Journal of Heredity

Juncus bufonius L. s.l. is a species complex with several ploidy levels, for which species delimitation remains unclear due to a lack of reliable morphological characters and the paucity of molecular studies. To clarify taxonomic and geographic relationships in the complex, we combined genomic, cytometric and morphological data from a broad latitudinal range from England down to Spain. We collected morphometric and cytometric data from 31 populations, and genomic data were obtained through Hyb-Seq using the Angiosperm353 kit for a subset of individuals. These three datasets were combined to explore phylogenetic relationships, population structure, and the validity of four previously proposed morphospecies (J. bufonius s.str., a hexaploid; J. minutulus, a tetraploid; and J. ranarius and J. hybridus, both diploids). Sequencing supported the separation of diploids and polyploids as two distinct taxa, but morphometric characters used previously to describe morphospecies showed continuous variation with no diagnostic value, and were not congruent with genomic and cytometric data. Polyploids likely originated through allopolyploidisation from diploids and tetraploids. Phylogenetic lineages were extensively mixed geographically, both for diploid and polyploid taxa, which suggests repeated long-distance dispersal events for both diploids and polyploids, and no separation of taxa by geography. Splitting of diploids into J. ranarius and J. hybridus was not supported. We recommend J. ranarius be treated as a synonym of J. hybridus, and that tetraploids and hexaploids be grouped under J. bufonius. The observed geographical patterns are consistent with high rates of seed dispersal by migratory waterbirds.

Animal translocations are becoming increasingly popular as a tool for conservationists. Demographic factors can be crucial determinants dictating translocation viability in the short term. Translocated populations pass through artificial bottlenecks and can suffer from founder effects. Reduction in genetic variation relative to their source populations is likely, limiting their adaptive potential. Founder events can increase frequencies of deleterious alleles due to elevated rates of inbreeding and inbreeding depression. Here, we describe the effects of human-driven, serial population translocations on the genetic diversity of critically endangered Anegada iguanas (Cyclura pinguis) in the British Virgin Islands. Though founding populations were extremely small (N=8, N=4), the census sizes of translocated iguana populations increased dramatically over the first twenty years. This implies that these translocations were successful from a demographic perspective despite the small number of animals used, indicating a genetic paradox. To quantify genetic signatures in these bottlenecked populations, blood samples were collected from the source population and two translocated populations and genotyped at 21 microsatellite loci. We found that allele frequencies in translocated populations differed significantly from those of the source, with the translocated populations having less genetic diversity. However, common methods for estimating presence of genetic bottlenecks were non-significant. Estimates of internal relatedness by age class suggest that inbreeding depression may be elevated after translocation, likely reflecting the small initial population sizes associated with these translocation events. Anecdotally, our work shows that translocations may result in subtle genetic erosion that has long-term population viability impacts, even when census size indicates success.

ContextGenetic diversity is essential for the persistence and future adaptation of species. However, human-driven habitat fragmentation results in population isolation, often leading to rapid loss of genetic diversity and adaptive capacity. Genetic management of focal taxa may be overlooked in many threatened species conservation programs. The Endangered southeastern Australian mallee emu-wren Stipiturus mallee is a species that may benefit from genetic management. Its current range encompasses patchily distributed sub-populations, prone to bottlenecks and genetic drift. Thus, the reintroduction to areas from which the species has been locally extirpated requires careful selection of founders to maximise genetic diversity. AimsWe analyse reduced-representation genomic data from seven sampling areas across the global meta-population to design a translocation strategy that maximises heterozygosity and retention of mallee emu-wren allelic diversity. MethodsWe estimated genetic structure, genetic diversity within, and differentiation between subpopulations, thus testing previous inference based on 12 length-variable loci of low population differentiation with 10,840 genome-wide SNP loci. We also estimated effective population sizes to identify populations in need of genetic augmentation, Finally, we used metapop2 simulations to estimate the relative contributions of each population to global genetic diversity of the species and to estimate the source and number of founders that would maximise heterozygosity and allelic richness in a hypothetical newly established population. Key resultsWe found weak genetic structure across all sampling areas, supporting previous conclusions that the global mallee emu-wren population should be considered a single genetic unit for management purposes. Low but significant Weir and Cockerham pairwise FST among locations indicated differentiation between sampling areas, suggesting that contemporary gene flow is restricted. Effective population sizes for the two regions supporting the largest numbers of mallee emu-wrens were below the threshold associated with reduced adaptive potential. ConclusionsThe genetic health and adaptive potential of sampled mallee emu-wren sub-populations are at risk. Implications The global mallee emu-wren meta-population would likely benefit from genetic augmentation, including reciprocal gene flow between extant sub-populations. To maximise genetic diversity in newly established populations, managers should prioritise gene-pool mixing with founders sourced from all sampled areas.

