title: Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards.
abstract: BACKGROUND
  High-throughput sequencing using targeted enrichment and transcriptomic methods enables rapid construction of phylogenomic data sets incorporating hundreds to thousands of loci. These advances have enabled access to an unprecedented amount of nucleotide sequence data, but they also pose new questions. Given that the loci targeted for enrichment are often highly conserved, how informative are they at different taxonomic scales, especially at the intraspecific/phylogeographic scale? We investigate this question using Australian scincid lizards in the Eugongylus group (Squamata: Scincidae). We sequenced 415 anchored hybrid enriched (AHE) loci for 43 individuals and mined 1650 exons (1648 loci) from transcriptomes (transcriptome mining) from 11 individuals, including multiple phylogeographic lineages within several species of Carlia, Lampropholis, and Saproscincus skinks. We assessed the phylogenetic information content of these loci at the intergeneric, interspecific, and phylogeographic scales. As a further test of the utility at the phylogeographic scale, we used the anchor hybrid enriched loci to infer lineage divergence parameters using coalescent models of isolation with migration.
  
  
  RESULTS
  Phylogenetic analyses of both data sets inferred very strongly supported trees at all taxonomic levels. Further, AHE loci yielded estimates of divergence times between closely related lineages that were broadly consistent with previous population-level analyses.
  
  
  CONCLUSIONS
  Anchored-enriched loci are useful at the deep phylogeny and phylogeographic scales. Although overall phylogenetic support was high throughout the Australian Eugongylus group phylogeny, there were nonetheless some conflicting or unresolved relationships, especially regarding the placement of Pseudemoia, Cryptoblepharus, and the relationships amongst closely-related species of Tasmanian Niveoscincus skinks.
authors.affiliation: School of Biological Sciences, Heydon-Laurence Building A08, University of Sydney, Sydney, NSW, 2006, Australia. mbrandley@gmail.com.|New York University - Sydney, The Rocks, NSW, 2000, Australia. mbrandley@gmail.com.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Brandley
authors.affiliation: Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Canberra, ACT 0200, Australia. jason.bragg@anu.edu.au.
authors.forename: Jason G
authors.initials: JG
authors.lastname: Bragg
authors.affiliation: Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720, USA. sonal.singhal1@gmail.com.|Department of Integrative Biology, University of California, 3060 Valley Life Sciences Building, Berkeley, CA, 94720, USA. sonal.singhal1@gmail.com.
authors.forename: Sonal
authors.initials: S
authors.lastname: Singhal
authors.affiliation: School of Biological Sciences, Monash University, Clayton, Melbourne, VIC, 3800, Australia. david.chapple@monash.edu.
authors.forename: David G
authors.initials: DG
authors.lastname: Chapple
authors.affiliation: Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720, USA. cjennings@berkeley.edu.|Department of Integrative Biology, University of California, 3060 Valley Life Sciences Building, Berkeley, CA, 94720, USA. cjennings@berkeley.edu.
authors.forename: Charlotte K
authors.initials: CK
authors.lastname: Jennings
authors.affiliation: Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306, USA. arlemmon@gmail.com.
authors.forename: Alan R
authors.initials: AR
authors.lastname: Lemmon
authors.affiliation: Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL, 32306, USA. chorusfrog@bio.fsu.edu.
authors.forename: Emily Moriarty
authors.initials: EM
authors.lastname: Lemmon
authors.affiliation: School of Biological Sciences, Heydon-Laurence Building A08, University of Sydney, Sydney, NSW, 2006, Australia. mike.thompson@sydney.edu.au.
authors.forename: Michael B
authors.initials: MB
authors.lastname: Thompson
authors.affiliation: Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Canberra, ACT 0200, Australia. craig.moritz@anu.edu.au.|The Commonwealth Scientific and Industrial Research Organization Ecosystem Sciences Division, GPO Box 1700, Canberra, ACT, 2601, Australia. craig.moritz@anu.edu.au.
authors.forename: Craig
authors.initials: C
authors.lastname: Moritz
mesh_terms: D000818:Animals; D001315:Australia; D019143:Evolution, Molecular; D008116:Lizards / Q000145:classification* / Q000235:genetics* / Q000502:physiology; D010802:Phylogeny; D058974:Phylogeography; D017422:Sequence Analysis, DNA