A molecular phylogeny shows the single origin of the Pyrenean subterranean Trechini ground beetles (Coleoptera: Carabidae).

Trechini ground beetles include some of the most spectacular radiations of cave and endogean Coleoptera, but the origin of the subterranean taxa and their typical morphological adaptations (loss of eyes and wings, depigmentation, elongation of body and appendages) have never been studied in a formal phylogenetic framework. We provide here a molecular phylogeny of the Pyrenean subterranean Trechini based on a combination of mitochondrial (cox1, cyb, rrnL, tRNA-Leu, nad1) and nuclear (SSU, LSU) markers of 102 specimens of 90 species. We found all Pyrenean highly modified subterranean taxa to be monophyletic, to the exclusion of all epigean and all subterranean species from other geographical areas (Cantabrian and Iberian mountains, Alps). Within the Pyrenean subterranean clade the three genera (Geotrechus, Aphaenops and Hydraphaenops) were polyphyletic, indicating multiple origins of their special adaptations to different ways of life (endogean, troglobitic or living in deep fissures). Diversification followed a geographical pattern, with two main clades in the western and central-eastern Pyrenees respectively, and several smaller lineages of more restricted range. Based on a Bayesian relaxed-clock approach, and using as an approximation a standard mitochondrial mutation rate of 2.3% MY, we estimate the origin of the subterranean clade at ca. 10 MY. Cladogenetic events in the Pliocene and Pleistocene were almost exclusively within the same geographical area and involving species of the same morphological type.

Putative origin and function of the intergenic region between COI and COII of Apis mellifera L. mitochondrial DNA.

The mitochondrial genome of honeybees is characterized by the presence of a long intergenic sequence located between the COI and COII genes. In addition, the length of this sequence varies between and within subspecies. Four length categories (200, 250, 450 and 650 bp) have been found in 63 sampled colonies. Analysis of the sequence of the largest type reveals the existence of two units: P (54 bp, 100% A + T) and Q (196 bp, 93.4% A + T). The lengths encountered in the sample are explained by the following combinations: Q, PQ, PQQ and PQQQ. According to similarities in primary and secondary structures, the sequence Q has been divided into three parts: Q1 (similar to the 3' end of the COI gene), Q2 (similar to the neighboring tRNA(leu) gene) and Q3 (highly similar to the P sequence). These relationships led us to hypothesize that these sequences, which do not have any counterpart in Drosophila yakuba mitochondrial DNA (mtDNA), arose by tandem duplication. The usual location of length variation in mtDNA control regions prompted us to examine the hypothesis that this COI-COII intergenic region might contain an origin of replication. High A + T content, stability profile, hairpin and cloverleaf putative secondary structures are all in favor of this hypothesis.

Microsatellite variation in honey bee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models.

Samples from nine populations belonging to three African (intermissa, scutellata and capensis) and four European (mellifera, ligustica, carnica and cecropia) Apis mellifera subspecies were scored for seven microsatellite loci. A large amount of genetic variation (between seven and 30 alleles per locus) was detected. Average heterozygosity and average number of alleles were significantly higher in African than in European subspecies, in agreement with larger effective population sizes in Africa. Microsatellite analyses confirmed that A. mellifera evolved in three distinct and deeply differentiated lineages previously detected by morphological and mitochondrial DNA studies. Dendrogram analysis of workers from a given population indicated that super-sisters cluster together when using a sufficient number of microsatellite data whereas half-sisters do not. An index of classification was derived to summarize the clustering of different taxonomic levels in large phylogenetic trees based on individual genotypes. Finally, individual population x loci data were used to test the adequacy of the two alternative mutation models, the infinite allele model (IAM) and the stepwise mutation models. The better fit overall of the IAM probably results from the majority of the microsatellites used including repeats of two or three different length motifs (compound microsatellites).

Evolutionary history of the honey bee Apis mellifera inferred from mitochondrial DNA analysis.

Variability of mitochondrial DNA (mtDNA) of the honey bee Apis mellifera L. has been investigated by restriction and sequence analyses on a sample of 68 colonies from ten different subspecies. The 19 mtDNA types detected are clustered in three major phylogenetic lineages. These clades correspond well to three groups of populations with distinct geographical distributions: branch A for African subspecies (intermissa, monticola, scutellata, andansonii and capensis), branch C for North Mediterranean subspecies (caucasica, carnica and ligustica) and branch M for the West European populations (mellifera subspecies). These results partially confirm previous hypotheses based on morphometrical and allozymic studies, the main difference concerning North African populations, now assigned to branch A instead of branch M. The pattern of spatial structuring suggests the Middle East as the centre of dispersion of the species, in accordance with the geographic areas of the other species of the same genus. Based on a conservative 2% divergence rate per Myr, the separation of the three branches has been dated at about 1 Myr BP.

