Allele frequency dynamics in a pedigreed natural population

Multi-generational fitness legacies of natural immigration: theoretical and empirical perspectives and opportunities

Natural dispersal between populations, and resulting immigration, influences population size and genetic variation and is therefore a key process driving reciprocal interactions between ecological and evolutionary dynamics. Here, population dynamic and evolutionary outcomes fundamentally depend not only on the relative fitnesses of natural immigrants and existing residents, but also on the fitness of their various descendants manifested in natural environments. Yet, the fitnesses of different sets of natural immigrants' descendants have rarely been explicitly or rigorously estimated or rationalised in the context of wild spatially structured populations. We therefore still have surprisingly limited capability to understand or predict the ultimate multi-generational impacts of natural immigration on population and evolutionary dynamics. Key theoretical frameworks that predict fitness outcomes of outcrossing between lineages have been developed and widely utilised in the contexts of agriculture and speciation research. These frameworks have also been applied in conservation genetics research to predict positive (widely termed "heterosis") and negative (widely termed "outbreeding depression") outcomes in the context of genetic rescue of highly inbred populations. However, these frameworks have rarely been utilised explicitly to guide analyses of multi-generational legacies of regular natural immigrants in the context of evolutionary ecology, precluding inferences on the basis of, and implications of, sub-population divergence. Accordingly, to facilitate translation of concepts and inspire new empirical efforts, we first review and synthesise key bodies of theory on multi-generational fitness outcomes, developed in the contexts of crosses between inbred lines and between different species. Such theory reveals how diverse fitness outcomes can be generated by common underlying mechanisms, depending on the genetic architecture of fitness, the forms of genotype-phenotype-fitness maps, and the relative roles of adaptive and non-adaptive mechanisms in population differentiation. Interestingly, such theory predicts particularly diverse fitness outcomes of crosses between weakly diverged lineages, constituting the parameter space where spatially structured populations lie. We then conduct a systematic literature review to assess the degree to which multi-generational outcomes of crosses between structured natural populations have actually been quantified. Our review shows a surprising paucity of empirical studies that quantify multi-generational fitness consequences of outcrossing resulting from natural immigration in the wild. Furthermore, studies undertaking experimental crosses among populations have used inconsistent methodologies, precluding quantitative or even qualitative overall conclusions. To initiate new progress, we outline how long-standing and recent methodological developments, including cutting-edge statistical and genomic tools, could be combined with field data sets to quantify the multi-generational fitness outcomes of crosses between residents and immigrants in nature. We thereby highlight key theoretical and empirical gaps that now need to be filled to further our understanding of dispersal-mediated drivers and constraints on eco-evolutionary dynamics arising in structured populations.

Effect of assortative mating and sexual selection on polygenic barriers to gene flow

Assortative mating and sexual selection are widespread in nature and can play an important role in speciation by facilitating the buildup and maintenance of reproductive isolation (RI). However, their contribution to genome-wide suppression of gene flow during RI is rarely quantified. Here, we consider a polygenic "magic" trait that is divergently selected across two populations connected by migration, while also serving as the basis of assortative mating, thus generating sexual selection on one or both sexes. We obtain theoretical predictions for divergence at individual trait loci by assuming that the effect of all other loci on any locus can be encapsulated via an effective migration rate, which bears a simple relationship to measurable fitness components of migrants and various early-generation hybrids. Our analysis clarifies how "tipping points" (characterized by an abrupt collapse of adaptive divergence) arise, and when assortative mating can shift the critical level of migration beyond which divergence collapses. We quantify the relative contributions of viability and sexual selection to genome-wide barriers to gene flow and discuss how these depend on existing divergence levels. Our results suggest that effective migration rates provide a useful way of understanding genomic divergence, even in scenarios involving multiple, interacting mechanisms of RI.

Food, weather, and population density, not number of helpers, drive overwinter survival in Florida Scrub-Jays

Survival is affected by many ecological factors including food, weather, population density, and predation pressure, but documenting survival rates together with all these associated variables requires long-term observational and ecological data from a large, marked population. We used 33 years of data on Florida Scrub-Jay (Aphelocoma coerulescens) demography, local weather, and food availability to assess determinants of jay survival during the non-breeding season (September to February). We used the known-fate model from program MARK to analyze the probability of survival for breeders and juveniles while independently testing multiple covariates. Breeder survival increased when territory size was larger, decreased when local population density was higher, and did not vary with mean daily minimum temperature in the winter. Juvenile survival slightly increased with mean daily minimum temperature in the winter but showed no association with territory size or local population density. For both breeders and juveniles, odds of survival increased with presence of both breeders in the territory and higher acorn availability, and decreased with higher total winter rainfall. Neither breeder nor juvenile survival was correlated with number of helpers or juveniles in the group. Our results emphasize the importance of environmental variables in driving adult and juvenile survival in this declining endangered bird.

Estimating effective population size trajectories from time-series identity-by-descent segments

Long, identical haplotypes shared between pairs of individuals, known as identity-by-descent (IBD) segments, result from recently shared co-ancestry. Various methods have been developed to utilize IBD sharing for demographic inference in contemporary DNA data. Recent methodological advances have extended the screening for IBD segments to ancient DNA (aDNA) data, making demographic inference based on IBD also possible for aDNA. However, aDNA data typically have varying sampling times, but most demographic inference methods for modern data assume that sampling is contemporaneous. Here, we present Ttne (Time-Transect Ne), which models time-transect sampling to infer recent effective population size trajectories. Using simulations, we show that utilizing IBD sharing in time series increased resolution to infer recent fluctuations in effective population sizes compared with methods that only use contemporaneous samples. To account for IBD detection errors common in empirical analyses, we implemented an approach to estimate and model IBD detection errors. Finally, we applied Ttne to two aDNA time transects: individuals associated with the Copper Age Corded Ware Culture and Medieval England. In both cases, we found evidence of a growing population, a signal consistent with archaeological records.

Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants

Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 60-fold range in effective population size. We find rapid evolution of genome architecture, including ~100 Mb variation in genome size driven by dynamic satellite landscapes with unexpectedly long (> 10 kb) repeat units and widespread variation in gene content, influencing gene expression. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with strong evidence of adaptive fixation only in large populations. Our results demonstrate how population size shapes the distribution of SVs and the importance of pangenomes to characterizing genomic diversity.

Estimating realized relatedness in free-ranging macaques by inferring identity-by-descent segments

Biological relatedness is a key consideration in studies of behavior, population structure, and trait evolution. Except for parent-offspring dyads, pedigrees capture relatedness imperfectly. The number and length of identical-by-descent DNA segments (IBD) yield the most precise relatedness estimates. Here, we leverage different methods for estimating IBD segments from low-depth whole genome resequencing data to demonstrate the feasibility and value of resolving fine-scaled gradients of relatedness in free-living animals. Using primarily 4 to 6× depth data from a rhesus macaque (Macaca mulatta) population with long-term pedigree data, we show that we can infer the number and length of IBD segments across the genome with high accuracy even at 0.5× sequencing depth. In line with expectations based on simulation, the resulting estimates demonstrate substantial variation in genetic relatedness within kin classes, leading to overlapping distributions between kin classes. By comparing the IBD-based estimates with pedigree and short tandem repeat-based methods, we show that IBD estimates are more reliable and provide more detailed information on kinship. The inferred IBD segments also identify cryptic genetic relatives not represented in the pedigree and reveal elevated recombination rates in females relative to males, which enables the majority of close maternal and paternal kin to be distinguished with genotype data alone. Our findings represent a breakthrough in the ability to study the predictors and consequences of genetic relatedness in natural populations, contributing to our understanding of a fundamental component of population structure in the wild.

