text: primary cultured cell

text: enrichment culture

text: Alveolar macrophages in culture media 6hours

text: primary cell culture

text: Sus scrofa

text: FAANG


status: PUBLIC

characteristic: SRA accession

characteristic: cell culture protocol

text: primary cultured cell

characteristic: cell type

text: 37oC in 5% CO2, RPMI 1640 media + fetal cattle serum 10%, L-glutamine 2mM, Penicillin-Streptomycin 1%, Gentamicin 100 mg/mL

characteristic: culture conditions

text: enrichment culture

characteristic: culture type

characteristic: description

text: primary cell culture

characteristic: material

characteristic: number of passages

text: Sus scrofa

characteristic: organism

text: FAANG

characteristic: project

text: RNAseq data from pig alveolar macrophages stimulated with LPS and Poly IC

characteristic: submission description

characteristic: submission identifier

characteristic: submission title

type: derived from

type: has member

Iowa State University (ISU)

Role: institution

Address: Iowa State University, Department of Animal Science, 806 Stange Road, 2255 Kildee Hall. Ames, IA 50010

Name: The United States Department of Agriculture (USDA)

Role: funder

Address: 1920 Dayton Ave, Ames, IA 50010

Christopher Tuggle

FirstName: Christopher

LastName: Tuggle

Role: investigator

Juber Herrera

FirstName: Juber

LastName: Herrera

Role: experiment performer

Role: submitter


text: primary cultured cell

text: enrichment culture

text: Alveolar macrophages stimulated 2 hours with Poly (I:C)

text: primary cell culture

text: Sus scrofa

text: FAANG


text: primary cultured cell

text: enrichment culture

text: Alveolar macrophages stimulated 6 hours with LPS

text: primary cell culture

text: Sus scrofa

text: FAANG


text: Regent honeyeater

characteristic: common name

text: Regent honeyeater contemoprary sample from the Museum of Victoria 80

text: Australia

characteristic: geographic location (country and/or sea)

text: Capertee

characteristic: geographic location (region and locality)

characteristic: lat lon

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Female

characteristic: sex

text: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879-1960), 102 ‘recent’ (1989-2012) and 52 ‘current’ (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species’ life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

text: Genomic impact of severe population decline in a nomadic songbird

text: Tissue

characteristic: tissue type

Name: Ecogenomics and Bioinformatics Lab (EBL)

Address: Frank Fenner Building 141, Canberra, ACT 2601 Australia

George Olah

FirstName: George

LastName: Olah


characteristic: SRA accession

text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 34

text: Australia

text: Capertee

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: specimen voucher

text: Blood


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 35

characteristic: description

text: Australia

text: Capertee

text: Ross Crates

characteristic: material

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 18

text: Australia

text: St. Marys

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: submission description

characteristic: submission identifier

text: Toe pad


text: Regent honeyeater

characteristic: common name

text: Regent honeyeater museum specimen from the American Museum of Natural History 31

text: Australia

text: Ashburton

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission title

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 78

text: Australia

characteristic: geographic location (country and/or sea)

text: Sutton

characteristic: geographic location (region and locality)

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Extracted DNA


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 66

text: Australia

text: Armidale

characteristic: lat lon

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Extracted DNA


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 4

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Female

characteristic: sex

text: Blood


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 64

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Extracted DNA

characteristic: tissue type


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 49

text: Australia

text: Cumbo Rd, NSW

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Blood


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 33

text: Australia

text: Capertee

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 98

characteristic: description

text: Australia

text: Quorrobolong

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Tissue


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 9

text: Australia

text: Cooks R.

