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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2020

The influence of roads on the fine-scale population genetic structure of the dengue vector Aedes aegypti (Linnaeus)

Dengue is endemic in tropical and subtropical countries and is transmitted mainly by Aedes aegypti. Mosquito movement can be affected by human-made structures such as roads that can act as a barrier. Roads can influence the population genetic structure of Ae. aegypti. We investigated the genetic structure and gene flow of Ae. aegypti as influenced by a primary road, Espana Boulevard (EB) with 2000-meter-long stretch and 24-meters-wide in a very fine spatial scale. We hypothesized that Ae. aegypti populations separated by EB will be different due to the limited gene flow as caused by the barrier effect of the road. A total of 376 adults and larval Ae. aegypti were collected from June to September 2017 in 21 sites across EB. North (N1-N11) and South (S1-S10) comprised of 211 and 165 individuals, respectively. All mosquitoes were genotyped at 11 microsatellite loci. AMOVA FST indicated significant genetic differentiation across the road. The constructed UPGMA dendrogram found 4 genetic groups revealing the clear separation between North and South sites across the road. On the other hand, Bayesian cluster analysis showed four genetic clusters (K = 4) wherein each individual samples have no distinct genetic cluster thus genetic admixture. Moreover, significant positive spatial autocorrelation was observed at 100 - 200 m distance class, suggesting dispersal potential of the adult mosquitoes within a 200 m spatial scale. Our results suggest that human-made landscape features such as primary roads are potential barriers to mosquito movement thereby limiting its gene flow across the road. This information is valuable in designing an effective mosquito control program in a very fine spatial scale. Author SummaryDengue, a mosquito-borne viral infection is a serious health problem in tropical and subtropical countries such as Philippines. Most dengue prevention programs aim to eradicate its mosquito vector, Aedes aegypti. A successful population control program is reliant in understanding the mosquito behavior and ecology including how human-made structures such as roads influence its expansion and movement. Previous studies have discovered the barrier effect of roads in the movement of mosquitoes. In this study, we examined the influence of roads in the population genetic structure of Ae. aegypti in a fine spatial scale using 11 microsatellite markers. We found significant genetic differentiation of mosquito populations across the road. Our results suggest limited gene flow across the road and supports our hypothesis that roads are potential barriers to mosquito dispersal. This information can be used in designing an effective mosquito population control zones in perceived barrier to mosquito dispersal such as roads.

molecular biology↗
bioRxiv2020

HeartBioPortal2.0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations

Cardiovascular disease (CVD) is the leading cause of death worldwide for both genders and across most racial and ethnic groups. However, different races and ethnicities exhibit different rates of cardiovascular disease and its related cardiorenal and metabolic co-morbidities, suggesting differences in genetic predisposition and risk of onset, as well as socioeconomic and lifestyle factors (diet, exercise, etc.) that act upon an individuals unique underlying genetic background. Here we present HeartBioPortal2.0, a major update to HeartBioPortal, the worlds largest CVD genetics data precision medicine platform for harmonized CVD-relevant genetic variants, which now enables search and analysis of human genetic information related to heart disease across ethnically diverse populations and cardiovascular/renal/metabolic quantitative traits pertinent to CVD pathophysiology. HeartBioPortal2.0 is structured as a cloud-based computing platform and knowledge portal that consolidates a multitude of CVD-relevant next-generation sequencing data modalities into a single powerful query and browsing interface between data and user via a user-friendly web application publicly available to the scientific research community. Since its initial release, HeartBioPortal2.0 has added new cardiovascular/renal/metabolic disease relevant gene expression data as well as genetic association data from numerous large-scale genome-wide association study (GWAS) consortiums such as CARDIoGRAMplusC4D, TOPMed, FinnGen, AFGen, MESA, MEGASTROKE, UK Biobank, CHARGE, Biobank Japan, MyCode, among other studies. In addition, HeartBioPortal2.0 now includes support for quantitative traits and ethnically diverse populations, allowing users to investigate the shared genetic architecture of any gene or its variants across the continuous cardiometabolic spectrum from health (e.g., blood pressure traits) to disease (hypertension), facilitating the understanding of CVD trait genetics that inform health-to-disease transitions and endophenotypes. Custom visualizations in the new and improved user interface (UI), including performance enhancements and new security features such as user authentication collectively re-imagine HeartBioPortals user experience and provide a data commons that co-locates data, storage and computing infrastructure in the context of studying the genetic basis behind the leading cause of global mortality. Database URLhttps://www.heartbioportal.com/

bioinformatics↗
bioRxiv2020

Genetic diversity and population structure of razor clam Sinonovacula constricta in Ariake Bay, Japan, revealed using RAD-Seq SNP markers.

