Phylogeographic patterns of genetic diversity in the common spadefoot toad, Pelobates fuscus (Anura: Pelobatidae), reveals evolutionary history, postglacial range expansion and secondary contact

The conservation paradox of an introduced population of a threatened species: spadefoot toads in the coastal dunes of the Netherlands

Species that are threatened in their native range may actually prosper as introduced populations. To investigate how such introduced populations were established involves determining from where within the natural range the founder individuals originated. This can be accomplished through mtDNA barcoding. The common spadefoot toad (Pelobates fuscus) naturally occurs in the south and east of the Netherlands and has shown a rapid decline. Yet, a flourishing introduced population was recently discovered in the coastal dunes in the west of the country. We use mtDNA barcoding to determine the provenance of the introduced population. We sampled both native and introduced populations from the Netherlands and compared our sequences to haplotypes from across the entire distribution range. The mtDNA haplotypes found in the introduced population are distinct from those naturally occurring in the Netherlands and point towards an origin in the Pannonian Basin, on the boundary between Central and Southeastern Europe. Paradoxically, the thriving P. fuscus population in the Dutch coastal dunes should be considered a conservation risk to local biodiversity, even though within the native range in the Netherlands the species is severely threatened. Our study illustrates the complicated conservation questions associated with species that are both native and invasive.

Long-term monitoring of common spadefoot toad activity in a European steppe using barn owl pellets

Background

One third of the worldwide amphibian species are threatened, therefore, efficient monitoring efforts are needed. Amphibians which adopt a hidden lifestyle, such as the common spadefoot toad, are often missed with standard surveying efforts. Spadefoot toads can be identified in regurgitated pellets of the barn owl, which provides an effective way to estimate toad activity. In our study we analyzed frequency of spadefoot toad remains from 2004 to 2016 in a steppe landscape in eastern Austria.

Methods

We used an automated model selection procedure together with a GLM analysis using a zero inflated error Poisson distribution, to analyze the presence of Pelobates fuscus in barn owl pellets. All analyses were done in the statistical software R, and the scripts to reproduce our results are available within this publication. Our approach may provide a template for other researchers to use for their own pellet data.

Conclusions

Our analysis suggested that activity of the common spadefoot toad is mainly influenced by rainfalls, while time of the year and temperature had small but significant effects. Interestingly, our data confirmed the possibility of a second breeding period in summer, triggered by heavy rainfalls. There were no indications for a population decrease in the observed years and locations. Our study shows that barn owl pellets can be used effectivley to assess pelobatid activity in an area. This might constitute a useful monitoring tool for conservation management for amphibians.

The eastern boundary of the geographic range of the Pallas’ spadefoot Pelobates vespertinus (Anura, Amphibia) is limited by overwintering temperatures

We studied the relationship between the geographic distribution of the Pallas’ spadefoot (Pelobates vespertinus) and the soil temperature regime at the eastern boundary of this species’ range (south-western West Siberia and northwest Kazakhstan). This species overwinters underground, burrowing down to 1.5 m or deeper and has poor frost tolerance – it is unable to withstand temperatures below 0 °C, therefore, the temperature at its overwintering depth has to be above zero. A cartographic approach to identifying the distribution of zero isotherms was used. Winter soil temperatures at depths of 80 cm, 120 cm, 160 cm and 240 cm were plotted, based on deep soil thermometer data and the outline of the spadefoot’s range was compared with close-to-zero isotherms in deep soil. Within the range of this species, the depth of the position of zero isotherms increases eastwards: from 80 cm in European Russia, to more than 160 cm in the south-west of Western Siberia. The eastern boundary of the species’ range lies in the forest-steppe, steppe and semi-desert zones in the Tobol-Ishim interfluve and further south, on the left bank area of the Turgai River. This boundary clearly coincides with the zero isotherm, which lies here at a depth of 160 cm, forming an impermeable barrier to the spadefoot’s distribution.

