The Aegean archipelago: a natural laboratory of evolution, ecology and civilisations

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.

Taxonomy of Dianthus (Caryophyllaceae) - overall phylogenetic relationships and assessment of species diversity based on a first comprehensive checklist of the genus

In this study, we present an overall phylogenetic framework for Dianthus using four plastid regions (matK-trnK-psbA, rpl32-trnL, trnQ-rps16) and nuclear ITS and a species-level checklist for the genus developed by using all available databases and the literature. The trees from the plastid dataset depict a clade of Dianthus that also includes Velezia and a few taxa of Petrorhagia. New combinations in Dianthus are provided for these species. The checklist of Dianthus in this new delimitation covers 1781 names, with 384 accepted species, 150 subspecies, 12 heterotypic varieties and two forms (not counting autonyms), 1050 synonyms, 22 hybrid names and 172 unresolved names, 3 names were excluded. Implications for the evolution of flower characters, life forms, biogeography, as well as sectional classification are discussed based on the phylogenetic framework.

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.

Abundance and population characteristics of the invasive sea urchin Diadema setosum (Leske, 1778) in the south Aegean Sea (eastern Mediterranean)

Background

The Indo-Pacific sea urchin Diadema setosum has invaded the Mediterranean Sea and has spread along many locations in the southeastern part of the basin, where established populations exist on the shallow subtidal rocky shore. Diadema setosum is a ubiquitous species, of particular ecological importance due to the high levels of grazing pressure it imposes on benthic communities. Its biology, however, is not adequately studied, especially along its introduced range of distribution. The present study examines the population status of D. setosum outside its native range, in the Dodecanese island complex, south Aegean Sea. Thirty-four stations located across 16 islands were surveyed by scientific SCUBA-diving (up to a depth of 10 m) in December 2019 and June-July 2020. Samplings included: (i) visual census along transects to estimate relative abundance and population density, and (ii) random collection of specimens from densely populated stations to assess biometry and reproductive condition (histological examination of gonads) of D. setosum.

Results

Diadema setosum was found in 21 out of the 34 surveyed stations. The species had sparse populations of well-hidden individuals in rocky crevices, but with dense localized patches in Agathonisi, Leros, Kalymnos, Pserimos, Symi, Alimia and Chalki islands. In those seven islands, mean population density was 2.5 ± 1.48 individuals m⁻². Diadema setosum had denser populations in shallower depths but larger dimensions in deeper; these results suggest segregated density and size patterns along a depth gradient. The size structure, according to the size frequency distribution of the test diameter, was unimodal with a fitted mode at 4.0–4.5 and 6.5–7.0 cm in shallow and deep populations, respectively. The examined morphometric relationships followed negative allometry, as previously suggested for the species within its native range of distribution, and test diameter appeared to be a good predictor of biomass. Diadema setosum specimens had immature gonads in winter and mature in summer, suggesting a synchronous reproductive pattern. These results conform to previous data from temperate populations of the species.

Conclusions

Differences in local environmental conditions, e.g. hydrodynamics and habitat type, together with biotic interactions, e.g. recruitment and competition, probably shape D. setosum population in the south Aegean distributional range. The establishment of D. setosum has severe implications on benthic communities and local sea urchin populations demanding management measures to prevent the forecasted further expansion of this invasive species.

Spatial and Ecological Drivers of Genetic Structure in Greek Populations of Alkanna tinctoria (Boraginaceae), a Polyploid Medicinal Herb