The razor clam Sinonovacula constricta is a commercially important bivalve in Japan. The current distribution of this species in Japan is limited to Ariake Bay, where the fishery stock is declining. It is necessary to understand the genetic population structure of this species in order to restore the fishery stock while preserving the genetic diversity of the clam. Here, we report for the first time the genetic population structure of S. constricta in Ariake Bay, Japan. Paired-end restriction site-associated DNA sequencing (RAD-Seq) analyzed samples of S. constricta collected from seven mudflats located along Ariake Bay. Two different genetic populations exist in Ariake Bay, one inhabiting wild habitats and the other inhabiting the transplanted area of artificial seedlings. Our results suggest that genetic differentiation occurred between these two populations (Fst value = 0.052), and a high level of genetic differentiation is maintained between the two groups. In the future, monitoring the interbreeding status of the two genetically distinct populations and the genetic differentiation within each population is important for conserving the genetic diversity of S. constricta in Japan.

zoology↗
bioRxiv2020

Genetic ancestry predicts male-female affiliation in a natural baboon hybrid zone

Opposite-sex social relationships are important predictors of fitness in many animals, including several group-living mammals. Consequently, understanding sources of variance in the tendency to form opposite-sex relationships is important for understanding social evolution. Genetic contributions are of particular interest due to their importance in long-term evolutionary change, but little is known about genetic effects on male-female relationships in social mammals, especially outside of the mating context. Here, we investigate the effects of genetic ancestry on male-female affiliative behavior in a hybrid zone between the yellow baboon (Papio cynocephalus) and the anubis baboon (P. anubis), in a population in which male-female social bonds are known predictors of lifespan. We place our analysis within the context of other social and demographic predictors of affiliative behavior in baboons. Genetic ancestry was the most consistent predictor of opposite-sex affiliative behavior we observed, with the exception of strong effects of dominance rank. Our results show that increased anubis genetic ancestry is associated with subtly, but significantly higher rates of opposite-sex affiliative behavior, in both males and females. Additionally, pairs of anubis-like males and anubis-like females were the most likely to socially affiliate, resulting in moderate assortativity in grooming and proximity behavior as a function of genetic ancestry. Our findings indicate that opposite-sex affiliative behavior partially diverged during baboon evolution to differentiate yellow and anubis baboons, despite overall similarities in their social structures and mating systems. Further, they suggest that affiliative behavior may simultaneously promote and constrain baboon admixture, through additive and assortative effects of ancestry, respectively. HIGHLIGHTSO_LIOpposite-sex social relationships can have important fitness consequences. C_LIO_LIIn hybrid baboons, genetic ancestry predicted male-female affiliative behavior. C_LIO_LIBoth an individuals genetic ancestry and that of its social partner mattered. C_LIO_LIMale-female affiliation was assortative with respect to genetic ancestry. C_LIO_LIDominance rank and group demography also influenced male-female social affiliation. C_LI

evolutionary biology↗
bioRxiv2020

Quantitative genetic basis of floral design in a natural plant population

The amount of genetic variation of floral traits and the degree to which they are genetically correlated are important parameters for the study of plant evolution. Estimates of these parameters can reveal the effect of historical selection relative to neutral processes such as mutation and drift, and allow us to predict the short-term evolutionary trajectory of a population under various selective regimes. Here, we assess the heritability and genetic correlation of the floral design of a native N. American tetraploid plant, Silene stellata (Caryophyllaceae), in a natural population. Specifically, we use a linear mixed model to estimate the genetic parameters based on a genealogy reconstructed from highly variable molecular markers. Overall, we found significant heritabilities in five out of nine studied traits. The level of heritability was intermediate (0.027 - 0.441). Interestingly, the floral trait showing the highest level of genetic variation was previously shown to be under strong sexually conflicting selection, which may serve as a mechanism for maintaining the observed genetic variation. Additionally, we also found prevalent positive genetic correlations between floral traits. Our results suggest that S. stellata is capable of responding to phenotypic selection on its floral design, while the abundant positive genetic correlations could also constrain the evolutionary trajectories to certain directions. Furthermore, this study demonstrates the utility and feasibility of marker-based approaches for estimating genetic parameters in natural populations.

evolutionary biology↗
bioRxiv2021

A complex genetic architecture in zebrafish relatives Danio quagga and D. kyathit underlies development of stripes and spots

