Deep roots of the Messinian salinity crisis

Founder events and subsequent genetic bottlenecks underlie karyotype evolution in the Ibero-North African endemic Carex helodes

BACKGROUND AND AIMS

Despite chromosomal evolution being one of the major drivers of diversification in plants, we do not yet have a clear view of how new chromosome rearrangements become fixed within populations, which is a crucial step forward for understanding chromosomal speciation.

METHODS

In this study, we test the role of genetic drift in the establishment of new chromosomal variants in the context of hybrid dysfunction models of chromosomal speciation. We genotyped 178 individuals from seven populations (plus 25 seeds from one population) across the geographical range of Carex helodes (Cyperaceae). We also characterized karyotype geographical patterns of the species across its distribution range. For one of the populations, we performed a detailed study of the fine-scale, local spatial distribution of its individuals and their genotypes and karyotypes.

KEY RESULTS

Synergistically, phylogeographical and karyotypic evidence revealed two main genetic groups: southwestern Iberian Peninsula vs. northwestern African populations; and within Europe our results suggest a west-to-east expansion with signals of genetic bottlenecks. Additionally, we inferred a pattern of descending dysploidy, plausibly as a result of a west-to-east process of post-glacial colonization in Europe.

CONCLUSIONS

Our results give experimental support to the role of geographical isolation, drift and inbreeding in the establishment of new karyotypes, which is key in the speciation models of hybrid dysfunction.

Phylogenomic and population genomic analyses reveal the spatial-temporal dynamics of diversification of the Nigella arvensis complex (Ranunculaceae) in the Aegean archipelago

The continental-shelf islands of the Aegean Sea provide an ideal geographical setting for evolutionary-biogeographical studies but disentangling the relationships between palaeogeographical history and the times, orders of modes of taxon divergence is not straightforward. Here, we used phylogenomic and population genomic approaches, based on orthologous gene sequences and transcriptome-derived SNP data, to reconstruct the spatial-temporal evolution of the Aegean Nigella arvensis complex (Ranunculaceae; 11 out of 12 taxa). The group's early diversification in the Early/Mid-Pliocene (c. 3.77 Mya) resulted in three main lineages (Greek mainland vs. central Aegean + Turkish mainland/eastern Aegean islands), while all extant taxa are of Late Plio-/Early Pleistocene origin (c. 3.30-1.59 Mya). Demographic modelling of the outcrossing taxa uncovered disparate modes of (sub)speciation, including divergence with gene flow on the Greek mainland, para- or peripatric diversification across eastern Aegean islands, and a 'mixing-isolation-mixing (MIM)' mode of subspeciation in the Cyclades. The two selfing species (N. stricta, N. doerfleri) evolved independently from the outcrossers. Present-day island configurations are clearly insufficient to explain the spatial-temporal history of lineage diversification and modes of (sub)speciation in Aegean Nigella. Moreover, our identification of positively selected genes in almost all taxa calls into question that this plant group represents a case of 'non-adaptive' radiation. Our study revealed an episodic diversification history of the N. arvensis complex, giving new insight into the modes and drivers of island speciation and adaption across multiple spatiotemporal scales.

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.

Faecal Microbiota Divergence in Allopatric Populations of Podarcis lilfordi and P. pityusensis, Two Lizard Species Endemic to the Balearic Islands

Gut microbial communities provide essential functions to their hosts and are known to influence both their ecology and evolution. However, our knowledge of these complex associations is still very limited in reptiles. Here we report the 16S rRNA gene faecal microbiota profiles of two lizard species endemic to the Balearic archipelago (Podarcis lilfordi and P. pityusensis), encompassing their allopatric range of distribution through a noninvasive sampling, as an alternative to previous studies that implied killing specimens of these IUCN endangered and near-threatened species, respectively. Both lizard species showed a faecal microbiome composition consistent with their omnivorous trophic ecology, with a high representation of cellulolytic bacteria taxa. We also identified species-specific core microbiota signatures and retrieved lizard species, islet ascription, and seasonality as the main factors in explaining bacterial community composition. The different Balearic Podarcis populations are characterised by harbouring a high proportion of unique bacterial taxa, thus reinforcing their view as unique and divergent evolutionary entities.

The story of a rock-star: multilocus phylogeny and species delimitation in the starred or roughtail rock agama, Laudakia stellio (Reptilia: Agamidae)

Situated at the junction of three continents, Europe, Asia and Africa, the Eastern Mediterranean is an ideal region to study the effects of palaeogeography, ecology and long human presence on animal evolution. Laudakia stellio (Squamata: Agamidae) is found across this region and offers an excellent opportunity for such studies. The high morphological variation across their range suggests that these lizards might represent a species complex. This is the first study exploring their evolutionary history, using molecular markers and individuals from all described subspecies. We employed the latest phylogenetic and species-delimitation methods to identify all distinct evolutionary lineages, their genetic variation and divergence times. The phenotypical diversity of L. stellio matches its genetic differentiation: almost all subspecies correspond to well-supported retrieved subclades and additional distinct lineages representing intermediate morphs have been retrieved. ‘Laudakia stellio’ represents three distinct evolutionary entities that diverged during the Plio-Pleistocene transition, which we propose as distinct species. One includes Greek and Turkish populations, as well as cryptic Anatolian lineages. The second comprises all other Near East populations and the third is endemic to Cyprus. Our results indicate a role of humans in shaping present distribution patterns, and highlight the importance of the Aegean, Anatolia and the Levant as glacial refugia and diversity hotspots.

