The genetic architecture underlying the evolution of a rare piscivorous life history form in brown trout after secondary contact and strong introgression

Identifying the genetic basis underlying phenotypic divergence and reproductive isolation is a longstanding problem in evolutionary biology. Genetic signals of adaptation and reproductive isolation are often confounded by a wide range of factors, such as variation in demographic history or genomic features. Brown trout ( ) in the Loch Maree catchment, Scotland, exhibit reproductively isolated divergent life history morphs, including a rare piscivorous (ferox) life history form displaying larger body size, greater longevity and delayed maturation compared to sympatric benthivorous brown trout. Using a dataset of 16,066 SNPs, we analyzed the evolutionary history and genetic architecture underlying this divergence. We found that ferox trout and benthivorous brown trout most likely evolved after recent secondary contact of two distinct glacial lineages, and identified 33 genomic outlier windows across the genome, of which several have most likely formed through selection. We further identified twelve candidate genes and biological pathways related to growth, development and immune response potentially underpinning the observed phenotypic differences. The identification of clear genomic signals divergent between life history phenotypes and potentially linked to reproductive isolation, through size assortative mating, as well as the identification of the underlying demographic history, highlights the power of genomic studies of young species pairs for understanding the factors shaping genetic differentiation

Analysis of among-site variation in substitution patterns

Substitution patterns among nucleotides are often assumed to be constant in phylogenetic analyses. Although variation in the average rate of substitution among sites is commonly accounted for, variation in the relative rates of specific types of substitution is not. Here, we review details of methodologies used for detecting and analyzing differences in substitution processes among predefined groups of sites. We describe how such analyses can be performed using existing phylogenetic tools, and discuss how new phylogenetic analysis tools we have recently developed can be used to provide more detailed and sensitive analyses, including study of the evolution of mutation and substitution processes. As an example we consider the mitochondrial genome, for which two types of transition deaminations (C⇒T and A⇒G) are strongly affected by single-strandedness during replication, resulting in a strand asymmetric mutation process. Since time spent single-stranded varies along the mitochondrial genome, their differential mutational response results in very different substitution patterns in different regions of the genome

Nuclear Encoded Proteins Important in Mitochondrial Genome Stability

The mitochondrion is widely known to be the site of cellular respiration and the factory of cellular energy. Similar to the nucleus, mitochondria house genetic material (mtDNA), which is responsible for the production of proteins essential to mechanisms required for cellular respiration. Furthermore, if there is a mutation or deletion in the mtDNA there can be ramifications in terms of energy production, which will hinder cell viability. Additionally, mutations in the mtDNA are associated with certain neuromuscular diseases as well as contributing to the aging process. The focus of this research is to identify genes that contribute to the maintenance of the mtDNA. Our data from genetic assays indicate that loss of the Clu1p protein exhibits an increase respiration loss as well as increase spontaneous point mutations. In addition, loss of Clu1p alters mitochondrial morphology

Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth

One of the most endangered vertebrates, the Devils Hole pupfish Cyprinodon diabolis, survives in a nearly impossible environment: a narrow subterranean fissure in the hottest desert on earth, Death Valley. This species became a conservation icon after a landmark 1976 US Supreme Court case affirming federal groundwater rights to its unique habitat. However, one outstanding question about this species remains unresolved: how long has diabolis persisted in this hellish environment? We used next-generation sequencing of over 13 000 loci to infer the demographic history of pupfishes in Death Valley. Instead of relicts isolated 2–3 Myr ago throughout repeated flooding of the entire region by inland seas as currently believed, we present evidence for frequent gene flow among Death Valley pupfish species and divergence after the most recent flooding 13 kyr ago. We estimate that Devils Hole was colonized by pupfish between 105 and 830 years ago, followed by genetic assimilation of pelvic fin loss and recent gene flow into neighbouring spring systems. Our results provide a new perspective on an iconic endangered species using the latest population genomic methods and support an emerging consensus that timescales for speciation are overestimated in many groups of rapidly evolving species

Recombination facilitates neofunctionalization of duplicate genes via originalization

<p>Abstract</p> <p>Background</p> <p>Recently originalization was proposed to be an effective way of duplicate-gene preservation, in which recombination provokes the high frequency of original (or wild-type) allele on both duplicated loci. Because the high frequency of wild-type allele might drive the arising and accumulating of advantageous mutation, it is hypothesized that recombination might enlarge the probability of neofunctionalization (P_neo) of duplicate genes. In this article this hypothesis has been tested theoretically.</p> <p>Results</p> <p>Results show that through originalization recombination might not only shorten mean time to neofunctionalizaiton, but also enlarge P_neo.</p> <p>Conclusions</p> <p>Therefore, recombination might facilitate neofunctionalization via originalization. Several extensive applications of these results on genomic evolution have been discussed: 1. Time to nonfunctionalization can be much longer than a few million generations expected before; 2. Homogenization on duplicated loci results from not only gene conversion, but also originalization; 3. Although the rate of advantageous mutation is much small compared with that of degenerative mutation, P_neocannot be expected to be small.</p

Molecular evolution at homoeologous loci in allotetraploid cotton (Malvaceae: Gossypium hirsutum L)

Duplicated genes created during polyploid formation (\u27homoeologues\u27) may experience a variety of fates depending upon the evolutionary forces operating on these loci. Homoeologue divergence may be limited if selection operates to maintain duplicate gene function, or divergence may be permitted if selective pressure on a functionally redundant locus is relaxed. In an attempt to determine the fate of duplicate loci in a polyploid genome, I have isolated and described sequence evolution at 15 sets of homoeologous loci from allotetraploid cotton (Gossypium L.) and the corresponding orthologues from its progenitor diploid genomes. Homoeology and orthology relationships of these loci have been demonstrated by in-situ hybridization for the 5S rDNA array, and by comparative linkage mapping for 12 low-copy anonymous loci and two known cellulose synthase genes, CelA1 and CelA2. In combination, these results demonstrate that relaxation of selective pressure (as indicated by an increase in the substitution rate) at duplicate loci subsequent to polyploidization may be minimal across the majority of loci in this duplicated genome. Ten of these loci (which correspond to mapped anonymous PstI-genomic probes) show rate equivalency between polyploid subgenomes and between subgenomes and their progenitor diploid genomes, indicating that selection continues to limit divergence at these loci. In contrast, the remaining five loci (5SrDNA, A1550, A1713, CelA1 and CelA2) show significant rate differences among the genomes tested. Two of these loci (CelA1 and CelA2) are known to be preferentially expressed in developing cotton fiber, and they show significantly elevated substitution rates in the D- and A-subgenome lineages, respectively. In addition, CelA2 from the A-subgenome of G. hirsutum has experienced a marked rate acceleration since polyploidization, and has accumulated a greater than expected number of non-synonymous substitutions without exhibiting the hallmarks of pseudogenization. These results indicate that cellulose synthase A2 may be responding to directional or diversifying selection, perhaps as a consequence of human-mediated selection upon fiber quality attributes