Adaptation enables natural populations to survive in a changing environment. Understanding the mechanics of adaptation is therefore crucial for learning about the evolution and ecology of natural populations, and for better conservation and management of natural resources such as fish stocks. In this review we focus on the impact of random sweepstakes on selection in highly fecund populations. In random sweepstakes the distribution of individual recruitment success is highly skewed, resulting in a huge variance in the number of offspring contributed by the individuals present in any given generation. We also describe selective sweepstakes which are well approximated by recurrent selective sweeps of strongly beneficial allelic types arising by mutation. We demonstrate that both types of sweepstakes reproduction may facilitate rapid adaptation. Finally, we review an important case study in which a model of recurrent selective sweeps is shown to essentially explain population genomic data of the highly fecund Atlantic cod, with broad implications for studying the evolution and ecology of highly fecund populations across domains of life.
How changes in biodiversity affect disease, particularly in the face of large-scale land-use change, is a contentious topic in disease ecology that has implications for public health and conservation policy. The ‘dilution effect’ hypothesis argues that declines in biodiversity are associated with increased disease risk, but this can be challenging to demonstrate because many pathogens have complex life cycles such that changes to the species composition and abundance of hosts can influence the density and infection prevalence of vectors via multiple mechanisms. Key to addressing this debate is a quantification of interactions between hosts, vectors, and pathogens. In their recent study published in Molecular Ecology, Kocher et al. (2022) captured thousands of sandflies, some species of which are vectors for the Leishmania protozoan that causes Leishmaniasis, across a human footprint gradient in French Guiana (Fig. 1). By implementing DNA metabarcoding of vectors combined with an innovative modeling approach, they effectively quantified the nuanced relationships between changes in land-use, mammalian host diversity, vector abundance, and parasite prevalence. In support of the dilution effect hypothesis, Kocher et al. found that sites with higher mammal diversity were associated with lower relative abundance of reservoir hosts and higher Leishmania infection prevalence in sandflies. However, while infection prevalence was lower when mammal diversity was high, the density of sandfly vectors was higher, which resulted in a weak overall effect of mammal diversity on the density of infected vectors, the most important indicator of Leishmania transmission risk.
The genomics revolution continues to change how ecologists and evolutionary biologists study the evolution and maintenance of biodiversity. It is now easier than ever to generate large molecular data sets consisting of hundreds to thousands of independently evolving nuclear loci to estimate a suite of evolutionary and demographic parameters. However, any inferences will be incomplete or inaccurate if incorrect taxonomic identities and perpetuated throughout the analytical pipeline. Due to decades of research and comprehensive online databases, sequencing of mitochondrial DNA (mtDNA), chloroplast DNA (cpDNA) and select nuclear genes can provide researchers with a cost effective and simple means to verify the species identity of samples prior to subsequent phylogeographic and population genomic analysis. The addition of these sequences to genomic studies can also shed light on other important evolutionary questions such as explanations for gene tree-species tree discordance, species limits, sex-biased dispersal patterns, and mtDNA introgression. Although the mtDNA and cpDNA genomes often should not be used exclusively to make historical inferences given their well-known limitations, the addition of these data to modern genomic studies adds little cost and effort while simultaneously providing a wealth of useful data that can have significant implications for both basic and applied research.
Traditional agrosystems, where humans, crops and microbes have coevolved over long periods, can serve as models to understand the eco-evolutionary determinants of disease dynamics and help the engineering of durably resistant agrosystems. Here, we investigated the genetic and phenotypic relationship between rice (Oryza sativa) landraces and their rice blast pathogen (Pyricularia oryzae) in the traditional Yuanyang terraces of flooded rice paddies in China, where rice landraces have been grown and bred over centuries without significant disease outbreaks. Analyses of genetic subdivision revealed that indica rice plants clustered according to landrace names. Three new diverse lineages of rice blast specific to the Yuanyang terraces coexisted with lineages previously detected at the worldwide scale. Population subdivision in the pathogen population did not mirror pattern of population subdivision in the host. Measuring the pathogenicity of rice blast isolates on landraces revealed generalist life histories. Our results suggest that the implementation of disease control strategies based on the emergence or maintenance of a generalist lifestyle in pathogens may sustainably reduce the burden of disease in crops.