Call a spade a spade: taxonomy and distribution of Pelobates, with description of a new Balkan endemic

The genomic era contributes to update the taxonomy of many debated terrestrial vertebrates. In an accompanying work, we provided a comprehensive molecular assessment of spadefoot toads (Pelobates) using genomic data. Our results call for taxonomic updates in this group. First, nuclear phylogenomics confirmed the species-level divergence between the Iberian P.cultripes and its Moroccan relative P.varaldii. Second, we inferred that P.fuscus and P.vespertinus, considered subspecies until recently, feature partial reproductive isolation and thus deserve a specific level. Third, we evidenced cryptic speciation and diversification among deeply diverged lineages collectively known as Pelobatessyriacus. Populations from the Near East correspond to the Eastern spadefoot toad P.syriacus sensu stricto, which is represented by two subspecies, one in the Levant (P.s.syriacus) and the other in the rest of the range (P.s.boettgeri). Populations from southeastern Europe correspond to the Balkan spadefoot toad, P.balcanicus. Based on genetic evidence, this species is also polytypic: the nominal P.b.balcanicus inhabits the Balkan Peninsula; a new subspecies P.b.chloeaessp. nov. appears endemic to the Peloponnese. In this paper, we provide an updated overview of the taxonomy and distribution of all extant Pelobates taxa and describe P.b.chloeaessp. nov.

Phylogeography of a cryptic speciation continuum in Eurasian spadefoot toads (Pelobates)

Cryptic phylogeographic diversifications provide unique models to examine the role of phylogenetic divergence on the evolution of reproductive isolation, without extrinsic factors such as ecological and behavioural differentiation. Yet, to date very few comparative studies have been attempted within such radiations. Here, we characterize a new speciation continuum in a group of widespread Eurasian amphibians, the Pelobates spadefoot toads, by conducting multilocus (restriction site associated DNA sequencing and mitochondrial DNA) phylogenetic, phylogeographic and hybrid zone analyses. Within the P. syriacus complex, we discovered species-level cryptic divergences (>5 million years ago [My]) between populations distributed in the Near-East (hereafter P. syriacus sensu stricto [s.s.]) and southeastern Europe (hereafter P. balcanicus), each featuring deep intraspecific lineages. Altogether, we could scale hybridizability to divergence time along six different stages, spanning from sympatry without gene flow (P. fuscus and P. balcanicus, >10 My), parapatry with highly restricted hybridization (P. balcanicus and P. syriacus s.s., >5 My), narrow hybrid zones (~15 km) consistent with partial reproductive isolation (P. fuscus and P. vespertinus, ~3 My), to extensive admixture between Pleistocene and refugial lineages (≤2 My). This full spectrum empirically supports a gradual build up of reproductive barriers through time, reversible up until a threshold that we estimate at ~3 My. Hence, cryptic phylogeographic lineages may fade away or become reproductively isolated species simply depending on the time they persist in allopatry, and without definite ecomorphological divergence.

Evolutionary melting pots: a biodiversity hotspot shaped by ring diversifications around the Black Sea in the Eastern tree frog (Hyla orientalis)

Hotspots of intraspecific genetic diversity, which are of primary importance for the conservation of species, have been associated with glacial refugia, that is areas where species survived the Quaternary climatic oscillations. However, the proximate mechanisms generating these hotspots remain an open issue. Hotspots may reflect the long-term persistence of large refugial populations; alternatively, they may result from allopatric differentiation between small and isolated populations, that later admixed. Here, we test these two scenarios in a widely distributed species of tree frog, Hyla orientalis, which inhabits Asia Minor and southeastern Europe. We apply a fine-scale phylogeographic survey, combining fast-evolving mitochondrial and nuclear markers, with a dense sampling throughout the range, as well as ecological niche modelling, to understand what shaped the genetic variation of this species. We documented an important diversity centre around the Black Sea, composed of multiple allopatric and/or parapatric diversifications, likely driven by a combination of Pleistocene climatic fluctuations and complex regional topography. Remarkably, this diversification forms a ring around the Black Sea, from the Caucasus through Anatolia and eastern Europe, with terminal forms coming into contact and partially admixing in Crimea. Our results support the view that glacial refugia generate rather than host genetic diversity and can also function as evolutionary melting pots of biodiversity. Moreover, we report a new case of ring diversification, triggered by a large, yet cohesive dispersal barrier, a very rare situation in nature. Finally, we emphasize the Black Sea region as an important centre of intraspecific diversity in the Palearctic with implications for conservation.

