Multiple auto- and allopolyploidisations marked the Pleistocene history of the widespread Eurasian steppe plant Astragalus onobrychis (Fabaceae)

Evolution, range formation and a revised taxonomy of the disjunctly distributed European members of Astragalus sect. Caprini, an intricate group including highly endangered species of dry grasslands

The Eurasian steppes are among the largest and most threatened biomes on Earth. During cold periods of the Pleistocene, the zonal Eurasian steppes had a much larger extent as compared to interglacial periods, and repeatedly expanded into large areas of present-day forested temperate Europe. Conversely, during warm periods, forest expansion recurrently forced Eurasian steppe biota into disjunct and small warm-stage refugia, i.e. today's extrazonal steppes. The rare, threatened and disjunctly distributed northwestern African and European members of Astragalus sect. Caprini constitute an ideal model for gaining insights into the evolutionary dynamics of typical steppe biota. Here, we reconstructed the spatiotemporal diversification of northwestern African and European members of Astragalus sect. Caprini based on a combination of RADseq data, single gene markers (internal transcribed spacer, plastid ycf1), genome size measurements and multivariate morphometrics. We outline an evolutionary scenario in which the group originated in the Irano-Turanian region and started to diversify shortly after the Mid-Pleistocene-Transition (ca. 0.5 to 0.7 Ma). While lineages occurring in (sub-)mediterranean mountain ranges diverged early, lineages occurring in northern lowland steppes are much younger (ca. 0.2 to 0.3 Ma), emphasizing the importance of southern European mountain ranges as long-term refugia. Recurrent colonization of the western Mediterranean region by eastern Mediterranean lineages and secondary contacts of currently spatially isolated lineages have significantly (co-)shaped the genetic structure within the group; we assume that these events may be a consequence of cold-stage range expansions. Based on combined genetic and morphometric data, we suggest treating the ten lineages introduced in this study as independent species, contrasting previous taxonomic treatments.

Anatomy of a mega-radiation: Biogeography and niche evolution in Astragalus

PREMISE

Astragalus (Fabaceae), with more than 3000 species, represents a globally successful radiation of morphologically highly similar species predominant across the northern hemisphere. It has attracted attention from systematists and biogeographers, who have asked what factors might be behind the extraordinary diversity of this important arid-adapted clade and what sets it apart from close relatives with far less species richness.

METHODS

Here, for the first time using extensive phylogenetic sampling, we asked whether (1) Astragalus is uniquely characterized by bursts of radiation or whether diversification instead is uniform and no different from closely related taxa. Then we tested whether the species diversity of Astragalus is attributable specifically to its predilection for (2) cold and arid habitats, (3) particular soils, or to (4) chromosome evolution. Finally, we tested (5) whether Astragalus originated in central Asia as proposed and (6) whether niche evolutionary shifts were subsequently associated with the colonization of other continents.

RESULTS

Our results point to the importance of heterogeneity in the diversification of Astragalus, with upshifts associated with the earliest divergences but not strongly tied to any abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. Biogeographic shifts have a strong association with the abiotic environment and highlight the importance of central Asia as a biogeographic gateway.

CONCLUSIONS

Our investigation shows the importance of phylogenetic and evolutionary studies of logistically challenging "mega-radiations." Our findings reject any simple key innovation behind high diversity and underline the often nuanced, multifactorial processes leading to species-rich clades.

Evolution of the Sabulina verna group (Caryophyllaceae) in Europe: A deep split, followed by secondary contacts, multiple allopolyploidization and colonization of challenging substrates

One of the major goals of contemporary evolutionary biology is to elucidate the relative roles of allopatric and ecological differentiation and polyploidy in speciation. In this study, we address the taxonomically intricate Sabulina verna group, which has a disjunct Arctic-alpine postglacial range in Europe and occupies a broad range of ecological niches, including substrates toxic to plants. Using genome-wide ddRAD sequencing combined with morphometric analyses based on extensive sampling of 111 natural populations, we aimed to disentangle internal evolutionary relationships and examine their correspondence with the pronounced edaphic and ploidy diversity within the group. We identified two spatially distinct groups of diploids: a widespread Arctic-alpine group and a spatially restricted yet diverse Balkan group. Most tetraploids exhibited a considerably admixed ancestry derived from both these groups, suggesting their allopolyploid origin. Four genetic clusters in congruence with geography and mostly supported by morphological traits were recognized in the diploid Arctic-alpine group. Tetraploids are split into two distinct and geographically vicariant groups, indicating their repeated polytopic origin. Furthermore, our results also revealed at least five-fold parallel colonization of toxic substrates (serpentine and metalliferous), altogether demonstrating a complex interaction between geography, challenging substrates and polyploidy in the evolution of the group. Finally, we propose a new taxonomic treatment of this complex.

