The Alboran volcanic-arc modulated the Messinian faunal exchange and salinity crisis

Late Miocene transformation of Mediterranean Sea biodiversity

Understanding deep-time marine biodiversity change under the combined effects of climate and connectivity changes is fundamental for predicting the impacts of modern climate change in semi-enclosed seas. We quantify the Late Miocene-Early Pliocene [11.63 to 3.6 million years (Ma)] taxonomic diversity of the Mediterranean Sea for calcareous nannoplankton, dinocysts, foraminifera, ostracods, corals, molluscs, bryozoans, echinoids, fishes, and marine mammals. During this time, marine biota was affected by global climate cooling and the restriction of the Mediterranean's connection to the Atlantic Ocean that peaked with the Messinian salinity crisis. Although the net change in species richness from the Tortonian to the Zanclean varies by group, species turnover is greater than 30% in all cases, reflecting a high degree of reorganization of the marine ecosystem after the crisis. The results show a clear perturbation already in the pre-evaporitic Messinian (7.25 to 5.97 Ma), with patterns differing among groups and subbasins.

Assessing citizen science data quality for bird monitoring in the Iberian Peninsula

Citizen science data on biodiversity has experienced significant growth, largely driven by advancements in technology that facilitate data sharing. In recent years, mobile applications have provided a substantial boost to both the collection and sharing of this data. While this accessible information is undoubtedly valuable, we must consider the numerous biases present in this data when used for high-quality research. In this study, we analyse citizen science data for the birds of the Iberian Peninsula, comprising over 23 million unique records after filtering for duplicates (i.e., instances where the same observation was uploaded more than once). Using a 10 × 10 km square grid, we present information on well-surveyed cells (completeness) as well as temporal, taxonomic, geographical, and land use coverages. We found that the completeness of information is generally high, with better coverage around densely populated areas such as major cities and coastal regions, as well as popular birding destinations, which are frequently visited. The Mediterranean ecoregion and wetlands exhibit the highest levels of surveying. Furthermore, we observed an increase in temporal coverage since the 1980s and broad taxonomic coverage across all bird orders in the Iberian region. Our results underscore the utility of citizen science for many locations, as expressed in 10 × 10 km cells. However, they also highlight the inadequate data completeness across part of the territory, particularly in forested or sparsely inhabited areas. These findings not only identify cells suitable for bird diversity or conservation studies but also indicate areas where citizen-driven bird recording efforts should be encouraged.

Novel phylogenomic inference and 'Out of Asia' biogeography of cobras, coral snakes and their allies

Estimation of evolutionary relationships among lineages that rapidly diversified can be challenging, and, in such instances, inaccurate or unresolved phylogenetic estimates can lead to erroneous conclusions regarding historical geographical ranges of lineages. One example underscoring this issue has been the historical challenge posed by untangling the biogeographic origin of elapoid snakes, which includes numerous dangerously venomous species as well as species not known to be dangerous to humans. The worldwide distribution of this lineage makes it an ideal group for testing hypotheses related to historical faunal exchanges among the many continents and other landmasses occupied by contemporary elapoid species. We developed a novel suite of genomic resources, included worldwide sampling, and inferred a robust estimate of evolutionary relationships, which we leveraged to quantitatively estimate geographical range evolution through the deep-time history of this remarkable radiation. Our phylogenetic and biogeographical estimates of historical ranges definitively reject a lingering former 'Out of Africa' hypothesis and support an 'Out of Asia' scenario involving multiple faunal exchanges between Asia, Africa, Australasia, the Americas and Europe.

Spatial genetic structure in European marbled newts revealed with target enrichment by sequence capture

European marbled newts come in two species that have abutting ranges. The northern species, Triturus marmoratus, is found in France and the northern part of the Iberian Peninsula, whereas the southern species, T. pygmaeus, is found in the southwestern corner of the Iberian Peninsula. We study the intraspecific genetic differentiation of the group because morphological data show geographical variation and because the Iberian Peninsula is a recognized center of speciation and intraspecific genetic diversity for all kinds of organisms, amphibians included. We use target enrichment by sequence capture to generate c. 7 k nuclear DNA markers. We observe limited genetic exchange between the species, which confirms their distinctiveness. Both species show substantial genetic structuring that is only in part mirrored by morphological variation. Genetically differentiated groups are found in the south (T. marmoratus) and west (T. pygmaeus) of the species ranges. Our observations highlight the position of the Iberian Peninsula as a hotspot for genetic differentiation.

