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bioRxiv2020

Influence of historical and human factors on genetic structure and diversity patterns in peripheral populations: implications for the conservation of Moroccan trout

O_LIThe brown trout s.l. has been the focus of numerous phylogeographic and conservation studies due to its socioeconomic importance, its marked genetic and phenotypic differentiation and its broad distribution range. Especially interesting evolutionary patterns are observed for populations occupying peripheral areas of a distribution range, such as in the case of the highly isolated trout populations in Morocco. C_LIO_LIContinuous stocking programs may conceal natural genetic patterns, making it challenging to discern evolutionary patterns. In Morocco, trout stocking programs have been implemented to increase the genetic diversity of native populations by pooling fish of different origins in the Ras el Ma hatchery (Azrou region) and then stocking them in the different basins. In this study, phylogenetic and phylogeographic patterns, as well as genetic structure and diversity, of Moroccan trout populations were analyzed to evaluate the impact of continuous fish stocking on evolutionary processes in order to better distinguish between natural and human-mediated patterns. C_LIO_LITwo mitochondrial and nine microsatellite markers were analyzed for all populations along the entire distribution range of brown trout in Morocco. Phylogenetic and phylogeographic analyses rendered two highly divergent evolutionary lineages, one comprising populations in the Draa Basin and a second grouping the remaining Moroccan populations. Divergence of the Draa lineage occurred during the Upper Pliocene, whilst differentiation within the second lineage coincided with the onset of the Pleistocene. C_LIO_LIGenetic structuring among populations was evident. Nevertheless, populations exhibiting higher levels of genetic diversity were those affected by human-mediated processes, making it difficult to associate this diversity with natural processes. In fact, highly geographically isolated, not stocked populations showed the lowest values of genetic diversity. Although stocking management may increase the genetic diversity of these populations, it could also lead to the loss of local adaptive genotypes. Hence, current trout conservation programs should be revised. C_LI

evolutionary biology↗

bioRxiv2020

Feedback Between Coevolution and Epidemiology Can Help or Hinder the Maintenance of Genetic Variation in Host-Parasite Models

Understanding if and when coevolution helps maintains genetic variation in hosts of a directly-transmissible pathogen is fundamental to quantifying the prevalence and impact of coevolution on disease epidemiology. Here, we extend our previous work on the maintenance of genetic variation in a classic matching-alleles coevolutionary model by exploring the effects of ecological and epidemiological feedbacks, where both allele frequencies and population sizes are allowed to vary over time. In general, we find that coevolution rarely maintains more host genetic variation than expected under neutral genetic drift alone. When and if coevolution maintains or depletes genetic variation relative to neutral drift is determined, predominantly, by two factors: the deterministic stability of the Red Queen allele frequency cycles and the frequency at which pathogen fixation occurs, as this results in directional selection and the depletion of genetic variation in the host. Compared to purely coevolutionary models with constant host and pathogen population sizes, ecological and epidemiological feedbacks stabilize Red Queen cycles deterministically, but population fluctuations in the pathogen increase the rate of pathogen fixation, especially in epidemiological models. Taken together our results illustrate the importance of considering the ecological and epidemiological context in which coevolution occurs when examining the impact of Red Queen cycles on genetic variation.