Is there a massive glacial-Holocene flora continuity in Central Europe?

The prevailing paradigm about the Quaternary ecological and evolutionary history of Central European ecosystems is that they were repeatedly impoverished by regional extinctions of most species during the glacial periods, followed by massive recolonizations from southern and eastern refugia during interglacial periods. Recent literature partially contradicts this view and provides evidence to re-evaluate this Postglacial Recolonization Hypothesis and develop an alternative one. We examined the long-term history of the flora of the Carpathian (Pannonian) Basin by synthesising recent advances in ecological, phylogeographical, palaeoecological and palaeoclimatological research, and analysing the cold tolerance of the native flora of a test area (Hungary, the central part of the Carpathian Basin). We found that (1) many species have likely occurred there continuously since before the Last Glacial Maximum (LGM); (2) most of the present-day native flora (1404 species, about 80%) can occur in climates as cold as or colder than the LGM (mean annual temperature ≤+3.5°C); and (3) grasslands and forests can be species-rich under an LGM-like cold climate. These arguments support an alternative hypothesis, which we call the Flora Continuity Hypothesis. It states that long-term continuity of much of the flora in the Carpathian Basin is more plausible than regional extinctions during the LGM followed by massive postglacial recolonizations. The long-term continuity of the region's flora may have fundamental implications not only for understanding local biogeography and ecology (e.g. the temporal scale of processes), but also for conservation strategies focusing on protecting ancient species-rich ecosystems and local gene pools.

Phylogenomics and plastome evolution of Indigofera (Fabaceae)

Introduction

Indigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of Indigofera taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of Indigofera.

Methods

Here, we newly assembled 18 chloroplast genomes of Indigofera. We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae.

Results and discussion

The chloroplast genomes of Indigofera exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which trnK-rbcL, ndhF-trnL, and ycf1 were considered as candidate DNA barcodes for species identification of Indigofera. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on complete chloroplast genome and protein-coding genes (PCGs) generated a well-resolved phylogeny of Indigofera and allied species. Indigofera monophyly was strongly supported, and four monophyletic lineages (i.e., the Pantropical, East Asian, Tethyan, and Palaeotropical clades) were resolved within the genus. The species pairwise Ka/Ks ratios showed values lower than 1, and 13 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis using the branch-site model, eight of which were associated with photosynthesis. Positive selection of accD suggested that Indigofera species have experienced adaptive evolution to selection pressures imposed by their herbivores and pathogens. Our study provided insight into the structural variation of chloroplast genomes, phylogenetic relationships, and adaptive evolution in Indigofera. These results will facilitate future studies on species identification, interspecific and intraspecific delimitation, adaptive evolution, and the phylogenetic relationships of the genus Indigofera.

Phylogenomic inference and demographic model selection suggest peripatric separation of the cryptic steppe ant species Plagiolepis pyrenaica stat. rev

The ant Plagiolepis taurica Santschi, 1920 (Hymenoptera, Formicidae) is a typical species of the Eurasian steppes, a large grassland dominated biome that stretches continuously from Central Asia to Eastern Europe and is represented by disjunct outposts also in Central and Western Europe. The extent of this biome has been influenced by the Pleistocene climate, and steppes expanded recurrently during cold stages and contracted in warm stages. Consequently, stenotopic steppe species such as P. taurica repeatedly went through periods of demographic expansion and severe isolation. Here, we explore the impact of these dynamics on the genetic diversification within P. taurica. Delimitation of P. taurica from other Plagiolepis species has been unclear since its initial description, which raised questions on both its classification and its spatiotemporal diversification early on. We re-evaluate species limits and explore underlying mechanisms driving speciation by using an integrative approach based on genomic and morphometric data. We found large intraspecific divergence within P. taurica and resolved geographically coherent western and eastern genetic groups, which likewise differed morphologically. A morphometric survey of type material showed that Plagiolepis from the western group were more similar to P. barbara pyrenaica Emery, 1921 than to P. taurica; we thus lift the former from synonymy and establish it as separate species, P. pyrenaica stat. rev. Explicit evolutionary model testing based on genomic data supported a peripatric speciation for the species pair, probably as a consequence of steppe contraction and isolation during the mid-Pleistocene. We speculate that this scenario could be exemplary for many stenotopic steppe species, given the emphasized dynamics of Eurasian steppes.

Genotyping-by-sequencing reveals range expansion of Adonis vernalis (Ranunculaceae) from Southeastern Europe into the zonal Euro-Siberian steppe

The Euro-Siberian steppe flora consists of warm- and cold-adapted species, which may have responded differently to Pleistocene glacials and interglacials. Genotyping-by-sequencing individuals from across the distribution range of the pheasant's eye (Adonis vernalis), we aimed to gain insight into steppe florogenesis based on the species' evolutionary history. Although the primary area of origin of the species group comprising A. vernalis, A. villosa and A. volgensis is in Asia, our results indicate that recent populations of A. vernalis are not of Asian origin but evolved in the southern part of Europe during the Pleistocene, with Spanish populations clearly genetically distinct from the Southeastern European populations. We inferred that A. vernalis migrated eastwards from the sub-Mediterranean forest-steppes of Southeastern Europe into the continental forest-steppe zone. Eastern European populations had the highest private allelic richness, indicating long-term large population sizes in this region. As a thermophilic species, A. vernalis seems unlikely to have survived in the cold deserts of the Last Glacial Maximum in Western Siberia, so this region was likely (re)colonized postglacially. Overall, our results reinforce the importance of identifying the area of origin and the corresponding ecological requirements of steppe plants in order to understand the composition of today's steppe flora.

From Western Asia to the Mediterranean Basin: Diversification of the Widespread Euphorbia nicaeensis Alliance (Euphorbiaceae)

The Mediterranean Basin is an important biodiversity hotspot and one of the richest areas in the world in terms of plant diversity. Its flora parallels in several aspects that of the Eurasian steppes and the adjacent Irano-Turanian floristic region. The Euphorbia nicaeensis alliance spans this immense area from the western Mediterranean to Central Asia. Using an array of complementary methods, ranging from phylogenomic and phylogenetic data through relative genome size (RGS) estimation to morphometry, we explored relationships and biogeographic connections among taxa of this group. We identified the main evolutionary lineages, which mostly correspond to described taxa. However, despite the use of highly resolving Restriction Site Associated DNA (RAD) sequencing data, relationships among the main lineages remain ambiguous. This is likely due to hybridisation, lineage sorting triggered by rapid range expansion, and polyploidisation. The phylogenomic data identified cryptic diversity in the Mediterranean, which is also correlated with RGS and, partly, also, morphological divergence, rendering the description of a new species necessary. Biogeographic analyses suggest that Western Asia is the source area for the colonisation of the Mediterranean by this plant group and highlight the important contribution of the Irano-Turanian region to the high diversity in the Mediterranean Basin. The diversification of the E. nicaeensis alliance in the Mediterranean was triggered by vicariance in isolated Pleistocene refugia, morphological adaptation to divergent ecological conditions, and, to a lesser extent, by polyploidisation.

Extensive polyploid clonality was a successful strategy for seagrass to expand into a newly submerged environment

Polyploidy has the potential to allow organisms to outcompete their diploid progenitor(s) and occupy new environments. Shark Bay, Western Australia, is a World Heritage Area dominated by temperate seagrass meadows including Poseidon's ribbon weed, Posidonia australis. This seagrass is at the northern extent of its natural geographic range and experiences extremes in temperature and salinity. Our genomic and cytogenetic assessments of 10 meadows identified geographically restricted, diploid clones (2n = 20) in a single location, and a single widespread, high-heterozygosity, polyploid clone (2n = 40) in all other locations. The polyploid clone spanned at least 180 km, making it the largest known example of a clone in any environment on earth. Whole-genome duplication through polyploidy, combined with clonality, may have provided the mechanism for P. australis to expand into new habitats and adapt to new environments that became increasingly stressful for its diploid progenitor(s). The new polyploid clone probably formed in shallow waters after the inundation of Shark Bay less than 8500 years ago and subsequently expanded via vegetative growth into newly submerged habitats.

