Back to the suture: the distribution of intraspecific genetic diversity in and around anatolia

Genome-Wide Data Uncover Cryptic Diversity With Multiple Reticulation Events in the Balkan-Anatolian Cardamine (Brassicaceae) Species Complex

Plant species diversity may be considerably underestimated, especially in evolutionarily complex genera and in diversity hotspots that have enabled long-term species persistence and diversification, such as the Balkan Peninsula. Here, we address the topic of underexplored plant diversity and underlying evolutionary and biogeographic processes by investigating the hygrophytic mountain species complex of Cardamine acris s.l. distributed in the Balkans (three subspecies within C. acris) and northwestern Anatolia (C. anatolica). We performed a series of phylogenetic and phylogeographic analyses based on restriction-site associated DNA sequencing (RADseq) and target enrichment (Hyb-Seq) data in combination with habitat suitability modelling. We found C. anatolica as a clade nested within the Balkan C. acris, probably resulting from a founder event, and uncovered three allopatric cryptic lineages within C. acris subsp. acris, allowing us to recognise a total of six entities in this complex. We observed the deepest genetic split within C. acris subsp. acris in the western Balkans, which was at odds with taxonomy and showed no distribution gap. We inferred vicariance as the most likely process for population divergence in the Balkans, accompanied by gene flow between the recognised entities, which was consistent with the modelled habitat suitability dynamics. Furthermore, we discovered several polyploid populations in C. acris, representing both pure intra- and inter-lineage hybrid polyploids, but detected only minor traces of hybridization with related congeners. Overall, our results illustrate that diverse evolutionary processes may influence the history of mountain plant species in the Balkan Peninsula, including vicariance, reticulation, polyploidization and cryptic diversification.

Phylogenomics reveal species limits and inter-relationships in the narrow-range endemic lycian salamanders

Salamanders of the genus Lyciasalamandra are represented by as many as 20 narrow-range endemic taxa inhabiting the Mediterranean coast of Turkey and a handful of Aegean Islands. Despite recent molecular phylogenetic studies, the genus is rife with uncertainty about the number of contained species and their phylogenetic relationships, both of which can interfere with needed conservation actions. To test species limits and infer interrelationships we generated as many as 113,176 RAD loci containing 229,427 single nucleotide polymorphisms (SNPs), for 110 specimens of Lyciasalamandra representing 19 of the 20 described taxa. Through a conservative species delimitation approach, we found support for eight species in the genus which broadly agree with currently described species-level diversity. We then use multiple coalescent-based species tree methods to resolve relationships in this relatively old, synchronous species radiation. We recommend synonymization of the largely over-split subspecific taxa, and the elevation of L. luschani finikensis to full species status as L. finikensis. Our hope is that this revised taxonomic framework provides a stable foundation for conservation management in these fragile, microendemic taxa.

A consequential one-night stand: Episodic historical hybridization leads to mitochondrial takeover in sympatric desert ant-eating spiders

Disentangling the genomic intricacies underlying speciation and the causes of discordance between sources of evidence can offer remarkable insights into evolutionary dynamics. The ant-eating spider Zodarion nitidum, found across the Middle East and Egypt, displays yellowish and blackish morphs that co-occur sympatrically. These morphs additionally differ in behavioral and physiological features and show complete pre-mating reproductive isolation. In contrast, they possess similar sexual features and lack distinct differences in their mitochondrial DNA. We analyzed both Z. nitidum morphs and outgroups using genome-wide and additional mitochondrial DNA data. The genomic evidence indicated that Yellow and Black are reciprocally independent lineages without signs of recent admixture. Interestingly, the sister group of Yellow is not Black but Z. luctuosum, a morphologically distinct species. Genomic gene flow analyses pinpointed an asymmetric nuclear introgression event, with Yellow contributing nearly 5 % of its genome to Black roughly 320,000 years ago, intriguingly aligning with the independently estimated origin of the mitochondrial DNA of Black. We conclude that the blackish and yellowish morphs of Z. nitidum are long-diverged distinct species, and that the ancient and modest genomic introgression event registered resulted in a complete mitochondrial takeover of Black by Yellow. This investigation underscores the profound long-term effects that even modest hybridization events can have on the genome of organisms. It also exemplifies the utility of phylogenetic networks for estimating historical events and how integrating independent lines of evidence can increase the reliability of such estimations.

Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region

Cryptic diversity poses a great obstacle in our attempts to assess the current biodiversity crisis and may hamper conservation efforts. The gekkonid genus Mediodactylus, a well-known case of hidden species and genetic diversity, has been taxonomically reclassified several times during the last decade. Focusing on the Mediterranean populations, a recent study within the M. kotschyi species complex using classic mtDNA/nuDNA markers suggested the existence of five distinct species, some being endemic and some possibly threatened, yet their relationships have not been fully resolved. Here, we generated genome-wide SNPs (using ddRADseq) and applied molecular species delimitation approaches and population genomic analyses to further disentangle these relationships. Τhe most extensive nuclear dataset, so far, encompassing 2,360 loci and ∼ 699,000 bp from across the genome of Mediodactylus gecko, enabled us to resolve previously obscure phylogenetic relationships among the five, recently elevated, Mediodactylus species and to support the hypothesis that the taxon includes several new, undescribed species. Population genomic analyses within each of the proposed species showed strong genetic structure and high levels of genetic differentiation among populations.

The Silk roads: phylogeography of Central Asian dice snakes (Serpentes: Natricidae) shaped by rivers in deserts and mountain valleys

Influenced by rapid changes in climate and landscape features since the Miocene, widely distributed species provide suitable models to study the environmental impact on their evolution and current genetic diversity. The dice snake Natrix tessellata, widely distributed in the Western Palearctic is one such species. We aimed to resolve a detailed phylogeography of N. tessellata with a focus on the Central Asian clade with 4 and the Anatolia clade with 3 mitochondrial lineages, trace their origin, and correlate the environmental changes that affected their distribution through time. The expected time of divergence of both clades began at 3.7 Mya in the Pliocene, reaching lineage differentiation approximately 1 million years later. The genetic diversity in both clades is rich, suggesting different ancestral areas, glacial refugia, demographic changes, and colonization routes. The Caspian lineage is the most widespread lineage in Central Asia, distributed around the Caspian Sea and reaching the foothills of the Hindu Kush Mountains in Afghanistan, and Eastern European lowlands in the west. Its distribution is limited by deserts, mountains, and cold steppe environments. Similarly, Kazakhstan and Uzbekistan lineages followed the Amu Darya and the Syr Darya water systems in Central Asia, with ranges delimited by the large Kyzylkum and Karakum deserts. On the western side, there are several lineages within the Anatolia clade that converged in the central part of the peninsula with 2 being endemic to Western Asia. The distribution of both main clades was affected by expansion from their Pleistocene glacial refugia around the Caspian Sea and in the valleys of Central Asia as well as by environmental changes, mostly through aridification.

