Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low-coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine-scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population-specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving numbers of individuals and genetic diversity. Notably, we highlight the importance of the Northern Temperate-Greater Antilles migratory population as containing the largest proportion of individuals in the species. Finally, we highlight valuable considerations for other population assignment studies aimed at using lcWGS. Our results have broad implications for improving our understanding of the ecology and evolution of migratory species through conservation genomics approaches.

Chromosomal inversions have been identified in many natural populations and can be responsible for novel traits and fast adaptation. In zebra finch, an inversion in the Z chromosome has a pleiotropic effect on multiple traits but especially on sperm. Males heterokaryotypic for the inversion have sperm with a longer midpiece and higher velocity. They have higher fertility and siring success than homokaryotypic males. To understand the effect the Z inversion on these traits, we examined young males at different stages of testis development using two homokaryotypic lines and heterokaryotypes. We sampled both testis and liver tissue to identify gene expression differences. In testis, 520 differentially expressed genes were found and most of them were located on chromosome Z. They were functionally enriched for sperm-related traits. In liver, 420 differentially expressed genes were not enriched for any specific functions but showed also an overrepresentation on chromosome Z. In both tissues, this overrepresentation was located near the distal end of Z but also in the middle of the chromosome. For the heterokaryotype, we observed several genes with expression patterns more similar to one or the other karyotype, based on similarity to homokaryotype invidividuals. This was confirmed with SNPs for three genes, and interestingly one gene, dmgdh, had allele-specific expression originating from only one inversion-allele in the testis, yet both inversion alleles were expressed in the liver. This allele-specific difference in tissue-specific expression demonstrates a pleiotropic effect of the inversion and thus suggests a mechanism for divergent phenotypic effects resulting from an inversion.

Geographic isolation and chromosome evolution are two of the major drivers of diversification in eukaryotes in general, and specifically, in plants. On one hand, range shifts induced by Pleistocene glacial oscillations deeply shaped the evolutionary trajectories of species in the Northern Hemisphere. On the other hand, karyotype variability within species or species complexes may have adaptive potential as different karyotypes may represent different recombination rates and linkage groups that may be associated with locally adapted genes or supergenes. Organisms with holocentric chromosomes are ideal to study the link between local adaptation and chromosome evolution, due to their high cytogenetic variability, especially when it seems to be related to environmental variation. Here, we integrate the study of the phylogeography, chromosomal evolution and ecological requirements of a plant species complex distributed in the Western Euro-Mediterranean region (Carex gr. laevigata, Cyperaceae). We aim to clarify the relative influence of these factors on population differentiation and ultimately on speciation. We obtained a well-resolved RADseq phylogeny that sheds light on the phylogeographic patterns of molecular and chromosome number variation, which are compatible with south-to-north postglacial migration. In addition, landscape genomics analyses identified candidate loci for local adaptation, and also strong significant associations between the karyotype and the environment. We conclude that karyotype distribution in C. gr. laevigata has been constrained by both range shift dynamics and local adaptation. Our study demonstrates that chromosome evolution may be responsible, at least partially, for microevolutionary patterns of population differentiation and adaptation in Carex.

Telomeres are chromosome protectors that shorten during cell replication and in stressful conditions. Developing individuals are susceptible to telomere erosion when their growth is fast and resources limited. This is critical because the rate of telomere attrition in early life is linked to health and life span of adults. The metabolic telomere attrition hypothesis (MeTA) suggests that telomere dynamics can respond to biochemical signals conveying information about the organism’s energetic state. Among these signals are glucocorticoids (hormones that promote catabolic processes, potentially impairing costly telomere maintenance) and nucleotides, which activate anabolic pathways though the cellular enzyme target of rapamycin (TOR) preventing telomere attrition. During the energetically demanding growth phase, the regulation of telomeres in response to two contrasting signals—one promoting telomere maintenance and the other inducing attrition—provides an ideal experimental setting to test MeTa. We studied nestlings of a rapidly developing free-living passerine, the great tit (Parus major), that either received glucocorticoids (Cort-chicks), nucleotides (Nuc-chicks), or a combination of both (NucCort-chicks) all compared with controls (Cnt-chicks). Contrary to Cort-chicks, which showed telomere attrition, NucCort-chicks, did not. NucCort-chicks was the only group showing increased gene expression of telo2 (proxy for TOR activation), of mitochondrial enzymes linked to ATP production (atp5f1a-atp5f1b-cox6a1-cox4) and a higher efficiency in aerobically producing ATP. NucCort-chicks had also a higher expression of telomere maintenance genes (trf2) and of enzymatic antioxidant genes (gpx4-sod1). The findings show that nucleotides availability is crucial for preventing telomere erosion during fast growth in stressful environments.