Genome Size Variation in Dianthus sylvestris Wulfen sensu lato (Caryophyllaceae)

Genome size (GS) is an important characteristic that may be helpful in delimitation of taxa, and multiple studies have shown correlations between intraspecific GS variation and morphological or environmental factors, as well as its geographical segregation. We estimated a relative GS (RGS) of 707 individuals from 162 populations of Dianthus sylvestris with a geographic focus on the Balkan Peninsula, but also including several populations from the European Alps. Dianthus sylvestris is morphologically variable species thriving in various habitats and six subspecies have been recognized from the Balkan Peninsula. Our RGS data backed-up with chromosome counts revealed that the majority of populations were diploid (2n = 30), but ten tetraploid populations have been recorded in D. sylvestris subsp. sylvestris from Istria (Croatia, Italy). Their monoploid RGS is significantly lower than that of the diploids, indicating genome downsizing. In addition, the tetraploids significantly differ from their diploid counterparts in an array of morphological and environmental characteristics. Within the diploid populations, the RGS is geographically and only partly taxonomically correlated, with the highest RGS inferred in the southern Balkan Peninsula and the Alps. We demonstrate greater RGS variation among the Balkan populations compared to the Alps, which is likely a result of more pronounced evolutionary differentiation within the Balkan Peninsula. In addition, a deep RGS divergence within the Alps likely points to persistence of the alpine populations in different Pleistocene refugia.

Congruent evolutionary responses of European steppe biota to late Quaternary climate change

Quaternary climatic oscillations had a large impact on European biogeography. Alternation of cold and warm stages caused recurrent glaciations, massive vegetation shifts, and large-scale range alterations in many species. The Eurasian steppe biome and its grasslands are a noteworthy example; they underwent climate-driven, large-scale contractions during warm stages and expansions during cold stages. Here, we evaluate the impact of these range alterations on the late Quaternary demography of several phylogenetically distant plant and insect species, typical of the Eurasian steppes. We compare three explicit demographic hypotheses by applying an approach combining convolutional neural networks with approximate Bayesian computation. We identified congruent demographic responses of cold stage expansion and warm stage contraction across all species, but also species-specific effects. The demographic history of the Eurasian steppe biota reflects major paleoecological turning points in the late Quaternary and emphasizes the role of climate as a driving force underlying patterns of genetic variance on the biome level.

Stability in the South, Turbulence Toward the North: Evolutionary History of Aurinia saxatilis (Brassicaceae) Revealed by Phylogenomic and Climatic Modelling Data

The Balkan Peninsula played an important role in the evolution of many Mediterranean plants and served as a major source for post-Pleistocene colonisation of central and northern Europe. Its complex geo-climatic history and environmental heterogeneity significantly influenced spatiotemporal diversification and resulted in intricate phylogeographic patterns. To explore the evolutionary dynamics and phylogeographic patterns within the widespread eastern Mediterranean and central European species Aurinia saxatilis, we used a combination of phylogenomic (restriction-site associated DNA sequencing, RADseq) and phylogenetic (sequences of the plastid marker ndhF) data as well as species distribution models generated for the present and the Last Glacial Maximum (LGM). The inferred phylogenies retrieved three main geographically distinct lineages. The southern lineage is restricted to the eastern Mediterranean, where it is distributed throughout the Aegean area, the southern Balkan Peninsula, and the southern Apennine Peninsula, and corresponds to the species main distribution area during the LGM. The eastern lineage extends from the eastern Balkan Peninsula over the Carpathians to central Europe, while the central lineage occupies the central Balkan Peninsula. Molecular dating places the divergence among all the three lineages to the early to middle Pleistocene, indicating their long-term independent evolutionary trajectories. Our data revealed an early divergence and stable in situ persistence of the southernmost, eastern Mediterranean lineage, whereas the mainland, south-east European lineages experienced more complex and turbulent evolutionary dynamics triggered by Pleistocene climatic oscillations. Our data also support the existence of multiple glacial refugia in southeast Europe and highlight the central Balkan Peninsula not only as a cradle of lineage diversifications but also as a source of lineage dispersal. Finally, the extant genetic variation within A. saxatilis is congruent with the taxonomic separation of peripatric A. saxatilis subsp. saxatilis and A. saxatilis subsp. orientalis, whereas the taxonomic status of A. saxatilis subsp. megalocarpa remains doubtful.

