Genetic Drift Research Articles

Evolutionary predictions for a parasite metapopulation: Modelling salmon louse resistance to pest controls in aquaculture.

Pests often evolve resistance to pest controls used in agriculture and aquaculture. The rate of pest adaptation is influenced by the type of control, the selective pressure it imposes, and the gene flow between farms. By understanding how these factors influence evolution at the metapopulation level, pest management strategies that prevent resistance from evolving can be developed. We developed a model for the metapopulation and evolutionary dynamics of the salmon louse (Lepeophtheirus salmonis), which is a major parasite affecting salmon aquaculture. Different management scenarios were simulated across a network of salmon farms covering half of Norway, and their effects on louse epidemiology and evolution were investigated. We compared louse controls that differed in how they were deployed through time (discrete vs. continuous), how they impacted the louse life cycle, and in their overall efficacy. We adjusted the strength of selection imposed by treatments, the dominance effect of the resistant allele, and the geographic location at which resistance originated. Continuously acting strategies (e.g., louse-resistant salmon) were generally more effective than discrete strategies at controlling lice, especially when they increased louse mortality during early developmental stages. However, effective strategies also risked imposing frequent and/or strong selection on lice, thus driving rapid adaptation. Resistant alleles were more likely to be lost through genetic drift when they were recessive, had a low-fitness advantage, or originated in low-farm-density areas. The north-flowing current along the Norwegian coastline dispersed resistant genes from south to north, and limited gene flow in the opposite direction. We demonstrate how evolutionary models can produce quantitative predictions over large spatial and temporal scales and for a range of pest control scenarios. Quantitative outputs can be translated into practical management decisions applied at a regional level to minimise the risk of resistance developing.

SNP heterozygosity, relatedness and inbreeding of whole genomes from the isolated population of the Faroe Islands

BackgroundThe population of the Faroe Islands is an isolated population but very little is known about it from whole genome sequencing. The population of about 50000 people has a high incidence of rare diseases e.g., 1:300 for Primary Carnitine Deficiency. A screening programme was implemented, and eleven persons were also whole genome sequenced at x37 coverage for diagnostic purposes of those cases that were not affected by the known mutations. The purpose of our study is to utilize the high coverage data to explore the genomic variation and the ancestral history of the population. We study the SNP heterozygosity, the pairwise relatedness from kinship, the inbreeding from runs of homozygosity ROH, and we find the minor allele frequency distribution. We estimate the population ancestry and the timing of the founding event by using the whole genomes from eight consenting individuals.ResultsWe find the number of SNPs and the heterozygosity for the eight individual samples, and for merged samples, for which we also study the relatedness. We find close relatedness between the supposedly unrelated individuals. From ROH, we interpret the high relatedness as an ancient property of the isolated population. A bottleneck event is estimated starting between years sim 50-300 with a maximum consanguineous population in year sim 600 and similarly consanguineous between years 500-700. The ancestry analysis shows the population descends from founders of >99% European and <1% Admixed American ancestry. A distinct clustering near the central European and British populations of the 1000 Genome Project is likely the result of the population isolation and genetic drift. The minor allele frequency distribution suggests many rare variants.ConclusionsThe ancestry is mainly European while the inbreeding is higher compared to European populations and population isolates. The Faroese population has inbreeding more like ancient Europeans. We discovered a bottlenecked and consanguineous population event and estimated it starting in the 1st-4th century as compared to the oldest archaeological findings from the 4th-6th century.

Evaluating hybrid speciation and swamping in wild carnivores with a decision-tree approach.

Hybridization is an important evolutionary force with a principal role in the origin of new species, known as hybrid speciation. However, ongoing hybridization can create hybrid swamping, in which parental genomes are completely lost. This can become a biodiversity threat if it involves species that have adapted to certain environmental conditions and occur nowhere else. Because conservation scientists commonly have a negative attitude toward hybrids, it is important to improve understanding of the influence of interspecific gene flow on the persistence of species. We reviewed the literature on species hybridization to build a list of all known cases in the order Carnivora. To examine the relative impact, we also noted level of introgression, whether fertile offspring were produced, and whether there was mention of negative or positive evolutionary effects (hybrid speciation and swamping). To evaluate the conservation implications of hybrids, we developed a decision-making tree with which to determine which actions should be taken to manage hybrid species. We found 53 hybrids involving 68 unique taxa, which is roughly 23% of all carnivore species. They mainly involved monophyletic (83%) and sympatric species (75%). For 2 species, the outcome of the assessment was to eliminate or restrict the hybrids: Ethiopian wolf (Canis simensis) and Scottish wildcat (Felis silvestris silvestris). Both species hybridize with their domestic conspecifics. For all other cases, we suggest hybrids be protected in the same manner as native species. We found no evidence of genomic extinction in Carnivora. To the contrary, some species appear to be of hybrid origin, such as the Asiatic black bear (Ursus thibetanus) and African golden wolf (Canis lupaster). Other positive outcomes of hybridization are novel genetic diversity, adaptation to extreme environments, and increased reproductive fitness. These outcomes are particularly valuable for counterbalancing genetic drift and enabling adaptive introgression in a human-dominated world.