Local adaptation is often facilitated by loci clustered in relatively few regions of the genome, termed genomic islands of divergence. However, the mechanisms that create, mold, and maintain these islands are poorly understood. Here, we use sockeye salmon as a model species to investigate the mechanisms responsible for creating islands of divergence linked to adaptive variation. Previous research suggests that multiple islands are involved in adaptive radiation of sockeye salmon. However, these studies were based on low-density genomic methods that genotyped tens to thousands of loci, making it difficult to elucidate the mechanisms responsible for islands. We used whole genome resequencing to genotype millions of loci to investigate these mechanisms. We discovered 64 islands, 16 of which were shared between two isolated populations; these 16 islands were clustered in four genomic regions. Characterization of the shared regions suggested that three of four were likely created by chromosomal inversions, while the other was created by processes not involving structural variation. Additionally, all four regions were relatively small (< 600 kb), suggesting inversions and other low recombination regions do not have to span megabases to be important for adaptive divergence. In sum, our study demonstrates that heterogeneous selection can lead to a mosaic of islands created by different mechanisms within the same genome. Future studies should continue to investigate how gene flow, selection, and the architecture of genetic traits interact to influence the genomic landscape of adaptive divergence.

A document by Samuel May. Click on the document to view its contents.

Fish often spawn eggs with ovarian fluids that have been hypothesized to support sperm of some males over others (cryptic female choice). Alternatively, sperm reactions to ovarian fluids could reveal male strategies. We used wild-caught lake char (Salvelinus umbla) to experimentally test whether sperm react differently to the presence of ovarian fluid, depending on male breeding coloration, male inbreeding coefficients (based of 4,150 SNPs), or the kinship coefficients between males and females. Male coloration was positively linked to body size and current health (based on lymphocytosis and thrombocytosis) but was a poor predictor of inbreeding or kinship coefficients. We found that sperm of more colorful males were faster in diluted ovarian fluids than in water only, while sperm of paler males were faster in water than in ovarian fluids. We then let equal numbers of sperm compete for fertilizations in the presence or absence of ovarian fluids and genetically assigned 1,464 embryos (from 70 experimental trials) to their fathers. The presence of ovarian fluids significantly increased the success of the more colorful competitors. Sperm of less inbred competitors were more successful when tested in water only than in diluted ovarian fluids. The kinship coefficients had no significant effects on sperm traits or fertilization success in the presence of ovarian fluids, although parallel stress tests on embryos had revealed that females would profit more from mating with least related males rather than most colored ones. We conclude that sperm of more colorful males are best adapted to ovarian fluids, and that the observed reaction norms suggest male strategies rather than cryptic female choice.

The Special Issue brought together papers that highlighted the power of high-throughput sequencing (HTS) data to address classic questions in ecology and evolution, and/or use models/theory to infer key ecological and evolutionary processes, and make predictions, particularly focused on metabarcoding (amplicon) datasets in conjunction with complementary -omics data types. We highlight key papers that show the power of the new technology to address questions related to: (1) community assembly, and the interplay between competition, environmental filtering, and neutral processes, that can be inferred from the data, and how these change according to environmental conditions, and across successional and extended evolutionary time. (2) Interaction networks, and how these can show predictable changes over similar spatial and temporal gradients, providing insights into questions of biotic resilience. Studies also examined (3) cross scale interactions and those involving hosts and their microbiomes, with the critical development being the ease of comparison and integration across scales of organismic complexity, allowing insights at one scale to inform the other. The approach is also amenable to (4) studies of invasive species and biotic homogenization, providing insights of shifts in alpha and beta diversity across a wide range of spatial scales.