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.

Species are the fundamental analytical units of evolutionary processes; thus evidence-based species delimitation is a crucial step for understanding species radiations. However, the task of delimiting species is particularly challenging in the context of a syngameon--a group of distinct, but closely related species that have incomplete reproductive isolation and frequently hybridize in nature. This problem is further exacerbated by the presence of cryptic species--species that are phenotypically distinct, though difficult to distinguish with gross morphology alone. Heuchera subsect. Heuchera comprises both clear and cryptic species within a syngameon that has seen study from morphological, experimental, and phylogenetic aspects. This group has long been recognized for its taxonomic complexity, namely two recognized hybrid zones with extreme morphological variation and persistent non-monophyly among parental populations. Here, we reassess species limits within Heuchera subsect. Heuchera, focusing on the hybrid complex between H. americana and H. richardsonii and adjacent H. americana populations. We use a multipronged approach with deep population-level sampling to 1) assess the genetic structure of 655 individuals across the geographic range of the H. americana group to identify genetic lineages and 2) assess the phenotypic diagnosability of these lineages. Despite extensive admixture and gene tree conflict, we find multiple cohesive lineages with diagnosable phenotypes. We recognize five species and three varieties within the H. americana group, one new and four resurrected. Our results demonstrate that even highly reticulate syngameons can be partitioned into meaningful taxonomic units with multiple lines of evidence.

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.

We assembled and annotated a chromosome-level reference genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (QV = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This reference genome, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

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.

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.

Giant kelp, Macrocystis pyrifera, occurs across northern and southern Hemisphere temperate coasts and is at high risk from ocean warming. Few giant kelp forests remain across the Southeast Australian shelf, while a handful of forests are actively being restored. Genomic resources can greatly aid in the conservation of remnant populations and enhance restoration efforts. Reference genomes are a fundamental resource as they are a prerequisite to, or enhance, many analyses used in conservation genomics. A single reference genome is available for giant kelp, assembled from a Californian haploid specimen. However, increasing evidence of genetic divergence between Northern and Southern Hemisphere populations highlights the need for regionally representative reference genomes. Here, we present two genome assemblies from the diploid vegetative tissue of Australian giant kelp specimens. We performed de novo genome assembly using long-read sequencing (PacBio HiFi and ONT R10.4 Simplex) and scaffolded the assemblies with the ONT reads, assembling 98-99% of the genomes into 35 pseudo-chromosomes. Genome sizes ranged from 528-534 Mbp, with BUSCO completeness scores of 97-98% and QV scores of 51-52. Genome annotation identified 17,565-17,800 genes in the Australian genomes. Genomic divergence between the Australian and Californian giant kelp genomes was seven-fold greater than between Australian genomes (1.5% vs 0.2%), supporting a Northern-Southern Hemisphere genetic divergence. Functional divergence was also observed between Australian and Californian genomes, reflected by differing patterns of enrichment in gene ontologies linked to energy metabolism, proteostasis and stress responses. These two new genome assemblies will serve as valuable resources for ongoing research into Southern Hemisphere giant kelp genetics, while providing the basis for genomic-guided conservation and restoration of remnant giant kelp forests in Australia.

