title: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds.
abstract: Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased nonamplification, or disruptions that may result in decreased polymorphism in nontarget species. Furthermore, high mutation rates and constraints on allele size may also with evolutionary time, promote an increase in convergently evolved allele size classes, biasing measures of interspecific genetic differentiation. Here, we used next-generation sequencing to develop microsatellite markers from a shotgun genome sequence of the sub-Antarctic seabird, the thin-billed prion (Pachyptila belcheri), that we tested for cross-species amplification in other Pachyptila and related sub-Antarctic species. We found that heterozygosity decreased and the proportion of nonamplifying loci increased with phylogenetic distance from the target species. Surprisingly, we found that species trees estimated from interspecific FST provided better approximations of mtDNA relationships among the studied species than those estimated using DC , even though FST was more affected by null alleles. We observed a significantly nonlinear second order polynomial relationship between microsatellite and mtDNA distances. We propose that the loss of linearity with increasing mtDNA distance stems from an increasing proportion of homoplastic allele size classes that are identical in state, but not identical by descent. Therefore, despite high cross-species amplification success and high polymorphism among the closely related Pachyptila species, we caution against the use of microsatellites in phylogenetic inference among distantly related taxa.
authors.affiliation: Department of Zoology, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa.|Department of Integrative Biology and Evolution, Konrad Lorenz Institute for Ethology, University of Veterinary Medicine Vienna, Savoyenstr. 1a, A-1160, Vienna, Austria.
authors.forename: Yoshan
authors.initials: Y
authors.lastname: Moodley
authors.affiliation: Justus Liebig University Giessen, Department of Animal Ecology & Systematics, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany.
authors.forename: Juan F
authors.initials: JF
authors.lastname: Masello
authors.affiliation: Justus Liebig University Giessen, Department of Animal Ecology & Systematics, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany.|Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA, 6102, Australia.
authors.forename: Theresa L
authors.initials: TL
authors.lastname: Cole
authors.affiliation: Justus Liebig University Giessen, Department of Animal Ecology & Systematics, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany.
authors.forename: Luciano
authors.initials: L
authors.lastname: Calderon
authors.affiliation: Department of Integrative Biology and Evolution, Konrad Lorenz Institute for Ethology, University of Veterinary Medicine Vienna, Savoyenstr. 1a, A-1160, Vienna, Austria.
authors.forename: Gopi K
authors.initials: GK
authors.lastname: Munimanda
authors.affiliation: Ecogenics GmbH, Grabenstrasse 11a, 8952, Zurich-Schlieren, Switzerland.
authors.forename: Marco R
authors.initials: MR
authors.lastname: Thali
authors.affiliation: Department of Primary Industries, Parks, Water and Environment, GPO Box 44, Hobart, Tas., 7001, Australia.
authors.forename: Rachael
authors.initials: R
authors.lastname: Alderman
authors.affiliation: Royal Society for the Protection of Birds (RSPB), The Lodge, Sandy, Bedfordshire, SG19 2DL, UK.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Cuthbert
authors.affiliation: Section of Ornithology, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA, 90007, USA.|Feather Link Inc., 1013 Westchester Way, Cincinnati, OH, 45244, USA.
authors.forename: Manuel
authors.initials: M
authors.lastname: Marin
authors.affiliation: School of Environmental Sciences, Charles Sturt University, PO Box 789, Albury, NSW, 2640, Australia.
authors.forename: Melanie
authors.initials: M
authors.lastname: Massaro
authors.affiliation: Department of Conservation Biology, Estación Biológica de Doñana (EBD-CSIC), Avda. Américo Vespucio s/n, Seville, 41092, Spain.
authors.forename: Joan
authors.initials: J
authors.lastname: Navarro
authors.affiliation: British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Phillips
authors.affiliation: Percy FitzPatrick Institute, DST/NRF Centre of Excellence, University of Cape Town, Rondebosch, 7701, South Africa.
authors.forename: Peter G
authors.initials: PG
authors.lastname: Ryan
authors.affiliation: Justus Liebig University Giessen, Department of Animal Ecology & Systematics, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany.
authors.forename: Cristián G
authors.initials: CG
authors.lastname: Suazo
authors.affiliation: Centre d'Etudes Biologiques de Chizé, UMR 7372 CNRS-Université de La Rochelle, 79360, Villiers-en-Bois, France.
authors.forename: Yves
authors.initials: Y
authors.lastname: Cherel
authors.affiliation: Centre d'Etudes Biologiques de Chizé, UMR 7372 CNRS-Université de La Rochelle, 79360, Villiers-en-Bois, France.
authors.forename: Henri
authors.initials: H
authors.lastname: Weimerskirch
authors.affiliation: Justus Liebig University Giessen, Department of Animal Ecology & Systematics, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany.
authors.forename: Petra
authors.initials: P
authors.lastname: Quillfeldt
mesh_terms: D000818:Animals; D001717:Birds / Q000145:classification* / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D010802:Phylogeny
chemical_list: D004272:DNA, Mitochondrial
keywords: Pachyptila; Procellariiformes; cross-species transferability; genetic diversity; microsatellite; null alleles