Levels and Spatial Patterns of Effective Population Sizes in the Southern Damselfly (Coenagrion mercuriale): On the Need to Carefully Interpret Single-Point and Temporal Estimations to Set Conservation Guidelines

The effective population size (N e) is a key parameter in conservation and evolutionary biology, reflecting the strength of genetic drift and inbreeding. Although demographic estimations of N e are logistically and time-consuming, genetic methods have become more widely used due to increasing data availability. Nonetheless, accurately estimating N e remains challenging, with few studies comparing N e estimates across molecular markers types and estimators such as single-sample methods based on linkage disequilibrium or sibship analyses versus methods based on temporal variance in allele frequencies. This study aims at bridging this gap by analysing single-sample and temporally spaced populations in the southern damselfly (Coenagrion mercuriale), a bioindicator Odonata species of conservation concern found in southwestern Europe's freshwater stream networks. A total of 77 local populations were sampled from a semi-urbanised area located in eastern France near Strasbourg city, yielding 2842 individuals that were genotyped with microsatellites and 958 of which were also genotyped for 2092 SNPs. Spatial genetic structure was stable over time, suggesting porosity between alternate-year cohorts. When accounting for spatial genetic structure, single-sample and temporal estimations of N e were consistent for each set of molecular markers. Biologically meaningful results were obtained when the effect of migration was minimising by considering metapopulation N e estimates based on the level of genetic differentiation and population boundaries. In terms of applied conservation and management, most depicted metapopulations displayed large N e, indicating no immediate need for conservation measures to mitigate anthropogenic pressures, provided that a continuous suitable freshwater network is maintained. However, urbanisation negatively impacted N e levels in populations close to Strasbourg city. Because N e is used to inform conservation decisions, caution is crucial in interpreting N e estimates, especially in continuously distributed populations undergoing migration. Altogether, our study highlights the challenge of obtaining robust N e estimates and the necessity of careful interpretation to set relevant conservation guidelines.

Density dependence maintains long-term stability despite increased isolation and inbreeding in the Florida Scrub-Jay

Isolation caused by anthropogenic habitat fragmentation can destabilize populations. Populations relying on the inflow of immigrants can face reduced fitness due to inbreeding depression as fewer new individuals arrive. Empirical studies of the demographic consequences of isolation are critical to understand how populations persist through changing conditions. We used a 34-year demographic and environmental dataset from a population of cooperatively breeding Florida Scrub-Jays (Aphelocoma coerulescens) to create mechanistic models linking environmental and demographic factors to population growth rates. We found that the population has not declined despite both declining immigration and increasing inbreeding, owing to a coinciding response in breeder survival. We find evidence of density-dependent immigration, breeder survival and fecundity, indicating that interactions between vital rates and local density play a role in buffering the population against change. Our study elucidates the impacts of isolation on demography and how long-term stability is maintained via demographic responses.

Beyond genes-for-behaviour: The potential for genomics to resolve long-standing questions in avian brood parasitism

Behavioural ecology by definition of its founding 'Tinbergian framework' is an integrative field, however, it lags behind in incorporating genomic methods. 'Finding the gene/s for a behaviour' is still rarely feasible or cost-effective in the wild but as we show here, genomic data can be used to address broader questions. Here we use avian brood parasitism, a model system in behavioural ecology as a case study to highlight how behavioural ecologists could use the full potential of state-of-the-art genomic tools. Brood parasite-host interactions are one of the most easily observable and amenable natural laboratories of antagonistic coevolution, and as such have intrigued evolutionary biologists for decades. Using worked examples, we demonstrate how genomic data can be used to study the causes and mechanisms of (co)evolutionary adaptation and answer three key questions for the field: (i) Where and when should brood parasitism evolve?, (ii) When and how should hosts defend?, and (iii) Will coevolution persist with ecological change? In doing so, we discuss how behavioural and molecular ecologists can collaborate to integrate Tinbergen's questions and achieve the coherent science that he promoted to solve the mysteries of nature.

36-year study reveals stability of a wild wheat population across microhabitats

Long-term genetic studies of wild populations are very scarce, but are essential for connecting ecological and population genetics models, and for understanding the dynamics of biodiversity. We present a study of a wild wheat population sampled over a 36-year period at high spatial resolution. We genotyped 832 individuals from regular sampling along transects during the course of the experiment. Genotypes were clustered into ecological microhabitats over scales of tens of metres, and this clustering was remarkably stable over the 36 generations of the study. Simulations show that it is difficult to determine whether this spatial and temporal stability reflects extremely limited dispersal or fine-scale local adaptation to ecological parameters. Using a common-garden experiment, we showed that the genotypes found in distinct microhabitats differ phenotypically. Our results provide a rare insight into the population genetics of a natural population over a long monitoring period.

A new high-quality genome assembly and annotation for the threatened Florida Scrub-Jay (Aphelocoma coerulescens)

The Florida Scrub-Jay (Aphelocoma coerulescens), a Federally Threatened, cooperatively-breeding bird, is an emerging model system in evolutionary biology and ecology. Extensive individual-based monitoring and genetic sampling for decades has yielded a wealth of data, allowing for the detailed study of social behavior, demography, and population genetics of this natural population. Here, we report a linkage map and a chromosome-level genome assembly and annotation for a female Florida Scrub-Jay made with long-read sequencing technology, chromatin conformation data, and the linkage map. We constructed a linkage map comprising 4,468 SNPs that had 34 linkage groups and a total sex-averaged autosomal genetic map length of 2446.78 cM. The new genome assembly is 1.33 Gb in length, consisting of 33 complete or near-complete autosomes and the sex chromosomes (ZW). This highly contiguous assembly has an NG50 of 68 Mb and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 97.1% with respect to the Aves database. The annotated gene set has a BUSCO transcriptome completeness score of 95.5% and 17,964 identified protein-coding genes, 92.5% of which have associated functional annotations. This new, high-quality genome assembly and linkage map of the Florida Scrub-Jay provides valuable tools for future research into the evolutionary dynamics of small, natural populations of conservation concern.

