Phylogeography of the Italian wall lizard, Podarcis sicula, as revealed by mitochondrial DNA sequences

Smarter in the city? Lizards from urban and semi-natural habitats do not differ in a cognitive task in two syntopic species

Urbanization occurs at a global scale, imposing dramatic and abrupt environmental changes that lead to biodiversity loss. Yet, some animal species can handle these changes, and thrive in such artificial environments. One possible explanation is that urban individuals are equipped with better cognitive abilities, but most studies have focused on birds and mammals and yielded varied results. Reptiles have received much less attention, despite some lizard species being common city dwellers. The Italian wall lizard, Podarcis siculus, and the common wall lizard, Podarcis muralis, are two successful lizards in anthropogenic habitats that thrive in urban locations. To test for differences in a cognitive skill between urban and semi-natural environments, we investigated inhibitory control through a detour task in syntopic populations of the two species, across 249 lizards that were tested in partially artificial field settings. Sophisticated inhibitory control is considered essential for higher degrees of cognitive flexibility and other higher-level cognitive abilities. In this task, we confronted lizards with a transparent barrier, separating them from a desired shelter area that they could only reach by controlling their impulse to go straight and instead detour the barrier. We found no differences between lizards in urban and semi-natural environments, nor between species, but females overall performed better than males. Moreover, 48% of the lizards in our study did not perform a correct trial in any of the 5 trials, hinting at the difficulty of the task for these species. This study is among the first to address lizard cognition, through their inhibitory control, as a potential explanation for success in cities and highlights one should be careful with assuming that urban animals generally have enhanced cognitive performance, as it might be taxa, task, or condition dependent.

Physiological phenotypes differ among color morphs in introduced common wall lizards (Podarcis muralis)

Many species exhibit color polymorphisms which have distinct physiological and behavioral characteristics. However, the consistency of morph trait covariation patterns across species, time, and ecological contexts remains unclear. This trait covariation is especially relevant in the context of invasion biology and urban adaptation. Specifically, physiological traits pertaining to energy maintenance are crucial to fitness, given their immediate ties to individual reproduction, growth, and population establishment. We investigated the physiological traits of Podarcis muralis, a versatile color polymorphic species that thrives in urban environments (including invasive populations in Ohio, USA). We measured five physiological traits (plasma corticosterone and triglycerides, hematocrit, body condition, and field body temperature), which compose an integrated multivariate phenotype. We then tested variation among co-occurring color morphs in the context of establishment in an urban environment. We found that the traits describing physiological status and strategy shifted across the active season in a morph-dependent manner-the white and yellow morphs exhibited clearly different multivariate physiological phenotypes, characterized primarily by differences in plasma corticosterone. This suggests that morphs have different strategies in physiological regulation, the flexibility of which is crucial to urban adaptation. The white-yellow morph exhibited an intermediate phenotype, suggesting an intermediary energy maintenance strategy. Orange morphs also exhibited distinct phenotypes, but the low prevalence of this morph in our study populations precludes clear interpretation. Our work provides insight into how differences among stable polymorphisms exist across axes of the phenotype and how this variation may aid in establishment within novel environments.

Evolutionary Plasticity in Insular Lizard, Adapting over Reproduction, Metabolism, and Color Variation

The Italian wall lizard (Podarcis siculus) living on islets exhibits a melanic skin coloration and a suite of adaptive traits lacking in nearby mainland populations. On islets, the unpredictable environmental conditions and highly fluctuating population densities are believed to have produced reversed island syndrome (RIS). Several physiological, behavioral, and life-history changes based on the RIS could result from positive selection on increased activity of melanocortins. We hypothesize that phenotypes on islets are the product of a plastic variation depending on the regulation of specific genes. Focusing on control systems that determine the insular-adapted phenotype, we demonstrated that reproductive markers, involved in the hypothalamus-hypophysis-gonadal axis, and metabolism markers, flags for hypophysis-melanocortin receptors, are all up-regulated in island lizards under the RIS. This behavior, combined with the observed limited variation in the mitochondrial genome, agrees with the hypothesis that plasticity enables populations to persist in novel environmental conditions and that over time, natural selection will "fine-tune" the population to the environment by modifying the phenotype under selection. We believe that analysis of the transcriptome and the single gene expression, such that all the variations observed in the island populations, can be useful to shed light on evolutionary plasticity as a process affecting animals' populations in general.

Genetic depletion does not prevent rapid evolution in island-introduced lizards

Experimental introductions of species have provided some of the most tractable examples of rapid phenotypic changes, which may reflect plasticity, the impact of stochastic processes, or the action of natural selection. Yet to date, very few studies have investigated the neutral and potentially adaptive genetic impacts of experimental introductions. We dissect the role of these processes in shaping the population differentiation of wall lizards in three Croatian islands (Sušac, Pod Kopište, and Pod Mrčaru), including the islet of Pod Mrčaru, where experimentally introduced lizards underwent rapid (~30 generations) phenotypic changes associated with a shift from an insectivorous to a plant-based diet. Using a genomic approach (~82,000 ddRAD loci), we confirmed a founder effect during introduction and very low neutral genetic differentiation between the introduced population and its source. However, genetic depletion did not prevent rapid population growth, as the introduced lizards exhibited population genetic signals of expansion and are known to have reached a high density. Our genome-scan analysis identified just a handful of loci showing large allelic shifts between ecologically divergent populations. This low overall signal of selection suggests that the extreme phenotypic differences observed among populations are determined by a small number of large-effect loci and/or that phenotypic plasticity plays a major role in phenotypic changes. Nonetheless, functional annotation of the outlier loci revealed some candidate genes relevant to diet-induced adaptation, in agreement with the hypothesis of directional selection. Our study provides important insights on the evolutionary potential of bottlenecked populations in response to new selective pressures on short ecological timescales.