The Impact of Increased Homozygosity on Human Fertility: A Comprehensive Review.

This comprehensive review explores the multifaceted relationship between increased homozygosity and human fertility, delving into the genetic, ethical, cultural, and public health dimensions of this complex phenomenon. Homozygosity, characterized by identical alleles at specific gene loci, can result from consanguineous marriages, genetic drift, and population isolation. The review highlights key findings, including the heightened risk of recessive genetic disorders, the implications for immune system diversity, and the influence on complex traits and diseases. It underscores the critical role of genetic counseling in addressing these consequences, considering the ethical implications, and respecting cultural practices. The delicate balance between genetic diversity and cultural norms is emphasized, calling for increased awareness and community engagement. Looking ahead, the review suggests emerging technologies, longitudinal studies, and interdisciplinary research as crucial avenues for further exploration, with the ultimate goal of informing effective public health policies and interventions that safeguard genetic diversity and cultural traditions for future generations.

Disentangling the genetic diversity and population structure of Magnaporthe oryzae from Telangana State of Southren Peninsular India

Magnaporthe oryzae is a plant pathogenic fungus and model organism due to its agricultural impact and tractability that causes severe blast disease affecting rice. Due to its complex cryptic species, VNTRs and complex polyphyletic lineage due to the presence of many transposable elements. In the present study the internal transcribed spacers (ITS) of the ribosomal DNA sequences were used to characterize the 40 monoconidial M. oryzae strains from blast disease samples of the Telangana. Using DNAsp, performed a population genetics study on the sequencing data and discovered that rDNA sequence variation was highly polymorphic, with 0.01521 nucleotide diversity. In the present investigation 8 haplotype groups with Haplotype 2 (Hap_2) were reported to have with a broader genetic base. With a D value of −2.660 and a P 0.05 Tajima's neutrality test, the haplotype diversity is 0.52317, implying that there are variations in the pathogen isolates' sequences. The pathogen's apparent clonal reproductive behaviour was in contrast to the observed population structure, which suggested that genetic recombination may still be occurring within the pathogen population. The total number of variable sites (S) and mutations (Eta) were 63 and 73 respectively. Further, a haplotype network was constructed for the comparison of genealogical relationship's among (ITS) allele's using Population analysis with reticulate trees (PopArt software) a population genetics software to visualize the broader genetic base and genetic drift among the samples collected from the various locations of Telangana.

Scrutinising an inscrutable bark-nesting ant: Exploring cryptic diversity in the Rhopalomastix javana (Hymenoptera: Formicidae) complex using DNA barcodes, genome-wide MIG-seq and geometric morphometrics.

Overlooking cryptic species diversity has grave implications on assessments of climate change impacts on biodiversity, ecosystems and organismal populations. Discriminating between cryptic species has long been challenging even for seasoned taxonomists, as interspecies morphological differences are often indiscernible by visual observation. Multi-disciplinary methods involving genetic analyses in conjunction with quantitative morphological data, should therefore be used to investigate boundaries between cryptic species. We adopted an integrated approach combining analyses of mitochondrial COI barcodes, a genome-wide dataset obtained via multiplexed inter-simple sequence repeats (ISSRs) genotyping by sequencing (MIG-seq), and geometric morphometrics to investigate species divergences in the inscrutable Rhopalomastix javana species complex. Objective clustering of COI suggested five putative molecular species units divergent from each other by thresholds within 4.2-10.6% uncorrected pairwise distance. Phylogenetic analyses based on concatenated MIG-seq data also recovered and strongly supported the monophyly of five major lineages in agreement with COI clusters. Co-ancestry analyses based on MIG-seq data using fineRADstructure resolved variable patterns of admixture linked to geography, and potential genetic drift within some putative species. Geometric morphometric analyses of specimen images further detected statistically significant differences in at least one of three anatomical aspects (Head, Meso, Profile) between all pairs of putative species. Head shape (full-face view) was determined to be the most informative character for species diagnosis, with relatively high classification accuracy. Thin-plate spline deformation grids highlighted areas of high variation between species in each shape for deeper taxonomic scrutiny. The presence of species from multiple distinct lineages existing in near-sympatry firmly demonstrates that R. javana comprises more than one closely-related species, but exact species boundaries are difficult to ascertain. Differences in elevation and its associated abiotic effects on ant adaptations and reproductive phenology may contribute to restricting gene flow and maintaining species boundaries between sympatric populations of the R. javana complex. We further assess the advantages and limitations of geometric morphometrics as a taxonomic tool. Despite its drawbacks, our combined approach has helped draw important insights on cryptic diversity in R. javana, and also identified gaps of knowledge that await address. Results from this study will inform and prime future in-depth taxonomic investigation on the R. javana complex, including formal descriptions and establishment of the five putative species.