Latitude or altitude as the future refugium? A case for the future of forests in Asia Minor and its surroundings

At the current juncture with climate change, centennial projections of species distributions in biodiversity hotspots, using dynamic vegetation models may provide vital insight into conservation efforts. This study aims to answer: (1) if climate change progresses under a business-as-usual scenario of anthropogenic emissions for this century, how may the forest ranges be affected? (2) will there be potential regional extinctions of the taxa simulated? (3) may any site emerge as a potential refugium?

STUDY AREA

Anatolian Peninsula and its surroundings, longitudes 24-50° E, latitudes 33-46° N. Time Period: 1961-2100. Major Taxa Studied: 25 woody species and a C3 grass-type.

METHOD

Keeping a spatial window large enough to track potential changes in the vegetation range and composition especially in the mountain ranges within the study area, we parameterized a process-based regional-to-global dynamic vegetation model (LPJ-GUESS v 4.1), forced it with ERA5-Land reanalysis for the historical period, and five different bias-corrected centennial global circulation model (GCM) datasets under SSP5-8.5, and simulated the dynamic responses of key forest species. Bivariate spatio-temporal maps from the simulation results were constructed for final analysis.

RESULTS

A significant increase in woody taxa biomass for the majority of our study area, towards the end of the century was simulated, where temperate taxa with high tolerance for drought and a wider range of temperatures took dominance. The mountain ranges in our study area stood out as critical potential refugia for cold favoring species. There were no regional extinctions of taxa, however, important changes in areal dominance and potential future forest composition were simulated.

MAIN CONCLUSIONS

Our simulation results suggest a high potential for future forest cover in our study region by the end of the century under a high emissions scenario, sans human presence, with important changes in vegetation composition, including encroachment of grasslands ecosystems by woody taxa.

The 10,000-year biocultural history of fallow deer and its implications for conservation policy

Over the last 10,000 y, humans have manipulated fallow deer populations with varying outcomes. Persian fallow deer (Dama mesopotamica) are now endangered. European fallow deer (Dama dama) are globally widespread and are simultaneously considered wild, domestic, endangered, invasive and are even the national animal of Barbuda and Antigua. Despite their close association with people, there is no consensus regarding their natural ranges or the timing and circumstances of their human-mediated translocations and extirpations. Our mitochondrial analyses of modern and archaeological specimens revealed two distinct clades of European fallow deer present in Anatolia and the Balkans. Zooarchaeological evidence suggests these regions were their sole glacial refugia. By combining biomolecular analyses with archaeological and textual evidence, we chart the declining distribution of Persian fallow deer and demonstrate that humans repeatedly translocated European fallow deer, sourced from the most geographically distant populations. Deer taken to Neolithic Chios and Rhodes derived not from nearby Anatolia, but from the Balkans. Though fallow deer were translocated throughout the Mediterranean as part of their association with the Greco-Roman goddesses Artemis and Diana, deer taken to Roman Mallorca were not locally available Dama dama, but Dama mesopotamica. Romans also initially introduced fallow deer to Northern Europe but the species became extinct and was reintroduced in the medieval period, this time from Anatolia. European colonial powers then transported deer populations across the globe. The biocultural histories of fallow deer challenge preconceptions about the divisions between wild and domestic species and provide information that should underpin modern management strategies.

Ancient and modern DNA track temporal and spatial population dynamics in the European fallow deer since the Eemian interglacial

Anthropogenic factors have impacted the diversity and evolutionary trajectory of various species. This can be through factors such as pressure on population size or range, habitat fragmentation, or extensive manipulation and translocation. Here we use time-calibrated data to better understand the pattern and processes of evolution in the heavily manipulated European fallow deer (Dama dama). During the Pleistocene, fallow deer had a broad distribution across Europe and were found as far north as Britain during the Eemian interglacial. The last glacial period saw fallow deer retreat to southern refugia and they did not disperse north afterwards. Their recolonisation was mediated by people and, from northern Europe and the British Isles, fallow deer were transported around the world. We use ancient and modern mitochondrial DNA (mtDNA) and mitogenomic data from Eemian Britain to assess the pattern of change in distribution and lineage structure across Europe over time. We find founder effects and mixed lineages in the northern populations, and stability over time for populations in southern Europe. The Eemian sample was most similar to a lineage currently in Italy, suggesting an early establishment of the relevant refuge. We consider the implications for the integration of anthropogenic and natural processes towards a better understanding of the evolution of fallow deer in Europe.

Distribution patterns of Quercus ilex from the last interglacial period to the future by ecological niche modeling

The plants' geographic distribution is affected by natural or human-induced climate change. Numerous studies at both the global and regional levels currently focus on the potential changes in plant distribution areas. Ecological niche modeling can help predict the likely distribution of species according to environmental variables under different climate scenarios. In this study, we predicted the potential geographic distributions of Quercus ilex L. (holm oak), a keystone species of the Mediterranean ecosystem, for the Last Interglacial period (LIG: ~130 Ka), the Last Glacial Maximum (LGM: ~22 Ka), mid-Holocene (MH: ~6 Ka), and future climate scenarios (Representative Concentration Pathway (RCP) 4.5 and 8.5 scenarios) for 2050-2070 obtained from CCSM4 and MIROC-ESM global climate scenarios respectively. The models were produced with algorithms from the R-package "biomod2" and assessed by AUC of the receiver operating characteristic plot and true skill statistics. Aside from BIOCLIM (SRE), all model algorithms performed similarly and produced projections that are supported by good evaluation scores, although random forest (RF) slightly outperformed all the others. Additionally, distribution maps generated for the past period were validated through a comparison with pollen data acquired from the Neotoma Pollen Database. The results revealed that southern areas of the Mediterranean Basin, particularly coastal regions, served as long-term refugia for Q. ilex, which was supported by fossil pollen data. Furthermore, the models suggest long-term refugia role for Anatolia and we argue that Anatolia may have served as a founding population for the species. Future climate scenarios indicated that Q. ilex distribution varied by region, with some areas experiencing range contractions and others range expands. This study provides significant insights into the vulnerability of the Q. ilex to future climate change in the Mediterranean ecosystem and highlights the crucial role of Anatolia in the species' historical distribution.