Genotyping the phenotypic diversity in Aegean Natrixnatrixmoreotica (Bedriaga, 1882) (Reptilia, Serpentes, Natricidae)

We examined the mitochondrial identity of Aegean Natrixnatrixmoreotica representing different morphotypes, with a focus on new material from Milos and Skyros. We found no correlation between distinct morphotypes and mitochondrial identity. Our results support that grass snake populations are polyphenetic and that southern subspecies, including island populations, show a higher variability than northern ones.

The Intriguing Biogeographic Pattern of the Italian Wall Lizard Podarcis siculus (Squamata: Lacertidae) in the Tuscan Archipelago Reveals the Existence of a New Ancient Insular Clade

The Tuscan Archipelago is one of the most ancient and ecologically heterogeneous island systems in the Mediterranean. The biodiversity of these islands was strongly shaped by the Pliocene and Pleistocene sea regressions and transgression, resulting in different waves of colonization and isolation of species coming from the mainland. The Italian wall lizard, Podarcis siculus, is present on the following islands of the Tuscan Archipelago: Elba, Giglio, Giannutri, Capraia, Montecristo and Cerboli. The species in the area displays a relatively high morphological variability that in the past led to the description of several subspecies. In this study, both the genetic and morphological diversity of P. siculus of the Tuscan Archipelago were investigated. Specifically, the meristic characters and the dorsal pattern were analyzed, while the genetic relationships among these populations were explored with mtDNA and microsatellite nuclear markers to reconstruct the colonization history of the Archipelago. Our results converge in the identification of at least two different waves of colonization in the Archipelago: Elba, and the populations of Cerboli and Montecristo probably originate from historical introductions from mainland Tuscany, while those of Giglio and Capraia are surviving populations of an ancient lineage which colonized the Tuscan Archipelago during the Pliocene and which shares a common ancestry with the P. siculus populations of south-eastern Italy. Giannutri perhaps represents an interesting case of hybridization between the populations from mainland Tuscany and the Giglio-Capraia clade. Based on the high phenotypic and molecular distinctiveness of this ancient clade, these populations should be treated as distinct units deserving conservation and management efforts as well as further investigation to assess their taxonomic status.

Türkiye Podarcis siculus siculus (Rafinesque-Schmaltz, 1810) Populasyonlarının Kökenini Ortaya Çıkarmak için Tür Sınırlarının Belirlenmesi

Türkiye’ye insan eliyle getirilen Podarcis sicurus türünün kökeninin iki farklı kaynak populasyona dayanma olasılığı ya da farklı coğrafyalara taşınan örneklerin alttür seviyesinde farkılaşma olasılığı bulunmaktadır. Ada türlerinde gözlemlenen hızlı evrimleşme süreçleri, taşınmış ve izole olmuş popülasyonlarda da benzer şekilde ortaya çıkabilmektedir. Bu çalışmada Türkiye’den üç farklı lokaliteden; Zonguldak, İstanbul ve Samsun'dan elde edilen örneklerden dokular alınmıştır. mtDNA gen dizileri elde edilmiş ve Türkiye'ye ait Podarcis sicurus örnekleri ve Genbanktan indirilen dizilerle birleştirilmiştir. Filogenetik analizler ve tür sınırlama analizleri yapılmıştır. Buna göre, türün Türkiye'den elde edilen örnekleri coğrafik izolasyonlarına benzer şekilde iki farklı haplotipte gruplanmıştır. Bu grupların farklı kaynak grupları olduğu görülmüştür. Species delimination analizleri ise bu haplotiplerin farklılıklaşmasının alttür düzeyinde olabileceğini göstermektedir.

Biogeography of Italy revisited: genetic lineages confirm major phylogeographic patterns and a pre-Pleistocene origin of its biota