evolutionary biology↗

bioRxiv2020

Predicting intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data

The growing availability of genetic datasets, in combination with machine learning frameworks, offer great potential to answer long-standing questions in ecology and evolution. One such question has intrigued population geneticists, biogeographers, and conservation biologists: What determines intraspecific genetic diversity? This question is challenging to answer because many factors may influence genetic variation, including life history traits, historical influences, and geography, and the relative importance of these factors varies across taxonomic and geographic scales. Furthermore, interpreting the influence of numerous, potentially correlated variables is difficult with traditional statistical approaches. To address these challenges, we combined repurposed data with machine learning and investigated predictors of genetic diversity, focusing on Nearctic amphibians as a case study. We aggregated species traits, range characteristics, and >42,000 genetic sequences for 299 species using open-access scripts and various databases. After identifying important predictors of nucleotide diversity with random forest regression, we conducted follow-up analyses to examine the roles of phylogenetic history, geography, and demographic processes on intraspecific diversity. Although life history traits were not important predictors for this dataset, we found significant phylogenetic signal in genetic diversity within amphibians. We also found that salamander species at northern latitudes contain lower genetic diversity. Data repurposing and machine learning provide valuable tools for detecting patterns with relevance for conservation, but concerted efforts are needed to compile meaningful datasets with greater utility for understanding global biodiversity.

evolutionary biology↗

bioRxiv2020

Genetic structure and molecular diversity of Brazilian grapevine germplasm: management and use in the breeding programs

The management of germplasm banks is complex, especially when many accessions are involved. Microsatellite markers are an efficient tool for assessing the genetic diversity of germplasm collections, optimizing their use in breeding programs. This study genetically characterizes a large collection of 410 grapevine accessions maintained at the Agronomic Institute of Campinas (IAC) (Brazil). The accessions were genotyped with 17 highly polymorphic microsatellite markers. Genetic data were analyzed to determine the genetic structure of the germplasm, quantify its allelic diversity, suggest the composition of a core collection, and discover cases of synonymy, duplication, and misnaming. A total of 304 alleles were obtained, and 334 unique genotypes were identified. The molecular profiles of 145 accessions were confirmed according to the literature and databases, and the molecular profiles of more than 100 genotypes were reported for the first time. The analysis of the genetic structure revealed different levels of stratification. The primary division was between accessions related to Vitis vinifera and V. labrusca, followed by their separation from wild grapevine. A core collection of 120 genotypes captured 100% of all detected alleles. The accessions selected for the core collection may be used in future phenotyping efforts, in genome association studies, and for conservation purposes. Genetic divergence among accessions has practical applications in grape breeding programs, as the choice of relatively divergent parents will maximize the frequency of progeny with superior characteristics. Together, our results can enhance the management of grapevine germplasm and guide the efficient exploitation of genetic diversity to facilitate the development of new grape cultivars for fresh fruits, wine, and rootstock.

molecular biology↗

bioRxiv2020

Relatedness and genetic structure of big brown bat (Eptesicus fuscus) maternity colonies in an urban-wildland interface provides insight into rabies transmission dynamics

Big brown bats (Eptesicus fuscus) are the bat species most frequently found to be rabid in North America and are a key source of sylvatic rabies in wildlife. Females can form summer maternity colonies in urban areas, often using access holes in the exterior of buildings to roost in relatively large numbers. In Flagstaff, Arizona, these roosts are commonly found in houses adjacent to golf courses, where habitat quality (food, water, shelter) is high for bats and for mesocarnivores such as striped skunks (Mephitis mephitis) and gray foxes (Urocyon cinereoargenteus). Periodic rabies outbreaks in Flagstaff involving all three of these mammals are primarily caused by an E. fuscus variant of the disease. However, little is known about E. fuscus social behavior during the summer months and how it may drive space use and hence disease exposure to conspecifics and mesocarnivores. To address this knowledge gap, we collected 88 unique genetic samples via buccal swabs from E. fuscus captured at four maternity roosts surrounding a golf course during summer of 2013. We used 7 microsatellite loci to estimate genetic relatedness among individuals and genetic structure within and among colonies in order to infer whether females selected roosts based on kinship, and used genetics and radio telemetry to determine the frequency of roost switching. We found roost switching through genetics (two mother and adult daughter pairs at the same and different roosts) and telemetry, and no evidence of elevated genetic relatedness within colonies or genetic structure between colonies. These results have important implications for disease transmission dynamics in that social cohesion based on relatedness does not act to constrain the virus to a particular roost area. Instead, geographic mobility may increase disease exposure to neighboring areas. We discuss mitigating actions for bat conservation and public health.