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: specimen voucher

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 34

text: Australia

text: Canberra

characteristic: material

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Male

text: Blood


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 19

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission description

characteristic: submission identifier

text: Blood


text: Regent honeyeater

characteristic: common name

text: Regent honeyeater museum specimen from the Queensland Museum 1

text: Australia

text: Greymare

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission title

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 3

text: Australia

characteristic: geographic location (country and/or sea)

text: Armidale

characteristic: geographic location (region and locality)

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879-1960), 102 ‘recent’ (1989-2012) and 52 ‘current’ (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species’ life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the Museum of Victoria 1

text: Australia

text: Abbotsford

characteristic: lat lon

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Genomic impact of severe population decline in a nomadic songbird

text: Toe pad


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 2

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Male

characteristic: sex

text: Blood


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 10

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood

characteristic: tissue type


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 3

text: Australia

text: Northern NSW

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 27

characteristic: description

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: specimen voucher

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 3

text: Australia

text: Tree Gully

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Male

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the Australian Museum 2

text: Australia

text: Parramatta

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission description

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 12

text: Australia

text: Capertee

characteristic: material

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission identifier

text: Blood


text: Regent honeyeater

characteristic: common name

text: Regent honeyeater contemoprary sample from the Museum of Victoria 96

text: Australia

text: Quorrobolong

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission title

text: Tissue


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 79

text: Australia

characteristic: geographic location (country and/or sea)

text: Sutton

characteristic: geographic location (region and locality)

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Extracted DNA


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 39

text: Australia

text: Northern NSW

text: Ross Crates

characteristic: lat lon

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 65

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Female

characteristic: sex

text: Extracted DNA


characteristic: SRA accession

text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 40

text: Australia

text: Northern NSW

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Feather

characteristic: tissue type


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 32

text: Australia

text: Ashburton

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 38

text: Australia

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Toe pad


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 26

text: Australia

text: Capertee

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879-1960), 102 ‘recent’ (1989-2012) and 52 ‘current’ (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species’ life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 1

characteristic: description

text: Australia

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: specimen voucher

text: Genomic impact of severe population decline in a nomadic songbird

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 42

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Male

characteristic: submission description

text: Blood


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 32

text: Australia

text: Capertee

text: Ross Crates

characteristic: material

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission identifier

text: Blood


text: Regent honeyeater

characteristic: common name

text: Regent honeyeater contemoprary sample from the Museum of Victoria 11

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission title

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 17

text: Australia

characteristic: geographic location (country and/or sea)

text: St. Marys

characteristic: geographic location (region and locality)

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the South Australian Museum 10

text: Australia

text: Coromandel Valley

characteristic: lat lon

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Toe pad


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 18

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Female

characteristic: sex

text: Blood


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 13

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood

characteristic: tissue type


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 81

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Tissue


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 24

text: Australia

text: Capertee

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Blood


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 1

characteristic: description

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: specimen voucher

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 67

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Female

characteristic: submission description

text: Extracted DNA


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 89

text: Australia

text: Capertee

characteristic: material

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission identifier

text: Tissue


text: Regent honeyeater

characteristic: common name

text: Regent honeyeater museum specimen from the American Museum of Natural History 23

text: Australia

text: Dandenong

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: submission title

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 30

text: Australia

characteristic: geographic location (country and/or sea)

text: Ashburton

characteristic: geographic location (region and locality)

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 50

text: Australia

text: Goulburn River NP

characteristic: lat lon

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879-1960), 102 ‘recent’ (1989-2012) and 52 ‘current’ (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species’ life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 43

text: Australia

text: Chiltern

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Male

characteristic: sex

text: Genomic impact of severe population decline in a nomadic songbird

text: Blood


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater museum specimen from the Museum of Victoria 7

text: Australia

text: Eskdale district

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Toe pad

characteristic: tissue type


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 91

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Tissue


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 35

text: Australia

text: Canberra

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 76

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Extracted DNA


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 4

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 23

text: Australia

text: Capertee

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 97

characteristic: description

text: Australia

text: Quorrobolong

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Tissue


text: Regent honeyeater

text: Regent honeyeater museum specimen from the South Australian Museum 9

text: Australia

text: Germanton (Now Holbrook)

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

characteristic: specimen voucher

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 2

text: Australia

text: Strathbalbyn

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: submission description

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 14

text: Australia

text: Capertee

characteristic: material

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission identifier

text: Blood


text: Ross Crates

text: Regent honeyeater

characteristic: common name

text: Regent honeyeater fresh sample from the wild 17

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission title

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 8

text: Australia

characteristic: geographic location (country and/or sea)

text: Cooks R.