Warm-adapted species survived the cold stages of the past glacial-interglacial cycles in southern European peninsulas and recolonized major parts of Central and Northern Europe in the wake of postglacial warming. However, many of the genetic lineages which differentiated within these refugia predate even the Pleistocene. One of these refugia is the Italian Peninsula with its surrounding islands. In this meta-analysis, we compiled phylogeographic patterns of multiple species across this region. We transformed existing geographic information on 78 animal and plant species (with a total of 471 genetic lineages) within 17 predefined areas into presence/absence matrices. We elaborated three matrices: (i) only old lineages exclusively distinguished by deep splits, (ii) only young lineages distinguished by shallow (i.e. recent) splits, and (iii) presence/absence of the respective species. To infer biogeographic relationships between the predefined areas, we performed bootstrapped neighbour joining cluster analyses on these three matrices. In addition, we reviewed the geological history of Italy to identify causes of the observed biogeographic patterns. We found Sardinia and Corsica to be biogeographically closely linked with each other, and that they diverge strongly from all other regions. Sicily also diverges strongly from all other regions, while the intra-island differentiation was comparatively low. On the Italian mainland, Calabria exhibited the most pronounced biogeographic differentiation, often with several lineages present, resulting from old vicariance events within the region. Furthermore, southern Apulia and the Po Plain with adjoining areas of northern peninsular Italy displayed considerable distinctiveness. Admixture prevailed in the areas between these three regions. The ancient isolation of Sicily, as well as Sardinia plus Corsica, resulted in endemic lineages with only moderate recent exchange with adjacent mainland regions. Pronounced diversification occurs within the Italian Peninsula. The complex tectonic activities, such as shifting (micro)plates, submergence of major parts of peninsular Italy with the genesis of numerous Pliocene islands, in combination with the climatic cycles during the Pleistocene have most likely generated the current biogeographic pattern of species. Immigrations from the Balkan Peninsula into northern Italy partly accounted for the distinctiveness of this region.

Fossil-calibrated time tree of Podarcis wall lizards provides limited support for biogeographic calibration models

Podarcis wall lizards are endemic to the Mediterranean Basin where they represent the predominant reptile group. Despite being extensively used as model organisms in evolutionary and ecological studies their phylogeny and historical biogeography are still incompletely resolved. Moreover, molecular clock calibrations used in wall lizard phylogeography are based on the assumption of vicariant speciation triggered by the abrupt Mediterranean Sea level rise at the end of the Messinian salinity crisis (MSC). However, the validity of this biogeographic calibration remains untested. In this study we inferred a robust time tree based on multilocus data and fossil calibrations using both gene concatenation and species-tree approaches and including models with gene-flow. We found five deeply divergent, geographically coherent, and well-supported clades comprising species from i) Iberian Peninsula and North Africa; ii) Western Mediterranean islands, iii) Sicilian and Maltese islands; and iv-v) Balkan region and Aegean islands. The mitochondrial tree shows some inconsistencies with the species tree that warrant future investigation. Diversification of main clades is estimated in a short time frame during the Middle Miocene and might have been associated with a period of global climate cooling with the establishment of a marked climatic zonation in Europe. Cladogenetic events within the main clades are scattered throughout the time tree, from the Late Miocene to the Early Pleistocene, suggesting that speciation events in wall lizards reflect a complex interplay between regional topography, climate and geological history rather than a shared major climatic or paleogeographic event. Our absolute time estimates, as well as a relative dating approach, demonstrate that the assumption of a causal link between sea-level rise at the end of the MSC and the diversification of many island endemics is not justified. This study reinforces the notion that multiple dispersal and vicariant events, at different time frames, are required to explain current allopatric distributions and to account for the historical assembly of Mediterranean biota, and cautions against the use of biogeographic calibrations based on the assumption of vicariance.

Rapid Dietary Shift in Podarcis siculus Resulted in Localized Changes in Gut Function

AbstractNatural dietary shifts offer the opportunity to address the nutritional physiological characters required to thrive on a particular diet. Here, we studied the nutritional physiology of Podarcis siculus, with populations on Pod Mrčaru, Croatia, that have become omnivorous and morphologically distinct (including the development of valves in the hindgut) from their insectivorous source population on Pod Kopište. We compared gut structure and function between the two island populations of this lizard species and contrasted them with an insectivorous mainland out-group population in Zagreb. On the basis of the adaptive modulation hypothesis, we predicted changes in gut size and structure, digestive enzyme activities, microbial fermentation products (short-chain fatty acids [SCFAs]), and plant material digestibility concomitant with this dietary change. The Pod Mrčaru population had heavier guts than the mainland population, but there were no other differences in gut structure. Most of the enzymatic differences we detected were between the island populations and the out-group population. The Pod Mrčaru lizards had higher amylase and trehalase activities in their hindguts compared with the Pod Kopište population, and the Pod Kopište lizards had greater SCFA concentrations in their hindguts than the omnivorous Pod Mrčaru population. Interestingly, the differences between the Pod Mrčaru and Pod Kopište populations are primarily localized to the hindgut and are likely influenced by microbial communities and a higher food intake by the Pod Mrčaru lizards. Although subtle, the changes in hindgut digestive physiology impact the digestibility of plant material in adult lizards-Pod Mrčaru lizards had higher digestibility of herbivorous and omnivorous diets fed over several weeks in the laboratory than did their source population.

Evaluating the island effect on phenotypic evolution in the Italian wall lizard, Podarcis siculus (Reptilia: Lacertidae)

Islands are compelling natural laboratories for studying evolutionary processes. Nevertheless, the existence of general rules underlying morphological evolution on islands remains an unresolved issue. In this study, we investigated the insular phenotypic variability of the Italian wall lizard (Podarcis siculus) on a large geographical scale, in order to assess the putative existence of an island effect on three morphological head traits: shape, size and degree of sexual dimorphism. A geometric morphometric analysis was performed on 30 island and 24 mainland populations, involving a total of 992 specimens, and we analysed differences in both mean trait values and variances (disparity). We found increased shape disparity in insular lizards with respect to mainland ones. On the other hand, both size disparity and mean head dimensions of males decreased on islands, leading to a reduction in sexual dimorphism. Our results provide evidence for a multidirectional morphological diversification on islands concerning head shape of both sexes, while directional and canalizing selection likely occurred for head size, but only in males. Our findings improve our knowledge on the effect of insularity in Podarcis siculus, and highlight the need for an exstensive sampling scheme and a multi-trait methodological approach.