ecology↗

bioRxiv2020

Common causes drive negative correlations between nuclear genetic and species level biodiversity

The processes that give rise to species richness gradients are not well understood, but may be linked to resource-based limits on the number of species a region can support. Ecological limits placed on regional species richness would also limit population sizes, suggesting that these processes could also generate genetic diversity gradients. If true, we might better understand how broad-scale biodiversity patterns are formed by identifying the common causes of genetic diversity and species richness. We develop a hypothetical framework based on the consequences of regional variation in ecological limits to simultaneously explain spatial patterns of species richness and neutral genetic diversity. Repurposing raw genotypic data spanning 38 mammal species sampled across 801 sites in North America, we show that estimates of genome-wide genetic diversity and species richness share spatial structure. Notably, species richness hotspots tend to harbor lower levels of within-species genetic variation. A structural equation model encompassing eco-evolutionary processes related to resource availability, habitat heterogeneity, and human disturbance explained 78% of variation in genetic diversity and 74% of the variation in species richness. These results suggest we can infer broad-scale patterns of species and genetic diversity using two simple environmental measures of resource availability and ecological opportunity.

evolutionary biology↗

bioRxiv2020

A forward genetic screen identifies Dolk as a regulator of startle magnitude through the potassium channel subunit Kv1.1

The acoustic startle response is an evolutionary conserved avoidance behavior. Disruptions in startle behavior, in particular startle magnitude, are a hallmark of several human neurological disorders. While the neural circuitry underlying startle behavior has been studied extensively, the repertoire of genes and genetic pathways that regulate this locomotor behavior has not been explored using an unbiased genetic approach. To identify such genes, we took advantage of the stereotypic startle behavior in zebrafish larvae and performed a forward genetic screen coupled with whole genome analysis. This identified mutants in eight genes critical for startle behavior, including two genes encoding proteins associated with human neurological disorders, Dolichol kinase (Dolk), a broadly expressed regulator of the glycoprotein biosynthesis pathway, and the potassium Shaker-like channel subunit Kv1.1. We demonstrate that Kv1.1 acts independently of supraspinal inputs to regulate locomotion, suggesting its site of action is within spinal circuitry. Moreover, we show that Kv1.1 protein is mis-localized in dolk mutants, suggesting they act in a common genetic pathway to regulate movement magnitude. Combined, our results identify a diverse set of eight genes all associated with human disorders that regulate zebrafish startle behavior and reveal a previously unappreciated role for Dolk and Kv1.1 in regulating movement magnitude via a common genetic pathway. Author summaryUnderlying all animal behaviors are neural circuits, which are controlled by numerous molecular pathways that direct neuron development and activity. To identify and study these molecular pathways that control behavior, we use a simple vertebrate behavior, the acoustic startle response, in the larval zebrafish. In response to an intense noise, larval zebrafish will quickly turn and swim away to escape. From a genetic screen, we have identified a number of mutants that behave in abnormal ways in response to an acoustic stimulus. We cloned these mutants and identified eight genes that regulate startle behavior. All eight genes are associated with human disorders, and here we focus on two genes, dolk and kcna1a, encoding Dolk, a key regulator of protein glycosylation, and the potassium channel Kv1.1, respectively. We demonstrate that loss of dolk or kcna1a causes larval zebrafish to perform exaggerated swim movements and that Dolk is required for Kv1.1 protein localization to axons of neurons throughout the nervous system, providing strong evidence that dolk and kcna1a act in a common molecular pathway. Combined, our studies provide new insights into the genetic regulation of startle behavior.

