Contrasting evolutionary histories of the legless lizards slow worms (Anguis) shaped by the topography of the Balkan Peninsula

Evolutionary history and systematics of European blind mole rats (Rodentia: Spalacidae: Nannospalax): Multilocus phylogeny and species delimitation in a puzzling group

Species delimitation is a powerful approach to assist taxonomic decisions in challenging taxa where species boundaries are hard to establish. European taxa of the blind mole rats (genus Nannospalax) display small morphological differences and complex chromosomal evolution at a shallow evolutionary divergence level. Previous analyses led to the recognition of 25 'forms' in their distribution area. We provide a comprehensive framework to improve knowledge on the evolutionary history and revise the taxonomy of European blind mole rats based on samples from all but three of the 25 forms. We sequenced two nuclear-encoded genetic regions and the whole mitochondrial cytochrome b gene for phylogenetic tree reconstructions using concatenation and coalescence-based species-tree estimations. The phylogenetic analyses confirmed that Aegean N. insularis belongs to N. superspecies xanthodon, and that it represents the second known species of this superspecies in Europe. Mainland taxa reached Europe from Asia Minor in two colonisation events corresponding to two superspecies-level taxa: N. superspecies monticola (taxon established herewith) reached Europe c. 2.1 million years ago (Mya) and was followed by N. superspecies leucodon (re-defined herewith) c. 1.5 Mya. Species delimitation allowed the clarification of the taxonomic contents of the above superspecies. N. superspecies monticola contains three species geographically confined to the western periphery of the distribution of blind mole rats, whereas N. superspecies leucodon is more speciose with six species and several additional subspecies. The observed geographic pattern hints at a robust peripatric speciation process and rapid chromosomal evolution. The present treatment is thus regarded as the minimum taxonomic content of each lineage, which can be further refined based on other sources of information such as karyological traits, crossbreeding experiments, etc. The species delimitation models also allowed the recognition of a hitherto unnamed blind mole rat taxon from Albania, described here as a new subspecies.

Unrecognized diversity, genetic structuring, and phylogeography of the genus Triplophysa (Cypriniformes: Nemacheilidae) sheds light on two opposite colonization routes during Quaternary glaciation that occurred in the Qilian Mountains

In recent years, the influence of historical geological and climatic events on the evolution of flora and fauna in the Tibetan Plateau has been a hot research topic. The Qilian Mountain region is one of the most important sources of biodiversity on the Qinghai-Tibet Plateau. Many species existed in the region during the Pleistocene glacial oscillation, and the complex geographical environment provided suitable conditions for the survival of local species. The shrinkage, expansion, and transfer of the distribution range and population size of species have significant effects on genetic diversity and intraspecific differentiation. To reveal the effects of geological uplift and climate oscillation on the evolution of fish populations in the Qilian Mountains, we investigated the genetic structure, phylogenetic relationship, and phylogeographical characteristics of genus Triplophysa species in the Qilian Mountains using the mitochondrial DNA gene (COI), three nuclear genes (RAG1, sRH, and Myh6) and 11 pairs of nuclear microsatellite markers. We collected 11 species of genus Triplophysa living in the Qilian Mountains, among which Triplophysa hsutschouensis and Triplophysa papillosolabiata are widely distributed in the rivers on the northern slope of the Qilian Mountains. There was a high degree of lineage differentiation among species, and the genetic diversity of endemic species was low. The different geographical groups of T. papillosolabiata presented some allogeneic adaptation and differentiation, which was closely related to the changes in the river system. Except for the population expansion event of T. hsutschouensis during the last glacial period of the Qinghai-Tibet Plateau (0.025 MYA), the population sizes of other plateau loach species remained stable without significant population expansion. Starting from the east and west sides of the Qilian Mountains, T. hsutschouensis, and T. papillosolabiata showed two species colonization routes in opposite directions. The geological events of the uplift of the Qinghai-Tibet Plateau and the climatic oscillation of the Quaternary glaciation had a great influence on the genetic structure of the plateau loach in the Qilian Mountains, which promoted the genetic differentiation of the plateau loach and formed some unique new species. The results of this study have important guiding significance for fish habitat protection in the Qilian Mountains.

