Complex hybridization patterns in European pond turtles (Emys orbicularis) in the Pyrenean Region

Hybrid zones are natural laboratories allowing insights in genetic processes like lineage diversification, speciation and introgression. Using large sampling, 15 microsatellite loci and a mitochondrial marker, we examined the Pyrenean contact zone of three pond turtle taxa (Emys orbicularis orbicularis, E. o. galloitalica, E. o. occidentalis). The Pyrenees are a biogeographically important region separating many lineages endemic to the Iberian Peninsula from their Western European counterparts. We discovered limited admixture, reflecting a complex biogeographic scenario. Simulations using Approximate Bayesian Computing supported that E. o. orbicularis invaded the Iberian Peninsula in the Holocene, circumventing the Pyrenees along the Mediterranean coast, and hybridized in the northern peninsula with the local coastal subspecies galloitalica, and to a lesser extent, with occidentalis. While E. o. occidentalis, and in particular E. o. orbicularis, expanded their ranges considerably during Holocene warming, E. o. galloitalica remained largely confined to its former Iberian refuge. Admixture among the three taxa is surprisingly low, and a future taxonomic investigation that includes the unstudied subspecies of E. orbicularis from North Africa, Eastern Europe and Asia has to determine whether their current status properly reflects their evolutionary divergence or whether certain taxa should be regarded as full species

Where are you from, stranger? The enigmatic biogeography of North African pond turtles (Emys orbicularis) .

Abstract The European pond turtle (Emys orbicularis) is a Nearctic element in the African fauna and thought to have invaded North Africa from the Iberian Peninsula. All North African populations are currently identified with the subspecies E. o. occidentalis. However, a nearly range-wide sampling in North Africa used for analyses of mitochondrial and microsatellite DNA provides evidence that only Moroccan populations belong to this taxon, while eastern Algerian and Tunisian pond turtles represent an undescribed distinct subspecies. These two taxa are most closely related to E. o. galloitalica with a native distribution along the Mediterranean coast of northern Spain through southern France to western and southern Italy. This group is sister to a clade comprising several mitochondrial lineages and subspecies of E. orbicularis from Central and Eastern Europe plus Asia, and the successive sisters are E. o. hellenica and E. trinacris. Our results suggest that E. orbicularis has been present in North Africa longer than on the Iberian Peninsula and that after an initial invasion of North Africa by pond turtles from an unknown European source region, there was a phase of diversification in North Africa, followed by a later re-invasion of Europe by one of the African lineages. The differentiation of pond turtles in North Africa parallels a general phylogeographic paradigm in amphibians and reptiles, with deeply divergent lineages in the western and eastern Maghreb. Acknowledging their genetic similarity, we propose to synonymize the previously recognized Iberian subspecies E. o. fritzjuergenobsti with E. o. occidentalis sensu stricto. The seriously imperiled Moroccan populations of E. o. occidentalis represent two Management Units different in mitochondrial haplotypes and microsatellite markers. The conservation status of eastern Algerian pond turtles is unclear, while Tunisian populations are endangered. Considering that Algerian and Tunisian pond turtles represent an endemic taxon, their situation throughout the historical range should be surveyed to establish a basis for conservation measures

No signs of inbreeding despite long-term isolation and habitat fragmentation in the critically endangered Montseny brook newt (Calotriton arnoldi)

Endemic species with restricted geographic ranges potentially suffer the highest risk of extinction. If these species are further fragmented into genetically isolated subpopulations, the risk of extinction is elevated. Habitat fragmentation is generally considered to have negative effects on species survival, despite some evidence for neutral or even positive effects. Typically, non-negative effects are ignored by conservation biology. The Montseny brook newt (Calotriton arnoldi) has one of the smallest distribution ranges of any European amphibian (8 km2) and is considered critically endangered by the International Union for Conservation of Nature. Here we apply molecular markers to analyze its population structure and find that habitat fragmentation owing to a natural barrier has resulted in strong genetic division of populations into two sectors, with no detectable migration between sites. Although effective population size estimates suggest low values for all populations, we found low levels of inbreeding and relatedness between individuals within populations. Moreover, C. arnoldi displays similar levels of genetic diversity to its sister species Calotriton asper, from which it separated around 1.5 million years ago and which has a much larger distribution range. Our extensive study shows that natural habitat fragmentation does not result in negative genetic effects, such as the loss of genetic diversity and inbreeding on an evolutionary timescale. We hypothesize that species in such conditions may evolve strategies (for example, special mating preferences) to mitigate the effects of small population sizes. However, it should be stressed that the influence of natural habitat fragmentation on an evolutionary timescale should not be conflated with anthropogenic habitat loss or degradation when considering conservation strategies

Evidence of positive selection associated with placental loss in tiger sharks

Background: All vertebrates initially feed their offspring using yolk reserves. In some live-bearing species these yolk reserves may be supplemented with extra nutrition via a placenta. Sharks belonging to the Carcharhinidae family are all live-bearing, and with the exception of the tiger shark (Galeocerdo cuvier), develop placental connections after exhausting yolk reserves. Phylogenetic relationships suggest the lack of placenta in tiger sharks is due to secondary loss. This represents a dramatic shift in reproductive strategy, and is likely to have left a molecular footprint of positive selection within the genome. Results: We sequenced the transcriptome of the tiger shark and eight other live-bearing shark species. From this data we constructed a time-calibrated phylogenetic tree estimating the tiger shark lineage diverged from the placental carcharhinids approximately 94 million years ago. Along the tiger shark lineage, we identified five genes exhibiting a signature of positive selection. Four of these genes have functions likely associated with brain development (YWHAE and ARL6IP5) and sexual reproduction (VAMP4 and TCTEX1D2). Conclusions: Our results indicate the loss of placenta in tiger sharks may be associated with subsequent adaptive changes in brain development and sperm production