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.

Population genomics of wall lizards reflects the dynamic history of the Mediterranean Basin

The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan Peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, which were largely discordant with the phylogenetic relationship of mitochondrial DNA. The most recent common ancestor of extant P. muralis was likely distributed in the Italian Peninsula, and experienced an “Out-of-Italy” expansion following the Messinian salinity crisis (∼5 Mya), resulting in the differentiation into the extant lineages on the Iberian, Italian, and Balkan Peninsulas. Introgression analysis revealed that both inter- and intraspecific gene flows have been pervasive throughout the evolutionary history of P. muralis. For example, the Southern Italy lineage has a hybrid origin, formed through admixture between the Central Italy lineage and an ancient lineage that was the sister to all other P. muralis. More recent genetic differentiation is associated with the onset of the Quaternary glaciations, which influenced population dynamics and genetic diversity of contemporary lineages. These results demonstrate the pervasive role of Mediterranean geology and climate for the evolutionary history and population genetic structure of extant species.

The roles of possible geographic barriers and geological events on the phylogeographic structure of the Eastern broad toothed field mouse (Apodemus mystacinus)

The Eastern broad toothed field mouse, Apodemus mystacinus, is a rodent species distributed in Turkey, the Middle East, and a few Aegean Islands. The aim of this study is to analyse the phylogeographic structure of A. mystacinus and possible causes of its differentiation, on the basis of mitochondrial and nuclear DNA sequences using a large number of new samples from Turkey. In this context, partial mitochondrial sequences of cytochrome b (Cytb), control region (D-loop) and a nuclear interphotoreceptor retinoid-binding protein (IRBP) gene were used to reveal the geographical differentiation among A. mystacinus populations and the validity of its subspecies. The estimated divergence times revealed that the first separation of A. mystacinus into three distinct groups (subspecies of A. mystacinus: A. m. mystacinus, A. m. smyrnensis, and A. m. euxinus) begun 0.641 Mya. The possible physical barriers in Anatolia such as high mountains and rivers could interrupt the gene flow between A. mystacinus populations. The results of the present study indicated that A. mystacinus might have used the high rocky areas along the Anatolian Diagonal as a dispersal way. Moreover, mitochondrial data in this study suggested for the first time that A. m. rhodius is synonymous with the nominative subspecies A. m. mystacinus.

Genetic hypervariability of a Northeastern Atlantic venomous rockfish

BACKGROUND

Understanding the interplay between climate and current and historical factors shaping genetic diversity is pivotal to infer changes in marine species range and communities' composition. A phylogeographical break between the Atlantic and the Mediterranean has been documented for several marine organisms, translating into limited dispersal between the two basins.

METHODS

In this study, we screened the intraspecific diversity of 150 individuals of the Madeira rockfish (Scorpaena maderensis) across its distributional range (seven sampling locations in the Atlantic and Mediterranean basins) using the mitochondrial control region and the nuclear S7 first intron.

RESULTS

The present work is the most comprehensive study done for this species, yielding no genetic structure across sampled locations and no detectable Atlantic-Mediterranean break in connectivity. Our results reveal deep and hyper-diverse bush-like genealogies with large numbers of singletons and very few shared haplotypes. The genetic hyper-diversity found for the Madeira rockfish is relatively uncommon in rocky coastal species, whose dispersal capability is limited by local oceanographic patterns. The effect of climate warming on the distribution of the species is discussed.

A new genus and species of Hydrobiidae Stimpson, 1865 (Caenogastropoda, Truncatelloidea) from Peloponnese, Greece

Minute caenogastropod brackish-water gastropods, formerly classified as Hydrobia, are important elements of the brackish-water fauna and were objects of intensive study for many years. Until now, five genera have been distinguished, most of them represented by a number of species, but rather indistinguishable without molecular data (cytochrome oxidase subunit I - COI). In the eastern Mediterranean region, they are still poorly studied. In this paper, we present a new species of "Hydrobia" from the brackish Moustos spring, Arkadia, eastern Peloponnese, Greece. The shell, protoconch, radula, female reproductive organs, and penis are described and illustrated, together with the molecular (COI) relationships with other hydrobiids. All data confirm that these snails represent a distinct taxon, which must be classified as a new species belonging to a new genus. The formal descriptions are given. The closest, sister taxon is Salenthydrobia Wilke, 2003. The molecularly estimated time of divergence, 5.75 ± 0.49 Mya, coincides with 5.33 Mya, which is the time of the Oligocene flooding that terminated the Messinian salinity crisis. During the latter period, brackish "Lago-Mare" habitats were most probably suitable for the last common ancestor of Salenthydrobia and the newly described genus. Later, the Pliocene flooding isolated the Apennine and Peloponnese populations, promoting speciation.