Phylogenomics of Anguis and Pseudopus (Squamata, Anguidae) indicates Balkan-Apennine mitochondrial capture associated with the Messinian event

A dated phylogenetic hypothesis on the evolutionary history of the extant taxa of the Western Palearctic lizards Anguis and Pseudopus is revised using genome-wide nuclear DNA and mitogenomes. We found overall concordance between nuclear and mitochondrial DNA phylogenies, with one significant exception - the Apennine A. veronensis. In mitochondrial DNA, this species forms a common clade with the earliest diverging lineage, the southern Balkan endemic A. cephallonica, while it clusters together with A. fragilis in nuclear DNA. The nuclear phylogeny conforms to the morphology, which is relatively similar between A. veronensis and A. fragilis. The most plausible explanation for the mitonuclear discordance is ancient mitochondrial capture from the Balkan ancestor of A. cephallonica to the Apennine population of the A. fragilis-veronensis ancestor. We hypothesize that this capture occurred only in a geographically restricted population. The dating of this presumed mitochondrial introgression and capture coincides with the Messinian event, when the Balkan and Apennine Peninsulas were presumably largely connected. The dated nuclear phylogenomic reconstruction estimated the divergence of A. cephallonica around 12 Mya, while the sister clade representing the A. fragilis species complex consisting of the sister species A. fragilis-A. veronensis and A. colchica-A. graeca further diversified around 7 Mya. The depth of nuclear divergence among the evolutionary lineages of Pseudopus (0.5-1.2 Mya) supports their subspecies status.

Hidden in plain sight: novel molecular data reveal unexpected genetic diversity among paramphistome parasites (Digenea: Paramphistomoidea) of European water frogs

Parasites might represent a helpful tool in understanding the historical dispersion and phylogeography of their hosts. In order to reveal whether the migration routes and diversification of hosts can be traceable in the genetic structures of their parasites, we investigated the diversity of paramphistomoid trematodes of Pelophylax frogs in 2 geographically distant European regions. Water frogs belonging to the genus Pelophylax represent a striking example of a species with a high variety of ecological adaptations and a rich evolutionary history. The parasites were collected from 2 Balkan endemic species, P. epeiroticus and P. kurtmuelleri, and 2 species in Slovakia, P. esculentus and P. ridibundus. While in Slovakia, Pelophylax frogs harboured 2 species, the diplodiscid Diplodiscus subclavatus and the cladorchiid Opisthodiscus diplodiscoides, only the former was recorded in the south-western Balkans. Remarkably high genetic diversity (16 unique mitochondrial cox1 haplotypes, recognized among 60 novel sequences) was observed in D. subclavatus, and subsequent phylogenetic analyses revealed a strong population-genetic structure associated with geographical distribution. We also evidenced the existence of 2 divergent D. subclavatus cox1 haplogroups in the south-western Balkans, which might be associated with the historical diversification of endemic water frogs in the regional glacial microrefugia.

Phenotypic differentiation of the slow worm lizards (Squamata: Anguis) across their contact zone in Central Europe

Background

The application of molecular-phylogenetic approaches to taxonomy has had a dramatic effect on our understanding of the diversity of reptiles. These approaches have allowed researchers to reveal previously hidden lineages as well as taxonomic overestimation in morphologically plastic taxa. Slow worms, legless lizards of the genus Anguis (Squamata: Anguidae), were previously considered to comprise either one or two species, and morphology-based intraspecific taxonomy of Anguis fragilis remained controversial throughout the 20th century. After the discovery of deep genetic divergences within the genus, its taxonomy was reconsidered, and as a result, five extant species have been recognized. In order to better understand the patterns of their interspecific differentiation, here we studied phenotypic differences between the two most widespread of them—A. fragilis and A. colchica, and their putative hybrids across the contact zone of both species in Central Europe.

Methods

We used multivariate and univariate statistics and analyzed ten metric, eleven meristic, and six categorical phenotypic variables in material comprising a total of 326 individuals. We also genotyped individuals from the contact zone for one mitochondrial and two nuclear DNA fragments in order to delineate the distribution of individuals of hybrid and non-hybrid origin. The clines in morphological traits were studied using HZAR.

Results

We show that the two species are morphologically differentiated. Anguis fragilis has a less robust head, fewer scales covering the body, lower frequency of the external ear opening presence, lower frequency of separated prefrontal scales, higher frequency of prefrontal scales in contact with each other, and body coloration more similar to the juvenile coloration than A. colchica. Slow worms from the contact/hybrid zone are characterized by an intermediate morphology, with more similarities to A. fragilis than to A. colchica.

