Journal of Heredity

Gene flow to marginal populations at a species range edge can facilitate rapid adaptation by increasing genetic diversity, reducing inbreeding depression, and introducing novel alleles. In highly inbred populations, hybrid vigor is often observed in the first generation (F1), but hybrid breakdown may diminish fitness in subsequent generations. Thus, benefits of gene flow may be overestimated when only F1 performance is assessed. We tested whether gene flow among populations of the annual plant Erythranthe laciniata (A. Gray) G.L. Nesom, from similar and contrasting environments, confers persistent fitness advantages across F1 and F2 generations at the high-elevation edge of its range in the California Sierra Nevada. Gene flow was experimentally introduced through pollen transfer between cold-edge populations, between cold edge and central populations, and within local cold edge populations, and compared to self-fertilized offspring, the predominant mating strategy of E. laciniata. For F1 progeny, we measured morphological, phenological, and fitness traits in a common garden located near the cold-climate range limit during 2008-2009, a relatively average year, and for F2 progeny in 2009-2010, a relatively wet year. Although F1 crosses showed no initial performance advantage measured in the previous year, F2 progeny from center-to-edge and edge-to-edge crosses significantly outperformed selfed and locally outcrossed lines in fruit mass, total pedicels, biomass, and height. Our findings demonstrate that gene flow can confer long-term fitness benefits, especially among populations adapted to similar selective pressures, and highlight the potential of assisted gene flow to bolster or rescue peripheral populations facing climate change. SIGNIFICANCE STATEMENTSpecies living at the edges of their geographic ranges often have small, isolated populations with limited genetic diversity, which can restrict their ability to adapt to environmental change. Gene flow from other populations may increase adaptive potential, but its long-term consequences remain uncertain because most studies evaluate only first-generation hybrids. Using experimental crosses in the mountain wildflower Erythranthe laciniata, we show that gene flow can produce stronger fitness benefits in second-generation hybrids than in the first generation at a high-elevation range edge. These results suggest that recombination among populations can generate advantageous genetic combinations that emerge over multiple generations. Our findings highlight the potential for assisted gene flow to enhance adaptation and persistence of range-edge populations under climate change.

Conservation interventions are increasingly required for species threatened by population declines and isolation due to anthropogenic pressures. Small, isolated populations are particularly vulnerable to the loss of genetic diversity, increased inbreeding, and the accumulation of deleterious mutations. Translocations or supplementation of allopatric individuals for genetic rescue may be the only way to increase genetic diversity to increase population persistence via increased adaptive potential. Here, we use an experimentally admixed population of sand lizards on a small island in Sweden as a valuable model of genetic rescue. This population was established approximately 20 years ago (5-6 generations) resulting in increased fecundity and hatchling viability. This population was founded from crossings between individuals from an inbred population from the nearby mainland and individuals sourced from populations in southern Sweden. Low-coverage whole-genome sequencing revealed elevated genetic diversity and reduced realized genetic load in this admixed population relative to the source populations. Ancestry analyses indicated a greater contribution of southern Swedish genetic variation, potentially reflecting contribution of beneficial adaptive variation from this region that may underlie the positive population effects. This system provides valuable empirical insights into the long-term genomic consequences of genetic rescue in this model vertebrate population.