Fossil-calibrated time tree of Podarcis wall lizards provides limited support for biogeographic calibration models

Podarcis wall lizards are endemic to the Mediterranean Basin where they represent the predominant reptile group. Despite being extensively used as model organisms in evolutionary and ecological studies their phylogeny and historical biogeography are still incompletely resolved. Moreover, molecular clock calibrations used in wall lizard phylogeography are based on the assumption of vicariant speciation triggered by the abrupt Mediterranean Sea level rise at the end of the Messinian salinity crisis (MSC). However, the validity of this biogeographic calibration remains untested. In this study we inferred a robust time tree based on multilocus data and fossil calibrations using both gene concatenation and species-tree approaches and including models with gene-flow. We found five deeply divergent, geographically coherent, and well-supported clades comprising species from i) Iberian Peninsula and North Africa; ii) Western Mediterranean islands, iii) Sicilian and Maltese islands; and iv-v) Balkan region and Aegean islands. The mitochondrial tree shows some inconsistencies with the species tree that warrant future investigation. Diversification of main clades is estimated in a short time frame during the Middle Miocene and might have been associated with a period of global climate cooling with the establishment of a marked climatic zonation in Europe. Cladogenetic events within the main clades are scattered throughout the time tree, from the Late Miocene to the Early Pleistocene, suggesting that speciation events in wall lizards reflect a complex interplay between regional topography, climate and geological history rather than a shared major climatic or paleogeographic event. Our absolute time estimates, as well as a relative dating approach, demonstrate that the assumption of a causal link between sea-level rise at the end of the MSC and the diversification of many island endemics is not justified. This study reinforces the notion that multiple dispersal and vicariant events, at different time frames, are required to explain current allopatric distributions and to account for the historical assembly of Mediterranean biota, and cautions against the use of biogeographic calibrations based on the assumption of vicariance.

Polyploidy Expands the Range of Centaurium (Gentianaceae)

The Mediterranean region is one of the most important worldwide hotspots in terms of number of species and endemism, and multiple hypotheses have been proposed to explain how diversification occurred in this area. The contribution of different traits to the diversification process has been evaluated in different groups of plants. In the case of Centaurium (Gentianaceae), a genus with a center of diversity placed in the Mediterranean region, polyploidy seems to have been an important driver of diversification as more than half of species are polyploids. Moreover, ploidy levels are strongly geographically structured across the range of the genus, with tetraploids distributed towards more temperate areas in the north and hexaploids in more arid areas towards the south. We hypothesize that the diversification processes and biodiversity patterns in Centaurium are explained by the coupled formation of polyploid lineages and the colonization of different areas. A MCC tree from BEAST2 based on three nuclear DNA regions of a total of 26 taxa (full sampling, of 18 species and 8 subspecies) was used to perform ancestral area reconstruction analysis in "BioGeoBEARS." Chromosome evolution was analyzed in chromEvol and diversification in BAMM to estimate diversification rates. Our results suggest that two major clades diverged early from the common ancestor, one most likely in the western Mediterranean and the other in a widespread area including west and central Asia (but with high uncertainty in the exact composition of this widespread area). Most ancestral lineages in the western clade remained in or around the western Mediterranean, and dispersal to other areas (mainly northward and eastward), occurred at the tips. Contrarily, most ancestral lineages in the widespread clade had larger ancestral areas. Polyploidization events in the western clade occurred at the tips of the phylogeny (with one exception of a polyploidization event in a very shallow node) and were mainly tetraploid, while polyploidization events occurred in the widespread clade were at the tips and in an ancestral node of the phylogeny, and were mainly hexaploid. We show how ancestral diploid lineages remained in the area of origin, whereas recent and ancestral polyploidization could have facilitated colonization and establishment in other areas.

Phylogenetic Placement and Phylogeography of Large-Flowered Lotus Species (Leguminosae) Formerly Classified in Dorycnium: Evidence of Pre-Pleistocene Differentiation of Western and Eastern Intraspecific Groups

The Mediterranean region is a center of species and genetic diversity of many plant groups, which served as a source of recolonization of temperate regions of Eurasia in Holocene. We investigate the evolutionary history of species currently classified in Lotus sect. Bonjeanea in the context of the evolution of the genus Lotus as a whole, using phylogenetic, phylogeographic and dating analyses. Of three species of the section, L. rectus and L. hirsutus have wide Mediterranean distribution while L. strictus has a disjunctive range in Bulgaria, Turkey, Armenia, Eastern Kazakhstan, and adjacent parts of Russia and China. We used entire nuclear ribosomal ITS1-5.8S-ITS2 region (nrITS) and a plastid dataset (rps16 and trnL-F) to reconstruct phylogenetic relationships within Lotus with an extended representation of Bonjeanea group. We analyzed the phylogeographic patterns within each species based on the plastid dataset. For divergence time estimation, the nrITS dataset was analyzed. Our results confirmed the non-monophyletic nature of the section Bonjeanea. They indicate that Lotus is likely to have diverged about 15.87 (9.99-19.81) million years ago (Ma), which is much older than an earlier estimate of ca. 5.54 Ma. Estimated divergence ages within L. strictus, L. rectus, and L. hisrutus (6.1, 4.94, and 4.16 Ma, respectively) well predate the onset of the current type of Mediterranean climate. Our data suggest that relatively ancient geological events and/or climatic changes apparently played roles in early diversification of Lotus and its major clades, as well as in formation of phylogeographic patterns, in at least some species.