Reconstructing hotspots of genetic diversity from glacial refugia and subsequent dispersal in Italian common toads (Bufo bufo)

Genetic diversity feeds the evolutionary process and allows populations to adapt to environmental changes. However, we still lack a thorough understanding of why hotspots of genetic diversity are so 'hot'. Here, we analysed the relative contribution of bioclimatic stability and genetic admixture between divergent lineages in shaping spatial patterns of genetic diversity in the common toad Bufo bufo along the Italian peninsula. We combined population genetic, phylogeographic and species distribution modelling (SDM) approaches to map ancestral areas, glacial refugia, and secondary contact zones. We consistently identified three phylogeographic lineages, distributed in northern, central and southern Italy. These lineages expanded from their ancestral areas and established secondary contact zones, before the last interglacial. SDM identified widespread glacial refugia in peninsular Italy, sometimes located under the present-day sea-level. Generalized linear models indicated genetic admixture as the only significant predictor of the levels of population genetic diversity. Our results show that glacial refugia contributed to preserving both levels and patterns of genetic diversity across glacial-interglacial cycles, but not to their formation, and highlight a general principle emerging in Mediterranean species: higher levels of genetic diversity mark populations with substantial contributions from multiple genetic lineages, irrespective of the location of glacial refugia.

Distribution and conservation status of the herpetofauna of Dugi Otok Island, Croatia

The first overview of the amphibians and reptiles of Dugi Otok Island, Northern Dalmatia, is presented, based on the published data and new records collected during the last twenty years. A total of 15 species are present on the island, of which only one was not recorded on our surveys. In comparison to other islands of Northern Dalmatia, Dugi Otok is the second most diverse island in terms of herpetofauna, just after Pag Island. The main threats to the amphibians and reptiles on the island are the disappearance and degradation of aquatic habitats, the abandonment and succession of traditional agricultural fields and olive groves and the increasing presence of several invasive species.

Differences in cautiousness between mainland and island Podarcis siculus populations are paralleled by differences in brain noradrenaline/adrenaline concentrations

Adaptive behavior is shaped by the type and intensity of selection pressures coming from the environment, such as predation risk and resource availability, and can be modulated by individual's neuroendocrine profile involving steroid hormones and the brain-stem monoaminergic circuits projecting to forebrain structures. Boldness when faced with a predator and exploration/activity when confronted with a new environment reflect the degree of cautiousness and/or "risk-taking" of an individual. In this study we have explored to which extent two populations of Podarcis siculus occupying different ecological niches: mainland (ML) and an islet (ISL) differ in the level of cautiousness and whether these differences are paralleled by differences in their monoaminergic profiles. Boldness was tested in the field as antipredator behavior, while novel space and object explorations were tested in a laboratory setting in an open field apparatus. Finally, serotonin, dopamine, noradrenaline (NA) and adrenaline (ADR) concentrations were measured in whole brain samples by ELISA. Lizards from ML population spent significantly more time hiding after a predator encounter in the field, displayed lower intensity of novel space exploration in a laboratory setting, and contained significantly higher whole-brain concentrations of NA and ADR than their ISL counterparts. Parallelism between the level of risk-taking behavior and concentrations of neurotransmitters mediating alertness and reaction to stress suggests that the differing environmental factors on ML and ISL may have shaped the degree of cautiousness in the residing lizard populations by affecting the activity of NA/ADR neural circuits.

Proximate and ultimate drivers of variation in bite force in the insular lizards Podarcis melisellensis and Podarcis sicula

Bite force is a key performance trait in lizards because biting is involved in many ecologically relevant tasks, including foraging, fighting and mating. Several factors have been suggested to impact bite force in lizards, such as head morphology (proximate factors), or diet, intraspecific competition and habitat characteristics (ultimate factors). However, these have been generally investigated separately and mostly at the interspecific level. Here we tested which factors drive variation in bite force at the population level and to what extent. Our study includes 20 populations of two closely related lacertid species, Podarcis melisellensis and Podarcis sicula, which inhabit islands in the Adriatic. We found that lizards with more forceful bites have relatively wider and taller heads, and consume more hard prey and plant material. Island isolation correlates with bite force, probably by driving resource availability. Bite force is only poorly explained by proxies of intraspecific competition. The linear distance from a large island and the proportion of difficult-to-reduce food items consumed are the ultimate factors that explain most of the variation in bite force. Our findings suggest that the way in which morphological variation affects bite force is species-specific, probably reflecting the different selective pressures operating on the two species.

Bacteria and parasites in Podarcis sicula and P. sicula klemmerii

Background

New epidemiological data on bacterial and parasitic infections in 24 Italian wall lizards, namely Podarcis sicula (mainland population) and P. sicula klemmerii (insular population) in southern Italy were provided. To achieve this goal, samples were collected from individuals belonging to the two populations and analysed by microbiological and parasitological methods.

