Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow‐mouth frogs

Alexander, Alana; Su, Yong‐Chao; Oliveros, Carl H.; Olson, Karen V.; Travers, Scott L.; Brown, Rafe M.

doi:10.1111/evo.13133

Cited by 47 publications

(33 citation statements)

References 92 publications

(151 reference statements)

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“…2 left), the representative of the Lycaenidae family. The two families, Riodinidae and Lycaenidae, are known to be close to each other from morphological and DNA evidence (Alexander et al, 2017; Robbins, 1988; Wahlberg et al, 2005). Terminal branches leading to Calephelis and Calycopis are long compared to others, as well as the branch leading to the ancestor of Riodinidae and Lycaenidae.…”

Section: Resultsmentioning

confidence: 99%

The first complete genomes of Metalmarks and the classification of butterfly families

Cong

Shen

et al. 2017

Genomics

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Sequencing complete genomes of all major phylogenetic groups of organisms opens unprecedented opportunities to study evolution and genetics. We report draft genomes of Calephelis nemesis and Calephelis virginiensis, representatives of the family Riodinidae. They complete the genomic coverage of butterflies at the family level. At 809 and 855 Mbp, respectively, they become the largest available Lepidoptera genomes. Comparison of butterfly genomes shows that the divergence between Riodinidae and Lycaenidae dates to the time when other families started to diverge into subfamilies. Thus, Riodinidae may be considered a subfamily of Lycaenidae. Calephelis species exhibit unique gene expansions in actin-disassembling factor, cofilin, and chitinase. The functional implications of these gene expansions are not clear, but they may aid molting of caterpillars covered in extensive setae. The two Calephelis species diverged about 5 million years ago and they differ in proteins involved in metabolism, circadian clock, regulation of development, and immune responses.

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Section: Resultsmentioning

confidence: 99%

The first complete genomes of Metalmarks and the classification of butterfly families

Cong

Shen

et al. 2017

Genomics

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“…Ultra-conserved elements have been previously used in frogs, with ~50% success capture rate (e.g. Alexander et al 2016;Pie et al 2018;Streicher et al 2018). For this study, we selected a subset of the orthologous UCEs previously sequenced from Kaloula (Microhylidae: Alexander et al 2016).…”

Section: Reduced-ranoidea Marker Selectionmentioning

confidence: 99%

“…We introduce FrogCap, a publicly available collection of molecular markers for all frogs that can be adapted into sequence capture probe sets that includes markers from a variety of data types (exons, introns, UCEs, markers sequenced previously using traditional/Sanger methods, independent markers to extract variants). We provide a modular, large, and flexible collection of tested markers and probes corresponding to ~15,000 markers, which unifies previous sequencing via the inclusion of "legacy" Sanger sequencing markers traditionally used in phylogenetic studies (Figure 1;Frost et al 2006;Pyron & Wiens 2011;Feng et al 2017) and UCEs that have been successfully captured in anurans (Alexander et al 2016;Streicher et al 2018). The FrogCap marker set is designed to be modular, such that subsets of the markers can be selected based on the probe set size, type of research question, and the taxonomic scale being addressed.…”

Section: Introductionmentioning

confidence: 99%

FrogCap: A modular sequence capture probe set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales

Hutter

Cobb

Portik

et al. 2019

Preprint

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Despite the increasing use of high-throughput sequencing in phylogenetics, many phylogenetic relationships remain difficult to resolve because of conflict between gene trees and species trees. Selection of different types of markers (i.e. protein-coding exons, non-coding introns, ultraconserved elements) is becoming important to alleviate these phylogenomic challenges. For evolutionary studies in frogs, we introduce the new publicly available FrogCap suite of genomic resources, which is a large and flexible collection of probes corresponding to ~15,000 markers that unifies previous frog sequencing work. FrogCap is designed to be modular, such that subsets of markers can be selected based on the phylogenetic scale of the intended study. FrogCap uses a variety of molecular marker types that include newly obtained exons and introns, previously sequenced UCEs, and Sanger-sequencing markers, which span a range of alignment lengths (100-12,000 base pairs). We tested three probe sets from FrogCap using 105 samples across five phylogenetic scales, comparing probes designed using a consensus-or genome-based approach. We also tested the effects of using different bait kit sizes on depth of coverage and missing data. We found that larger bait kits did not result in lowered depth of coverage or increased missing data. We also found that sensitivity, specificity, and missing data are not related to genetic distance in the consensus-based probe design, suggesting that this approach has greater success and overcomes a major hurdle in probe design. We observed sequence capture success (in terms of missing data, quantity of sequence data, recovered marker length, and number of informative sites) and compared them at all phylogenetic scales. The incorporation of different molecular marker types allowed recovery of the variation required for resolving difficult phylogenetic relationships and for performing population genetic studies. Altogether, FrogCap is a valuable and adaptable resource for performing high-throughput sequencing projects across variable timescales.

