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Revisiting the number of self‐incompatibility alleles in finite populations: From old models to new results

Under gametophytic self-incompatibility (GSI), plants are heterozygous at the self-incompatibility locus (S-locus) and can only be fertilized by pollen with a different allele at that locus. The last century has seen a heated debate about the correct way of modeling the allele diversity in a GSI population that was never formally resolved. Starting from an individual-based model, we derive the deterministic dynamics as proposed by Fisher (1958), and compute the stationary S-allele frequency distribution. We find that the stationary distribution proposed by Wright (1964) is close to our theoretical prediction, in line with earlier numerical confirmation. Additionally, we approximate the invasion probability of a new S-allele, which scales inversely with the number of resident S-alleles. Lastly, we use the stationary allele frequency distribution to estimate the population size of a plant population from an empirically obtained allele frequency spectrum, which complements the existing estimator of the number of S-alleles. Our expression of the stationary distribution resolves the long-standing debate about the correct approximation of the number of S-alleles and paves the way to new statistical developments for the estimation of the plant population size based on S-allele frequencies.

Predicting spatio-temporal population patterns of Borrelia burgdorferi, the Lyme disease pathogen

The causative bacterium of Lyme disease, Borrelia burgdorferi, expanded from an undetected human pathogen into the etiologic agent of the most common vector-borne disease in the United States over the last several decades. Systematic field collections of the tick vector reveal increases in the geographic range and population size of B. burgdorferi that coincided with increases in human Lyme disease incidence across New York State. Here we investigate the impact of environmental features on the population dynamics of B. burgdorferi. Analytical models developed using field collections of nearly 19,000 nymphal Ixodes scapularis and spatially- and temporally-explicit environmental features accurately explained the variation of B. burgdorferi population sizes across space and time. Importantly, the model identified environmental features that can be used to predict the biogeographical patterns of B. burgdorferi-infected ticks into future years and in previously unsampled areas. Forecasting the distribution and abundance of a pathogen at fine geographic scales offers a powerful strategy to mitigate a serious public health threat.

Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time

Aim: We tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene. Location: Solimões River, Western Amazon, South America. Taxon: Myrmoborus lugubris, Thamnophilus cryptoleucus and Myrmotherula assimilis. Methods: We explored spatial patterns of genetic diversity and connectivity among sampled localities using thousands of Ultra-Conserved Elements. Range expansions were tested with alternative methods. We quantified habitat preference for the analyzed species to test whether the occupation of dynamic habitats could predict spatial patterns of genetic diversity. Results: Our study did not support shared population range expansions related to historical regionalized changes in habitat availability. We found considerable variation in the spatial distribution of the genetic diversity between studied taxa, and that species with higher levels of specialization to dynamic environments have a more heterogeneous distribution of genetic diversity and reduced levels of gene flow across space. Main conclusions: Our results suggest that demographic expansions along the Solimões River might be linked to spatially homogeneous oscillation in the distribution of floodplain environments, promoting effective population size changes but not range expansion. We found that habitat specificity might be a good predictor of population connectivity along the Amazonian floodplains.

Population genetic structure and demographic history of Rhodeus atremius suigensis, an endangered bitterling in Japan

