Postglacial species displacement in Triturus newts deduced from asymmetrically introgressed mitochondrial DNA and ecological niche models

Higher temperature induces oxidative stress in hybrids but not in parental species: A case study of crested newts

Ectotherms are particularly sensitive to global warming due to their limited capacity to thermoregulate, which can impact their performance and fitness. From a physiological standpoint, higher temperatures often enhance biological processes that can induce the production of reactive oxygen species and result in a state of cellular oxidative stress. Temperature alters interspecific interactions, including species hybridization. Hybridization under different thermal conditions could amplify parental (genetic) incompatibilities, thus affecting a hybrid's development and distribution. Understanding the impact of global warming on the physiology of hybrids and particularly their oxidative status could help in predicting future scenarios in ecosystems and in hybrids. In the present study, we investigated the effect of water temperature on the development, growth and oxidative stress of two crested newt species and their reciprocal hybrids. Larvae of Triturus macedonicus and T. ivanbureschi, and their T. macedonicus-mothered and T. ivanbureschi-mothered hybrids were exposed for 30 days to temperatures of 19°C and 24°C. Under the higher temperature, the hybrids experienced increases in both growth and developmental rates, while parental species exhibited accelerated growth (T. macedonicus) or development (T. ivanbureschi). Warm conditions also had different effects on the oxidative status of hybrid and parental species. Parental species had enhanced antioxidant responses (catalase, glutathione peroxidase, glutathione S-transferase and SH groups), which allowed them to alleviate temperature-induced stress (revealed by the absence of oxidative damage). However, warming induced an antioxidant response in the hybrids, including oxidative damage in the form of lipid peroxidation. These findings point to a greater disruption of redox regulation and metabolic machinery in hybrid newts, which can be interpreted as the cost of hybridization that is likely linked to parental incompatibilities expressed under a higher temperature. Our study aims to improve mechanistic understanding of the resilience and distribution of hybrid species that cope with climate-driven changes.

The Bank Vole (Clethrionomys glareolus) as a Model System for Adaptive Phylogeography in the European Theater

The legacy of climatic changes during the Pleistocene glaciations allows inferences to be made about the patterns and processes associated with range expansion/colonization, including evolutionary adaptation. With the increasing availability of population genomic data, we have the opportunity to examine these questions in detail and in a variety of non-traditional model species. As an exemplar, here we review more than two decades of work by our group and others that illustrate the potential of a single “non-model model” mammal species - the bank vole (Clethrionomys glareolus), which is particularly well suited to illustrate the complexities that may be associated with range expansion and the power of genomics (and other datasets) to uncover them. We first summarize early phylogeographic work using mitochondrial DNA and then describe new phylogeographic insights gained from population genomic analysis of genome-wide SNP data to highlight the bank vole as one of the most compelling examples of a forest mammal, that survived in cryptic extra-Mediterranean (“northern”) glacial refugia in Europe, and as one of the species in which substantial replacement and mixing of lineages originating from different refugia occurred during end-glacial colonization. Our studies of bank vole hemoglobin structure and function, as well as our recent ecological niche modeling study examining differences among bank vole lineages, led us to develop the idea of “adaptive phylogeography.” This is what we call the study of the role of adaptive differences among populations in shaping phylogeographic patterns. Adaptive phylogeography provides a link between past population history and adaptation that can ultimately help predict the potential of future species responses to climate change. Because the bank vole is part of a community of organisms whose range has repeatedly contracted and then expanded in the past, what we learn from the bank vole will be useful for our understanding of a broad range of species.

