Allopatric diversification and evolutionary melting pot in a North African Palearctic relict: The biogeographic history of Salamandra algira

Hidden in the sand: Phylogenomics unravel an unexpected evolutionary history for the desert-adapted vipers of the genus Cerastes

The desert vipers of the genus Cerastes are a small clade of medically important venomous snakes within the family Viperidae. According to published morphological and molecular studies, the group is comprised by four species: two morphologically similar and phylogenetically sister taxa, the African horned viper (Cerastes cerastes) and the Arabian horned viper (Cerastes gasperettii); a more distantly related species, the Saharan sand viper (Cerastes vipera), and the enigmatic Böhme's sand viper (Cerastes boehmei), only known from a single specimen in captivity allegedly captured in Central Tunisia. In this study, we sequenced one mitochondrial marker (COI) as well as genome-wide data (ddRAD sequencing) from 28 and 41 samples, respectively, covering the entire distribution range of the genus to explore the population genomics, phylogenomic relationships and introgression patterns within the genus Cerastes. Additionally, and to provide insights into the mode of diversification of the group, we carried out niche overlap analyses considering climatic and habitat variables. Both nuclear phylogenomic reconstructions and population structure analyses have unveiled an unexpected evolutionary history for the genus Cerastes, which sharply contradicts the morphological similarities and previously published mitochondrial approaches. Cerastes cerastes and C. vipera are recovered as sister taxa whilst C. gasperettii is a sister taxon to the clade formed by these two species. We found a relatively high niche overlap (OI > 0.7) in both climatic and habitat variables between C. cerastes and C. vipera, contradicting a potential scenario of sympatric speciation. These results are in line with the introgression found between the northwestern African populations of C. cerastes and C. vipera. Finally, our genomic data confirms the existence of a lineage of C. cerastes in Arabia. All these results highlight the importance of genome-wide data over few genetic markers to study the evolutionary history of species.

Phylogeographic and Paleoclimatic Modelling Tools Improve Our Understanding of the Biogeographic History of Hierophis viridiflavus (Colubridae)

Phylogeographic and paleoclimatic modelling studies have been combined to infer the role of Pleistocene climatic oscillations as drivers of the genetic structure and distribution of Mediterranean taxa. For the European whip snake, Hierophis viridiflavus, previous studies based on paleoclimatic modelling have depicted a low reliability in the pattern of past climatic suitability across the central Mediterranean Basin, which barely fits the species' genetic structure. In this study, we combined phylogeographic and paleoclimatic modelling tools to improve our understanding of the biogeographic history of H. viridiflavus, particularly extending the sampling and phylogeographic inferences to previously under-sampled regions. Phylogeographic analyses recovered two major clades that diverged at the beginning of the Pleistocene and had diversified in different ways by the late Pleistocene: the east clade (composed of three subclades) and the west clade (with no further structure). Paleoclimatic models highlighted the temperate character of H. viridiflavus, indicating range contractions during both the last inter-glacial and last glacial maximum periods. Range expansions from southern-located climatic refugia likely occurred in the Bølling-Allerød and Middle Holocene periods, which are supported by signals of demographic growth in the west clade and South-East-North subclade. Overall, this work improves our understanding of the historical biogeography of H. viridiflavus, providing further insights into the evolutionary processes that occurred in the Mediterranean Basin hotspot.

First ecological assessment of the endangered Lichtenfelder’s Tiger Gecko (Goniurosaurus lichtenfelderi) from northern Vietnam: Micro-habitat and macro-climatic niche comparisons between island and mainland populations

The Lichtenfelder’s Tiger Gecko, Goniurosaurus lichtenfelderi is currently known only from northern Vietnam and southern China. Because of its restricted distribution, the species is potentially threatened by extinction due to anthropogenic impacts. Recently, the species has been listed in the IUCN Red List of Threatened Species as “Vulnerable” and included in CITES Appendix II and the Vietnam Governmental Decree – Group IIB. However, conservation activities to safeguard wild populations of G. lichtenfelderi have not yet been implemented due to a lack of detailed information about the population status and its ecological requirements. In this study, the micro-habitat use of G. lichtenfelderi was assessed. As a result of our field surveys, we found this species in evergreen forest areas with a high percentage of vegetation coverage and in close proximity to medium or small stream sections with rocky shelters on granitic formations. Canopy coverage, three micro-climatic variables (air, substrate temperature and humidity), weather condition and substrate type were the most important characteristics explaining the variation in the micro-habitat use of G. lichtenfelderi. Coupled with a macro-ecological (climate niche) approach, the complex niches of G. lichtenfelderi were defined by comparing them between two geographically distant populations in island and mainland sites. We found high similarities in macro-climatic and micro-habitat niches between the island and mainland populations of G. lichtenfelderi. Based on the ecological information, we recommend conservation actions to protect the core refugia of G. lichtenfelderi and reduce negative influences of anthropogenic impacts on wild populations in the future.