Vertebrate pigmentation is a fundamentally important, multifaceted phenotype. Zebrafish, Danio rerio, has been a valuable model for understanding genetics and development of pigment pattern formation due to its genetic and experimental tractability, advantages that are shared across several Danio species having a striking array of pigment patterns. Here, we use the sister species D. quagga and D. kyathit, with stripes and spots, respectively, to understand how natural genetic variation impacts phenotypes at cellular and organismal levels. We first show that D. quagga and D. kyathit phenotypes resemble those of wild-type D. rerio and several single locus mutants of D. rerio, respectively, in a morphospace defined by pattern variation along dorsoventral and anteroposterior axes. We then identify differences in patterning at the cellular level between D. quagga and D. kyathit by repeated daily imaging during pattern development and quantitative comparisons of adult phenotypes, revealing that patterns are similar initially but diverge ontogenetically. To assess the genetic architecture of these differences, we employ reduced-representation sequencing of second-generation hybrids. Despite the similarity of D. quagga to D. rerio, and D. kyathit to some D. rerio mutants, our analyses reveal a complex genetic basis for differences between D. quagga and D. kyathit, with several quantitative trait loci contributing to variation in overall pattern and cellular phenotypes, epistatic interactions between loci, and abundant segregating variation within species. Our findings provide a window into the evolutionary genetics of pattern-forming mechanisms in Danio and highlight the complexity of differences that can arise even between sister species. Further studies of natural genetic diversity underlying pattern variation in D. quagga and D. kyathit should provide insights complementary to those from zebrafish mutant phenotypes and more distant species comparisons. Author SummaryPigment patterns of fishes are diverse and function in a wide range of behaviors. Common pattern themes include stripes and spots, exemplified by the closely related minnows Danio quagga and D. kyathit, respectively. We show that these patterns arise late in development owing to alterations in the development and arrangements of pigment cells. In the closely related model organism zebrafish (D. rerio) single genes can switch the pattern from stripes to spots. Yet, we show that pattern differences between D. quagga and D. kyathit have a more complex genetic basis, depending on multiple genes and interactions between these genes. Our findings illustrate the importance of characterizing naturally occuring genetic variants, in addition to laboratory induced mutations, for a more complete understanding of pigment pattern development and evolution.

developmental biology↗
bioRxiv2021

Herpes simpex virus 2 (HSV-2) evolves faster in cell culture than HSV-1 by generating greater genetic diversity

Herpes simplex virus type 1 and 2 (HSV-1 and HSV-2, respectively) are prevalent human pathogens of clinical relevance that establish long-life latency in the nervous system. They have been considered, along with the Herpesviridae family, to exhibit a low level of genetic diversity during viral replication. However, the high ability shown by these viruses to rapidly evolve under different selective pressures does not correlates with that presumed genetic stability. High-throughput sequencing has revealed that heterogeneous or plaque-purified populations of both serotypes contain a broad range of genetic diversity, in terms of number and frequency of minor genetic variants, both in vivo and in vitro. This is reminiscent of the quasispecies phenomenon traditionally associated with RNA viruses. Here, by plaque-purification of two selected viral clones of each viral subtype, we reduced the high level of genetic variability found in the original viral stocks, to more genetically homogeneous populations. After having deeply characterized the genetic diversity present in the purified viral clones as a high confidence baseline, we examined the generation of de novo genetic diversity under culture conditions. We found that both serotypes gradually increased the number of de novo minor variants, as well as their frequency, in two different cell types after just five and ten passages. Remarkably, HSV-2 populations displayed a much higher raise of nonconservative de novo minor variants than the HSV-1 counterparts. Most of these minor variants exhibited a very low frequency in the population, increasing their frequency over sequential passages. These new appeared minor variants largely impacted the coding diversity of HSV-2, and we found some genes more prone to harbor higher variability. These data show that herpesviruses generate de novo genetic diversity differentially under equal in vitro culture conditions. This might have contributed to the evolutionary divergence of HSV-1 and HSV-2 adapting to different anatomical niche, boosted by selective pressures found at each epithelial and neuronal tissue. AUTHOR SUMMARYHerpesviruses are highly human pathogens that establish latency in neurons of the peripheral nervous system. Colonization of nerve endings is required for herpes simplex virus (HSV) persistence and pathogenesis. HSV-1 global prevalence is much higher than HSV-2, in addition to their preferential tendency to infect the oronasal and genital areas, respectively. How these closely related viruses have been adapting and evolving to replicate and colonize these two different anatomical areas remains unclear. Herpesviruses were presumed to mutate much less than viruses with RNA genomes, due to the higher fidelity of the DNA polymerase and proofreading mechanisms when replicating. However, the worldwide accessibility and development of high-throughput sequencing technologies have revealed the heterogenicity and high diversity present in viral populations clinically isolated. Here we show that HSV-2 mutates much faster than HSV-1, when compared under similar and controlled cell culture conditions. This high mutation rate is translated into an increase in coding diversity, since the great majority of these new mutations lead to nonconservative changes in viral proteins. Understanding how herpesviruses differentially mutate under similar selective pressures is critical to prevent resistance to anti-viral drugs.