In asexual reproduction, meiosis must be bypassed or altered to maintain ploidy from mother to daughter without fertilization. Most of the ways meiosis can be modified to this end are expected to reduce heterozygosity within individuals; however, many asexual species are highly heterozygous. Asexual reproduction is especially common among species of microscopic, desiccation-tolerant animals such as rotifers, nematodes, and tardigrades, but the cellular and genetic mechanisms underlying asexual reproduction have not been definitively documented in any species of tardigrade. Here, we show that the asexual tardigrade Hypsibius exemplaris fails to complete the cell division of meiosis I, followed by a complete meiosis II-like division, and reproduction proceeds without detectable loss of heterozygosity. We used a combined cytological and genomic approach to characterize the mechanism of reproduction and pattern of allele inheritance in this species. Furthermore, we identified heterozygous variants in a subset of transcriptionally active genes consistent with loss of function in one allele, suggesting that maintained heterozygosity in this species allowed divergence between alleles over time. This work establishes the meiotic mechanism and inheritance pattern of reproduction in H. exemplaris, which provides a framework for interpreting genetic variation in this organism as a laboratory model. Additionally, our finding that meiosis is modified in H. exemplaris via a mechanism that maintains heterozygosity across the genome adds to a growing body of evidence that maintaining heterozygosity is not detrimental to the long-term survival of asexual eukaryotes. Article SummaryAnimals that reproduce asexually must alter meiosis, a highly conserved process of two cell divisions normally used to make eggs and sperm. This study represents the first combined cytological and genetic characterization of how meiosis is modified in a tardigrade. The authors found that the model tardigrade Hypsibius exemplaris modifies meiosis by skipping the first cell division, but completing the second. Additionally, they found that this species preserves heterozygosity across the genome and from generation to generation. Finally, some genes show evidence of sequence divergence between alleles, supporting a broader conclusion that maintaining heterozygosity influences how asexual species genomes evolve.

Parthenogenesis is relatively rare and often regarded as an evolutionary dead end. Despite this, certain parthenogenetic animal species have endured for millions of years, but it is unclear what enables the persistence of some parthenogenetic lineages. Transitions from sexual to parthenogenetic reproduction can occur through different evolutionary processes that give rise to diverse cytological reproductive mechanisms. These mechanisms are likely to influence genetic diversity, especially in the early stages after the transition to parthenogenesis and may thus affect lineage persistence. To understand such evolutionary transitions, we used experimental crosses to investigate the mechanism of parthenogenesis and the immediate genetic consequences of switching from sexual to parthenogenetic reproduction in the facultatively parthenogenetic phasmid Megacrania batesii. We obtained DNA sequence data from multiple lineages propagated over three generations via sex, parthenogenesis, or transitions between reproductive modes. We quantified heterozygosity and within-family genetic variation and compared the genetic patterns with predictions for known mechanisms of parthenogenesis. We found that a single generation of parthenogenesis typically resulted in (near-)complete loss of heterozygosity and an absence of within-family genetic variation, consistent with automixis with gamete duplication or terminal fusion and little/no recombination. However, we also found evidence of variation in the mechanism of parthenogenesis among lineages and even within the same individual, associated with drastic differences in the amount of heterozygosity and within-family genetic variation maintained across generations. Our findings show that considerable variation in parthenogenetic mechanisms can exist within populations and suggest that such variation could influence the persistence and evolution of parthenogenetic lineages.

Understanding evolutionary processes is greatly facilitated by high-quality data on genetic variation. We report the development of a genomic toolkit for a recently bottlenecked, long-term studied species, the Seychelles warbler (Ptimerl dezil; Acrocephalus sechellensis). This toolkit comprises a reference genome assembled into 31 chromosomes, together with functional annotations and reference-panel-free imputation of whole-genome sequences from 1,935 individuals. The genomic data have been used to assign the sequenced individuals into a genetic pedigree. Individual genomic data are associated with a suite of phenotypic metadata, amassed from three decades of fieldwork in this closed, long-term monitored population. We compared sex and parentage assigned using the genomic data with the previously recorded sex and parentage metadata to identify and correct 41 sample DNA samples labelled with the wrong identity. This population resource enables a wide range of analyses, that include, but are not limited to phylogenetics, metabarcoding, recombination rates, linkage patterns, adaptation, heritability, demographic history, selection, and inbreeding estimates. We wish to encourage interest from researchers seeking to collaborate on future analyses and data collection. Overall, our methods demonstrate the potential of next generation sequencing and statistical tools to provide dense genomic datasets at large sample sizes for wild populations.