Results

A wide range of bacteria (e.g. Pantoea spp., Citrobacter spp., Morganella spp., Pseudomonas, Enterobacter spp., Staphylococcus spp. and Escherichia coli) and parasites (e.g. Ophionyssus natricis, coccidia, Dicrocoelidae) were detected in both P. sicula and P. sicula klemmerii individuals. Insular population presented similar bacterial and parasitic diversity to its mainland counterpart. Ampicillin was the antimicrobial with the highest resistance rate.

Conclusion

This study highlighted various bacteria and parasites, some of them potentially zoonotic. Further studies are needed to better understand the epidemiology and transmission routes of these pathogens along with their impact on the welfare and behaviour of Italian wall lizards.

Spotlight on islands: on the origin and diversification of an ancient lineage of the Italian wall lizard Podarcis siculus in the western Pontine Islands

Groups of proximate continental islands may conceal more tangled phylogeographic patterns than oceanic archipelagos as a consequence of repeated sea level changes, which allow populations to experience gene flow during periods of low sea level stands and isolation by vicariant mechanisms during periods of high sea level stands. Here, we describe for the first time an ancient and diverging lineage of the Italian wall lizard Podarcis siculus from the western Pontine Islands. We used nuclear and mitochondrial DNA sequences of 156 individuals with the aim of unraveling their phylogenetic position, while microsatellite loci were used to test several a priori insular biogeographic models of migration with empirical data. Our results suggest that the western Pontine populations colonized the islands early during their Pliocene volcanic formation, while populations from the eastern Pontine Islands seem to have been introduced recently. The inter-island genetic makeup indicates an important role of historical migration, probably due to glacial land bridges connecting islands followed by a recent vicariant mechanism of isolation. Moreover, the most supported migration model predicted higher gene flow among islands which are geographically arranged in parallel. Considering the threatened status of small insular endemic populations, we suggest this new evolutionarily independent unit be given priority in conservation efforts.

Phylogenetic relationships of Podarcis siculus (Rafinesque-Schmaltz, 1810) and Podarcis tauricus (Pallas, 1814) in Turkey, based on mitochondrial DNA

The Italian wall lizard and the Balkan wall lizard have a series of taxonomic revisions. However, their phylogenetic relationships still remain uncertain in Turkey. In the present study, we have assessed taxonomic relationships, both of Podarcis siculus and Podarcis tauricus through estimation of phylogenetic relationships among 43 and 42 specimens, respectively, using mtDNA (16 S rRNA and cytb) from great main populations in Turkey. The genetic distances among the populations of P. siculus in Turkey were very low and they were ranged from 0.2 to 1.6% in 16 S rRNA while they were ranged from 0.0% to 3.3% in cytb. On the other hand, the p-distances among the populations of P. tauricus were ranged from 0.0 to 0.6% in 16 S rRNA while they were 0.2% cytb in Turkey. Finally, most of the topologically identical trees of phylogenetic analyses and p-distances showed that monophyly was found in extant populations of P. siculus and P. tauricus. The nominate subspecies, P. s. siculus and P. t. tauricus are representatives of these lizards in Turkey.

Extra-Mediterranean glacial refugia in a Mediterranean faunal element: the phylogeography of the chalk-hill blue Polyommatus coridon (Lepidoptera, Lycaenidae)

Most warm-adapted Central European species are thought to have survived ice ages exclusively in Mediterranean refugia. During recent years, this point of view has been questioned. Therefore, we tested the hypothesis that extra-Mediterranean refugia also played a role in warm-adapted insect species and selected the chalk-hill blue, Polyommatus coridon. We sequenced two mitochondrial loci (COI, CR) in 150 individuals from 30 populations covering nearly the complete range. Minimum spanning networks and other statistical analyses concordantly revealed four genetic lineages with strong phylogeographic signal: a western group in Italy, France and western/central Germany, an eastern lineage in the Balkan Peninsula, the Carpathian Basin and eastern Central Europe, an Alpine group with populations in the Alps and southern Germany and a Pyrenean group. Our results are generally consistent with previous analyses for P. coridon based on allozymes and DNA sequences, but provide additional insights. We propose that these four lineages have evolved during allopatry in different glacial refugia, two in typical Mediterranean refugia (Apennines and Balkan Peninsulas), but two in extra-Mediterranean areas south of the Alps and Pyrenees. This supports survival of warm-adapted organisms in these regions in close geographic proximity to the refugia of high mountain species.

A combination of long term fragmentation and glacial persistence drove the evolutionary history of the Italian wall lizard Podarcis siculus

BACKGROUND

The current distribution of genetic diversity is the result of a vast array of microevolutionary processes, including short-term demographic and ecological mechanisms and long-term allopatric isolation in response to Quaternary climatic fluctuations. We investigated past processes that drove the population differentiation and spatial genetic distribution of the Italian wall lizard Podarcis siculus by means of sequences of mitochondrial cytb (n = 277 from 115 localities) and nuclear mc1r and β-fibint7genes (n = 262 and n = 91, respectively) from all its distribution range. The pattern emerging from the genetic data was compared with current and past (last glacial maximum) species distribution modeling (SDM).