Geo-Climatic Changes and Apomixis as Major Drivers of Diversification in the Mediterranean Sea Lavenders (Limonium Mill.)

The Mediterranean realm, comprising the Mediterranean and Macaronesian regions, has long been recognized as one of the world's biodiversity hotspots, owing to its remarkable species richness and endemism. Several hypotheses on biotic and abiotic drivers of species diversification in the region have been often proposed but rarely tested in an explicit phylogenetic framework. Here, we investigate the impact of both species-intrinsic and -extrinsic factors on diversification in the species-rich, cosmopolitan Limonium, an angiosperm genus with center of diversity in the Mediterranean. First, we infer and time-calibrate the largest Limonium phylogeny to date. We then estimate ancestral ranges and diversification dynamics at both global and regional scales. At the global scale, we test whether the identified shifts in diversification rates are linked to specific geological and/or climatic events in the Mediterranean area and/or asexual reproduction (apomixis). Our results support a late Paleogene origin in the proto-Mediterranean area for Limonium, followed by extensive in situ diversification in the Mediterranean region during the late Miocene, Pliocene, and Pleistocene. We found significant increases of diversification rates in the "Mediterranean lineage" associated with the Messinian Salinity Crisis, onset of Mediterranean climate, Plio-Pleistocene sea-level fluctuations, and apomixis. Additionally, the Euro-Mediterranean area acted as the major source of species dispersals to the surrounding areas. At the regional scale, we infer the biogeographic origins of insular endemics in the oceanic archipelagos of Macaronesia, and test whether woodiness in the Canarian Nobiles clade is a derived trait linked to insular life and a biotic driver of diversification. We find that Limonium species diversity on the Canary Islands and Cape Verde archipelagos is the product of multiple colonization events followed by in situ diversification, and that woodiness of the Canarian endemics is indeed a derived trait but is not associated with a significant shift to higher diversification rates. Our study expands knowledge on how the interaction between abiotic and biotic drivers shape the uneven distribution of species diversity across taxonomic and geographical scales.

New approaches to species delimitation and population structure of anthozoans: Two case studies of octocorals using ultraconserved elements and exons

As coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological variation and slowly evolving molecular markers confound species identification. New approaches to species delimitation in corals are needed to overcome these challenges. Here, we test whether target enrichment of ultraconserved elements (UCEs) and exons can be used for delimiting species boundaries and population structure within species of corals by focusing on two octocoral genera, Alcyonium and Sinularia, as exemplary case studies. We designed an updated bait set (29,181 baits) to target-capture 3,023 UCE and exon loci, recovering a mean of 1,910 ± 168 SD per sample with a mean length of 1,055 ± 208 bp. Similar numbers of loci were recovered from Sinularia (1,946 ± 227 SD) and Alcyonium (1,863 ± 177 SD). Species-level phylogenies were highly supported for both genera. Clustering methods based on filtered single nucleotide polymorphisms delimited species and populations that are congruent with previous allozyme, DNA barcoding, reproductive and ecological data for Alcyonium, and offered further evidence of hybridization among species. For Sinularia, results were congruent with those obtained from a previous study using restriction site associated DNA sequencing. Both case studies demonstrate the utility of target-enrichment of UCEs and exons to address a wide range of evolutionary and taxonomic questions across deep to shallow timescales in corals.

Climate-driven vicariance and long-distance dispersal explain the Rand Flora pattern in the liverwort Exormotheca pustulosa (Marchantiophyta)

The ‘Rand flora’ is a biogeographical disjunction which refers to plant lineages occurring at the margins of the African continent and neighbouring oceanic archipelagos. Here, we tested whether the phylogeographical pattern of Exormotheca pustulosa Mitt. was the result of vicariance induced by past climatic changes or the outcome of a series of recent long-distance dispersal events. Two chloroplast markers (rps4-trnF region and psbA-trnH spacer) and one nuclear marker (ITS2) were analysed. Phylogenetic and phylogeographical relationships were inferred as well as divergence time estimates and ancestral areas. Exormotheca possibly originated in Eastern Africa during the Late Oligocene/Early Miocene while Exormotheca putulosa diversified during the Late Miocene. Three main E. pustulosa groups were found: the northern Macaronesia/Western Mediterranean, the South Africa/Saint Helena and the Cape Verde groups. The major splits among these groups occurred during the Late Miocene/Pliocene; diversification was recent, dating back to the Pleistocene. Climate-driven vicariance and subsequent long-distance dispersal events may have shaped the current disjunct distribution of E. pustulosa that corresponds to the Rand Flora pattern. Colonization of Macaronesia seems to have occurred twice by two independent lineages. The evolutionary history of E. pustulosa populations of Cape Verde warrants further study.