Independent evolutionary transitions to pueriparity across multiple timescales in the viviparous genus Salamandra

The ability to bear live offspring, viviparity, has evolved multiple times across the tree of life and is a remarkable adaptation with profound life-history and ecological implications. Within amphibians the ancestral reproductive mode is oviparity followed by a larval life stage, but viviparity has evolved independently in all three amphibian orders. Two types of viviparous reproduction can be distinguished in amphibians; larviparity and pueriparity. Larviparous amphibians deliver larvae into nearby ponds and streams, while pueriparous amphibians deliver fully developed juveniles and thus do not require waterbodies for reproduction. Among amphibians, the salamander genus Salamandra is remarkable as it exhibits both inter- and intraspecific variation in the occurrence of larviparity and pueriparity. While the evolutionary relationships among Salamandra lineages have been the focus of several recent studies, our understanding of how often and when transitions between modes occurred is still incomplete. Furthermore, in species with intraspecific variation, the reproductive mode of a given population can only be confirmed by direct observation of births and thus the prevalence of pueriparous populations is also incompletely documented. We used sequence capture to obtain 1,326 loci from 94 individuals from across the geographic range of the genus, focusing on potential reproductive mode transition zones. We also report additional direct observations of pueriparous births for 20 new locations and multiple lineages. We identify at least five independent transitions from the ancestral mode of larviparity to pueriparity among and within species, occurring at different evolutionary timescales ranging from the Pliocene to the Holocene. Four of these transitions occurred within species. Based on a distinct set of markers and analyses, we also confirm previous findings of introgression between species and the need for taxonomic revisions in the genus. We discuss the implications of our findings with respect to the evolution of this complex trait, and the potential of using five independent convergent transitions for further studies on the ecological context in which pueriparity evolves and the genetic architecture of this specialized reproductive mode.

Multiple paternity in the pueriparous North African fire salamander, Salamandra algira, supports polyandry as a successful mating strategy in low fecundity Salamandra lineages

Multiple paternity is widespread in nature and despite costs, it has many associated benefits like increased genetic diversity and fertilization success. It has been described in many viviparous systems, suggesting the existence of some fitness advantages counteracting the inherent costs of viviparity, such as fecundity reduction and high parental investment. Reproductively polymorphic species, like the urodele Salamandra algira, which shows two types of viviparity: larviparity (i.e., delivering aquatic larvae), and pueriparity (i.e., delivering terrestrial metamorphosed juveniles), are suitable systems to study the relationship between reproductive modes and polygamous mating. Here, multiple paternity is confirmed in a pueriparous lineage of S. algira, as previously verified for the pueriparous lineages of the reproductively polymorphic species S. salamandra, suggesting polyandry is a successful mating strategy in pueriparous systems with reduced brood sizes. We discuss the potential benefits of polyandry in the context of viviparity evolution in urodeles.

Physical and ecological isolation contribute to maintain genetic differentiation between fire salamander subspecies

Landscape features shape patterns of gene flow among populations, ultimately determining where taxa lay along the continuum between panmixia to complete reproductive isolation. Gene flow can be restricted, leading to population differentiation in two non-exclusive ways: "physical isolation", in which geographic distance in combination with the landscape features restricts movement of individuals promoting genetic drift, and "ecological isolation", in which adaptive mechanisms constrain gene flow between different environments via divergent natural selection. In central Iberia, two fire salamander subspecies occur in parapatry across elevation gradients along the Iberian Central System mountains, while in the adjacent Montes de Toledo Region only one of them occurs. By integrating population and landscape genetic analyses, we show a ubiquitous role of physical isolation between and within mountain ranges, with unsuitable landscapes increasing differentiation between populations. However, across the Iberian Central System, we found strong support for a significant contribution of ecological isolation, with low genetic differentiation in environmentally homogeneous areas, but high differentiation across sharp transitions in precipitation seasonality. These patterns are consistent with a significant contribution of ecological isolation in restricting gene flow among subspecies. Overall, our results suggest that ecological divergence contributes to reduce genetic admixture, creating an opportunity for lineages to follow distinct evolutionary trajectories.

