Species detection and identification in sexual organisms using population genetic theory and DNA sequences.

Phylogenetic trees of DNA sequences of a group of specimens may include clades of two kinds: those produced by stochastic processes (random genetic drift) within a species, and clades that represent different species. The ratio of the mean pairwise sequence difference between a pair of clades (K) to...

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Autor principal:	C William Birky
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cd36b66e36b34619b78b14cc3bd26fe0
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spelling	oai:doaj.org-article:cd36b66e36b34619b78b14cc3bd26fe02021-11-18T08:02:41ZSpecies detection and identification in sexual organisms using population genetic theory and DNA sequences.1932-620310.1371/journal.pone.0052544https://doaj.org/article/cd36b66e36b34619b78b14cc3bd26fe02013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23308113/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Phylogenetic trees of DNA sequences of a group of specimens may include clades of two kinds: those produced by stochastic processes (random genetic drift) within a species, and clades that represent different species. The ratio of the mean pairwise sequence difference between a pair of clades (K) to the mean pairwise sequence difference within a clade (θ) can be used to determine whether the clades are samples from different species (K/θ ≥ 4) or the same species (K/θ<4) with probability ≥ 0.95. Previously I applied this criterion to delimit species of asexual organisms. Here I use data from the literature to show how it can also be applied to delimit sexual species using four groups of sexual organisms as examples: ravens, spotted leopards, sea butterflies, and liverworts. Mitochondrial or chloroplast genes are used because these segregate earlier during speciation than most nuclear genes and hence detect earlier stages of speciation. In several cases the K/θ ratio was greater than 4, confirming the original authors' intuition that the clades were sufficiently different to be assigned to different species. But the K/θ ratio split each of two liverwort species into two evolutionary species, and showed that support for the distinction between the common and Chihuahuan raven species is weak. I also discuss some possible sources of error in using the K/θ ratio; the most significant one would be cases where males migrate between different populations but females do not, making the use of maternally inherited organelle genes problematic. The K/θ ratio must be used with some caution, like all other methods for species delimitation. Nevertheless, it is a simple theory-based quantitative method for using DNA sequences to make rigorous decisions about species delimitation in sexual as well as asexual eukaryotes.C William BirkyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 1, p e52544 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q C William Birky Species detection and identification in sexual organisms using population genetic theory and DNA sequences.
description	Phylogenetic trees of DNA sequences of a group of specimens may include clades of two kinds: those produced by stochastic processes (random genetic drift) within a species, and clades that represent different species. The ratio of the mean pairwise sequence difference between a pair of clades (K) to the mean pairwise sequence difference within a clade (θ) can be used to determine whether the clades are samples from different species (K/θ ≥ 4) or the same species (K/θ<4) with probability ≥ 0.95. Previously I applied this criterion to delimit species of asexual organisms. Here I use data from the literature to show how it can also be applied to delimit sexual species using four groups of sexual organisms as examples: ravens, spotted leopards, sea butterflies, and liverworts. Mitochondrial or chloroplast genes are used because these segregate earlier during speciation than most nuclear genes and hence detect earlier stages of speciation. In several cases the K/θ ratio was greater than 4, confirming the original authors' intuition that the clades were sufficiently different to be assigned to different species. But the K/θ ratio split each of two liverwort species into two evolutionary species, and showed that support for the distinction between the common and Chihuahuan raven species is weak. I also discuss some possible sources of error in using the K/θ ratio; the most significant one would be cases where males migrate between different populations but females do not, making the use of maternally inherited organelle genes problematic. The K/θ ratio must be used with some caution, like all other methods for species delimitation. Nevertheless, it is a simple theory-based quantitative method for using DNA sequences to make rigorous decisions about species delimitation in sexual as well as asexual eukaryotes.
format	article
author	C William Birky
author_facet	C William Birky
author_sort	C William Birky
title	Species detection and identification in sexual organisms using population genetic theory and DNA sequences.
title_short	Species detection and identification in sexual organisms using population genetic theory and DNA sequences.
title_full	Species detection and identification in sexual organisms using population genetic theory and DNA sequences.
title_fullStr	Species detection and identification in sexual organisms using population genetic theory and DNA sequences.
title_full_unstemmed	Species detection and identification in sexual organisms using population genetic theory and DNA sequences.
title_sort	species detection and identification in sexual organisms using population genetic theory and dna sequences.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/cd36b66e36b34619b78b14cc3bd26fe0
work_keys_str_mv	AT cwilliambirky speciesdetectionandidentificationinsexualorganismsusingpopulationgenetictheoryanddnasequences
_version_	1718422633497755648

Species detection and identification in sexual organisms using population genetic theory and DNA sequences.

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