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“…Mitochondrial ("mt") sequence data are often obtained as "by-catch", given that mitochondrial genomes are not targeted during library preparation, during sequence capture dataset sequencing. We used a pipeline developed by Alexander et al (2017) and freely available on github (https://github.com/laninsky/Pulling-out-mitogenomes-from-UCE-data/) to assemble whole mitochondrial genomes for the individuals sequenced in this study. Briefly, we used NCBI BLAST (Altschul et al 1990) and the mitochondrial genome of Liolaemus chehuachekenk (assembled into a single contig during de novo assembly and verified in NCBI BLAST) to serve as a reference library.…”

Section: Bioinformatics and Dataset Assemblymentioning

confidence: 99%

“…Alternatively, when parent species are well-differentiated and belong to independent clades, the alleles of hybrid individuals are readily recovered in the two different clades (e.g. Leaché and McGuire 2006;Alexander et al 2017). Furthermore, when an entire species/population is of hybrid origin, or when hybrid individuals are represented by a single consensus genotype (e.g., not phased alleles), phylogenetic support values will be reduced (due to the ambiguous placement of the admixed genotypes/individuals); this fact has been formalized into software that detects hybrids (Schneider et al 2016).…”

Section: Detecting Hybridization With Sequence Datamentioning

confidence: 99%

Phylogenomic evidence for a recent and rapid radiation of lizards in the Patagonian Liolaemus fitzingerii species group

Grummer¹,

Morando²,

Ávila³

et al. 2018

Molecular Phylogenetics and Evolution

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Rapid evolutionary radiations are difficult to resolve because divergence events are nearly synchronous and gene flow among nascent species can be high, resulting in a phylogenetic "bush". Large datasets composed of sequence loci from across the genome can potentially help resolve some of these difficult phylogenetic problems. A suitable test case is the Liolaemus fitzingerii species group of lizards, which includes twelve species that are broadly distributed in Argentinean Patagonia. The species in the group have had a complex evolutionary history that has led to high morphological variation and unstable taxonomy. We generated a sequence capture dataset for 28 ingroup individuals of 580 nuclear loci, alongside a mitogenomic dataset, to infer phylogenetic relationships among species in this group. Relationships among species were generally weakly supported with the nuclear data, and along with an inferred age of ∼2.6 million years old, indicate either rapid evolution, hybridization, incomplete lineage sorting, non-informative data, or a combination thereof. We inferred a signal of mito-nuclear discordance, indicating potential hybridization between L. melanops and L. martorii, and phylogenetic network analyses provided support for 5 reticulation events among species. Phasing the nuclear loci did not provide additional insight into relationships or suspected patterns of hybridization. Only one clade, composed of L. camarones, L. fitzingerii, and L. xanthoviridis was recovered across all analyses. Genomic datasets provide molecular systematists with new opportunities to resolve difficult phylogenetic problems, yet the lack of phylogenetic resolution in Patagonian Liolaemus is biologically meaningful and indicative of a recent and rapid evolutionary radiation. The phylogenetic relationships of the Liolaemus fitzingerii group may be best modeled as a reticulated network instead of a bifurcating phylogeny.

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Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow‐mouth frogs

Cited by 47 publications

References 92 publications

The first complete genomes of Metalmarks and the classification of butterfly families

The first complete genomes of Metalmarks and the classification of butterfly families

FrogCap: A modular sequence capture probe set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales

Phylogenomic evidence for a recent and rapid radiation of lizards in the Patagonian Liolaemus fitzingerii species group

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