Telomerase activity and telomere maintenance in certain somatic cells of human adults support the proliferative capacity of these cells and thus contribute to their regenerative potential, and telomerase activity and telomere length are commonly considered lifespan predictors. Eusocial insects provide excellent models for aging research based on their extraordinary caste-related lifespan differences that contradict the typical mammalian fecundity/lifespan trade-off. Telomerase activity is upregulated in the reproductive, long-lived individuals of eusocial insects such as queens and kings, and telomerase activity may act as a key factor in their extended longevity. But, as documented by the presence of telomerase in somatic tissues of numerous invertebrate and vertebrate species, the connection between telomerase activity and the predicted lifespan is not clear. Here, I ask whether somatic telomerase activity in eusocial reproductives may serve its non-canonical function to protect its individuals against the metabolic stress due to reproduction and reflect a more common phenomenon among species. Here, I propose a hypothesis that the presence of telomerase activity in somatic cells reflects a different reproduction strategy of species.
Low vagility species may hold strong genetic signatures of past biogeographic processes but are also vulnerable to habitat loss. Flightless grasshoppers of the morabine group were once widespread in south-eastern Australia including Tasmania but are becoming restricted to remnant patches of vegetation, with local ranges impacted by agriculture and development as well as management. Habitat fragmentation can generate genetically differentiated “island” populations with low genetic variation. However, following revegetation, populations could be re-established and gene flow increased. Here we characterise SNP based genetic variation in a widespread chromosomal race of the morabine Vandiemenella viatica (race 19) to investigate the genetic health of remnant populations and to provide guidelines for restoration efforts. We update the distribution of this race to new sites in Victoria and Tasmania, and show that V. viatica populations from northern Tasmania and eastern Victoria have reduced genetic variation compared to other mainland populations. In contrast there was no effect of habitat fragment size on genetic variation. Tasmanian V. viatica populations fell into two groups, one connected genetically to eastern Victoria and the other connected to south-western Victoria. Mainland populations showed isolation by distance. These patterns are consistent with expectations from past biogeographic processes rather than local recent population fragmentation and emphasize the importance of small local reserves in preserving genetic variation. The study highlights how genomic analyses can combine information on genetic variability and population structure to identify biogeographic patterns within a species, which in turn can inform decisions on potential source populations for translocations.
Divergence in the face of high dispersal capabilities is a documented but poorly understood phenomenon. The white-tailed eagle (Haliaeetus albicilla) has a large geographic dispersal capability and should theoretically be able to maintain genetic homogeneity across its dispersal range. However, following analysis of the genomic variation of white-tailed eagles, from both historical and contemporary samples, clear signatures of ancient biogeographic substructure across Europe and the North-East Atlantic is observed. The greatest genomic differentiation was observed between island (Greenland and Iceland) and mainland (Denmark, Norway and Estonia) populations. The two island populations share a common ancestry from a single mainland population, distinct from the other sampled mainland populations, and despite the potential for high connectivity between Iceland and Greenland they are well separated from each other and are characterized by inbreeding and little variation. Temporal differences also highlight a pattern of regional populations persisting despite the potential for admixture. All sampled populations generally showed a decline in effective population size over time, which may have been shaped by four historical events: I) isolation of refugia during the last glacial period 110-115,000 years ago, II) population divergence following the colonization of the deglaciated areas ~10,000 years ago, III) human population expansion, which led to the settlement in Iceland ~1,100 years ago, and IV) human persecution and exposure to toxic pollutants during the last two centuries.