characteristic: geographic location (region and locality)

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 90

text: Australia

text: Capertee

characteristic: lat lon

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Tissue


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 82

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Male

characteristic: sex

text: Tissue


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 16

text: Australia

text: St. Marys

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879-1960), 102 ‘recent’ (1989-2012) and 52 ‘current’ (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species’ life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

text: Toe pad

characteristic: tissue type


text: Regent honeyeater

text: Regent honeyeater museum specimen from the Museum of Victoria 3

text: Australia

text: Healesville

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Genomic impact of severe population decline in a nomadic songbird

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 22

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 29

text: Australia

text: Ashburton

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Toe pad


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 45

text: Australia

text: Capertee

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 68

characteristic: description

text: Australia

text: Chiltern

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Male

text: Extracted DNA


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 30

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: specimen voucher

characteristic: submission description

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the South Australian Museum 3

text: Australia

text: Blackwood

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission identifier

text: Toe pad


text: Regent honeyeater

characteristic: common name

text: Regent honeyeater contemoprary sample from the Museum of Victoria 51

text: Australia

text: Goulburn River NP

characteristic: material

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 27

text: Australia

characteristic: geographic location (country and/or sea)

text: Castlemaine

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: submission title

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 36

text: Australia

text: Canberra

characteristic: geographic location (region and locality)

characteristic: lat lon

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the South Australian Museum 1

text: Australia

text: Clarendon,

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Male

text: Toe pad


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 53

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: sex

text: Extracted DNA


text: Regent honeyeater

text: Regent honeyeater museum specimen from the Museum of Victoria 6

text: Australia

text: Whittlesea

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Toe pad

characteristic: tissue type


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 19

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 21

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 5

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879-1960), 102 ‘recent’ (1989-2012) and 52 ‘current’ (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species’ life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the Queensland Museum 2

text: Australia

text: Chinchilla

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Genomic impact of severe population decline in a nomadic songbird

text: Toe pad


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 44

text: Australia

text: Northern NSW

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Feather


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 48

characteristic: description

text: Australia

text: Northern NSW

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Male

text: Feather


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 7

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission description

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 23

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: submission identifier

text: Blood


text: Ross Crates

text: Regent honeyeater

characteristic: common name

text: Regent honeyeater fresh sample from the wild 13

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: specimen voucher

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 15

text: Australia

characteristic: geographic location (country and/or sea)

text: St. Marys

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 83

text: Australia

text: Capertee

characteristic: material

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission title

text: Tissue


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 13

text: Australia

text: Bimberry, Manilara

characteristic: geographic location (region and locality)

characteristic: lat lon

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 69

text: Australia

text: Chiltern

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Female

text: Extracted DNA


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 28

text: Australia

text: Castlemaine

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 11

text: Australia

text: Hogarah, near Sydney

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: sex

text: Toe pad

characteristic: tissue type


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 52

text: Australia

text: Munghorn East

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 87

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Tissue


text: Regent honeyeater

text: Regent honeyeater museum specimen from the South Australian Museum 2

text: Australia

text: Happy Valley

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the Museum of Victoria 5

text: Australia

text: Tooborac

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879-1960), 102 ‘recent’ (1989-2012) and 52 ‘current’ (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species’ life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

text: Toe pad


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 29

text: Australia

text: Capertee

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Genomic impact of severe population decline in a nomadic songbird

text: Feather


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 12

characteristic: description

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Female

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 37

text: Australia

text: Canberra

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission description

characteristic: submission identifier

text: Blood


text: Regent honeyeater

characteristic: common name

text: Regent honeyeater contemoprary sample from the Museum of Victoria 56

text: Australia

text: Chiltern

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Extracted DNA


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 47

text: Australia

characteristic: geographic location (country and/or sea)

