Graber, L. C. | bioRxiv Science

bioRxiv2023

Comparative phylogenomic analyses of SNP versus full locus datasets: insights and recommendations for researchers

PremiseIn phylogenomic analyses, no consensus exists on whether using single nucleotide polymorphisms (SNPs) or including flanking regions (full locus) is best, nor how strictly missing data should be filtered. Moreover, empirical evidence on whether SNP-only trees are suitable for downstream phylogenetic comparative methods such as divergence time estimation and ancestral state reconstructions is lacking. MethodsUsing GBS data from 22 taxa of Glycine, we addressed the effects of SNP vs. locus usage and filtering stringency on phylogenomic inference and phylogenetic comparative methods. We compared branch length, node support, and divergence time estimation across eight datasets with varying amounts of missing data and total size. ResultsOur results reveal five aspects of phylogenomic data usage: 1. tree topology is largely congruent regardless of data type or filtering parameters; 2. filtering missing data too strictly reduces the confidence in some relationships; 3. absolute branch lengths vary by two orders of magnitude between datasets; 4. data type and branch length variation have little effect on divergence time estimation; 5. phylograms significantly alter the estimation of ancestral states. DiscussionWhen conducting phylogenomic analyses we recommend not to filter datasets too strictly to minimize the risk of misleading topologies, low support, and inaccurate divergence times.

evolutionary biology↗

bioRxiv2021

Evaluating the contribution of aestivation to the persistence of malaria mosquitoes through the Sahelian dry season using stable isotopes

Data suggests the malaria vector Anopheles coluzzii persists in the Sahel by dry-season aestivation though evidence is scant. We have marked Anopheles mosquitoes using deuterium (2H) to assess the contribution of aestivation to persistence of mosquitoes through the seven-month dry season. If local aestivation is the only way A. coluzzii persists, the frequency of marked mosquitoes should remain stable throughout, whereas finding no marked mosquitoes would be evidence against aestivation. Larval sites were spiked with 2H at the end of the 2017 wet season in two Sahelian villages in Mali. We monitored 2H-enriched populations until the onset of rains. By the end of the enrichment period, 33% of A. coluzzii mosquitoes were clearly marked. Expectedly, 2H levels in marked mosquitoes degraded over time, resulting in a partial overlap of the marked and non-marked 2H distributions. We utilized three methods to estimate the fraction of marked mosquitoes in the population. Seven months after enrichment, 7% of the population had 2H values above the highest pre-enrichment value. An excess of 21% exceeded the 3rd quartile of the pre-enrichment population. A finite mixed population model showed 2.5% represented a subpopulation of marked mosquitoes with elevated 2H, compatible with our predictions. We provide evidence that aestivation is a major persistence mechanism of A. coluzzii in the Sahel, contributing at least 20% of the adults at the onset of rains, suggesting A. coluzzii utilizes multiple persistence strategies enabling its populations rapid buildup, facilitating subsequent malaria resurgence. These may complicate vector control and malaria elimination campaigns. Significance statementHere we estimated the contribution of aestivation to the persistence of mosquitoes through the seven-month long dry season, by marking a known fraction of the adult population through larval site 2H-spiking by the end of the wet season and assessing the change in this fraction through the dry season, until after the onset of the first rain of the subsequent wet season. In a mark-release-recapture study using stable isotopes, we provide compelling evidence that the primary Sahelian malaria vector Anopheles coluzzii aestivates on a population-scale, contributing at least 20% of the adults which reestablish the population of the subsequent wet season. The capacity to use multiple strategies of persistence in time and space might complicate vector control and elimination campaigns.

ecology↗