Islands as a crossroad of evolutionary lineages: A case study of Centaurea sect. Centaurea (Compositae) from Sardinia (Mediterranean Basin)

The Mediterranean Basin is a biodiversity hotspot, where islands play a key role because of their high biological diversity, degree of endemicity and human pressure. One of these islands, Sardinia, is a good evolutionary laboratory, especially for the study of complex genera, such as Centaurea. In particular, endemic species of Centaurea sect. Centaurea from Sardinia provides an interesting case study of plant evolution on continental islands. We attempted to clarify the processes leading to the diversification of Centaurea species on Sardinia using bi-parentally inherited nuclear markers and maternally inherited plastid markers. Our plastid results revealed the presence of five lineages of sect. Centaurea on the island. Three of them were defined as three species: C. ferulacea, C. filiformis and C. horrida. The other two lineages highlighted the complex evolutionary history of the two polyploids C. corensis and C. magistrorum. Multiple colonization events from the mainland involving the C. deusta and C. paniculata lineages among others, have led to the diversity of sect. Centaurea on Sardinia. One colonization event likely followed a southern path via the land connection between the mainland, the Calabrian Plate and Sardinia. A second pathway likely followed a northern connection, probably through the Tuscan Archipelago. Implications of these findings on conservation efforts for Centaurea endemics on Sardinia are also discussed.

Earthquake crisis unveils the growth of an incipient continental fault system

Large continental faults extend for thousands of kilometres to form boundaries between rigid tectonic blocks. These faults are associated with prominent topographic features and can produce large earthquakes. Here we show the first evidence of a major tectonic structure in its initial-stage, the Al-Idrissi Fault System (AIFS), in the Alboran Sea. Combining bathymetric and seismic reflection data, together with seismological analyses of the 2016 M_w 6.4 earthquake offshore Morocco – the largest event ever recorded in the area – we unveil a 3D geometry for the AIFS. We report evidence of left-lateral strike-slip displacement, characterise the fault segmentation and demonstrate that AIFS is the source of the 2016 events. The occurrence of the M_w 6.4 earthquake together with historical and instrumental events supports that the AIFS is currently growing through propagation and linkage of its segments. Thus, the AIFS provides a unique model of the inception and growth of a young plate boundary fault system.

The Al-Idrissi Fault System in the Alboran Sea is a major tectonic structure in its initial stage. By using bathymetric and seismic reflection data, the authors unravel a 3D geometry for the AIFS, which corresponds to a crustal-scale boundary and provides a unique model of the inception and growth of a young plate boundary fault system.

A pre-Miocene Irano-Turanian cradle: Origin and diversification of the species-rich monocot genus Gagea (Liliaceae)

The Irano-Turanian (IT) floristic region is considered an important center of origin for many taxa. However, there is a lack of studies dealing with typical IT genera that also occur in neighboring areas. The species-rich monocot genus Gagea Salisb. shows a center of diversity in IT region and a distribution in adjacent regions, therefore representing a good study object to investigate spatial and temporal relationships among IT region and its neighboring areas (East Asia, Euro-Siberia, Himalaya, and Mediterranean). We aimed at (a) testing the origin of the genus and of its major lineages in the IT region, (b) reconstructing divergence times, and (c) reconstructing colonization events. To address these problems, sequences of the ribosomal DNA internal transcribed spacer (ITS) region of 418 individuals and chloroplast intergenic spacers sequences (psbA-trnH, trnL-trnF) of 497 individuals, representing 116 species from all sections of the genus and nearly its entire distribution area were analyzed. Divergence times were estimated under a random molecular clock based on nrITS phylogeny, which was the most complete data set regarding the representation of species and distribution areas. Ancestral distribution ranges were estimated for the nrITS data set as well as for a combined data set, revealing that Gagea most likely originated in southwestern Asia. This genus first diversified there starting in the Early Miocene. In the Middle Miocene, Gagea migrated to the Mediterranean and to East Asia, while migration into Euro-Siberia took place in the Late Miocene. During the Pleistocene, the Arctic was colonized and Gagea serotina, the most widespread species, reached North America. The Mediterranean basin was colonized multiple times from southwestern Asia or Euro-Siberia. Most of the currently existing species originated during the last 3 Ma.

A pre-Miocene Irano-Turanian cradle: Origin and diversification of the species-rich monocot genus Gagea (Liliaceae)