microbiology↗
bioRxiv2021

The role of genetic diversity and arbuscular mycorrhizal fungal diversity in population recovery of the semi-natural grassland plant species Succisa pratensis

BackgroundEcosystem restoration is as a critical tool to counteract the decline of biodiversity and recover vital ecosystem services. Restoration efforts, however, often fall short of meeting their goals. Although functionally important levels of biodiversity can significantly contribute to the outcome of ecosystem restoration, they are often overlooked. One such important facet of biodiversity is within-species genetic diversity, which is fundamental to population fitness and adaptation to environmental change. Also the diversity of arbuscular mycorrhizal fungi (AMF), obligate root symbionts that regulate nutrient and carbon cycles, potentially plays a vital role in mediating ecosystem restoration outcome. In this study, we investigated the relative contribution of intraspecific population genetic diversity, AMF diversity, and their interaction, to population recovery of Succisa pratensis, a key species of nutrient poor semi natural grasslands. We genotyped 180 individuals from 12 populations of S. pratensis and characterized AMF composition in their roots, using microsatellite markers and next generation amplicon sequencing, respectively. We also investigated whether the genetic makeup of the host plant species can structure the composition of root-inhabiting AMF communities. ResultsOur analysis revealed that population allelic richness was strongly positively correlated to relative population growth, whereas AMF richness and its interaction with population genetic diversity did not significantly contribute. The variation partitioning analysis showed that, after accounting for soil and spatial variables, the plant genetic makeup explained a small but significant part of the unique variation in AMF communities. ConclusionsOur results confirm that population genetic diversity can contribute to population recovery, highlighting the importance of within-species genetic diversity for the success of restoration. We could not find evidence, however, that population recovery benefits from the presence of more diverse AMF communities. Our analysis also showed that the genetic makeup of the host plant structured root-inhabiting AMF communities, suggesting that the plant genetic makeup may be linked to genes that control symbiosis development.

ecology↗
bioRxiv2021

Genetic advantage and equality of opportunity in education: Two definitions and an empirical application

The literature of Equality of Opportunity (EOp) has long acknowledged the existence of talents, innate ability or genetic ability. Nonetheless, attempts to explicitly incorporate a measure of innate ability in the quantification of EOp have been rare. On the other hand, the literature of social-science genetics has found credible genetic-based components of EOp, without an explicit quantification of overall EOp. In addition, there exists prevalent disagreement within both kinds of literature on whether innate ability should be perceived as a fair or unfair source of advantage. This paper proposes to quantify EOp while explicitly including a genetic-based measure of innate ability. It proposes two formal definitions of EOp that draw on both stances regarding the compensation of innate ability. Novel testable implications are derived. The educational attainment polygenic index is used as a measure of innate ability while correcting for genetic nurture and accounting for the correlation between genes and other circumstances. An empirical application in the US Health and Retirement Study finds that the share of inequality of opportunity is 26% under the view that genetic differences are unfair sources of advantage and 21% otherwise. A comparative analysis over cohorts reveals that the trend in EOp depends on the definition adopted; if genetic advantage is a fair source of inequality then EOp has improved; the opposite holds if one considers genetic advantage an unfair source of inequality. These results highlight the importance of accounting for genetic differences in the EOp framework.

genomics↗
bioRxiv2021

The ecology and quantitative genetics of seed and seedling traits in upland and lowland ecotypes of a perennial grass