Most eukaryotes reproduce using partial clonality, for which appropriate population genetic models remain limited. This gap constrains our ability to accurately reconstruct past population dynamics, predict future trajectories, and infer the evolutionary processes involved. We present a Wright-Fisher-like model tailored for tracking the mean and the variance of genotype frequencies over generations at one locus with multiple alleles in a same finite-sized population with mutation. Different initial conditions and rates of clonality generate unique mean trajectories of genotype frequencies. Partially clonal populations converge to the same unique stable equilibrium as exclusively sexual populations, that only depends on the reciprocal mutation rates between alleles. The dynamics unfold in two phases: First, genotype frequencies move towards Hardy-Weinberg proportions; Then iterate along the Hardy-Weinberg proportions until reaching the stable equilibrium. Mean allele frequencies and gene diversity remain unchanged by different rates of clonality along the trajectories. Instead, clonality influences the speed at which populations return to Hardy-Weinberg proportions and thus shapes the temporal sequence of genotype frequency distributions over generations. Variance around each mean trajectory depends only on parental genotype frequency distributions and population size, not on clonality. Taken together, these explain why both negative and positive Fis values are expected in partially clonal populations, and why variance of Fis across loci is a reliable proxy for inferring clonal rates. Our model will enable the analysis and prediction of changes in genotype frequencies within monitored populations, and will support future inference methods relying on time-series genotyping data from a target population. HighlightsO_LIOut of equilibrium, sexual and clonal populations share the same two-step dynamics. C_LIO_LIFirst, return to Hardy-Weinberg parabola impacted by rates of clonality; Then, iteration along this parabola until reaching equilibrium that only depends on mutation rates C_LIO_LIIncreasing clonality change the speed and direction of mean dynamics out of Hardy-Weinberg parabola without affecting mean allele frequencies C_LIO_LIVariance around mean dynamics depends on parental genotype frequencies and population size but not affected by clonality C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/717696v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@1207e9dorg.highwire.dtl.DTLVardef@587d2dorg.highwire.dtl.DTLVardef@18224eborg.highwire.dtl.DTLVardef@145e2ed_HPS_FORMAT_FIGEXP M_FIG C_FIG

Successful establishment of a species in a new range is a useful way to understand the impact of demography and selection on the evolution of globally distributed species. In particular, introductions influence genetic diversity and population structure in the introduced range in unpredictable ways. Additionally, introgressive hybridization is often associated with successful establishment in new ranges. In this study, we explore the impact of introgressive hybridization on the polyploid Capsella bursa-pastoris in the New York City metropolitan area. We find Capsella bursa-pastoris in the New York City metropolitan area likely originated from multiple introductions from northern Eurasia, and that populations across the New York City metropolitan area are generally panmictic. As with Capsella bursa-pastoris in Eurasia, we discover evidence of introgression from the diploid Capsella rubella in this population. By evaluating ancestry in regions across the genome, we find introgressed regions are rich in gene content and contribute to genetic diversity in this population. These results suggest that introgressive hybridization before introductions may buffer species from the negative effects of population bottlenecks and allow for successful establishment.

Tigriopus copepods are found in splash pools on all seven continents from the equator to Arctic and Antarctic regions. Given their geographic distribution, frequent exposure to extreme environmental conditions in the high intertidal zone, and strong signatures of local adaptation, these copepods have become models for exploring patterns of adaptation to stressful environments. However, most studies focus on a relatively small subset of Tigriopus species, and there are few genome resources representing the diversity of Tigriopus species and populations. Here, we combine long-read, Pacific Biosciences HiFi data with short-read, Illumina HiC and RNA-seq data to assemble and annotate a genome sequence representing a Tigriopus population from the coast of central Chile. Based on the level of divergence that we observed in mitochondrial genes, we also performed a comparison of morphological characteristics between individuals of this population and members of the T. angulatus complex. The haplotypes that we assembled (qhTigAngs1.1.hap1 & qhTigAngs1.1.hap2) are placed into 12 major scaffolds (N50 18-19 Mbp, L50 6-7), equivalent to the number of chromosomes in other Tigriopus species. BUSCO and k-mer analyses of each haplotype and BUSCO analyses of gene models are relatively complete (95-99%) with respect to gene and k-mer content. Analyses of mitochondrial data also suggest that the Chilean population of Tigriopus we sampled may represent a novel species that we call Tigriopus aff. angulatus. These genomic resources will help us understand the diversity and structure of Tigriopus species and populations as well as facilitate future comparisons of adaptation across parallel environmental gradients.