Demographic events can shape genetic diversity through genetic drift, often leaving a persistent signal in the genetic characteristics of species. Rhodeus atremius suigensis is an endangered bitterling fish endemic to the Okayama Plain, Japan. In this study, we inferred its demographic history and genetic structure using a comprehensive analysis of the mtDNA ND1 gene, microsatellite markers (MS) and MHC class IIB gene. Based on mtDNA, R. a. suigensis included two sublineages; A and B. While <a name="OLE_LINK85"></a><a name="OLE_LINK88"></a>the former was widely distributed, the latter was restricted to eastern populations<a name="OLE_LINK11"></a><a name="OLE_LINK12"></a> that were monomorphic in MHC. Phylogenetic analysis revealed that R. a. suigensis, together with R. a. atremius, experienced a substantial bottleneck in the middle Pleistocene. In MS and MHC, genetic diversity was low in all populations; ranked as the lowest among bitterling species. Bayesian clustering suggested that two clusters of MS had been widely introgressed in the centre of its distribution. These clusters seem to have been formed by the disruption of the distribution in the last Pleistocene, and later admixed by a large-scale reclamation in the Okayama Plain since the 16th century, which triggered a decline in effective population size (Ne) in many populations. Based on coalescence analysis, all populations reached their lowest Ne around the middle of the 20th century. Accordingly, R. a. suigensis seems to have experienced two large bottlenecks in the past. While the first bottleneck was probably due to climatic changes in the middle Pleistocene, the second is due to anthropogenic degradation and fragmentation of habitats in recent years.

opencc-by-4.0Apr 2022View details →

zenodo36/100

Genetic Population Structure of the Waved Whelk (Buccinum undatum) in the western North Atlantic

R studio script files that includes original SNP data files used to determine the spatial genetic structure of Buccinum undatum in the western North Atlantic. Attached R-code is used to generate population genetic analyses, including a pairwise FST heatmap, principal component analyses, and admixture analyses.

Population structure and demographic history of the gastropod Thaisella chocolata (Duclos, 1832) from the Southeast Pacific inferred from mitochondrial DNA analyses

The present-day population structure of a species reflects the combination of oceanographic currents, life-history traits, and historical events. However, little is known about the mechanisms that have shaped the gene lineage distribution of marine species inhabiting the Southeast Pacific. Here we provide a comprehensive phylogeographical study of a species distributed along the Southeast Pacific coastal region by analyzing the endemic gastropod Thaisella chocolata (Duclos, 1832). Sequencing of mitochondrial cytochrome c oxidase subunit 1 (CO1) and 16S rRNA revealed strikingly high haplotypic nucleotide and genetic diversity but a lack of significant population differentiation within the survey area. In addition, a star-shaped phylogeny and significantly negative Tajima's D and Fu's Fs tests of neutrality suggested historical occurrence of rapid demographic expansion. Mismatch distributions and Bayesian inference analyses also confirmed T. chocolata to have undergone two ancestral demographic expansions. Calculations suggested that these expansions began in the lower and middle Pleistocene epoch, likely due to continental shelf development and climatic conditions. These findings could help establish a genetic baseline for T. chocolata as the first step toward sustainable spatial management of this species, as well as understand this species' response to future climate change.

opencc-zeroDec 2021View details →

Population genomics of an emergent tri-species hybrid zone

Isolating barriers that drive speciation are commonly studied in the context of two-species hybrid zones. There is however evidence that more complex introgressive relationships are common in nature. Here, we use field observations and genomic analysis, including the sequencing and assembly of a novel reference genome, to study an emergent hybrid zone involving two colliding hybrid zones of three woodpecker species: red-breasted, red-naped, and yellow-bellied sapsuckers (Sphyrapicus ruber, S. nuchalis, and S. varius). Surveys of the area surrounding Prince George, British Columbia, Canada, show that all three species are sympatric, and Genotyping-by-Sequencing identifies hybrids from each species pair and birds with ancestry from all three species. Observations of phenotypes and genotypes of mated pairs provide evidence for assortative mating, though there is some heterospecific pairing. Hybridization is more extensive in this tri-species hybrid zone than in two di-species hybrid zones. However, there is no evidence of a hybrid swarm, and admixture is constrained to contact zones, so we classify this region as a tension zone and invoke selection against hybrids as a likely mechanism maintaining species boundaries. Analysis of sapsucker age classes does not show disadvantages in hybrid survival to adulthood, so we speculate the selection upholding the tension zone may involve hybrid fecundity. Gene flow among all sapsuckers in di-species hybrid zones suggests introgression likely occurred before the formation of this tri-species hybrid zone and might result from bridge hybridization, vagrancies, or other three-species interactions.

Summary data for plots in: Eco-evolutionary extinction and recolonization dynamics reduce genetic load and increase time to extinction in highly inbred populations

Understanding how genetic and ecological effects can interact to shape genetic loads within and across local populations is key to understanding ongoing persistence of systems that should otherwise be susceptible to extinction through mutational meltdown. Classic theory predicts short persistence times for metapopulations comprising small local populations with low connectivity, due to accumulation of deleterious mutations. Yet, some such systems have persisted over evolutionary time, implying the existence of mechanisms that allow metapopulations to avoid mutational meltdown. We first hypothesize a mechanism by which the combination of stochasticity in the numbers and types of mutations arising locally (genetic stochasticity), resulting in local extinction and recolonization through evolving dispersal, facilitates metapopulation persistence. We then test this mechanism using a spatially and genetically explicit individual-based model. We show that genetic stochasticity in highly structured metapopulations can result in local extinctions, which can favour increased dispersal, thus allowing recolonization of empty habitat patches. This causes fluctuations in metapopulation size and transient gene flow, which reduces genetic load and increases metapopulation persistence over evolutionary time. Our suggested mechanism and simulation results provide an explanation for the conundrum presented by the continued persistence of highly structured populations with inbreeding mating systems that occur in diverse taxa.

Local field potentials reflect cortical population dynamics in a region-specific and frequency-dependent manner

The spiking activity of populations of cortical neurons is well described by a small number of population-wide covariance patterns, the "latent dynamics". These latent dynamics are largely driven by the same correlated synaptic currents across the circuit that determine the generation of local field potentials (LFP). Yet, the relationship between latent dynamics and LFPs remains largely unexplored. Here, we characterised this relationship for three different regions of primate sensorimotor cortex during reaching. The correlation between latent dynamics and LFPs was frequency-dependent and varied across regions. However, for any given region, this relationship remained stable across behaviour: in each of the primary motor and premotor cortices, the LFP-latent dynamics correlation profile was remarkably similar between movement planning and execution. These robust associations between LFPs and neural population latent dynamics help bridge the wealth of studies reporting neural correlates of behaviour using either type of recording.

The effect of migration and variation on populations of Escherichia coli adapting to complex fluctuating environments

Migration, a critical evolutionary force, can have contrasting effects on adaptation. It can aid as well as impede adaptation. The effects of migration on microbial adaptation have been studied primarily in simple constant environments. Very little is known about the effects of migration on adaptation to complex, fluctuating environments. In our study, we subjected replicate populations of Escherichia coli, adapting to complex and unpredictably fluctuating environments to different proportions of clonal ancestral immigrants. Contrary to the results from simple/constant environments, the presence of clonal immigrants reduced all measured proxies of fitness. However, migration from a source population with a greater variance in fitness resulted in no change in fitness w.r.t the no-migration control, except at the highest level of migration. Thus, the presence of variation in the immigrants could counter the adverse effects of migration in complex and unpredictably fluctuating environments. Our study demonstrates that the effects of migration are strongly dependent on the nature of the destination environment and the genetic makeup of immigrants. These results enhance our understanding of the influences of migrating populations, which could help better predict the consequences of migration.

Data from: Population genomics reveal deep divergence and strong geographical structuring in the Hengduan Mountains

We used restriction site-associated DNA sequencing to generate 1,907 single nucleotide polymorphisms (SNPs) and four-kb of plastid sequence in species of the Gentiana hexaphylla complex (Gentianaceae). We performed genetic clustering with spatial and non-spatial models, phylogenetic reconstructions, and ancestral range estimation, with the aim of addressing the processes influencing the diversification of G. hexaphylla in the HM. Here, the SNP data and plastid sequence alignments are provided.

Estimation of breeding population size using DNA-based pedigree reconstruction in brown bears

Robust estimates of demographic parameters are critical for effective wildlife conservation and management, but are difficult to obtain for elusive species. We estimated the breeding and adult population sizes, as well as the minimum population size, in a high-density brown bear population on the Shiretoko Peninsula, in Hokkaido, Japan, using DNA-based pedigree reconstruction. A total of 1,288 individuals, collected in and around the Shiretoko Peninsula between 1998 and 2020, were genotyped at 21 microsatellite loci. Among them, 499 individuals were identified by intensive genetic sampling conducted in two consecutive years (2019 and 2020) mainly by noninvasive methods (e.g., hair and fecal DNA). Among them, both parents were assigned for 330 bears, and either maternity or paternity was assigned to 47 and 76 individuals, respectively. The subsequent pedigree reconstruction indicated a range of breeding and adult (≥4 years old) population sizes: 128–173 for female breeders and 66–91 male breeders, and 155–200 for female adults and 84–109 male adults. The minimum population size was estimated to be 449 (252 females and 197 males) in 2019. Long-term continuous genetic sampling prior to a short-term intensive survey would enable parentage to be identified in a population with a high probability, thus enabling reliable estimates of breeding population size for elusive species. --

opencc-by-4.0Dec 2022View details →

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How extreme drought events , introduced species, and disease interact to impact influence threatened amphibian populations

Long term dataset of amphibian breeding in the Bay Area of California. We used this  7-y dataset (2013–2019) on amphibian breeding activity that encompassed a recent extreme drought event to assess 1) how breeding activities of these taxa differed during and after drought conditions and 2) the additive and interactive relationships of drought, chytrid fungal infection (Bd), and invasive species with the presence and abundance of larval amphibians.

Weak population genetic structure in Eurasian spruce bark beetle over large regional scales in Sweden

The Eurasian spruce bark beetle, Ips typographus, is a major pest, capable of killing spruce forests during large population outbreaks. Recorded dispersal distances of individual beetles are typically within hundreds of meters or a few kilometres. However, the connectivity between populations at larger distances and longer time spans and how this is affected by the habitat is less studied, despite its importance for understanding at which distances local outbreaks may spread. Previous population genetic studies in I. typographus typically used low resolution markers. Here, we use genome-wide data to assess population structure and connectivity of I. typographus in Sweden. We used 152 individuals from 19 population samples, distributed over 830 km from Strömsund (63º 46' 8'' N) in the north to Nyteboda (56º 8' 50'' N) in the south, to capture processes at a large regional scale, and a transect sampling design adjacent to a recent outbreak to capture processes at a smaller scale (76 km). Using restriction site-associated DNA sequencing (RADseq) markers capturing 1409-1997 SNPs throughout the genome, we document a weak genetic structure over the large scale, potentially indicative of high connectivity with extensive gene flow. No differentiation was detected at the smaller scale. We find indications of isolation-by-distance both for relative (FST) and absolute divergence (Dxy). The two northernmost populations are most differentiated from the remaining populations, and diverge in parallel to the southern populations for a set of outlier loci. In conclusion, the population structure of I. typographus in Sweden is weak, suggesting a high capacity to disperse and establish outbreak populations in new territories.

Connectivity among thermal habitats buffers the effects of warm climate on life-history traits and population dynamics

1. Contemporary climate change affects population dynamics, but its influence varies with landscape structure. It is still unclear whether landscape fragmentation buffers or enhances the effects of climate on population size and on the age and body size of individuals composing these populations. 2. This study aims to investigate the impacts of warm climates on lizard life-history traits and population dynamics in habitats varying in their connectivity. 3. We monitored common lizard (Zootoca vivipara) populations for three years in an experimental system in which both climatic conditions and connectivity among habitats were simultaneously manipulated. We considered two climatic treatments (i.e., present-day climate and warm climate (+1.4°C than present-day climate)) and two connectivity treatments (i.e., a connected treatment in which individuals could move from one climate to the other and an isolated treatment in which movement between climates was not possible). We monitored survival, reproduction, growth, dispersal, age and body size of each individual in the system as well as population density through time. 4. We found that the influence of warm climates on the life-history traits and population dynamics depended on the connectivity among thermal habitats. Populations in warm climates were i) composed of younger individuals only when isolated; ii) larger in population size only in connected habitats; and iii) composed of larger age-specific individuals independently of the landscape configuration. The connectivity among habitats altered population responses to climate warming likely through asymmetries in the flow and phenotype of dispersers between thermal habitats. 5. Our results demonstrate that landscape fragmentation can drastically change the dynamics and persistence of populations facing climate change.

Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis

The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two-species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host Medicago truncatula with a community of 88 Ensifer meliloti strains. Multi-strain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single-strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, i.e., genotype-by-genotype, effects on rhizobia fitness and some annotated rhizobia genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation-selection balance. Consistent with the lack of positive selection acting on host genes, we found that among-host variation in growth was similar whether plants were grown with rhizobia or N-fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multi-strain contexts.

Data from: Genetic patterns of Magnolia in the Lesser Antilles: Stepwise colonisation leading to highly inbred island 'populations'

Aim: Test for genetic signatures of island biogeographic patterns, using a slowly evolving, recent colonist with a low dispersal capability in an island chain without linear chronosequence; evaluate the multiple-endemic status of the species; and quantify genetic diversity of extant island populations. Location: The Lesser Antilles (Caribbean). Taxon: Magnolia dodecapetala (Magnoliaceae). Methods: Genetic diversity was characterised using Sanger sequencing of 21 individuals amplified for 11 DNA markers, plus microsatellite data of 195 individuals genotyped with 19 simple sequence repeat (SSR) markers. Sanger sequencing data were used to construct a Bayesian phylogenetic hypothesis, while SSR markers were used to run approximate Bayesian computation (ABC) demographic analyses and calculate population statistics. Results: Both types of molecular data support stepwise colonization, decoupled from known island ages. The ABC analyses support a north to south migration while the Sanger sequencing data indicates a mixture of island progression rule and stepping stone dispersal. The SSR data show strong genetic structuring per island and significant inbreeding in all populations except in Saint Lucia. The lowest genetic diversity is found in the population from Saint Vincent. A high amount of genetic linkage occurs in a subpopulation from Dominica. Main conclusions: Biogeographic patterns for the complex geological setting of the Lesser Antilles are uncovered using a slowly evolving study species. All genetic data support treating each island as distinct Management Units for conservation and call for a re-evaluation of the species limits. Inbreeding threatens the survival of island populations and the populations of Saint Vincent and Dominica represent conservation priorities.

Grassland bird population declines at three Breeding Bird Survey spatial scales in contrast to a large native prairie

Grassland biomes in North America are threatened by agricultural intensification with implications for grassland associated bird populations via habitat loss, alteration, pesticide use and declining landscape heterogeneity. Despite decades of conservation concern, steep declines of North American grassland bird populations continue. Key to optimizing conservation effort is understanding how land-use practices, such as agriculture, across the annual cycle affects population status. Determining the relative influence of impacts on grassland bird declines is difficult given that the most robust estimates of population trends, the North American Breeding Bird Survey (BBS), are from surveys throughout agriculturally dominated regions. Our goal was to explore whether agriculture during the breeding season is a major driver of grassland bird declines. We derived trends for 16 grassland bird species spanning 23 years (1994-2016) at a large (459 km2), native prairie site, Suffield National Wildlife Area (SNWA) in Alberta, Canada. We compared those trends to the BBS across three spatial scales, a regional monitoring scheme with higher than average native grass cover (GBM), BCR 11 - Canada (Canada) and all of BCR 11 (BCR 11). Trends measured as annual percent change and credible interval varied greatly among species and survey strata. Across all species, declines were greatest for Canada (-1.3%, CI: -2.8, 0.0) and BCR 11 (-1.9%, CI: -3.2, -0.6). This contrasts with positive mean trends for GBM routes (1.0%, CI: -0.4, 2.3) and the SNWA data (1.7%, CI: 0.3, 3.3). Six of 16 species at SNWA were increasing with one decreasing. Five species increased at GBM and four declined. Canada had 10 species declines and three increases and BCR 11 had 10 declines and no increases. None of six grassland obligate species declined at SNWA, two declined at GBM, and all six declined over the two larger BBS strata. Our results showing fewer negative population trends at a large native grassland site compared to BBS at three spatial scales across the North American prairies support the prediction that agricultural intensification on breeding grounds is a major driver of declining populations and protection of remaining native grasslands should remain a key component of grassland bird conservation efforts.