text: Northern NSW

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: specimen voucher

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 20

text: Australia

text: Capertee

characteristic: material

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission title

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 86

text: Australia

text: Lurg

characteristic: geographic location (region and locality)

characteristic: lat lon

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Tissue


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 12

text: Australia

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Toe pad


characteristic: SRA accession

text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 31

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: sex

text: Feather


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 16

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood

characteristic: tissue type


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 10

characteristic: description

text: Australia

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 6

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Female

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 25

text: Australia

text: Melton

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission description

text: Toe pad


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 38

text: Australia

text: Northern NSW

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission identifier

text: Blood


text: Regent honeyeater

characteristic: common name

text: Regent honeyeater contemoprary sample from the Museum of Victoria 40

text: Australia

characteristic: geographic location (country and/or sea)

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 25

text: Australia

text: Capertee

characteristic: material

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879-1960), 102 ‘recent’ (1989-2012) and 52 ‘current’ (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species’ life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

text: Blood


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 22

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: specimen voucher

text: Genomic impact of severe population decline in a nomadic songbird

characteristic: submission title

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 6

text: Australia

text: Gosford

characteristic: geographic location (region and locality)

characteristic: lat lon

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Toe pad


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 7

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Female

text: Blood


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 92

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: sex

text: Tissue


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 77

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Extracted DNA

characteristic: tissue type


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 21

characteristic: description

text: Australia

text: Blackwood

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 61

text: Australia

text: Chiltern

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Male

text: Extracted DNA


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 36

text: Australia

text: Moorabool

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: submission description

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the South Australian Museum 8

text: Australia

text: Cherry Gardens

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 46

text: Australia

text: Chiltern

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 29

text: Australia

text: Chiltern

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 102

text: Australia

text: Quorrobolong

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Tissue


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 15

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 6

text: Australia

text: Capertee

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

characteristic: common name

text: Regent honeyeater contemoprary sample from the Museum of Victoria 93

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: submission identifier

text: Tissue


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 5

text: Australia

characteristic: geographic location (country and/or sea)

text: Gosford

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879-1960), 102 ‘recent’ (1989-2012) and 52 ‘current’ (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species’ life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 20

text: Australia

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: specimen voucher

text: Genomic impact of severe population decline in a nomadic songbird

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 35

text: Australia

text: Lang Lang

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission title

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 47

text: Australia

text: Cumbo Rd, NSW

characteristic: geographic location (region and locality)

characteristic: material

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 62

text: Australia

text: Chiltern

characteristic: lat lon

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Extracted DNA


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater museum specimen from the South Australian Museum 7

text: Australia

text: Gawler

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 30

text: Australia

text: Chiltern

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Blood

characteristic: tissue type


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 37

characteristic: description

text: Australia

text: Northern NSW

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: sex

text: Feather


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 16

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Male

characteristic: submission description

text: Blood


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 21

text: Australia

text: Capertee

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

characteristic: common name

text: Regent honeyeater contemoprary sample from the Museum of Victoria 17

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission identifier

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 1

text: Australia

characteristic: geographic location (country and/or sea)

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 50

text: Australia

text: Goulburn River

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: specimen voucher

characteristic: submission title

text: Feather


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 94

text: Australia

text: Capertee

characteristic: geographic location (region and locality)

characteristic: material

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Tissue


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 51

text: Australia

text: Goulburn River

text: Ross Crates

characteristic: lat lon

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Feather


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 19

text: Australia

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Female

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 34

characteristic: description

text: Australia

text: Ashburton

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879-1960), 102 ‘recent’ (1989-2012) and 52 ‘current’ (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species’ life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

text: Toe pad

characteristic: tissue type


text: Regent honeyeater

text: Regent honeyeater museum specimen from the South Australian Museum 6

text: Australia

text: Blackwood

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Female

characteristic: sex

text: Genomic impact of severe population decline in a nomadic songbird

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 63

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission description

text: Extracted DNA


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 48

text: Australia

text: Cumbo Rd, NSW

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 36

text: Australia

text: Capertee

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Feather


text: Regent honeyeater

characteristic: common name

text: Regent honeyeater contemoprary sample from the Museum of Victoria 31

text: Australia

text: Canberra

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: submission identifier

text: Blood


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 20

text: Australia

characteristic: geographic location (country and/or sea)