Strong population contractions can leave a persistent genomic legacy that can influence populations long after their demographic recovery. While bottlenecks facilitate the removal of strongly deleterious mutations, the effectiveness of purging may be limited in historically small populations. The Kirtlands warbler (Setophaga kirtlandii) is a rare North American songbird with an ancestrally small population. After narrowly evading extinction, they are one of few species that have been delisted from federal protections in the USA. Despite their recovery, a previous study showed evidence for recent inbreeding and a high burden of deleterious mutations that may have not been purged despite strong bottlenecks. Historical DNA offers a unique opportunity to understand the consequences of recent demographic declines on genetic diversity. Here, we use DNA from over 100-year-old museum specimens to estimate changes in genetic load in the Kirtlands warblers pre- and post-bottleneck. We validate our results with forward-in-time genetic simulations and explore how sample size and missing data can affect estimates. Both empirical data and simulations suggest a reduced ability to purge deleterious mutations in this historically small population. Our simulations also highlight that limited sampling design and data quality can constrain the ability to detect changes.

Populations of the Caribbean reef-building coral, Acropora palmata, have declined sharply since their population genetic structure was first characterized in the early 2000s. Previous analyses comprehensively sampled coral colonies across the Caribbean and western North Atlantic but genomic resolution was limited by the number of loci assayed. These analyses indicated extensive asexual reproduction via fragmentation, high outcrossing at the genet level, and a distinct east-west population split. To advance basic research and inform genetic management of this endangered species, we present an updated population genomic assessment using a species-specific microarray to analyze over 4,000 samples representing [~]1,500 genets from 12 geographic regions. Data were contributed by more than 30 research and restoration groups. Our analysis identifies nine spatially structured genetic clusters, with low average pairwise FST values of between 0.01 to 0.125. Interestingly, legacy genets from the Florida Reef Tract were admixed between two clusters, one dominant in the Mesoamerican Reef Tract on the western flank and the other cluster appearing in genets from Cuba to the south. Migration surface analyses highlight the influence of major current systems on gene flow. Isolation by distance was evident along the Greater Antilles but weak along the Florida Reef Tract. Kinship among wild genets was low across sites, suggesting limited local relatedness; however, assisted sexual reproduction in restoration efforts may disrupt natural kinship patterns. These findings refine our understanding of A. palmatas genetic architecture and underscore the importance of incorporating genomic data into conservation strategies.

The fitness of immigrants and their descendants determines the effectiveness of gene flow. Genetic incompatibilities or outbreeding depression can limit the spread of novel alleles, while highly fit immigrant lineages can hasten introgression. These fitness effects of gene flow can also differ between generations as immigrant and resident haplotypes recombine. Understanding the genetic factors that shape immigrant fitness over multiple generations is increasingly important as habitat fragmentation threatens populations by reducing genetic variation and leading to increased levels of inbreeding. Few studies have measured the multigenerational fitness of immigrant lineages, especially within populations that had histories of high gene flow. We used 33 years of life history and pedigree data on a population of Florida scrub-jays (Aphelocoma coerulescens) with historically high immigration to quantify the fitness of immigrants and their descendants. We compared the fitness of immigrants and residents as well as their resulting descendants (F1, F2, etc.) to determine the composite genetic effects responsible for fitness differences. We found evidence of additive benefits of immigrant ancestry and heterosis driven by non-additive effects that persists for multiple generations. These results are promising for conservation efforts aiming to increase connectivity and illustrate the complex dynamics that determine the rates of introgression in natural populations.

Assessing genetic diversity is essential for conserving endangered populations, yet comprehensive genomic evaluations remain limited for many declining species. Here, we investigated inbreeding levels and effective population sizes (Ne) of caribou (Rangifer tarandus) in western Canada, where populations have experienced pronounced declines over the past centuries due to anthropogenic pressures and climate change. We analyzed 33,346 Single Nucleotide Polymorphisms (SNPs) from 759 individuals representing 45 subpopulations within six metapopulations to: (1) assess inbreeding using runs of homozygosity (ROHs), (2) estimate contemporary and historical Ne, and (3) evaluate relationships between census size (Nc), inbreeding, and Ne. Small and endangered subpopulations, predominantly in southern regions, generally exhibited high inbreeding (FROH > 0.1), although some larger populations also showed elevated levels. Most subpopulations displayed a mixture of short and long ROHs, indicating both ancient shared ancestry and recent inbreeding. Twelve subpopulations had Ne <50, and 28 subpopulations and all metapopulations had Ne < 500, suggesting compromised short-term viability and long-term adaptive potential. Nc significantly predicted inbreeding (R{superscript 2} = 0.25), whereas contemporary Ne did not. Historical Ne reconstructions revealed a north-to-south gradient in bottleneck timing: northern populations declined in [~]1700-1780, central populations in [~]1780-1860, and southern populations in [~]1860-1940, likely driven by sequential impacts of climate shifts and anthropogenic disturbances. Our findings identify at-risk populations requiring urgent genetic intervention and demonstrate that integrating inbreeding and Ne estimates provides a robust framework for caribou recovery and the management of fragmented wildlife populations.