Piecing the barcoding puzzle of Palearctic water frogs (Pelophylax) sheds light on amphibian biogeography and global invasions

Palearctic water frogs (genus Pelophylax) are an outstanding model in ecology and evolution, being widespread, speciose, either threatened or threatening to other species through biological invasions, and capable of siring hybrid offspring that escape the rules of sexual reproduction. Despite half a century of genetic research and hundreds of publications, the diversity, systematics and biogeography of Pelophylax still remain highly confusing, in no small part due to a lack of correspondence between studies. To provide a comprehensive overview, we gathered >13,000 sequences of barcoding genes from >1700 native and introduced localities and built multigene mitochondrial (~17 kb) and nuclear (~10 kb) phylogenies. We mapped all currently recognized taxa and their phylogeographic lineages (>40) to get a grasp on taxonomic issues, cyto-nuclear discordances, the genetic makeup of hybridogenetic hybrids, and the origins of introduced populations. Competing hypotheses for the molecular calibration were evaluated through plausibility tests, implementing a new approach relying on predictions from the anuran speciation continuum. Based on our timetree, we propose a new biogeographic paradigm for the Palearctic since the Paleogene, notably by attributing a prominent role to the dynamics of the Paratethys, a vast paleo-sea that extended over most of Europe. Furthermore, our results show that distinct marsh frog lineages from Eastern Europe, the Balkans, the Near East, and Central Asia (P. ridibundus ssp.) are naturally capable of inducing hybridogenesis with pool frogs (P. lessonae). We identified 14 alien lineages (mostly of P. ridibundus) over ~20 areas of invasions, especially in Western Europe, with genetic signatures disproportionally pointing to the Balkans and Anatolia as the regions of origins, in line with exporting records of the frog leg industry and the stocks of pet sellers. Pelophylax thus emerges as one of the most invasive amphibians worldwide, and deserves much higher conservation concern than currently given by the authorities fighting biological invasions.

Oceanic currents maintain the genetic structure of non-marine coastal taxa in the western Mediterranean Sea

Coastal habitats are amongst the most dynamic on Earth, due to their simultaneous exposure to terrestrial, oceanic and atmospheric processes. Coastal taxa are therefore often ecologically specialised and adapted to withstand frequent shifts in sea level, wave exposure, temperature or salinity. This specialisation often resulting in significant cryptic diversity. Previous molecular studies have suggested that genetic differentiation in non-marine coastal organisms may be influenced by oceanic currents and fronts, but the extent to which such processes affect dispersal and evolution of such taxa remains unclear. Here we explore whether population genetic structure in two supralittoral rockpool beetle species (genus Ochthebius) can be predicted from the general circulation pattern of the marine currents and associated oceanic fronts. We simulated dispersal using a Lagrangian particle tracking model and compared this with population genetic structure inferred from COI (mitochondrial) and wingless (nuclear) genes applying linear models and Mantel tests. We show that a biophysical model based on oceanic currents and fronts in the western Mediterranean Sea is a much better predictor of observed population genetic structure than isolation by distance in both species. Our results show that oceanic processes, besides shaping contemporary population connectivity in fully marine organisms, also exert a meaningful influence on terrestrially-derived coastal taxa such as supralittoral rockpool beetles - the first time this mode of dispersal has been demonstrated in an insect.

Evidence for a developing plate boundary in the western Mediterranean

The current diffuse-strain model of the collision between Africa and Eurasia in the western Mediterranean predicts a broad region with deformation distributed among numerous faults and moderate-magnitude seismicity. However, the model is untested because most deformation occurs underwater, at poorly characterized faults of undetermined slip. Here we assess the diffuse-strain model analysing two active offshore fault systems associated with the most prominent seafloor relief in the region. We use pre-stack depth migrated seismic images to estimate, for the first time, the total Plio-Holocene slip of the right-lateral Yusuf and reverse Alboran Ridge structurally linked fault system. We show that kinematic restoration of deformational structures predicts a slip of 16 ± 4.7 km for the Alboran Ridge Fault and a minimum of 12 km for the Yusuf Fault. Thus, this fault system forms a well-defined narrow plate boundary that has absorbed most of the 24 ± 5 km Plio-Holocene Africa-Eurasia convergence and represents an underappreciated hazard.

