Approximate Bayesian Computation Untangles Signatures of Contemporary and Historical Hybridization between Two Endangered Species.

Contemporary gene flow, when resumed after a period of isolation, can have crucial consequences for endangered species, as it can both increase the supply of adaptive alleles and erode local adaptation. Determining the history of gene flow and thus the importance of contemporary hybridization, however, is notoriously difficult. Here, we focus on two endangered plant species, Arabis nemorensis and A. sagittata, which hybridize naturally in a sympatric population located on the banks of the Rhine. Using reduced genome sequencing, we determined the phylogeography of the two taxa but report only a unique sympatric population. Molecular variation in chloroplast DNA indicated that A. sagittata is the principal receiver of gene flow. Applying classical D-statistics and its derivatives to whole-genome data of 35 accessions, we detect gene flow not only in the sympatric population but also among allopatric populations. Using an Approximate Bayesian computation approach, we identify the model that best describes the history of gene flow between these taxa. This model shows that low levels of gene flow have persisted long after speciation. Around 10 000 years ago, gene flow stopped and a period of complete isolation began. Eventually, a hotspot of contemporary hybridization was formed in the unique sympatric population. Occasional sympatry may have helped protect these lineages from extinction in spite of their extremely low diversity.

Species diversity of Arabis alpina L. communities in two Pb/Zn mining areas with different smelting history in Yunnan Province, China.

In order to explore the species compositions and species diversity (Dominance (Do), Shannon-Wiener index (H'), Simpson diversity index (Dsi), Species richness (DMG), Pielou evenness index (Epi) and Frequency (Fr)) of twenty Arabis alpina L. var. parviflora Franch communities, field investigation was conducted in Huize county, Yunnan province, China. Some 20 A. alpina communities were distributed in two traditional smelting tailing piles of Minbingyingjiying (TST) and Shangduoduo village (SDD) with different Pb smelting history. The morphological characteristics (plant height, branch number, basal leaf length, basal leaf width and root morphology) of A. alpina, contents and accumulation characteristics of eight potentially toxic metals (As, Cd, Cr, Cu, Pb, Zn, Al, Fe) in soil and plants were analyzed. The results showed that the morphological characteristics of A. alpina were mean plant height 12.25 cm, the basal leaf length 17.69 cm, leaf width 5.40 cm, the total root length 117.86 cm plant-1, the root diameter 0.90 mm. The leaves of A. alpina in SDD were longer and narrower with higher plant height compared with in TST. The main companion plants of A. alpina were Sporobolus fertilis (Steud.) W. D. Clayt, Arenaria orbiculata Royle ex Edgew. et Hook. F. and Eulalia speciosa. (Debeaux). The H' and Dsi were 0.56-2.04 and 0.44-0.95, respectively. The plant species numbers, H', Dsi and Epi of A. alpina communities in TST were higher than those in SDD. Pb contents in shoot of two A. alpina samples were more than 1000 mg kg-1, Cd content in shoot of one A. alpina sample >100 mg kg-1 and Zn contents in shoot of seven A. alpina samples >10,000 mg kg-1 with the enrichment factors and transport coefficients greater than 1. The results indicate that A. alpina as a Zn, Pb and Cd hyperaccumulator, could be used for long-term phytoremediation of soils contaminated by Cd, Pb and Zn. Species diversity of A. alpina community during long-term natural vegetation restoration was high in the middle succession with single-peak model, and A. alpina would be dominant in the succession climax stage in potentially toxic metal contamination areas.

Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae).

Advances in high-throughput sequencing have promoted the collection of reference genomes and genome-wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single-nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Here, we sequenced the full genomes of 304 individuals of Arabis alpina sampled from four nearby natural populations to genotype SNPs as well as polymorphic long terminal repeat retrotransposons (polymorphic TEs; i.e., presence/absence of TE insertions at specific loci). We identified 291,396 SNPs and 20,548 polymorphic TEs, comparing their contributions to genomic diversity and divergence across populations. Few SNPs were shared among populations and overall showed high population-specific variation, whereas most polymorphic TEs segregated among populations. The genomic context of these two classes of variants further highlighted candidate adaptive loci having a putative impact on functional genes. In particular, 4.96% of the SNPs were identified as nonsynonymous or affecting start/stop codons. In contrast, 43% of the polymorphic TEs were present next to Arabis genes enriched in functional categories related to the regulation of reproduction and responses to biotic as well as abiotic stresses. This unprecedented data set, mapping variation gained from SNPs and complementary polymorphic TEs within and among populations, will serve as a rich resource for addressing microevolutionary processes shaping genome variation.

Repetitive flanking sequences challenge microsatellite marker development: a case study in the lepidopteran Melanargia galathea.

Microsatellite DNA families (MDF) are stretches of DNA that share similar or identical sequences beside nuclear simple-sequence repeat (nSSR) motifs, potentially causing problems during nSSR marker development. Primers positioned within MDFs can bind several times within the genome and might result in multiple banding patterns. It is therefore common practice to exclude MDF loci in the course of marker development. Here, we propose an approach to deal with multiple primer-binding sites by purposefully positioning primers within the detected repetitive element. We developed a new protocol to determine the family type and the primer position in relation to MDFs using the software packages repark and repeatmasker together with an in-house R script. We re-evaluated newly developed nSSR markers for the lepidopteran Marbled White (Melanargia galathea) and explored the implications of our results with regard to published data sets of the butterfly Euphydryas aurinia, the grasshopper Stethophyma grossum, the conifer Pinus cembra and the crucifer Arabis alpina. For M. galathea, we show that it is not only possible to develop reliable nSSR markers for MDF loci, but even to benefit from their presence in some cases: We used one unlabelled primer, successfully binding within an MDF, for two different loci in a multiplex PCR, combining this family primer with uniquely binding and fluorescently labelled primers outside of MDFs, respectively. As MDFs are abundant in many taxa, we propose to consider these during nSSR marker development in taxa concerned. Our new approach might help in reducing the number of tested primers during nSSR marker development.

