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.

Parnassius apollo (Linnaeus, 1758) is probably the most renowned Eurasian montane butterfly. Its specialized ecology makes it very sensitive to habitat and climate changes, so that it is now experiencing range contraction and local extinction across most of its range. We sequenced 869 bp of the mitochondrial DNA (mtDNA) cytochrome oxidase I gene in 78 P. apollo populations (201 individuals) in order to: (1) assess the phylogeographic pattern of the species; (2) shed light on the historical biogeographic processes that shaped the distribution of the species; and (3) identify geographic population units of special value for the conservation of the species' genetic diversity. Our analyses revealed a very strong phylogeographic structure in P. apollo, which displays a number of distinctive mtDNA lineages populating geographically distinct areas. Overall sequence divergence is relatively shallow, and is consistent with a recent (late Pleistocene) colonization of most of the range. We propose that P. apollo is best viewed as an atypical glacial invader in southern and western Europe, the isolated, montane populations of which, threatened by climate warming, retain a large fraction of the species evolutionary heritage. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101, 169–183

Mitochondrial DNA length variation in DicentrurchusZubrux is the outcome of the simultaneous variation in the copy number of two tandem repeat arrays located in the D-loop region. The repeated sequences, named R17 and R48, are 17 and 48 bp long, respectively. On the basis of 209 individuals collected in eight Mediterranean localities, length variation and its partitioning between the two repeat arrays have been characterized and quantified by means of frequency distributions of repeat copy number and genetic diversity estimates. The median copy numbers are 4 and 11 for the R17 and R48 repeat arrays, respectively. For both repeat arrays, continuity in step variation and the occurrence of both frequent and rare arrangements was observed. More than 50% of the individuals are heteroplasmic for up to four variants. Within populations, heteroplasmy ranges between 33.3% and 70.0% of the individuals. A large proportion of the total gene diversity (29.1%) occurs within individuals and the greatest proportion (66.6%) is found between individuals within populations, while only 4.3% is due to variation between populations. Although the interpopulation component of the diversity is rather low, the significant differentiation of the two Eastern populations from all the other Western samples suggests the occurrence of a phylogeographic component of the genetic divergence between the Mediterranean populations, which is only recognizable on a large geographic scale.

The difficult and controversial attribution of Hipparchia (Parahipparchia) populations to species or subspecies rank led us to use a comparative, quantitative approach to clarify evolutionary and taxonomic relationships among taxa. Seventeen populations from the Mediterranean area belonging to nine presumptive species or subspecies were sampled, and multivariate analyses were employed to study three character sets: allozymes, morphometric profiles of male genitalia, and quantitative descriptors of wing pattern and shape. Comparative analyses of distance matrices, trees and ordination patterns enabled us to outline evolutionary relationships among taxa and to assess the relative value of each character set. Congruent relationships among taxa were obtained from allozymes and male genital morphometrics, suggesting that divergence in genital morphology is a fairly good marker of the overall genetic divergence. O n the other hand, discordant results from wing pattern descriptors suggest these might be subjected to different evolutionary trajectories and rates because of their particular adaptive significance, and might not represent reliable tracers of phylogeny.

Morphometric analyses were carried out for 14 cave dwelling populations of Dolichopoda (Orthoptera, Rhaphidophoridae) from peninsular Italy belonging to the faetitiae-genzcu/ata complex. The selected set of variables includes linear measures of body parts and appendages whose variation is expected to be adaptive and to reflect the degree of specialization to the cave environment.Inter-population morphometric variation was compared with the patterns of allozyme variation, investigated electrophoretically in a previous paper, by means of ordination and classification multivariate analyses. Results from this comparison reject the hypothesis of parallel geographic variation of morphometric indices and allele frequencies, revealing independent trends for the two sets of characters.