Biology subjects

Wagner, N. D.

Publications and source records attributed to Wagner, N. D..

3 recordsLinked to original sources

bioRxiv2020

Conservation genomics of an Australian orchid complex with implications for the taxonomic and conservation status of Corybas dowlingii

This study assessed genomic diversity in an Australian species complex in the helmet orchids to clarify taxonomic delimitation and conservation status of the threatened species Corybas dowlingii, a narrow endemic from southeast Australia. Taxonomic delimitation between the three closely related species C. aconitiflorus, C. barbarae, and C. dowlingii has been mainly based on floral traits which exhibit varying degrees of overlap, rendering species delimitation in the complex difficult. Genomic data for the species complex was generated using double-digest restriction-site associated DNA (ddRAD) sequencing. Maximum likelihood, NeighborNet, and Bayesian structure analyses showed genetic differentiation within the species complex and retrieved genomic signatures consistent with hybridisation and introgression between C. aconitiflorus and C. barbarae, and an intermediate genetic position of C. dowlingii indicating a hybrid origin of the species. The genetic structure analysis showed varying levels of genetic admixture for several C. aconitiflorus, C. barbarae, and C. dowlingii samples, thus further corroborating the presence of hybridisation and introgression within the species complex. The taxonomic status of C. dowlingii D.L.Jones was revised to C. x dowlingii D.L.Jones stat. nov. to reflect its hybrid origin. The conservation status of C. x dowlingii was assessed based on key ecological and ethical aspects, and recommendations made regarding its conservation status in Australian conservation legislation.

genetics↗

bioRxiv2020

RAD sequencing data reveal a radiation of willow species (Salix L., Salicaceae) in the Hengduan Mountains and adjacent areas

The Hengduan Mountains (HDM) in South West China are an important hotspot of plant diversity and endemism and considered to be a secondary diversification center for the woody plant genus Salix (Salicaceae). This study aimed to reconstruct the spatio-temporal evolution of the Salix Chamaetia-Vetrix clade in the HDM and to test for the occurrence of a radiation. We inferred phylogenetic relationships based on more than 34,000 RAD loci of 27 species. Phylogenetic analyses recovered a well-resolved tree topology with two major clades, the Eurasian and the HDM clade and a divergence time of c. 23.9 Ma. The HDM clade comprises two subclades. The species of the HDM clade originated in north HDM and adjacent areas and then dispersed into the south HDM, westwards to the Himalayas and eastwards to the Qinling Mountains. Niche modelling analyses revealed that during the last glacial maximum, range contractions were observed in the northern areas, while southward expansions resulted in range overlaps. The reconstruction of putative adaptive character evolution of plant height, inflorescence and flower morphology indicate that adaptations to altitudinal distribution contributed to the diversification of the HDM willows. Our data indicate that a radiation occurred in HDM within the Salix Chamaetia-Vetrix clade. Dispersal within the mountain system and to adjacent regions as well as survival in glacial refugia have shaped the biogeographical history of the clade. Differentiation along altitudinal zonation concomitant to morphological adaptations to colder climates may be important ecological factors for the high species diversity of Salix in this area.

evolutionary biology↗

bioRxiv2019

Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data

AO_SCPLOWBSTRACTC_SCPLOWDespite the general progress in using next generation sequencing techniques for evolutionary research questions, the analysis of polyploid species is still hampered by the lack of suitable analytical tools and the statistical difficulties of dealing with more than two alleles per locus. Polyploidization and especially allopolyploidy leads to new combinations of traits by combining genomes of two or more parental species. This enhances the adaptive potential and often results in speciation. However, multiple origins of polyploids, backcrossing to the parental species and post-origin evolution can strongly influence the genome composition of polyploid species. Here, we used RAD sequencing, which revealed 23,393 loci and 320,010 high quality SNPs, to analyze the relationships and origin of seven polyploid species of the diverse genus Salix by utilizing a phylogenomic and a network approach, as well as analyzing the genetic structure and composition of the polyploid genome in comparison to putative parental species. We adapted the SNiPloid pipeline that was originally developed to analyse SNP composition of recently established allotetraploid crop lineages to RAD sequencing data by using concatenated RAD loci as reference. Our results revealed a well-resolved phylogeny of 35 species of Eurasian shrub willows (Salix subg. Chamaetia/Vetrix), including 28 diploid and 7 polyploid species. Polyploidization in willows appears to be predominantly connected to hybridization, i.e. to an allopolyploid origin of species. More ancient allopolyploidization events involving hybridization of more distantly related, ancestral lineages were observed for two hexaploid and one octoploid species. Our data suggested a more recent allopolyploid origin for the included tetraploids within the major subclades and identified putative parental taxa that appear to be plausible in the context of geographical, morphological and ecological patterns. SNiPloid and HyDe analyses disentangled the different genomic signatures resulting from hybrid origin, backcrossing, and secondary post-origin evolution in the polyploid species. All tetraploids showed a considerable post-origin, species-specific proportion of SNPs. The amount of extant hybridization appears to be related to the degree of geographical and ecological isolation of species. Our data demonstrate that high-quality RAD sequencing data are suitable and highly informative for the analysis of the origin and relationships of polyploid species. The combination of the traditional tools RAxML, STRUCTURE, SplitsTree and recently developed programs like SNAPP, HyDe and SNiPloid established a bioinformatic pipeline for unraveling the complexity of polyploid genomes.

evolutionary biology↗