Species delimitation and relationships: The dance of the seven veils

Abstract

An increasing number of studies using genetic data at the generic and species levels reveal complex patterns of relationships among populations and species. Incomplete lineage sorting and reticulation are, for instance, commonly observed in low-rank phylogenies. These two processes falsify the simplifying assumptions often used when reconstructing phylogenetic relationships or when assigning specimens to species using barcodes, i.e., the absence of ancestral polymorphism or the obligate dichotomous relationship among species. We recognize seven processes that act as veils to obscure species boundaries and relationships and lead to erroneous interpretations if not diagnosed and analysed properly. These processes include the transfer of genetic material from plastids or mitochondria to the nuclear genome (NuPt, NuMt), hybridization, the stochasticity of lineage sorting within and among species, genome organization, species demography, selection, genetic and geographic structure. Most of these processes have a direct impact on species effective population sizes, a central parameter to be considered. Failure to take the seven processes into account can affect the accuracy of barcode-based identification, in particular between closely related species. It can also bias the delimitation of species, result in inaccurate estimations of species relationships and lead to incorrect estimation of species ages. We suggest that these problems can be identified and, to some extent, mitigated by ensuring that the full spatial and genetic ranges of the species are sampled, and by the use of information from all genomes of the species. By analysing numerous loci, each as a separate entity in a coalescence framework, it is possible to take into account stochasticity as well as variation in genome effective population sizes. Such a critical approach would allow the use of genetic data to make realistic assessments of species delimitation, affinities and ages, and should promote a more biologically realistic view of species and speciation.

Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada

“…The observed differences in taxonomic resolution for the three barcodes are undoubtedly influenced by selection, species demography, hybridization, lineage sorting, and phylogeographic structure (reviewed by [52]). The higher resolution of matK compared to rbcL reflects the different selective pressures acting on these genes.…”

“…The low levels of sequence variation in several plant families likely reflects the joint impacts of polyploidization, hybridization, phylogeographic effects such as allele surfing during range expansions, and demographic effects including bottlenecks which reduce intra- and inter-specific variation [52; 60; 61]. These effects are more prominent in Arctic communities that might explain the frequent failure of both nuclear and plastid markers in discriminating species in this region [52; 62; 63; 64; 65].…”

“…These effects are more prominent in Arctic communities that might explain the frequent failure of both nuclear and plastid markers in discriminating species in this region [52; 62; 63; 64; 65]. Although these processes (singly or in combination) compromise the effectiveness of DNA barcoding in discriminating plant species, they do provide an opportunity to understand the factors that shape plant populations and genomes.…”

“…However, the same lack of resolution was observed with our ITS2 data and in a more detailed analysis of 22 species [26], indicating that the lack of divergence extends into the nuclear genome. This difficulty in differentiating Salix species using molecular markers may reflect hybridization, introgression, recent speciation, allele surfing via range expansion, and low rates of molecular evolution [52; 59; 67; 68; 69]. More extensive phylogenetic studies targeting nuclear markers or whole plastid genomes are necessary to clarify the processes driving the unusually low divergences in Salix .…”

Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences – a case study in the tree genus Milicia

“…If we remove from consideration the West African cluster of M. regia K1, the divergence time of K6 and its relatedness to Kenyan cluster K5 composed of M. excelsa (Fig. 5b and c) supported the first hypothesis as this phenomenon is quite common in recently diverging species with large effective population size [74]. The chloroplast capture scenario is also acceptable.…”