Microevolutionary change in wild stickleback: Using integrative time-series data to infer responses to selection

A central goal in evolutionary biology is to understand how different evolutionary processes cause trait change in wild populations. However, quantifying evolutionary change in the wild requires linking trait change to shifts in allele frequencies at causal loci. Nevertheless, datasets that allow for such tests are extremely rare and existing theoretical approaches poorly account for the evolutionary dynamics that likely occur in ecological settings. Using a decade-long integrative phenome-to-genome time-series dataset on wild threespine stickleback (Gasterosteus aculeatus), we identified how different modes of selection (directional, episodic, and balancing) drive microevolutionary change in correlated traits over time. Most strikingly, we show that feeding traits changed by as much 25% across 10 generations which was driven by changes in the genetic architecture (i.e., in both genomic breeding values and allele frequencies at genetic loci for feeding traits). Importantly, allele frequencies at genetic loci related to feeding traits changed at a rate greater than expected under drift, suggesting that the observed change was a result of directional selection. Allele frequency dynamics of loci related to swimming traits appeared to be under fluctuating selection evident in periodic population crashes in this system. Our results show that microevolutionary change in a wild population is characterized by different modes of selection acting simultaneously on different traits, which likely has important consequences for the evolution of correlated traits. Our study provides one of the most thorough descriptions to date of how microevolutionary processes result in trait change in a natural population.

To Prosper, Live Long: Understanding the Sources of Reproductive Skew and Extreme Reproductive Success in Structured Populations

AbstractIn many species, a few individuals produce most of the next generation. How much of this reproductive skew is driven by variation among individuals in fixed traits, how much by external factors, and how much by random chance? And what does it take to have truly exceptional lifetime reproductive output (LRO)? In the past, we and others have partitioned the variance of LRO as a proxy for reproductive skew. Here we explain how to partition LRO skewness itself into contributions from fixed trait variation, four forms of "demographic luck" (birth state, fecundity luck, survival trajectory luck, and growth trajectory luck), and two kinds of "environmental luck" (birth environment and environment trajectory). Each of these is further partitioned into contributions at different ages. We also determine what we can infer about individuals with exceptional LRO. We find that reproductive skew is largely driven by random variation in lifespan, and exceptional LRO generally results from exceptional lifespan. Other kinds of luck frequently bring skewness down rather than increasing it. In populations where fecundity varies greatly with environmental conditions, getting a good year at the right time can be an alternate route to exceptional LRO, so that LRO is less predictive of lifespan.

Allele frequency dynamics under sex-biased demography and sex-specific inheritance in a pedigreed jay population

Sex-biased demography, including sex-biased survival or migration, can alter allele frequency changes across the genome. In particular, we can expect different patterns of genetic variation on autosomes and sex chromosomes due to sex-specific differences in life histories, as well as differences in effective population size, transmission modes, and the strength and mode of selection. Here, we demonstrate the role that sex differences in life history played in shaping short-term evolutionary dynamics across the genome. We used a 25-year pedigree and genomic dataset from a long-studied population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of sex-biased demography and inheritance in shaping genome-wide allele frequency trajectories. We used gene dropping simulations to estimate individual genetic contributions to future generations and to model drift and immigration on the known pedigree. We quantified differential expected genetic contributions of males and females over time, showing the impact of sex-biased dispersal in a monogamous system. Due to female-biased dispersal, more autosomal variation is introduced by female immigrants. However, due to male-biased transmission, more Z variation is introduced by male immigrants. Finally, we partitioned the proportion of variance in allele frequency change through time due to male and female contributions. Overall, most allele frequency change is due to variance in survival and births. Males and females make similar contributions to autosomal allele frequency change, but males make higher contributions to allele frequency change on the Z chromosome. Our work shows the importance of understanding sex-specific demographic processes in characterizing genome-wide allele frequency change in wild populations.

AGT, CYP11B2 & ADRB2 gene polymorphism & essential hypertension (HT): A meta-analysis

Background & objectives The results of the genetic association studies between the selected candidate genes and hypertension (HT) contradicted across different populations. Majority of the meta-analyses carried out did not consider population genetic ancestry as a confounding factor. Therefore, this meta-analysis attempted to consolidate and re-evaluate the findings of the association between the selected candidate variants (AGT-rs699, CYP11B2-rs1799998, ADRB2-rs1042713 and rs1042714) and HT, by categorizing the genotyping data based on known genetic ancestry, and/or major geographical populations. Methods Publications were retrieved from PubMed, Cochrane and World of Science. The included articles were further divided into different populations based on their known genetic and/or geographical ancestry. Results AGTrs699-G was significantly associated with HT among Indians for (i) allele [P=0.03, Odds ratio (OR): 1.37, 95% Confidence Interval (CI): 1.03-1.82], and (ii) dominant mode of inheritance (P=0.009, OR:1.45, 95% CI: 1.09-1.91). CYP11B2rs1799998-G was significantly associated with HT in Europeans for (i) allele (P=6.9 × 10-5, OR: 0.82, 95% CI: 0.74-0.9), (ii) recessive (P=6.38 × 10-5, OR: 0.7, 95% CI: 0.59-0.83) and (iii) dominant mode of inheritance (P=0.008, OR: 0.81, 95% CI: 0.7-0.94). ADRB2-rs1042713-G was significantly associated with HT in east Asians for (i) allele (P=0.01, OR: 1.26, 95% CI: 1.05-1.51), and (ii) recessive mode of inheritance (P=0.04, OR: 1.36, 95% CI: 1.01-1.83). Interpretation & conclusions Different genotype and allele frequencies in diverse populations result in different genetic associations with HT across populations. This meta-analysis finding provides an update and summary of the genetic association between the selected simple nucleotide polymorphism (SNPs) and HT across different populations and essential insights into selecting appropriate pharmacogenetic marker(s) for effective HT management in populations of different ancestries.

Impacts of increasing isolation and environmental variation on Florida Scrub-Jay demography

Isolation caused by anthropogenic habitat fragmentation can destabilize populations. Populations relying on the inflow of immigrants can face reduced fitness due to inbreeding depression as fewer new individuals arrive. Empirical studies of the demographic consequences of isolation are critical to understand how populations persist through changing conditions. We used a 34-year demographic and environmental dataset from a population of cooperatively-breeding Florida Scrub-Jays ( Aphelocoma coerulescens ) to create mechanistic models linking environmental and demographic factors to population growth rates. We found that the population has not declined despite both declining immigration and increasing inbreeding, owing to a coinciding response in breeder survival. We find evidence of density-dependent immigration, breeder survival, and fecundity, indicating that interactions between vital rates and local density play a role in buffering the population against change. Our study elucidates the impacts of isolation on demography and how long-term stability is maintained via demographic responses.

A new approach to geostatistical synthesis of historical records reveals capuchin spatial responses to climate and demographic change

Recent proliferation of GPS technology has transformed animal movement research. Yet, time-series data from this recent technology rarely span beyond a decade, constraining longitudinal research. Long-term field sites hold valuable historic animal location records, including hand-drawn maps and semantic descriptions. Here, we introduce a generalised workflow for converting such records into reliable location data to estimate home ranges, using 30 years of sleep-site data from 11 white-faced capuchin (Cebus imitator) groups in Costa Rica. Our findings illustrate that historic sleep locations can reliably recover home range size and geometry. We showcase the opportunity our approach presents to resolve open questions that can only be addressed with very long-term data, examining how home ranges are affected by climate cycles and demographic change. We urge researchers to translate historical records into usable movement data before this knowledge is lost; it is essential to understanding how animals are responding to our changing world.

