Phylogenomic history of enigmatic pygmy perches

Implications for biogeography, taxonomy and conservation

Sean J. Buckley, Fabricius M.C.B. Domingos, Catherine R.M. Attard, Chris J. Brauer, Jonathan Sandoval-Castillo, Ryan Lodge, Peter J. Unmack, Luciano B. Beheregaray

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater fishes that have a puzzling biogeographic disjunction across southern Australia. Current understanding of pygmy perch phylogenetic relationships suggests past east–west migrations across a vast expanse of now arid habitat in central southern Australia, a region lacking contemporary rivers. Pygmy perches also represent a threatened group with confusing taxonomy and potentially cryptic species diversity. Here, we present the first study of the evolutionary history of pygmy perches based on genome-wide information. Data from 13 991 ddRAD loci and a concatenated sequence of 1 075 734 bp were generated for all currently described and potentially cryptic species. Phylogenetic relationships, biogeographic history and cryptic diversification were inferred using a framework that combines phylogenomics, species delimitation and estimation of divergence times. The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east–west events of divergence within the group across the Australian continent. These results also resolved discordance between nuclear and mitochondrial data from a previous study. In addition, we propose three cryptic species within a southwestern species complex. The finding of potentially new species demonstrates that pygmy perches may be even more susceptible to ecological and demographic threats than previously thought. Our results have substantial implications for improving conservation legislation of pygmy perch lineages, especially in southwestern Western Australia.

Original languageEnglish
Article number172125
Pages (from-to)1-17
Number of pages17
JournalRoyal Society Open Science
Volume5
Issue number6
DOIs
Publication statusPublished - 13 Jun 2018

Fingerprint

biogeography
genome
history
divergence
phylogenetics
species complex
species diversity
legislation
phylogeny
new species
habitat
fish
river
continent

Cite this

Buckley, S. J., Domingos, F. M. C. B., Attard, C. R. M., Brauer, C. J., Sandoval-Castillo, J., Lodge, R., ... Beheregaray, L. B. (2018). Phylogenomic history of enigmatic pygmy perches: Implications for biogeography, taxonomy and conservation. Royal Society Open Science, 5(6), 1-17. [172125]. https://doi.org/10.1098/rsos.172125
Buckley, Sean J. ; Domingos, Fabricius M.C.B. ; Attard, Catherine R.M. ; Brauer, Chris J. ; Sandoval-Castillo, Jonathan ; Lodge, Ryan ; Unmack, Peter J. ; Beheregaray, Luciano B. / Phylogenomic history of enigmatic pygmy perches : Implications for biogeography, taxonomy and conservation. In: Royal Society Open Science. 2018 ; Vol. 5, No. 6. pp. 1-17.
@article{688fba4c03094fa9a7f5ac8967919078,
title = "Phylogenomic history of enigmatic pygmy perches: Implications for biogeography, taxonomy and conservation",
abstract = "Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater fishes that have a puzzling biogeographic disjunction across southern Australia. Current understanding of pygmy perch phylogenetic relationships suggests past east–west migrations across a vast expanse of now arid habitat in central southern Australia, a region lacking contemporary rivers. Pygmy perches also represent a threatened group with confusing taxonomy and potentially cryptic species diversity. Here, we present the first study of the evolutionary history of pygmy perches based on genome-wide information. Data from 13 991 ddRAD loci and a concatenated sequence of 1 075 734 bp were generated for all currently described and potentially cryptic species. Phylogenetic relationships, biogeographic history and cryptic diversification were inferred using a framework that combines phylogenomics, species delimitation and estimation of divergence times. The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east–west events of divergence within the group across the Australian continent. These results also resolved discordance between nuclear and mitochondrial data from a previous study. In addition, we propose three cryptic species within a southwestern species complex. The finding of potentially new species demonstrates that pygmy perches may be even more susceptible to ecological and demographic threats than previously thought. Our results have substantial implications for improving conservation legislation of pygmy perch lineages, especially in southwestern Western Australia.",
keywords = "Cryptic species, DdRAD-seq, Freshwater fish, Historical biogeography, Nannoperca, Phylogeography",
author = "Buckley, {Sean J.} and Domingos, {Fabricius M.C.B.} and Attard, {Catherine R.M.} and Brauer, {Chris J.} and Jonathan Sandoval-Castillo and Ryan Lodge and Unmack, {Peter J.} and Beheregaray, {Luciano B.}",
year = "2018",
month = "6",
day = "13",
doi = "10.1098/rsos.172125",
language = "English",
volume = "5",
pages = "1--17",
journal = "Royal Society Open Science",
issn = "2054-5703",
publisher = "The Royal Society",
number = "6",

