Using Population Genetic Theory and DNA Sequences for Species Detection and Identification in Asexual Organisms

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.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.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

Rapid Evolution of Enormous, Multichromosomal Genomes in Flowering Plant Mitochondria with Exceptionally High Mutation Rates

A pair of species within the genus Silene have evolved the largest known mitochondrial genomes, coinciding with extreme changes in mutation rate, recombination activity, and genome structure

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 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

Models of successive times after speciation (A–C) with sampling at stage C (D).

<p>The bases of the inverted shaded isosceles triangles in A–C represent populations with effective size N_e individuals, while the vertex represent the most recent common ancestor. The altitude of the triangles represents coalescent time = 2N_e generations. The vertical bar represents a barrier to gene flow that splits the population in two. The inset in B shows some of the genes (black circles) and their relationships. Red and yellow circles in C and D are samples of genes. Nucleotide diversities π of the two species are estimated by the mean sequence differences a_ia_j and b_ibj; θ is a function of π and the sample sizes. K is the mean of the sequence differences a_ib_i, corrected for multiple hits.</p

Neighbor-joining tree of partial sequences of the chloroplast genes AtpB and rbcL genes from liverworts.

<p>Sequence distances were small and not corrected for multiple hits. Dashed lines indicate clades supported by less than 500/1000 bootstrap replicas. Black squares indicate clades that are species identified by Heinrichs et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052544#pone.0052544-Heinrich1" target="_blank">[44]</a> and verified using Kθ; red squares are species delimited by K/θ but not distinguished by Heinrichs et al. The probability of reciprocal monophyly in the populations from which the individuals were sampled was >0.95 in each case.</p

Neighbor-joining tree of raven cox1 sequences.

<p>Closed circles indicate clades that are different species, with D/θ>>4 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052544#pone-0052544-t001" target="_blank">Table 1</a>). Open circles indicate the Chihuahuan raven (C. cryptoleucus) and the Pacific clade of the common raven, which have D/θ<4 and thus are not different species by the criterion used here.</p