The Irano-Turanian (IT) floristic region is considered an important center of origin for many taxa. However, there is a lack of studies dealing with typical IT genera that also occur in neighboring areas. The species-rich monocot genus Gagea Salisb. shows a center of diversity in IT region and a distribution in adjacent regions, therefore representing a good study object to investigate spatial and temporal relationships among IT region and its neighboring areas (East Asia, Euro-Siberia, Himalaya, and Mediterranean). We aimed at (a) testing the origin of the genus and of its major lineages in the IT region, (b) reconstructing divergence times, and (c) reconstructing colonization events. To address these problems, sequences of the ribosomal DNA internal transcribed spacer (ITS) region of 418 individuals and chloroplast intergenic spacers sequences (psbA-trnH, trnL-trnF) of 497 individuals, representing 116 species from all sections of the genus and nearly its entire distribution area were analyzed. Divergence times were estimated under a random molecular clock based on nrITS phylogeny, which was the most complete data set regarding the representation of species and distribution areas. Ancestral distribution ranges were estimated for the nrITS data set as well as for a combined data set, revealing that Gagea most likely originated in southwestern Asia. This genus first diversified there starting in the Early Miocene. In the Middle Miocene, Gagea migrated to the Mediterranean and to East Asia, while migration into Euro-Siberia took place in the Late Miocene. During the Pleistocene, the Arctic was colonized and Gagea serotina, the most widespread species, reached North America. The Mediterranean basin was colonized multiple times from southwestern Asia or Euro-Siberia. Most of the currently existing species originated during the last 3 Ma.

Mediterranean isolation preconditioning the Earth System for late Miocene climate cooling

A global Neogene cooling trend culminated ~7 million years ago with the onset of Greenland glaciation. Increased ocean-atmosphere interaction and low- to high-latitude circulation are thought to be key factors in reorganizing late Miocene global temperature and precipitation patterns, but the drivers of this reorganization have yet to be identified. Here, we present new information about the evolution of the Atlantic-Mediterranean gateway that generated Mediterranean overflow. We use sedimentary and palaeogeographic evidence to constrain the timing and dimensions of this gateway and document the initiation of a saline plume of water within the North Atlantic. Today, this saline jet entrains and transports Eastern North Atlantic water and its dissolved inorganic carbon into the interior of the ocean, contributing to the drawdown of CO₂ and the sensitivity of the ocean to atmospheric changes. We show that during the Miocene this transport emerged simultaneously with gateway restriction and propose that the resulting interaction of ocean-surface and ocean-interior carbon inventories would have greatly enhanced ocean-atmosphere exchange, preconditioning the Earth System for late Miocene cooling.

Reinterpretation of an endangered taxon based on integrative taxonomy: The case of Cynara baetica (Compositae)

The Strait of Gibraltar, the gateway between the Atlantic Ocean and the Mediterranean Sea, has a convulsive geological history, with recurring closing and opening events since the late Miocene. As a consequence, this region has played a major role in the evolutionary history of many species. Cynara baetica (Compositae) is a diploid perennial herb distributed in both sides of this strait. It is currently subdivided into two subspecies: C. baetica subsp. baetica for the Spanish populations, and C. baetica subsp. maroccana for the Moroccan ones. Following three different approximations of species delimitation, including phylogenetic and population genetic analyses (based on three AFLP primer combinations and two intergenic spacers of cpDNA), ecological niche modeling (ENM) and morphological studies, this taxon is investigated and reinterpreted. The results obtained showed a clear genetic, morphological and ecological differentiation between the two taxa and the important role played by the Strait of Gibraltar as a geographical barrier. Based on this evidence, the current taxonomic treatment is modified (both taxa should recover their specific rank) and specific conservation guidelines are proposed for the newly delimited taxa.

Tracking the Serpentinite Feet of the Mediterranean Salt Giant

Interpretation of seismic profiles and results of scientific drillings in the Mediterranean subseafloor provided indication of gigantic salt deposits which rarely crop out on land, such as in Sicily. The salt giants were ascribed to the desiccation, driven by the solar energy, of the entire basin. Nevertheless, the evaporite model hardly explains deep-sea salt deposits. This paper considers a different hypothesis suggesting that seawater reached NaCl saturation during serpentinization of ultramafic rocks. Solid salts and brine pockets were buried within the serpentinite bodies being later (e.g., in the Messinian) released, due to serpentinite breakdown, and discharged at seafloor as hydrothermal heavy brines. Therefore, sea-bottom layers of brine at gypsum and halite saturation were formed. The model is applicable to the Mediterranean area since geophysical data revealed relicts of an aged (hence serpentinized) oceanic lithosphere, of Tethyan affinity, both in its western “Atlantic” extension (Gulf of Cádiz) and in eastern basins, and xenoliths from Hyblean diatremes (Sicily) provided evidence of buried serpentinites in the central area. In addition, the buoyant behavior of muddled serpentinite and salts (and hydrocarbons) gave rise to many composite diapirs throughout the Mediterranean area. Thus, the Mediterranean “salt giant” consists of several independent geobodies of serpentinite and salts.