The Reproductive Success of Triturus ivanbureschi × T. macedonicus F1 Hybrid Females (Amphibia: Salamandridae)

Simple Summary

Two moderately related large-bodied newt species endemic to the Balkan Peninsula, the Balkan crested newt (Triturus ivanbureschi) and the Macedonian crested newt (T. macedonicus), coexist and hybridize in central Serbia. Many generations of mutual hybrid crossings and backcrossings with parental species shaped the genetic composition of hybrid populations. Natural populations have admixed nuclear DNA (nuDNA) of parental species and T. ivanbureschi mitochondrial DNA (mtDNA), which is usually maternally inherited. The mechanisms that direct gene flow and shape the first generations of hybrids could explain the formation of hybrid zones and their maintenance in nature. We followed and compared life history traits related to reproduction of the first generation of reciprocal hybrids obtained by experimental crossing. Our results suggested that possible incompatibilities between mitochondrial and nuclear genomes, which could lead to the exclusion of T. macedonicus mtDNA in natural populations, most likely act at later stages of development or subsequent hybrid generations. Results from this study add to the growing knowledge of Triturus hybrid biology and ecology, which is the baseline for conservation programs necessary to protect these highly endangered amphibians.

Abstract

Two large-bodied newt species, Triturus ivanbureschi and T. macedonicus, hybridize in nature across the Balkan Peninsula. Consequences of hybridization upon secondary contact of two species include species displacement and asymmetrical introgression of T. ivanbureschi mtDNA. We set an experimental reciprocal cross of parental species and obtained two genotypes of F₁ hybrids (with T. ivanbureschi or T. macedonicus mtDNA). When hybrids attained sexual maturity, they were engaged in mutual crossings and backcrossing with parental species. We followed reproductive traits over two successive years. Our main aim was to explore the reproductive success of F₁ females carrying different parental mtDNA. Additionally, we tested for differences in reproductive success within female genotypes depending on the crossing with various male genotypes (hybrids or parental species). Both female genotypes had similar oviposition periods, number of laid eggs and hatched larvae but different body and egg sizes. Overall reproductive success (percentage of egg-laying females and viability of embryos) was similar for both genotypes. The type of crossing led to some differences in reproductive success within female genotypes. The obtained results suggest that processes that led to exclusion of T. macedonicus mtDNA in natural populations may be related to the survival at postembryonic stages of F₂ generation or reproductive barriers that emerged in subsequent hybrid generations.

The Origin of Isolated Populations of the Mountain Weevil, Liparus glabrirostris-The Flagship Species for Riparian Habitats

Liparus glabrirostris is one of the largest European weevils, and it has been recently proposed as the flagship species for threatened riparian habitats in the mountains. For effective conservation of its populations (and associated habitats), it is crucial to understand its history, contemporary distribution, genetic diversity and predict changes in the range, including its highly isolated populations on the Baltic coast. Here, we examined numerous populations of L. glabrirostris across almost the entire species range using phylogeography and species niche modeling (SNM) approaches. Analyses of mtDNA and nucDNA markers revealed the existence of 2 major mitochondrial lineages generally separated between 1) the Alpine region and 2) the Bohemian Massif, the Carpathians, and the Baltic coast areas. Genetic diversity in nuclear genes was more complicated with no clear division between populations. The origin of Baltic populations was derived from the Carpathians, but there were probably multiple expansion events to the north. SNM suggested the existence of glacial refugia for L. glabrirostris, mainly in the Alps and the Southern Carpathians. Current predictions of species range were found to be generally congruent with zoogeographic data; however, the Baltic coast was not really supported as a suitable area for L. glabrirostris. An important prediction of future distribution (2050-2070 CE) suggests a shrinkage of the L. glabrirostris range and extinction of some of its populations (particularly those isolated on lower altitudes). Based on the aforementioned data, proposals for the protection of this species are proposed, including the designation of several evolutionary units of conservation importance.

The effect of short-term fasting on the oxidative status of larvae of crested newt species and their hybrids