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: specimen voucher

text: Blood


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 5

text: Australia

text: Capertee

characteristic: geographic location (region and locality)

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission title

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the South Australian Museum 4

text: Australia

text: Kingscote, Kangaroo Island

characteristic: lat lon

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the Australian Museum 1

text: Australia

text: Sutherland shire

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Toe pad


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 33

text: Australia

text: Canberra

characteristic: material

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 18

characteristic: description

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 2

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Blood

characteristic: tissue type


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 49

text: Australia

text: Northern NSW

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: submission description

text: Tissue


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 95

text: Australia

text: Quorrobolong

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: sex

text: Tissue


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 4

text: Australia

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 33

text: Australia

text: Ashburton

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879-1960), 102 ‘recent’ (1989-2012) and 52 ‘current’ (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species’ life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 32

text: Australia

text: Canberra

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Genomic impact of severe population decline in a nomadic songbird

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 73

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Extracted DNA


text: Regent honeyeater

text: Regent honeyeater museum specimen from the South Australian Museum 5

text: Australia

text: Blackwood

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 41

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 26

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 58

text: Australia

text: Chiltern

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Extracted DNA


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 41

text: Australia

text: Northern NSW

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Feather


text: Ross Crates

text: Regent honeyeater

characteristic: common name

text: Regent honeyeater fresh sample from the wild 10

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission identifier

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 28

text: Australia

characteristic: geographic location (country and/or sea)

text: Chiltern

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 99

text: Australia

text: Quorrobolong

characteristic: geographic location (region and locality)

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Tissue


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 88

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission title

text: Tissue


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 24

text: Australia

text: Bayswater

characteristic: lat lon

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: specimen voucher

text: Toe pad


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater museum specimen from the South Australian Museum 12

text: Australia

text: Toongabbie

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 59

characteristic: description

text: Australia

text: Chiltern

characteristic: material

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Extracted DNA


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 27

text: Australia

text: Chiltern

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

characteristic: scientific name

text: Female

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 100

text: Australia

text: Quorrobolong

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879-1960), 102 ‘recent’ (1989-2012) and 52 ‘current’ (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species’ life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

characteristic: submission description

text: Tissue

characteristic: tissue type


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 44

text: Australia

text: Chiltern

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: sex

text: Genomic impact of severe population decline in a nomadic songbird

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 74

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Extracted DNA


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 9

text: Australia

text: Capertee

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Ross Crates

text: Regent honeyeater

characteristic: common name

text: Regent honeyeater fresh sample from the wild 25

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission identifier

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 37

text: Australia

characteristic: geographic location (country and/or sea)

text: Mulgrave

characteristic: geographic location (region and locality)

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the South Australian Museum 11

text: Australia

text: Square waterhole

characteristic: lat lon

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission title

text: Toe pad


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 7

text: Australia

text: Cooks R.

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: specimen voucher

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 60

characteristic: description

text: Australia

text: Chiltern

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Extracted DNA


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 45

text: Australia

text: Chiltern

characteristic: material

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Female

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 101

text: Australia

text: Quorrobolong

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Female

characteristic: submission description

text: Tissue


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 8

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: sex

text: Blood

characteristic: tissue type


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 75

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Extracted DNA


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 22

text: Australia

text: Dandenong

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Toe pad


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 46

text: Australia

text: Capertee

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

characteristic: common name

text: Regent honeyeater contemoprary sample from the Museum of Victoria 8

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission identifier

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 84

text: Australia

characteristic: geographic location (country and/or sea)

text: Capertee

characteristic: geographic location (region and locality)

