A Complete Species-Level Phylogeny of the Erythrura Parrotfinches (Aves: Estrildidae)

DeCicco, Lucas H.; DeRaad, Devon A.; Ostrow, Emily N.; Moyle, Robert G.

doi:10.2139/ssrn.4387240

Cited by 1 publication

(5 citation statements)

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“…Studies using similar SNP calling protocols have shown the effectiveness of SNP datasets extracted from UCE enriched reads (e.g. McCormack et al, 2016;Decicco et al, 2023;DeRaad et al, 2023;McCormack et al 2023), including in comparisons with other reduced capture methods such as RAD-Seq (Harvey et al, 2016;Manthey et al, 2020). Studies in arthropods have commonly applied UCEs and other target capture methods for resolving deeper time-scales (E.g.…”

Section: Performance Of Analysesmentioning

confidence: 99%

“…3 samples removed). Because of the lack of an appropriate reference genome, we generated a pseudo-reference genome (e.g., McCormack et al 2016;DeRaad et al 2023) for read mapping and SNP calling. In brief, this approach involves the de novo assembly of UCE loci using phyluce (Faircloth, 2016), which can then be used as reference sequence for mapping cleaned UCE reads from each sample and performing SNP calling.…”

Section: Population Geneticsmentioning

confidence: 99%

“…Blaimer et al, 2016;Branstetter et al, 2023;Freitas et al, 2023;Goodman et al, 2023) and are especially well documented in birds (e.g. Lim and Braun, 2016;Moyle et al, 2016;Salter et al 2022;Hruska et al, 2023;Decicco et al, 2023;. It is likely that processing captured data outside of Phyluce (e.g.…”

Section: Performance Of Analysesmentioning

confidence: 99%

“…mapping reads to a reference genome, aligning manually with MAFFT to adjust parameters., etc.) as in Decicco et al (2023) could remedy some of these effects.…”

Section: Performance Of Analysesmentioning

confidence: 99%

“…To further examine geographic structure within the complex, we harvest single nucleotide polymorphisms (SNPs) from our UCE alignments to use as input for genetic clustering analyses. To call SNPs from UCE alignments we extended previous approaches (McCormack et al 2016;DeRaad et al 2023), adding the novel step of constructing a chimeric UCE reference sequence set so that all captured UCEs across all sampled taxa are available for read mapping and SNP calling. This method effectively maximized the size of our SNP dataset, despite the lack of availability of an appropriate reference genome for this group.…”

Section: Introductionmentioning

confidence: 99%

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A shallow-scale phylogenomics approach reveals parallel patterns of diversification among sympatric populations of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)

Baca,

Gustafson,

DeRaad

et al. 2023

Preprint

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TheNotomicrus trailispecies group (Coleoptera: Noteridae) is a lineage of aquatic beetles distributed throughout South America and extends into Mexico and the West Indies. Previous research has revealed a species complex within this group, with multiple distinct clades sharing overlapping distributions and lineages attributed toN. trailiand the closely relatedN. gracilipesrecovered as polyphyletic. Here, we perform targeted capture of ultraconserved elements (UCEs) to examine relationships and patterns of evolution within theN. trailigroup. First, we use short-read whole genome sequencing of four noterid genera to design a noterid-specific UCE probe set (Noteridae 3.4Kv1) targeting over 3,400 unique loci. Using this probe set, we capture UCE data from population-level sampling of 44trailigroup specimens from across the Neotropics, with an emphasis on the Guiana Shield where distributions of several putativeN. trailigroup populations overlap. We subject the resulting data matrix to various trimming and data completeness treatments and reconstruct the phylogeny with both concatenated maximum likelihood and coalescent congruent methods. We recover robust phylogenetic estimates that identify several phylogenetically distinct clades within thetrailigroup that share overlapping distributions. To test for the genetic distinctiveness of populations, we extract single nucleotide polymorphism (SNP) data from UCE alignments and examine patterns of genetic clustering using principal component analyses (PCAs) and STRUCTURE. Population genetic results are highly concordant with recovered phylogenetic structure, revealing a high degree of co-ancestry shared within identified clades, contrasting with limited ancestry sharing between clades. We recover a pattern consistent with repeated diversification and dispersal of thetrailigroup in the Neotropics, highlighting the efficacy of a tailored UCE approach for facilitating shallow-scale phylogenetic reconstructions and population genetic analyses, which can reveal novel aspects of coleopteran phylogeography.

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Section: Performance Of Analysesmentioning

confidence: 99%

Section: Population Geneticsmentioning

confidence: 99%

Section: Performance Of Analysesmentioning

confidence: 99%

“…mapping reads to a reference genome, aligning manually with MAFFT to adjust parameters., etc.) as in Decicco et al (2023) could remedy some of these effects.…”

Section: Performance Of Analysesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

A shallow-scale phylogenomics approach reveals parallel patterns of diversification among sympatric populations of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)

Baca,

Gustafson,

DeRaad

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

A Complete Species-Level Phylogeny of the Erythrura Parrotfinches (Aves: Estrildidae)

Cited by 1 publication

References 0 publications

A shallow-scale phylogenomics approach reveals parallel patterns of diversification among sympatric populations of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)

A shallow-scale phylogenomics approach reveals parallel patterns of diversification among sympatric populations of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)

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