Indirect genetic effects describe phenotypic variation that results from differences in the genotypic composition of social partners. Such effects represent heritable sources of environmental variation in eusocial organisms because individuals are typically reared by their siblings. In the fire ant Solenopsis invicta, a social supergene exhibits striking indirect genetic effects on worker regulation of colony queen number, such that the genotypic composition of workers at the supergene determines whether colonies contain a single or multiple queens. We assessed the direct and indirect genetic effects of this supergene on gene expression in brains and abdominal tissues from lab-reared workers and compared these with previously published data from field-collected pre-reproductive queens. We found that direct genetic effects caused larger gene expression changes and were more consistent across tissue types and castes than indirect genetic effects. Indirect genetic effects influenced the expression of many loci but were generally restricted to the abdominal tissues. Further, indirect genetic effects were only detected when the genotypic composition of social partners differed throughout the development and adult life of focal workers, and were often only significant with relatively lenient statistical cutoffs. Our study provides insight into direct and indirect genetic effects of a social supergene on gene regulatory dynamics across tissues and castes in a complex society.
Linear infrastructure stands as one of the main culprits of anthropogenically caused biodiversity decline. As it fragments landscapes, it ultimately results in a myriad of direct and indirect ecological consequences for wildlife. As transportation networks will continue to grow under increasing human population growth, biodiversity will continue to decline making the need to understand and mitigate their impact on species an urgent need for conservation worldwide. The implementation of mitigation measures to alleviate the barrier effect produced by linear transport infrastructure on local fauna is not new, and research has shown that their effectiveness has been shown to be influenced by their design, their placement and the biology of the impacted species. Our understanding of their effectiveness in preventing the longer-term impacts of linear transport infrastructure on habitat connectivity via gene flow, however, remains poorly understood. Here, we used a pre- and post-habitat fragmentation genetic dataset collected as part of an extensive Koala Management Program to ask questions about the immediate and predicted longer-term genetic consequences of linear transport infrastructure on the impacted species. Importantly, using forward migration simulations, we show that to preserve connectivity would need to result in around 20% of the population mixing to avoid long-term genetic drift. These results have important consequences for the management of species at the forefront of linear infrastructure. In particular, the study shows the importance of considering gene flow in our assessment of the effectiveness of fauna crossings.
By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while new can be asked. Such questions include how different local environments influence both adaptive and neutral genomic variation within and among populations, providing insights not only into local adaptation of natural populations, but also into their responses to global change and the exploitation-induced evolution. Here, under a seascape genomic approach, ddRAD genomic data were used along with environmental information to uncover the underlying processes (migration, selection) shaping European sardines (Sardina pilchardus) of the Western Mediterranean and adjacent Atlantic waters. This information can be relevant to the (re)definition of fishery stocks, and their short-term adaptive potential. We found that studied sardine samples form two clusters, detected using both neutral and adaptive (outlier) loci suggesting that natural selection and local adaptation play a key role in driving genetic change among the Atlantic and the Mediterranean sardines. Temperature and especially the trend in the number of days with sea surface temperature (SST) above 19oC was crucial at all levels of population structuring with implications on species’ key biological processes, especially reproduction. Our findings provide evidence for a dynamic equilibrium where population structure is maintained by physical and biological factors under the opposing influences of migration and selection. Given its dynamic nature, such a system postulates a continuous monitoring under a seascape genomic approach that can benefit by incorporating a temporal as well as a more detailed spatial dimension.