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879-1960), 102 ‘recent’ (1989-2012) and 52 ‘current’ (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species’ life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

text: Tissue


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 15

text: Australia

text: Northern NSW

text: Ross Crates

characteristic: lat lon

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Genomic impact of severe population decline in a nomadic songbird

characteristic: submission title

text: Blood


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 14

text: Australia

text: St. Marys

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: specimen voucher

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater museum specimen from the Museum of Victoria 4

characteristic: description

text: Australia

text: Eltham

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 38

text: Australia

text: Capertee

characteristic: material

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Female

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 55

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

characteristic: submission description

text: Extracted DNA


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 70

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: sex

text: Extracted DNA

characteristic: tissue type


text: Regent honeyeater

text: Regent honeyeater museum specimen from the Museum of Victoria 2

text: Australia

text: Bankstown

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 9

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 54

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Extracted DNA


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 85

text: Australia

text: Indigo Valley

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Tissue


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 14

text: Australia

text: Capertee

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Blood


text: Ross Crates

text: Regent honeyeater

characteristic: common name

text: Regent honeyeater fresh sample from the wild 43

text: Australia

text: Northern NSW

text: Ross Crates

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: submission identifier

text: Blood


text: Regent honeyeater

text: Regent honeyeater museum specimen from the American Museum of Natural History 26

text: Australia

characteristic: geographic location (country and/or sea)

text: Castlemaine

characteristic: geographic location (region and locality)

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Toe pad


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 39

text: Australia

text: Capertee

characteristic: lat lon

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: submission title

text: Blood


characteristic: SRA accession

text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 71

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Extracted DNA


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 24

characteristic: description

text: Australia

text: Capertee

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

text: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879-1960), 102 ‘recent’ (1989-2012) and 52 ‘current’ (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species’ life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

text: Blood


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 28

text: Australia

text: Capertee

text: Ross Crates

text: polygamy

characteristic: mating type

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Male

characteristic: specimen voucher

text: Genomic impact of severe population decline in a nomadic songbird

text: Blood


text: Ross Crates

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 11

text: Australia

text: Capertee

text: Ross Crates

characteristic: material

text: polygamy

text: Anthochaera phrygia

characteristic: organism

text: Anthochaera phrygia

text: Male

text: Blood


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 57

text: Australia

text: Chiltern

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

characteristic: scientific name

text: Male

characteristic: submission description

text: Extracted DNA


text: Regent honeyeater

text: Regent honeyeater contemoprary sample from the Museum of Victoria 72

text: Australia

text: Armidale

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

characteristic: sex

text: Extracted DNA

characteristic: tissue type


text: Ross Crates

characteristic: collected by

text: Regent honeyeater

text: Regent honeyeater fresh sample from the wild 42

text: Australia

text: Capertee

text: Ross Crates

characteristic: identified by

text: polygamy

text: Anthochaera phrygia

text: Anthochaera phrygia

text: Female

text: Blood


text: abomasal lymph node

characteristic: cell type

text: sheep

characteristic: common name

text: CH (Spanish Churra Sheep)

characteristic: derived from

text: Adult Churra sheep abomasal lymph node transcriptome high-quality variants 1 - High-quality variants ( variants detected by both GATK and samtools) obtained from abomasal lymph node transcriptome of 12 adult churra sheep (6 resistant and 6 susceptible) subjected to an experimental infection with T. circumcincta and merged into a single dataset

text: Spain

text: Castilla y Leon

text: Ovis aries

text: Ovis aries

text: Female

text: ALN (abomasal lymph node )

characteristic: subject

text: In this project the RNA-seq technology was exploited to analyze the transcriptome of target tissues affected by the Teladorsagia circumcincta infection in two groups (6 resistsant and 6 susceptible) of adult ewes showing different statuses against gastrointestinal nematode (GIN) infection with the aim of identifying genes and variants linked to GIN infection resistance in sheep.

characteristic: submission identifier

text: Analysis of mucosal and abomasal lymphnode transcriptome for the identification of genes involved in nematode resistance gastrointestinal tract in adult sheep.

Department of Animal Production

Address: University of Leon, Campus de Vegazana s/n, 24071 León, Spain.