Background and Aims: Quantifying genetic variation is fundamental to understand a species' demographic trajectory and its ability to adapt to future changes. In comparison with diploids, however, genetic variation and factors fostering genetic divergence remain poorly studied in polyploids due to analytical challenges. Here, by employing a ploidy-aware framework, we investigated the genetic structure and its determinants in polyploid Alkanna tinctoria (Boraginaceae), an ancient medicinal herb that is the source of bioactive compounds known as alkannin and shikonin (A/S). From a practical perspective, such investigation can inform biodiversity management strategies. Methods: We collected 14 populations of A. tinctoria within its main distribution range in Greece and genotyped them using restriction site-associated DNA sequencing. In addition, we included two populations of A. sieberi. By using a ploidy-aware genotype calling based on likelihoods, we generated a dataset of 16,107 high-quality SNPs. Classical and model-based analysis was done to characterize the genetic structure within and between the sampled populations, complemented by genome size measurements and chromosomal counts. Finally, to reveal the drivers of genetic structure, we searched for associations between allele frequencies and spatial and climatic variables. Key Results: We found support for a marked regional structure in A. tinctoria along a latitudinal gradient in line with phytogeographic divisions. Several analyses identified interspecific admixture affecting both mainland and island populations. Modeling of spatial and climatic variables further demonstrated a larger contribution of neutral processes and a lesser albeit significant role of selection in shaping the observed genetic structure in A. tinctoria. Conclusion: Current findings provide evidence of strong genetic structure in A. tinctoria mainly driven by neutral processes. The revealed natural genomic variation in Greek Alkanna can be used to further predict variation in A/S production, whereas our bioinformatics approach should prove useful for the study of other non-model polyploid species.

Past connections with the mainland structure patterns of insular species richness in a continental-shelf archipelago (Aegean Sea, Greece)

Recent research in island biogeography has highlighted the important role of late Quaternary sea-level fluctuations in shaping biogeographic patterns in insular systems but focused on oceanic systems. Through this study, we aim investigate how late Quaternary sea-level fluctuations shaped species richness patterns in continental-shelf island systems. Focusing on the Aegean archipelago, we first compiled maps of the area's geography using published data, under three sea-level stands: (a) current; (b) median sea-level over the last nine glacial-interglacial cycles (MSL); and (c) Last Glacial Maximum (LGM). We gathered taxon-island occurrences for multiple chorotypes of angiosperms, butterflies, centipedes, and reptiles. We investigated the impact of present-day and past geographic settings on chorological groups by analyzing island species-area relationships (ISARs) and using generalized linear mixed models (GLMMs) selection based on multiple metrics of goodness of fit. Our results confirm that the Aegean's geography has changed dramatically since the LGM, whereas the MSL only modestly differs from the present configuration. Apart for centipedes, paleogeographic changes affected both native and endemic species diversity through altering connections between land-bridge islands and the mainland. On land-bridge islands, we detected over-representation of native species and under-representation of endemics. Unlike oceanic islands, sea-level-driven increase of isolation and area contraction did not strongly shape patterns of species richness. Furthermore, the LGM configurations rather than the MSL configuration shaped patterns of endemic species richness. This suggests that even short episodes of increased connectivity with continental populations are sufficient to counteract the genetic differentiation of insular populations. On the other hand, the over-representation of native nonendemic species on land-bridge islands reflected MSL rather than LGM mainland connections. Our study shows that in terms of processes affecting species richness patterns, continental archipelagos differ fundamentally from oceanic systems because episodic connections with the mainland have profound effects on the biota of land-bridge islands.

Multiple Drivers of High Species Diversity and Endemism Among Alyssum Annuals in the Mediterranean: The Evolutionary Significance of the Aegean Hotspot

The Mediterranean Basin is a significant hotspot of species diversity and endemism, with various distribution patterns and speciation mechanisms observed in its flora. High species diversity in the Mediterranean is also manifested in the monophyletic lineage of Alyssum annuals (Brassicaceae), but little is known about its origin. These species include both diploids and polyploids that grow mainly in open and disturbed sites across a wide elevational span and show contrasting distribution patterns, ranging from broadly distributed Eurasian species to narrow island endemics. Here, we investigated the evolution of European representatives of this lineage, and aimed to reconstruct their phylogeny, polyploid and genome size evolution using flow cytometric analyses, chloroplast and nuclear high- and low-copy DNA markers. The origin and early diversification of the studied Alyssum lineage could be dated back to the Late Miocene/Pliocene and were likely promoted by the onset of the Mediterranean climate, whereas most of the extant species originated during the Pleistocene. The Aegean region represents a significant diversity center, as it hosts 12 out of 16 recognized European species and comprises several (sub)endemics placed in distinct phylogenetic clades. Because several species, including the closest relatives, occur here sympatrically without apparent niche differences, we can reject simple allopatric speciation via vicariance as well as ecological speciation for most cases. Instead, we suggest scenarios of more complex speciation processes that involved repeated range shifts in response to sea-level changes and recurrent land connections and disconnections since the Pliocene. In addition, multiple polyploidization events significantly contributed to species diversity across the entire distribution range. All seven polyploids, representing both widespread species and endemics to the western or eastern Mediterranean, were inferred to be allopolyploids. Finally, the current distribution patterns have likely been affected also by the human factor (farming and grazing). This study illustrates the complexity of evolutionary and speciation processes in the Mediterranean flora.