Discussion

None of the analyzed characters alone proved to be fully diagnostic, although more than 90% of all individuals could be successfully assigned to one or another species based on numbers of scales around the body. Our results indicate concordant, coincident, and steep clines in character states change. We present several hypotheses on the origin and evolutionary maintenance of the morphological divergence between both species and suggest that different evolutionary histories of the taxa rather than recently acting selection explain the observed morphological variation.

Morphological and genetic differentiation in the anguid lizard Pseudopus apodus supports the existence of an endemic subspecies in the Levant

The Levant represents one of the most important reptile diversity hotspots and centers of endemism in the Western Palearctic. The region harbored numerous taxa in glacial refugia during the Pleistocene climatic oscillations. Due to the hostile arid conditions in the warmer periods they were not always able to spread or come into contact with populations from more distant regions. One large and conspicuous member of the Levantine herpetofauna is the legless anguid lizardPseudopus apodus. This species is distributed from the Balkans to Central Asia with a portion of its range running along the eastern Mediterranean coast. Mitochondrial and nuclear DNA sequences, microsatellite genotypes, and morphology show that populations in this region differ from the two named subspecies and presumably had a long independent evolutionary history during the Quaternary. Here we describe the Levantine population as a new subspecies and present biogeographic scenarios for its origin and diversification. The new subspecies is genetically highly diverse, and it forms a sister lineage toPseudopusfrom the remaining parts of the range according to mtDNA. It is the largest-bodied of the three subspecies, but occupies the smallest range.

Stability in the Balkans: phylogeography of the endemic Greek stream frog, Rana graeca

We still have little knowledge concerning the phylogeography of amphibians and reptiles from the Balkan Peninsula compared with the other two Mediterranean peninsulas. This raises concerns for endemic taxa from these peninsulas, because it might interfere with further conservation efforts. Here we focus on the endemic Greek stream frog (Rana graeca) and reconstruct its biogeography and evolutionary history. Using four genetic markers (Cytb, 16S, COI and BDNF) in > 350 sequences covering the whole distribution range, we conducted phylogenetic, demographic and ecological niche analyses, which revealed the phylogeography of this species. Surprisingly, this examination of R. graeca reveals a very shallow level of intraspecific genetic variability through the Balkans, with two main, statistically supported lineages having a partly sympatric distribution. The most variable marker was Cytb, which showed 19 haplotypes in 123 analysed sequences in the whole species distribution area. Here presented genetic data, together with the environmental niche projection and demographic analyses suggest that R. graeca was probably affected only marginally by climatic oscillations, with the Hellenides as the most suitable area for the occurrence of the species in different geological periods. This is consistent with the observed genetic diversity, which is mostly related to these mountains. Although the species shows a certain level of phenotypic variability and ecological preferences, this might be related to species plasticity affected by the micro-climatic conditions in small areas, which merits further research. Comparing phylogeography of other amphibian and reptile species in the Balkans, we showed that the observed pattern represents a new view on the phylogeography of the Balkan herpetofauna.

DNA barcoding reveals distinct population of Dopasia gracilis (Squamata: Anguidae) in Mizoram, Northeast India

The DNA barcode data of Asian Glass Lizard, Dopasia gracilis, is limited in the global database, especially from India. The present study aimed to generate a barcode sequence of morphologically identified D. gracilis from the Mizoram state in northeast India and compared with other Anguidae species. The studied species showed monophyletic clustering in the Bayesian analysis (BA) phylogeny with strong posterior probability support and also discriminated sufficient Kimura 2 parameter genetic distances. The barcode data of D. gracilis revealed high intra-species genetic variability and formed two clusters in BA phylogeny. The Templeton, Crandall, and Sing network also depicted four different haplotypes within the barcode sequences of D. gracilis. The DNA sequences generated from northeast India showed 6.5-6.6% and 7.3% genetic distances with the sequences generated from Yunnan Province and Tibetan Plateau, respectively. Considering the high genetic distances, multiple clustering, and distinct haplotypes, the present study assumed the presence of possible cryptic diversity of D. gracilis in the Indochina sub-region and a distinct population in northeast India. We recommended the generation of more DNA information from different localities to elucidate the actual diversity of D. gracilis within the known range distribution.

