Biology subjects

Pearman, P. B.

Publications and source records attributed to Pearman, P. B..

3 recordsLinked to original sources

bioRxiv2025

Universal single-copy genes and 16S rDNA present incongruent evolutionary histories in Vibrio

A common technique for the study of the diversity and evolution of microbial communities is 16S rDNA sequencing. However, high sequence identity and variable copy number constrain the application of 16S rDNA in differentiation of closely related taxa and estimation of species relative abundance in environmental samples. A promising alternative is the use of universal single-copy genes (USCGs) as phylogenetic markers. We develop this by analyzing a set of USCG loci from the genus Vibrio, which holds over 100 species of substantial ecological and epidemiological relevance. The phylogenetic histories of these loci, of representative copies of 16S and 23S rDNA genes, and of a collection of 16S rDNA partial sequences were reconstructed using Bayesian inference. Taxon resolution was assessed according to consensus tree topology and clade credibility values. In addition, the congruence among posterior distributions of phylogenetic estimates of the different loci was calculated using Robinson-Foulds distances and visualized with non-metric multidimensional scaling (NMDS). Phylogenetic analyses reveal that USCG loci produce highly resolved trees in comparison to those of 16S and 23S rDNA sequences. We also observe relatively high congruence among phylogenies of USCG loci while rDNA phylogenies diverge from these. The loci mfd and uvrC are highlighted for further research on Vibrio evolution and analysis of environmental samples. Moreover, possible sources of phylogenetic incongruence between USCG and rDNA loci include differential susceptibility to horizontal gene transfer, as potentially explained by the complexity hypothesis, or lack of phylogenetic information due to limited sequence variability in rDNA sequences.

microbiology↗

bioRxiv2025

Independent colonisations of serpentine habitats highlight species-specific evolutionary histories of lineage diversification

Serpentine soils are characterized by high levels of heavy metals, low nutrient availability, and water scarcity, presenting significant ecological challenges for plant species. Nonetheless, some species have adapted successfully to these conditions. We investigate the population genomic structure, evolutionary history and phenotypic differentiation of three diploid generalist plant species, Lavandula stoechas L., Halimium atriplicifolium (Lam) Spach. subsp. atriplicifolium, and Phlomis purpurea L., all of which inhabit adjacent serpentine and non-serpentine soils in the Malaga region in the southern Iberian Peninsula (Spain). We explore whether populations from serpentine and non-serpentine soils represent distinct evolutionary lineages and whether there is genomic and phenotypic differentiation associated with serpentine conditions. We measured plant height and specific leaf area (SLA) to detect potential ecotypic variation associated with soil type. A ddRADseq SNP dataset was generated for each species, representing 10 populations from serpentine and 10 from non-serpentine soils. We ordinated genotype data to assess genomic variation, conducted an ADMIXTURE analysis to infer ancestral groups, and used Treemix analyses to investigate phylogenetic relationships and gene flow events between populations. Isolation by distance (IBD) analyses evaluated the role of geographic separation in observed genomic differentiation. Our results reveal species-specific patterns of genomic, and to some extent phenotypic, differentiation between serpentine and non-serpentine populations, with evidence of multiple colonisations of serpentine sites in all three species. The study highlights the role of historical differentiation and subsequent gene flow in shaping the genomic structure of plant populations, alongside observed variation in phenotypic traits across environments.

evolutionary biology↗

bioRxiv2023

Conserving genetic diversity during climate change:Niche marginality and discrepant monitoring capacity in Europe

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. Genetic diversity has been largely neglected in biodiversity monitoring, and when addressed is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. Genetic monitoring supports the conservation and management of fisheries, game, and threatened populations. It also can contribute to the assessment of predicted and realized impacts of climate change, and their management. We report the first accounting of genetic monitoring efforts among countries in Europe (their genetic monitoring capacity, GMC) to determine where GMC suggests the combination of national infrastructure, political support and resources for continued and expanded monitoring. Overlaying GMC with areas where species ranges approach current and future climate niche limits (i.e., niche marginality) helps identify whether GMC coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area extent, financial resources, and conservation policy influence GMC, high values of which inconsistently match joint species patterns of climate niche marginality. Populations at niche margins likely hold genetic diversity that is important to adaptation to changing climate, and our results illuminate the need in Europe for expanded genetic monitoring across the climate gradients occupied by species, a need arguably greatest in southeastern European countries.

ecology↗