Little hope for the polyploid endemic Pyrenean Larkspur (Delphinium montanum): Evidences from population genomics and Ecological Niche Modeling

Species endemic to restricted geographical ranges represent a particular conservation issue, be it for their heritage interest. In a context of global change, this is particularly the case for plants which belong to high-mountain ecosystems and, because of their ecological requirements, are doomed to survive or disappear on their "sky islands". The Pyrenean Larkspur (Delphinium montanum, Ranunculaceae) is endemic to the Eastern part of the Pyrenees (France and Spain). It is now only observable at a dozen of localities and some populations show signs of decline, such as a recurrent lack of flowering. Implementing population genomics approach (e.g., RAD-seq like) is particularly useful to understand genomic patterns of diversity and differentiation in order to provide recommendations in term of conservation. However, it remains challenging for species such as D. montanum that are autotetraploid with a large genome size (1C-value >10 pg) as most methods currently available were developed for diploid species. A Bayesian framework able to call genotypes with uncertainty allowed us to assess genetic diversity and population structure in this system. Our results show evidence for inbreeding (mean G IS = 0.361) within all the populations and substantial population structure (mean G ST = 0.403) at the metapopulation level. In addition to a lack of connectivity between populations, spatial projections of Ecological Niche Modeling (ENM) analyses under different climatic scenarios predict a dramatic decrease of suitable habitat for D. montanum in the future. Based on these results, we discuss the relevance and feasibility of different conservation measures.

Low-coverage reduced representation sequencing reveals subtle within-island genetic structure in Aldabra giant tortoises

Aldabrachelys gigantea (Aldabra giant tortoise) is one of only two giant tortoise species left in the world and survives as a single wild population of over 100,000 individuals on Aldabra Atoll, Seychelles. Despite this large current population size, the species faces an uncertain future because of its extremely restricted distribution range and high vulnerability to the projected consequences of climate change. Captive-bred A. gigantea are increasingly used in rewilding programs across the region, where they are introduced to replace extinct giant tortoises in an attempt to functionally resurrect degraded island ecosystems. However, there has been little consideration of the current levels of genetic variation and differentiation within and among the islands on Aldabra. As previous microsatellite studies were inconclusive, we combined low-coverage and double-digest restriction-associated DNA (ddRAD) sequencing to analyze samples from 33 tortoises (11 from each main island). Using 5426 variant sites within the tortoise genome, we detected patterns of within-island population structure, but no differentiation between the islands. These unexpected results highlight the importance of using genome-wide genetic markers to capture higher-resolution genetic structure to inform future management plans, even in a seemingly panmictic population. We show that low-coverage ddRAD sequencing provides an affordable alternative approach to conservation genomic projects of non-model species with large genomes.

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.

Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework

Multi-locus genetic data are pivotal in phylogenetics. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. In phylogeography, the use of HTS has concentrated on a few taxonomic groups, and the amount of data used to resolve a phylogeographic pattern often seems arbitrary. We explore the performance of two genetic marker sampling strategies and the effect of marker quantity in a comparative phylogeographic framework focusing on six species (arthropods and plants). The same analyses were applied to data inferred from amplified fragment length polymorphism fingerprinting (AFLP), a cheap, non-HTS based technique that is able to straightforwardly produce several hundred markers, and from restriction site associated DNA sequencing (RADseq), a more expensive, HTS-based technique that produces thousands of single nucleotide polymorphisms. We show that in four of six study species, AFLP leads to results comparable with those of RADseq. While we do not aim to contest the advantages of HTS techniques, we also show that AFLP is a robust technique to delimit evolutionary entities in both plants and animals. The demonstrated similarity of results from the two techniques also strengthens biological conclusions that were based on AFLP data in the past, an important finding given the wide utilization of AFLP over the last decades. We emphasize that whenever the delimitation of evolutionary entities is the central goal, as it is in many fields of biodiversity research, AFLP is still an adequate technique.