Cryptic diversity in the smooth snake (Coronella austriaca)

The smooth snake, Coronella austriaca, is a common snake species widespread in the Western Palearctic region. It does not form conspicuous morphological variants and, although several evolutionary lineages have been distinguished based on the analyses of the mitochondrial DNA sequences, only two subspecies with very limited distribution have been traditionally recognized. Here we present an mtDNA phylogeography of the species using geographically extended sampling while incorporating biogeographically important areas that have not been analyzed before, such as Anatolia, Crimea, and Iran. We find that the smooth snake comprises 14 distinct phylogenetic clades with unclear mutual relationships, characterized by complex genetic structure and relatively deep divergences; some of them presumably of Miocene origin. In general, the biogeographic pattern is similar to other Western Palearctic reptiles and illustrates the importance of the main European peninsulas as well as the Anatolian mountains, Caucasus, and Alborz Mts. in Iran for the evolution of the present-day diversity. Considerable genetic structure present in the smooth snake populations within these large areas indicates the existence of several regional Plio-Pleistocene refugia that served as reservoirs for dispersal and population expansions after the glacial periods. The current taxonomy of C. austriaca does not reflect the rich genetic diversity, deep divergences, and overall evolutionary history revealed in our study and requires a thorough revision. This will only be possible with an even higher-resolution sampling and integrative approach, combining analyses of multiple genetic loci with morphology, and possibly other aspects of the smooth snake biology.

Multilocus phylogeography of the brown-spotted pitviper Protobothrops mucrosquamatus (Reptilia: Serpentes: Viperidae) sheds a new light on the diversification pattern in Asia

Understanding the influence of geographical events and climate changes on genetic diversity is essential in explaining current patterns of genetic structure and geographic distribution of organisms. We inferred phylogenetic relationships, investigated historical demography, explored the evolutionary history, and clarified intraspecific taxonomy of Protobothrops mucrosquamatus, which is one of the commonest and most wide-ranging Asian pitvipers. A total of 184 samples from 54 localities were sequenced and analyzed for two mitochondrial gene fragments and two nuclear genes. Phylogenetic reconstruction based on mtDNA sequences revealed the existence of a minimum of five geographically structured and well-supported lineages within P. mucrosquamatus. Based on the mtDNA gene tree, and the geographic relationship between populations allied by matrilineal lineages, a complex longitudinal and latitudinal diversification pattern was uncovered in P. mucrosquamatus. The estimated date of the origin of the species (about 5.3 Ma) and divergence of the intraspecific lineages match the rapid uplifting of Qinghai-Xizang Plateau, and is also consistent with those of some other co-distributed Asian pitvipers. Formation of the two island lineages (Taiwan and Hainan) was generally congruent with the first isolation of the islands, but the two lineages showed different relationships with the continental Asian populations in comparison with some other pitvipers. Population historical demographic analyses, based on three methods, showed that all lineages have experienced slight population expansion in and around the Dali Glacial. Tests of intraspecific taxonomy indicated that no cryptic taxon is present within this widely distributed snake.

High cryptic diversity of bitterling fish in the southern West Palearctic

South-east Europe, along with the adjacent region of south-west Asia, is an important biodiversity hotspot with high local endemism largely contributed by contemporary continental lineages that retreated to southern refugia during colder Quaternary periods. We investigated the genetic diversity of the European bitterling fish (Rhodeus amarus) species complex (Cyprinidae) across its range in the western Palearctic, but with a particular emphasis in the region of Balkan, Pontic and Caspian refugia. We genotyped 12 polymorphic microsatellite loci and a partial sequence of mitochondrial gene cytochrome b (CYTB) for a set of 1,038 individuals from 60 populations. We used mtDNA sequences to infer phylogenetic relationships and historical demography, and microsatellite markers to describe fine-scale genetic variability and structure. Our mtDNA analysis revealed six well-supported lineages, with limited local co-occurrence. Two lineages are distributed throughout central and western Europe (lineages "A" and "B"), with two zones of secondary contact. Another two lineages were restricted to the Ponto-Aegean region of Greece (lineages "C" and "D") and the final two lineages were restricted south of the Caucasus mountains (lineage "E" from the Black Sea watershed and lineage "F" from the Caspian watershed). A signal of recent expansion was revealed in the two widespread lineages and the Ponto-Aegean lineage "C". The geographic distribution of clusters detected by nuclear microsatellites corresponded well with mitochondrial lineages and demonstrated finely sub-structured populations. A profound population structure suggested a significant role of genetic drift in differentiation among lineages. Lineage divergence in the Ponto-Aegean and Caspian regions are substantial, supporting the validity of two described endemic species (Rhodeus meridionalis as lineage "D" and Rhodeus colchicus as lineage "E") and invite taxonomic evaluation of the other two southern lineages (Thracean "C" and Caspian "F").