neuroscience↗

bioRxiv2020

Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells

The discovery that somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) - cells that can be differentiated into any cell type of the three germ layers - has provided a foundation for in vitro human disease modelling1,2, drug development1,2, and population genetics studies3,4. In the majority of instances, the expression levels of genes, plays a critical role in contributing to disease risk, or the ability to identify therapeutic targets. However, while the effect of the genetic background of cell lines has been shown to strongly influence gene expression, the effect has not been evaluated at the level of individual cells. Differences in the effect of genetic variation on the gene expression of different cell-types, would provide significant resolution for in vitro research using preprogramed cells. By bringing together single cell RNA sequencing15-21 and population genetics, we now have a framework in which to evaluate the cell-types specific effects of genetic variation on gene expression. Here, we performed single cell RNA-sequencing on 64,018 fibroblasts from 79 donors and we mapped expression quantitative trait loci (eQTL) at the level of individual cell types. We demonstrate that the large majority of eQTL detected in fibroblasts are specific to an individual sub-type of cells. To address if the allelic effects on gene expression are dynamic across cell reprogramming, we generated scRNA-seq data in 19,967 iPSCs from 31 reprogramed donor lines. We again identify highly cell type specific eQTL in iPSCs, and show that that the eQTL in fibroblasts are almost entirely disappear during reprogramming. This work provides an atlas of how genetic variation influences gene expression across cell subtypes, and provided evidence for patterns of genetic architecture that lead to cell-types specific eQTL effects.

genomics↗

bioRxiv2020

Impact of vector control on effective population sizes; empirical evidence for a control- based genetic bottleneck in the tsetse fly Glossina fuscipes

We investigated genetic variation at 37 newly-developed microsatellite loci in populations of the tsetse fly Glossina fuscipes fuscipes captured from the upper and lower reaches of a single hydrographical network within an endemic Human African Trypanosomiasis focus. Our primary aim was to assess the impact of vector control using insecticide-treated baits (Tiny Targets) on genetic structure. We initially used STRUCTURE to delineate geographical boundaries of two stable ancestral reference populations without any history of vector control but marked for either vector control ( intervention) or no control ( non-intervention). We then used the ADMIXTURE model to assess genetic divergence in temporal populations collected after vector control implementation. We applied the Linkage Disequilibrium method to explicitly measure spatial and temporal changes in effective population size (Ne). We observed a significant reduction in Ne coincident with vector control, whereas Ne remained stable in the non-intervention area. Our empirical findings show how classical population genetics approaches detected within a short period of time, a significant genetic bottleneck associated with vector control, and opens up the possibility of using routine genomic surveillance. We have also generated a resource of new genetic markers for studies on the population genetics of tsetse at finer-scale resolution. FundingThis work was funded through a Wellcome Trust Masters Fellowship in Public Health and Tropical Medicine awarded to Allan Muhwezi (103268/Z/13/Z).

evolutionary biology↗

bioRxiv2020

Landscape and climatic features drive genetic differentiation processes in a South American coastal plant

* BackgroundHistorical and ecological processes shape patterns of genetic diversity in plant species. Colonization to new environments and geographical landscape features determine, amongst other factors, genetic diversity within- and differentiation between-populations. We analyse the genetic diversity and population structure of Calibrachoa heterophylla to infer the influence of abiotic landscape features on the level of gene flow in this coastal species of the South Atlantic Coastal Plain. * ResultsThe C. heterophylla populations located on early-deposited coastal plain regions show higher genetic diversity than those closer to the sea. The genetic differentiation follows a pattern of isolation-by-distance. Landscape features, such as water bodies and wind corridors, and geographical distances equally explain the observed genetic differentiation, whereas the precipitation seasonality exhibits a strong signal for isolation-by-environment in marginal populations. The estimated levels of gene flow suggest that marginal populations had restricted immigration rates enhancing differentiation. * ConclusionsTopographical features related to coastal plain deposition history influence population differentiation in C. heterophylla. Gene flow is mainly restricted to nearby populations and facilitated by wind fields, albeit without any apparent influence of large water bodies. Furthermore, differential rainfall regimes in marginal populations seem to promote genetic differentiation.