Small marsupials in the family Dasyuridae are a key component of Australias arid and semi-arid fauna, whose high species richness is proposed to reflect an opportunity-driven adaptive radiation. Despite growing interest in this group from both ecological and evolutionary perspectives, genomic data for most species is non-existent, or limited to a few marker loci. Here, we generated a chromosome-level reference genome and a de novo mitochondrial genome for the desert-dwelling Wongai ningaui (Ningaui ridei). The nuclear genome assembly is highly contiguous, with a scaffold N50 of 594.484 MB and high BUSCO gene recovery (93.84%). Additionally, we produced a draft assembly for the related, semi-arid slender-tailed dunnart (Sminthopsis murina). We then used these assemblies to explore the demographic histories of these species. We find evidence for contrasting patterns of population growth during the late Pleistocene and early Holocene, corresponding with differences in local climate, potentially consistent with differences in optimal habitat. The new genomic resources and demographic findings presented here provide a foundation for future studies on adaptive specialisation in this group of Australian marsupials. Significance StatementDasyurid marsupials are the primary carnivorous and insectivorous mammals in Australia. This diverse family includes species such as the endangered Tasmanian devil (Sarcophilus harrisii) and quolls (Genus Dasyurus), as well as an emerging laboratory model species, the fat-tailed dunnart (Sminthopsis crassicaudata). Despite the species richness within dasyurids, most species remain under-studied. This is particularly true of arid and semi-arid zone species, who are often small in size, live in remote habitats and are cryptic by nature. By creating genome assemblies for two dasyurid species, this study provides resources to support a variety of phylogenetic, population genetic and evolutionary developmental lines of research. Importantly, the studys finding that arid and semi-arid dasyurids show distinct trajectories of demographic change in response to historical climatic shifts may point to local adaptations with implications for the resilience of these species to ongoing and future climate change.

Transitions from sexual to asexual reproduction are well-documented across different taxa. However, despite extensive efforts, the regulatory changes underlying the emergence of asexuality remain largely undiscovered in the majority of species studied. Artemia brine shrimp have multiple closely related sexual and obligate parthenogenetic lineages, making them a promising model for addressing this question. While earlier work suggested that asexuals use a modified meiosis, and inferred a likely role for the Z-chromosome in its transmission, no master regulator or genetic changes have been put forward as the root causes for the shift. Here, we generate single-nucleus RNAseq data of the female reproductive system of individuals from the Aibi lake population of Artemia parthenogenetica and its closely related obligate sexual species Artemia sp. Kazakhstan. We identify the germline cell clusters in the female reproductive system and perform differential expression analysis to infer substantial transcriptional differences at genes putatively involved in cell cycle and oocyte development between the meiotic cells of the two species. Additionally, we use whole-genome sequencing of 32 individuals from two backcrossing experiments to narrow down the genomic regions associated with the transmission of asexuality to an 8 megabase region of the Z chromosome. Within the identified regions, two adjacent genes with known functions in oogenesis, ITPR and USP8, show differential expression and genetic differentiation between sexuals and asexuals, making them promising candidate drivers of asexuality in this species. Significance statementWhile most animals reproduce sexually, many do not, and why and how these shifts occur remains an open question. This paper presents a systematic investigation of the molecular changes that underlie the transition from sexual to asexual reproduction in brine shrimp. We combine multiple computational and experimental approaches to look for differences between close sexual and asexual lineages. We find that a subset of meiotic germ cells is regulated differently in the two, and that two important oogenesis genes are the likely drivers of asexuality. This work is unique in providing an in-depth characterization of the combined genetic and regulatory changes underlying this key transition in reproductive modes.