Plants have evolved diverse reproductive allocation strategies and seed traits to aid in dispersal, persistence in the seed bank, and establishment. In particular, seed size, dormancy, and early seedling vigor are thought to be key functional traits with important recruitment and fitness consequences across abiotic stress gradients. Selection for favored seed-trait combinations, or against maladaptive combinations, is likely an important driver shaping recruitment strategies. Here, we test for seed-trait plasticity and local adaptation in contrasting upland and lowland ecotypes of Panicum hallii with field experiments in native versus foreign habitats. Furthermore, we test whether seed traits have been under directional selection in P. hallii using the v-test (Fraser 2020) based on trait variance in a genetic cross. Finally, we evaluate the genetic architecture of ecotypic divergence for these traits with Quantitative Trait Locus (QTL) mapping. Field experiments reveal little plasticity but support a hypothesis of local adaptation among ecotypes based on recruitment. Patterns of segregation within recombinant hybrids provides strong support for directional selection driving ecotypic divergence in seeds traits. Genetic mapping revealed a polygenic architecture with evidence of genetic correlation between seed mass, dormancy, and seedling vigor. Our results suggest that the evolution of these traits may involve constraints that affect the direction of adaptive divergence. For example, seed size and germination percentage shared two colocalized QTL with antagonistic additive effects. This supports the hypothesis of a functional genetic relationship between these traits, resulting in either large seed/strong dormancy or small seed/weak dormancy trait combinations. Overall, our study provides insights into the factors facilitating and potentially constraining ecotypic differentiation in seed traits. Impact SummarySeed size and dormancy are key functional traits with important recruitment and fitness consequences. Theory suggests tradeoffs and plasticity in offspring quantity and quality are important in seed evolution. The genetics of seed size and dormancy traits have been studied extensively, but these studies are mostly limited to model system or domesticated crops. We also know very little about the genetic architecture and evolution of seed-based life history traits especially considering adaptation to xeric and mesic habitats. Here, we explored the genetic basis of trade-offs between seed size and dormancy in a C4 perennial grass, Panicum hallii, endemic to North America. We planted seeds of recombinant inbred lines from a cross between a xeric and mesic ecotype of P.hallii and mapped quantitative trait (QTL) loci for seed size, dormancy and seedling vigor traits. We detected a genetic basis of trade-offs between seed size and dormancy, suggesting that natural selection strongly favored specific trait combinations in ecotype formation. We further explored the role of seed size variation on seedling and adult recruitment in contrasting habitats. Our data showed that seed size was under strong selection through recruitment. Overall, our results demonstrate that adaptive differentiation for seed size and early life stages are important factors in adaptation to contrasting habitats.

evolutionary biology↗
bioRxiv2021

Declining population sizes and loss of genetic diversity in commercial fishes: a simple method for a first diagnostic

Exploited fish species may have or are experiencing declines in population sizes coupled with a decrease in genetic diversity. This can lead to the loss of adaptive potential to face current and future environmental changes. However, little is known about this subject while research on it is urgently needed. Thus, this study aims to answer a simple, even naive question, given the complexity of the subject: Could we use a simple method to obtain information on the loss of genetic diversity in exploited fish species? We investigated the use of the levels of genetic diversity in the widely used genetic marker Cytochrome C Oxidase subunit I (COI) mitochondrial gene. Estimates of genetic diversity in COI were obtained for populations of seven fish species with different commercial importance from the East China Sea. These estimates were contrasted against a large dataset of fish species distributed worldwide (N=1426), a dataset of East-Asian fish species (N=118), two farmed species with expected low genetic diversity, and four long-term managed species from the Mediterranean Sea. We found that estimates of genetic diversity in COI match the expectations from theoretical predictions, known population declines, and fishing pressures. Thus, the answer to our question is affirmative and we conclude that estimates of genetic diversity in COI provide an effective first diagnostic of the conservation status of exploited fish species. This simple and cost-effective tool can help prioritize research, management, and conservation on species with suspected loss of genetic diversity potentially eroding their adaptive potential to global change.

ecology↗
bioRxiv2022

Developmentally determined intersectional genetic strategies to dissect adult somatosensory circuit function

Improvements in the speed and cost of expression profiling of neuronal tissues offer an unprecedented opportunity to define ever finer subgroups of neurons for functional studies. In the spinal cord, single cell RNA sequencing studies1,2 support decades of work on spinal cord lineage studies3-5, offering a unique opportunity to probe adult function based on developmental lineage. While Cre/Flp recombinase intersectional strategies remain a powerful tool to manipulate spinal neurons6-8, the field lacks genetic tools and strategies to restrict manipulations to the adult mouse spinal cord at the speed at which new tools develop. This study establishes a new workflow for intersectional mouse-viral strategies to dissect adult spinal function based on developmental lineages in a modular fashion. To restrict manipulations to the spinal cord, we generate a brain-sparing Hoxb8FlpO mouse line restricting Flp recombinase expression to caudal tissue. Recapitulating endogenous Hoxb8 gene expression9, Flp-dependent reporter expression is present in the caudal embryo starting day 9.5. This expression restricts Flp activity in the adult to the caudal brainstem and below. Hoxb8FlpO heterozygous and homozygous mice do not develop any of the sensory or locomotor phenotypes evident in Hoxb8 heterozygous or mutant animals10,11, suggesting normal developmental function of the Hoxb8 gene and protein in Hoxb8FlpO mice. Compared to the variability of brain recombination in available caudal Cre and Flp lines12,13 Hoxb8FlpO activity is not present in the brain above the caudal brainstem, independent of mouse genetic background. Lastly, we combine the Hoxb8FlpO mouse line with dorsal horn developmental lineage Cre mouse lines to express GFP in developmentally determined dorsal horn populations. Using GFP-dependent Cre recombinase viruses14 and Cre recombinase-dependent inhibitory chemogenetics, we target developmentally defined lineages in the adult. We show how developmental knock-out versus transient adult silencing of the same ROR{beta} lineage neurons affects adult sensorimotor behavior. In summary, this new mouse line and viral approach provides a blueprint to dissect adult somatosensory circuit function using Cre/Flp genetic tools to target spinal cord interneurons based on genetic lineage. In briefWe describe the generation of a Hoxb8FlpO mouse line that targets Flp-recombinase expression to the spinal cord, dorsal root ganglia, and caudal viscera. This line can be used in intersectional Cre/Flp strategies to restrict manipulations to the caudal nervous system. Additionally, we describe an intersectional genetics+viral strategy to convert developmental GFP expression into adult Cre expression, allowing for modular incorporation of viral tools into intersectional genetics. This approach allows for manipulation of a developmentally determined lineage in the adult. This strategy is also more accessible than traditional intersectional genetics, and can adapt to the constantly evolving available viral repertoire. Highlights- A new Hoxb8FlpO mouse line allows Flp-dependent recombination in the spinal cord, dorsal root ganglia, and caudal viscera. - We observed no ectopic brain expression across mouse genetic backgrounds with the Hoxb8FlpO mouse line. - Combining this new mouse line for intersectional genetics and a viral approach, we provide a novel pipeline to target and manipulate developmentally defined adult spinal circuits.