evolutionary biology↗

bioRxiv2020

Genetic diversity and population structure analyses in the Alpine plum (Prunus brigantina Vill.) confirm its affiliation to the Armeniaca section

In-depth characterization of the genetic diversity and population structure of wild relatives of crops is of paramount importance for genetic improvement and biodiversity conservation, and is particularly crucial when the wild relatives of crops are endangered. In this study, we therefore sampled the Alpine plum (Briancon apricot) Prunus brigantina Vill. across its natural distribution in the French Alps, where its populations are severely fragmented and its population size strongly impacted by humans. We analysed 71 wild P. brigantina samples with 34 nuclear markers and studied their genetic diversity and population structure, with the aim to inform in situ conservation measures and build a core collection for long-term ex-situ conservation. We also examined the genetic relationships of P. brigantina with other species in the Prunophora subgenus, encompassing the Prunus (Eurasian plums), Prunocerasus (North-American plums) and Armeniaca (apricots) sections, to check its current taxonomy. We detected a moderate genetic diversity in P. brigantina and a Bayesian model-based clustering approach revealed the existence of three genetically differentiated clusters, endemic to three geographical regions in the Alps, which will be important for in situ conservation measures. Based on genetic diversity and population structure analyses, a subset of 36 accessions were selected for ex-situ conservation in a core collection that encompasses the whole detected P. brigantina allelic diversity. Using a dataset of cultivated apricots and wild cherry plums (P. cerasifera) genotyped with the same markers, we detected gene flow neither with European P. armeniaca cultivars nor with diploid plums. In contrast with previous studies, dendrograms and networks placed P. brigantina closer to Armeniaca species than to Prunus species. Our results thus confirm the classification of P. brigantina within the Armeniaca section; it also illustrates the importance of the sampling size and design in phylogenetic studies.

evolutionary biology↗

bioRxiv2020

The Genetic Variation Landscape of African Swine Fever Virus Reveals Frequent Positive Selection on Amino Acid Replacements

African swine fever virus (ASFV) is a lethal disease agent that causes high mortality in swine population and devastating loss in swine industries. The development of efficacious vaccines has been hindered by the gap in knowledge concerning genetic variation of ASFV and the genetic factors involved in host adaptation and virus-host interactions. In this study, we performed a meta-genetic study of ASFV aiming to profile the variation landscape and identify genetic factors with signatures of positive selection and relevance to host adaptation. Our data reveals a high level of genetic variability of ASFV shaped by both diversifying selection and selective sweep. The selection signatures are widely distributed across the genome with the diversifying selection falling within 29 genes and selection sweep within 25 genes, highlighting strong signals of adaptive evolution of ASFV. Further examination of the sequence properties reveals the link of the selection signatures with virus-host interactions and adaptive flexibility. Specifically, we discovered a site at 157th of the key antigen protein EP402R under diversifying selection, which is located in the cytotoxic T-cell epitope related with the low level of cross-reaction in T-cell response. Importantly, two multigene families MGF360 and MGF505, the host range factors of ASFV, exhibit divergent selection among the paralogous members, conferring sequence pools for genetic diversification and adaptive capability. By integrating the genes with selection signatures into a unified framework of interactions between ASFV and hosts, we showed that the genes are involved in multiple processes of host immune interaction and virus life cycles, and may play crucial roles in circumventing host defense systems and enhancing adaptive fitness. Our findings will allow enhanced understanding of genetic basis of rapid spreading and adaptation of ASFV among the hosts.

evolutionary biology↗

bioRxiv2020

South Asian patient population genetics reveal strong founder effects and high rates of homozygosity - new resources for precision medicine