Atlas of the Echiniscidae (Heterotardigrada) of the Worldpart I: West Palaearctic Echiniscus species

Traditionally Eurocentric tardigrade taxonomy has started to dissect endemics from very few truly cosmopolitan or widely distributed species, originally described mostly from the West Palaearctic, in the last decade. Obviously, the most problematic for taxonomic identification are species in large genera containing over 100 species in the case of Tardigrada. In limno-terrestrial heterotardigrades, only Echiniscus C.A.S. Schultze, 1840 fulfils this criterion, being a perfect example of taxonomic inflation. In Echiniscidae, this phenomenon results predominantly from the historical fallacy of attaching more importance to chaetotaxy than to the analysis of dorsal plate sculpturing. In this paper, the first of a series on echiniscids of the World, we review the current state of knowledge on the West Palaearctic Echiniscus species. Echiniscus granulatus (Doyre, 1840) and E. spinulosus (Doyre, 1840) are re-described based on multiple population data. Echiniscus lapponicus Thulin, 1911 and E. militaris Murray, 1911 are provided with the first SEM and molecular data, respectively. Following synonymies are made based on analyses of ample comparative material, type series, and redescriptions: E. blumi schizofilus Barto, 1941 syn. nov. and E. trojanus Maucci, 1973 syn. nov. of E. blumi blumi Richters, 1903; E. inocelatus Miheli, 1938 syn. nov., E. heterospinosus Maucci, 1954 syn. nov. and E. egnatiae Durante Pasa & Maucci, 1979 syn. nov. of E. granulatus; Echiniscus merokensis suecicus Thulin, 1911 syn. nov., E. columinis Murray, 1911 syn. nov., E. batramiae Iharos, 1936 syn. nov., E. jagodici Miheli, 1951 syn. nov. and E. laterospinosus Rudescu, 1964 syn. nov. of E. merokensis merokensis Richters, 1904; E. hexacanthus Maucci, 1973 syn. nov. of E. militaris Murray, 1911; E. carusoi Pilato, 1972 syn. nov. of E. spinulosus; E. osellai Maucci, 1974 syn. nov. of E. trisetosus Cunot, 1932. Two new nomina dubia are proposed: E. apuanus M. Bertolani, 1946 sp. dub. (and a probable synonymy with E. merokensis suggested) and E. pajstunensis Barto, 1941 sp. dub. Two new nomina inquirenda are established: E. marleyi Li, 2007 sp. inq. (another chaetotaxy-based morphotype of the Echiniscus blumi-canadensis complex) and E. punctus McInnes, 1995 sp. inq. (the lack of reliable morphological criteria separating it from E. granulatus). We summarise the morphological, phylogenetic and biogeographic information for the West Palaearctic Echiniscus species, and conclude with a total of 21 valid and identifiable taxa. We predict this number will decrease further with solving the species delimitation issues within the Echiniscus blumi-canadensis complex. Among these 21 taxa, 13 species (62%) are to be found solely in the Western Palaearctic and/or entire Holarctic regions. This augments the many recent findings that tardigrades are typically biogeographically structured and form clearly defined faunae.

Hybrid zone analysis confirms cryptic species of banded newt and does not support competitive displacement since secondary contact

When two putatively cryptic species meet in nature, hybrid zone analysis can be used to estimate the extent of gene flow between them. Two recently recognized cryptic species of banded newt (genus Ommatotriton) are suspected to meet in parapatry in Anatolia, but a formal hybrid zone analysis has never been conducted. We sample populations throughout the range, with a focus on the supposed contact zone, and genotype them for 31 nuclear DNA SNP markers and mtDNA. We determine the degree of genetic admixture, introgression, and niche overlap. We reveal an extremely narrow hybrid zone, suggesting strong selection against hybrids, in line with species status. The hybrid zone does not appear to be positioned at an ecological barrier, and there is significant niche overlap. Therefore, the hybrid zone is best classified as a tension zone, maintained by intrinsic selection against hybrids. While the two banded newt species can evidently backcross, we see negligible introgression and the pattern is symmetric, which we interpret as supporting the fact that the hybrid zone has been practically stationary since its origin (while extensive hybrid zone movement has been suggested in other newt genera in the region). Our study illustrates the use of hybrid zone analysis to test cryptic species status.

Evolution of hygrophytic plant species in the Anatolia-Caucasus region: insights from phylogenomic analyses of Cardamine perennials

BACKGROUND AND AIMS

Southwestern Asia is a significant centre of biodiversity and a cradle of diversification for many plant groups, especially xerophytic elements. In contrast, little is known about the evolution and diversification of its hygrophytic flora. To fill this gap, we focus on Cardamine (Brassicaceae) species that grow in wetlands over a wide altitudinal range. We aimed to elucidate their evolution, assess the extent of presumed historical gene flow between species, and draw inferences about intraspecific structure.

METHODS

We applied the phylogenomic Hyb-Seq approach, ecological niche analyses and multivariate morphometrics to a total of 85 Cardamine populations from the target region of Anatolia-Caucasus, usually treated as four to six species, and supplemented them with close relatives from Europe.

KEY RESULTS

Five diploids are recognized in the focus area, three of which occur in regions adjacent to the Black and/or Caspian Sea (C. penzesii, C. tenera, C. lazica), one species widely distributed from the Caucasus to Lebanon and Iran (C. uliginosa), and one western Anatolian entity (provisionally C. cf. uliginosa). Phylogenomic data suggest recent speciation during the Pleistocene, likely driven by both geographic separation (allopatry) and ecological divergence. With the exception of a single hybrid (allotetraploid) speciation event proven for C. wiedemanniana, an endemic of southern Turkey, no significant traces of past or present interspecific gene flow were observed. Genetic variation within the studied species is spatially structured, suggesting reduced gene flow due to geographic and ecological barriers, but also glacial survival in different refugia.