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

What process triggered the Mediterranean Sea restriction remains debated since the discovery of the Messinian Salinity Crisis (MSC). Recent hypotheses infer that the MSC initiated after the closure of the Atlantic-Mediterranean Betic and Rifean corridors, being modulated through restriction at the Gibraltar Strait. These hypotheses however, do not integrate contemporaneous speciation patterns of the faunal exchange between Iberia and Africa and several geological features like the evaporite distribution. Exchange of terrestrial biota occurred before, during and after the MSC, and speciation models support an exchange path across the East Alborán basin (EAB) located a few hundreds of km east of the Gibraltar Strait. Yet, a structure explaining jointly geological and biological observations has remained undiscovered. We present new seismic data showing the velocity structure of a well-differentiated 14–17-km thick volcanic arc in the EAB. Isostatic considerations support that the arc-crust buoyancy created an archipelago leading to a filter bridge across the EAB. Sub-aerial erosional unconformities and onlap relationships support that the arc was active between ~10–6 Ma. Progressive arc build-up leading to an archipelago and its later subsidence can explain the extended exchange of terrestrial biota between Iberia and Africa (~7–3 Ma), and agrees with patterns of biota speciation and terrestrial fossil distribution before the MSC (10–6.2 Ma). In this scenario, the West Alboran Basin (WAB) could then be the long-postulated open-marine refuge for the Mediterranean taxa that repopulated the Mediterranean after the MSC, connected to the deep restricted Mediterranean basin through a sill at the Alboran volcanic arc archipelago.

Diversification in continental island archipelagos: new evidence on the roles of fragmentation, colonization and gene flow on the genetic divergence of Aegean Nigella (Ranunculaceae)

Background and Aims

Disentangling the relative roles of past fragmentation (vicariance), colonization (dispersal) and post-divergence gene flow in the genetic divergence of continental island organisms remains a formidable challenge. Amplified fragment length polymorphisms (AFLPs) were used to (1) gain further insights into the biogeographical processes underlying the Pleistocene diversification of the Aegean Nigella arvensis complex; (2) evaluate the role of potential key factors driving patterns of population genetic variability (mating system, geographical isolation and historical contingencies); and (3) test the robustness of conclusions previously drawn from chloroplast (cp) DNA.

Methods

Genetic diversity was analysed for 235 AFLP markers from 48 populations (497 individuals) representing 11 taxa of the complex using population genetic methods and Bayesian assignment tests.

Key Results

Most designated taxa are identifiable as genetically distinct units. Both fragmentation and dispersal-driven diversification processes occurred at different geological time scales, from Early to Late Pleistocene, specifically (1) sea barrier-induced vicariant speciation in the Cyclades, the Western Cretan Strait and Ikaria; and (2) bi-regional colonizations of the 'Southern Aegean Island Arc' from the Western vs. Eastern Aegean mainland, followed by allopatric divergences in Crete vs. Rhodos and Karpathos/Kasos. Outcrossing island taxa experienced drift-related demographic processes that are magnified in the two insular selfing species. Population genetic differentiation on the mainland seems largely driven by dispersal limitation, while in the Central Aegean it may still be influenced by historical events (island fragmentation and sporadic long-distance colonization).

Conclusions

The biogeographical history of Aegean Nigella is more complex than expected for a strictly allopatric vicariant model of divergence. Nonetheless, the major phylogeographical boundaries of this radiation are largely congruent with the geography and history of islands, with little evidence for ongoing gene exchange between divergent taxa. The present results emphasize the need to investigate further biological and landscape features and contemporary vs. historical processes in driving population divergence and taxon diversification in Aegean plant radiations.

Different diversity-dependent declines in speciation rate unbalances species richness in terrestrial slugs

Two genera of terrestrial slugs (Arion and Geomalacus) display a striking disproportion in species richness in the Iberian Peninsula. While there are 17 Iberian endemic species in Arion, morphological criteria only recognize four species within Geomalacus. Sequence data were used to test whether these differences could result from: (1) cryptic diversity within Geomalacus; (2) an earlier origin for Arion (older clades are expected to accumulate more species); (3) distinct patterns of diversification rates (higher initial speciation rates in Arion), and (4) some combination of the above factors (e.g., an older clade with higher speciation rates). Species delimitation tests based on mitochondrial and nuclear data revealed eight cryptic lineages within Geomalacus that lessened the asymmetry; nevertheless, the disparity required further investigation. No meaningful differences in crown group ages of each recovered clade were found. Regardless the different premises of the two equally plausible diversification models (similar initial speciation rates vs. higher initial speciation rates in Geomalacus), both coincide on diversity-dependent diversification for the two groups but weaker rate declines in Arion best explains the observed asymmetry in species richness. Also, the broader environmental tolerance combined with a faster dispersal and wider distribution may have represented an evolutionary advantage for Arion.

The Mediterranean Overflow in the Gulf of Cadiz: A rugged journey

The pathways and transformations of dense water overflows, which depend on small-scale interactions between flow dynamics and erosional-depositional processes, are a central piece in the ocean's large-scale circulation. A novel, high-resolution current and hydrographic data set highlights the intricate pathway travelled by the saline Mediterranean Overflow as it enters the Atlantic. Interaction with the topography constraints its spreading. Over the initial 200 km west of the Gibraltar gateway, distinct channels separate the initial gravity current into several plunging branches depth-sorted by density. Shallow branches follow the upper slope and eventually detach as buoyant plumes. Deeper branches occupy mid slope channels and coalesce upon reaching a diapiric ridge. A still deeper branch, guided by a lower channel wall marked by transverse furrows, experiences small-scale overflows which travel downslope to settle at mid-depths. The Mediterranean salt flux into the Atlantic has implications for the buoyancy balance in the North Atlantic. Observations on how this flux enters at different depth levels are key to accurately measuring and understanding the role of Mediterranean Outflow in future climate scenarios.