Evolutionary history of the oriental fire-bellied toad (Bombina orientalis) in Northeast China

The evolutionary history of a species is generally affected by the combination of geological events and climate fluctuations. By analyzing the population features, genetic structure and the effective population historical dynamics of existing species, the population evolutionary history can be reestablished. In recent years, geological evidence shows that the Yilan-Yitong fault zone located in Northeast Asia experienced strong and frequent geological changes in the late Quaternary period. Species population history has been shaped by the combination of the complex climatic conditions of the Quaternary and Pleistocene glacial interglacial cycles and palaeogeological events in Northeast Asia and it has become a research focus for evolutionary biology researchers. In this study, mitochondrial and microsatellite molecular markers were used to reveal the population features, genetic structure, and the effective population historical dynamics of the Oriental fire-bellied toad (Bombina orientalis). The results showed that the strong seismic activity of the Yilan-Yitong fault zone in the late Quaternary period was the main reason for the population differentiation of Oriental fire-bellied toad in northeast China. The Quaternary Pleistocene glacial interglacial cycles led to the significant bottleneck effect of the western population located in the Maoer mountain area. As a result, the western population has low genetic diversity. Recent gene flow between eastern and western populations and historical evidence of population expansion proved that the dispersal behavior of the western populations was the main cause of the low genetic diversity and mitochondrial and nuclear discordance. Human economic activity may be the mainly driving factor. These evidences showed that the comprehensive influence of geology, climate, human activities and other factors should be considered in the process of exploring the evolutionary history of species.

Landscape resistance constrains hybridization across contact zones in a reproductively and morphologically polymorphic salamander

Explicitly accounting for phenotypic differentiation together with environmental heterogeneity is crucial to understand the evolutionary dynamics in hybrid zones. Species showing intra-specific variation in phenotypic traits that meet across environmentally heterogeneous regions constitute excellent natural settings to study the role of phenotypic differentiation and environmental factors in shaping the spatial extent and patterns of admixture in hybrid zones. We studied three environmentally distinct contact zones where morphologically and reproductively divergent subspecies of Salamandra salamandra co-occur: the pueriparous S. s. bernardezi that is mostly parapatric to its three larviparous subspecies neighbours. We used a landscape genetics framework to: (i) characterise the spatial location and extent of each contact zone; (ii) assess patterns of introgression and hybridization between subspecies pairs; and (iii) examine the role of environmental heterogeneity in the evolutionary dynamics of hybrid zones. We found high levels of introgression between parity modes, and between distinct phenotypes, thus demonstrating the evolution to pueriparity alone or morphological differentiation do not lead to reproductive isolation between these highly divergent S. salamandra morphotypes. However, we detected substantial variation in patterns of hybridization across contact zones, being lower in the contact zone located on a topographically complex area. We highlight the importance of accounting for spatial environmental heterogeneity when studying evolutionary dynamics of hybrid zones.

Species versus within-species niches: a multi-modelling approach to assess range size of a spring-dwelling amphibian

Species Distribution Models (SDMs) can be used to estimate potential geographic ranges and derive indices to assess species conservation status. However, habitat-specialist species require fine-scale range estimates that reflect resource dependency. Furthermore, local adaptation of intraspecific lineages to distinct environmental conditions across ranges have frequently been neglected in SDMs. Here, we propose a multi-stage SDM approach to estimate the distributional range and potential area of occupancy (pAOO) of Neurergus kaiseri, a spring-dwelling amphibian with two climatically-divergent evolutionary lineages. We integrate both broad-scale climatic variables and fine-resolution environmental data to predict the species distribution while examining the performance of lineage-level versus species-level modelling on the estimated pAOO. Predictions of habitat suitability at the landscape scale differed considerably between evolutionary level models. At the landscape scale, spatial predictions derived from lineage-level models showed low overlap and recognised a larger amount of suitable habitats than species-level model. The variable dependency of lineages was different at the landscape scale, but similar at the local scale. Our results highlight the importance of considering fine-scale resolution approaches, as well as intraspecific genetic structure of taxa to estimate pAOO. The flexible procedure presented here can be used as a guideline for estimating pAOO of other similar species.

Phylogenomic inference of species and subspecies diversity in the Palearctic salamander genus Salamandra

The salamander genus Salamandra is widespread across Europe, North Africa, and the Near East and is renowned for its conspicuous and polymorphic colouration and diversity of reproductive modes. The phylogenetic relationships within the genus, and especially in the highly polymorphic species S. salamandra, have been very challenging to elucidate, leaving its real evolutionary history and classification at species and subspecies levels a topic of debate and contention. However, the distribution of diversity and species delimitation within the genus are critically important for identifying evolutionarily significant units for conservation and management, especially in light of threats posed by the pathogenic chytrid fungus Batrachochytrium salamandrivorans that is causing massive declines of S. salamandra populations in central Europe. Here, we conducted a phylogenomic analysis from across the taxonomic and geographic breadth of the genus Salamandra in its entire range. Bayesian, maximum likelihood and network-based phylogenetic analyses of up to 4905 ddRADseq-loci (294,300 nucleotides of sequence) supported the distinctiveness of all currently recognised species (Salamandra algira, S. atra, S. corsica, S. infraimmaculata, S. lanzai, and S. salamandra), and all five species for which we have multiple exemplars were confirmed as monophyletic. Within S. salamandra, two main clades can be distinguished: one clade with the Apenninic subspecies S. s. gigliolii nested within the Iberian S. s. bernardezi/fastuosa; and a second clade comprising all other Iberian, Central and East European subspecies. Our analyses revealed that some of the currently recognized subspecies of S. salamandra are paraphyletic and may require taxonomic revision, with the Central- and Eastern-European subspecies all being poorly differentiated at the analysed genomic markers. Salamandra s. longirostris - sometimes considered a separate species - was nested within S. salamandra, consistent with its subspecies status. The relationships identified within and between Salamandra species provide valuable context for future systematic and biogeographic studies, and help elucidate critical evolutionary units for conservation and taxonomy.