Phylogenetic relationships and divergence dating in the Glass Lizards (Anguinae)

The Glass Lizards are a subfamily (Anguinae) of Anguid Lizards with an elongated limbless body plan that occur throughout the Northern Hemisphere primarily in North America, Europe, and Asia, but also have a presence in North Africa and Indonesia. We used twenty-five nuclear loci (15,191 bp) and 2090 bp of the mtDNA genome to generate a phylogeny containing all known species groups to explore species relationships within the group as well as divergence dating. We also examined the group in the context of a coalescent species tree analysis and species delimitation. All major lineages were found to be monophyletic with potential cryptic diversity in some. The Anguinae first appeared in the Eocene and most lineages were present by the beginning of the Miocene. The Anguinae originated in Europe from an Anguidae ancestor that crossed the Thulean land bridge, spreading to Asia after the drying of the Turgai Sea, then across Beringia as the climate permitted. A species tree analyses found support for the major Anguinae lineages and species delimitation supported accepted species.

Tracing the maternal origin of the common wall lizard (Podarcis muralis) on the northern range margin in Central Europe

The maternal origin of isolated populations of the common wall lizard (Podracis muralis) in the Czech Republic, representing the north-eastern range border of the species, was addressed. We compared mitochondrial DNA sequences of the cytochrome b gene of samples from these populations with those from within the continuous range in Slovakia, the northern Balkan region, and those available from previous studies. We recorded five main haplogroups in the studied region, with all available Central European samples belonging to the same haplogroup. The star-like structure of this haplogroup suggests a scenario of relatively recent, post-glacial population expansion, which is further supported by a coalescent-based demographic analysis. The presence of unique haplotypes in two of the three isolated Czech populations together with close phylogenetic relationships to adjacent Slovak populations suggests either autochthonous origin or human-mediated introductions from geographically and genetically closest populations. We therefore support conservation programs for all three isolated Czech populations.

Extra-Mediterranean glacial refuges in barred and common grass snakes (Natrix helvetica, N. natrix)

Extra-Mediterranean glacial refugia of thermophilic biota, in particular in northern latitudes, are controversial. In the present study we provide genetic evidence for extra-Mediterranean refugia in two species of grass snake. The refuge of a widely distributed western European lineage of the barred grass snake (Natrix helvetica) was most likely located in southern France, outside the classical refuges in the southern European peninsulas. One genetic lineage of the common grass snake (N. natrix), distributed in Scandinavia, Central Europe and the Balkan Peninsula, had two distinct glacial refuges. We show that one was located in the southern Balkan Peninsula. However, Central Europe and Scandinavia were not colonized from there, but from a second refuge in Central Europe. This refuge was located in between the northern ice sheet and the Alpine glaciers of the last glaciation and most likely in a permafrost region. Another co-distributed genetic lineage of N. natrix, now massively hybridizing with the aforementioned lineage, survived the last glaciation in a structured refuge in the southern Balkan Peninsula, according to the idea of 'refugia-within-refugia'. It reached Central Europe only very recently. This study reports for the first time the glacial survival of a thermophilic egg-laying reptile species in Central Europe.

Microevolution of the noble crayfish (Astacus astacus) in the Southern Balkan Peninsula

Background

The noble crayfish (Astacus astacus) displays a complex historical and contemporary genetic status in Europe. The species divergence has been shaped by geological events (i.e. Pleistocene glaciations) and humanly induced impacts (i.e. translocations, pollution, etc.) on its populations due to species commercial value and its niche degradation. Until now, limited genetic information has been procured for the Balkan area and especially for the southernmost distribution of this species (i.e. Greece). It is well known that the rich habitat diversity of the Balkan Peninsula offers suitable conditions for genetically diversified populations. Thus, the present manuscript revisits the phylogenetic relationships of the noble crayfish in Europe and identifies the genetic make-up and the biogeographical patterns of the species in its southern range limit.