Conventional models propose multiple fault systems across a diffuse deformation zone absorbing plate convergence in the western Mediterranean. Here the authors show new data supporting the active development of a single plate boundary fault system, representing an underappreciated seismic and tsunami hazard.

The Strait of Gibraltar is an ineffective palaeogeographic barrier for some flightless darkling beetles (Coleoptera: Tenebrionidae: Pimelia)

The geographic distribution of a species is shaped by its biology and by environmental and palaeogeographic factors that interact at different spatial-temporal scales, which leads to distributions and diversification patterns observed between and within lineages. The darkling beetle genus Pimelia has been diversifying for more than 31.2 Mya showing different colonization patterns after the opening of the Gibraltar Strait 5 Mya. Three of the 14 subgenera of Pimelia have populations on both sides of the Strait. Through extensive sampling and the analysis of three molecular markers, we determine levels of intra- and interspecific genetic variation, identify evolutionary lineages in subgenera, estimate their temporal origin and distribution ranges and discuss the historical basis for the geographic and diversification patterns of Pimelia around the Strait. This single geographical feature acted both as a barrier and as a dispersal route for different Pimelia species. The Strait has represented a strong barrier for the subgenus Magrebmelia since the Middle Miocene. However, the subgenera Amblyptera and Amblypteraca share repetitive signatures of post-Messinian colonization across the Strait, possibly driven by stochastic or ‘catastrophic’ events such as tsunamis. Our demographic analyses support Wallace’s hypothesis on insect dispersal stochasticity. Some taxonomic changes, including the designation of a lectotype for Pimelia maura, are also proposed.

Biogeographic and demographic history of the Mediterranean snakes Malpolon monspessulanus and Hemorrhois hippocrepis across the Strait of Gibraltar

BACKGROUND

The contribution of North Africa to the assembly of biodiversity within the Western Palaearctic is still poorly documented. Since the Miocene, multiple biotic exchanges occurred across the Strait of Gibraltar, underlying the high biogeographic affinity between the western European and African sides of the Mediterranean basin. We investigated the biogeographic and demographic dynamics of two large Mediterranean-adapted snakes across the Strait and assess their relevance to the origin and diversity patterns of current European and North African populations.

RESULTS

We inferred phylogeographic patterns and demographic history of M. monspessulanus and H. hippocrepis, based on range-wide multilocus data, combined with fossil data and species distribution modelling, under present and past bioclimatic envelopes. For both species we identified endemic lineages in the High Atlas Mountains (Morocco) and in eastern Iberia, suggesting their persistence in Europe during the Pleistocene. One lineage is shared between North Africa and southern Iberia and likely spread from the former to the latter during the sea-level low stand of the last glacial stage. During this period M. monspessulanus shows a sudden demographic expansion, associated with increased habitat suitability in North Africa. Lower habitat suitability is predicted for both species during interglacial stages, with suitable areas restricted to coastal and mountain ranges of Iberia and Morocco. Compiled fossil data for M. monspessulanus show a continuous fossil record in Iberia at least since the Pliocene and throughout the Pleistocene.

CONCLUSIONS

The previously proposed hypothesis of Pleistocene glacial extinction of both species in Europe is not supported based on genetic data, bioclimatic envelopes models, and the available fossil record. A model of range retraction to mountain refugia during arid periods and of glacial expansion (demographic and spatial) associated to an increase of Mediterranean habitats during glacial epochs emerges as a general pattern for mesic vertebrates in North Africa. Moreover, the phylogeographic pattern of H. hippocrepis conforms to a well-established biogeographic partition between western and eastern Maghreb.