Magmatic pulse driven by sea-level changes associated with the Messinian salinity crisis

Between 5 and 6 million years ago, during the so-called Messinian salinity crisis, the Mediterranean basin became a giant salt repository. The possibility of abrupt and kilometre-scale sea-level changes during this extreme event is debated. Messinian evaporites could signify either deep- or shallow-marine deposits, and ubiquitous erosional surfaces could indicate either subaerial or submarine features. Significant and fast reductions in sea level unload the lithosphere, which can increase the production and eruption of magma. Here we calculate variations in surface load associated with the Messinian salinity crisis and compile the available time constraints for pan-Mediterranean magmatism. We show that scenarios involving a kilometre-scale drawdown of sea level imply a phase of net overall lithospheric unloading at a time that appears synchronous with a magmatic pulse from the pan-Mediterranean igneous provinces. We verify the viability of a mechanistic link between unloading and magmatism using numerical modelling of decompression partial mantle melting and dike formation in response to surface load variations. We conclude that the Mediterranean magmatic record provides an independent validation of the controversial kilometre-scale evaporative drawdown and sheds new light on the sensitivity of magmatic systems to the surface forcing.

Global biogeography, cryptic species and systematic issues in the shrimp genus Hippolyte Leach, 1814 (Decapoda: Caridea: Hippolytidae) by multimarker analyses

Hippolyte is a genus of small bodied marine shrimps, with a global distribution. Here, we studied the phylogenetic and biogeographic relationships amongst the species of this genus with two mitochondrial and two nuclear markers, using Bayesian Inference, Maximum Likelihood, genetic divergence, molecular clock and S-DIVA. In addition, the Indo-West Pacific genus Alcyonohippolyte was included. Based on sequences from 57 specimens of 27 species, we recovered a robust biogeographic scenario that shows the Indo-West Pacific as the probable ancestral area of the genus Hippolyte, which emerged in the Paleocene, followed by dispersal in three general directions: (1) South Pacific, (2) eastern Atlantic and Mediterranean Sea and (3) Americas, the latter with a primary colonization in the eastern Pacific followed by a radiation into the western Atlantic. Our analysis reveals that the species of the H. ventricosa group do not constitute a monophyletic group and Alcyonohippolyte does not constitute a reciprocally monophyletic group to Hippolyte, with both genera herein synonimised. The relationships and systematic status of several transisthmian and Atlantic species are clarified.

Asymmetrical dispersal and putative isolation-by-distance of an intertidal blenniid across the Atlantic-Mediterranean divide

Transition zones are of high evolutionary interest because unique patterns of spatial variation are often retained. Here, we investigated the phylogeography of the peacock blenny, Salaria pavo, a small marine intertidal fish that inhabits rocky habitats of the Mediterranean and the adjacent Atlantic Ocean. We screened 170 individuals using mitochondrial and nuclear sequence data from eight locations. Four models of genetic structure were tested: panmixia, isolation-by-distance, secondary contact and phylogeographic break. Results indicated clear asymmetric migration from the Mediterranean to the Atlantic but only marginally supported the isolation-by-distance model. Additionally, the species displays an imprint of demographic expansion compatible with the last glacial maximum. Although the existence of a refugium in the Mediterranean cannot be discarded, the ancestral lineage most likely originated in the Atlantic, where most of the genetic diversity occurs.

Mitogenomic phylogeny of cone snails endemic to Senegal

Cone snails attain in Senegal one of their highest peaks of species diversity throughout the continental coast of Western Africa. A total of 15 endemic species have been described, all placed in the genus Lautoconus. While there is ample data regarding the morphology of the shell and the radular tooth of these species, virtually nothing is known regarding the genetic diversity and phylogenetic relationships of one of the most endangered groups of cones. In this work, we determined the complete or near-complete (only lacking the control region) mitochondrial (mt) genomes of 17 specimens representing 11 endemic species (Lautoconus belairensis, Lautoconus bruguieresi, Lautoconus cacao, Lautoconus cloveri, Lautoconus cf. echinophilus, Lautoconus guinaicus, Lautoconus hybridus, Lautoconus senegalensis, Lautoconus mercator, Lautoconus taslei, and Lautoconus unifasciatus). We also sequenced the complete mt genome of Lautoconus guanche from the Canary Islands, which has been related to the cones endemic to Senegal. All mt genomes share the same gene arrangement, which conforms to the consensus reported for Conidae, Neogastropoda and Caenogastropoda. Phylogenetic analyses using probabilistic methods recovered three major lineages, whose divergence coincided in time with sea level and ocean current changes as well as temperature fluctuations during the Messinian salinity crisis and the Plio-Pleistocene transition. Furthermore, the three lineages corresponded to distinct types of radular tooth (robust, small, and elongated), suggesting that dietary specialization could be an additional evolutionary driver in the diversification of the cones endemic to Senegal. The reconstructed phylogeny showed several cases of phenotypic convergence (cryptic species) and questions the validity of some species (ecotypes or phenotypic plasticity), both results having important taxonomic and conservation consequences.