Population-scale genetic studies can identify drug targets and allow disease risk to be predicted with resulting benefit for management of individual health risks and system-wide allocation of health care delivery resources. Although population-scale projects are underway in many parts of the world, genetic variation between population groups means that additional projects are warranted. South Asia has a population whose genetics is the least characterized of any of the worlds major populations. Here we describe GenomeAsia studies that characterize population structure in South Asia and that create tools for economical and accurate genotyping at population-scale. Prior work on population structure characterized isolated population groups, the relevance of which to large-scale studies of disease genetics is unclear. For our studies we used whole genome sequence information from 4,807 individuals recruited in the health care delivery systems of Pakistan, India and Bangladesh to ensure relevance to population-scale studies of disease genetics. We combined this with WGS data from 927 individuals from isolated South Asian population groups, and developed a custom SNP array (called SARGAM) that is optimized for future human genetic studies in South Asia. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of homozygosity that approach 100 times that seen in outbred populations. We describe founder effects that increase the power to associate functional variants with disease processes and that make South Asia a uniquely powerful place for population-scale genetic studies.

genomics↗

bioRxiv2020

Hidden genetic variation in plasticity increases the potential to adapt to novel environments

Rapid environmental change is forcing populations into novel environments where plasticity will no longer maintain fitness. When populations are exposed to novel environments, evolutionary theory predicts that genetic variation in fitness will increase and should be associated with genetic differences in plasticity. If true, then genetic variation in plasticity can increase adaptive potential in novel environments, and population persistence via rapid adaptation is more likely. To test whether genetic variation in fitness increases in novel environments and is associated with plasticity, we transplanted 8,149 clones of 314 genotypes of a Sicilian daisy (Senecio chrysanthemifolius) within and outside its native range, and quantified genetic variation in fitness, and plasticity in leaf traits and gene expression. Although mean fitness declined by 87% in the novel environment, genetic variance in fitness increased threefold and was correlated with plasticity in leaf traits. High fitness genotypes showed greater plasticity in gene expression, but lower plasticity in most leaf traits. Interestingly, genotypes with greater fitness in the novel environment had the lowest fitness at the native site. These results suggest that standing genetic variation in plasticity could help populations to persist and adapt to novel environments, despite remaining hidden in native environments.

evolutionary biology↗

bioRxiv2020

DNA transduction in Sodalis species: implications for the genetic modification of uncultured endosymbionts of insects

Bacteriophages (phages) are ubiquitous in nature. These viruses play a number of central roles in microbial ecology and evolution by, for instance, promoting horizontal gene transfer (HGT) among bacterial species. The ability of phages to mediate HGT through transduction has been widely exploited as an experimental tool for the genetic study of bacteria. As such, bacteriophage P1 represents a prototypical generalized transducing phage with a broad host range that has been extensively employed in the genetic manipulation of Escherichia coli and a number of other model bacterial species. Here we demonstrate that P1 is capable of infecting, lysogenizing and promoting transduction in members of the bacterial genus Sodalis, including the maternally inherited insect endosymbiont Sodalis glossinidius. While establishing new tools for the genetic study of these bacterial species, our results suggest that P1 may be used to deliver DNA to many Gram negative endosymbionts in their insect host, thereby circumventing a culturing requirement to genetically manipulate these organisms. SummaryA large number of economically important insects maintain intimate associations with maternally inherited endosymbiotic bacteria. Due to the inherit nature of these associations, insect endosymbionts cannot be usually isolated in pure culture nor genetically manipulated. Here we use a broad-host range bacteriophage to deliver exogenous DNA to an insect endosymbiont and a closely related free-living species. Our results suggest that broad host range bacteriophages can be used to genetically alter insect endosymbionts in their insect host and, as a result, bypass a culturing requirement to genetically alter these bacteria.

microbiology↗

bioRxiv2020

Dispersal rate and riverine network connectivity shape the genetic diversity of freshwater amphipod metapopulations