Anthropogenic biological invasions represent major concerns but enable us to investigate rapid evolutionary changes and adaptation to novel environments. The goldfish Carassius auratus with sexual diploids and asexual triploids coexisting in natural waters, is one of the most widespread invasive fishes in Tibet, providing an ideal model to study evolutionary processes during invasion in different reproductive forms from the same vertebrate. Here, using whole-genome resequencing data of 151 C. auratus individuals from invasive and native ranges, we found different patterns of genomic responses between diploid and triploid populations during their invasion to Tibet. For diploids, although invasive individuals derived from two different genetically distinct sources and had a relative higher diversity (π) at the population level, their individual genetic diversity (genome-wide observed heterozygosity) was significantly lower (21.4%) than that of source individuals. Population structure analysis revealed that the invasive individuals formed a specific genetic cluster distinct from the source populations. Runs of homozygosity analysis showed low inbreeding only in invasive individuals, and only the invasive population experienced a recent decline in effective population size reflecting founder events. For triploids, however, invasive populations showed no loss of individual genetic diversity and no genetic differentiation relative to source populations. Regions of putative selective sweeps between invasive and source populations of diploids mainly involved genes associated with mannosidase activity and embryo development. Our results suggest invasive diploids deriving from distinct sources still lost individual genetic diversity resulting from recent inbreeding and founder events and selective sweeps, and invasive triploids experienced no genetic change owing to their reproduction mode of gynogenesis that precludes inbreeding and founder effects and may make them more powerful invaders.
Pregnancy, the post-fertilization period when embryos are incubated within the body, is a dynamic multistage process that has convergently evolved in many vertebrates. To increase independence from environmental fluctuations and protect offspring from predation, challenges had to be initially overcome. The most obvious, when considering such an intimate relation between the parent and its semi-allogenic offspring, was the pressing need to dodge immunity-associated embryo rejection. In mammals, immunological tolerance was found to be dependent on the active modulation of the immune system. Even though supporting much of the current knowledge on vertebrate pregnancy, mammals lack extant transitional stages that could help reconstruct the evolutionary pathway of this fascinatingly complex reproduction mode. In this issue of Molecular Ecology, Parker et al. (2022) selected an untraditional model - the seahorse and pipefish family, whose species evolved male pregnancy across an almost continuous gradient of complexity, from external oviparity to internal gestation. By contrasting gene expression profiles of syngnathids with distinct brooding architectures, this study allowed for the observation of subtle evolutionary adaptations, while confirming the existence of remarkable similarities to ‘female’ pregnancy (e.g., the evolution of male pregnancy in pouched species occurred alongside immune downregulation, and inflammation seems vital during early pregnancy stages). In a world where the debate on sex-roles takes centre stage, Parker et al. (2022) appeasing results hint at the fact that the strongly convergent evolution of vertebrate pregnancy was seemingly unaffected by which sex carries the burden of gestation.
Host-parasite interactions can cause strong demographic fluctuations accompanied by selective sweeps of resistance/infectivity alleles. Both demographic bottlenecks and frequent sweeps are expected to reduce the amount of segregating genetic variation and therefore might constrain adaption during coevolution. Recent studies, however, suggest that the interaction of demographic and selective processes is a key component of coevolutionary dynamics and may rather positively affect levels of genetic diversity available for adaptation. Here, we provide direct experimental testing of this hypothesis by disentangling the effect of demography, selection, and of their interaction in an experimental host-parasite system. We grew 12 populations of unicellular algae (Chlorella variabilis) that experienced either growth followed by constant population sizes (3 populations), demographic fluctuations (3 populations), selection induced by exposure to a virus (3 populations), or demographic fluctuations together with virus-induced selection (3 populations). After 50 days, we conducted whole-genome sequencing of each algal population. We observed more genetic diversity in populations that jointly experienced selection and demographic fluctuations than in populations where these processes were experimentally separated. In addition, in those 3 populations that jointly experienced selection and demographic fluctuations, experimentally measured diversity exceeds expected values of diversity that account for the cultures’ population sizes. Our results suggest that eco-evolutionary feedbacks can positively affect genetic diversity and provide the necessary empirical measures to guide further improvements of theoretical models of adaptation during host-parasite coevolution.
