Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex

Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phyl...

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Main Authors: Chan, Kin O., Hutter, Carl R., Wood, Perry L., Grismer, L. L., Das, Indraneil, Brown, Rafe M.
Format: Article
Language:English
Published: John Wiley & Sons, Inc 2020
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Online Access:http://ir.unimas.my/id/eprint/31951/1/Gene%20flow%20creates%20a%20mirage%20of%20cryptic%20species%20in%20a%20Southeast%20Asian%20spotted%20stream%20frog%20complex.pdf
http://ir.unimas.my/id/eprint/31951/
https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.15603
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spelling my.unimas.ir.319512023-03-30T06:33:55Z http://ir.unimas.my/id/eprint/31951/ Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex Chan, Kin O. Hutter, Carl R. Wood, Perry L. Grismer, L. L. Das, Indraneil Brown, Rafe M. Q Science (General) QL Zoology Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation. John Wiley & Sons, Inc 2020 Article PeerReviewed text en http://ir.unimas.my/id/eprint/31951/1/Gene%20flow%20creates%20a%20mirage%20of%20cryptic%20species%20in%20a%20Southeast%20Asian%20spotted%20stream%20frog%20complex.pdf Chan, Kin O. and Hutter, Carl R. and Wood, Perry L. and Grismer, L. L. and Das, Indraneil and Brown, Rafe M. (2020) Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex. Molecular Ecology. pp. 1-18. https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.15603 10.1111/mec.15603
institution Universiti Malaysia Sarawak
building Centre for Academic Information Services (CAIS)
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaysia Sarawak
content_source UNIMAS Institutional Repository
url_provider http://ir.unimas.my/
language English
topic Q Science (General)
QL Zoology
spellingShingle Q Science (General)
QL Zoology
Chan, Kin O.
Hutter, Carl R.
Wood, Perry L.
Grismer, L. L.
Das, Indraneil
Brown, Rafe M.
Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex
description Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
format Article
author Chan, Kin O.
Hutter, Carl R.
Wood, Perry L.
Grismer, L. L.
Das, Indraneil
Brown, Rafe M.
author_facet Chan, Kin O.
Hutter, Carl R.
Wood, Perry L.
Grismer, L. L.
Das, Indraneil
Brown, Rafe M.
author_sort Chan, Kin O.
title Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex
title_short Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex
title_full Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex
title_fullStr Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex
title_full_unstemmed Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex
title_sort gene flow creates a mirage of cryptic species in a southeast asian spotted stream frog complex
publisher John Wiley & Sons, Inc
publishDate 2020
url http://ir.unimas.my/id/eprint/31951/1/Gene%20flow%20creates%20a%20mirage%20of%20cryptic%20species%20in%20a%20Southeast%20Asian%20spotted%20stream%20frog%20complex.pdf
http://ir.unimas.my/id/eprint/31951/
https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.15603
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