Theory predicts that the distribution of genetic diversity in a landscape is strongly dependent on the connectivity of the metapopulation and the dispersal of individuals between patches. However, the influence of explicit spatial configurations such as dendritic landscapes on the genetic diversity and structure of metapopulations is still understudied, and theoretical corroborations of empirical patterns are largely lacking. Here, we used real-world microsatellite data and stochastic simulations of two metapopulations of freshwater amphipods in a 28,000 km2 riverine network to study the influence of spatial connectivity and dispersal strategies on their spatial genetic diversity and structure. We found a significant imprint of the riverine network connectivity on the genetic diversity of both amphipod species. Data from 95 sites showed that allelic richness and observed heterozygosity significantly increased towards more central nodes of the network. In simulation models, dispersal rate was suggested to be the key factor explaining the empirically observed distribution of genetic diversity. Contrary to often-claimed expectations, however, the relevance of directionality of dispersal was only minor. Surprisingly, also the consideration of site-specific carrying capacities, for example by assuming a direct dependency of population size with local river size, substantially decreased the model fit to empirical data. This highlights that directional dispersal and the spatial arrangement of population sizes may have a smaller relevance in shaping population genetic diversity of riverine organisms than previously thought, and that dispersal along the river network is the single-most important determinant of population genetic diversity.

ecology↗

bioRxiv2020

Landscape configuration of an Amazonian island-like ecosystem drives population structure and genetic diversity of a habitat-specialist bird

ContextAmazonian white-sand ecosystems (campinas) are open vegetation patches which form a natural island-like system in a matrix of tropical rainforest. Due to their clear distinction from the surrounding matrix, the spatial characteristics of campina patches may affect the genetic diversity and composition of their specialized organisms such as the small and endemic passerine Elaenia ruficeps. ObjectivesHere, we estimate the relative contribution of the current extension, configuration and geographical context of campina patches to the patterns of genetic diversity and population structure of E. ruficeps. MethodsWe sampled individuals of E. ruficeps from three landscapes in Central Amazonia with contrasting campina spatial distribution, from landscapes with large and connected patches to landscapes with small and isolated patches. We estimate population structure, genetic diversity, and contemporary and historical migration within and among the three landscapes and used landscape metrics as predictor variables. Furthermore, we estimate genetic isolation by distance and resistance among individuals sampled within landscapes. ResultsWe identified three genetically distinct populations with asymmetrical gene flow among landscapes and a decreasing migration rate with distance. Within each landscape, we found low genetic differentiation without genetic isolation by distance nor by resistance. In contrast, we found differentiation and spatial correlation between landscapes. ConclusionsOur results uncover population dynamics of E. ruficeps through time. Together with previous studies, this suggests that both regional context and landscape structure shape the connectivity among populations of campina specialist birds, and that Amazonian landscapes, together with their associated biota, have responded to recent climatic changes.

ecology↗

bioRxiv2021

Cascading indirect genetic effects in a clonal vertebrate

Understanding how individual differences among organisms arise and how their effects propagate through groups of interacting individuals are fundamental questions in biology.Individual differences can arise from genetically-based variation in the conspecifics with which an individual interacts, and these effects might then be propagated to other individuals. Using a clonal species, the Amazon molly (Poecilia formosa), we test the hypothesis that such indirect genetic effects (IGE) propagate beyond individuals that experience them firsthand. We tested this hypothesis by exposing genetically identical Amazon mollies to social partners of different genotypes, and then moving these individuals to new social groups in which they were the only member to have experienced the IGE. We found that genetically different social environments induced different levels of aggression experienced by the focal animals, and that these genetically-based social effects carried over into new social groups to influence the behavior of individuals that did not directly experience the previous social environments. Our data reveal that IGE can cascade beyond the individuals that directly experience them to influence phenotypes even when there is no genetically-based variation present within interacting groups. Theoretical and empirical expansion of the quantitative genetic framework developed for IGE to include cascading and other types of carry-over effects will improve understanding of social behavior and its evolution.

animal behavior and cognition↗