publication . Article . Other literature type . 2015

Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards

Jason Bragg; David Chapple; Michael Thompson;
Open Access
  • Published: 11 Apr 2015 Journal: BMC Evolutionary Biology, volume 15 (eissn: 1471-2148, Copyright policy)
  • Publisher: Springer Nature
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 indi...
Subjects
free text keywords: Ecology, Evolution, Behavior and Systematics, Research Article, Anchored phylogenomics, Coalescence, Phylogeography, Skink, Transcriptome, Ultraconserved elements
73 references, page 1 of 5

Lemmon, EM, Lemmon, AR. High-throughput genomic data in systematics and phylogenetics. Ann Rev Ecol Evol Syst. 2013; 44: 99-121 [OpenAIRE] [DOI]

Faircloth, BC, Sorenson, L, Santini, F, Alfaro, ME. A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS ONE. 2013; 8: e65923 [OpenAIRE] [PubMed] [DOI]

Johnson, BR, Borowiec, ML, Chiu, JC, Lee, EK, Atallah, J, Ward, PS. Phylogenomics resolves evolutionary relationships among ants, bees, and wasps. Curr Biol. 2013; 23: 2565 [OpenAIRE] [DOI]

Simon, S, Narechania, A, DeSalle, R, Hadrys, H. Insect phylogenomics: exploring the source of incongruence using new transcriptomic data. Genome Biol Evol. 2012; 4: 1295-309 [OpenAIRE] [PubMed] [DOI]

5.Wen J, Xiong Z, Nie Z-L, Mao L, Zhu Y, Kan X-Z et al. Transcriptome sequences resolve deep relationships of the grass family. PLoS ONE 2013, e74394.

Peters, RS, Meusemann, K, Petersen, M, Mayer, C, Wilbrandt, J, Ziesmann, T. The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data. BMC Evol Biol. 2013; 14: 52 [OpenAIRE] [PubMed] [DOI]

Faircloth, BC, McCormack, JE, Crawford, NG, Harvey, MG, Brumfield, RT, Glenn, TC. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst Biol. 2012; 61: 717-26 [OpenAIRE] [PubMed] [DOI]

Bi, K, Vanderpool, D, Singhal, S, Linderoth, T, Moritz, C, Good, JM. Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC Genomics. 2012; 13: 403 [OpenAIRE] [PubMed] [DOI]

Lemmon, AR, Emme, SA, Lemmon, EM. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol. 2012; 61: 727-44 [OpenAIRE] [PubMed] [DOI]

Bybee, SM, Bracken-Grissom, HD, Hermansen, RA, Clement, MJ, Crandall, KA, Felderc, DL. Directed next generation sequencing for phylogenetics: an example using Decapoda (Crustacea). Zool Anz. 2011; 250: 497-506 [OpenAIRE] [DOI]

O’Neill, EM, Schwartz, R, Bullock, CT, Williams, JS, Shaffer, HB, Aguilar-Miguel, X. Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex. Mol Ecol. 2013; 22: 111-29 [OpenAIRE] [PubMed] [DOI]

Barrow, LN, Ralicki, HF, Emme, SA, Moriarty Lemmon, E. Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing. Mol Phylogenet Evol. 2014; 75: 78-90 [OpenAIRE] [PubMed] [DOI]

Miller, MR, Atwood, TS, Eames, BF, Eberhart, JK, Yan, Y-L, Postlethwait, JH. RAD marker microarrays enable rapid mapping of zebrafish mutations. Genome Biol. 2007; 8: R105 [OpenAIRE] [PubMed] [DOI]

Baird, NA, Etter, PD, Atwood, TS, Currey, MC, Shiver, AL, Lewis, ZA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE. 2008; 3: e3376 [OpenAIRE] [PubMed] [DOI]

Peterson, BK, Weber, JN, Kay, EH, Fisher, HS, Hoekstra, HE. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE. 2012; 7: e37135 [OpenAIRE] [PubMed] [DOI]

73 references, page 1 of 5
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 indi...
Subjects
free text keywords: Ecology, Evolution, Behavior and Systematics, Research Article, Anchored phylogenomics, Coalescence, Phylogeography, Skink, Transcriptome, Ultraconserved elements
73 references, page 1 of 5

Lemmon, EM, Lemmon, AR. High-throughput genomic data in systematics and phylogenetics. Ann Rev Ecol Evol Syst. 2013; 44: 99-121 [OpenAIRE] [DOI]

Faircloth, BC, Sorenson, L, Santini, F, Alfaro, ME. A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS ONE. 2013; 8: e65923 [OpenAIRE] [PubMed] [DOI]

Johnson, BR, Borowiec, ML, Chiu, JC, Lee, EK, Atallah, J, Ward, PS. Phylogenomics resolves evolutionary relationships among ants, bees, and wasps. Curr Biol. 2013; 23: 2565 [OpenAIRE] [DOI]

Simon, S, Narechania, A, DeSalle, R, Hadrys, H. Insect phylogenomics: exploring the source of incongruence using new transcriptomic data. Genome Biol Evol. 2012; 4: 1295-309 [OpenAIRE] [PubMed] [DOI]

5.Wen J, Xiong Z, Nie Z-L, Mao L, Zhu Y, Kan X-Z et al. Transcriptome sequences resolve deep relationships of the grass family. PLoS ONE 2013, e74394.

Peters, RS, Meusemann, K, Petersen, M, Mayer, C, Wilbrandt, J, Ziesmann, T. The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data. BMC Evol Biol. 2013; 14: 52 [OpenAIRE] [PubMed] [DOI]

Faircloth, BC, McCormack, JE, Crawford, NG, Harvey, MG, Brumfield, RT, Glenn, TC. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst Biol. 2012; 61: 717-26 [OpenAIRE] [PubMed] [DOI]

Bi, K, Vanderpool, D, Singhal, S, Linderoth, T, Moritz, C, Good, JM. Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC Genomics. 2012; 13: 403 [OpenAIRE] [PubMed] [DOI]

Lemmon, AR, Emme, SA, Lemmon, EM. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol. 2012; 61: 727-44 [OpenAIRE] [PubMed] [DOI]

Bybee, SM, Bracken-Grissom, HD, Hermansen, RA, Clement, MJ, Crandall, KA, Felderc, DL. Directed next generation sequencing for phylogenetics: an example using Decapoda (Crustacea). Zool Anz. 2011; 250: 497-506 [OpenAIRE] [DOI]

O’Neill, EM, Schwartz, R, Bullock, CT, Williams, JS, Shaffer, HB, Aguilar-Miguel, X. Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex. Mol Ecol. 2013; 22: 111-29 [OpenAIRE] [PubMed] [DOI]

Barrow, LN, Ralicki, HF, Emme, SA, Moriarty Lemmon, E. Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing. Mol Phylogenet Evol. 2014; 75: 78-90 [OpenAIRE] [PubMed] [DOI]

Miller, MR, Atwood, TS, Eames, BF, Eberhart, JK, Yan, Y-L, Postlethwait, JH. RAD marker microarrays enable rapid mapping of zebrafish mutations. Genome Biol. 2007; 8: R105 [OpenAIRE] [PubMed] [DOI]

Baird, NA, Etter, PD, Atwood, TS, Currey, MC, Shiver, AL, Lewis, ZA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE. 2008; 3: e3376 [OpenAIRE] [PubMed] [DOI]

Peterson, BK, Weber, JN, Kay, EH, Fisher, HS, Hoekstra, HE. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE. 2012; 7: e37135 [OpenAIRE] [PubMed] [DOI]

73 references, page 1 of 5
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