Microsatellite analysis of sperm admixture in honeybee.

Sperm usage was investigated in an instrumentally inseminated honeybee queen. Her progeny were examined in the first 3 months of the egg-laying period using a microsatellite marker. Frequencies of different subfamilies differed significantly from one month to another. However, there was no evidence for sperm displacement or sperm precedence of a specific male in the worker progeny. The variance of subfamily proportions decreased over time suggesting that sperm admixture in the spermatheca was incomplete at the beginning of the egg-laying period of the queen and improved progressively during the first months after mating.

Hybrid origins of honeybees from italy (Apis mellifera ligustica) and sicily (A. m. sicula).

The genetic variability of honeybee populations Apis mellifera ligustica, in continental Italy, and of A. m. sicula, in Sicily, was investigated using nuclear (microsatellite) and mitochondrial markers. Six populations (236 individual bees) and 17 populations (664 colonies) were, respectively, analysed using eight microsatellite loci and DraI restriction fragment length polymorphism (RFLP) of the cytochrome oxidase I (COI)-cytochrome oxidase II (COII) region. Microsatellite loci globally confirmed the southeastern European heritage of both subspecies (evolutionary branch C). However, A. m. ligustica mitochondrial DNA (mtDNA) appeared to be a composite of the two European (M and C) lineages over most of the Italian peninsula, and only mitotypes from the African (A) lineage were found in A. m. sicula samples. This demonstrates a hybrid origin for both subspecies. For A. m. ligustica, the most widely exported subspecies, this hybrid origin has long been obscured by the fact that in the main area of queen production (from which most of the previous ligustica bee samples originated) the M mitochondrial lineage is absent, whereas it is present almost everywhere else in Italy. This presents a new view of the evolutionary history of European honeybees. For instance, the Iberian peninsula was considered as the unique refuge for the M branch during the quaternary ice periods. Our results show that the Apennine peninsula played a similar role. The differential distribution of nuclear and mitochondrial markers observed in Italy seems to be a general feature of introgressed honeybee populations. Presumably, it stems from the social nature of the species in which both genome compartments are differentially affected by the two (individual and colonial) reproduction levels.

Genetic diversity of the honeybee in Africa: microsatellite and mitochondrial data.

A total of 738 colonies from 64 localities along the African continent have been analysed using the DraI RFLP of the COI-COII mitochondrial region. Mitochondrial DNA of African honeybees appears to be composed of three highly divergent lineages. The African lineage previously reported (named A) is present in almost all the localities except those from north-eastern Africa. In this area, two newly described lineages (called O and Y), putatively originating from the Near East, are observed in high proportion. This suggests an important differentiation of Ethiopian and Egyptian honeybees from those of other African areas. The A lineage is also present in high proportion in populations from the Iberian Peninsula and Sicily. Furthermore, eight populations from Morocco, Guinea, Malawi and South Africa have been assayed with six microsatellite loci and compared to a set of eight additional populations from Europe and the Middle East. The African populations display higher genetic variability than European populations at all microsatellite loci studied thus far. This suggests that African populations have larger effective sizes than European ones. According to their microsatellite allele frequencies, the eight African populations cluster together, but are divided in two subgroups. These are the populations from Morocco and those from the other African countries. The populations from southern Europe show very low levels of 'Africanization' at nuclear microsatellite loci. Because nuclear and mitochondrial DNA often display discordant patterns of differentiation in the honeybee, the use of both kinds of markers is preferable when assessing the phylogeography of Apis mellifera and to determine the taxonomic status of the subspecies.

Geographical overlap of two mitochondrial genomes in Spanish honeybees (Apis mellifera iberica).

Restriction enzyme cleavage maps of mitochondrial DNA from the Spanish honeybee, Apis mellifera iberica (Hymenoptera: Apidae), were compared with those from the European subspecies A. m. mellifera, A. m. ligustica, and A. m. carnica, and the African subspecies A. m. intermissa and A. m. scutellata. The mitochondrial DNA (mtDNA) of the two African subspecies can be distinguished by restriction fragment polymorphisms revealed by Hinf I digests. Two distinct mtDNA types were found among Spanish honeybees: a west European mellifera-like type, which predominates in the north of Spain, and an African intermissa-like type, which predominates in the south. Spain appears to be a region of contact and hybridization between the two subspecies A. m. intermissa and A. m. mellifera, which respectively represent African and west European honeybee lineages. This natural boundary between European and African honeybee populations in the Old World may provide a model for predicting the eventual outcome of the colonization of North America by introduced African honeybees.