Biology subjects

Oxelman, B.

Publications and source records attributed to Oxelman, B..

5 recordsLinked to original sources

bioRxiv2023

Phylogeny inference under time-decaying migration and varying information content

AO_SCPLOWBSTRACTC_SCPLOWPostspeciation gene flow is widespread across the Tree of Life but is ignored as a cause of gene tree discordance under the standard multispecies coalescent. Where interspecific migration has occurred but is not modelled explicitly, effective population sizes, divergence times and topology can be seriously misestimated. Isolation-with-migration and multispecies coalescent-with-introgression models explicitly model migration but include additional parameters that limit their computational viability with even moderately sized molecular data sets. Here we simulate the evolution of sequences which vary in molecular information content under the coalescent while allowing continuous, tree-wide gene flow/migration between contemporaneous branches, the rate of which decreases with time since divergence. Using simulated sequences, we evaluate the performance of DENIM under rapidly to gradually time-decaying migration and benchmark its performance against the standard MSC method StarBeast3. DENIM consistently outperforms StarBeast3, both in phylogenetic accuracy and computational performance per core. Rapidly decaying migration is associated with improved topology and divergence time estimates under both DENIM and StarBeast3. While species tree estimation accuracy is not improved by increasing the number of loci from 30 to 60 under either method, model convergence is slowed considerably. By contrast, increasing sequence length to 10,000 bp has no clear effect on convergence rates, but shows a tendency towards increased accuracy in DENIM. We apply DENIM and StarBeast3 with a 36-locus empirical bat data set and recover species trees identical in topology to those obtained with 12,931 loci. Our work demonstrates that DENIM can deliver accurate phylogenetic estimates in the presence of both deep coalescence and empirically realistic migration patterns using as few as 30 loci with single-core runtimes of 2-3 days.

evolutionary biology↗

bioRxiv2021

Minimal clustering and species delimitation based on multi-locus alignments vs SNPs: the case of the Seriphium plumosum L. complex (Gnaphalieae: Asteraceae)

We applied species delimitation methods based on the Multi-Species Coalescent (MSC) model to 500+ loci derived from genotyping-by-sequencing on the South African Seriphium plumosum (Asteraceae) species complex. The loci were represented either as multiple sequence alignments or single nucleotide polymorphisms (SNPs), and analysed by the STACEY and Bayes Factor Delimitation (BFD)/SNAPP methods, respectively. Both methods supported species taxonomies where virtually all of the 32 sampled individuals, each representing its own geographical population, were identified as separate species. Computational efforts required to achieve adequate mixing of MCMC chains were considerable, and the species/minimal cluster trees identified similar strongly supported clades in replicate runs. The resolution was, however, higher in the STACEY trees than in the SNAPP trees, which is consistent with the higher information content of full sequences. The computational efficiency, measured as effective sample sizes of likelihood and posterior estimates per time unit, was consistently higher for STACEY. A random subset of 56 alignments had similar resolution to the 524-locus SNP data set. The STRUCTURE-like sparse Non-negative Matrix Factorisation (sNMF) method was applied to six individuals from each of 48 geographical populations and 28023 SNPs. Significantly fewer (13) clusters were identified as optimal by this analysis compared to the MSC methods. The sNMF clusters correspond closely to clades consistently supported by MSC methods, and showed evidence of admixture, especially in the western Cape Floristic Region. We discuss the significance of these findings, and conclude that it is important to a priori consider the kind of species one wants to identify when using genome-scale data, the assumptions behind the parametric models applied, and the potential consequences of model violations may have.

evolutionary biology↗

bioRxiv2018

Evolution of sex determination and heterogamety changes in section Otites of the genus Silene

Switches in heterogamety occasionally occur both in animals and plants, although plant sex determination systems are mostly more recently evolved than those of animals, and have had less time for switches to occur. However, our previous research revealed a switch in heterogamety in section Otites of the plant genus Silene.\n\nHere we analyse in detail the evolution of genetic sex determination in section Otites, which is estimated to have evolved about 0.55 MYA. Our study confirms female heterogamety in S. otites and newly reveals female heterogamety in S. borysthenica. Sequence analyses and genetic mapping show that the sex-linked regions of these two species are the same, but the region in S. colpophylla, a close relative with male heterogamety, is different. The sex chromosome pairs of S. colpophylla and S. otites each correspond to an autosome of the other species, and both differ from the XY pair in S. latifolia, in a different section of the genus. Our phylogenetic analysis suggests a possible change from female to male heterogamety within Silene section Otites, making these species suitable for detailed studies of the events involved.

evolutionary biology↗

bioRxiv2018

De novo transcriptome assembly, annotation, and identification of low-copy number genes in the flowering plant genus Silene (Caryophyllaceae)

Phylogenetic methods that rely on information from multiple, unlinked genes have recently been developed for resolving complex situations where evolutionary relationships do not conform to bifurcated trees and are more adequately depicted by networks. Such situations arise when successive interspecific hybridizations in combination with genome duplications have shaped species phylogenies. Several processes such as homoeolog loss and deep coalescence can potentially hamper our ability to recover the historical signal correctly. Consequently the prospect of reconstructing accurate phylogenies lies in the combination of several low-copy nuclear markers that when, used in concert, can provide homoeologs for all the ancestral genomes and help to disentangle gene tree incongruence due to deep coalescence events. Expressed sequence tag (EST) databases represent valuable resource for the identification of genes in organisms with uncharacterized genomes and for development of molecular markers. The genus Silene L. is a prime example of a plant group whose evolutionary history involves numerous events of hybridization and polyploidization. As for many groups there is currently a shortage of low-copy nuclear markers, for which phylogenetic usefulness has been demonstrated. Here, we present two EST libraries for two species of Silene that belong to large phylogenetic groups not previously investigated with next generation technologies. The assembled and annotated transcriptomes are used for identifying low copy nuclear regions, suitable for sequencing.

bioinformatics↗

bioRxiv2018

Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for non-model organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach is that it recovers a consistent set of loci, each with high sequencing depth, which leads to more confidence in the assembly of target sequences. High sequencing depth can also be used to identify phylogenetically informative allelic variation within sequenced individuals, but allele sequences are infrequently assembled in phylogenetic studies.\n\nInstead, many scientists perform their phylogenetic analyses using contig sequences which result from the de novo assembly of sequencing reads into contigs containing only canonical nucleobases, and this may reduce both statistical power and phylogenetic accuracy. Here, we develop an easy-to-use pipeline to recover allele sequences from sequence capture data, and we use simulated and empirical data to demonstrate the utility of integrating these allele sequences to analyses performed under the Multispecies Coalescent (MSC) model. Our empirical analyses of Ultraconserved Element (UCE) locus data collected from the South American hummingbird genus Topaza demonstrate that phased allele sequences carry sufficient phylogenetic information to infer the genetic structure, lineage divergence, and biogeographic history of a genus that diversified during the last three million years. The phylogenetic results support the recognition of two species, and suggest a high rate of gene flow across large distances of rainforest habitats but rare admixture across the Amazon River. Our simulations provide evidence that analyzing allele sequences leads to more accurate estimates of tree topology and divergence times than the more common approach of using contig sequences.

evolutionary biology↗