Development of an Arabis alpina genomic contig sequence data set and application to single nucleotide polymorphisms discovery.

The alpine plant Arabis alpina is an emerging model in the ecological genomic field which is well suited to identifying the genes involved in local adaptation in contrasted environmental conditions, a subject which remains poorly understood at molecular level. This study presents the assembly of a pool of A. alpina genomic fragments using next-generation sequencing technologies. These contigs cover 172 Mb of the A. alpina genome (i.e. 50% of the genome) and were shown to contain sequences giving positive hits against 96% of the 458 CEGMA core genes (Core Eukaryotic Genes Mapping Approach), a set of highly conserved eukaryotic genes. Regions presenting high nucleic sequence identity with 77% of the close relative Arabidopsis thaliana's genes were found with an unbiased distribution across the different functional categories of A. thaliana genes. This new resource was tested using a resequencing assay to identify polymorphic sites. Sixteen samples were successfully analysed and 127,041 single-nucleotide polymorphisms identified. This contig data set will contribute to improving our understanding of the ecology of Arabis alpina, thus constituting an important resource for future ecological genomic studies.

Systematics and evolution of Arctic-Alpine Arabis alpina (Brassicaceae) and its closest relatives in the eastern Mediterranean.

PREMISE OF THE STUDY: The high mountains in southern Anatolia and the eastern Mediterranean are assumed to play a major role as a primary center of genetic diversity and species richness in Eurasia. We tested this hypothesis by focusing on the widespread perennial arctic-alpine Arabis alpina and its sympatrically distributed closest relatives in the eastern Mediterranean. METHODS: Plastid (trnL intron, trnL-F intergenic spacer) and nuclear (ITS) DNA sequence analysis was used for phylogenetic reconstruction. Broad-scale plastid haplotype analyses were conducted to infer ancestral biogeographic patterns. KEY RESULTS: Five Arabis species, identified from the eastern Mediterranean (Turkey mainland and Cyprus), evolved directly and independently from A. alpina, leaving Arabis alpina as a paraphyletic taxon. These species are not affected by hybridization or introgression, and species divergence took place at the diploid level during the Pleistocene. CONCLUSIONS: Pleistocene climate fluctuations produced local altitudinal range-shifts among mountain glacial survival areas, resulting not only in the accumulation of intraspecific genotype diversity but also in the formation of five local species. We also show that the closest sister group of Arabis alpina consists exclusively of annuals/winter annuals and diverged prior to Pleistocene climatic fluctuations during the colonization of the lowland Mediterranean landscape. These findings highlight that Anatolia is not only a center of species richness but also a center for life-history diversification.

Pleistocene colonization of afro-alpine 'sky islands' by the arctic-alpine Arabis alpina.

The afro-alpine region comprises the high mountains of Ethiopia and tropical East Africa, which represent biological 'sky islands' with high level of endemism. However, some primarily arctic-alpine plants also occur in the afro-alpine mountains. It has been suggested that these plants are Tertiary relicts, but a recent worldwide study of Arabis alpina suggests that this species colonized the region twice during the Pleistocene. Here we investigate the detailed colonization history of A. alpina in the afro-alpine region based on chloroplast DNA sequences from 11 mountain systems. The results confirm the twice-into-Africa scenario. The Asian lineage is confined to the mountains closest to the Arabian Peninsula, on opposite sides of the Rift Valley (Simen Mts and Gara Muleta in Ethiopia), suggesting long-distance dispersal of this lineage. The African lineage is divided into two phylogeographic groups with distinct geographic distribution. The observed pattern is consistent with isolation of the African lineage in at least two interglacial refugia, located on separated highlands, followed by range expansion in cooler period(s), when the afro-alpine habitat extended further down the mountains. Several long-distance dispersal events, also across the Rift Valley, are suggested by single haplotypes observed outside the area occupied by the phylogeographic groups they belonged to.

Multiple hybrid formation in natural populations: concerted evolution of the internal transcribed spacer of nuclear ribosomal DNA (ITS) in North American Arabis divaricarpa (Brassicaceae).

DNA sequence variation of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA from Arabis holboellii, A. drummondii, and its putative hybrid A. divaricarpa was analyzed to study hybrid speciation in a species system geographically covering nearly the entire North American continent. Based on molecular systematics the investigated species are better combined under the genus Boechera. Multiple intraindividual ITS copies were detected in numerous accessions of A. divaricarpa, and, to a minor extent, in the parental taxa. Comparative phylogenetic analysis demonstrates that reticulate evolution is common. Consequently, concerted evolution of ITS regions resulted in different types of ITS fragments not only in hybrid populations but also in one of the parental taxa, A. holboellii. Hybrid formation often occurred independently at different sites and at different times, which is reflected by ITS copies resampling the original parental sequence variation in different ways. Some biogeographic structuring of genetic diversity is apparent and mirrors postglacial migration routes. Hybridization, reticulation, and apomixis are assumed to be the major forces driving speciation processes in this species complex. Analysis of conserved regions and secondary structures of the ITS region provided no evidence that, in this system, hybrid ITS evolution is predominantly driven in a particular direction. However, two regions in the ITS1 and ITS2, respectively, show higher mutation rates than expected from outgroup comparisons. Strong evidence for the occurrence of apomixis in A. holboellii and A. divaricarpa has come from pollen size measurements and estimations of pollen quality, which favor the hypothesis that A. drummondii served as paternal hybridization partner more frequently than A. holboellii.