Tropical freshwater lakes are well-known for their high biodiversity, and the East African Great Lakes in particular are renowned for their endemic cichlid fish adaptive radiations. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, evolutionary trajectories within lineages, impacts of environmental drivers, or the scope and nature of now-extinct diversity remain largely unknown. Time-structured paleodata from geologically young fossil records, such as fossil counts and particularly ancient DNA data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous ancient DNA (aDNA). Despite generally low endogenous content and high sample drop-out, high-throughput sequencing and in some cases sequence capture allowed for taxonomic assignment to family or tribe level and phylogenetic placement of individuals. Even skeletal remains weighing less than 1 mg and up to 2700 years of age could be phylogenetically placed. We find that the relationship of degradation of aDNA with the thermal age of samples is similar to that described for terrestrial samples from cold environments adjusted for elevated temperatures. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in water oxygenation at deposition. Our study demonstrates that sediments of tropical lakes preserve genetic information on rapidly diversifying taxa over time scales of millennia.

Epigenetic modifications, like DNA methylation, generate phenotypic diversity in fish and ultimately lead to adaptive evolutionary processes. Euryhaline marine species that migrate between salinity contrasted habitats have received little attention regarding the role of salinity on whole-genome DNA methylation. Investigation of salinity-induced DNA methylation in fish will help to better understand the potential role of this process in salinity acclimation. Using whole genome bisulfite sequencing, we compared DNA methylation patterns in European sea bass (Dicentrarchus labrax) juveniles in seawater and after freshwater transfer. We targeted the gill as a crucial organ involved in plastic responses to environmental changes. To investigate the function of DNA methylation in gills, we performed RNAseq and assessed DNA methylome-transcriptome correlations. We showed a negative correlation between gene expression levels and DNA methylation levels in promoters, first introns and exons. A significant effect of salinity on DNA methylation dynamics with an overall DNA hypomethylation in freshwater-transferred fish compared to seawater controls was demonstrated. This suggests a role of DNA methylation changes in salinity acclimation. Genes involved in key functions as metabolism, ion transport and transepithelial permeability (junctional complexes) were differentially methylated and expressed between salinity conditions. Expression of genes involved in mitochondrial metabolism was increased as well as the expression of DNA methyltransferases 3a. This study reveals novel aspects on the link of DNA methylation and gene expression patterns.

Phytoplankton have short generation times, flexible reproduction strategies, large population sizes, and high standing genetic diversity, traits that should facilitate rapid evolution under directional selection. We quantified local adaptation of copper tolerance in a population of the diatom Skeletonema marinoi from a mining exposed inlet in the Baltic Sea and in a non-exposed population 100 km away. We hypothesized that mining pollution has driven evolution of elevated copper tolerance in the impacted population of S. marinoi. Assays of 58 strains originating from sediment resting stages revealed no difference in the average tolerance to copper between the two populations. However, variation within populations was greater at the mining site, with three strains displaying hyper-tolerant phenotypes. In an artificial evolution experiment, we used a novel intraspecific metabarcoding locus to track selection and quantify fitness of all 58 strains during co-cultivation in one control and one toxic copper treatment. As expected, the hyper-tolerant strains enabled rapid evolution of copper tolerance in the mining exposed population through selection on available strain diversity. Within 42 days, in each experimental replicate a single strain dominated (30-99% abundance) but different strains dominated the different treatments. The reference population developed tolerance beyond expectations primarily due to slowly developing plastic response in one strain, suggesting that different modes of copper tolerance are present in the two populations. Our findings provide novel empirical evidence that standing genetic diversity of phytoplankton resting stage allows populations to evolve rapidly (20-50 generations) and flexibly on timescales relevant for seasonal bloom progressions.