RESULTS

We identified seven deeply divergent parapatric clades which presumably remained isolated in different refugia scattered mainly throughout the Tyrrhenian coast. Conversely, the Adriatic coast showed only two haplogroups with low genetic variability. These results appear to agree with the SDM prediction at the last glacial maximum (LGM) indicating a narrow area of habitat suitability along the Tyrrhenian coast and much lower suitability along the Adriatic one. However, the considerable land exposure of the Adriatic coastline favored a glacial colonization of the Balkan Peninsula.

CONCLUSIONS

Our population-level historical demography showed a common trend consistent with glacial expansions and regional persistence during the last glacial maximum. This complex genetic signature appears to be inconsistent with the expectation of the expansion-contraction model and post-LGM (re)colonizations from southern refugia. Hence it is one of an increasing number of cases in which these assumptions are not met, indicating that long-term fragmentation and pre-LGM events such as glacial persistence were more prominent in shaping genetic variation in this temperate species.

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.

Complex within a Complex: Integrative Taxonomy Reveals Hidden Diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and Unexpected Relationships with a Song Divergent Relative

Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premating barriers and have been used extensively to reveal hidden taxonomic diversity in morphologically similar species. The Palaearctic Cicadetta montana species complex is an excellent example where distinct song patterns have disclosed multiple recently described species. Indeed, two taxa turned out to be especially diverse in that they form a “complex within the complex”: the Cicadetta cerdaniensis song group (four species studied previously) and Cicadetta brevipennis (examined in details here). Based on acoustic, morphological, molecular, ecological and spatial data sampled throughout their broad European distribution, we find that Cicadetta brevipennis s. l. comprises five lineages. The most distinct lineage is identified as Cicadetta petryi Schumacher, 1924, which we re-assign to the species level. Cicadetta brevipennis litoralis Puissant & Hertach ssp. n. and Cicadetta brevipennis hippolaidica Hertach ssp. n. are new to science. The latter hybridizes with Cicadetta brevipennis brevipennis Fieber, 1876 at a zone inferred from intermediate song patterns. The fifth lineage requires additional investigation. The C. cerdaniensis and the C. brevipennis song groups exhibit characteristic, clearly distinct basic song patterns that act as reproductive barriers. However, they remain completely intermixed in the Bayesian and maximum likelihood COI and COII mitochondrial DNA phylogenies. The closest relative of each of the four cerdaniensis group species is a brevipennis group taxon. In our favoured scenario the phylogenetic pairs originated in common Pleistocene glacial refuges where the taxa speciated and experienced sporadic inter-group hybridization leading to extensive introgression and mitochondrial capture.

Three in One--Multiple Faunal Elements within an Endangered European Butterfly Species

Ice ages within Europe forced many species to retreat to refugia, of which three major biogeographic basic types can be distinguished: "Mediterranean", "Continental" and "Alpine / Arctic" species. However, this classification often fails to explain the complex phylogeography of European species with a wide range of latitudinal and altitudinal distribution. Hence, we tested for the possibility that all three mentioned faunal elements are represented within one species. Our data was obtained by scoring 1,307 Euphydryas aurinia individuals (46 European locations) for 17 allozyme loci, and sequencing a subset of 492 individuals (21 sites) for a 626 base pairs COI fragment. Genetic diversity indices, F statistics, hierarchical analyses of molecular variance, individual-based clustering, and networks were used to explore the phylogeographic patterns. The COI fragment represented 18 haplotypes showing a strong geographic structure. All but one allozyme loci analysed were polymorphic with a mean F_ST of 0.20, supporting a pronounced among population structure. Interpretation of both genetic marker systems, using several analytical tools, calls for the recognition of twelve genetic groups. These analyses consistently distinguished different groups in Iberia (2), Italy, Provence, Alps (3), Slovenia, Carpathian Basin, the lowlands of West and Central Europe as well as Estonia, often with considerable additional substructures. The genetic data strongly support the hypothesis that E. aurinia survived the last glaciation in Mediterranean, extra-Mediterranean and perialpine refugia. It is thus a rare example of a model organism that combines attributes of faunal elements from all three of these sources. The observed differences between allozymes and mtDNA most likely result from recent introgression of mtDNA into nuclear allozyme groups. Our results indicate discrepancies with the morphologically-based subspecies models, underlining the need to revise the current taxonomy.

Persistence and dispersal in a Southern Hemisphere glaciated landscape: the phylogeography of the spotted snow skink (Niveoscincus ocellatus) in Tasmania

Background

The aim of this research was to identify the effects of Pleistocene climate change on the distribution of fauna in Tasmania, and contrast this with biotic responses in other temperate regions in the Northern and Southern Hemisphere that experienced glacial activity during this epoch. This was achieved by examining the phylogeographic patterns in a widely distributed Tasmanian endemic reptile, Niveoscincus ocellatus. 204 individuals from 29 populations across the distributional range of N. ocellatus were surveyed for variation at two mitochondrial genes (ND2, ND4), and two nuclear genes (β-globin, RPS8). Phylogenetic relationships were reconstructed using a range of methods (maximum parsimony, Bayesian inference and haplotype networks), and the demographic histories of populations were assessed (AMOVA, Tajima’s D, Fu’s Fs, mismatch distributions, extended Bayesian skyline plots, and relaxed random walk analyses).