Is it time for genetic reinforcement of French Iberian ibex populations?

An evolutionary significant unit of the Iberian ibex (Capra pyrenaica), the Pyrenean ibex or “bucardo” (Capra pyrenaica pyrenaica) became extinct in its natural range, the Pyrenees, at the beginning of the twentieth-first century. Several years later (2014–2021) more than 250 specimens (C. p. victoriae) coming from the same donor population from central Spain were released in four localities of the French Pyrenees. Despite an initial fast demographic increase, the genetic variability of these populations remains low. Moreover, it is expected that genetic variability continues to decline due to genetic drift and that inbreeding accumulates. Here we revise options for genetic rescue or reinforcement of these populations involving future release of animals from different extant Spanish populations, mainly those belonging to the subpecies C. p. hispanica. The future hybridization between both phenotypes or “subspecies” may occur anyways in the next years, since currently there is a natural expansion of C. P. hispanica populations from the southern Pyrenees (Spanish side).

Preserving Pure Siamese Crocodile Populations: A Comprehensive Approach Using Multi-Genetic Tools.

Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) in captive populations represent a serious challenge for conservation and reintroduction programs due to the impact of anthropogenic activities. A previous study used microsatellite and mitochondrial DNA data to establish the criteria for identifying species and their hybrids; however, the results may have been influenced by biased allelic frequencies and genetic drift within the examined population. To overcome these limitations and identify the true signals of selection, alternative DNA markers and a diverse set of populations should be employed. Therefore, this study used DArT sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in both species and confirm the genetic scenario of the parental species and their hybrids. A population of saltwater crocodiles from Australia was used to compare the distribution of species-diagnostic SNPs. Different analytical approaches were compared to diagnose the level of hybridization when an admixture was present, wherein three individuals had potential backcrossing. Approximately 17.00-26.00% of loci were conserved between the Siamese and saltwater crocodile genomes. Species-diagnostic SNP loci for Siamese and saltwater crocodiles were identified as 8051 loci and 1288 loci, respectively. To validate the species-diagnostic SNP loci, a PCR-based approach was used by selecting 20 SNP loci for PCR primer design, among which 3 loci were successfully able to differentiate the actual species and different hybridization levels. Mitochondrial and nuclear genetic information, including microsatellite genotyping and species-diagnostic DNA markers, were combined as a novel method that can compensate for the limitations of each method. This method enables conservation prioritization before release into the wild, thereby ensuring sustainable genetic integrity for long-term species survival through reintroduction and management programs.

Genomic evolution of island birds from the view of the Swinhoe's pheasant (Lophura swinhoii).

Island endemic birds account for the majority of extinct vertebrates in the past few centuries. To date, the evolutionary characteristics of island endemic bird's is poorly known. In this research, we de novo assembled a high-quality chromosome-level reference genome for the Swinhoe's pheasant, which is a typical endemic island bird. Results of collinearity tests suggest rapid ancient chromosome rearrangement that may have contributed to the initial species radiation within Phasianidae, and a role for the insertions of CR1 transposable elements in rearranging chromosomes in Phasianidae. During the evolution of the Swinhoe's pheasant, natural selection positively selected genes involved in fecundity and body size functions, at both the species and population levels, which reflect genetic variation associated with island adaptation. We further tested for variation in population genomic traits between the Swinhoe's pheasant and its phylogenetically closely related mainland relative the silver pheasant, and found higher levels of genetic drift and inbreeding in the Swinhoe's pheasant genome. Divergent demographic histories of insular and mainland bird species during the last glacial period may reflect the differing impact of insular and continental climates on the evolution of species. Our research interprets the natural history and population genetic characteristics of the insular endemic bird the Swinhoe's pheasant, at a genome-wide scale, provides a broader perspective on insular speciation, and adaptive evolution and contributes to the genetic conservation of island endemic birds.

A genomic analysis of the University of Nebraska Replicated Recurrent Selection program.

The inbred-hybrid system of maize breeding closely resembles a reciprocal full-sib (RFS) selection program. Studying changes in genetic variation as a result of RFS selection can help illuminate long-standing questions regarding the relative roles of selection and genetic drift and help understand the nature of adaptation occurring in selection programs. The University of Nebraska-Lincoln Replicated Recurrent Selection (UNL-RpRS) program underwent eight cycles of replicated RFS and S1-progeny selection, making it a powerful system to study genomic changes accompanying selection for inter-population performance. The objectives of this study were to identify regions of the genome under selection after eight cycles of selection and evaluate the effect eight cycles of selection for inter-population full-sib performance had in expanding genome-wide and localized population structure. We address these questions with a large set of individuals sampled from the UNL-RpRS program with dense genotyping-by-sequence data. We found evidence of parallel selection signatures in the UNL-RpRS program, with a region on chromosome 7 being implicated in three of the four selection systems studied. Regions that displayed selection signatures across independently run selection programs represent regions likely to be capitalizing on standing genetic variation and support a soft sweep model of adaptation. We did not find selection to be a strong force in diverging populations undergoing RFS. This could be due to the nature of adaptation occurring in these populations, underlying gene action, or a result of unstable genetic topographies.

Concurrent invasions of European starlings in Australia and North America reveal population‐specific differentiation in shared genomic regions

AbstractA species' success during the invasion of new areas hinges on an interplay between the demographic processes common to invasions and the specific ecological context of the novel environment. Evolutionary genetic studies of invasive species can investigate how genetic bottlenecks and ecological conditions shape genetic variation in invasions, and our study pairs two invasive populations that are hypothesized to be from the same source population to compare how each population evolved during and after introduction. Invasive European starlings (Sturnus vulgaris) established populations in both Australia and North America in the 19th century. Here, we compare whole‐genome sequences among native and independently introduced European starling populations to determine how demographic processes interact with rapid evolution to generate similar genetic patterns in these recent and replicated invasions. Demographic models indicate that both invasive populations experienced genetic bottlenecks as expected based on invasion history, and we find that specific genomic regions have differentiated even on this short evolutionary timescale. Despite genetic bottlenecks, we suggest that genetic drift alone cannot explain differentiation in at least two of these regions. The demographic boom intrinsic to many invasions as well as potential inversions may have led to high population‐specific differentiation, although the patterns of genetic variation are also consistent with the hypothesis that this infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors). We use targeted sampling of replicated invasions to identify and evaluate support for multiple, interacting evolutionary mechanisms that lead to differentiation during the invasion process.

Relict stands of Central European oaks: Unravelling autochthony and genetic structure based on a multi-population study

Central European white oaks expanded rapidly after the last glacial period and reached their current distribution range during the early Holocene. They have been an important resource of timber, fuelwood and animal feed for humans, who actively promoted their presence in forests and other landscape types at least since the early historical times. Besides stands with intensive management, putatively relict populations of three native oak species can be found on unproductive sites with restricted accessibility. Here, we apply chloroplast and nuclear microsatellite markers in order to address the autochthony of relict and managed stands and compare the spatial distribution of genetic variation between them. Based on data from more than 150 populations, we demonstrate that oak autochthony was preserved throughout historical times which is likely the result of traditional silvicultural treatment. This is supported by the fact that the spatial pattern of chloroplast haplotype distribution still reflects the post-glacial recolonization in both relict and old managed stands. We observed significant admixture of haplotypes only in stands established after the Second World War, which is attributable to the transfer of reproductive material used for afforestation. In terms of nuclear genetic variation, we observed marked differences among species. Quercus pubescens exhibited a pronounced genetic structure. Genetic drift and limited gene flow among its small and isolated populations in our study area might have contributed to this pattern. Varying extent of genetic introgression with other sympatric oak species could offer an additional explanation. On the contrary, the gene pools of Q. petraea and Q. robur are highly homogenous, displaying only weak isolation-by-distance. We found no significant differences of genetic diversity and differentiation between relict and managed stands. This suggests that seed transfer mostly occurred within our study area, even in those stands established in post-war times, verifying previous findings which point out limited human interference. We recommend consideration of population genetic structure for gene conservation, with a finer resolution of gene conservation units needed for Q. pubescens due to its spatial genetic structure. Both relict and old managed stands, species-pure or mixed, are suitable for conservation, as they host autochthonous gene pools. Coppice-with-standard management could contribute to preservation of autochthony. In the face of climate change, it is also important to maintain the evolutionary potential of the stands, by facilitating generative reproduction and allowing for hybridization in mixed stands.

