Genetic data are currently providing a large amount of new information on past distribution of species and are contributing to a new vision of Pleistocene ice ages. Nonetheless, an increasing number of studies on the 'time dependency' of mutation rates suggest that date assessments for evolutionary events of the Pleistocene might be overestimated. We analysed mitochondrial (mt) DNA (COI) sequence variation in 225 Parnassius mnemosyne individuals sampled across central and eastern Europe in order to assess (i) the existence of genetic signatures of Pleistocene climate shifts; and (ii) the timescale of demographic and evolutionary events. Our analyses reveal a phylogeographical pattern markedly influenced by the Pleistocene/Holocene climate shifts. Eastern Alpine and Balkan populations display comparatively high mtDNA diversity, suggesting multiple glacial refugia. On the other hand, three widely distributed and spatially segregated lineages occupy most of northern and eastern Europe, indicating postglacial recolonization from different refugial areas. We show that a conventional 'phylogenetic' substitution rate cannot account for the present distribution of genetic variation in this species, and we combine phylogeographical pattern and palaeoecological information in order to determine a suitable intraspecific rate through a Bayesian coalescent approach. We argue that our calibrated 'time-dependent' rate (0.096 substitutions/ million years), offers the most convincing time frame for the evolutionary events inferred from sequence data. When scaled by the new rate, estimates of divergence between Balkan and Alpine lineages point to c. 19 000 years before present (last glacial maximum), and parameters of demographic expansion for northern lineages are consistent with postglacial warming (5-11 000 years before present).

No abstract

The chironomid midges Belgica antarctica,\ud Eretmoptera murphyi (subfamily Orthocladiinae) and\ud Parochlus steinenii (subfamily Podonominae), are the\ud only Diptera species currently found in Antarctica. The\ud relationships between these species and a range of further\ud taxa of Chironomidae were examined by sequencing\ud domains 1 and 3–5 of 28S ribosomal RNA. The resulting\ud molecular relationships between B. antarctica and\ud E. murphyi, within Orthocladiinae, were highly supported\ud by validation analyses, confirming their position\ud within Chironomidae, as generated by classical taxonomy.\ud Within Podonominae, P. steinenii from the Maritime\ud Antarctic was more closely related to material from\ud sub-Antarctic South Georgia than to material from\ud Patagonia. Taking advantage of the availability of a\ud molecular substitution rate calculated for this gene in\ud Diptera, a dating of divergence between our study taxa\ud was tentatively established. The divergence dates obtained\ud were 49 million years (Myr), between B. antarctica\ud and E. murphyi, and 68.5 Myr between these species\ud and the closest Orthocladiinae taxon tested from Patagonia,\ud suggesting that B. antarctica and E. murphyi were\ud representatives of an ancient lineage. As both are endemic\ud to their respective tectonic microplates, their\ud contemporary distribution is, therefore, likely to have\ud been shaped by vicariance rather than dispersal

All species concepts are rooted in reproductive, and ultimately genealogical, relations. Genetic data are thus the most important source of information for species delimitation. Current ease of access to genomic data and recent computational advances are blooming a plethora of coalescent-based species delimitation methods. Despite their utility as objective approaches to identify species boundaries, coalescent-based methods (1) rely on simplified demographic models that may fail to capture some attributes of biological species, (2) do not make explicit use of the geographic information contained in the data, and (3) are often computationally intensive. In this article, we present a case of species delimitation in the Erebia tyndarus species complex, a taxon regarded as a classic example of problematic taxonomic resolution. Our approach to species delimitation used genomic data to test predictions rooted in the biological species concept and in the criterion of coexistence in sympatry. We (1) obtained restriction-site associated DNA (RAD) sequencing data from a carefully designed sample, (2) applied two genotype clustering algorithms to identify genetic clusters, and (3) performed within-clusters and between-clusters analyses of isolation by distance as a test for intrinsic reproductive barriers. Comparison of our results with those from a Bayes factor delimitation coalescent-based analysis, showed that coalescent-based approaches may lead to overconfident splitting of allopatric populations, and indicated that incorrect species delimitation is likely to be inferred when an incomplete geographic sample is analyzed. While we acknowledge the theoretical justification and practical usefulness of coalescent-based species delimitation methods, our results stress that, even in the phylogenomic era, the toolkit for species delimitation should not dismiss more traditional, biologically grounded, approaches coupling genomic data with geographic information.

No abstract