Beatriz Gutiérrez-Gil

FirstName: Beatriz

LastName: Gutiérrez-Gil

Juan Jose Arranz

FirstName: Juan Jose

LastName: Arranz

Praveen Krishna Chitneedi

FirstName: Praveen Krishna

LastName: Chitneedi


characteristic: SRA accession

text: abomasal lymph node

text: sheep

text: CH (Spanish Churra Sheep)

text: Adult Churra sheep abomasal lymph node transcriptome high-quality variants 8 - High-quality variants ( variants detected by both GATK and samtools) obtained from abomasal lymph node transcriptome of 12 adult churra sheep (6 resistant and 6 susceptible) subjected to an experimental infection with T. circumcincta and merged into a single dataset

text: Spain

characteristic: geographic location (country and/or sea)

text: Castilla y Leon

characteristic: geographic location (region and locality)

text: Ovis aries

text: Ovis aries

text: Female

text: ALN (abomasal lymph node )

characteristic: submission title


text: abomasal lymph node

text: sheep

text: CH (Spanish Churra Sheep)

text: Adult Churra sheep abomasal lymph node transcriptome high-quality variants 4 - High-quality variants ( variants detected by both GATK and samtools) obtained from abomasal lymph node transcriptome of 12 adult churra sheep (6 resistant and 6 susceptible) subjected to an experimental infection with T. circumcincta and merged into a single dataset

characteristic: description

text: Spain

text: Castilla y Leon

text: Ovis aries

text: Ovis aries

text: Female

text: ALN (abomasal lymph node )


text: abomasal lymph node

text: sheep

text: CH (Spanish Churra Sheep)

text: Adult Churra sheep abomasal lymph node transcriptome high-quality variants 9 - High-quality variants ( variants detected by both GATK and samtools) obtained from abomasal lymph node transcriptome of 12 adult churra sheep (6 resistant and 6 susceptible) subjected to an experimental infection with T. circumcincta and merged into a single dataset

text: Spain

text: Castilla y Leon

text: Ovis aries

characteristic: organism

text: Ovis aries

text: Female

text: ALN (abomasal lymph node )


text: abomasal lymph node

text: sheep

text: CH (Spanish Churra Sheep)

text: Adult Churra sheep abomasal lymph node transcriptome high-quality variants 11 - High-quality variants ( variants detected by both GATK and samtools) obtained from abomasal lymph node transcriptome of 12 adult churra sheep (6 resistant and 6 susceptible) subjected to an experimental infection with T. circumcincta and merged into a single dataset

text: Spain

text: Castilla y Leon

text: Ovis aries

text: Ovis aries

characteristic: scientific name

text: Female

text: ALN (abomasal lymph node )


text: abomasal lymph node

text: sheep

text: CH (Spanish Churra Sheep)

text: Adult Churra sheep abomasal lymph node transcriptome high-quality variants 5 - High-quality variants ( variants detected by both GATK and samtools) obtained from abomasal lymph node transcriptome of 12 adult churra sheep (6 resistant and 6 susceptible) subjected to an experimental infection with T. circumcincta and merged into a single dataset

text: Spain

text: Castilla y Leon

text: Ovis aries

text: Ovis aries

text: Female

text: ALN (abomasal lymph node )

characteristic: submission description


text: abomasal lymph node

text: sheep

text: CH (Spanish Churra Sheep)

text: Adult Churra sheep abomasal lymph node transcriptome high-quality variants 7 - High-quality variants ( variants detected by both GATK and samtools) obtained from abomasal lymph node transcriptome of 12 adult churra sheep (6 resistant and 6 susceptible) subjected to an experimental infection with T. circumcincta and merged into a single dataset

text: Spain

text: Castilla y Leon

text: Ovis aries

text: Ovis aries

text: Female

characteristic: sex

text: ALN (abomasal lymph node )


text: abomasal lymph node

text: sheep

text: CH (Spanish Churra Sheep)