Understanding population structure is critical for effective fisheries management in species with complex life histories and variable recruitment. Southern flounder (Paralichthys lethostigma) is a valuable flatfish species with declining populations in the Southeast United States. Improved management may depend on a better understanding of fine-scale and temporal population genetic structure in this region; however, such structure remains poorly characterized. To address our lack of understanding of the spatial and temporal population structure of this important species, we used double digest reduced-representation genome sequencing (ddRADSeq) on juveniles from estuaries in North Carolina and Texas between 2014 and 2023. We found significant genetic differentiation between the Gulf of Mexico and Atlantic populations, supporting the management of these regions as distinct stocks. By contrast, we detected significant variance in genetic structure within Texas and North Carolina populations that was not consistent across sampling years between estuaries in close proximity. The population genetic structure of southern flounder suggests significant, temporally variable genetic differences within estuarine locations that may result from variation in larval dispersal and recruitment patterns. Our findings highlight the value of integrating fine-scale, multi-year genetic data to capture temporal dynamics and avoid misleading conclusions based on single-year or broad-scale sampling.

1Effective population size (Ne) is a critical parameter for evaluating the evolutionary and persistence potential of endangered populations and for designing sustainable conservation strategies. Captive breeding and release programs are widely used across taxa to reduce risk of extinction when natural reproduction is insufficient or no longer possible, making it essential to assess their consequences. We used the case study of the landlocked Saimaa salmon (Salmo salar), one of the most critically en-dangered salmonid populations in Europe, with unique evolutionary significance due to its isolation from other populations since the last glaciation. Using long-term demographic data (1969-2024) from wild-caught founders of a captive breeding and release program, we estimated the effective population size under multiple scenarios of variance in reproductive success. Across scenarios, Ne ranged from 33 to 81 individuals, representing 32%-75% of the census size. Captive breeding practices aimed at equalizing parental contributions during fertilization and early life stages increased Ne by 12% compared to natural reproductive conditions. However, variation in survival after early developmental stages, typically beyond direct management control, remained a key determinant of Ne. Despite recent increases in the number of founders, the population remains genetically vulnerable due to historical bottlenecks. These results highlight that while captive breeding programs can partially mitigate genetic risks, their effectiveness depends critically on both controlled and uncontrolled sources of variance in reproductive success. Strengthening such programs may require combining breeding management with habitat restoration and, where appropriate, genetic rescue to ensure the long-term evolutionary potential of such unique and endangered populations.

Whole genome duplication is a common mutation in eukaryotes with far-reaching phenotypic effects. The resulting morphological, physiological, and fitness consequences and how they affect the survival probability of newly polyploid lineages are intensively studied, but very little is known about the effect of genome doubling on the short-term evolvability of populations. Understanding the effect of polyploidization on the adaptive potential of populations is of crucial importance to predict the future of polyploid populations. In this paper, I investigate the immediate consequences of genome doubling on the genetic variance of populations. To do so, I performed numerical iterations and simulations of how the genetic variance of a quantitative trait changes after polyploidization, under different genetic architectures (additivity, dominance, and epistasis). I found that genetic variance generally decreases after genome doubling. Non-additive gene actions can make autotetraploid populations genetically more diverse than their diploid progenitors in rare cases, notably with overdominance and directional epistasis. By collecting estimates from the agronomic literature, I found that both dominance and epistatic variance contribute to the genetic variance of polyploid populations. These results bring new insights into the adaptive potential of newly formed tetraploid populations, and call for further experimental investigations of how polyploidization is associated with a short-term decrease in evolvability.