Results

There was a high degree of mitochondrial haplotype diversity (96 unique haplotypes) and phylogeographic structure, where spatially distinct groups were associated with Tasmania’s Northeast and a large area covering Southeast and Central Tasmania. Phylogeographic structure was also present within each major group, but the degree varied regionally, being highest in the Northeast. Only the Southeastern group had a signature of demographic expansion, occurring during the Pleistocene but post-dating the Last Glacial Maximum. In contrast, nuclear DNA had low levels of variation and a lack of phylogeographic structure, and further loci should be surveyed to corroborate the mitochondrial inferences.

Conclusions

The phylogeographic patterns of N. ocellatus indicate Pleistocene range and demographic expansion in N. ocellatus, particularly in the Southeast and Central areas of Tasmania. Expansion in Central and Southeastern areas appears to have been more recent in both demographic and spatial contexts, than in Northeast Tasmania, which is consistent with inferences for other taxa of greater stability and persistence in Northeast Tasmania during the Last Glacial Maximum. These phylogeographic patterns indicate contrasting demographic histories of populations in close proximity to areas directly affected by glaciers in the Southern Hemisphere during the LGM.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0397-y) contains supplementary material, which is available to authorized users.

Widespread primary, but geographically restricted secondary, human introductions of wall lizards, Podarcis muralis

Establishing the introduction pathways of alien species is a fundamental task in invasion biology. The common wall lizard, Podarcis muralis, has been widely introduced outside of its native range in both Europe and North America, primarily through escaped pets or deliberate release of animals from captive or wild populations. Here, we use Bayesian clustering, approximate Bayesian computation (ABC) methods and network analyses to reconstruct the origin and colonization history of 23 non-native populations of wall lizards in England. Our analyses show that established populations in southern England originate from at least nine separate sources of animals from native populations in France and Italy. Secondary introductions from previously established non-native populations were supported for eleven (47%) populations. In contrast to the primary introductions, secondary introductions were highly restricted geographically and appear to have occurred within a limited time frame rather than being increasingly common. Together, these data suggest that extant wall lizard populations in England are the result of isolated accidental and deliberate releases of imported animals since the 1970s, with only local translocation of animals from established non-native populations. Given that populations introduced as recently as 25 years ago show evidence of having adapted to cool climate, discouraging further translocations may be important to prevent more extensive establishment on the south coast of England.

What triggers the rising of an intraspecific biodiversity hotspot? Hints from the agile frog

Hotspots of genetic diversity are regions of utmost importance for species survival and conservation, and their intimate link with the geographic location of glacial refugia has been well established. Nonetheless, the microevolutionary processes underlying the generation of hotspots in such regions have only recently become a fervent field of research. We investigated the phylogeographic and population genetic structure of the agile frog, Rana dalmatina, within its putative refugium in peninsular Italy. We found this region to harbour far more diversity, phylogeographic structure, and lineages of ancient origin than that by the rest of the species' range in Europe. This pattern appeared to be well explained by climate-driven microevolutionary processes that occurred during both glacial and interglacial epochs. Therefore, the inferred evolutionary history of R. dalmatina in Italy supports a view of glacial refugia as 'factories' rather than as repositories of genetic diversity, with significant implications for conservation strategies for hotspots.

Assessing the Spatial Scale Effect of Anthropogenic Factors on Species Distribution

Patch context is a way to describe the effect that the surroundings exert on a landscape patch. Despite anthropogenic context alteration may affect species distributions by reducing the accessibility to suitable patches, species distribution modelling have rarely accounted for its effects explicitly. We propose a general framework to statistically detect the occurrence and the extent of such a factor, by combining presence-only data, spatial distribution models and information-theoretic model selection procedures. After having established the spatial resolution of the analysis on the basis of the species characteristics, a measure of anthropogenic alteration that can be quantified at increasing distance from each patch has to be defined. Then the distribution of the species is modelled under competing hypotheses: H0, assumes that the distribution is uninfluenced by the anthropogenic variables; H1, assumes the effect of alteration at the species scale (resolution); and H2, H3 … Hn add the effect of context alteration at increasing radii. Models are compared using the Akaike Information Criterion to establish the best hypothesis, and consequently the occurrence (if any) and the spatial scale of the anthropogenic effect. As a study case we analysed the distribution data of two insular lizards (one endemic and one naturalised) using four alternative hypotheses: no alteration (H0), alteration at the species scale (H1), alteration at two context scales (H2 and H3). H2 and H3 performed better than H0 and H1, highlighting the importance of context alteration. H2 performed better than H3, setting the spatial scale of the context at 1 km. The two species respond differently to context alteration, the introduced lizard being more tolerant than the endemic one. The proposed approach supplies reliably and interpretable results, uses easily available data on species distribution, and allows the assessing of the spatial scale at which human disturbance produces the heaviest effects.