In nature, animals often face periods without food caused by seasonal fluctuations and/or prey scarcity. An organism's physiological response to imposed energetic limitations is followed by changes in mitochondrial functioning (adjustment of energy metabolism) and a reduction of non-essential processes. However, this energy-saving strategy can have its costs. In this study, we examined oxidative stress as one of the possible physiological costs of short-term, two-week-long food deprivation on developing amphibian larvae of the crested newts Triturus macedonicus and Triturus ivanbureschi and their hybrids. We investigated whether this exogenous factor additionally affected the oxidative status (fitness-related trait) of hybrid individuals. The fasting treatment led to lower growth and a lower body mass and body condition index of individuals. The results revealed that the antioxidant system (AOS) of food-deprived larvae could not cope in a proper manner with reactive oxygen species production under limited energy availability, leading to higher lipid oxidative damage. The lowest AOS response was observed for H₂O₂ scavenging parameters (catalase, glutathione peroxidase, and total glutathione), which together with the elevated activity of superoxide dismutase suggested increased H₂O₂ concentrations. Comparison between parental species and their hybrids showed that hybrid individuals suffered greater oxidative damage (as demonstrated by higher concentrations of lipid peroxides), indicating that they were more susceptible to fasting-induced oxidative stress. Overall, this study illustrates that: (i) an oxidative event is one of the costs amphibian larvae face during short-term periods of fasting, (ii) hybrids are less capable of dealing with this stressful condition, which can lower their chances of survival in a changing environment.

The Effect of Shelter on Oxidative Stress and Aggressive Behavior in Crested Newt Larvae (Triturus spp.)

Shelters are important for animal survival. Provision of adequate hiding places allow animals to express their natural sheltering behavior and it can have different positive effects on cortisol levels, physiological processes and mental performance. Although the absence of a refuge activates some stress response, its effect on oxidative stress has not been adequately examined. This study investigated whether the presence/absence of a shelter modifies the oxidative status (the antioxidant system and oxidative damage) and aggressive behavior of crested newt larvae (Triturus macedonicus and its hybrid with T. ivanbureschi). Our results show that individuals reared with shelters had lower values of the tested antioxidant parameters (catalase, glutathione peroxidase, glutathione S-transferase and glutathione), indicating a lower production of reactive species than individuals reared without shelter. The same pattern was observed in both T. macedonicus and its hybrid. Contrary to the activation of some physiological pathways, shelter availability did not significantly affect the rate of intraspecific aggressive behavior. The physiological benefits of shelter use can be manifested as a lower requirement for investment in the energy necessary for the maintenance of the upregulated antioxidant defenses, activation of repair systems and synthesis of endogenous antioxidants. This study highlights the importance of shelter provision, which may be valuable in habitat restoration and animal conservation studies.

Discordant patterns of introgression across a narrow hybrid zone between two cryptic lineages of an Iberian endemic newt

The study of natural hybrid zones can illuminate aspects of lineage divergence and speciation in morphologically cryptic taxa. We studied a hybrid zone between two highly divergent but morphologically similar lineages (south-western and south-eastern) of the Iberian endemic Bosca's newt (Lissotriton boscai) in SW Iberia with a multilocus dataset (microsatellites, nuclear and mitochondrial genes). STRUCTURE and NEWHYBRIDS analyses retrieved few admixed individuals, which classified as backcrosses involving parental individuals of the south-western lineage. Our results show asymmetric introgression of mtDNA beyond the contact from this lineage into the south-eastern lineage. Analysis of nongeographic introgression patterns revealed asymmetries in the direction of introgression, but except for mtDNA, we did not find evidence for nonconcordant introgression patterns across nuclear loci. Analysis of a 150-km transect across the hybrid zone showed broadly coincident cline widths (ca. 3.2-27.9 km), and concordant cline centres across all markers, except for mtDNA that is displaced ca. 60 km northward. Results from ecological niche modelling show that the hybrid zone is in a climatically homogenous area with suitable habitat for the species, suggesting that contact between the two lineages is unlikely to occur further south as their distributions are currently separated by an extensive area of unfavourable habitat. Taken together, our findings suggest the genetic structure of this hybrid zone results from the interplay of historical (biogeographic) and population-level processes. The narrowness and coincidence of genetic clines can be explained by weak selection against hybrids and reflect a degree of reproductive isolation that is consistent with cryptic speciation.

