Phylogeographic analysis of Anatolian bats highlights the importance of the region for preserving the Chiropteran mitochondrial genetic diversity in the Western Palaearctic

Geographic Genetic Structure of Alectoris chukar in Türkiye: Post-LGM-Induced Hybridization and Human-Mediated Contaminations

Türkiye is considered an important evolutionary area for Chukar partridge (Alectoris chukar), since it is both a potential ancestral area and a diversification center for the species. Using 2 mitochondrial (Cty-b and D-loop) and 13 polymorphic microsatellite markers, we investigated the geographic genetic structure of A. chukar populations to determine how past climatic fluctuations and human activities have shaped the gene pool of this species in Türkiye. Our results indicate, firstly, that only A. chukar of the genus Alectoris is present in Türkiye (Anatolia and Thrace), with no natural or artificial gene flow from congenerics. Secondly, the geographic genetic structure of the species in Türkiye has been shaped by topographic heterogeneity, Pleistocene climatic fluctuations, and artificial transport by humans. Third, there appears to be three genetic clusters: Thracian, Eastern, and Western. Fourth, the post-LGM demographic expansion of the Eastern and Western populations has formed a hybrid zone in Central Anatolia (~8 kyBP). Fifth, the rate of China clade-B contamination in Türkiye is about 8% in mtDNA and about 12% in nuDNA, with the Southeastern Anatolian population having the highest contamination. Sixth, the Thracian population was the most genetically distinct, with the lowest genetic diversity and highest level of inbreeding and no China clad-B contamination. These results can contribute to the conservation regarding A. chukar populations, especially the Thracian population.

Patterns of mtDNA introgression suggest population replacement in Palaearctic whiskered bat species

Secondary contacts can play a major role in the evolutionary histories of species. Various taxa diverge in allopatry and later on come into secondary contact during range expansions. When they meet, their interactions and the extent of gene flow depend on the level of their ecological differentiation and the strength of their reproductive isolation. In this study, we present the multilocus phylogeography of two cryptic whiskered bat species, Myotis mystacinus and M. davidii, with a particular focus on their putative sympatric zone. Our findings suggest that M. mystacinus and M. davidii evolved in allopatry and came into secondary contact during range expansions. Individuals in the area of secondary contact, in Anatolia and the Balkans, have discordant population assignments based on the mitochondrial and the nuclear datasets. These observed patterns suggest that the local M. mystacinus populations hybridized with expanding M. davidii populations, which resulted in mitochondrial introgression from the former. In the introgression area, M. mystacinus individuals with concordant nuclear and mitochondrial genotypes were identified in relatively few locations, suggesting that the indigenous populations might have been largely replaced by invading M. davidii. Changing environmental conditions coupled with ecological competition is the likely reason for this replacement. Our study presents one possible example of a historical population replacement that was captured in phylogeographic patterns.

Porous barriers? Assessment of gene flow within and among sympatric long-eared bat species

Species are the basic units for measuring biodiversity and for comprehending biological interactions. Yet, their delineation is often contentious, especially in groups that are both diverse and phenotypically conservative. Three cryptic species of long-eared bats, Plecotus auritus, P. austriacus, and P. macrobullaris, co-occur over extensive areas of Western Europe. The latter is a fairly recent discovery, questioning the overall diversity of the entire Plecotus complex. Yet, high morphological and acoustic similarities compromise the reliable identification of long-eared bats in the field. We postulate that such extensive phenotypic overlap, along with the recurrent observation of morphologically intermediate individuals, may hide rampant interspecific hybridization. Based on a geographic sampling centered on areas of sympatry in the Alps and Corsica, we assessed the level of reproductive isolation of these three Plecotus species with mitochondrial and nuclear markers, looking at both inter- and intraspecific genetic population structuring. No sign of hybridization was detected between these three species that appear well separated biologically. Genetic structuring of populations, however, reflected different species-specific responses to environmental connectivity, that is, to the presence of orographic or sea barriers. While the Alpine range and the Ligurian Sea coincided with sharp genetic discontinuities in P. macrobullaris and P. austriacus, the more ubiquitous P. auritus showed no significant population structuration. There were clear phylogeographic discrepancies between microsatellite and mitochondrial markers at the intraspecific level, however, which challenges the reliance on simple barcoding approaches for the delineation of sound conservation units.

Two Mitochondrial Barcodes for one Biological Species: The Case of European Kuhl's Pipistrelles (Chiroptera)

The Kuhl's pipistrelle (Pipistrellus kuhlii) is a Western Palaearctic species of bat that exhibits several deeply divergent mitochondrial lineages across its range. These lineages could represent cryptic species or merely ancient polymorphism, but no nuclear markers have been studied so far to properly assess the taxonomic status of these lineages. We examined here two lineages occurring in Western Europe, and used both mitochondrial and nuclear markers to measure degrees of genetic isolation between bats carrying them. The sampling focused on an area of strict lineage sympatry in Switzerland but also included bats from further south, in North Africa. All individuals were barcoded for the COI gene to identify their mitochondrial lineages and five highly polymorphic microsatellite loci were used to cluster them according to their nuclear genotypes. Despite this low number of nuclear markers, all North African nuclear genotypes were grouped in a highly distinct subpopulation when compared with European samples sharing the same mitochondrial barcodes. The reverse situation prevailed in Switzerland where bats carrying distinct barcodes had similar nuclear genotypes. There was a weak east/west nuclear structure of populations, but this was independent of mitochondrial lineages as bats carrying either variant were completely admixed. Thus, the divergent mitochondrial barcodes present in Western Europe do not represent cryptic species, but are part of a single biological species. We argue that these distinct barcodes evolved in allopatry and came recently into secondary contact in an area of admixture north of the Alps. Historical records from this area and molecular dating support such a recent bipolar spatial expansion. These results also highlight the need for using appropriate markers before claiming the existence of cryptic species based on highly divergent barcodes.

Systematic position and taxonomy of Pipistrellus deserti (Chiroptera: Vespertilionidae)

is a small, pale-coloured bat occurring in the most arid parts of the Sahara, in Morocco, Algeria, Libya, Egypt, and the Sudan, and marginally also in sub-Saharan Africa. Although most authors consider