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Using population genetic theory and DNA sequences for species detection and identification in asexual organisms.

ABSTRACT: BACKGROUND:It is widely agreed that species are fundamental units of biology, but there is little agreement on a definition of species or on an operational criterion for delimiting species that is applicable to all organisms. METHODOLOGY/PRINCIPAL FINDINGS:We focus on asexual eukaryotes as the simplest case for investigating species and speciation. We describe a model of speciation in asexual organisms based on basic principles of population and evolutionary genetics. The resulting species are independently evolving populations as described by the evolutionary species concept or the general lineage species concept. Based on this model, we describe a procedure for using gene sequences from small samples of individuals to assign them to the same or different species. Using this method of species delimitation, we demonstrate the existence of species as independent evolutionary units in seven groups of invertebrates, fungi, and protists that reproduce asexually most or all of the time. CONCLUSIONS/SIGNIFICANCE:This wide evolutionary sampling establishes the general existence of species and speciation in asexual organisms. The method is well suited for measuring species diversity when phenotypic data are insufficient to distinguish species, or are not available, as in DNA barcoding and environmental sequencing. We argue that it is also widely applicable to sexual organisms.

SUBMITTER: Birky CW

PROVIDER: S-EPMC2869354 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature

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Using population genetic theory and DNA sequences for species detection and identification in asexual organisms.

Birky C William CW Adams Joshua J Gemmel Marlea M Perry Julia J

PloS one 20100513 5

<h4>Background</h4>It is widely agreed that species are fundamental units of biology, but there is little agreement on a definition of species or on an operational criterion for delimiting species that is applicable to all organisms.<h4>Methodology/principal findings</h4>We focus on asexual eukaryotes as the simplest case for investigating species and speciation. We describe a model of speciation in asexual organisms based on basic principles of population and evolutionary genetics. The resultin ...[more]

PMID: 20498705

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Project description:Paphiopedilum is among the most popular ornamental orchid genera due to its unique slipper flowers and attractive leaf coloration. Most of the Paphiopedilum species are in critical danger due to over-exploitation. They were listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which prevents their being traded across borders. While most Paphiopedilum species are distinctive, owing to their respective flowers, their vegetative features are more similar and undistinguished. Hence, the conservation of these species is challenging, as most traded specimins are immature and non-flowered. An urgent need exists for effective identification methods to prevent further illegal trading of Paphiopedilum species. DNA barcoding is a rapid and sensitive method for species identification, at any developmental stage, using short DNA sequences. In this study, eight loci, i.e., ITS, LEAFY, ACO, matK, trnL, rpoB, rpoC1, and trnH-psbA, were screened for potential barcode sequences on the Vietnamese Paphiopedilum species. In total, 17 out of 22 Paphiopedilum species were well identified. The studied DNA sequences were deposited to GenBank, in which Paphiopedilum dalatense accessions were introduced for the first time. ACO, LEAFY, and trnH-psbA were limited in amplification rate for Paphiopedilum. ITS was the best single barcode. Single ITS could be used along with nucleotide polymorphism characteristics for species discrimination. The combination of ITS + matK was the most efficient identification barcode for Vietnamese Paphiopedilum species. This barcode also succeeded in recognizing misidentified or wrongly-named traded samples. Different bioinformatics programs and algorithms for establishing phylogenetic trees were also compared in the study to propose quick, simple, and effective tools for practical use. It was proved that both the Bayesian Inference method in the MRBAYES program and the neighbor-joining method in the MEGA software met the criteria. Our study provides a barcoding database of Vietnamese Paphiopedilum which may significantly contribute to the control and conservation of these valuable species.

Dataset Information

Using population genetic theory and DNA sequences for species detection and identification in asexual organisms.

Publications

Using population genetic theory and DNA sequences for species detection and identification in asexual organisms.

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