Acquisition of new genes often results in the emergence of novel functions and is a key step in lineage-specific adaptation. As the only group of sessile crustaceans, barnacles establish permanent attachment through initial cement secretion at the larval phase followed by continuous cement secretion in juveniles and adults. However, the origins and evolution of barnacle larval and adult cement proteins remain poorly understood. By performing microdissection of larval cement glands, transcriptome and shotgun proteomics and immunohistochemistry validation, we identified 30 larval and 27 adult cement proteins of the epibiotic turtle barnacle Chelonibia testudinaria, of which the majority are stage- and barnacle-specific. While only two proteins, SIPC and CP100K, were expressed in both larvae and adults, detection of protease inhibitors and the cross-linking enzyme lysyl oxidase paralogs in larvae and adult cement suggested functional convergence. Other barnacle specific cement proteins such as CP100k and CP52k likely share a common origin dating back at least to the divergent of Rhizocephala and Thoracica. Different CP52k paralogs could be detected in larval and adult cement, suggesting stage-specific cement proteins may arise from duplication followed by changes in expression timing of the duplicates. Interestingly, the biochemical properties of larval- and adult-specific CP52k paralogs exhibited remarkable differences, reflecting the composition of cement in different life stages of turtle barnacle might be chemically different. We conclude that de novo gene formation and duplicate neofunctionalization are pivotal to the evolution of lineage-specific cement toolkits in barnacles, which may explain how barnacles can inhabit diverse marine substrata.

Population genomics applied to game species conservation can help delineate management units, ensure appropriate harvest levels, and identify populations needing genetic rescue to safeguard their adaptive potential. The ruffed grouse (Bonasa umbellus) is rapidly declining in much of the eastern USA due to a combination of forest maturation and habitat fragmentation. More recently, mortality from West Nile Virus may have affected connectivity of local populations; however, genetic approaches have never explicitly investigated this issue. In this study, we sequenced 54 individual low-coverage (~5X) grouse genomes to characterize population structure and assess migration rates across the landscape to identify potential barriers to gene flow. Surprisingly, we identified two genomic clusters with no clear geographic correlation, with large blocks of genomic differentiation associated with chromosomes 4 and 20, likely due to chromosomal inversions. After excluding these putative inversions from the data set, we found weak but non-significant signals of population subdivision. Estimated gene flow revealed reduced rates of migration in areas with extensive habitat fragmentation, while areas with more habitat continuity showed higher rates of genetic connectivity. Our findings provide a benchmark for wildlife managers to compare and scale the genetic diversity and structure of ruffed grouse populations in Pennsylvania and across the eastern USA, as well as reveal unexpected structural variation in the grouse genome that requires further study to understand its possible effects on individual fitness and population distribution.

Introduced and invasive species make excellent natural experiments for investigating rapid evolution. Here, we describe the effects of genetic drift and rapid genetic adaptation in pink salmon (Oncorhynchus gorbuscha) that were accidentally introduced to the Great Lakes via a single introduction event 31-generations ago. Using whole-genome resequencing for 134 fish spanning five sample groups across the native and introduced range, we estimate that the progenitor population’s effective population size was 146,886 at the time of introduction, whereas the founding population’s effective population size was just 72—a 2040-fold decrease. As expected with a severe bottleneck, we show reductions in genome-wide measures of genetic diversity, specifically a 37.7% reduction in the number of SNPs and an 8.2% reduction in observed heterozygosity. Despite this decline in genetic diversity, we provide evidence for putative selection at 47 loci across multiple chromosomes in the introduced populations, including missense variants in genes associated with circadian rhythm, immunological response, and maturation, which match expected or known phenotypic changes in the Great Lakes. For one of these genes, we use a species-specific agent-based model to rule out genetic drift and conclude that a strong response to selection occurred in a period gene (per2) that plays a predominant role in determining an organism’s daily clock, matching large day length differences experienced by introduced salmon during important phenological periods. Together, these results inform how populations might evolve rapidly to new environments, even with a small pool of standing genetic variation.

