Biology subjects

Hoerandl, E.

Publications and source records attributed to Hoerandl, E..

4 recordsLinked to original sources

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↗

bioRxiv2020

Phylogenomics supported by geometric morphometrics reveals delimitation of sexual species within the polyploid apomictic Ranunculus auricomus complex (Ranunculaceae)

Species are the basic units of biodiversity and evolution. Nowadays, they are widely considered as ancestor-descendant lineages. Their definition remains a persistent challenge for taxonomists due to lineage evolutionary role and circumscription, i.e., persistence in time and space, ecological niche or a shared phenotype of a lineage. Recognizing and delimiting species is particularly methodically challenging in fast-evolving, evolutionary young species complexes often characterized by low genetic divergence, hybrid origin, introgression and incomplete lineage sorting (ILS). Ranunculus auricomus is a large Eurasian apomictic polyploid complex that probably has arisen from the hybridization of a few sexual progenitor species. However, even delimitation and relationships of diploid sexual progenitors have been unclearly ranging from two to twelve species. Here, we present an innovative workflow combining phylogenomic methods based on 86,782 parameter-optimized RADseq loci and target enrichment of 663 nuclear genes together with geometric morphometrics to delimit sexual species in this evolutionary young complex (< 1 Mya). For the first time, we revealed a fully resolved and well-supported maximum likelihood (ML) tree phylogeny congruent to neighbor-net network and STRUCTURE results based on RADseq data. In a few clades, we found evidence of discordant patterns indicated by quartet sampling (QS) and reticulation events in the neighbor-net network probably caused by introgression and ILS. Together with coalescent-based species delimitation approaches based on target enrichment data, we found five main genetic lineages, with an allopatric distribution in Central and Southern Europe. A concatenated geometric morphometric data set including basal and stem leaves, as well as receptacles, revealed the same five main clusters. We accept those five morphologically differentiated, geographically isolated, genetic main lineages as species: R. cassubicifolius s.l. (incl. R. carpaticola), R. flabellifolius, R. envalirensis s.l. (incl. R. cebennensis), R. marsicus and R. notabilis s.l. (incl. R. austroslovenicus, R. calapius, R. mediocompositus, R. peracris and R. subcarniolicus). Our comprehensive workflow combing phylogenomic methods supported by geometric morphometrics proved to be successful in delimiting closely related sexual taxa and applying an evolutionary species concept, which is also transferable to other evolutionarily young species complexes.

evolutionary biology↗

bioRxiv2020

Phylogenomics unravels speciation patterns in temperate-montane plant species: a case study on the recently radiating Ranunculus auricomus species complex

The time frame and geographical patterns of diversification processes in European temperate-montane herbs are still not well understood. We used the sexual species of the Ranunculus auricomus complex as a model system to understand how vicariance vs. dispersal processes in the context of Pleistocene climatic fluctuations have triggered speciation in temperate-montane plant species. We employed Target Enrichment sequence data from about 600 nuclear genes and coalescent-based species tree inference methods to resolve phylogenetic relationships among the sexual taxa of the complex. We estimated absolute divergence times and, using ancestral range reconstruction, we tested if speciation was rather enhanced by vicariance or dispersal processes. Phylogenetic relationships among taxa were fully resolved. Incongruence among species trees mainly concerned the intraspecific relationships in R. notabilis s.l., R. cassubicifolius s.l., and the position of the tetraploid R. marsicus. Speciation events took place in a very short time at the end of the Mid-Pleistocene Transition (830-580 ka). A second wave of intraspecific geographical differentiation within and around the European mountain systems happened between 200-100 ka. Ancestral range reconstruction supports the existence of a widespread European ancestor of the R. auricomus complex. Vicariance processes have triggered allopatric speciation in temperate-montane plant species during the climatic deterioration occurred in the last phase of the Mid-Pleistocene Transition. Vegetation restructuring from forest into tundra could have confined these forest species into isolated glacial refugia. During subsequent warming periods, range expansions of these locally distributed species could have been hampered by congeneric competitors in the same habitat.

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↗