Testing the evolutionary constraints of metamorphosis: The ontogeny of head shape in Triturus newts

In vertebrates with complex, biphasic, life cycles, larvae have a distinct morphology and ecological preferences compared to metamorphosed juveniles and adults. In amphibians, abrupt and rapid metamorphic changes transform aquatic larvae to terrestrial juveniles. The main aim of this study is to test whether, relative to larval stages, metamorphosis (1) resets the pattern of variation between ontogenetic stages and species, (2) constrains intraspecific morphological variability, and (3) similar to the "hour-glass" model reduces morphological disparity. We explore postembryonic ontogenetic trajectories of head shape (from hatching to completed metamorphosis) of two well-defined, morphologically distinct Triturus newts species and their F1 hybrids. Variation in head shape is quantified and compared on two levels: dynamic (across ontogenetic stages) and static (at a particular stage). Our results show that the ontogenetic trajectories diverge early during development and continue to diverge throughout larval stages and metamorphosis. The high within-group variance and the largest disparity level (between-group variance) characterize the metamorphosed stage. Hence, our results indicate that metamorphosis does not canalize head shape variation generated during larval development and that metamorphosed phenotype is not more constrained relative to larval ones. Therefore, metamorphosis cannot be regarded as a developmental constraint, at least not for salamander head shape.

Genomic and mitochondrial evidence of ancient isolations and extreme introgression in the four-lined snake

Comparing mitochondrial and genomic phylogenies is an essential tool for investigating speciation processes, because each genome carries different inheritance properties and evolutionary characteristics. Furthermore, mitonuclear discordance may arise from ecological adaptation, historic isolation, population size changes, and sex-biased dispersal. Closely related taxa are expected to experience gene flow; however, this may not be true for insular populations or populations isolated in refugia. The four-lined snake Elaphe quatuorlineata has a fragmented distribution, separating populations of the Italian and Balkan Peninsulas, whereas several insular Aegean populations of significantly smaller body size (Cyclades island group and Skyros Island, Greece) are currently considered distinct subspecies. We constructed the species-tree phylogeny of this species utilizing genome-wide single nucleotide polymorphisms and a gene-tree based on complete cytochrome b sequences, aiming to detect convergence and discrepancies between biparentally and maternally inherited genomes. Population structuring, phylogenetic patterns and migration events among geographically defined lineages supported our hypothesis of isolation in multiple sub-refugia. Where biogeographical barriers did not restrict subsequent dispersal, extensive genetic exchange occurred between mainland Balkan populations. This process has led to the mitochondrial sweep of an ancestral mitolineage that survived only in peripheral (East Greece) and insular populations (North Cyclades and Skyros). The Central Cyclades represent an ancient lineage for both molecular markers that emerged almost 3.3 Mya. Considering their distinct morphology, insular E. quatuorlineata populations should be the future focus of an extensive sampling, especially since the mitonuclear discordance observed in this species could be related to ecological adaptations, such as the island-dwarfism phenomenon.

Hybridization and extensive mitochondrial introgression among fire salamanders in peninsular Italy

Discordance between mitochondrial and nuclear patterns of population genetic structure is providing key insights into the eco-evolutionary dynamics between and within species, and their assessment is highly relevant to biodiversity monitoring practices based on DNA barcoding approaches. Here, we investigate the population genetic structure of the fire salamander Salamandra salamandra in peninsular Italy. Both mitochondrial and nuclear markers clearly identified two main population groups. However, nuclear and mitochondrial zones of geographic transition between groups were located 600 km from one another. Recent population declines in central Italy partially erased the genetic imprints of past hybridization dynamics. However, the overall pattern of genetic variation, together with morphological and fossil data, suggest that a rampant mitochondrial introgression triggered the observed mitonuclear discordance, following a post-glacial secondary contact between lineages. Our results clearly show the major role played by reticulate evolution in shaping the structure of Salamandra salamandra populations and, together with similar findings in other regions of the species' range, contribute to identify the fire salamander as a particularly intriguing case to investigate the complexity of mechanisms triggering patterns of mitonuclear discordance in animals.

The study of larval tail morphology reveals differentiation between two Triturus species and their hybrids

In amphibians, morphological differentiation and disparity at the larval and post-metamorphic ontogenetic stages can diverge, owing to various contrasting environments and different selective pressures. In the monophyletic clade of nineTriturusnewt species, five different morphotypes can be recognized, but information on larval morphology is limited. Here we explore divergence of larval morphology inTriturus ivanbureschi,T. macedonicus, and their F1 hybrids. These two genetically and morphologically distinct crested newt species hybridize in nature and form a relatively wide hybrid zone in the central part of the Balkan Peninsula. Using a geometric morphometric approach and multivariate statistics, we evaluated differences of tail size and shape, colouration pattern, and the presence of a tail filament at the mid-larval stage in larvae reared under controlled laboratory conditions. We chose the tail as the main propulsive organ crucial for locomotion, feeding, and escaping predators. We found thatTriturus ivanbureschiandT. macedonicuslarvae differ in tail shape, but not in tail size. Two groups of F1 hybrid larvae (obtained from reciprocal crossing) were similar to each other, but differed from the parental species in size and shape of the tail, colouration pattern, and the presence of a tail filament. Our results indicate that, like adults, larvae diverge morphologically and hybrid larvae do not exhibit intermediate morphology of the parental species.

A signature of dynamic biogeography: enclaves indicate past species replacement

Understanding how species have replaced each other in the past is important to predicting future species turnover. While past species replacement is difficult to detect after the fact, the process may be inferred from present-day distribution patterns. Species with abutting ranges sometimes show a characteristic distribution pattern, where a section of one species range is enveloped by that of the other. Such an enclave could indicate past species replacement: when a species is partly supplanted by a competitor, but a population endures locally while the invading species moves around and past it, an enclave forms. If the two species hybridize and backcross, the receding species is predicted to leave genetic traces within the expanding one under a scenario of species replacement. By screening dozens of genes in hybridizing crested newts, we uncover genetic remnants of the ancestral species, now inhabiting an enclave, in the range of the surrounding invading species. This independent genetic evidence supports the past distribution dynamics we predicted from the enclave. We suggest that enclaves provide a valuable tool in understanding historical species replacement, which is important because a major conservation concern arising from anthropogenic climate change is increased species replacement in the future.

Stabilization of a salamander moving hybrid zone

When related species meet upon postglacial range expansion, hybrid zones are frequently formed. Theory predicts that such zones may move over the landscape until equilibrium conditions are reached. One hybrid zone observed to be moving in historical times (1950–1979) is that of the pond‐breeding salamanders Triturus cristatus and Triturus marmoratus in western France. We identified the ecological correlates of the species hybrid zone as elevation, forestation, and hedgerows favoring the more terrestrial T. marmoratus and pond density favoring the more aquatic T. cristatus. The past movement of the zone of ca. 30 km over three decades has probably been driven by the drastic postwar reduction of the “bocage” hedgerow landscape, favoring T. cristatus over T. marmoratus. No further hybrid zone movement was observed from 1979 to the present. To explain the changing dynamics of the hybrid zone, we propose that it stalled, either because an equilibrium was found at an altitude of ca. 140 m a.s.l. or due to pond loss and decreased population densities. While we cannot rule out the former explanation, we found support for the latter. Under agricultural intensification, ponds in the study area are lost at an unprecedented rate of 5.5% per year, so that remaining Triturus populations are increasingly isolated, hampering dispersal and further hybrid zone movement.

Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens

Background

The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea—an area demarcated by the biogeographic breaks between Wallace’s and Lydekker’s lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi’s three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships.

Results

Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace’s line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data.

Conclusions

The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7–12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0650-z) contains supplementary material, which is available to authorized users.

Homeotic transformations and number changes in the vertebral column of Triturus newts

We explored intraspecific variation in vertebral formulae, more specifically the variation in the number of thoracic vertebrae and frequencies of transitional sacral vertebrae in Triturus newts (Caudata: Salamandridae). Within salamandrid salamanders this monophyletic group shows the highest disparity in the number of thoracic vertebrae and considerable intraspecific variation in the number of thoracic vertebrae. Triturus species also differ in their ecological preferences, from predominantly terrestrial to largely aquatic. Following Geoffroy St. Hilaire's and Darwin's rule which states that structures with a large number of serially homologous repetitive elements are more variable than structures with smaller numbers, we hypothesized that the variation in vertebral formulae increases in more elongated species with a larger number of thoracic vertebrae. We furthermore hypothesized that the frequency of transitional vertebrae will be correlated with the variation in the number of thoracic vertebrae within the species. We also investigated potential effects of species hybridization on the vertebral formula. The proportion of individuals with a number of thoracic vertebrae different from the modal number and the range of variation in number of vertebrae significantly increased in species with a larger number of thoracic vertebrae. Contrary to our expectation, the frequencies of transitional vertebrae were not correlated with frequencies of change in the complete vertebrae number. The frequency of transitional sacral vertebra in hybrids did not significantly differ from that of the parental species. Such a pattern could be a result of selection pressure against transitional vertebrae and/or a bias towards the development of full vertebrae numbers. Although our data indicate relaxed selection for vertebral count changes in more elongated, aquatic species, more data on different selective pressures in species with different numbers of vertebrae in the two contrasting, terrestrial and aquatic environments are needed to test for causality.