CONCLUSIONS

This study highlights the importance of the refugial regions of the Black and Caspian Seas for both harbouring and generating hygrophytic species diversity in Southwestern Asia. It also supports the significance of evolutionary links between Anatolia and the Balkan Peninsula. Reticulation and polyploidization played a minor evolutionary role here in contrast to the European relatives.

DNA barcoding of the genus Alburnoides Jeitteles, 1861 (Actinopterygii, Cyprinidae) from Anatolia, Turkey

The present study investigated the ability of DNA barcoding to reliably identify the endemic freshwater species in Turkey, known as biodiversity hotspots. The barcode region (652 bp) of the mitochondrial cytochrome c oxidase subunit I (COI) was used to barcode 153 individuals from 13 morphologically identified species of the genus Alburnoides. Based on the Kimura two-parameter (K2P) evolution model, the average interspecific distance (0.0595) was 31-fold higher than the average intraspecific distance (0.0019). There was a clear-cut barcode gap (0.0158–0.0187) between maximum intraspecific distance (A. tzanevi and A. velioglui) and minimum nearest-neighbour distance (A. freyhofi and A. kurui) for Anatolian Alburnoides species and a common genetic threshold of 0.0158 sequence divergence was defined for species delimitation. The multiple species delimitation methods (ABGD, ASAP, GMYC and bPTP) revealed a total of 11 molecular operational taxonomic units (MOTUs) for 13 morphospecies. Neighbour-joining (NJ), Maximum Likelihood (ML) and Bayesian Inference (BI) tree analysis indicated that all haplotypes were clustered into two major clades, which corresponded to eleven Alburnoides species clusters, with strong bootstrap support. Furthermore, all the specimens clustered in concurrence with the morpho-taxonomic status of the species, except for two species (A. coskuncelebii and A. emineae) that were morphologically differentiated, but showed overlap in variation for COI-based DNA barcode data with other species. Overall, present results identified that COI-based DNA barcoding is effective for species identification and cataloguing of genus Alburnoides in Turkey.

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.

Easternmost distribution of Bufo bufo (Linnaeus, 1758) in Türkiye: implications for the putative contact zone between B. bufo and B. verrucosissimus

The geographic range of a species is crucial for obtaining information on the exact distribution of the species. The geographic data are important for delimiting distinct species or exploring the degree of differentiation among different populations of a species. The local details of species boundaries facilitate the study of the importance of phylogeographic background, secondary contacts, and hybrid zones, along with the relations between the species and its extrinsic environmental factors. In the present study, the range boundaries of Bufo bufo and Bufo verrucosissimus in the north-eastern region of Türkiye were delineated using an integrative taxonomic approach that utilized a combination of molecular and morphological data. According to the mtDNA results of the present study, B. bufo inhabits a single distribution from İyidere town to Çayeli town in Rize, while B. verrucosissimus is distributed from Şavşat town of Artvin to Ardeşen town in Rize. In addition, the two species coexist in Pazar, Hemşin, and Çamlıhemşin towns in Rize. The demographic analyses indicated a distinct population expansion for the B. verrucosissimus species after the Last Glacial Maximum, while the same did not occur for B. bufo. The univariate and multivariate statistical analyses conducted for the morphological data of the two species corroborated the presence of a putative contact zone between B. bufo and B. verrucosissimus. In summary, the present study resolved the non-distinct geographic boundaries between B. bufo and B. verrucosissimus species and also revealed the easternmost distribution of B. bufo in Türkiye. In addition, important evidence on the putative contact zone between the two species was indicated using an integrative taxonomic approach.

Investigating the Impact of a Curse: Diseases, Population Isolation, Evolution and the Mother's Curse

The mitochondrion was characterized for years as the energy factory of the cell, but now its role in many more cellular processes is recognized. The mitochondrion and mitochondrial DNA (mtDNA) also possess a set of distinct properties, including maternal inheritance, that creates the Mother's Curse phenomenon. As mtDNA is inherited from females to all offspring, mutations that are harmful to males tend to accumulate more easily. The Mother's Curse is associated with various diseases, and has a significant effect on males, in many cases even affecting their reproductive ability. Sometimes, it even leads to reproductive isolation, as in crosses between different populations, the mitochondrial genome cannot cooperate effectively with the nuclear one resulting in a mito-nuclear incompatibility and reduce the fitness of the hybrids. This phenomenon is observed both in the laboratory and in natural populations, and have the potential to influence their evolution and speciation. Therefore, it turns out that the study of mitochondria is an exciting field that finds many applications, including pest control, and it can shed light on the molecular mechanism of several diseases, improving successful diagnosis and therapeutics. Finally, mito-nuclear co-adaptation, paternal leakage, and kin selection are some mechanisms that can mitigate the impact of the Mother's Curse.

DNA barcoding and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae) in Anatolia

The DNA barcoding approach was used for the determination of evolutionary relationships and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae). The COI barcode region (615 bp amplicon) was used to barcode 444 individuals from 64 morphologically identified species in the genus Oxynoemacheilus and 189 haplotypes were identified. The average of the interspecific p distance (9.59%) was about 21-fold higher than the average intraspecific distance (0.44%). A general genetic threshold of 1.46% sequence divergence was defined for species delimitation. The multiple species delimitation methods (BCM, GMYC, bPTP and TCS) revealed a total of 62 molecular operational taxonomic units for 64 morphospecies with a new loach species from the BuyukMelen River. Neighbour-joining, maximum likelihood and Bayesian inference analyses indicated that all haplotypes were clustered into 62 clades, which corresponded to Oxynoemacheilus species, with strong bootstrap support (≥95%). Furthermore, all samples grouped in concurrence with the taxonomic status of the species except for species groups (O. germencicus-O. cinicus-O. mesudae and O. leontinae-O. namiri) that were showed intraspecific overlap in genetic diversity for COI-based barcodes. In conclusion, our analyses indicate that COI-based barcodes provide reliable species discrimination. Therefore, we currently recommend COI barcodes as the suitable barcode for genus Oxynoemacheilus.