}

Buckley, SJ, Domingos, FMCB, Attard, CRM, Brauer, CJ, Sandoval-Castillo, J, Lodge, R, Unmack, PJ & Beheregaray, LB 2018, 'Phylogenomic history of enigmatic pygmy perches: Implications for biogeography, taxonomy and conservation', Royal Society Open Science, vol. 5, no. 6, 172125, pp. 1-17. https://doi.org/10.1098/rsos.172125

Phylogenomic history of enigmatic pygmy perches : Implications for biogeography, taxonomy and conservation. / Buckley, Sean J.; Domingos, Fabricius M.C.B.; Attard, Catherine R.M.; Brauer, Chris J.; Sandoval-Castillo, Jonathan; Lodge, Ryan; Unmack, Peter J.; Beheregaray, Luciano B.

In: Royal Society Open Science, Vol. 5, No. 6, 172125, 13.06.2018, p. 1-17.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Phylogenomic history of enigmatic pygmy perches

T2 - Implications for biogeography, taxonomy and conservation

AU - Buckley, Sean J.

AU - Domingos, Fabricius M.C.B.

AU - Attard, Catherine R.M.

AU - Brauer, Chris J.

AU - Sandoval-Castillo, Jonathan

AU - Lodge, Ryan

AU - Unmack, Peter J.

AU - Beheregaray, Luciano B.

PY - 2018/6/13

Y1 - 2018/6/13

N2 - Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater fishes that have a puzzling biogeographic disjunction across southern Australia. Current understanding of pygmy perch phylogenetic relationships suggests past east–west migrations across a vast expanse of now arid habitat in central southern Australia, a region lacking contemporary rivers. Pygmy perches also represent a threatened group with confusing taxonomy and potentially cryptic species diversity. Here, we present the first study of the evolutionary history of pygmy perches based on genome-wide information. Data from 13 991 ddRAD loci and a concatenated sequence of 1 075 734 bp were generated for all currently described and potentially cryptic species. Phylogenetic relationships, biogeographic history and cryptic diversification were inferred using a framework that combines phylogenomics, species delimitation and estimation of divergence times. The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east–west events of divergence within the group across the Australian continent. These results also resolved discordance between nuclear and mitochondrial data from a previous study. In addition, we propose three cryptic species within a southwestern species complex. The finding of potentially new species demonstrates that pygmy perches may be even more susceptible to ecological and demographic threats than previously thought. Our results have substantial implications for improving conservation legislation of pygmy perch lineages, especially in southwestern Western Australia.

AB - Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater fishes that have a puzzling biogeographic disjunction across southern Australia. Current understanding of pygmy perch phylogenetic relationships suggests past east–west migrations across a vast expanse of now arid habitat in central southern Australia, a region lacking contemporary rivers. Pygmy perches also represent a threatened group with confusing taxonomy and potentially cryptic species diversity. Here, we present the first study of the evolutionary history of pygmy perches based on genome-wide information. Data from 13 991 ddRAD loci and a concatenated sequence of 1 075 734 bp were generated for all currently described and potentially cryptic species. Phylogenetic relationships, biogeographic history and cryptic diversification were inferred using a framework that combines phylogenomics, species delimitation and estimation of divergence times. The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east–west events of divergence within the group across the Australian continent. These results also resolved discordance between nuclear and mitochondrial data from a previous study. In addition, we propose three cryptic species within a southwestern species complex. The finding of potentially new species demonstrates that pygmy perches may be even more susceptible to ecological and demographic threats than previously thought. Our results have substantial implications for improving conservation legislation of pygmy perch lineages, especially in southwestern Western Australia.

KW - Cryptic species

KW - DdRAD-seq

KW - Freshwater fish

KW - Historical biogeography

KW - Nannoperca

KW - Phylogeography

UR - http://www.scopus.com/inward/record.url?scp=85048525743&partnerID=8YFLogxK

UR - http://www.mendeley.com/research/phylogenomic-history-enigmatic-pygmy-perches-implications-biogeography-taxonomy-conservation-1

U2 - 10.1098/rsos.172125

DO - 10.1098/rsos.172125

M3 - Article

VL - 5

SP - 1

EP - 17

JO - Royal Society Open Science

JF - Royal Society Open Science

SN - 2054-5703

IS - 6

M1 - 172125

ER -

Buckley SJ, Domingos FMCB, Attard CRM, Brauer CJ, Sandoval-Castillo J, Lodge R et al. Phylogenomic history of enigmatic pygmy perches: Implications for biogeography, taxonomy and conservation. Royal Society Open Science. 2018 Jun 13;5(6):1-17. 172125. https://doi.org/10.1098/rsos.172125