neuroscience↗
bioRxiv2022

Mating system and speciation I: accumulation of genetic incompatibilities in allopatry

Self-fertilisation is widespread among hermaphroditic species across the tree of life. Selfing has many consequences on the genetic diversity and the evolutionary dynamics of populations, which may in turn affect macroevolutionary processes such as speciation. On the one hand, because selfing increases genetic drift and reduces migration rate among populations, selfing may be expected to promote speciation. On the other hand, because selfing reduces the efficacy of selection, selfing may be expected to hamper ecological speciation. To better understand under which conditions and in which direction selfing affects the build-up of reproductive isolation, an explicit population genetics model is required. Here, we focus on the interplay between genetic drift, selection and genetic linkage by studying speciation without gene flow. We test how fast populations with different rates of selfing accumulate mutations leading to genetic incompatibilities. When speciation requires the population to pass through a fitness valley caused by underdominant and compensatory mutations, selfing reduces the depth and/or breadth of the valley, and thus overall facilitates the fixation of incompatibilities. When speciation does not require the population to pass through a fitness valley, as for Bateson-Dobzhanzky-Muller incompatibilities (BDMi), the lower effective population size and higher genetic linkage in selfing populations facilitates the fixation of incompatibilities. Interestingly, and contrary to intuitive expectations, local selection does not always accelerate the build-up of reproductive isolation in outcrossing relative to selfing populations. Our work helps to clarify how selfing lineages may speciate and diversify over time, and emphasizes the need to account for interactions among segregating mutations within populations to better understand macroevolutionary dynamics. Author summaryHermaphroditic organisms may use their male gametes to fertilise their own female gametes, and species vary greatly in how much they self-fertilise. Self-fertilisation induces many genetic modifications in the population, which may ultimately affect the rates at which lineages diversify. Here we aim to build predictions on how self-fertilisation affects the rate at which reproductive isolation arises between geographically isolated populations. Specifically, we develop theoretical models in which populations varying in their rates of self-fertilisation may fixate mutations leading to reproductive isolation. We first explored scenarios in which reproductive isolation is made by mutations whose fixations necessitate the population to experience temporally deleterious effects (i.e., a fitness valley), and found that self-fertilisation reduces the breadth and depth of the fitness valley and thereby overall facilitates the accumulation of such mutations. Second, we explored scenarios in which genetic incompatibilities are caused by interactions between derived alleles of different genes (i.e., BDMi). By allowing the BDMi to occur within populations, we found that self-fertilisation reduces the manifestation of BDMi within population, and thereby facilitates their fixation. This effect prevails even in the face of local adaptation. Thus, our study clarifies how fast species are expected to arise in self-fertilisation lineages.

evolutionary biology↗
bioRxiv2022

Testing Wright's Intermediate Population Size Hypothesis - When Genetic Drift is a Good Thing