Mapping QTL associated with resistance to Pseudomonas syringae pv. actinidiae in kiwifruit (Actinidia chinensis var. chinensis)

Pseudomonas syringae pv. actinidiae (Psa) is a bacterial pathogen of kiwifruit. This pathogen causes leaf-spotting, cane dieback, wilting, cankers (lesions), and in severe cases, plant death. Families of diploid A. chinensis seedlings grown in the field show a range of susceptibilities to the disease with up to 100% of seedlings in some families succumbing to Psa. But the effect of selection for field resistance to Psa on the alleles that remain in surviving seedlings has not been assessed. The objective of this work was to analyse, the effect of plant removal from Psa on the allele frequency of an incomplete-factorial-cross population. This population was founded using a range of genotypically distinct diploid A. chinensis var. chinensis parents to make 28 F1 families. However, because of the diversity of these families, low numbers of surviving individuals, and a lack of samples from dead individuals, standard QTL mapping approaches were unlikely to yield good results. Instead, a modified bulk segregant analysis (BSA) overcame these drawbacks while reducing the costs of sampling and sample processing, and the complexity of data analysis. Because the method was modified, part one of this work was used to determine the signal strength required for a QTL to be detected with BSA. Once QTL detection accuracy was known, part two of this work analysed the 28 families from the incomplete-factorial-cross population that had multiple individuals removed due to Psa infection. Each family was assigned to one of eight bulks based on a single parent that contributed to the families. DNA was extracted in bulk by grinding sampled leaf discs together before DNA extraction. Each sample bulk was compared against a bulk made up of WGS data from the parents contributing to the sample bulk. The deviation in allele frequency from the expected allele frequency within surviving populations using the modified BSA method was able to identify 11 QTLs for Psa that were present in at least two analyses. The identification of these Psa resistance QTL will enable marker development to selectively breed for resistance to Psa in future kiwifruit breeding programs.

Multi-generation genetic contributions of immigrants reveal cryptic elevated and sex-biased effective gene flow within a natural meta-population

Impacts of immigration on micro-evolution and population dynamics fundamentally depend on net rates and forms of resulting gene flow into recipient populations. Yet, the degrees to which observed rates and sex ratios of physical immigration translate into multi-generational genetic legacies have not been explicitly quantified in natural meta-populations, precluding inference on how movements translate into effective gene flow and eco-evolutionary outcomes. Our analyses of three decades of complete song sparrow (Melospiza melodia) pedigree data show that multi-generational genetic contributions from regular natural immigrants substantially exceeded those from contemporary natives, consistent with heterosis-enhanced introgression. However, while contributions from female immigrants exceeded those from female natives by up to three-fold, male immigrants' lineages typically went locally extinct soon after arriving. Both the overall magnitude, and the degree of female bias, of effective gene flow therefore greatly exceeded those which would be inferred from observed physical arrivals, altering multiple eco-evolutionary implications of immigration.

Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques

Biological relatedness is a key consideration in studies of behavior, population structure, and trait evolution. Except for parent-offspring dyads, pedigrees capture relatedness imperfectly. The number and length of DNA segments that are identical-by-descent (IBD) yield the most precise estimates of relatedness. Here, we leverage novel methods for estimating locus-specific IBD from low coverage whole genome resequencing data to demonstrate the feasibility and value of resolving fine-scaled gradients of relatedness in free-living animals. Using primarily 4-6× coverage data from a rhesus macaque (Macaca mulatta) population with available long-term pedigree data, we show that we can call the number and length of IBD segments across the genome with high accuracy even at 0.5× coverage. The resulting estimates demonstrate substantial variation in genetic relatedness within kin classes, leading to overlapping distributions between kin classes. They identify cryptic genetic relatives that are not represented in the pedigree and reveal elevated recombination rates in females relative to males, which allows us to discriminate maternal and paternal kin using genotype data alone. Our findings represent a breakthrough in the ability to understand the predictors and consequences of genetic relatedness in natural populations, contributing to our understanding of a fundamental component of population structure in the wild.

The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics

In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies formalized in a structure called an ancestral recombination graph (ARG). An ARG extensively encodes the ancestry of the genome(s) and thus is replete with valuable information for addressing diverse questions in evolutionary biology. Despite its potential utility, technological and methodological limitations, along with a lack of approachable literature, have severely restricted awareness and application of ARGs in evolution research. Excitingly, recent progress in ARG reconstruction and simulation have made ARG-based approaches feasible for many questions and systems. In this review, we provide an accessible introduction and exploration of ARGs, survey recent methodological breakthroughs, and describe the potential for ARGs to further existing goals and open avenues of inquiry that were previously inaccessible in evolutionary genomics. Through this discussion, we aim to more widely disseminate the promise of ARGs in evolutionary genomics and encourage the broader development and adoption of ARG-based inference.

Effective fitness under fluctuating selection with genetic drift

The natural environment fluctuates for virtually every population of organisms. As a result, the fitness of a mutant may vary temporally. While commonly used for summarizing the effect of fluctuating selection on the mutant, geometric mean fitness can be misleading under some circumstances due to the influence of genetic drift. Here, we show by mathematical proof and computer simulation that, with genetic drift, the geometric mean fitness does not accurately reflect the overall effect of fluctuating selection. We propose an alternative measure based on the average expected allele frequency change caused by selection and demonstrate that this measure-effective fitness-better captures the overall effect of fluctuating selection in the presence of drift.

Temporal collections to study invasion biology

Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community-level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.

The era of the ARG: an empiricist's guide to ancestral recombination graphs

In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies formalized in a structure called an ancestral recombination graph (ARG). An ARG extensively encodes the ancestry of the genome(s) and thus is replete with valuable information for addressing diverse questions in evolutionary biology. Despite its potential utility, technological and methodological limitations, along with a lack of approachable literature, have severely restricted awareness and application of ARGs in empirical evolution research. Excitingly, recent progress in ARG reconstruction and simulation have made ARG-based approaches feasible for many questions and systems. In this review, we provide an accessible introduction and exploration of ARGs, survey recent methodological breakthroughs, and describe the potential for ARGs to further existing goals and open avenues of inquiry that were previously inaccessible in evolutionary genomics. Through this discussion, we aim to more widely disseminate the promise of ARGs in evolutionary genomics and encourage the broader development and adoption of ARG-based inference.

The estimation of reproductive values from pedigrees

Quantifying fitness is important to understand adaptive evolution. Reproductive values are useful for making fitness comparisons involving different categories of individuals, like males and females. By definition, the reproductive value of a category is the expected per capita contribution of the members of that category to the gene pool of future generations. Life history theory reveals how reproductive values can be determined via the estimation of life-history parameters, but this requires an adequate life-history model and intricate algebraic calculations. Recently, an alternative pedigree-based method has become popular, which estimates the expected genetic contribution of individuals to future generations by tracking their descendants down the pedigree. This method is versatile and intuitively appealing, but it is unknown if the method produces estimates of reproductive values that are accurate and precise. To investigate this, we implement various life-history scenarios (for which the "true" reproductive values can be calculated) in individual-based simulations, use the simulation data to estimate reproductive values with the pedigree method, and compare the results with the true target values. We show that the pedigree-based estimation of reproductive values is either biased (in the short term) or imprecise (in the long term). This holds even for simple life histories and under idealized conditions. We conclude that the pedigree method is not a good substitute for the traditional method to quantify reproductive values.

Beyond simple adaptation: Incorporating other evolutionary processes and concepts into eco-evolutionary dynamics

Studies of eco-evolutionary dynamics have integrated evolution with ecological processes at multiple scales (populations, communities and ecosystems) and with multiple interspecific interactions (antagonistic, mutualistic and competitive). However, evolution has often been conceptualised as a simple process: short-term directional adaptation that increases population growth. Here we argue that diverse other evolutionary processes, well studied in population genetics and evolutionary ecology, should also be considered to explore the full spectrum of feedback between ecological and evolutionary processes. Relevant but underappreciated processes include (1) drift and mutation, (2) disruptive selection causing lineage diversification or speciation reversal and (3) evolution driven by relative fitness differences that may decrease population growth. Because eco-evolutionary dynamics have often been studied by population and community ecologists, it will be important to incorporate a variety of concepts in population genetics and evolutionary ecology to better understand and predict eco-evolutionary dynamics in nature.

The long-lasting legacy of reproduction: lifetime reproductive success shapes expected genetic contributions of humans after 10 generations

An individual's lifetime reproductive success (LRS) measures its realized genetic contributions to the next generation, but how well does it predict this over longer periods? Here we use human genealogical data to estimate expected individual genetic contributions (IGC) and quantify the degree to which LRS, relative to other fitness proxies, predicts IGC over longer periods. This allows an identification of the life-history stages that are most important in shaping variation in IGC. We use historical genealogical data from two non-isolated local populations in Switzerland to estimate the stabilized IGC for 2230 individuals approximately 10 generations after they were born. We find that LRS explains 30% less variation in IGC than the best predictor of IGC, the number of grandoffspring. However, albeit less precise than the number of grandoffspring, we show that LRS does provide an unbiased prediction of IGC. Furthermore, it predicts IGC better than lifespan, and accounting for offspring survival to adulthood does not improve the explanatory power. Overall, our findings demonstrate the value of human genealogical data to evolutionary biology and suggest that reproduction-more than lifespan or offspring survival-impacts the long-term genetic contributions of historic humans, even in a population with appreciable migration.

Genetic and demographic consequences of range contraction patterns during biological annihilation

Species range contractions both contribute to, and result from, biological annihilation, yet do not receive the same attention as extinctions. Range contractions can lead to marked impacts on populations but are usually characterized only by reduction in extent of range. For effective conservation, it is critical to recognize that not all range contractions are the same. We propose three distinct patterns of range contraction: shrinkage, amputation, and fragmentation. We tested the impact of these patterns on populations of a generalist species using forward-time simulations. All three patterns caused 86-88% reduction in population abundance and significantly increased average relatedness, with differing patterns in declines of nucleotide diversity relative to the contraction pattern. The fragmentation pattern resulted in the strongest effects on post-contraction genetic diversity and structure. Defining and quantifying range contraction patterns and their consequences for Earth's biodiversity would provide useful and necessary information to combat biological annihilation.

Genetic Signature of Pinctada fucata Inferred from Population Genomics: Source Tracking of the Invasion in Mischief Reef of Nansha Islands

Among the anthropogenic stresses that marine ecosystems face, biological invasions are one of the major threats. Recently, as a result of increasingly intense anthropogenic disturbance, numerous marine species have been introduced to their non-native ranges. However, many introduced species have uncertain original sources. This prevents the design and establishment of methods for controlling or preventing these introduced species. In the present study, genomic sequencing and population genetic analysis were performed to detect the geographic origin of the introduced Pinctada fucata population in the Mischief Reef of the South China Sea. The results of population genetic structure analysis showed a close relationship between the Mischief Reef introduced population and the Lingshui population, indicating that Lingshui may be the potential geographical origin. Furthermore, lower heterozygosity and nucleotide diversity were observed in the introduced population in Mischief Reef, indicating lower genetic diversity than in other native populations. We also identified some selected genomic regions and genes of the introduced population, including genes related to temperature and salinity tolerance. These genes may play important roles in the adaptation of the introduced population. Our study will improve our understanding of the invasion history of the P. fucata population. Furthermore, the results of the present study will also facilitate further control and prevention of invasion in Mischief Reef, South China Sea.

Impact of Helicobacter pylori virulence markers on clinical outcomes in adult populations

BACKGROUND

In recent years, associations between specific virulence markers of Helicobacter pylori (H. pylori) and gastrointestinal disorders have been suggested.

AIM

To investigate the presence of virulence factors including vacuolating cytotoxin A genotypes (s1m1, s1m2, s2m1, and s2m2), cytotoxin-associated gene A (CagA), and urease activity in H. pylori strains isolated from Arab and Jewish populations in northern Israel and to assess associations between these factors and patients’ demographics and clinical outcomes.

METHODS

Patients (n = 108) who underwent gastroscopy at the Baruch Padeh Medical Center, Poriya due to symptomatic gastroduodenal pathologies as part of H. pylori diagnosis were enrolled in the study. Gastric biopsy specimens were collected from the antrum of the stomach. Clinical condition was assessed by clinical pathology tests. Bacteria were isolated on modified BD Helicobacter Agar (BD Diagnostics, Sparks, MD, United States). Bacterial DNA was extracted, and PCR was performed to detect CagA and vacuolating cytotoxin A genes. Urease activity was assessed using a rapid urease test.

RESULTS

A significant correlation was found between disease severity and patient ethnicity (P = 0.002). A significant correlation was found between CagA presence and the s1m1 genotype (P = 0.02), which is considered the most virulent genotype. Further, a higher level of urease activity was associated with isolates originating from the Jewish population. Moreover, higher urease activity levels were measured among CagA-/s1m1 and CagA-/s2m2 isolates.

CONCLUSION

Our study highlights the importance of incorporating molecular methods for detection of virulence markers of H. pylori in order to tailor optimal treatments for each patient. Further investigation should be performed regarding associations between H. pylori virulence factors and ethnicity.

Semantic and Population Analysis of the Genetic Targets Related to COVID-19 and Its Association with Genes and Diseases

SARS-CoV-2 is a coronavirus responsible for one of the most serious, modern worldwide pandemics, with lasting and multifaceted effects. By late 2021, SARS-CoV-2 has infected more than 180 million people and has killed more than 3 million. The virus gains entrance to human cells through binding to ACE2 via its surface spike protein and causes a complex disease of the respiratory system, termed COVID-19. Vaccination efforts are being made to hinder the viral spread, and therapeutics are currently under development. Toward this goal, scientific attention is shifting toward variants and SNPs that affect factors of the disease such as susceptibility and severity. This genomic grammar, tightly related to the dark part of our genome, can be explored through the use of modern methods such as natural language processing. We present a semantic analysis of SARS-CoV-2-related publications, which yielded a repertoire of SNPs, genes, and disease ontologies. Population data from the 1000 Genomes Project were subsequently integrated into the pipeline. Data mining approaches of this scale have the potential to elucidate the complex interaction between COVID-19 pathogenesis and host genetic variation; the resulting knowledge can facilitate the management of high-risk groups and aid the efforts toward precision medicine.

Taking quantitative genomics into the wild

We organized this special issue to highlight new work and review recent advances at the cutting edge of 'wild quantitative genomics'. In this editorial, we will present some history of wild quantitative genetic and genomic studies, before discussing the main themes in the papers published in this special issue and highlighting the future outlook of this dynamic field.

The genomic scale of fluctuating selection in a natural plant population

This study characterizes evolution at ≈1.86 million Single Nucleotide Polymorphisms (SNPs) within a natural population of yellow monkeyflower (Mimulus guttatus). Most SNPs exhibit minimal change over a span of 23 generations (less than 1% per year), consistent with neutral evolution in a large population. However, several thousand SNPs display strong fluctuations in frequency. Multiple lines of evidence indicate that these 'Fluctuating SNPs' are driven by temporally varying selection. Unlinked loci exhibit synchronous changes with the same allele increasing consistently in certain time intervals but declining in others. This synchrony is sufficiently pronounced that we can roughly classify intervals into two categories, "green" and "yellow," corresponding to conflicting selection regimes. Alleles increasing in green intervals are associated with early life investment in vegetative tissue and delayed flowering. The alternative alleles that increase in yellow intervals are associated with rapid progression to flowering. Selection on the Fluctuating SNPs produces a strong ripple effect on variation across the genome. Accounting for estimation error, we estimate the distribution of allele frequency change per generation in this population. While change is minimal for most SNPs, diffuse hitchhiking effects generated by selected loci may be driving neutral SNPs to a much greater extent than classic genetic drift.

Screening of Candidate Genes Associated with Brown Stripe Resistance in Sugarcane via BSR-seq Analysis

Sugarcane brown stripe (SBS), caused by the fungal pathogen Helminthosporium stenospilum, is one of the most serious threats to sugarcane production. However, its outbreaks and epidemics require suitable climatic conditions, resulting in the inefficient improvement of the SBS resistance by phenotype selection. The sugarcane F1 population of SBS-resistant YT93-159 × SBS-susceptible ROC22 was used for constructing the bulks. Bulked segregant RNA-seq (BSR-seq) was then performed on the parents YT93-159 (T01) and ROC22 (T02), and the opposite bulks of 30 SBS-susceptible individuals mixed bulk (T03) and 30 SBS-resistant individuals mixed bulk (T04) collected from 287 F1 individuals. A total of 170.00 Gb of clean data containing 297,921 SNPs and 70,426 genes were obtained. Differentially expressed genes (DEGs) analysis suggested that 7787 and 5911 DEGs were identified in the parents (T01 vs. T02) and two mixed bulks (T03 vs. T04), respectively. In addition, 25,363 high-quality and credible SNPs were obtained using the genome analysis toolkit GATK for SNP calling. Subsequently, six candidate regions with a total length of 8.72 Mb, which were located in the chromosomes 4B and 7C of sugarcane wild species Saccharum spontaneum, were identified, and 279 genes associated with SBS-resistance were annotated by ED algorithm and ΔSNP-index. Furthermore, the expression profiles of candidate genes were verified by quantitative real-time PCR (qRT-PCR) analysis, and the results showed that eight genes (LRR-RLK, DHAR1, WRKY7, RLK1, BLH4, AK3, CRK34, and NDA2) and seven genes (WRKY31, CIPK2, CKA1, CDPK6, PFK4, CBL2, and PR2) of the 20 tested genes were significantly up-regulated in YT93-159 and ROC22, respectively. Finally, a potential molecular mechanism of sugarcane response to H. stenospilum infection is illustrate that the activations of ROS signaling, MAPK cascade signaling, Ca2+ signaling, ABA signaling, and the ASA-GSH cycle jointly promote the SBS resistance in sugarcane. This study provides abundant gene resources for the SBS resistance breeding in sugarcane.

On the hidden temporal dynamics of plant adaptation

Adaptation to a wide range of environments is a major driver of plant diversity. It is now possible to catalog millions of potential adaptive genomic differences segregating between environments within a plant species in a single experiment. Understanding which of these changes contributes to adaptive phenotypic divergence between plant populations is a major goal of evolutionary biologists and crop breeders. In this review, we briefly highlight the approaches frequently used to understand the genetic basis of adaptive phenotypes in plants, and we discuss some of the limitations of these methods. We propose that direct observation of the process of adaptation using multigenerational studies and whole genome sequencing is a crucial missing component of recent studies of plant adaptation because it complements several shortcomings of sampling-based techniques.

Parent-offspring inference in inbred populations

Genealogical relationships are fundamental components of genetic studies. However, it is often challenging to infer correct and complete pedigrees even when genome-wide information is available. For example, inbreeding can obscure genetic differences between individuals, making it difficult to even distinguish first-degree relatives such as parent-offspring from full siblings. Similarly, genotyping errors can interfere with the detection of genetic similarity between parents and their offspring. Inbreeding is common in natural, domesticated, and experimental populations and genotyping of these populations often has more errors than in human data sets, so efficient methods for building pedigrees under these conditions are necessary. Here, we present a new method for parent-offspring inference in inbred pedigrees called specific parent-offspring relationship estimation (spore). spore is vastly superior to existing pedigree-inference methods at detecting parent-offspring relationships, in particular when inbreeding is high or in the presence of genotyping errors, or both. spore therefore fills an important void in the arsenal of pedigree inference tools.

Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus)

BACKGROUND

Development of large single nucleotide polymorphism (SNP) arrays can make genomic data promptly available for conservation problematic. Medium and high-density panels can be designed with sufficient coverage to offer a genome-wide perspective and the generated genotypes can be used to assess different genetic metrics related to population structure, relatedness, or inbreeding. SNP genotyping could also permit sexing samples with unknown associated metadata as it is often the case when using non-invasive sampling methods favored for endangered species. Genome sequencing of wild species provides the necessary information to design such SNP arrays. We report here the development of a SNP-array for endangered Rangifer tarandus using a multi-platform sequencing approach from animals found in diverse populations representing the entire circumpolar distribution of the species.