Processes governing genetic diversity and adaptive potential in reef-building corals are of interest both for fundamental evolutionary biology and for reef conservation. Here, we investigated the possibility of “sweepstakes reproductive success” (SRS) in a broadcast spawning coral Acropora hyacinthus at Yap Island, Micronesia. SRS is an extreme yearly variation in the number of surviving offspring among parents. It is predicted to generate genetically differentiated, low genetic diversity recruit cohorts, containing close kin individuals. We have tested these predictions by comparing genetic composition of size classes (adults and juveniles) at several sites on the island of Yap, Micronesia. We did see the genome-wide dip in genetic diversity in juveniles compared to adults at two of the four sites; however, both adults and juveniles varied in genetic diversity across sites, and there was no detectable genetic structure among juveniles, which does not conform to the classical SRS scenario. Yet, we have identified a pair of juvenile siblings at the site where juveniles had the lowest genetic diversity compared to adults, an observation that is hard to explain without invoking SRS. While further support for SRS is needed to fully settle the issue, we show that incorporating SRS into the Indo-West Pacific coral metapopulation adaptation model had surprisingly little effect on mean rates of coral cover decline during warming. Still, SRS notably increases year-to-year variation in coral cover throughout the simulation.
An exhaustive assessment of biodiversity is a major challenge of ecological research, and molecular approaches such as the metabarcoding of environmental DNA are boosting our ability to perform biodiversity inventories. Are we actually able to assess the whole community, to unravel the intricate interactions between organisms and the impacts of global changes on the different trophic levels? The majority of metabarcoding papers published in the last years used just one or two markers and analyzed a limited number of taxonomic groups. Nevertheless, approaches are emerging that might allow “all-taxa biological inventories”. Exhaustive biodiversity assessments can be attempted by combining a large number of specific primers, by exploiting the power of universal primers, or by combining specific and universal primers to obtain good information on key taxa while limiting the overlooked biodiversity. Multiplexes of primers and shotgun sequencing may provide a better coverage of biodiversity compared to standard metabarcoding, but still require major methodological advances. We identify the strengths and limitations of different approaches, and suggest new development lines that might improve broad scale biodiversity analyses in the near future.
Community-level traits as a way to partly circumvent the culturing problem in mycorrhizal trait-based ecology?Chagnon, P.-L.Data availability statement: No new data has been generated in this manuscript.Traits are the intermediate by which species respond to environmental filters and influence ecosystem functions. With the myriad of biogeochemical processes controlled by fungi, the past decade has witnessed a rising interest in applying trait-based approaches, core to the toolkit of plant and animal ecophysiologists, to fungi. One of the first challenges to tackle when working on fungal ecophysiology is to circumscribe the very definition of what we consider a fungal trait. Traits are characteristics/features possessed by an individualthat can influence how it interacts with its environment. Here the individual scale is both important, and problematic. Important because the very goal of comparative ecology is to measure traits on individuals belonging to known species. This allows to populate trait databases, and syntheses of such databases can reveal key trade-offs and trait syndromes that govern species’ life-histories. The scale of the individual is problematic, however, because it is hard to define for soil fungi, and because a rare minority of fungi can be sampled at the individual scale in the environment (e.g., macroscopic sporocarps, ectomycorrhizal root tips, lichen thalli). Beyond this minority, the individual organisms can only be accessed/sampled through establishing fungal cultures, which probably represents one of the main bottlenecks in the development of fungal trait databases. In this issue, Zhang et al. (2022) show how interesting insights in fungal trait-based ecology can be gained by working at the community level.In their study, Zhang et al. (2022) adapted a protocol developed by Neumann & George (2005) to capture mycorrhizal fungal hyphae using ingrowth bags. If we assume that most hyphae recovered through this technique are mycorrhizal, the washed hyphae can be characterized through various chemical/morphological downstream analyses. Measuring such traits for biomass recovered from whole communities is akin to estimating community-weighted mean (CWM) traits, which are central to many aspects of ecophysiology. Various paradigms/theories in community ecology assume some form of equilibrium between species and their environment (Leibold et al., 2004). If we assume (1) a heterogeneous