Pollinator data from: Pollinator movement activity influences genetic diversity and differentiation of spatially isolated populations of clonal forest herbs

In agricultural landscapes, forest herbs live in small, spatially isolated forest patches. For their long-term survival, their populations depend on animals as genetic linkers that provide pollen- or seed-mediated gene flow among different forest patches. However, whether insect pollinators serve as genetic linkers among spatially isolated forest herb populations in agricultural landscapes remains to be shown. Here, we used population genetic methods to analyze: (A) the genetic diversity and genetic differentiation of populations of two common, slow-colonizing temperate forest herb species (Polygonatum multiflorum (L.) All. and Anemone nemorosa L.) in spatially isolated populations within three agricultural landscapes in Germany and Sweden and (B) the movement activity of their most relevant associated pollinator species, i.e., the bumblebee Bombus pascuorum (Scopoli, 1763) and the hoverfly Melanostoma scalare (Fabricus, 1794), respectively, which differ in their mobility. We tested whether the indicated pollinator movement activity affected the genetic diversity and genetic differentiation of the forest herb populations. Bumblebee movement indicators that solely indicated movement activity between the forest patches affected both genetic diversity and genetic differentiation of the associated forest herb P. multiflorum in a way that can be explained by pollen-mediated gene flow among the forest herb populations. In contrast, movement indicators reflecting the total movement activity at a forest patch (including within-forest patch movement activity) showed unexpected effects for both plant-pollinator pairs that might be explained by accelerated genetic drift due to enhanced sexual reproduction. Our integrated approach revealed that bumblebees serve as genetic linkers of associated forest herb populations, even if they are more than 2 km apart from each other. No such evidence was found for the forest-associated hoverfly species which showed significant genetic differentiation among forest patches itself. Our approach also indicated that a higher within-forest patch movement activity of both pollinator species might enhance sexual recruitment and thus diminishes the temporal buffer that clonal growth provides against habitat fragmentation effects.

High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan

Understanding patterns of genetic structure and adaptive variation in natural populations is crucial for informing conservation and management. Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish (Coregonus clupeaformis) within Lake Michigan, USA. However, ambiguity in genetic stock assignments suggested those neutral microsatellite markers did not provide adequate power for delineating lake whitefish stocks in this system, prompting calls for a genomics approach to investigate stock structure. Here, we generated a dense genomic dataset to characterize population structure and investigate patterns of neutral and adaptive genetic diversity among lake whitefish populations in Lake Michigan. Using Rapture sequencing, we genotyped 829 individuals collected from 17 baseline populations at 197,588 SNP markers after quality filtering. Although the overall pattern of genetic structure was similar to the previous microsatellite study, our genomic data provided several novel insights. Our results indicated a large genetic break between the northwestern and eastern sides of Lake Michigan, and we found a much greater level of population structure on the eastern side compared to the northwestern side. Collectively, we observed five genomic islands of adaptive divergence on five different chromosomes. Each island displayed a different pattern of population structure, suggesting that combinations of genotypes at these adaptive regions are facilitating local adaptation to spatially heterogenous selection pressures. Additionally, we identified a large linkage disequilibrium block of ~8.5 Mb on chromosome 20 that is suggestive of a putative inversion but with a low frequency of the minor haplotype. Our study provides a comprehensive assessment of population structure and adaptive variation that can help inform management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management.