RESULTS

From a very large comprehensive catalog of SNPs detected over the entire sample set (N = 894), a total of 63,336 SNPs were selected. SNP selection accounted for SNPs evenly distributed across the entire genome (~ every 50Kb) with known minor alleles across populations world-wide. In addition, a subset of SNPs was selected to represent rare and local alleles found in Eastern Canada which could be used for ecotype and population assignments - information urgently needed for conservation planning. In addition, heterozygosity from SNPs located in the X-chromosome and genotyping call-rate of SNPs located into the SRY gene of the Y-chromosome yielded an accurate and robust sexing assessment. All SNPs were validated using a high-throughput SNP-genotyping chip.

CONCLUSION

This design is now integrated into the first genome-wide commercially available genotyping platform for Rangifer tarandus. This platform would pave the way to future genomic investigation of populations for this endangered species, including estimation of genetic diversity parameters, population assignments, as well as animal sexing from genetic SNP data for non-invasive samples.

Reproductive isolation via polygenic local adaptation in sub-divided populations: Effect of linkage disequilibria and drift

This paper considers how polygenic local adaptation and reproductive isolation between hybridizing populations is influenced by linkage disequilibria (LD) between loci, in scenarios where both gene flow and genetic drift counteract selection. It shows that the combined effects of multi-locus LD and genetic drift on allele frequencies at selected loci and on heterozygosity at neutral loci are predicted accurately by incorporating (deterministic) effective migration rates into the diffusion approximation (for selected loci) and into the structured coalescent (for neutral loci). Theoretical approximations are tested against individual-based simulations and used to investigate conditions for the maintenance of local adaptation on an island subject to one-way migration from a differently adapted mainland, and in an infinite-island population with two habitats under divergent selection. The analysis clarifies the conditions under which LD between sets of locally deleterious alleles allows these to be collectively eliminated despite drift, causing sharper and (under certain conditions) shifted migration thresholds for loss of adaptation. Local adaptation also has counter-intuitive effects on neutral (relative) divergence: F_ST is highest for a pair of subpopulations belonging to the same (rare) habitat, despite the lack of reproductive isolation between them.

Environmental adaptation often involves spatially heterogeneous selection at many genetic loci. Thus, the evolutionary consequences of hybridisation between populations adapted to different environments depend on the coupled dynamics of multiple loci under selection, migration and genetic drift, making them challenging to predict. Here, I introduce theoretical approximations that accurately capture the effect of such coupling on allele frequencies at individual loci, while also accounting for the stochastic effects of genetic drift. I then use these approximations to study hybridisation in a metapopulation consisting of many interconnected subpopulations, where each subpopulation belongs to one of two habitats under divergent selection. The analysis clarifies how subpopulations belonging to a rare habitat can maintain local adaptation despite high levels of migration if net selection against multi-locus genotypes is stronger than a threshold which depends on the relative abundances of the two habitats. Further, local adaptation in a metapopulation can significantly elevate F_ST between subpopulations belonging to the same habitat, even though these are not reproductively isolated. These findings highlight the importance of carefully considering the genetic architecture and spatial context of divergence when interpreting patterns of genomic differentiation between speciating populations.

Quantitative evaluation of nonlinear methods for population structure visualization and inference

Population structure (also called genetic structure and population stratification) is the presence of a systematic difference in allele frequencies between subpopulations in a population as a result of nonrandom mating between individuals. It can be informative of genetic ancestry, and in the context of medical genetics, it is an important confounding variable in genome-wide association studies. Recently, many nonlinear dimensionality reduction techniques have been proposed for the population structure visualization task. However, an objective comparison of these techniques has so far been missing from the literature. In this article, we discuss the previously proposed nonlinear techniques and some of their potential weaknesses. We then propose a novel quantitative evaluation methodology for comparing these nonlinear techniques, based on populations for which pedigree is known a priori either through artificial selection or simulation. Based on this evaluation metric, we find graph-based algorithms such as t-SNE and UMAP to be superior to principal component analysis, while neural network-based methods fall behind.

The effective family size of immigrant founders predicts their long-term demographic outcome: From Québec settlers to their 20th-century descendants

Population history reconstruction, using extant genetic diversity data, routinely relies on simple demographic models to project the past through ascending genealogical-tree branches. Because genealogy and genetics are intimately related, we traced descending genealogies of the Québec founders to pursue their fate and to assess their contribution to the present-day population. Focusing on the female and male founder lines, we observed important sex-biased immigration in the early colony years and documented a remarkable impact of these early immigrants on the genetic make-up of 20th-century Québec. We estimated the immigrants’ survival ratio as a proportion of lineages found in the 1931–60 Québec to their number introduced within the immigration period. We assessed the effective family size, EFS, of all immigrant parents and their Québec-born descendants. The survival ratio of the earliest immigrants was the highest and declined over centuries in association with the immigrants’ EFS. Parents with high EFS left plentiful married descendants, putting EFS as the most important variable determining the parental demographic success throughout time for generations ahead. EFS of immigrant founders appears to predict their long-term demographic and, consequently, their genetic outcome. Genealogically inferred immigrants’ "autosomal" genetic contribution to 1931–60 Québec from consecutive immigration periods follow the same yearly pattern as the corresponding maternal and paternal lines. Québec genealogical data offer much broader information on the ancestral diversity distribution than genetic scrutiny of a limited population sample. Genealogically inferred population history could assist studies of evolutionary factors shaping population structure and provide tools to target specific health interventions.

What is the best fitness measure in wild populations? A case study on the power of short-term fitness proxies to predict reproductive value

Fitness is at the core of evolutionary theory, but it is difficult to measure accurately. One way to measure long-term fitness is by calculating the individual’s reproductive value, which represents the expected number of allele copies an individual passes on to distant future generations. However, this metric of fitness is scarcely used because the estimation of individual’s reproductive value requires long-term pedigree data, which is rarely available in wild populations where following individuals from birth to death is often impossible. Wild study systems therefore use short-term fitness metrics as proxies, such as the number of offspring produced. This study compared two frequently used short-term metrics for fitness obtained at different offspring life stages (eggs, hatchlings, fledglings and recruits), and compared their ability to predict reproductive values derived from the genetic pedigree of a wild passerine bird population. We used twenty years of precise field observations and a near-complete genetic pedigree to calculate reproductive success, individual growth rate and de-lifed fitness as lifetime fitness measures, and as annual de-lifed fitness. We compared the power of these metrics to predict reproductive values and lineage survival to the end of the study period. The three short-term fitness proxies predict the reproductive values and lineage survival only when measured at the recruit stage. There were no significant differences between the different fitness proxies at the same offspring stages in predicting the reproductive values and lineage survival. Annual fitness at one year old predicted reproductive values equally well as lifetime de-lifed fitness. However, none of the short-term fitness proxies were strongly associated with the reproductive values. The commonly used short-term fitness proxies best predict long-term fitness when measured at recruitment stage. Thus, because lifetime fitness measured at recruit stage and annual fitness in the first year of life were the best proxies of long-term fitness in short-lived birds, we encourage their future use.