environment, (2) species as reproductively isolated units competing for space/resources and (3) traits as determinants of their reproductive success, correlations between species traits and environmental parameters are naturally expected to arise (Shipley et al., 2011). Under specific stable environmental conditions, a species bearing certain traits should have a higher probability to (1) occur and (2) become abundant in such environment. At the community level, we thus expect a correlation between CWM traits (the sum of species mean traits weighted by their relative abundances), and environmental parameters (box 1). With mycorrhizal fungi, we can have a reasonable access to species’ relative abundances through sequence-based profiles of communities, but the species × traits matrix remains inaccessible. The shortcut taken by Zhang et al. (2022) is to take measurements of traits (here, hyphal C:N:P stoichiometry) at the community level directly.Does the species × traits become dispensable in mycorrhizal ecology? Certainly not. Bringing mycorrhizal fungi into cultures, identifying traits likely to represent important trade-offs in fungal resource management strategies (Chagnon et al., 2013), ensuring reproducible measurement of such traits and establishing common resources to share such traits (Kattge et al., 2020; Zanne et al., 2020) remains a priority of mycorrhizal ecophysiology. Opinions (Chagnon et al., 2013) and definitions (Chaudhary et al., 2020) will only be useful if followed by actual work to populate databases currently storing the very fragmentary data on fungal traits. We cannot leave aside this important work at the species and individual scales, because evolutionary trade-offs defining resource management and life history strategies emerge at those very scales, not at the community level (Grime & Pierce, 2012).Trait-environment relationships, however, can inform us on the way environmental pressures may select for particular species characteristics, and in this regard, progress can be made over much shorter timescales than the work expected to rely on permanent culture banks and individual-level trait measurements. Zhang et al. (2022), for example, identified an increase in hyphal P concentrations in response to warming and drought treatments, illustrating hyphal stoichiometry as a potentially important “response trait” for mycorrhizal fungi. The upcoming challenge with stoichiometry is now to link form and function. What is the purpose of enhanced mycelial P for the fungus? Luxury uptake and storage as polyphosphates, which may confer bargaining power to the fungus? Increased cellular concentration of “growth-related molecules” (sensu Zhang et al., 2022) such as RNA? This remains to be elucidated. The same is true for nitrogen, which can be present in both growth- and function-related proteins, or in cell wall components slowing down necromass decomposition (Fernandez et al., 2019). This will influence how likely are fungal hyphae to contribute to soil organic pools of different turnover times (See et al., 2022; Klink et al., 2022).We can probably identify many other traits that we expect to be (1) measurable at the community level and (2) associated with environmental filters. Spore size and wall ornamentations could be linked to dispersal dynamics (e.g., Chaudhary et al., 2020). Cell wall thickness could be linked with susceptibility to fungivory (as a constitutive structural defense), and could be expected to be associated with predation risk, but also community-level productivity. Generally, structural defenses are expected to be maximal under harsh conditions promoting conservative species with long-lived, constitutively defended tissues (Coley, 1988). Hyphal allocation allometry to the root vs. the soil habitats already has received considerable attention (e.g., Maherali & Klironomos, 2007), although the assumption that extensive soil foraging is associated with more efficient P return to host can be questioned (Jakobsen et al., 1992). Community-level allometric measurements could be coupled with soil nutrient availability along natural or experimental gradients could clarify this issue. Relative mycelial investments in the soil, however, is a multifaceted trait that bears implication for other aspects of fungal growth and dispersal, namely the colonization of new patches (emerging roots), the exposition to parasites/predators, and the interactions with non-mycorrhizal microorganisms potentially including hyphosphere mutualists. In other words, soil hyphae are not strictly foraging units, but may also serve dispersal, chemical warfare and interkingdom cooperation. This may decrease the probability of finding clear univariate linkages between hyphal allometry and single environmental filters such as nutrient availability. Other traits requiring our attention are biomass growth and turnover rates. Tissue maximal growth rate and lifespan are central to the definition of ecological strategies (e.g., Westoby et al., 2002; Darling et al., 2012). In principle, this can be measured at the community level for mycorrhizal fungi, although the experimental approach should be selected wisely. Traditional approaches to measuring biomass accumulation in