Biology subjects

Mee, J. A.

Publications and source records attributed to Mee, J. A..

6 recordsLinked to original sources

bioRxiv2024

Same trait, different genes: pelvic spine loss in three brook stickleback populations in Alberta

The genetic basis of phenotypic or adaptive parallelism can reveal much about constraints on evolution. This study investigated the genetic basis of a canonically parallel trait: pelvic spine reduction in sticklebacks. Pelvic reduction has a highly parallel genetic basis in threespine stickleback in populations around the world, always involving a deletion of the pel1 enhancer of Pitx1. We conducted a genome-wide association study to investigate the genetic basis of pelvic spine reduction in three populations of brook stickleback in Alberta, Canada. Pelvic reduction did not involve Pitx1 in any of the three populations. Instead, pelvic reduction in one population involved a mutation in an exon of Tbx4, and it involved a mutation in an intron of Lmbr1 in the other two populations. Hence, the parallel phenotypic evolution of pelvic spine reduction across stickleback genera, and among brook stickleback populations, has a non-parallel genetic basis. This suggests that there may be redundancy in the genetic basis of this adaptive polymorphism, but it is not clear whether a lack of parallelism indicates a lack of constraint on the evolution of this adaptive trait. Whether the different pleiotropic effects of different mutations have different fitness consequences, or whether certain pelvic reduction mutations confer specific benefits in certain environments, remains to be determined. Lay SummaryIn this study, we looked for the genetic basis of a well-studied trait in stickleback fish: the pelvic spines. This structure (i.e. the pelvic girdle and attached spines) has a shared developmental basis (and is homologous to) the pelvic bones and hind limbs of all tetrapods (including humans). We know from studying mice, fish, humans, and even manatees that there are several genes that could affect the development of pelvic spines and hind limbs. In one species of stickleback, the threespine stickleback, however, a single gene called Pitx1 is always involved in the loss of pelvic spines in populations that have adapted to freshwater lakes. This replicated evolution of the same trait in the same environmental conditions is called parallel evolution. Its remarkable that Pitx1 is always the gene underlying this adaptive loss of spines in freshwater threespine stickleback populations. We were interested in whether this "genetic parallelism" extended to other species of stickleback that have also evolved the loss of pelvic spines. We looked at three populations of brook stickleback (which are never found in the ocean), each of which contains individuals with and without pelvic spines. We found that the Pitx1 genetic parallelism does not extend to brook stickleback, and, in fact, the genetic basis of pelvic spine loss differs between populations. In Muir Lake and Astotoin Lake, pelvic spine loss results from a mutation in the Lmbr1 gene, and in Shunda Lake, pelvic spine loss results from a mutation in the Tbx4 gene.

evolutionary biology↗

bioRxiv2023

Pelvic spine reduction affects diet but not gill raker morphology in two polymorphic brook stickleback (Culaea inconstans) populations

Pelvic spine polymorphism occurs in several species in the stickleback family (Gasterosteidae). Given the similar phenotypic polymorphisms in multiple stickleback species, we sought to determine the extent of parallelism in the ecological correlates of pelvic spine reduction. Based on a metabarcoding analysis of brook stickleback gut contents in two polymorphic populations, we found significant diet differences were associated with pelvic spine reduction, but we found no clear or consistent trend supporting a tendency for benthic feeding in pelvic-reduced brook stickleback. These results contrast with those found in threespine stickleback where pelvic spine reduction is often associated with a benthic diet. Hence, we found non-parallel consequences of spine polymorphism across species. Furthermore, a difference in gill raker morphology has been frequently observed between ecomorphs with differen diets in many fish species. But, we found no evidence of any difference in gill raker morphology associated with pelvic spine polymorphism in brook stickleback.

evolutionary biology↗

bioRxiv2023

Conditionally deleterious mutation load accumulates in genomic islands but can be purged with sufficient genotypic redundancy