Complete mitogenomes of Turkish tree squirrels, Sciurus anomalus and S. vulgaris, (Sciuridae: Rodentia: Mammalia) and their phylogenetic status within the tribe Sciurini

The genus Sciurus, a member of the family Sciuridae, is widely distributed in the Holarctic region. To better understand mitogenomic characteristics and to reveal internal phylogenetic relationships of the genus, 20 complete mitogenomes of Turkish tree squirrels were successfully sequenced for the first time, including 19 for S. anomalus (from 16,505 bp to 16,510 bp) and one for S. vulgaris (16,511 bp). The mitogenomes of two species were AT-biased. All tRNAs for two species displayed a typical clover-leaf structure, except for tRNA^Ser(AGY). The tRNA Serine1 (S1)-GCT structure lacked the dihydrouridine (DHU) loop and stem. Based on mitogenomic dataset for phylogeny of Sciurinae, phylogenetic analyses (Bayesian Inference and Maximum Likelihood) did not support monophyly of Sciurus and proposed that S. anomalus, the most basal taxa in the Sciurini tribe, had at least five mitogenome lineages, which were also supported by network analysis. The dissimilarities among the five linegaes of S. anomalus ranged from 0.0042 (0.42%) to 0.0062 (0.62%) using K2P sequence pairwise distances. In addition to this mitogenomic analysis result, phylogenetic analyses using the CYTB + D-loop dataset proposed the existence of at least nine lineages for S. anomalus, which was different than those of the previous studies. The current study proposed that the use of mitogenomic data for reconstructing the phylogeny of Turkey' Sciurus holds an important value for revealing evolutionary relationships.

Pliocene-Pleistocene dispersal bring along low inter species diversity between Vimba species based on multilocus analysis

This study investigates phylogenetic and phylogeographic relationships of Vimba species using mitochondrial cytochrome b (cyt b) (1023 bp) and cytochrome c oxidase subunit I (COI) barcoding region (652 bp) genes. Ninety-one samples from 36 populations for the cyt b gene and 67 samples from 20 populations for the COI were analyzed. We identified 29 haplotypes and calculated overall haplotype diversity as Hd: 0.907 ± 0.015 for cyt b. We also identified 13 COI haplotypes and calculated overall haplotype diversity as 0.826 ± 0.026 for this marker. The phylogenetic analysis of Vimba species reveals the presence of four clades, based on concatenated cyt b and COI sequences. The first and second clade consist of Vimba vimba Western lineage, and Vimba vimba Caspian lineage, while the third and fourth clade consist of Vimba mirabilis and Vimba melanops. Based on haplotype network analyses and phylogeographic inferences, the Vimba genus is monophyletic, and its species dispersed in the Pleistocene era.

The story of a rock-star: multilocus phylogeny and species delimitation in the starred or roughtail rock agama, Laudakia stellio (Reptilia: Agamidae)

Situated at the junction of three continents, Europe, Asia and Africa, the Eastern Mediterranean is an ideal region to study the effects of palaeogeography, ecology and long human presence on animal evolution. Laudakia stellio (Squamata: Agamidae) is found across this region and offers an excellent opportunity for such studies. The high morphological variation across their range suggests that these lizards might represent a species complex. This is the first study exploring their evolutionary history, using molecular markers and individuals from all described subspecies. We employed the latest phylogenetic and species-delimitation methods to identify all distinct evolutionary lineages, their genetic variation and divergence times. The phenotypical diversity of L. stellio matches its genetic differentiation: almost all subspecies correspond to well-supported retrieved subclades and additional distinct lineages representing intermediate morphs have been retrieved. ‘Laudakia stellio’ represents three distinct evolutionary entities that diverged during the Plio-Pleistocene transition, which we propose as distinct species. One includes Greek and Turkish populations, as well as cryptic Anatolian lineages. The second comprises all other Near East populations and the third is endemic to Cyprus. Our results indicate a role of humans in shaping present distribution patterns, and highlight the importance of the Aegean, Anatolia and the Levant as glacial refugia and diversity hotspots.

Taxonomic Revision of Eastern Part of Western Palaearctic Cordulegaster Using Molecular Phylogeny and Morphology, with the Description of Two New Species (Odonata: Anisoptera: Cordulegastridae)

Taxonomy of the genus Cordulegaster Leach in Brewster, 1815 in the Eastern part of the Western Palaearctic is poorly resolved. A two-step approach was applied: sequences of mitochondrial and nuclear DNA fragments were used to sort specimens; poorly known or new taxa with their phenotypic variation were described. The existence of two traditional groups (boltonii- and bidentata-group) was confirmed. Cordulegaster coronata Morton, 1916, however, belongs to a different group. Molecular-analysis supported three known and one new species (C. heros Theischinger, 1979, C. picta Selys, 1854, C. vanbrinkae Lohmann, 1993, and C. kalkmani sp. nov.) in the boltonii-group. In the bidentata-group, all specimens from West-Turkey belonged to C. insignis Schneider, 1845, all specimens further east to a complex of four closely related species, which we name charpentieri-complex (C. amasina Morton, 1916, stat. rev., C. mzymtae Bartenev, 1929 C. charpentieri (Kolenati, 1846), stat. rev. and C. cilicia sp. nov.). The following taxa: C. insignis nobilis Morton, 1916, syn. nov., C. nachitschevanica Skvortsov and Snegovaya, 2015, syn. nov. C. plagionyx Skvortsov and Snegovaya, 2015, syn. nov. and the Caucasian subspecies C. insignis lagodechica Bartenev, 1930, syn. nov., were synonymized with C. charpentieri. Finally, we provide a key for all Western Palaearctic Cordulegaster.

Next-generation phylogeography of the banded newts (Ommatotriton): A phylogenetic hypothesis for three ancient species with geographically restricted interspecific gene flow and deep intraspecific genetic structure

Technological developments now make it possible to employ many markers for many individuals in a phylogeographic setting, even for taxa with large and complex genomes such as salamanders. The banded newt (genus Ommatotriton) from the Near East has been proposed to contain three species (O. nesterovi, O. ophryticus and O. vittatus) with unclear phylogenetic relationships, apparently limited interspecific gene flow and deep intraspecific geographic mtDNA structure. We use parallel tagged amplicon sequencing to obtain 177 nuclear DNA markers for 35 banded newts sampled throughout the range. We determine population structure (with Bayesian clustering and principal component analysis), interspecific gene flow (by determining the distribution of species-diagnostic alleles) and phylogenetic relationships (by maximum likelihood inference of concatenated sequence data and based on a summary-coalescent approach). We confirm that the three proposed species are genetically distinct. A sister relationship between O. nesterovi and O. ophryticus is suggested. We find evidence for introgression between O. nesterovi and O. ophryticus, but this is geographically limited. Intraspecific structuring is extensive, with the only recognized banded newt subspecies, O. vittatus cilicensis, representing the most distinct lineage below the species level. While mtDNA mostly mirrors the pattern observed in nuclear DNA, all banded newt species show mito-nuclear discordance as well.