Results

Mitochondrial markers (i.e. COI and 16S) were used in order to elucidate the genetic structure and diversity of the noble crayfish in Europe. Two of the six European haplotypic lineages, were found exclusively in Greece. These two lineages exhibited greater haplotypic richness when compared with the rest four (of “Central European” origin) while they showed high genetic diversity. Divergence time analysis identified that the majority of this divergence was captured through Pleistocene, suggesting a southern glacial refugium (Greece, southern Balkans). Furthermore, six microsatellite markers were used in order to define the factors affecting the genetic structure and demographic history of the species in Greece. The population structure analysis revealed six to nine genetic clusters and eight putative genetic barriers. Evidence of bottleneck effects in the last ~5000 years (due to climatic and geological events and human activities) is also afforded. Findings from several other research fields (e.g. life sciences, geology or even archaeology) have been utilized to perceive the genetic make-up of the noble crayfish.

Conclusions

The southernmost part of Balkans has played a major role as a glacial refugium for A. astacus. Such refugia have served as centres of expansion to northern regions. Recent history of the noble crayfish in southern Balkans reveals the influence of environmental (climate, geology and/or topology) and anthropogenic factors.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0971-6) contains supplementary material, which is available to authorized users.

Complete mitochondrial genome of the Eastern slow worm, Anguis colchica (Nordmann, 1840)

Here, we present complete mitochondrial genome of the Eastern Slow Worm, Anguis colchica (Nordmann, 1840). Mitogenome complete sequence is 17,097 bp long and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one control region. Anguis colchica mitochondrial genome has the same gene order as other mitogenomes of Anguis spp. Their analyzed genome has base composition as: A (30.4%), T (24.6%), C (30.4%), G (14.6%), with an A + T bias (55%). Length of the all 22 tRNA genes varies from 65 to 73 bp with an average of 69 bp. Presented mitogenome will provide new data for phylogenetic analysis within the genus Anguis.

Complete mitochondrial genome of the Italian slow-worm Anguis veronensis Pollini, 1818, and its comparison with mitogenomes of other Anguis species

In this paper, we present complete mitochondrial genome of the Italian legless lizard species Anguis veronensis Pollini, 1818. The complete mtDNA consisted of 13 protein-coding genes, 22 tRNAs, and two rRNA genes which in total formed a DNA strand of 17,322 bp. Anguis veronensis mitogenome had the same gene order as two other compared Anguis spp., i.e. A. cephallonica and A. fragilis. The base composition of A. veronensis mitochondrial genome was A - 30.8%, T - 24.9%, C - 29.9%, G - 14.4%, with an A + T bias (55.7%). The newly described genome provides valuable data for future comparative mitogenomic analysis within Anguis genus.

Phylogeography and postglacial colonization of Central Europe by Anguis fragilis and Anguis colchica

Five slow-worm species are distributed in the Palearctic region. Two species, Anguis fragilis and A. colchica, are native to Central Europe, where only limited information on the phylogeography of the genus exists. Here, we examined the situation in Poland and surrounding regions, where a mitochondrial contact zone between the species is expected. We used new mitochondrial DNA sequences and available published data from Central Europe and the northern Balkans. Haplotypes of both species were recorded in the study area. Anguis fragilis is represented by a single haplogroup, while A. colchica by three haplogroups. This suggests four independent sources/refugia for postglacial colonization of northern Central Europe. The mitochondrial contact zone seems to mirror the borders between lowlands of the North European Plain and East European Plain, and the south-eastern Poland uplands, while the Vistula River does not constitute a barrier. The presence of both species, A. fragilis and A. colchica, in Poland should also be considered for protection by the Polish conservation legislation.

Distribution and diversity of reptiles in Albania: a novel database from a Mediterranean hotspot

Although Albania has a rich reptile fauna, efforts to reveal its diversity have so far been limited. To fill this gap, we collected available published and unpublished (museum collections, online sources) records of reptile occurrences and conducted several expeditions to search for reptiles in areas with few or no previous records. Our georeferenced database contains 3731 records of 40 species from between 1918 and 2015. Based on this comprehensive dataset, we prepared distribution maps for each reptile species of the country. Applying spatial statistics, we revealed that overall sampling effort was clustered, with hotspots associated with easily accessible areas and natural heritage sites. The maximum number of species per cell was 26 with an average of seven. Cells harbouring large reptile diversity were located along the Adriatic and Ionian coasts, on the western slopes of south Albanian mountains, i.e. in areas generally considered as Balkans biodiversity hotspots or potential historical refugia. We found that species presence and diversity is strongly influenced by landscape features. Diversity of land cover, altitudinal variation, temperature and precipitation variation explained the observed pattern in our models. Our study presents the largest database of reptile occurrences to date and is the first to analyse reptile diversity patterns in Albania. The database and the diversity patterns can provide a basis for future macroecological studies and conservation planning.