Speciation and DNA barcodes: testing the effects of dispersal on the formation of discrete sequence clusters

Abstract

Large-scale sequencing of short mtDNA fragments for biodiversity inventories ('DNA barcoding') indicates that sequence variation in animal mtDNA is highly structured and partitioned into discrete genetic clusters that correspond broadly to species-level entities. Here we explore how the migration rate, an important demographic parameter that is directly related to population isolation, might affect variation in the strength of mtDNA clustering among taxa. Patterns of mtDNA variation were investigated in two groups of beetles that both contain lineages occupying habitats predicted to select for different dispersal abilities: predacious diving beetles (Dytiscidae) in the genus Bidessus from lotic and lentic habitats across Europe and darkling beetles (Tenebrionidae) in the genus Eutagenia from sand and other soil types in the Aegean Islands. The degree of genetic clustering was determined using the recently developed 'mixed Yule coalescent' (MYC) model that detects the transition from between-species to within-population branching patterns. Lineages from presumed stable habitats, and therefore displaying lower dispersal ability and migration rates, showed greater levels of mtDNA clustering and geographical subdivision than their close relatives inhabiting ephemeral habitats. Simulations of expected patterns of mtDNA variation under island models showed that MYC clusters are only detected when the migration rates are much lower than the value of NmZ1 typically used to define the threshold for neutral genetic divergence. Therefore, discrete mtDNA clusters provide strong evidence for independently evolving populations or species, but their formation is suppressed even under very low levels of dispersal.

Bombus cullumanus—an extinct European bumblebee species?

“…Monaghan et al 2005;Papadopoulou et al 2008;Pons et al 2006). Unfortunately, fully quantitative models of these processes are only applicable in situations where many species are anticipated with multiple unique haplotypes within each (Monaghan et al 2009), which is not the case here.…”

“…Elsewhere, this kind of pattern has been interpreted as marking the separation between small intraspecific differences and larger interspecific differences (Monaghan et al 2005(Monaghan et al , 2009Pons et al 2006;Papadopoulou et al 2008). Such a strong distinction (corresponding to the much criticised 'barcoding gap') is not universal among bumblebees (e.g.…”

Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation

“…Today, however, consensus is changing towards a more phylogenetic approach to species classification (e.g. Papadopoulou et al 2008), typified by Cracraft's (1989) phylogenetic or diagnostic species concept (figure 1c; for further discussion of the relationships between Darwin's morphological concept, the biological concept and the phylogenetic concept of species, see figure 1 and appendix A). These newer ideas have led to rapid taxonomic inflation, especially in some charismatic vertebrate groups.…”

“…Two major types of phylogenetic species concepts are generally recognized (Baum 1992). First of all, species could be defined as monophyletic groups (Papadopoulou et al 2008), perhaps based on multiple gene genealogies (Baum & Shaw 1995). Others recommend using diagnostic characters possessed by clusters of individuals as a means to define species (Cracraft 1989); this is sometimes called the diagnostic concept of species.…”

Introduction. Speciation in plants and animals: pattern and process

“…The success of DNA barcoding is ultimately dependent upon the presence of suitable signal in the barcoding locus to differentially group sets of individuals into their respective species. Papadopoulou et al (2008) used a combination of simulated and empirical datasets to explore the conditions under which discrete clusters of sequences are likely to arise, focusing on their recently developed likelihood method for identifying species clusters from barcode data. To date, there has been strong correspondence between barcode clusters and taxonomic species in many published studies (e.g.…”