Comparative Analysis of Karyotypes of Two Cryptic Species of Pelobatid Frogs (Amphibia, Anura) of Ukraine

The paper first describes in detail the karyotype of Pelobates vespertinus (Pallas, 1771) in comparison with the karyotype of Pelobates fuscus (Laurenti, 1768). Comparative morphological analysis of chromosomes has shown that these two cryptic species have a symmetrical karyotype consisting of two-armed chromosomes. It has been established that their chromosome sets consist of 7 pairs of large chromosomes and 6 pairs of small ones. The species diff er by the position of the centromere in the chromosomes of the 10th and 11th pairs. The 10th pair of P. fuscus is metacentrics, the 11th pair is submetacentric; the 10th pair of P. vespertinus is submetacentric, and the 11th one is metacentrics. Secondary constrictions are on the short arms of the 7th chromosome pair. The chromosomal formula for both species is 4 meta-(m) + 7 submeta-(sm) + 2 subtelocentrics (st), 2n = 26, N.F. = 52. Absolute length of all the chromosomes in the karyotype of P. fuscus is somewhat larger than that one in the karyotype of P. vespertinus. The parameters of relative length are equivalent on average, but they diff er in individual chromosomes. On the background of established chromosomal differences between the cryptic species, reliable diagnostic features have not been identified.

Persistence across Pleistocene ice ages in Mediterranean and extra-Mediterranean refugia: phylogeographic insights from the common wall lizard

BACKGROUND

Pleistocene climatic oscillations have played a major role in structuring present-day biodiversity. The southern Mediterranean peninsulas have long been recognized as major glacial refugia, from where Northern Europe was post-glacially colonized. However, recent studies have unravelled numerous additional refugia also in northern regions. We investigated the phylogeographic pattern of the widespread Western Palaearctic lizard Podarcis muralis, using a range-wide multilocus approach, to evaluate whether it is concordant with a recent expansion from southern glacial refugia or alternatively from a combination of Mediterranean and northern refugia.

RESULTS

We analyzed DNA sequences of two mitochondrial (cytb and nd4) and three nuclear (acm4, mc1r, and pdc) gene fragments in individuals from 52 localities across the species range, using phylogenetic and phylogeographic methods. The complex phylogeographic pattern observed, with 23 reciprocally monophyletic allo- parapatric lineages having a Pleistocene divergence, suggests a scenario of long-term isolation in multiple ice-age refugia across the species distribution range. Multiple lineages were identified within the three Mediterranean peninsulas - Iberia, Italy and the Balkans - where the highest genetic diversity was observed. Such an unprecedented phylogeographic pattern - here called "refugia within all refugia" - compasses the classical scenario of multiple southern refugia. However, unlike the southern refugia model, various distinct lineages were also found in northern regions, suggesting that additional refugia in France, Northern Italy, Eastern Alps and Central Balkans allowed the long-term persistence of this species throughout Pleistocene glaciations.

CONCLUSIONS

The phylogeography of Podarcis muralis provides a paradigm of temperate species survival in Mediterranean and extra-Mediterranean glacial refugia. Such refugia acted as independent biogeographic compartments for the long-term persistence of this species, for the differentiation of its genetic lineages, and for the short-distance post-glacial re-colonization of neighbouring areas. This finding echoes previous findings from recent phylogeographic studies on species from temperate ecoregions, thus suggesting the need for a reappraisal of the role of northern refugia for glacial persistence and post-glacial assembly of Holarctic biota.