Pleistocene climate fluctuations drove demographic history of African golden wolves (Canis lupaster)

Pleistocene climate change impacted entire ecosystems throughout the world. In the northern hemisphere, the distribution of Arctic species expanded during glacial periods, while more temperate and mesic species contracted into climatic refugia, where isolation drove genetic divergence. Cycles of local cooling and warming in the Sahara region of northern Africa caused repeated contractions and expansions of savannah-like environments which connected mesic species isolated in refugia during interglacial times, possibly driving population expansions and contractions; divergence and geneflow in the associated fauna. Here, we use whole genome sequences of African golden wolves (Canis lupaster), a generalist mesopredator with a wide distribution in northern Africa to estimate their demographic history and past episodes of geneflow. We detect a correlation between divergence times and cycles of increased aridity-associated Pleistocene glacial cycles. A complex demographic history with responses to local climate change in different lineages was found, including a relict lineage north of the High Atlas Mountains of Morocco that has been isolated for more than 18,000 years, possibly a distinct ecotype.

Phylogeographic analyses point to long-term survival on the spot in micro-endemic Lycian salamanders

Lycian salamanders (genus Lyciasalamandra) constitute an exceptional case of micro-endemism of an amphibian species on the Asian Minor mainland. These viviparous salamanders are confined to karstic limestone formations along the southern Anatolian coast and some islands. We here study the genetic differentiation within and among 118 populations of all seven Lyciasalamandra species across the entire genus’ distribution. Based on circa 900 base pairs of fragments of the mitochondrial 16SrDNA and ATPase genes, we analysed the spatial haplotype distribution as well as the genetic structure and demographic history of populations. We used 253 geo-referenced populations and CHELSA climate data to infer species distribution models which we projected on climatic conditions of the Last Glacial Maximum (LGM). Within all but one species, distinct phyloclades were identified, which only in parts matched current taxonomy. Most haplotypes (78%) were private to single populations. Sometimes population genetic parameters showed contradicting results, although in several cases they indicated recent population expansion of phyloclades. Climatic suitability of localities currently inhabited by salamanders was significantly lower during the LGM compared to recent climate. All data indicated a strong degree of isolation among Lyciasalamandra populations, even within phyloclades. Given the sometimes high degree of haplotype differentiation between adjacent populations, they must have survived periods of deteriorated climates during the Quaternary on the spot. However, the alternative explanation of male biased dispersal combined with a pronounced female philopatry can only be excluded if independent nuclear data confirm this result.

A new subspecies of African fire salamander Salamandra algira (Urodela, Salamandridae) from the Middle Atlas Mountains, Morocco

A new subspecies within the Salamandra algira species complex from north-western Africa is described. Previous molecular analysis showed that the populations of S. algira splendens from north-western Morocco consisted of two well supported clades: clade 1 distributed in the Rif Mountains, from Chefchaouen (type locality) to Al Hoceima, and clade 2, located southern from clade 1 being isolated in the northern and central Middle Atlas Mountains. Clade 2 is herein described as a distinct subspecies: Salamandra algira atlantica ssp. nov. based on morphological data, allopatric range and molecular divergence. This new subspecies shows an uncorrected pairwise distance of 0.0265 from clade 1 based on cytochrome b DNA sequences. Salamandra algira atlantica ssp. nov. is a slender and large sized salamander with a highly variable colouration pattern. It can be distinguished from S. algira splendens by the greater proportion of coral red in the background colouration, being the only known subspecies of S. algira in which coral red can exceed the proportion of black. Variable number (0-5) of yellow to golden yellow dorsal blotches, but usually in lower numbers than the nominotypical subspecies. Salamandra algira atlantica ssp. nov. inhabits subhumid to humid forests and karstic systems at mid to high elevations. We briefly discuss the phylogenetic and taxonomic issues among the genus Salamandra which encompasses more valid species than currently recognised.