Evolutionary and Ecological Drivers of Local Adaptation and Speciation in a North American Avian Species Complex

Throughout the speciation process, genomic divergence can be differentially impacted by selective pressures, as well as gene flow and genetic drift. Disentangling the effects of these evolutionary mechanisms remains challenging, especially for non-model organisms. Accounting for complex evolutionary histories and contemporary population structure often requires sufficient sample sizes, for which the expense of full genomes remains prohibitive. Here, we demonstrate the utility of partial-genome sequence data for range-wide samples to shed light into the divergence process of two closely related ducks, the Mexican duck (Anas diazi) and mallard (A. platyrhynchos). We determine the role of selective and neutral processes during speciation of Mexican ducks by integrating evolutionary and demographic modelling with genotype-environment and genotype-phenotype association testing. First, evolutionary models and demographic analyses support the hypothesis that Mexican ducks originally diverged ~300,000 years ago in a climate refugia arising during a glacial period in in a southwestern North America, and that subsequent environmental selective pressures played a key role in divergence. Mexican ducks then showed cyclical demographic patterns that likely reflected repeated range expansions and contractions, along with bouts of gene flow with mallards during glacial cycles. Finally, we provide evidence that sexual selection acted on several phenotypic traits as a co-evolutionary process, facilitating the development of reproductive barriers that initially arose due to strong ecological selection. More broadly, this work reveals that the genomic and phenotypic patterns observed across species complexes are the result of myriad factors that contribute in dynamic ways to the evolutionary trajectories of a lineage.

A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population

Population genetics seeks to illuminate the forces shaping genetic variation, often based on a single snapshot of genomic variation. However, utilizing multiple sampling times to study changes in allele frequencies can help clarify the relative roles of neutral and non-neutral forces on short time scales. This study compares whole-genome sequence variation of recently collected natural population samples of Drosophila melanogaster against a collection made approximately 35 years prior from the same locality—encompassing roughly 500 generations of evolution. The allele frequency changes between these time points would suggest a relatively small local effective population size on the order of 10,000, significantly smaller than the global effective population size of the species. Some loci display stronger allele frequency changes than would be expected anywhere in the genome under neutrality—most notably the tandem paralogs Cyp6a17 and Cyp6a23, which are impacted by structural variation associated with resistance to pyrethroid insecticides. We find a genome-wide excess of outliers for high genetic differentiation between old and new samples, but a larger number of adaptation targets may have affected SNP-level differentiation versus window differentiation. We also find evidence for strengthening latitudinal allele frequency clines: northern-associated alleles have increased in frequency by an average of nearly 2.5% at SNPs previously identified as clinal outliers, but no such pattern is observed at random SNPs. This project underscores the scientific potential of using multiple sampling time points to investigate how evolution operates in natural populations, by quantifying how genetic variation has changed over ecologically relevant timescales.

Gene Flow and Genetic Structure Reveal Reduced Diversity between Generations of a Tropical Tree, Manilkara multifida Penn., in Atlantic Forest Fragments

The Atlantic Forest remnants in southern Bahia, Brazil, contain large tree species that have suffered disturbances in recent decades. Anthropogenic activities have led to a decrease in the population of many tree species and a loss of alleles that can maintain the evolutionary fitness of their populations. This study assessed patterns of genetic diversity, spatial genetic structure, and genetic structure among Manilkara multifida Penn. populations, comparing the genetic parameters of adult and juvenile trees. In particular, we collected leaves from adults and juveniles of M. multifida in two protected areas, the Veracel Station (EVC) and the Una Biological Reserve (UBR), located in threatened Atlantic Forest fragments. We observed a substantial decay in genetic variability between generations in both areas i.e., adults’ H_O values were higher (EVC = 0.720, UBR = 0.736) than juveniles’ (EVC = 0.463 and UBR = 0.560). Both juveniles and adults showed genetic structure between the two areas (θ = 0.017 for adults and θ = 0.109 for juveniles). Additionally, forest fragments indicated an unexpectedly short gene flow. Our results, therefore, highlight the pervasive effects of historical deforestation and other human disturbances on the genetic diversity of M. multifida populations within a key conservation region of the Atlantic Forest biodiversity hotspot.

Sex differences in deleterious mutational effects in Drosophila melanogaster: combining quantitative and population genetic insights

Fitness effects of deleterious mutations can differ between females and males due to: (i) sex differences in the strength of purifying selection; and (ii) sex differences in ploidy. Although sex differences in fitness effects have important broader implications (e.g., for the evolution of sex and lifespan), few studies have quantified their scope. Those that have belong to one of two distinct empirical traditions: (i) quantitative genetics, which focusses on multi-locus genetic variances in each sex, but is largely agnostic about their genetic basis; and (ii) molecular population genetics, which focusses on comparing autosomal and X-linked polymorphism, but is poorly suited for inferring contemporary sex differences. Here, we combine both traditions to present a comprehensive analysis of female and male adult reproductive fitness among 202 outbred, laboratory-adapted, hemiclonal genomes of Drosophila melanogaster. While we find no clear evidence for sex differences in the strength of purifying selection, sex differences in ploidy generate multiple signals of enhanced purifying selection for X-linked loci. These signals are present in quantitative genetic metrics-i.e., a disproportionate contribution of the X to male (but not female) fitness variation-and population genetic metrics-i.e., steeper regressions of an allele's average fitness effect on its frequency, and proportionally less nonsynonymous polymorphism on the X than autosomes. Fitting our data to models for both sets of metrics, we infer that deleterious alleles are partially recessive. Given the often-large gap between quantitative and population genetic estimates of evolutionary parameters, our study showcases the benefits of combining genomic and fitness data when estimating such parameters.

The promise and deceit of genomic selection component analyses

Selection component analyses (SCA) relate individual genotype to fitness components such as viability, fecundity and mating success. SCA are based on population genetic models and yield selection estimates directly in terms of predicted allele frequency change. This paper explores the statistical properties of gSCA: experiments that apply SCA to genome-wide scoring of SNPs in field sampled individuals. Computer simulations indicate that gSCA involving a few thousand genotyped samples can detect allele frequency changes of the magnitude that has been documented in field experiments on diverse taxa. To detect selection, imprecise genotyping from low-level sequencing of large samples of individuals provides much greater power than precise genotyping of smaller samples. The simulations also demonstrate the efficacy of 'haplotype matching', a method to combine information from a limited collection of whole genome sequence (the reference panel) with the much larger sample of field individuals that are measured for fitness. Pooled sequencing is demonstrated as another way to increase statistical power. Finally, I discuss the interpretation of selection estimates in relation to the Beavis effect, the overestimation of selection intensities at significant loci.

The relevance of pedigrees in the conservation genomics era

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.

The genomic consequences of hybridization

In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of natural hybridization, both historical and recent, there are still many unanswered questions about its genetic and evolutionary consequences. Recent work has suggested that the outcomes of hybridization in the genome may be in part predictable, but many open questions about the nature of selection on hybrids and the biological variables that shape such selection have hampered progress in this area. We synthesize what is known about the mechanisms that drive changes in ancestry in the genome after hybridization, highlight major unresolved questions, and discuss their implications for the predictability of genome evolution after hybridization.