text: Adult Churra sheep abomasal lymph node transcriptome high-quality variants 6 - High-quality variants ( variants detected by both GATK and samtools) obtained from abomasal lymph node transcriptome of 12 adult churra sheep (6 resistant and 6 susceptible) subjected to an experimental infection with T. circumcincta and merged into a single dataset

text: Spain

text: Castilla y Leon

text: Ovis aries

text: Ovis aries

text: Female

text: ALN (abomasal lymph node )


text: abomasal lymph node

text: sheep

text: CH (Spanish Churra Sheep)

text: Adult Churra sheep abomasal lymph node transcriptome high-quality variants 10 - High-quality variants ( variants detected by both GATK and samtools) obtained from abomasal lymph node transcriptome of 12 adult churra sheep (6 resistant and 6 susceptible) subjected to an experimental infection with T. circumcincta and merged into a single dataset

text: Spain

text: Castilla y Leon

text: Ovis aries

text: Ovis aries

text: Female

text: ALN (abomasal lymph node )


text: abomasal lymph node

text: sheep

text: CH (Spanish Churra Sheep)

text: Adult Churra sheep abomasal lymph node transcriptome high-quality variants 12 - High-quality variants ( variants detected by both GATK and samtools) obtained from abomasal lymph node transcriptome of 12 adult churra sheep (6 resistant and 6 susceptible) subjected to an experimental infection with T. circumcincta and merged into a single dataset

text: Spain

text: Castilla y Leon

text: Ovis aries

text: Ovis aries

text: Female

text: ALN (abomasal lymph node )


text: abomasal lymph node

text: sheep

text: CH (Spanish Churra Sheep)

text: Adult Churra sheep abomasal lymph node transcriptome high-quality variants 3 - High-quality variants ( variants detected by both GATK and samtools) obtained from abomasal lymph node transcriptome of 12 adult churra sheep (6 resistant and 6 susceptible) subjected to an experimental infection with T. circumcincta and merged into a single dataset

text: Spain

text: Castilla y Leon

text: Ovis aries

text: Ovis aries

text: Female

text: ALN (abomasal lymph node )


text: abomasal lymph node

text: sheep

text: CH (Spanish Churra Sheep)

text: Adult Churra sheep abomasal lymph node transcriptome high-quality variants 2 - High-quality variants ( variants detected by both GATK and samtools) obtained from abomasal lymph node transcriptome of 12 adult churra sheep (6 resistant and 6 susceptible) subjected to an experimental infection with T. circumcincta and merged into a single dataset

text: Spain

text: Castilla y Leon

text: Ovis aries

text: Ovis aries

text: Female

text: ALN (abomasal lymph node )


text: IL6 receptor deficiency sample

text: Israel

text: Homo sapiens

text: Homo sapiens

text: Male

text: Identifing a novel immunodeficiency

text: IL6 receptor deficiency

Name: Primary immunodeficiency research Laboratory

Address: Rager Ave 1 Beer Sheva 8410501

Amit Nahum

FirstName: Amit

LastName: Nahum


Horse 1

text: horse

text: Thoroughbred horse 1

text: equus caballus

text: equus caballus

text: Exclusion of Candidate Genes within Thrombin Signaling Pathway in Association with Atypical Equine Thrombasthenia in Thoroughbreds

Finno

Address: 1 Shields Ave, Davis CA 95616

Anna Dahlgren

FirstName: Anna

LastName: Dahlgren


Horse 7

text: horse

text: Thoroughbred horse 7

text: equus caballus

text: equus caballus


Horse 15

text: horse

text: Thoroughbred horse 15

text: equus caballus

text: equus caballus


Horse 14

text: horse

text: Thoroughbred horse 14

text: equus caballus

text: equus caballus


Horse 5

text: horse

text: Thoroughbred horse 5

text: equus caballus

text: equus caballus


Horse 13

text: horse

text: Thoroughbred horse 13

text: equus caballus

text: equus caballus


Horse 6

text: horse

text: Thoroughbred horse 6

text: equus caballus

text: equus caballus


Horse 12

text: horse

text: Thoroughbred horse 12

text: equus caballus

text: equus caballus