In his 1931 monograph, Sewall Wright predicted genetic drift would overwhelm selection in very small populations, and selection would dominate in large ones, but also concluded drift could facilitate selection in populations of intermediate size. The idea that drift and selection would act together in smaller populations has not been evaluated using analytical or numerical approaches even as empirical evidence of rapid evolution associated with population bottlenecks has continued to accumulate. I used forward-time simulations with random mating and discrete generations to test the hypothesis that drift can facilitate selection in small populations. I find evidence of drift facilitation of selection as increases in levels of{Delta} q in small populations (N<100) when selection is weak (s<0.2) and when allele frequencies are low (q<0.5). Fixation of beneficial mutations is accelerated by drift facilitation in small populations for recessive and codominant alleles, and less so for dominant alleles. Drift facilitation accelerated fixation of beneficial mutations in small populations compared to predictions from diffusion equations, while fixation time was longer than predicted in large populations. Drift facilitation increases the probability of fixation of new mutations in small populations. Accumulation of beneficial mutations (fixation flux) over several thousand generations was high in small populations and declined rapidly for large populations, which accumulated large amounts of standing genetic variation. Even though selection is more efficient in large populations, the increased time for allele replacement and lack of drift facilitation can result in substantially slower rates of adaptive evolution. Small populations were more susceptible to the accumulation of drift load, while larger populations maintained higher levels of segregation load. These results indicate that drift facilitation in small populations promotes purging of genetic load and accelerated fixation of beneficial mutations, and may account for the large number of observations of rapid adaptation during population bottlenecks. Impact Summary - After the recognition of Gregor Mendels contributions to our understanding of the inheritance of genetically-determined traits around 1900, there was confusion as to whether the type of variation Mendel studied could account for evolution by natural selection, as described by Charles Darwin. This controversy was resolved when three theoreticians (Ronald Fisher, Sewell Wright, and J.B.S. Haldane) published books that integrated Mendelian genetics with evolution. Their contributions (referred to as the Modern Synthesis), focused on evolutionary processes occurring within and among populations of a species, and established a mathematical foundation for our understanding of evolutionary biology. The mathematical models developed by the three architects of the modern synthesis, and those who followed, predicted that the effects of natural selection would be overwhelmed by random genetic changes (referred to as Genetic Drift) in small populations, and that genetic drift would be minimal, while selection would be most effective in large populations. Even though one of Wrights major conclusions was that genetic drift and selection would work together (Drift Facilitation) to promote adaptive evolution in intermediate-sized populations, this idea has been almost completely ignored since it was first introduced in 1931. In this study, I use simulations of evolution in natural populations to evaluate the potential for drift facilitation to promote evolution in small populations. My work largely confirms Wrights predictions; the removal of deleterious mutations and promotion of adaptive evolution are enhanced in population sizes ranging from about 10 to 100. These results indicate that our paradigm for our understanding of evolution within populations needs refinement to emphasize the importance of drift facilitation in small populations, and to recognize that periods of reduced population size are opportunities for enhanced levels of adaptive evolution. "In a population of intermediate size ... there is continual random shifting of gene frequencies ... which leads to a relatively rapid, continuing, irreversible, and largely fortuitous, but not degenerative series of changes, even under static conditions." Wright 1931, Page 157.

evolutionary biology↗
bioRxiv2022

Genetic diversity and structure in wild Robusta coffee (Coffea canephora A. Froehner) populations in Yangambi (DR Congo) and their relation with forest disturbance

Degradation and regeneration of tropical forests can strongly affect gene flow in understorey species, resulting in genetic erosion and changes in genetic structure. Yet, these processes remain poorly studied in tropical Africa. Coffea canephora is an economically important species, found in the understorey of tropical rainforests of Central and West Africa, and the genetic diversity harboured in its wild populations is vital for sustainable coffee production worldwide. Here, we aimed to quantify genetic diversity, genetic structure, and pedigree relations in wild C. canephora populations, and we investigated associations between these descriptors and forest disturbance and regeneration. Therefore, we sampled 256 C. canephora individuals within 24 plots across three forest categories in Yangambi (DR Congo), and used genotyping-by-sequencing to identify 18 894 SNPs. Overall, we found high genetic diversity, and no evidence of genetic erosion in C. canephora in disturbed old-growth forest, as compared to undisturbed old-growth forest. Additionally, an overall heterozygosity excess was found in all populations, which was expected for a self-incompatible species. Genetic structure was mainly a result of isolation-by-distance, reflecting geographical location, with low to moderate relatedness at finer scales. Populations in regrowth forest had lower allelic richness than populations in old-growth forest and were characterised by a lower inter-individual relatedness and a lack of isolation-by-distance, suggesting that they originated from different neighbouring populations and were subject to founder effects. Wild Robusta coffee populations in the study area still harbour high levels of genetic diversity, yet careful monitoring of their response to ongoing forest degradation remains required.

ecology↗
bioRxiv2022

A robotic system for automated genetic manipulation and analysis of Caenorhabditis elegans on agar media