Patterns of cranial ontogeny in lacertid lizards: morphological and allometric disparity

We explored the ontogenetic dynamics of the morphological and allometric disparity in the cranium shapes of twelve lacertid lizard species. The analysed species (Darevskia praticola, Dinarolacerta mosorensis, Iberolacerta horvathi, Lacerta agilis, L. trilineata, L. viridis, Podarcis erhardii, P. melisellensis, P. muralis, P. sicula, P. taurica and Zootoca vivipara) can be classified into different ecomorphs: terrestrial lizards that inhabit vegetated habitats (habitats with lush or sparse vegetation), saxicolous and shrub-climbing lizards. We observed that there was an overall increase in the morphological disparity (MD) during the ontogeny of the lacertid lizards. The ventral cranium, which is involved in the mechanics of jaw movement and feeding, showed higher levels of MD, an ontogenetic shift in the morphospace planes and more variable allometric patterns than more conserved dorsal crania. With respect to ecology, the allometric trajectories of the shrub-climbing species tended to cluster together, whereas the allometric trajectories of the saxicolous species were highly dispersed. Our results indicate that the ontogenetic patterns of morphological and allometric disparity in the lacertid lizards are modified by ecology and functional constraints and that the identical mechanisms that lead to intraspecific morphological variation also produce morphological divergence at higher taxonomic levels.

One species, three Pleistocene evolutionary histories: phylogeography of the Italian crested newt, Triturus carnifex

Phylogeographic patterns of temperate species from the Mediterranean peninsulas have been investigated intensively. Nevertheless, as more phylogeographies become available, either unique patterns or new lines of concordance continue to emerge, providing new insights on the evolution of regional biotas. Here, we investigated the phylogeography and evolutionary history of the Italian crested newt, Triturus carnifex, through phylogenetic, molecular dating and population structure analyses of two mitochondrial gene fragments (ND2 and ND4; overall 1273 bp). We found three main mtDNA lineages having parapatric distribution and estimated divergence times between Late Pliocene and Early Pleistocene. One lineage (S) was widespread south of the northern Apennine chain and was further geographically structured into five sublineages, likely of Middle Pleistocene origin. The second lineage (C) was widespread throughout the Padano-Venetian plain and did not show a clear phylogeographic structure. The third lineage (N) was observed in only two populations located on western Croatia/Slovenia. Results of analysis of molecular variance suggested that partitioning populations according to the geographic distribution of these lineages and sublineages explains 76% of the observed genetic variation. The phylogeographic structure observed within T. carnifex and divergence time estimates among its lineages, suggest that responses to Pleistocene environmental changes in this single species have been as diverse as those found previously among several codistributed temperate species combined. Consistent with the landscape heterogeneity, physiographic features, and palaeogeographical evolution of its distribution range, these responses encompass multiple refugia along the Apennine chain, lowland refugia in large peri-coastal plains, and a 'cryptic' northern refugium.

Vicariance divergence and gene flow among islet populations of an endemic lizard

Allopatry and allopatric speciation can arise through two different mechanisms: vicariance or colonization through dispersal. Distinguishing between these different allopatric mechanisms is difficult and one of the major challenges in biogeographical research. Here, we address whether allopatric isolation in an endemic island lizard is the result of vicariance or dispersal. We estimated the amount and direction of gene flow during the divergence of isolated islet populations and subspecies of the endemic Skyros wall lizard Podarcis gaigeae, a phenotypically variable species that inhabits a major island and small islets in the Greek archipelago. We applied isolation-with-migration models to estimate population divergence times, population sizes and gene flow between islet-mainland population pairs. Divergence times were significantly correlated with independently estimated geological divergence times. This correlation strongly supports a vicariance scenario where islet populations have sequentially become isolated from the major island. We did not find evidence for significant gene flow within P. g. gaigeae. However, gene-flow estimates from the islet to the mainland populations were positively affected by islet area and negatively by distance between the islet and mainland. We also found evidence for gene flow from one subspecies (P. g. weigandi) into another (P. g. gaigeae), but not in the other direction. Ongoing gene flow between the subspecies suggests that even in this geographically allopatric scenario with the sea posing a strong barrier to dispersal, divergence with some gene flow is still feasible.

Multiple lines of evidence for demographic and range expansion of a temperate species (Hyla sarda) during the last glaciation

Many temperate species experienced demographic and range contractions in response to climatic changes during Pleistocene glaciations. In this study, we investigate the evolutionary history of the Tyrrhenian tree frog Hyla sarda, a species inhabiting the Corsica-Sardinia island system (Western Mediterranean basin). We used sequence analysis of two mitochondrial (overall 1229 bp) and three nuclear (overall 1692 bp) gene fragments to assess the phylogeography and demographic history of this species, and species distribution modelling (SDM) to predict its range variation over time. Phylogeographic, historical demographic and SDM analyses consistently indicate that H. sarda does not conform to the scenario generally expected for temperate species but rather underwent demographic and range expansion mostly during the last glacial phase. Palaeogeographic data and SDM analyses suggest that such expansion was driven by the glaciation-induced increase in lowland areas during marine regression. This unusual scenario suggests that at least some temperate species may not have suffered the adverse effects of glacial climate on their population size and range extent, owing to the mitigating effects of other glaciations-induced palaeoenvironmental changes. We discuss previous clues for the occurrence of such a scenario in other species and some possible challenges with its identification. Early phylogeographic literature suggested that responses to the Pleistocene glacial-interglacial cycles were expected to vary among species and regions. Our results point out that such variation may have been greater than previously thought.