The distribution and taxonomy of Lissotriton newts in Turkey (Amphibia, Salamandridae)

Two and perhaps three taxa of Lissotriton newt occur in Turkey. Their species status is controversial. The distribution of these taxa and the taxonomic status of each are reviewed and discussed. A database of 128 Turkish Lissotriton localities was compiled and species distribution models were constructed. We reiterate that the presence of Lissotriton (vulgaris) lantzi in Turkey is disputed and needs confirmation. The range of Lissotriton (vulgaris) kosswigi is restricted to north-western Anatolia - given the small global range of this Turkey endemic, a closer look at its conservation status is warranted. The distribution of Lissotritonvulgarisschmidtleri covers western Asiatic and European Turkey. The findings support an allopatric distribution of the Turkish Lissotriton species. We reflect on the biological significance of previously reported morphological intermediates between Lissotriton (vulgaris) kosswigi and Lissotritonvulgarisschmidtleri in the light of the recent proposal to recognize kosswigi at the species level. The available data are in line with species status for Lissotriton (vulgaris) lantzi and Lissotriton (vulgaris) kosswigi. Although Lissotritonvulgarisschmidtleri is a genetically diverged taxon as well, the extent of gene flow with parapatric European Lissotriton taxa is as yet unknown.

Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts

The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted.

High levels of diversity uncovered in a widespread nominal taxon: continental phylogeography of the neotropical tree frog Dendropsophus minutus

Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km². One of them occupies an area of almost one million km² encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered.

Exploring the effect of asymmetric mitochondrial DNA introgression on estimating niche divergence in morphologically cryptic species

If potential morphologically cryptic species, identified based on differentiated mitochondrial DNA, express ecological divergence, this increases support for their treatment as distinct species. However, mitochondrial DNA introgression hampers the correct estimation of ecological divergence. We test the hypothesis that estimated niche divergence differs when considering nuclear DNA composition or mitochondrial DNA type as representing the true species range. We use empirical data of two crested newt species (Amphibia: Triturus) which possess introgressed mitochondrial DNA from a third species in part of their ranges. We analyze the data in environmental space by determining Fisher distances in a principal component analysis and in geographical space by determining geographical overlap of species distribution models. We find that under mtDNA guidance in one of the two study cases niche divergence is overestimated, whereas in the other it is underestimated. In the light of our results we discuss the role of estimated niche divergence in species delineation.

Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform

Next-generation sequencing is a fast and cost-effective way to obtain sequence data for nonmodel organisms for many markers and for many individuals. We describe a protocol through which we obtain orthologous markers for the crested newts (Amphibia: Salamandridae: Triturus), suitable for analysis of interspecific hybridization. We use transcriptome data of a single Triturus species and design 96 primer pairs that amplify c. 180 bp fragments positioned in 3-prime untranslated regions. Next, these markers are tested with uniplex PCR for a set of species spanning the taxonomical width of the genus Triturus. The 52 markers that consistently show a single band of expected length at gel electrophoreses for all tested crested newt species are then amplified in five multiplex PCRs (with a plexity of ten or eleven) for 132 individual newts: a set of 84 representing the seven (candidate) species and a set of 48 from a presumed hybrid population. After pooling multiplexes per individual, unique tags are ligated to link amplicons to individuals. Subsequently, individuals are pooled equimolar and sequenced on the Ion Torrent next-generation sequencing platform. A bioinformatics pipeline identifies the alleles and recodes these to a genotypic format. Next, we test the utility of our markers. baps allocates the 84 crested newt individuals representing (candidate) species to their expected (candidate) species, confirming the markers are suitable for species delineation. newhybrids, a hybrid index and hiest confirm the 48 individuals from the presumed hybrid population to be genetically admixed, illustrating the potential of the markers to identify interspecific hybridization. We expect the set of markers we designed to provide a high resolving power for analysis of hybridization in Triturus.