The roles of possible geographic barriers and geological events on the phylogeographic structure of the Eastern broad toothed field mouse (Apodemus mystacinus)

The Eastern broad toothed field mouse, Apodemus mystacinus, is a rodent species distributed in Turkey, the Middle East, and a few Aegean Islands. The aim of this study is to analyse the phylogeographic structure of A. mystacinus and possible causes of its differentiation, on the basis of mitochondrial and nuclear DNA sequences using a large number of new samples from Turkey. In this context, partial mitochondrial sequences of cytochrome b (Cytb), control region (D-loop) and a nuclear interphotoreceptor retinoid-binding protein (IRBP) gene were used to reveal the geographical differentiation among A. mystacinus populations and the validity of its subspecies. The estimated divergence times revealed that the first separation of A. mystacinus into three distinct groups (subspecies of A. mystacinus: A. m. mystacinus, A. m. smyrnensis, and A. m. euxinus) begun 0.641 Mya. The possible physical barriers in Anatolia such as high mountains and rivers could interrupt the gene flow between A. mystacinus populations. The results of the present study indicated that A. mystacinus might have used the high rocky areas along the Anatolian Diagonal as a dispersal way. Moreover, mitochondrial data in this study suggested for the first time that A. m. rhodius is synonymous with the nominative subspecies A. m. mystacinus.

Population genetics and phylogeography of Tabanus bromius (Diptera: Tabanidae)

Background

Tabanus bromius (Diptera: Tabanidae) is one of the most notable Tabanidae species of veterinary and medical importance distributed throughout the Palearctic region. In this study, we investigate the genetic diversity and the phylogeographic structure of T. bromius sampled from Turkey, Croatia, and Iran.

Methods

For this purpose, a 686-base-pair (bp) fragment of mitochondrial DNA cytochrome oxidase I gene (COI) and 1339 bp of the nuclear DNA internal transcribed spacer (ITS) were sequenced from 247 individuals representing 15 populations.

Results

The sequences generated 169 COI haplotypes and 90 ITS alleles. A higher haplotype/allele diversity (h = 0.9909 for the COI gene and Ad = 0.8193 for the ITS region) compared to a low nucleotide diversity (π = 0.020605 for COI gene and π = 0.013667 for the ITS region), present for a high number of singleton and private haplotypes/alleles imply population expansion in the past. The results of phylogenetic analysis led to the uncovering of geographically significant groupings of lineages with regard to the entrance of the species into Anatolia and the location of major geographic barriers. According to current data, the species appears to have entered Turkey from Caucasia and Iran. A molecular clock applied to the COI data suggests that T. bromius diverged from the outgroup species nearly 8.83 million years ago, around the end of the Miocene era.

Conclusions

The results of this study indicate remarkable genetic diversity across the studied range of the species. High haplotype/allele versus low nucleotide diversity and demographic analyses implied that the T. bromius populations have undergone a series of expansions and retreats in the past. Our current findings suggest that T. bromius split from outgroups around the Late Miocene. Subsequent diversification events during the climatic and environmental fluctuation times of the Late Pliocene and Early Pleistocene periods also significantly influenced the species, resulting in the formation of some major genetic lineages. The phylogenetic analyses indicate that T. bromius most likely entered Turkey from the Caucasus region and Iran.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04970-5.

Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx

Previous molecular studies of the wide-ranging Eurasian lynx Lynx lynx focused mainly on its northern Palearctic populations, with the consequence that the reconstruction of this species’ evolutionary history did not include genetic variation present in its southern Palearctic distribution. We sampled a previously not considered Asian subspecies (L. l. dinniki), added published data from another Asian subspecies (L. l. isabellinus), and reassessed the Eurasian lynx mtDNA phylogeny along with previously published data from northern Palearctic populations. Our mitogenome-based analyses revealed the existence of three major clades (A: Central Asia, B: SE Europe/SW Asia, C: Europe and Northern Asia) and at least five lineages, with diversification in Lynx lynx commencing at least 28kyr earlier than hitherto estimated. The subspecies L. l. isabellinus harbors the most basal matriline, consistent with the origin of Lynx lynx in this subspecies’ current range. L. l. dinniki harbors the second most basal matriline, which is related to, and may be the source of, the mtDNA diversity of the critically endangered Balkan lynx L. l. balcanicus. Our results suggest that the Anatolian peninsula was a glacial refugium for Eurasian lynx, with previously unconsidered implications for the colonization of Europe by this species.

Conservation genetics of the European fallow deer: a reply to Marchesini et al

In this letter, we revisit a study we published in 2017, following comment in a paper by Marchesini et al. published in this volume. We provide some further analyses that help us to reinforce the original conclusions of our earlier paper, and to address the points raised by Marchesini et al. We conclude that the concerns raised in their review do not alter the inference we presented earlier, and we identify issues with analyses presented by Marchesini et al. that limit their utility. The key points of inference remain that this species in Europe shows remarkably low levels of diversity within populations and strong structure among populations which can be explained by a combination of natural and anthropogenic processes.

Allele Sorting as a Novel Approach to Resolving the Origin of Allotetraploids Using Hyb-Seq Data: A Case Study of the Balkan Mountain Endemic Cardamine barbaraeoides

Mountains of the Balkan Peninsula are significant biodiversity hotspots with great species richness and a large proportion of narrow endemics. Processes that have driven the evolution of the rich Balkan mountain flora, however, are still insufficiently explored and understood. Here we focus on a group of Cardamine (Brassicaceae) perennials growing in wet, mainly mountainous habitats. It comprises several Mediterranean endemics, including those restricted to the Balkan Peninsula. We used target enrichment with genome skimming (Hyb-Seq) to infer their phylogenetic relationships, and, along with genomic in situ hybridization (GISH), to resolve the origin of tetraploid Cardamine barbaraeoides endemic to the Southern Pindos Mts. (Greece). We also explored the challenges of phylogenomic analyses of polyploid species and developed a new approach of allele sorting into homeologs that allows identifying subgenomes inherited from different progenitors. We obtained a robust phylogenetic reconstruction for diploids based on 1,168 low-copy nuclear genes, which suggested both allopatric and ecological speciation events. In addition, cases of plastid-nuclear discordance, in agreement with divergent nuclear ribosomal DNA (nrDNA) copy variants in some species, indicated traces of interspecific gene flow. Our results also support biogeographic links between the Balkan and Anatolian-Caucasus regions and illustrate the contribution of the latter region to high Balkan biodiversity. An allopolyploid origin was inferred for C. barbaraeoides, which highlights the role of mountains in the Balkan Peninsula both as refugia and melting pots favoring species contacts and polyploid evolution in response to Pleistocene climate-induced range dynamics. Overall, our study demonstrates the importance of a thorough phylogenomic approach when studying the evolution of recently diverged species complexes affected by reticulation events at both diploid and polyploid levels. We emphasize the significance of retrieving allelic and homeologous variation from nuclear genes, as well as multiple nrDNA copy variants from genome skim data.

