Evolutionary Applications

Most pathogens are generalists capable of infecting multiple host species or strains. Trade-offs in performance among different hosts are expected to limit the evolution of generalism. Despite the commonness of generalism, the variation in infectivity, transmission, and trade-offs in performance among host species have rarely been studied in the wild. To understand the ecological and evolutionary drivers of multi-host pathogen infectivity and transmission potential, I studied disease severity, transmission dynamics, and infectivity variation of downy mildew pathogen Peronospora sparsa on its three host plants Rubus arcticus , R...

Mexican native maize ( Zea mays ssp. mays ) is adapted to a wide range of climatic and edaphic conditions. Here, we focus specifically on the potential role of root anatomical variation in this adaptation. Given the investment required to characterize root anatomy, we present a machine-learning approach using environmental descriptors to project trait variation from a relatively small training panel onto a larger panel of genotyped and georeferenced Mexican maize accessions. The resulting models defined potential biologically relevant clines across a complex environment that we used subsequently for genotype-environment association...

Most species will not be able to migrate fast enough to cope with climate change, nor evolve quickly enough with current levels of genetic variation. Exacerbating the problem are anthropogenic influences on adaptive potential, including the prevention of gene flow through habitat fragmentation and the erosion of genetic diversity in small, bottlenecked populations. Facilitated adaptation, or assisted evolution, offers a way to augment adaptive genetic variation via artificial selection, induced hybridization, or genetic engineering...

Harvest in walleye Sander vitreus fisheries is size-selective and could influence phenotypic traits of spawners; however, contributions of individual spawners to recruitment are unknown. We used parentage analyses using single nucleotide polymorphisms to test whether parental traits were related to the probability of offspring survival in Escanaba Lake, Wisconsin. From 2017 to 2020, 1339 adults and 1138 juveniles were genotyped and 66% of the offspring were assigned to at least one parent. Logistic regression indicated the probability of reproductive success (survival of age-0 to first fall) was positively (but weakly) related to total length and growth rate in females, but not age...

Since the emergence of a transmissible cancer, devil facial tumour disease (DFT1), in the 1980s, wild Tasmanian devil populations have been in decline. In 2016, a second, independently evolved transmissible cancer (DFT2) was discovered raising concerns for survival of the host species. Here, we applied experimental and modelling frameworks to examine competition dynamics between the two transmissible cancers in vitro. Using representative cell lines for DFT1 and DFT2, we have found that in monoculture, DFT2 grows twice as fast as DFT1 but reaches lower maximum cell densities...

Modern fisheries management strives to balance opposing goals of protection for weak stocks and opportunity for harvesting healthy stocks. Test fisheries can aid management of anadromous fishes if they can forecast the strength and timing of an annual run with adequate time to allow fisheries planning. Integration of genetic stock identification (GSI) can further maximize utility of test fisheries by resolving run forecasts into weak- and healthy-stock subcomponents. Using 5 years (2017-2022) of test fishery data, our study evaluated accuracy, resolution, and lead time of predictions for stock-specific run timing and abundance of Columbia River spring Chinook salmon ( Oncorhynchus tshawytscha )...

Characterizing patterns of genetic connectivity in marine species is of critical importance given the anthropogenic pressures placed on the marine environment. For sessile species, population connectivity can be shaped by many processes, such as pelagic larval duration, oceanographic boundaries and currents. This study combines restriction-site associated DNA sequencing (RADseq) and passive particle dispersal modelling to delineate patterns of population connectivity in the pink sea fan, Eunicella verrucosa , a temperate octocoral...

Molecular mechanisms driving the escalation of pyrethroid resistance in the major malaria mosquitoes of Central Africa remain largely uncharacterized, hindering effective management strategies. Here, resistance intensity and the molecular mechanisms driving it were investigated in a population of Anopheles coluzzii from northern Cameroon. High levels of pyrethroid and organochloride resistance were observed in An. coluzzii population, with no mortality for 1× permethrin; only 11% and 33% mortalities for 5× and 10× permethrin diagnostic concentrations, and <2% mortalities for deltamethrin and DDT, respectively...

While Atlantic salmon ( Salmo salar ) of the northernmost American populations is alimentary, economically, and culturally important for Ungava Inuit communities (Nunavik, Canada) and might play a key role in the persistence of the species in a global warming context, many mysteries remain about those remote and atypical populations. Thus, our first aim was to document the genomic structure of the Nunavik populations. The second objective was to determine whether salmon only migrating to the estuary without reaching the sea, apparently unique to those populations, represent distinct populations from the typical anadromous salmons and subsequently explore the genetic basis of migratory life-history tactics in the species...

The Aedes aegypti (Linnaeus, 1762) mosquito is the main vector of dengue, chikungunya and Zika and is well established today all over the world. The species comprises two forms: the ancestral form found throughout Africa and a global domestic form that spread to the rest of the tropics and subtropics. In Saudi Arabia, A. aegypti has been known in the southwest since 1956, and previous genetic studies clustered A. aegypti from Saudi Arabia with the global domestic form. The purpose of this study was to assess the genetic structure of A...