Spatial Phylogenetics, Biogeographical Patterns and Conservation Implications of the Endemic Flora of Crete (Aegean, Greece) under Climate Change Scenarios

Human-induced biodiversity loss has been accelerating since the industrial revolution. The climate change impacts will severely alter the biodiversity and biogeographical patterns at all scales, leading to biotic homogenization. Due to underfunding, a climate smart, conservation-prioritization scheme is needed to optimize species protection. Spatial phylogenetics enable the identification of endemism centers and provide valuable insights regarding the eco-evolutionary and conservation value, as well as the biogeographical origin of a given area. Many studies exist regarding the conservation prioritization of mainland areas, yet none has assessed how climate change might alter the biodiversity and biogeographical patterns of an island biodiversity hotspot. Thus, we conducted a phylogenetically informed, conservation prioritization study dealing with the effects of climate change on Crete’s plant diversity and biogeographical patterns. Using several macroecological analyses, we identified the current and future endemism centers and assessed the impact of climate change on the biogeographical patterns in Crete. The highlands of Cretan mountains have served as both diversity cradles and museums, due to their stable climate and high topographical heterogeneity, providing important ecosystem services. Historical processes seem to have driven diversification and endemic species distribution in Crete. Due to the changing climate and the subsequent biotic homogenization, Crete’s unique bioregionalization, which strongly reminiscent the spatial configuration of the Pliocene/Pleistocene Cretan paleo-islands, will drastically change. The emergence of the ‘Anthropocene’ era calls for the prioritization of biodiversity-rich areas, serving as mixed-endemism centers, with high overlaps among protected areas and climatic refugia.

A surprising new genus and species of cave-adapted Plusiocampinae Cycladiacampa irakleiae (Diplura, Campodeidae) from Irakleia Island, Cyclades Islands in the Aegean Archipelago (Greece)

The surprising discovery ofCycladiacampa irakleiae, a new genus and species, a cave-adapted campodeid dipluran highlights the paleobiogeographical importance of the insular Aegean cave-ecosystems. This new dipluran genus inhabits with other noticeable endemic cave-adapted invertebrate species in the isolated Spilaio Agiou Ioanni cave in Irakleia, a small island in the centre of the Cyclades Archipelago.C. irakleiaegen. nov. et sp. nov.is related with Stygiocampa species, a subgenus of Plusiocampa genus, with hereto six cave-adapted species inhabiting karst areas in Dinaric and the Rhopode Mountains. These species share similarities such as the absence of mesonotal and metanotal macrosetae, the abundance and shape of urosternal macrosetae, as well as the lack of medial posterior macrosetae on mesonotum and metanotum. This can be explained by a common ancestor that probably originated from Asia and expanded its distribution to the fragmented Europe since the Eocene-Oligocene, colonizing cave habitats in recent periods.Cycladiacampa irakleiaeis a remarkable addition to the fauna of the cave of Irakleia and should raise awareness on the need to enhance the study and conservation of the cave’s natural heritage.

