Biology subjects

Archer, F. I.

Publications and source records attributed to Archer, F. I..

3 recordsLinked to original sources

bioRxiv2025

The distribution of fitness effects varies phylogenetically across animals

1The distribution of fitness effects (DFE) describes the selection coefficients (s) of newly arising mutations and fundamentally influences population genetic processes. However, the extent and mechanisms of DFE variation have not been systematically investigated across species with divergent phylogenetic histories and ecological functions. Here, we inferred the DFE in natural populations of eleven animal (sub)species, including humans, mice, fin whales, vaquitas, wolves, collared flycatchers, pied flycatchers, halictid bees, Drosophila, and mosquitoes. We find that the DFE co-varies with phylogeny, where the expected mutation effects are more similar in closely related species (Pagels{lambda} = 0.84, P = 0.01). Additionally, mammals have a higher proportion of strongly deleterious mutations (22% to 47% in mammals; 0.0% to 5.4% in insects and birds) and a lower proportion of weakly deleterious mutations than insects and birds. Population size is significantly negatively correlated with the expected impact of new deleterious mutations (PGLS{lambda}, P = 0.03), and the proportion of new beneficial mutations ([Formula], P < 0.001). These findings align with Fishers Geometric Model (FGM), which defines organismal complexity as the number of phenotypes under selection. Consistent with the FGMs predictions, we observe that mutations are more deleterious in complex organisms, while beneficial mutations occur more frequently in smaller populations to compensate for the drift load. Our study demonstrates strong phylogenetic constraints in the evolution of a fundamental population genetics parameter, and proposes that, through mechanisms of global epistasis, long-term population size and organismal complexity drive variation in the DFE across animals. 2 Significance StatementUnderstanding how mutations affect fitness is fundamental in evolution, but little is known about how and why the distribution of fitness effects (DFE) varies across species. In this study, we examine the DFE in diverse animal populations and show that closely related species exhibit similar patterns of mutation effects, with new mutations being more deleterious in mammals compared with birds and insects. Our findings corroborate Fishers Geometric Model, which explains the variation in the DFE across species as a function of organismal complexity and long-term population size. By connecting organismal complexity and population size with the DFE, we offer a phylogenetic view into the selective forces shaping species adaptation and evolution.

evolutionary biology↗

bioRxiv2020

Reference genome and demographic history of the most endangered marine mammal, the vaquita

The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline resulting from inadvertent deaths due to the increasing use of large-mesh gillnets for more than 20 years. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analyzed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

genomics↗

bioRxiv2016

Mitogenome and nuclear DNA differentiation in spinner (Stenella longirostris) and pantropical spotted dolphins (S. attenuata) from the eastern tropical Pacific Ocean

Spinner dolphins (Stenella longirostris) and spotted dolphins (S. attenuata) show high intraspecific morphological diversity and endemic subspecies in the eastern tropical Pacific Ocean (ETP). Previous studies of mitochondrial DNA (mtDNA) have found low genetic differentiation among most of these groups, possibly due to demographic factors, ongoing gene flow, and/or recent divergence. These species were heavily depleted due to bycatch in the ETP yellowfin tuna fishery. Because population structure is important for accurate management of the recovery of these species, we collected whole mitochondrial genome sequences from 104 spinner and 76 spotted dolphins to test structure hypotheses at multiple hierarchical levels. Our results showed significant differences between subspecies of spotted (FST: 0.0125; P = 0.0402) and spinner dolphins (FST: 0.0133; P = 0.034), but no support for the division of existing offshore stocks of spotted dolphins or Tres Marias spinner dolphins. We compare these results to previous results of genome-wide nuclear SNP data and suggest high haplotype diversity, female dispersal, male philopatry, or relative power of the two datasets explains the differences observed. Our results further support a genetic basis for biologically meaningful management units at the subspecies level, and provide a critical component to mitigating historical and continued fishery interactions.

zoology↗