In sex-role reversed species, females are socially polyandrous and compete for multiple mates, whereas males conduct the majority of parental care. To understand the extent to which physiological differences between females and males are shaped by sex roles, we examined sex differences in gene expression in sex-role reversed northern jacanas (Jacana spinosa). Given that females compete for mating opportunities, and males cycle between courtship and parental care, we predicted that transcriptomic profiles would be more similar between females and courting males, in contrast to female and parenting males. Leveraging a high quality de novo genome assembly, we conducted RNA-seq on two brain regions associated with the regulation of social behavior: the preoptic area of the hypothalamus and the nucleus taeniae. The majority of genes differentially expressed between the sexes were male-biased. Of these male-biased genes, the majority were located on the Z-chromosome. Contrary to our prediction, the greatest difference in autosomal gene expression was between females and courting males, in the preoptic area of the hypothalamus. Several differentially expressed genes related to elements of hormone signaling that are likely to be behaviorally salient, including higher expression of androgen receptor in females relative to parenting males, and higher expression of prolactin receptor in males, regardless of breeding stage. Some sex-associated gene networks were also associated with competitive traits, whereas others were associated with aggressive behaviors, regardless of sex. Few genes were differentially expressed between courting and parenting males, yet some nonetheless had connections to behavioral endocrinology, including prolactin, thyroid and insulin-like growth factor pathways. Our investigation of sex differences in gene expression can help to reveal the molecular mechanisms underlying female competition and male parental care in socially polyandrous species. We conclude that social polyandry is not a simple reversal in the direction of sex-biased gene expression in the brain, but rather a result of complex genetic and hormonal interactions that warrants further study.

Genetic evidence for fluctuating selection has begun to accumulate for different species over the past few decades, especially for the Drosophila genus where studies have reported hundreds of loci undergoing putatively adaptive oscillations across successive seasons. However, most theoretical and simulation studies of fluctuating selection have relied on abstract or weakly parameterized models, making it difficult to assess their relevance for natural populations. In this study, we simulate multilocus seasonally fluctuating selection under a recently developed model and examine its effect on the variance effective population size (Ne) at a genome-wide scale. By recapitulating genomic, demographic, and evolutionary parameters from natural Drosophila populations in our simulations, we were able to reproduce allele frequency oscillations reported in recent studies and show that these lead to [~]50% genome-wide reductions in Ne. We also demonstrate that Ne reductions are well predicted by the maximum frequency amplitude among all adaptively fluctuating loci, and that the frequency amplitudes are largely determined by the number of adaptively fluctuating loci and the strength of their epistatic interactions. Our results demonstrate that fluctuating selection can substantially reduce effective population size and underscore the importance of temporally variable selection in shaping genome-wide patterns of variation beyond classical models. Article SummaryGenetic studies of fluctuating selection in natural populations have grown steadily over the past decade, with reports suggesting that hundreds of loci undergo adaptive oscillations over seasonal timescales in cosmopolitan Drosophila populations. By simulating seasonally fluctuating selection under a recently developed model and ecological scenarios informed by published studies, the authors show that this mode of selection can reduce effective population size by [~]50%, with the magnitude of the reduction correlated with the locus exhibiting the largest allele frequency fluctuations. These findings highlight fluctuating selection as an important factor shaping genome-wide patterns of genetic variation and effective population size.

The field of genetics of bird migration advances, driven by exponential refinements of sequencing and tracking technologies. In willow warblers (Phylloscopus trochilus), a complex repeat-rich region named MARB (Migration Associated Repeat Block) has recently been found to correlate with the routes taken by individual birds from Europe to their African wintering grounds. However, the genomic location of this region remains unknown. Here, we characterized MARB using a combination of approaches to understand how it evolved. We describe the region using long-read genome assemblies of two willow warbler subspecies (P. t. trochilus and P. t. acredula), two related species, the common chiffchaff (P. collybita) and the greenish warbler (P. trochiloides), and whole genome sequencing data from 76 willow warblers. Finally, we applied karyotyping and fluorescent in situ hybridization techniques on willow warbler spermatocytes to cytogenetically locate MARB. Due to the many repeats, we cannot order scaffolds in silico, but probe hybridization on the karyotype shows that MARB constitutes a single locus (~27.5 Mb) spanning most of the 11th largest chromosome in the willow warbler genome. Interestingly, the MARB regions of all species share several characteristics such as relatively high GC content (50%), a high density of specific repeat families and notably, more than 800 olfactory receptor sequences. Regions homologous to MARB may exist in several migrant bird genomes, though currently unassembled due to their complexity. Resolving these in species with similar migratory polymorphisms to willow warblers will be essential to determine whether MARB influences migratory behaviour across species.