Dispersal versus vicariance in the Aegean: combining molecular and morphological phylogenies of eastern Mediterranean Dendarus (Coleoptera: Tenebrionidae) sheds new light on the phylogeography of the Aegean area

The Aegean archipelago, as an ‘evolutionary laboratory of nature’, is an ideal model for research in phylogeography. In this area, the darkling beetles of the genus Dendarus (distributed from Morocco to the Caucasus) exhibit a high level of diversity with 36 species, 27 of which are island endemics. However, their taxonomy is complex and unstable, having undergone continuous revision to address extensive morphological and ecological plasticity. Here, we examine the phylogenetic relationships of 23 species from Greece and Turkey, using mitochondrial and nuclear DNA sequences and 61 morphological characters, to unveil their phylogeny in the Aegean. This helps to clarify phylogeographic scenarios and historical processes that shaped the observed patterns. The analyses reveal 13 distinct lineages with several para- and polyphyletic cases that correspond to three major phylogroups [south/south-east Aegean (D. foraminosus complex, D. rhodius, D. sporadicus, D. wettsteini); central to north Aegean, Turkey and mainland Greece (D. crenulatus, D. moesiacus group, D. sinuatus complex, D. stygius) and mainland Greece (D. messenius, D. paganettii)], indicating the need for further taxonomic re-evaluation. Lineage topology and phylogeography suggest a spatial and temporal sequence of geographic isolation, following either a vicariant or a dispersal model coincident with major palaeogeographic separations in the Aegean.

Habitat Islands on the Aegean Islands (Greece): Elevational Gradient of Chasmophytic Diversity, Endemism, Phytogeographical Patterns and need for Monitoring and Conservation

The Aegean archipelago, characterized as a natural laboratory for research concerning plant species diversity and phytogeography has a complex geological and paleogeographical history that varies among its phytogeographical areas. A different combination of factors of variable intensity and duration time drives patterns of its impressive plant species richness and endemism. Cliffs, a conspicuous feature of the Aegean landscape, consist of biologically closed communities that serve as refugia for obligate chasmophytes, the majority of which are Greek or Aegean endemics, and for this reason, they are also considered as habitat islands on the Aegean islands. A synoptic analysis is presented concerning chasmophytic plant diversity focusing on endemic obligate chasmophytes. Phytogeographical patterns of obligate chasmophytes, and especially the endemic ones as well as their elevational range and distribution and zeta diversity, are analyzed and discussed in the frame of climatic change, mentioning that the most threatened endemic obligate chasmophytes are those specialized in high elevation areas, and focusing on the need for monitoring and conservation.

Endemic plants of Crete in electronic trade and wildlife tourism: current patterns and implications for conservation

Background

The island of Crete is a biodiversity hotspot having 223 endemic vascular taxa (species and subspecies) as a result of its long isolation and the wide range of habitats it includes. We explore trends and patterns in the electronic trade of these unique genetic resources and in their involvement in wildlife tourism, the ways these two activities are performed and the associated potential threats on the plants' wild populations, and we also identify priority taxa requiring special attention. The main part of the study was conducted in 2016-2017 using English as a search language; an additional search was conducted in 2019 using German and French.

Results

We found e-commerce for 28 (13%) endemic taxa. These are traded by 65 nurseries from 14 countries, the UK primarily. Among the traded plants, 16 face extinction risk and/or are under protection status. Prices vary largely for the same taxon and form of sale. Lamiaceae is the family with the highest number of e-traded taxa, Tulipa bakeri is the most traded species, and the living plant is the commonest form of sale. Thirty-seven endemic taxa are advertised in the websites of travel agencies involved in wildlife tourism. Tulipa doerfleri is the most frequently encountered taxon in these websites, whereas Lamiaceae, Liliaceae and Orchidaceae are similarly represented. The additional search showed a very rapid increase in the e-trade of the Cretan endemis.

Conclusion

The two examined markets are similar in that geophytes play a prominent role and Lamiaceae rank first among the represented plant families, but differ in several aspects: only 22.6% of the taxa detected are common in both, obedience to rules exhibited by travel agencies is not usually the case with nurseries, and potential threats to wild populations are estimated as considerably higher for the traded plants. Sixteen endemic taxa of Crete were identified as requiring special attention.

