Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

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Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

Andermann, Tobias (author): Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences

Fernandes, A. M. (author)

Olsson, Urban, 1954 (author): Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences

Töpel, Mats H., 1973 (author): Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences

Pfeil, Bernard E., 1975 (author): Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences

Oxelman, Bengt, 1958 (author): Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences

Aleixo, A. (author)

Faircloth, B. C. (author)

Antonelli, Alexandre, 1978 (author): Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences

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2018-05-15
2019
English.
In: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 68:1, s. 32-46

Related links:: https://academic.oup...; show more...; https://gup.ub.gu.se...; https://doi.org/10.1...; show less...

Journal article (peer-reviewed)

Abstract Subject headings

Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for nonmodel organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach is that it recovers a consistent set of loci, each with high sequencing depth, which leads to more confidence in the assembly of target sequences. High sequencing depth can also be used to identify phylogenetically informative allelic variation within sequenced individuals, but allele sequences are infrequently assembled in phylogenetic studies. Instead, many scientists perform their phylogenetic analyses using contig sequences which result from the de novo assembly of sequencing reads into contigs containing only canonical nucleobases, and this may reduce both statistical power and phylogenetic accuracy. Here, we develop an easy-to-use pipeline to recover allele sequences from sequence capture data, and we use simulated and empirical data to demonstrate the utility of integrating these allele sequences to analyses performed under the multispecies coalescent model. Our empirical analyses of ultraconserved element locus data collected from the South American hummingbird genus Topaza demonstrate that phased allele sequences carry sufficient phylogenetic information to infer the genetic structure, lineage divergence, and biogeographic history of a genus that diversified during the last 3 myr. The phylogenetic results support the recognition of two species and suggest a high rate of gene flow across large distances of rainforest habitats but rare admixture across the Amazon River. Our simulations provide evidence that analyzing allele sequences leads to more accurate estimates of tree topology and divergence times than the more common approach of using contig sequences.

Subject headings

NATURVETENSKAP -- Biologi -- Biologisk systematik (hsv//swe)
NATURAL SCIENCES -- Biological Sciences -- Biological Systematics (hsv//eng)

Keyword

Aves
gene tree
heterozygous sites
mitochondrial genome
SNP
species tree
target enrichment
Trochilidae
divergence times
read alignment
target-capture
DNA-sequences
species
trees
gene trees
radiation
algorithms
markers
rivers
Evolutionary Biology

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ref (subject category)
art (subject category)

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NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Biological Syste ...

Articles in the publication: Systematic Biolo ...

By the university: University of Gothenburg

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