The nematode Caenorhabditis elegans is one of the most widely studied organisms in biology due to its small size, rapid life cycle, and manipulable genetics. Research with C. elegans depends on labor-intensive and time-consuming manual procedures, imposing a major bottleneck for many studies, especially those involving large numbers of animals. Here we describe the first general-purpose tool, WormPicker, a robotic system capable of performing complex genetic manipulations and other tasks by imaging, phenotyping, and transferring C. elegans on standard agar media. Our system uses a motorized stage to move an imaging system and a robotic arm over an array of plates. Machine vision tools identify animals and assay developmental stage, morphology, sex, expression of fluorescent reporters, and other phenotypes. Based on the results of these assays the robotic arm selectively transfers individual animals using an electrically self-sterilized wire loop, with the aid of machine vision and electrical capacitance sensing. Automated C. elegans manipulation shows reliability and throughput comparable to standard manual methods. We developed software to enable the system to autonomously carry out complex protocols. To validate the effectiveness and versatility of our methods we used the system to perform a collection of common C. elegans procedures, including genetic crossing, genetic mapping, and genomic integration of a transgene. Our robotic system will accelerate C. elegans research and opens possibilities for performing genetic and pharmacological screens that would be impractical using manual methods. Significance StatementThe nematode Caenorhabditis elegans is a powerful genetic model organism in life sciences due to its compact anatomy, short life cycle, and optical transparency. Current methods for worm genetics rely on laborious, time-consuming, and error-prone manual work. Here, we describe the first general-purpose automated tool capable of genetically manipulating C. elegans. Our robotic system will accelerate a broad variety of C. elegans research and opens possibilities for performing genetic and pharmacological screens that would be impractical using manual methods.

bioengineering↗
bioRxiv2023

Immigration and seasonal bottlenecks: High inbreeding despite high genetic diversity in an oscillating population of the biting midge, Culicoides sonorensis (Diptera: Ceratopogonidae)

Most population genetic studies concern spatial genetic differentiation, but far fewer aim at analyzing the temporal genetic changes that occur within populations. Vector species, including mosquitoes and biting midges, are often characterized by oscillating adult population densities, which may affect their dispersal, selection, and genetic diversity over time. Here, we used a population of Culicoides sonorensis from a single site in California to investigate short-term (intra-annual) and long-term (inter-annual) temporal variation in genetic diversity over a three year period. This biting midge species is the primary vector of several viruses affecting both wildlife and livestock, thus a better understanding of the population dynamics of this species can help inform epidemiological studies. We found no significant genetic differentiation between months or years, and no correlation between adult populations and the inbreeding coefficient (FIS). However, we show that repeated periods of low adult abundance during cooler winter months resulted in recurring bottleneck events. Interestingly, we also found a high number of private and rare alleles, which suggests both a large, stable population, as well as a constant influx of migrants from nearby populations. Overall, we showed that the high number of migrants maintains a high level of genetic diversity by introducing new alleles, while this increased diversity is counterbalanced by recurrent bottleneck events potentially purging unfit alleles each year. These results highlight the temporal influences on population structure and genetic diversity in C. sonorensis and provide insight into factors effecting genetic variation that may occur in other vector species with fluctuating populations.

molecular biology↗
bioRxiv2023

Genetic diversity and population structure of Epichloe fungal pathogens of plants in natural ecosystems

Understanding the population genetic processes driving the evolution of plant pathogens is of central interest to plant pathologists and evolutionary biologists alike. However, most studies focus on host-pathogen associations in agricultural systems of high genetic and environmental homogeneity and less is known about the genetic structure of pathogen populations infecting wild plants in natural ecosystems. We performed parallel population sampling of two pathogenic Epichloe species occurring sympatrically on different host grasses in natural and seminatural grasslands in Europe: E. typhina infecting Dactylis glomerata and E. clarkii infecting Holcus lanatus. We sequenced 422 haploid isolates and generated genome-wide SNP datasets to investigate genetic diversity and population structure. In both species geographically separated populations formed genetically distinct groups, however population separation was less distinct in E. typhina compared to E. clarkii. The patterns of among population admixture also differed between species across the same geographic range: we found higher levels of population genetic differentiation and a stronger effect of isolation by distance in E. clarkii compared to E. typhina, consistent with lower levels of gene flow in the former. This pattern may be explained by the different dispersal abilities of the two pathogens and is expected to be influenced by the genetic structure of host populations. In addition, genetic diversity was higher in E. typhina populations compared to E. clarkii, indicative of higher effective population size in E. typhina. These results suggest that the effect of genetic drift and the efficacy of selection may differ in the two species. Our study provides evidence of how ecologically similar species occupying the same geographical space can experience different evolutionary contexts, which could influence local adaptation and coevolutionary dynamics of these fungal pathogens.

evolutionary biology↗