The distribution of the crested and marbled newt species (Amphibia: Salamandridae: Triturus) – an addition to the New Atlas of Amphibians and Reptiles of Europe

In the recently published New Atlas of Amphibians and Reptiles of Europe (Sillero et al., 2014a), the distribution of the newt genusTrituruswas not resolved at the level of the species. The main reason for this was the lack of high quality distribution data from in and around the parapatric contact zones between species, where interspecific hybridization occurs. We are working extensively onTriturusand the (particularly genetic) data we have accumulated allow us to map the individualTriturusspecies at the appropriate scale. We here provide a database composed of distribution data for the individual species, at generally high resolution, particularly from in and around contact zones. Based on this database we produce maps at the 50 × 50 km UTM grid resolution as used in the new atlas and highlight those grid cells in which more than oneTriturusspecies occurs.

Tracing glacial refugia of Triturus newts based on mitochondrial DNA phylogeography and species distribution modeling

INTRODUCTION

The major climatic oscillations during the Quaternary Ice Age heavily influenced the distribution of species and left their mark on intraspecific genetic diversity. Past range shifts can be reconstructed with the aid of species distribution modeling and phylogeographical analyses. We test the responses of the different members of the genus Triturus (i.e. the marbled and crested newts) as the climate shifted from the previous glacial period (the Last Glacial Maximum, ~21 Ka) to the current interglacial.

RESULTS

We present the results of a dense mitochondrial DNA phylogeography (visualizing genetic diversity within and divergence among populations) and species distribution modeling (using two different climate simulations) for the nine Triturus species on composite maps.

CONCLUSIONS

The combined use of species distribution modeling and mitochondrial phylogeography provides insight in the glacial contraction and postglacial expansion of Triturus. The combined use of the two independent techniques yields a more complete understanding of the historical biogeography of Triturus than both approaches would on their own. Triturus newts generally conform to the 'southern richness and northern purity' paradigm, but we also find more intricate patterns, such as the absence of genetic variation and suitable area at the Last Glacial Maximum (T. dobrogicus), an 'extra-Mediterranean' refugium in the Carpathian Basin (T. cristatus), and areas where species displaced one another postglacially (e.g. T. macedonicus and western T. karelinii). We provide a biogeographical scenario for Triturus, showing the positions of glacial refugia, the regions that were postglacially colonized and the areas where species displaced one another as they shifted their ranges.

A multimarker phylogeography of crested newts (Triturus cristatus superspecies) reveals cryptic species

The crested newt Triturus cristatus superspecies is composed of five recognized species. One of these, T. karelinii sensu lato, comprises three geographically structured mitochondrial DNA lineages: 'eastern', 'central' and 'western T. karelinii'. Genetic divergence among these lineages is comparable to that of recognized crested newt species, but morphologically they are indistinguishable. Here, we conduct a multimarker phylogeographical survey to explore the evolutionary independence of these mitochondrial DNA lineages and we include representatives of the other species to guide our interpretation of the results. All markers show distinct patterns when analyzed singly (as a phylogeny or haplotype network) and none of them sort haplotypes fully in line with species or mitochondrial DNA lineage. A multilocus approach (BAPS and *BEAST) on the other hand shows that not only the recognized species, but also the three mitochondrial DNA lineages represent discrete nuclear DNA gene pools. A mismatch is found in the northwest of Asiatic Turkey, where several populations identified as 'central T. karelinii' based on nuclear DNA possesses 'western T. karelinii' mitochondrial DNA. We invoke asymmetric mitochondrial DNA introgression to explain this pattern and support this with a historical biogeographical scenario. The three spatial groups in T. karelinii sensu lato should be regarded as distinct species.