Biology subjects

Nürk, N. M.

Publications and source records attributed to Nürk, N. M..

3 recordsLinked to original sources

bioRxiv2026

Enrichment Probe Sets Combining Universal and Lineage-Specific Targets Help Resolve Recalcitrant Lineages

The combination of target capture sequencing (TCS) with low-coverage whole genome sequencing (lcWGS), an approach known as Hyb-Seq, has allowed the integration of natural history collections into the genomics revolution, transforming biodiversity research. To implement Hyb-Seq, a collection of genomic targets, often nuclear orthologs, is needed to design probes for TCS. In flowering plants, the universal Angiosperms353 probe set has been proven resolutive at multiple evolutionary scales, with caveats. Malpighiales is known to be one of the most challenging flowering plant orders to resolve. Within this order, the clusioid clade ([~]2.2K species, 94 genera, five families) is no exception. To resolve phylogenetic relationships in this recalcitrant clade, we design a custom probe set, the Clusioids626 kit, composed of 39,936 120-mer probes targeting 626 nuclear orthologs ([~]6.6M nucleotides). This probe set includes all Angiosperms353 targets and 273 clusioid-specific ones, carefully chosen taking copy-number, length evenness, and phylo-informativeness into account. We test our probe set on 70 accessions representing all families and tribes in the clusioid clade. On average, 50.4% of TCS reads mapped to our targets, recovering a median of [~]600 orthologs. Relationships for all clusioid families are fully resolved for our nuclear targets. Additionally, 105 plastid coding DNA sequences were retrieved from the lcWGS fraction. A strong cyto-nuclear conflict was detected. The Clusioids626 kit performs better than the universal Angiosperms353 enrichment panel alone. Our kit design workflow can be extended into other lineages for which a universal probe set exists but more resolution is needed.

evolutionary biology↗

bioRxiv2023

The dynamics of species divergence in South Africa's megadiverse Cape region.

Deciphering the ecological and geographic factors that influence the dynamics of population divergence can aid in understanding why some groups of organisms diversify more prolifically than others. One such diverse group is the heathers (Erica, Ericaceae), whose exceptional species richness in the Cape Floristic Region is enigmatic. Here, we study Erica abietina, a small but highly variable species complex with four described subspecies differing in geographic range, habitat, and floral characters associated with pollination. To understand the factors and forces that shaped its evolution, we evaluate the status of the subspecies and test for hybridisation, introgression, pollinator-driven divergence, and geographic population structure using genotyping-by-sequencing on samples across the entire distribution. We find that the four subspecies form variably distinct genetic groups, however, the most widespread subspecies exhibits cryptic diversity comprising two independent lineages that are geographically isolated and occur on different soil types. Phylogenetic results suggest that shifts between bird- and insect-pollination syndromes have occurred twice independently, with accompanying genetic divergence. However, for one pair of genetically distinct populations (FST{approx} 0.06) with different pollinators we uncover several individuals of hybrid origin at a site where they occur sympatrically. Together, these results suggest that floral differentiation driven by divergent selection acts in concert with geographic isolation to maintain reproductive isolation. Finally, we show that a reticulate history involving "ghost" introgression best explains the groups evolution. Our results reveal a highly dynamic system whose diversity has been shaped by a variety of interacting forces, and we suggest that such systems are likely to have contributed substantially to the diversity of Erica and the Cape flora in general.

evolutionary biology↗

bioRxiv2019

Diversification in evolutionary arenas -- assessment and synthesis

Understanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography, and the metaphorical concepts of adaptive radiation and evolutionary stasis describe two opposing aspects causing variation in diversification rates. Here we review the central concepts in the evolutionary diversification literature and synthesize these into a simple, general framework for studying rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions and across spatial and temporal scales. Our framework describes the diversification rate (d) as a function of the abiotic environment (a), the biotic environment (b) and clade-specific phenotypes or traits (c); thus d[~]a,b,c. We refer to the four components (a-d) and their interactions collectively as the Evolutionary Arena. We outline analytical approaches to this framework and present a case study on conifers, for which we parameterise the general model. We also discuss three conceptual examples: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating connectivity due to climatic oscillations; oceanic island radiations in the context of island formation and erosion; and biotically driven radiations of the Mediterranean orchid genus Ophrys. The results of the conifer case study are consistent with the long-standing scenario that low competition and high rates of niche evolution promote diversification. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework helps to identify and structure future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge.

evolutionary biology↗