mycorrhizal studies typically rely either on microcosms inoculated with fungal propagules, or on ingrowth bags. Both these approaches will select for colonists that can rapidly invade this new empty niche (a bulk sterile pot/ingrowth bag), thus biasing our estimates of growth rates in favor of those displayed by ruderal colonists (i.e., community-level trait not matching the community composition/structure). However, regarding biomass turnover rates, it could be envisaged to derive such estimate using stable isotope probing targeting a specific biomarker (e.g., NLFA 16:1ω5). The only drawback is that evaluating dilution rate of heavy carbon in such a biomarker rapidly makes the cost per sample prohibitive, hampering measurements of biomass turnover rates along environmental gradients, or in response to an experimental treatment.Despite the technical difficulties associated with measuring community-level traits, or the challenges to linking form and function, the approach put forth by Zhang et al. (2022) with hyphal stoichiometry are part of the equation to advance mycorrhizal ecophysiology, and should be extended to other traits. Meanwhile, the long-term objective for mycorrhizal ecophysiologists should still be to isolate and culture strains, and make these permanent resources for them and other research groups to measure traits in future studies. Intraspecific trait variation appears so important, at least for arbuscular mycorrhizal fungi (e.g., Munkvold et al., 2004; Antunes et al., 2011), that strain identity will be just as important as species identity in building trait databases. And as mycorrhizal ecophysiology matures, new traits will gain interest and have to be measured on those strains for which we have already measured a number of other traits. Plant and animal ecophysiologists have a permanent resource they can sample individuals from: it is called nature. Mycorrhizal ecologists are in need for such analogous resource: permanent culture banks. Thus, it seems that challenges lying ahead in mycorrhizal ecophysiology are multifaceted, encompassing the need for conceptual development, standard laboratory methods, but also creativity in getting long-term funding to maintain biological material.
Anthropogenic changes have altered the historical distributions of many North American taxa. As environments shift, ecological and evolutionary processes can combine in complex ways to either stimulate or inhibit range expansion. Here we examine the role of evolution in a rapid range expansion whose ecological context has been well-documented, Anna’s Hummingbird (Calypte anna). Previous work suggests that the C. anna range expansion is the result of an ecological release facilitated by human-mediated environmental changes, where access to new food sources have allowed further filling of the abiotic niche. We examine the role of gene flow and adaptation during range expansion from their native California north into Canada and east into New Mexico and Texas, USA. Using low coverage whole genome sequencing we found high genetic diversity, low divergence, and little evidence of selection on the northern and eastern expansion fronts. Additionally, there are few (if any) limits to gene flow across the native and expanded range. The lack of selective signals between core and expanded ranges could reflect i) an absence of novel selection pressure in the extended range (supporting the ecological release hypothesis), ii) swamping of adaptive variation due to high gene flow, or iii) limitations of genome scans for detecting small shifts in allele frequencies across many loci. Nevertheless, our results provide an example where strong selection is not apparent during a rapid, contemporary range shift.
Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations. Across island systems, contemporary patterns of genetic diversity reflect complex population demography, including colonisation events, bottlenecks, gene flow and genetic drift. Here, we investigate whether island founder events have prolonged effects on genome-wide diversity and runs of homozygosity (ROH) distributions, using whole genome resequencing from six populations across three archipelagos of Berthelot’s pipit (Anthus berthelotii) - a passerine which has undergone island speciation relatively recently. Pairwise sequential Markovian coalescent (PSMC) analyses estimated divergence from its sister species approximately two million years ago. Results indicate that all Berthelot’s pipit populations had shared ancestry until approximately 50,000 years ago, when the Madeiran archipelago populations were founded, while the Selvagens were colonised within the last 8,000 years. We identify extensive long ROH (>1 Mb) in genomes in the most recently colonised populations of Madeira and Selvagens which have experienced sequential island founder events and population crashes. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). Extensive long and short ROH in the Selvagens reflects strong recent inbreeding, small contemporary effective population size and past bottleneck effects, with as much as 37.7% of the autosomes comprised of ROH >250 kb in length. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations.