Integrative analyses of speciation and divergence in Psammodromus hispanicus (Squamata: Lacertidae)

Assessing vulnerability of reptile hotspots through temporal trends of global change factors in the Iberian Peninsula

Habitat degradation and climate change are major threats to the long-term persistence of reptile populations. However, their roles on primary productivity instability remain unclear at certain scales. Besides, the design of protected areas has often overlooked reptiles or assumed that their ecological requirements are represented under the umbrella of more charismatic species. Here, we assess the vulnerability of areas of high diversity of reptiles in the Iberian Peninsula to global change using data from satellite imagery. We focused on primary productivity, climate and land-use change because they are indicators of environmental variability that might impair ecosystem functioning and alter wildlife communities. We used linear regressions to detect monotonic temporal trends in primary productivity (through the enhanced vegetation index, EVI) and climate (mean temperature and accumulated precipitation) at two spatial resolutions (10-km² UTM squares and CORINE land-cover polygon level) over the period 2000-2020. We also determined how the strength of land-use and climate change affected the intensity of change in primary productivity at both spatial scales with multivariate linear regressions. We identified 339 hotspots (10-km² UTM squares) and monotonic increments of temperature, EVI or both occurred in 43 %, 16 % and 22 % of them, respectively. Positive trends of the EVI were related to increasing temperatures and changes in shrubland and forest cover. Within the hotspots with monotonic increments in EVI and temperature, EVI increments occurred in 65 % of the CORINE polygons that did not change their land-cover type, with stronger increases in tree crops. Finally, the Natura 2000 network provides only moderate protection to reptile hotspots, being most of the vegetation types relatively underrepresented. The proportion of forest and shrubland protected by the Natura 2000 network was higher in hotspots where EVI changed. Our procedures are relevant to prioritize hotspots requiring ground monitoring that allows economic and time savings.

A two-species distribution model for parapatric newts, with inferences on their history of spatial replacement

Related species often engage in abutting or overlapping contact zones with various strengths of interspecific competition. Biotic interactions such as these preclude the registration of the full profile of environmental variables that would describe the otherwise larger species ranges. Here, I advocate to forego full range species distribution modelling and instead focus on the ecography of the contact zone, for example with ‘two-species distribution models’ (TSDMs), in which presence data are contrasted against the background of environmental data. The newts Triturus cristatus and Triturus marmoratus meet in the west of France. A countrywide TSDM suggests that the contact zone of the species is located at a climatic gradient, in line with their north-eastern vs. south-western ranges. The species are also ecologically segregated by elevation and forestation, which is in line with a documented movement of the contact zone caused by hedgerow removal in lowland areas. Hindcasts for the Holocene suggest that the species contact zone was positioned at either the same place as at present or more to the south, depending on the amount of forestation. A forecast under climate warming predicts a fast movement to the north, but this scenario is deemed unrealistic. One reason is that recent habitat loss compromises dispersal and range expansion. Other species pairs to which TSDMs have been applied are listed for comparison.

Niche diversification of Mediterranean and southwestern Asian tortoises

Background

Tortoises of the genus Testudo are widely distributed throughout the Mediterranean region and southwestern Asia. However, the evolutionary mechanisms of diversification in this genus are still poorly understood.

Methods

In this study, we assessed the evolutionary patterns in the climate niches of five species and 11 subspecies of the genus Testudo using ecological niche models and evaluated the niche overlap based on species phylogenetic distances.

Results

The ecological models indicated that most species differ in their climate niches, but show overlap, with gradual transitions at range boundaries. As expected, the ecological divergence among subspecies was lower than that among species. Evaluation of the phylogenetic signal indicated that climate niches have been weakly conserved, but sister species also show high evolutionary divergence.

Phylogeography and ecological differentiation of strictly Mediterranean taxa: the case of the Iberian endemic Odontites recordonii

PREMISE

Ecological drivers for genetic differentiation in Mediterranean climates are still underexplored. We have used the strictly Mediterranean endemic Odontites recordonii as a model species to address this question. This species is one of the three Iberian representatives of the O. vernus group, which are morphologically similar. Thus, it was additionally necessary to clarify their phylogenetic relationships.

METHODS

We used amplified fragment length polymorphisms to reveal phylogenetic relationships within O. vernus group, and to reconstruct the phylogeographic patterns within O. recordonii. Additionally, ecological niche models were generated to detect refugia along the Quaternary climatic oscillations. And finally, alleles under natural selection were identified, and correlations between allele presences and environmental variables were calculated in order to shed light on the ecological drivers promoting differentiation.

RESULTS

The three species from the O. vernus group were recovered as distinct species. Three genetic groups were found within O. recordonii and a putative refugium was detected for each one. Eighty-one alleles could be under diversifying selection, and 58 alleles showed significant correlations with environmental variables, especially with temperature and precipitation seasonality and summer drought.

CONCLUSIONS

The three Iberian species of the O. vernus group are reciprocal monophyletic taxa. The three genetic groups of O. recordonii could have been restricted to narrow refugia during the Quaternary and displayed present distributions in accordance with bioclimatic conditions. Temperature and precipitation seasonality and the intensity of summer drought are definitory climatic parameters of Mediterranean-type climates, and they could have acted as drivers of genetic differentiation on O. recordonii.

Niche differentiation between deeply divergent phylogenetic lineages of an endemic newt: implications for Species Distribution Models

Species distribution models (SDMs) treat species as a single unit, neglecting intraspecific variation. Few studies address the impact of intraspecific variation on SDM performance, and none of them account for the well-known inter-algorithm variability in prediction performance. The endemic Iberian amphibian Lissotriton boscai comprises two geographically highly structured phylogenetic lineages, which allowed us to explore how intraspecific variation affects the overall performance of SDMs and the predicted ecological niche. We built species and lineage distribution models using three different presence-only algorithms. We also tested for niche overlap, niche equivalency and niche similarity, using an ordination technique. We found differences in the predicted potential distribution of the two lineages and the underlying environmental factors. Moreover, intraspecific differences in model predictive capacity existed irrespective of which algorithm was used to build the distribution models. This was coupled with lineages showing a low degree of niche overlap and occurring in relatively different environmental niches spaces. The intraspecific variation observed in L. boscai led to an improved intraspecific predictivity of the lineage level based-distribution models. There was partial spatial agreement between the niche overlap and independently reported secondary contact zones. Thus SDMs built only at the species level may be too naive to predict impacts of global change on species distributions.

Niche divergence of evolutionarily significant units with implications for repopulation programs of the world's largest amphibians

The niche divergence and potential climate change-induced loss of evolutionarily significant units (ESUs) of flagship amphibian species in China, the Chinese giant salamander clade, were investigated. We tested niche-related ecological hypotheses and identified suitable habitats that are essential for the conservation of ESUs in response to future climate change according to ecological niche models (ENMs). We predicted the localized habitat loss crisis of ESUs induced by global climate heating using the predicted climate derived from two representative concentration pathway (RCP) scenarios 2.6 and 8.5, respectively. In our study, a niche conservatism pattern was found between the two distinctive northern and southern ESUs with sufficient distributional records, but their niches were not equivalent. Furthermore, there was neither abrupt environmental change in nor remarkable biogeographic barriers between the suitable habitats of the species, as indicated by random linear, blob and ribbon range-breaking tests. Under the low-emission scenario RCP2.6, the northern ESU had a moderate loss of suitable range, while the southern ESU had range expansion in the 2070s. The climatic velocities were low in the ranges of both ESUs. However, under the high-emission scenario RCP8.5, the climatic velocities were found to become larger in the suitable ranges of both ESUs. Moreover, the northern ESU had severe habitat loss, bringing it to the edge of extinction, while the southern ESU also had intensified range loss. Considering this, climatic velocity can be an effective indicator of range loss. We argued conclusively that conservation prioritization of ESUs should effectively take into account the underlying geographic and ecological mechanisms driving the speciation process. The conservation of ESUs should consider the conservation of both evolutionary potential and ecological adaptation capacity of each lineage. The present study provided practical guidelines for repopulation programs for endangered species and the conservation of evolutionary diversity.

Influence of climate change on the predicted distributions of the genus Tympanoctomys (Rodentia, Hystricomorpha, Octodontidae), and their conservation implications

Viscacha rats (genus Tympanoctomys Yepes, 1942) are ecologically, physiologically, and behaviorally unusual octodontid rodents endemic to the Monte and Patagonian desert biomes of Argentina. The geographic ranges of the different species of Tympanoctomys have been described in general terms but have not been associated with spatial and climate data. Within species, populations are patchily distributed and genetically distinct. We investigated the predicted distribution of Tympanoctomys and the influence of climate fluctuations on their geographic range in historical, current, and future, scenarios. Our objectives were to characterize the environmental niche of the genus, propose a paleoclimatic context for the oldest fossils, characterize the environmental niches for T. barrerae and T. kirchnerorum, and forecast potential future distributions for these taxa. Ecological niche models were constructed using occurrence records from 1941 to the present wherein we identified several precipitation and temperature variables as important predictors of the geographic distributions of the genus, and the species T. barrerae and T. kirchnerorum. Based on our models’ results, we hypothesize that the distribution of Tympanoctomys has contracted from historical to modern times. At the species level, T. kirchnerorum likely experienced the most dramatic change, suffering a large contraction of its historical distribution resulting in its limited present distribution. Given these findings, projected future climate fluctuations and global warming are expected to affect the distributions and persistence of these species.

Niche models at inter- and intraspecific levels reveal hierarchical niche differentiation in midwife toads

Variation and population structure play key roles in the speciation process, but adaptive intraspecific genetic variation is commonly ignored when forecasting species niches. Amphibians serve as excellent models for testing how climate and local adaptations shape species distributions due to physiological and dispersal constraints and long generational times. In this study, we analysed the climatic factors driving the evolution of the genus Alytes at inter- and intraspecific levels that may limit realized niches. We tested for both differences among the five recognized species and among intraspecific clades for three of the species (Alytes obstetricans, A. cisternasii, and A. dickhilleni). We employed ecological niche models with an ordination approach to perform niche overlap analyses and test hypotheses of niche conservatism or divergence. Our results showed strong differences in the environmental variables affecting species climatic requirements. At the interspecific level, tests of equivalence and similarity revealed that sister species were non-identical in their environmental niches, although they neither were entirely dissimilar. This pattern was also consistent at the intraspecific level, with the exception of A. cisternasii, whose clades appeared to have experienced a lower degree of niche divergence than clades of the other species. In conclusion, our results support that Alytes toads, examined at both the intra- and interspecific levels, tend to occupy similar, if not identical, climatic environments.

A comparative atlas of the skull osteology of European lizards (Reptilia: Squamata)

The fossil record provides evidence of a long evolutionary history of European lizards. Since fossil lizards are regularly represented by bone remains, the knowledge of the origins of extant taxa and their distribution in time and space is hindered by the fact that their comparative osteology is not yet completely and adequately known. In spite of a rising interest in this topic since the end of the 20th century, a gap in our knowledge is still evident. We here report the first broad-scale comparative osteological analysis of the skulls of extant European lizards, highlighting significant differences that can be used in identification. This comparative study, including as many European species as possible, leads to the creation of a detailed diagnostic key for each single bone. Also, our data significantly improve the recognizability of extant European non-snake squamates, with 54% of the current diversity to be recognized based on the new results contra the previously estimated 31%. This recognizability is expected to further increase in the future, with new studies focusing on species that are either missing or poorly represented here, or applying promising advanced methodologies.

Ecological change predicts population dynamics and genetic diversity over 120 000 years

While ecological effects on short-term population dynamics are well understood, their effects over millennia are difficult to demonstrate and convincing evidence is scant. Using coalescent methods, we analysed past population dynamics of three lizard species (Psammodromus hispanicus, P. edwardsianus, P. occidentalis) and linked the results with climate change data covering the same temporal horizon (120 000 years). An increase in population size over time was observed in two species, and in P. occidentalis, no change was observed. Temporal changes in temperature seasonality and the maximum temperature of the warmest month were congruent with changes in population dynamics observed for the three species and both variables affected population density, either directly or indirectly (via a life-history trait). These results constitute the first solid link between ecological change and long-term population dynamics. The results moreover suggest that ecological change leaves genetic signatures that can be retrospectively traced, providing evidence that ecological change is a crucial driver of genetic diversity and speciation.

The evolution of colour pattern complexity: selection for conspicuousness favours contrasting within-body colour combinations in lizards

Many animals display complex colour patterns that comprise several adjacent, often contrasting colour patches. Combining patches of complementary colours increases the overall conspicuousness of the complex pattern, enhancing signal detection. Therefore, selection for conspicuousness may act not only on the design of single colour patches, but also on their combination. Contrasting long- and short-wavelength colour patches are located on the ventral and lateral surfaces of many lacertid lizards. As the combination of long- and short-wavelength-based colours generates local chromatic contrast, we hypothesized that selection may favour the co-occurrence of lateral and ventral contrasting patches, resulting in complex colour patterns that maximize the overall conspicuousness of the signal. To test this hypothesis, we performed a comparative phylogenetic study using a categorical colour classification based on spectral data and descriptive information on lacertid coloration collected from the literature. Our results demonstrate that conspicuous ventral (long-wavelength-based) and lateral (short-wavelength-based) colour patches co-occur throughout the lacertid phylogeny more often than expected by chance, especially in the subfamily Lacertini. These results suggest that selection promotes the evolution of the complex pattern rather than the acquisition of a single conspicuous colour patch, possibly due to the increased conspicuousness caused by the combination of colours with contrasting spectral properties.

Geographical and temporal body size variation in a reptile: roles of sex, ecology, phylogeny and ecology structured in phylogeny

Geographical body size variation has long interested evolutionary biologists, and a range of mechanisms have been proposed to explain the observed patterns. It is considered to be more puzzling in ectotherms than in endotherms, and integrative approaches are necessary for testing non-exclusive alternative mechanisms. Using lacertid lizards as a model, we adopted an integrative approach, testing different hypotheses for both sexes while incorporating temporal, spatial, and phylogenetic autocorrelation at the individual level. We used data on the Spanish Sand Racer species group from a field survey to disentangle different sources of body size variation through environmental and individual genetic data, while accounting for temporal and spatial autocorrelation. A variation partitioning method was applied to separate independent and shared components of ecology and phylogeny, and estimated their significance. Then, we fed-back our models by controlling for relevant independent components. The pattern was consistent with the geographical Bergmann's cline and the experimental temperature-size rule: adults were larger at lower temperatures (and/or higher elevations). This result was confirmed with additional multi-year independent data-set derived from the literature. Variation partitioning showed no sex differences in phylogenetic inertia but showed sex differences in the independent component of ecology; primarily due to growth differences. Interestingly, only after controlling for independent components did primary productivity also emerge as an important predictor explaining size variation in both sexes. This study highlights the importance of integrating individual-based genetic information, relevant ecological parameters, and temporal and spatial autocorrelation in sex-specific models to detect potentially important hidden effects. Our individual-based approach devoted to extract and control for independent components was useful to reveal hidden effects linked with alternative non-exclusive hypothesis, such as those of primary productivity. Also, including measurement date allowed disentangling and controlling for short-term temporal autocorrelation reflecting sex-specific growth plasticity.

Multilocus phylogeography of the common lizard Zootoca vivipara at the Ibero-Pyrenean suture zone reveals lowland barriers and high-elevation introgression

BACKGROUND

The geographic distribution of evolutionary lineages and the patterns of gene flow upon secondary contact provide insight into the process of divergence and speciation. We explore the evolutionary history of the common lizard Zootoca vivipara (= Lacerta vivipara) in the Iberian Peninsula and test the role of the Pyrenees and the Cantabrian Mountains in restricting gene flow and driving lineage isolation and divergence. We also assess patterns of introgression among lineages upon secondary contact, and test for the role of high-elevation trans-mountain colonisations in explaining spatial patterns of genetic diversity. We use mtDNA sequence data and genome-wide AFLP loci to reconstruct phylogenetic relationships among lineages, and measure genetic structure.

RESULTS

The main genetic split in mtDNA corresponds generally to the French and Spanish sides of the Pyrenees as previously reported, in contrast to genome-wide AFLP data, which show a major division between NW Spain and the rest. Both types of markers support the existence of four distinct and geographically congruent genetic groups, which are consistent with major topographic barriers. Both datasets reveal the presence of three independent contact zones between lineages in the Pyrenean region, one in the Basque lowlands, one in the low-elevation mountains of the western Pyrenees, and one in the French side of the central Pyrenees. The latter shows genetic evidence of a recent, high-altitude trans-Pyrenean incursion from Spain into France.

CONCLUSIONS

The distribution and age of major lineages is consistent with a Pleistocene origin and a role for both the Pyrenees and the Cantabrian Mountains in driving isolation and differentiation of Z. vivipara lineages at large geographic scales. However, mountain ranges are not always effective barriers to dispersal, and have not prevented a recent high-elevation trans-Pyrenean incursion that has led to asymmetrical introgression among divergent lineages. Cytonuclear discordance in patterns of genetic structure and introgression at contact zones suggests selection may be involved at various scales. Suture zones are important areas for the study of lineage formation and speciation, and our results show that biogeographic barriers can yield markedly different phylogeographic patterns in different vertebrate and invertebrate taxa.

Causes and evolutionary consequences of population subdivision of an Iberian mountain lizard, Iberolacerta monticola

Aim

The study of the factors that influence population connectivity and spatial distribution of genetic variation is crucial for understanding speciation and for predicting the effects of landscape modification and habitat fragmentation, which are considered severe threats to global biodiversity. This dual perspective is obtained from analyses of subalpine mountain species, whose present distribution may have been shaped both by cyclical climate changes over ice ages and anthropogenic perturbations of their habitats. Here, we examine the phylogeography, population structure and genetic diversity of the lacertid lizard Iberolacerta monticola, an endemism considered to be facing a high risk of extinction in several populations.

Location

Northwestern quadrant of the Iberian Peninsula.

Methods

We analyzed the mtDNA variation at the control region (454 bp) and the cytochrome b (598 bp) loci, as well as at 10 nuclear microsatellite loci from 17 populations throughout the distribution range of the species.

Results

According to nuclear markers, most sampling sites are defined as distinct, genetically differentiated populations, and many of them show traces of recent bottlenecks. Mitochondrial data identify a relatively old, geographically restricted lineage, and four to six younger geographically vicariant sister clades, whose origin may be traced back to the mid-Pleistocene revolution, with several subclades possibly associated to the mid-Bruhnes transition. Geographic range fragmentation of one of these clades, which includes lowland sites, is very recent, and most likely due to the accelerated loss of Atlantic forests by human intervention.

Main Conclusions

Altogether, the data fit a “refugia within refugia” model, some lack of pattern uniformity notwithstanding, and suggest that these mountains might be the cradles of new species of Iberolacerta. However, the changes operated during the Holocene severely compromise the long-term survival of those genetic lineages more exposed to the anthropogenic perturbations of their habitats.