Local adaptation frequently evolves in patches or environments that are connected via migration. In these cases, genomic regions that are linked to an adaptive locus experience reduced effective migration rates. Via individual-based simulations of a two-patch system, we show that this reduced effective migration results in the accumulation of conditionally deleterious mutations, but not universally deleterious mutations, adjacent to adaptive loci. When there is redundancy in the genetic basis of local adaptation (i.e. genotypic redundancy), turnover of adaptive loci allows conditionally deleterious mutation load to be purged. The amount of mutational load that accumulates adjacent to adaptive loci is dependent on redundancy, recombination rate, migration rate, population size, strength of selection, and the phenotypic effect size of adaptive alleles. Our results highlight the need to be cautious when interpreting patterns of local adaptation at the level of phenotype or fitness, as the genetic basis of local adaptation can be transient, and evolution may confer a degree of maladaptation to non-local environments.

evolutionary biology↗

bioRxiv2022

Convergent recruitment of Amh as the sex determination gene in two lineages of stickleback fish

Sex chromosomes vary greatly in their age and levels of differentiation across the tree of life. This variation is largely due to the rates of sex chromosome turnover in different lineages; however, we still lack an explanation for why sex chromosomes are so conserved in some lineages (e.g. Mammals, Birds) but so labile in others (e.g. Fish, Amphibians). Here we add to the information on sex chromosomes in stickleback, a valuable model lineage for the study of sex chromosome evolution, by identifying the sex chromosome and a strong candidate for the master sex determination gene in the brook stickleback, Culaea inconstans. Using whole genome sequencing of wild-caught samples and a lab cross, we identify AmhY, a male specific duplication of the gene Amh, as the candidate master sex determination gene. AmhY resides on Chromosome 20 in C. inconstans and is likely a recent duplication, as both AmhY and the sex linked region of Chromosome 20 show little sequence divergence. Importantly, this duplicate AmhY represents the second independent duplication and recruitment of Amh as the sex determination gene in stickleback and the eighth example now known across teleosts. We discuss this convergence in the context of sex chromosome turnovers and the role that the Amh/AmhrII pathway, which is crucial for sex determination, may play in the evolution of sex chromosomes in teleosts.

evolutionary biology↗

bioRxiv2021

Parallel and non-parallel divergence within polymorphic populations of brook stickleback, Culaea inconstans (Actinopterygii: Gasterosteidae)

Studying parallel evolution allows us to draw conclusions about the repeatability of adaptive evolution. Whereas populations likely experience similar selective pressures in similar environments, it is not clear if this will always result in parallel divergence of ecologically relevant traits. Our study investigates the extent of parallelism associated with the evolution of pelvic spine reduction in brook stickleback populations. We find that populations with parallel divergence in pelvic spine morphology do not exhibit parallel divergence in head and body morphology but do exhibit parallel divergence in diet. In addition, we compare these patterns associated with pelvic reduction in brook stickleback to well-studied patterns of divergence between spined and unspined threespine stickleback. Whereas spine reduction is associated with littoral habitats and a benthic diet in threespine stickleback, spine reduction in brook stickleback is associated with a planktonic diet. Hence, we find that pelvic spine divergence is associated with largely non-parallel ecological consequences across species.

evolutionary biology↗

bioRxiv2019

Unpacking conditional neutrality: genomic signatures of selection on conditionally beneficial and conditionally deleterious mutations

It is common to look for signatures of local adaptation in genomes by identifying loci with extreme levels of allele frequency divergence among populations. This approach to finding genes associated with local adaptation often assumes antagonistic pleiotropy, wherein alternative alleles are strongly favoured in alternative environments. Conditional neutrality has been proposed as an alternative to antagonistic pleiotropy, but conditionally neutral polymorphisms are transient and it is unclear how much outlier signal would be maintained under different forms of conditional neutrality. Here, we use individual-based simulations and a simple analytical heuristic to show that a pattern that mimics local adaptation at the phenotypic level, where each genotype has the highest fitness in its home environment, can be produced by the accumulation of mutations that are neutral in their home environment and deleterious in non-local environments. Because conditionally deleterious mutations likely arise at a rate many times higher than conditionally beneficial mutations, they can have a significant cumulative effect on fitness even when individual effect sizes are small. We show that conditionally deleterious mutations driving non-local maladaptation may be undetectable by even the most powerful genome scans, as differences in allele frequency between populations are typically small. We also explore the evolutionary effects of conditionally-beneficial mutations and find that they can maintain significant signals of local adaptation, and they would be more readily detectable than conditionally deleterious mutations using conventional genome scan approaches. We discuss implications for interpreting outcomes of transplant experiments and genome scans that are used to study the genetic basis of local adaptation.

evolutionary biology↗