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.

Revealing the genetic basis of local adaptation is a common goal of evolutionary biology, but despite theoretical progress, general expectations for the genetic architecture of local adaptation are still unclear. Theoretical analyses usually model simplified ecologies or simplified genetic architectures of adaptive traits, so the interplay of these factors is missing from our understanding. In this study, we use simulations to explore how the interplay of ecological and genetic parameters influences the evolution and genetic architecture of local adaptation. With these simulations, we ask: i) What are the features of alleles that made the largest contribution to local adaptation, and how are they affected by polygenicity of adaptive traits, migration rates, demographic history, and the spatial pattern of the environment? And ii) does allele age moderate the confounding effect from population structure in genotype-environmental associations (GEA)? We find that the frequency, number, and phenotypic effect size of locally adaptive alleles are sensitive to trait polygenicity and demographic history, and that these factors shape the evolutionary dynamics of local adaptation. We find that population expansions can leave legacies in the genetic architecture of local adaptation, reducing the expected number of adaptive alleles relative to models with constant population size, and this effect is long-lasting. Compared to range expansion, other ecological variables known to affect the genetic basis of local adaptation had limited effects. Finally, allele age moderated the confounding effect of population structure and modified the causal effect of environmental variables on genotypes. Alleles that arose around the time of environmental changes often made large contributions to local adaptation, but young alleles often had the highest false positive rates and were the most common age category. We describe how incorporating allele age and its interactions with population structure and environmental variables may increase the sensitivity and specificity of GEA analysis. Overall, this work demonstrates the critical importance that a species demographic history can have on its genetic architecture of local adaptation.

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.

The scaly-sided merganser, Mergus squamatus, is an Endangered piscivorous duck which has been declining since the late 1900s due to habitat loss, over-hunting, and climate change. Despite being a species of global conservation concern and subject to ex- and in-situ conservation efforts, genomic research has been limited, hindering our understanding of its population genetic status and evolutionary history. In this study, we present the first fully annotated, chromosome-level genome for the scaly-sided merganser, generated using Oxford Nanopore long reads, Illumina short reads, and Hi-C sequencing. The final assembly spans 1.1 Gb across 307 scaffolds, 64 of which are anchored into 35 chromosomes, covering 99.5% of the genome. The assembly shows high contiguity (N50 = 84.3Mb) and completeness, with a Benchmarking Universal Single-Copy Ortholog (BUSCO) score of 98%. Repeat sequences comprise 9.55% of the genome. Homology-based gene annotation identified [~]15,200 protein-coding genes. A complete 16,624 bp mitochondrial genome was also assembled and annotated. Synteny analysis revealed strong chromosomal conservation across the wider Anatidae family, with evidence of lineage-specific rearrangements. Pairwise Sequential Markovian Coalescence modelling indicates recent stability in the effective population size of the species, with past declines coinciding with Pleistocene glacial cycles. Our high-quality genome provides an essential resource for conservation genomic and evolutionary studies of the scaly-sided merganser, supporting ongoing efforts to manage and protect this threatened species.

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.

Estimation of the effective size (Ne) of large populations with a continuous distribution across wide geographic areas and limited dispersal of individuals has been elusive so far. Estimates of the contemporary Ne from genetic markers for such large, structured populations, typically of plant and marine species, tend to be strongly biased downwards, which has led to question their relevance. Here we show that a recently proposed estimation method of Ne from linkage disequilibrium between markers, which accounts for population structure, yields estimates of metapopulation Ne when the sampling area is sufficiently large. The method is applied to empirical data of maritime pine (Pinus pinaster Aiton). While previous estimates of Ne in pine populations were of the order of a few hundred individuals, we show that estimates of the metapopulation Ne can reach values of the order of tens of thousands of individuals. This result is especially relevant from a conservation point of view, as populations with Ne lower than 500 individuals are considered to be under the risk of extinction.