Changes in Fish Taxonomy Affect Freshwater Biogeographical Regionalisations: Insights from Greece

Freshwater fishes are key indicators for delineating biogeographical maps worldwide. However, controversy in regional-scale ichthyogeographic boundaries still persists, especially in areas of high species endemicity, such as in Greece. One problem concerns the taxonomy of the fishes because there have been extensive changes, mainly due to an increased splitting of species in recent years in Europe. Here, we explore why ichthyogeographic boundary disagreements and uncertainties in region-scale biogeographical units persist. We compare cluster analyses of river basin fish fauna in Greece using two taxonomic datasets: the older fish taxonomy (from 1991) and the current taxonomy that now follows the phylogenetic species concept (PSC), which has become widely established in Europe after 2007. Cluster analyses using the older fish taxonomy depicts only two major biogeographical regional divisions, while the current taxonomy defines four major regional divisions in mainland Greece. Interestingly, some older maps from the pre-PSC taxonomy era also similarly show four ichthyogeographic divisions in Greece and we can assume that the older biogeographical work did not solely use numerical taxonomy but followed an expert-guided synthesis; the older regional definitions have persisted quite well despite radical changes in Europe’s fish taxonomy. Through the prism of biodiversity conservation planning, we hope this review may help identify ways to help standardize policy-relevant biogeographical mapping.

Islands and hybrid zones: combining the knowledge from "Natural Laboratories" to explain phylogeographic patterns of the European brown hare

Background

The aim of the study was to use hybrid populations as well as island populations of the European brown hare (Lepus europaeus) to explore the effect of evolutionary events, such as the post-deglaciation translocations, spontaneous and human-mediated, local adaptation and the genetic drift in the shaping of the phylogeographic patterns of the species. For this purpose, we used molecular markers, both nuclear and mitochondrial, that are indicative for local adaptation as well as neutral markers to elucidate the patterns of population differentiation based on geographic isolation and the clade of origin. To broaden our analysis, we included data from our previous studies concerning mainland populations, to explore the genetic differentiation in the base of the geographic origin (mainland/island) of the populations.

Results

Our results suggest that local adaptation shapes the differentiation in both genomes, favoring specific alleles in nuclear genes (e.g. DQA) or haplotypes in mtDNA (e.g. Control Region, CR). mtDNA variation was found to be in a higher level and was able to give a phylogeographic signal for the populations. Furthermore, the degree of variation was influenced not only by the geographic origin, but also by the clade of origin, since specific island populations of Anatolian origin showed a greater degree of variation compared to specific mainland populations of the European clade. Concerning the hybrid population, we confirmed the existence of both clades in the territory and we provided a possible explanation for the lack of introgression between the clades.

Conclusion

Our results indicate that the Quaternary’s climatic oscillations played a major role in the shaping of the phylogeographic patterns of the species, by isolating populations in the distinct refugia, where they adapted and differentiate in allopatry, leading to genome incompatibilities observed nowadays.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1354-y) contains supplementary material, which is available to authorized users.

Hybridization-facilitated genome merger and repeated chromosome fusion after 8 million years

The small genus Ricotia (nine species, Brassicaceae) is confined to the eastern Mediterranean. By comparative chromosome painting and a dated multi-gene chloroplast phylogeny, we reconstructed the origin and subsequent evolution of Ricotia. The ancestral Ricotia genome originated through hybridization between two older genomes with n = 7 and n = 8 chromosomes, respectively, on the Turkish mainland during the Early Miocene (c. 17.8 million years ago, Ma). Since then, the allotetraploid (n = 15) genome has been altered by two independent descending dysploidies (DD) to n = 14 in Ricotia aucheri and the Tenuifolia clade (2 spp.). By the Late Miocene (c. 10 Ma), the latter clade started to evolve in the most diverse Ricotia core clade (6 spp.), the process preceded by a DD event to n = 13. It is noteworthy that this dysploidy was mediated by a unique chromosomal rearrangement, merging together the same two chromosomes as were merged during the origin of a fusion chromosome within the paternal n = 7 genome c. 20 Ma. This shows that within a time period of c. 8 Myr genome evolution can repeat itself and that structurally very similar chromosomes may originate repeatedly from the same ancestral chromosomes by different pathways (end-to-end translocation versus nested chromosome insertion).

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.