Frog phylogeny : A time-calibrated, species-level tree based on hundreds of loci and 5,242 species
Copyright © 2023 Elsevier Inc. All rights reserved..
Large-scale, time-calibrated phylogenies from supermatrix studies have become crucial for evolutionary and ecological studies in many groups of organisms. However, in frogs (anuran amphibians), there is a serious problem with existing supermatrix estimates. Specifically, these trees are based on a limited number of loci (15 or fewer), and the higher-level relationships estimated are discordant with recent phylogenomic estimates based on much larger numbers of loci. Here, we attempted to rectify this problem by generating an expanded supermatrix and combining this with data from phylogenomic studies. To assist in aligning ribosomal sequences for this supermatrix, we developed a new program (TaxonomyAlign) to help perform taxonomy-guided alignments. The new combined matrix contained 5,242 anuran species with data from 307 markers, but with 95% missing data overall. This dataset represented a 71% increase in species sampled relative to the previous largest supermatrix analysis of anurans (adding 2,175 species). Maximum-likelihood analyses generated a tree in which higher-level relationships (and estimated clade ages) were generally concordant with those from phylogenomic analyses but were more discordant with the previous largest supermatrix analysis. We found few obvious problems arising from the extensive missing data in most species. We also generated a set of 100 time-calibrated trees for use in comparative analyses. Overall, we provide an improved estimate of anuran phylogeny based on the largest number of combined taxa and markers to date. More broadly, we demonstrate the potential to combine phylogenomic and supermatrix analyses in other groups of organisms.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2023 |
|---|---|
| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:188 |
|---|---|
| Enthalten in: |
Molecular phylogenetics and evolution - 188(2023) vom: 24. Nov., Seite 107907 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Portik, Daniel M [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
Anurans |
|---|
| Anmerkungen: |
Date Completed 18.09.2023 Date Revised 25.09.2023 published: Print-Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1016/j.ympev.2023.107907 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM361317077 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM361317077 | ||
| 003 | DE-627 | ||
| 005 | 20231226084902.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231226s2023 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1016/j.ympev.2023.107907 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1204.xml |
| 035 | |a (DE-627)NLM361317077 | ||
| 035 | |a (NLM)37633542 | ||
| 035 | |a (PII)S1055-7903(23)00207-5 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Portik, Daniel M |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Frog phylogeny |b A time-calibrated, species-level tree based on hundreds of loci and 5,242 species |
| 264 | 1 | |c 2023 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 18.09.2023 | ||
| 500 | |a Date Revised 25.09.2023 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2023 Elsevier Inc. All rights reserved. | ||
| 520 | |a Large-scale, time-calibrated phylogenies from supermatrix studies have become crucial for evolutionary and ecological studies in many groups of organisms. However, in frogs (anuran amphibians), there is a serious problem with existing supermatrix estimates. Specifically, these trees are based on a limited number of loci (15 or fewer), and the higher-level relationships estimated are discordant with recent phylogenomic estimates based on much larger numbers of loci. Here, we attempted to rectify this problem by generating an expanded supermatrix and combining this with data from phylogenomic studies. To assist in aligning ribosomal sequences for this supermatrix, we developed a new program (TaxonomyAlign) to help perform taxonomy-guided alignments. The new combined matrix contained 5,242 anuran species with data from 307 markers, but with 95% missing data overall. This dataset represented a 71% increase in species sampled relative to the previous largest supermatrix analysis of anurans (adding 2,175 species). Maximum-likelihood analyses generated a tree in which higher-level relationships (and estimated clade ages) were generally concordant with those from phylogenomic analyses but were more discordant with the previous largest supermatrix analysis. We found few obvious problems arising from the extensive missing data in most species. We also generated a set of 100 time-calibrated trees for use in comparative analyses. Overall, we provide an improved estimate of anuran phylogeny based on the largest number of combined taxa and markers to date. More broadly, we demonstrate the potential to combine phylogenomic and supermatrix analyses in other groups of organisms | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, U.S. Gov't, Non-P.H.S. | |
| 650 | 4 | |a Anurans | |
| 650 | 4 | |a Divergence times | |
| 650 | 4 | |a Missing data | |
| 650 | 4 | |a Phylogenomics | |
| 650 | 4 | |a Supermatrix | |
| 700 | 1 | |a Streicher, Jeffrey W |e verfasserin |4 aut | |
| 700 | 1 | |a Wiens, John J |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Molecular phylogenetics and evolution |d 1993 |g 188(2023) vom: 24. Nov., Seite 107907 |w (DE-627)NLM013242059 |x 1095-9513 |7 nnns |
| 773 | 1 | 8 | |g volume:188 |g year:2023 |g day:24 |g month:11 |g pages:107907 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1016/j.ympev.2023.107907 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 188 |j 2023 |b 24 |c 11 |h 107907 | ||