Directional selection alters the genome via hard sweeps, soft sweeps, and polygenic selection. However, mapping polygenic selection is difficult because it does not leave clear signatures on the genome like a selective sweep. In populations with temporally stratified genotypes, the Generation Proxy Selection Mapping (GPSM) method identifies variants associated with generation number (or appropriate proxy) and thus variants undergoing directional allele frequency changes. Here, we use GPSM on two large datasets of beef cattle to detect associations between an animal's generation and 11 million imputed SNPs...

Genome-wide single nucleotide polymorphism (SNP) genotyping platforms have become increasingly popular in characterizing livestock and wildlife populations, replacing traditional methods such as microsatellite fragment analysis. Herein, we report the development and evaluation of a novel bison SNP panel for population management and conservation. Initially, 2474 autosomal SNPs were selected from existing bison whole-genome sequences and variable sites among bison on the GGSP bovine 50K Chip, based on minor allele frequency, data completeness, and chromosome location...

As coral reefs continue to decline due to climate change, the role of coral epigenetics (specifically, gene body methylation, GBM) in coral acclimatization warrants investigation. The evidence is currently conflicting. In diverse animal phyla, the baseline GBM level is associated with gene function: continuously expressed "housekeeping" genes are typically highly methylated, while inducible context-dependent genes have low or no methylation at all. Some authors report an association between GBM and the environment and interpret this observation as evidence of the GBM's role in acclimatization...

Climate-induced expansion of invasive hybridization (breeding between invasive and native species) poses a significant threat to the persistence of many native species worldwide. In the northern U.S. Rocky Mountains, hybridization between native cutthroat trout and non-native rainbow trout has increased in recent decades due, in part, to climate-driven increases in water temperature. It has been postulated that invasive hybridization may enhance physiological tolerance to climate-induced thermal stress because laboratory studies indicate that rainbow trout have a higher thermal tolerance than cutthroat trout...

The use of whole-genome sequence (WGS) data is expected to improve genomic prediction (GP) power of complex traits because it may contain mutations that in strong linkage disequilibrium pattern with causal mutations. However, a few previous studies have shown no or small improvement in prediction accuracy using WGS data. Incorporating prior biological information into GP seems to be an attractive strategy that might improve prediction accuracy. In this study, a total of 6334 pigs were genotyped using 50K chips and subsequently imputed to the WGS level...

Fish hatcheries are widely used to enhance fisheries and supplement declining wild populations. However, substantial evidence suggests that hatchery fish are subject to differential selection pressures compared to their wild counterparts. Domestication selection, or adaptation to the hatchery environment, poses a risk to wild populations if traits specific to success in the hatchery environment have a genetic component and there is subsequent introgression between hatchery and wild fish. Few studies have investigated domestication selection in hatcheries on a genomic level, and even fewer have done so in parallel across multiple hatchery-wild population pairs...

The majority of the transcribed genome does not have coding potential but these non-coding transcripts play crucial roles in transcriptional and post-transcriptional regulation of protein-coding genes. Regulation of gene expression is important in shaping an organism's response to environmental changes, ultimately impacting their survival and persistence as population or species face global change. However, the roles of long non-coding RNAs (lncRNAs), when confronted with environmental changes, remain largely unclear...

The dwarf surf clam, Mulinia lateralis , is considered as a model species for bivalves because of its rapid growth and short generation time. Recently, successful breeding of this species for multiple generations in our laboratory revealed its acquisition of adaptive advantages during artificial breeding. In this study, 310 individuals from five different generations were genotyped with 22,196 single nucleotide polymorphisms (SNPs) with the aim of uncovering the genetic basis of their adaptation to laboratory conditions...

Macaques (genus Macaca ) are the most widely distributed non-human primates, and their evolutionary history, gene expression profiles, and genetic differences have been extensively studied. However, the DNA methylomes of macaque species are not available in public databases, which hampers understanding of epigenetic differences among macaque species. Epigenetic modifications can potentially affect development, physiology, behavior, and evolution. Here, we investigated the methylation patterns of the Tibetan macaque ( M...

By the 1980s, after decades of declining numbers in the mid-1900s, Coho salmon ( Oncorhynchus kisutch ) were considered extirpated from the interior Columbia River. In the mid-1990s, the Confederated Tribes of the Umatilla Indian Reservation, the Confederated Tribes and Bands of the Yakama Nation, and the Nez Perce Tribe began successful reintroduction programs of Coho salmon upstream of Bonneville Dam, but which were initially sourced from lower Columbia River hatcheries. Here we present the first Coho salmon parentage-based tagging (PBT) baseline from seven hatchery programs located in the interior Columbia River basin, and two sites at or downstream of Bonneville Dam, composed of over 32,000 broodstock samples...