Late Miocene megalake regressions in Eurasia

The largest megalake in the geological record formed in Eurasia during the late Miocene, when the epicontinental Paratethys Sea became tectonically-trapped and disconnected from the global ocean. The megalake was characterized by several episodes of hydrological instability and partial desiccation, but the chronology, magnitude and impacts of these paleoenvironmental crises are poorly known. Our integrated stratigraphic study shows that the main desiccation episodes occurred between 9.75 and 7.65 million years ago. We identify four major regressions that correlate with aridification events, vegetation changes and faunal turnovers in large parts of Europe. Our paleogeographic reconstructions reveal that the Paratethys was profoundly transformed during regression episodes, losing ~ 1/3 of the water volume and ~ 70% of its surface during the most extreme events. The remaining water was stored in a central salt-lake and peripheral desalinated basins while vast regions (up to 1.75 million km²) became emergent land, suitable for development of forest-steppe landscapes. The partial megalake desiccations match with climate, food-web and landscape changes throughout Eurasia, although the exact triggers and mechanisms remain to be resolved.

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.

Patterns of morphological diversification in giant Berberomeloe blister beetles (Coleoptera: Meloidae) reveal an unexpected taxonomic diversity concordant with mtDNA phylogenetic structure

Delimiting species boundaries is a complex challenge usually hindered by overlooked morphological diversification or misinterpretation of geographically structured phenotypic variability. Independent molecular data are extremely useful to characterize and understand such morphological diversity. Morphological and molecular variability of the non-phoretic and apterous, widely distributed, giant blister beetles of the genus Berberomeloe, were investigated within and between lineages across most of the distributional range of the genus. We used two mtDNA gene fragments to characterize genetic variability and to produce a time-calibrated phylogeny of the genus. Our results reveal several mitochondrial lineages, allopatrically, parapatrically and sympatrically distributed. Most clades are not distinguishable between each other based on morphometrics. However, no morphometric overlap is observed between two closely related clades, one of them occurring in sympatry with a distantly congeneric species (B. insignis), suggesting that sympatry could trigger morphological diversification. Although most species share a morphometric space, they can be morphologically identified by a combination of easily observed characteristic qualitative features. Based on the concordance between mtDNA clades and morphological units, we describe six new species of Berberomeloe (B. castuo sp. nov., B. comunero sp. nov., B. indalo sp. nov, B. yebli sp. nov., B. payoyo sp. nov. and B. tenebrosus sp. nov.), revalidate two taxa (B. maculifrons comb. nov. and B. laevigatus comb. nov.) and redefine B. majalis.

Reconstructing evolution at the community level: A case study on Mediterranean amphibians

Reconstructing reliable timescales for species evolution is an important and indispensable goal of modern biogeography. However, many factors influence the estimation of divergence times, and uncertainty in the inferred time trees remains a major issue that is often insufficiently acknowledged. We here focus on a fundamental problem of time tree analysis: the combination of slow-evolving (nuclear DNA) and fast-evolving (mitochondrial DNA) markers in a single time tree. Both markers differ in their suitability to infer divergences at different time scales (the 'genome-timescale-dilemma'). However, strategies to infer shallow and deep divergences in a single time tree have rarely been compared empirically. Using Mediterranean amphibians as model system that is exceptional in its geographic and taxonomic completeness of available genetic information, we analyze 202 lineages of western Palearctic amphibians across the entire Mediterranean region. We compiled data of four nuclear and five mitochondrial genes and used twelve fossil calibration points widely acknowledged for amphibian evolution. We reconstruct time trees for an extensive lineage-level data set and compare the performances of the different trees: the first tree is based on primary fossil calibration and mitochondrial DNA, while the second tree is based on a combination of primary fossil and on secondary calibrations taken from a nuclear tree using mitochondrial DNA (two-step protocol). Focusing on a set of nodes that are most likely explained by vicariance, we statistically compare the reconstructed alternative time trees by applying a biogeographical plausibility test. Our two-step protocol outperformed the alternative approach in terms of spatial and temporal plausibility. It allows us to infer scenarios for Mediterranean amphibian evolution in eight geographic provinces. We identified several tectonic and climatic events explaining the majority of Mediterranean amphibian divergences, with Plio-Pleistocene climatic fluctuations being the dominant driver for intrageneric evolution. However, often more than one event could be invoked for a specific split. We give recommendations for the use of secondary calibrations in future molecular clock analyses at the community level.