Molecular Phylogeny of the Subgenus Karstomys Reveals Genetic Signature of Post-Glacial Colonization of Apodemus mystacinus (Rodentia: Muridae) in the Zagros Mountains from Different Refugia

Eastern broad-toothed field mouse, Apodemus mystacinus, is a rocky habitat dwelling rodent distributed in Asia Minor, the Levant, the Caucasus, and the Zagros Mountains. In this study, we investigated the phylogenetic relationship between different populations of A. mystacinus throughout its range, based on the mitochondrial cytb marker. Phylogenetic analyses revealed the existence of five separately evolving lineages within A. mystacinus, of which two previously unrecognized lineages were identified in the Zagros Mountains and the Levant. Divergence between two major clades of the subgenus Karstomys, corresponding to A. mystacinus and Apodemus epimelas, is inferred to coincide with the Messinian Salinity Crisis (Late Miocene), whereas the splits between major lineages of A. mystacinus are inferred to have occurred during the Pleistocene. Colonization of the Zagros may have occurred from different refugia via eastward migration of the Turkish population and then again by a more recent colonization from the Caucasus, after reopening of the land corridor between the Caucasus and the Zagros Mountains during the Holocene drought.

Large-scale spatial patterns of small-mammal communities in the Mediterranean region revealed by Barn owl diet

Due to mainly opportunistic hunting behaviour of Barn owl can be its diet composition used for assessing local structure of small-mammal community. We evaluated the structure of small-mammal communities in the Mediterranean region by analysing Barn owl diet using own pellets and literature data (85 localities comprising 182,343 prey individuals). Contrary to widely accepted macroecological theory, we found a latitudinal increase of small-mammal alpha diversity, a less distinct west–east increase and lower diversity on islands. The mean prey weight decreased with increasing latitude, while on islands it decreased with increasing island area. The mean prey weight on islands was further negatively affected by mean land modification by human and positively affected by its range. The diet diversity on islands was not affected either by island area or its distance from the mainland. Its composition largely conformed to the main pattern pronounced over whole the region: an unexpected homogeneity of small-mammal community structure. Despite high beta diversity and large between-sample variation in species composition, Crocidura (+ Suncus etruscus) and murids (Apodemus, Mus, Rattus, in marginal regions partly replaced by gerbillids, Meriones or Microtus) composed more than 90% of owl prey in 92% of samples. Peak abundances of these widespread species are associated with a dynamic mosaic of dense patches of sparse herb vegetation and evergreen sclerophyllous shrublands interspersing areas of human activity, the dominant habitat of the inner Mediterranean and richest food resource for foraging Barn owls. The respective small-mammal species can be looked upon as invasive elements accompanying large scale human colonization of the region since the Neolithic and replacing original island biota. Our study documented that desertification of the Mediterranean played an important role in shaping inverse latitudinal gradient in diversity of small-mammals that contradicts to widely accepted mecroecological theory.

From refugia to contact: Pine processionary moth hybrid zone in a complex biogeographic setting

Contact zones occur at the crossroad between specific dispersal routes and are facilitated by biogeographic discontinuities. Here, we focused on two Lepidoptera sister species that come in contact near the Turkish Straits System (TSS). We aimed to infer their phylogeographic histories in the Eastern Mediterranean and finely analyze their co-occurrence and hybridization patterns in this biogeographic context. We used molecular mitochondrial and nuclear markers to study 224 individuals from 42 localities. We used discordances between markers and complementary assignment methods to identify and map hybrids and parental individuals. We confirmed the parapatric distribution of Thaumetopoea pityocampa (Lepidoptera: Notodontidae) in the west and Thaumetopoea wilkinsoni in the east and identified a narrow contact zone. We identified several glacial refugia of T. wilkinsoni in southern Turkey with a strong east-west differentiation in this species. Unexpectedly, T. pityocampa crossed the TSS and occur in northern Aegean Turkey and some eastern Greek islands. We found robust evidence of introgression between the two species in a restricted zone in northwestern Turkey, but we did not identify any F1 individuals. The identified hybrid zone was mostly bimodal. The distributions and genetic patterns of the studied species were strongly influenced both by the Quaternary climatic oscillations and the complex geological history of the Aegean region. T. pityocampa and T. wilkinsoni survived the last glacial maximum in disjoint refugia and met in western Turkey at the edge of the recolonization routes. Expanding population of T. wilkinsoni constrained T. pityocampa to the western Turkish shore. Additionally, we found evidence of recurrent introgression by T. wilkinsoni males in several T. pityocampa populations. Our results suggest that some prezygotic isolation mechanisms, such as differences in timing of the adult emergences, might be a driver of the isolation between the sister species.

The Anatolian glacial refugium and human-mediated colonization: a phylogeographical study of the stone marten (Martes foina) in Turkey

The Anatolian Peninsula, comprising most of modern Turkey, is situated at the junction of Europe, the Middle East and Asia. Together with its complex geomorphological and climatic history, this has given rise to a rich fauna and flora, which exhibits a wide range of historical biogeographical patterns. The stone marten (Martes foina) is a small carnivore that is found across the temperate Palaearctic region including Anatolia, where it is often associated with habitats modified by humans, but few genetic data exist for this species. We sequenced a 1840-bp region of the mitochondrial genome from 97 martens sampled across the peninsula and intron 7 of the nuclear β-fibrinogen gene from 53 of these. Two mitochondrial lineages were recovered, with overlapping eastern and western distributions, but there was no geographical structure for the autosomal marker. Coalescent analyses indicated that both of the lineages originated during the Last Glacial Maximum, one of them within an eastern Anatolian refugium and the other in a western Anatolian or Balkan refugium. The western lineage colonized most of Europe in the Holocene, while the eastern lineage may be endemic to Anatolia, from where it colonized the Iberian Peninsula via human translocation. The presence of at least one refugial stone marten population highlights the importance of Anatolia to the preservation of genetic variation and biodiversity.