Physical and ecological isolation contribute to maintain genetic differentiation betweenfire salamander subspecies

Landscape features shape patterns of geneflow among populations, ultimately determining where taxa lay along thecontinuum between panmixia to complete reproductive isolation. Geneflow can be restricted, leading to populationdifferentiation in two non-exclusive ways:“physical isolation”, in which geographic distance in combination with thelandscape features restricts movement of individuals promoting genetic drift, and“ecological isolation”, in which adaptivemechanisms constrain geneflow between different environments via divergent natural selection. In central Iberia, twofiresalamander subspecies occur in parapatry across elevation gradients along the Iberian Central System mountains, while inthe 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 increasingdifferentiation between populations. However, across the Iberian Central System, we found strong support for a significantcontribution of ecological isolation, with low genetic differentiation in environmentally homogeneous areas, but highdifferentiation across sharp transitions in precipitation seasonality. These patterns are consistent with a significantcontribution of ecological isolation in restricting geneflow among subspecies. Overall, our results suggest that ecologicaldivergence contributes to reduce genetic admixture, creating an opportunity for lineages to follow distinct evolutionary trajectories.GV-A was supported by FCT–Foundation for Science and Technology (CEECIND/00937/2018). This research was supported by the European Science Foundation (Frontiers of Speciation Research, Exchange grant 3318), and by the European Commission (Synthesys grant ES-TAF-1486), granted to RJP. Partial funds were additionally provided by grants EVOVIV: PTDC/BIA-EVF/3036/2012 (FCT, Portugal) to GV-A, and CGL2017-83131-P (FEDER/Ministerio de Ciencia, Innovación y Universidades–Agencia Estatal de Investigación, Spain) to IMS.Peer reviewe

Evolutionary History and Not Heterochronic Modifications Associated with Viviparity Drive Head Shape Differentiation in a Reproductive Polymorphic Species, Salamandra salamandra

Identifying the evolutionary processes that underlie morphological variation at the intraspecific level is cornerstone for understanding the drivers of phenotypic diversity at higher macro-evolutionary scales. The fire salamander, Salamandra salamandra, exhibits exceptional intraspecific variation in multiple phenotypic traits (i.e. body size, head shape, coloration, reproductive modes). Pueriparity (females laying fully metamorphosed juveniles) in S. salamandra entails modifications during embryonic development in comparison to larviparity (females laying aquatic larvae), which is the ancestral reproductive mode. These heterochronic modifications involve a general acceleration of development and mainly focus on cephalic structures to facilitate intrauterine active feeding, which might impact head shape in the adult stage. In the present study, we (i) describe the main features of head shape variation in adults of the two distinct subspecies of Salamandra salamandra that independently evolved to pueriparity, and (ii) explore the morphological consequences of developmental and functional changes related to this major evolutionary shift. Our results show that evolutionary history, and not reproductive mode, is the main driver of head shape variation in S. salamandra. These results suggest different evolutionary processes acting differentially on each subspecies, at least at the adult stage. The present study highlights the importance of comparative studies integrating evolutionary histories and ontogenetic trajectories to explore the different sources of observed morphological diversification.This work is funded by the Ministerio de Economía y Competitividad (Grants Nos. CGL2012-40246-C02-02 and CGL2017-86924-P); by FEDER funds through the Operational Programme for Competitiveness Factors – COMPETE (FCOMP-01-0124-FEDER-028325 and POCI-01- 0145-FEDER-006821); and by National Funds through FCT – Foundation for Science and Technology (EVOVIV: PTDC/BIA-EVF/3036/2012; SALOMICS: PTDC/BIA-EVL/28475/2017). L.A.-R. was supported by a FPU grant (FPU14/03015) from the Ministerio de Educación, Cultura y Deporte (MECD, Spain) and and G.V.-A. and A.K. by IF contracts (IF/01425/2014 and IF/00641/2014, respectively). from Fundação para a Ciência e a Tecnologia (FCT, Portugal)

Challenges for assessing vertebrate diversity in turbid Saharan water-bodies using environmental DNA

The Sahara desert is the largest warm desert in the world and a poorly explored area. Small water-bodies occur across the desert and are crucial habitats for vertebrate biodiversity. Environmental DNA (eDNA) is a powerful tool for species detection and is being increasingly used to conduct biodiversity assessments. However, there are a number of difficulties with sampling eDNA from such turbid water-bodies and it is often not feasible to rely on electrical tools in remote desert environments. We trialled a manually powered filtering method in Mauritania, using pre-filtration to circumvent problems posed by turbid water in remote arid areas. From nine vertebrate species expected in the water-bodies, four were detected visually, two via metabarcoding, and one via both methods. Difficulties filtering turbid water led to severe constraints, limiting the sampling protocol to only one sampling point per study site, which alone may largely explain why many of the expected vertebrate species were not detected. The amplification of human DNA using general vertebrate primers is also likely to have contributed to the low number of taxa identified. Here we highlight a number of challenges that need to be overcome to successfully conduct metabarcoding eDNA studies for vertebrates in desert environments in Africa

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