Deciduous forests form the dominant natural vegetation of Europe today, but were restricted to small refugia during Pleistocene cold stages, implying an evolutionary past shaped by recurrent range contractions and expansions. Cold-stage forest refugia were probably widespread in southern and central Europe, with the northwestern Balkan Peninsula being of particular importance. However, the actual number and location of deciduous forest refugia, as well as the connections between them, remain disputed. Here, we address the evolutionary dynamics of the deciduous forest understorey species Euphorbia carniolica as a proxy for past forest dynamics. To do so, we obtained genomic and morphometric data from populations representing the species' entire range, investigated phylogenetic position and intraspecific genetic variation, tested explicit demographic scenarios and applied species distribution models. Our data support two disjoint groups linked to separate refugia on the northwestern and central Balkan Peninsula. We find that genetic differentiation between groups started in the early Pleistocene via vicariance, suggesting a larger distribution in the past. Both refugia acted as sources for founder events to the southeastern Alps and the Carpathians, whereas the latter were likely colonized before the last cold stage. In line with traditional views on the pre-Pleistocene origin of many southeastern European deciduous forest species, the origin of E. carniolica was dated to the late Pliocene. The fact that E. carniolica evolved at a time when a period of continuous forestation was ending in much of Eurasia provides an interesting biogeographical perspective on the past links between Eurasian deciduous forests and their biota.

The processes governing soil bacteria biogeography are still not fully understood. It remains unknown how the importance of environmental filtering and dispersal differs between bacterial taxonomic and functional biogeography, and whether their importance is scale-dependent. We sampled soils at 195 plots across the Tibet plateau, with distances among plots ranging from 20 m to 1 550 km. Taxonomic composition of bacterial community was characterized by 16S amplicon sequencing, and functional community composition by qPCR targeting 9 functional groups involved in N dynamics. Twelve climatic and soil characteristics were also measured. Both taxonomic and functional dissimilarities were more related to environmental dissimilarity than geographic distance. Taxonomic dissimilarity was mostly explained by soil pH and organic matter, while functional dissimilarity was mostly linked to moisture, temperature and N, P and C availabilities. The roles of environmental filtering and dispersal were, however, scale-dependent and varied between taxonomic and functional dissimilarities, with distance affecting taxonomic dissimilarity over short distances (<~300 km) and functional dissimilarity over long distances (>~600 km). The importance of different environmental predictors varied across scales more for functional than taxonomic dissimilarity. Our results demonstrate how biodiversity dimension (taxonomic versus functional) and spatial scale strongly influence the conclusions derived from bacterial biogeography studies.

An accurate inference of the chronological and biological age of individuals is fundamental to population ecology and our understanding of ageing itself, its evolution and the biological processes that affect or even cause ageing. In humans, epigenetic clocks based on the DNA methylation (DNAm) at selected CpG sites correlate highly with chronological age. Discrepancies between the inferred epigenetic and known chronological age predict morbidity and mortality, and therefore epigenetic clocks are thought to reflect biological age. Recently, a growing number epigenetic clocks in non-model organisms have been developed towards a diverse array of purposes in commercial, conservation and ageing research. Here we review those studies and conduct the first meta-analysis to assess the effects of different aspects of experimental protocol on the accuracy of epigenetic clocks for non-model species. Our analysis reveals higher coefficients of determination (R2) of chronological age for epigenetic clocks based on the HorvathMammalMethylChip4, compared to other DNAm quantification approaches. No dependence of (R2) was detected for the number of CpG sites in a clock; the sample size; the number or kind of tissue(s) used; the class of animals; or whether captive or wild animals were sampled to infer the epigenetic clocks. We further conclude that epigenetic clocks can predict chronological age with relatively high accuracy, suggesting great potential for the field of ecological epigenetics. We therefore encourage further research on the topic of ecological epigenetics in relation to ageing and, perhaps more importantly, discuss the potential of employing DNAm to assess key traits other than age.

Adaptation enables natural populations to survive in a changing environment. Understanding the mechanics of adaptation is therefore crucial for learning about the evolution and ecology of natural populations, and for better conservation and management of natural resources such as fish stocks. In this review we focus on the impact of random sweepstakes on selection in highly fecund populations. In random sweepstakes the distribution of individual recruitment success is highly skewed, resulting in a huge variance in the number of offspring contributed by the individuals present in any given generation. We also describe selective sweepstakes which are well approximated by recurrent selective sweeps of strongly beneficial allelic types arising by mutation. We demonstrate that both types of sweepstakes reproduction may facilitate rapid adaptation. Finally, we review an important case study in which a model of recurrent selective sweeps is shown to essentially explain population genomic data of the highly fecund Atlantic cod, with broad implications for studying the evolution and ecology of highly fecund populations across domains of life.