Phylo-comparative analyses reveal the dual role of drift and selection in reproductive character displacement

When incipient species meet in secondary contact, natural selection can rapidly reduce costly reproductive interactions by directly targeting reproductive traits. This process, called reproductive character displacement (RCD), leaves a characteristic pattern of geographic variation where divergence of traits between species is greater in sympatry than allopatry. However, because other forces can also cause similar patterns, care must be given in separating pattern from process. Here we show how the phylo-comparative method together with genomic data can be used to evaluate evolutionary processes at the population level in closely related species. Using this framework, we test the role of RCD in speciation of two cricket species endemic to Anatolian mountains by quantifying patterns of character displacement, rates of evolution and adaptive divergence. Our results show differing patterns of character displacement between species for reproductive vs. non-reproductive characters and strong patterns of asymmetric divergence. We demonstrate diversification results from rapid divergence of reproductive traits towards multiple optima under the dual influence of strong drift and selection. These results present the first solid evidence for RCD in Anatolian mountains, quantify the amount of drift and selection necessary for RCD to lead to speciation, and demonstrate the utility of phylo-comparative methods for quantifying evolutionary parameters at the population level.

Phylogeography and Population Structure of the Mediterranean Corn Borer, Sesamia nonagrioides (Lepidoptera: Noctuidae), Across Its Geographic Range

Sesamia nonagrioides (Lefèbvre) (Lepidoptera: Noctuidae), is a widespread insect pest in Africa, the Middle East, and Europe. However, its pest status varies across its distribution range. It is a major pest of maize in Europe and of sugarcane in Iran. In Africa, it is a major pest of maize in West Africa but not considered as a pest in East Africa. Recent surveys conducted in 2015 recorded S. nonagrioides to be a major pest of sugarcane in Ethiopia and reported the species for the first time in Botswana, outside its known geographic range. The genetic relationship of these records with the previously recorded population of S. nonagrioides was investigated using the cytochrome oxidase subunit I region of the mitochondrial genome. In total, 113 individuals across the geographic range of the species were analyzed and 63 haplotypes were identified. Phylogenetic analysis separated the populations into two clades with no distinct geographic distribution pattern. The genetic differentiation was also not associated with host plants and geographic distances. Results of the molecular analysis revealed the long-time establishment of S. nonagrioides population in Botswana and identified the newly recorded sugarcane population from Ethiopia as part of the wild host population in the country. The phylogeographic patterns observed among population of S. nonagrioides have probably been shaped by Pleistocene's climatic oscillations and geographic range expansions from different refugia with secondary contact and admixture. Possible reasons for the host-plant expansion by the Ethiopian population are discussed.

Ribosomal DNA polymorphisms reveal genetic structure and a phylogeographic pattern in the Burgundy truffle Tuber aestivum Vittad

Ectomycorrhizal ascomycetes belonging to the genus Tuber produce edible fruiting bodies known as truffles. Tuber aestivum, in particular, is a fungus appreciated worldwide and has a natural distribution throughout Europe. Most of the molecular studies conducted on this species have been focused on the question as to whether or not T. aestivum and the morphologically similar T. uncinatum are conspecific. Conversely, only a handful of studies have assessed the level and distribution of genetic diversity and occurrence of phylogeographic patterns in this species. Here, we analyzed the genetic diversity of T. aestivum over a wide geographic range, performing an extensive sampling of specimens from Turkey, which is novel, to the best of our knowledge. We compared the internal transcribed spacer (ITS) profiles of 45 samples collected in different Turkish areas with those of 144 samples from all over Europe. We identified 63 haplotypes, 32 of which were exclusively present in Turkey. The majority of these haplotyes were also population specific. Haplotype network analysis and statistical tests highlighted the presence of a genetic structure and phylogeographic pattern, with three spatially distinct genetic clusters (northeastern Europe, southern Europe, and Turkey), with Turkey representing a diversity hotspot. Based on these results, we hypothesize the presence of glacial refugia for T. aestivum in Turkey, whereas European populations likely experienced a population bottleneck. The possible occurrence of cryptic species among Turkish T. aestivum samples also emerged. Our results are of practical relevance for the marketing of T. aestivum truffles and mycorrhizal seedlings and the preservation of the biodiversity of this species.

Islands and hybrid zones: combining the knowledge from "Natural Laboratories" to explain phylogeographic patterns of the European brown hare

Background

The aim of the study was to use hybrid populations as well as island populations of the European brown hare (Lepus europaeus) to explore the effect of evolutionary events, such as the post-deglaciation translocations, spontaneous and human-mediated, local adaptation and the genetic drift in the shaping of the phylogeographic patterns of the species. For this purpose, we used molecular markers, both nuclear and mitochondrial, that are indicative for local adaptation as well as neutral markers to elucidate the patterns of population differentiation based on geographic isolation and the clade of origin. To broaden our analysis, we included data from our previous studies concerning mainland populations, to explore the genetic differentiation in the base of the geographic origin (mainland/island) of the populations.

Results

Our results suggest that local adaptation shapes the differentiation in both genomes, favoring specific alleles in nuclear genes (e.g. DQA) or haplotypes in mtDNA (e.g. Control Region, CR). mtDNA variation was found to be in a higher level and was able to give a phylogeographic signal for the populations. Furthermore, the degree of variation was influenced not only by the geographic origin, but also by the clade of origin, since specific island populations of Anatolian origin showed a greater degree of variation compared to specific mainland populations of the European clade. Concerning the hybrid population, we confirmed the existence of both clades in the territory and we provided a possible explanation for the lack of introgression between the clades.

Conclusion

Our results indicate that the Quaternary’s climatic oscillations played a major role in the shaping of the phylogeographic patterns of the species, by isolating populations in the distinct refugia, where they adapted and differentiate in allopatry, leading to genome incompatibilities observed nowadays.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1354-y) contains supplementary material, which is available to authorized users.