Revealing genetic diversity of wild Phalaenopsis orchids in Thailand through Random Amplified Polymorphic DNA markers

Abstract. Kate-ngam S, Jantasuriyarat C, Lakote P, Promchot T, Chueakaew C. 2023. Revealing genetic diversity of wild Phalaenopsis orchids in Thailand through Random Amplified Polymorphic DNA markers. Biodiversitas 24: 5409-5417. Wild Phalaenopsis orchids are widely distributed in Thailand, especially along the banks of the Mekong River. The tremendous decrease in the population of these orchids is a matter of concern for maintaining and preventing genetic loss in the natural ecosystem. This study aimed to determine the genetic diversity of 50 wild Phalaenopsis accessions collected from the northeastern of Thailand using random amplified polymorphic DNA (RAPD) markers. The 204 polymorphic bands generated from 27 RAPD primers were employed for fingerprinting these orchid accessions. Dice’s similarity coefficients ranged from 0.43 to 0.98, with an average of 0.65. In general, a dendrogram constructed based on the unweighted pair group method with arithmetic average (UPGMA) grouped these wild Phalaenopsis accessions into two clusters, namely P. pulcherrima and P. ubonensis clusters. The UPGMA clustering pattern and principal component analysis (PCA) corresponded well with their morphological classification and ploidy level. Our results suggest that this wild Phalaenopsis orchid exhibits a moderate level of relatedness. This might be a consequence of habitat destruction and human over-exploitation which limit gene flow and cause genetic drift among populations. The present finding supports the urgent need for a systematic conservation effort of this orchid species in Thailand.

Multilayer Profiling of MRD in Patients with Relapsed/Refractory CLL Treated with Venetoclax-Based Regimens in a Real-World Setting

Background Clinical trials have shown that patients with relapsed/refractory chronic lymphocytic leukemia (RR-CLL) treated with venetoclax monotherapy (Ven) or venetoclax-rituximab (VenR) often achieve unmeasurable MRD (uMRD) in peripheral blood (57% of VenR-patients achieved uMRD in peripheral blood at the 12 months landmark by FCM and/or ASO-PCR in the RCT MURANO; Kater AP. et al. JCO 2019 1). uMRD is a strong prognostic factor for progression free survival (PFS) in RR-CLL treated with venetoclax, but the rate of uMRD has not been systematically validated in RR-CLL cohorts treated in the real-world setting. Venetoclax imposes a strong selective pressure on the MRD clone, but the magnitude of the genetic drift of MRD persisting under venetoclax has not been quantified or qualified. Resistance to venetoclax can be mediated by selection of BCL2 mutant clones, but it is unknown if they already emerge in persistent cells of the MRD when the disease is in remission. Methods We analyzed peripheral blood of Swiss patients enrolled in the VeRVe study (NCT03342144), a prospective non-interventional observational study assessing effectiveness, safety, and quality of life in real-world patients with RR-CLL treated with Ven or VenR according to local label. MRD was measured by 8-color multi-parametric flow cytometry (FCM) following the European Research Initiative on CLL (ERIC) guidelines (sensitivity 10 -4), by high throughput sequencing (Ig-HTS, clonoSEQ® Assay) on gDNA from PBMCs (sensitivity 10 -6) and by NGS LyV4.0 CAPP-Seq ctDNA Assay on plasma ctDNA (sensitivity 10 -3) at diagnosis and at 12 months of treatment. To overcome the limitations imposed by the small size of MRD under venetoclax treatment, we leveraged ctDNA for clonal evolution profiling and for the detection of BCL2 mutations. Tumor gDNA was extracted from pre-treatment CLL cells purified by flow cytometry. Germline gDNA was extracted from PB leukocytes collected at the time of best MRD remission. Results In total, 28 patients were recruited. At the time of the analysis, 7 patients went off study before the one-year landmark, 4 patients have not yet reached the one-year landmark, resulting in 17 patients (Ven=5, VenR=12) assessable at the one-year landmark [17 analyzed by FCM, 16 by CAPP-seq (1 ongoing) and 12 by Ig-HTS (5 ongoing; 3 could not be evaluated because they failed Ig-HTS QC)]. At the 12 months landmark, uMRD was achieved in 58% of the assessed cases by FCM, 56% by CAPP-seq and 33% by Ig-HTS. FCM and CAPP-seq concordantly defined the MRD status in 76% of cases with κ=0.49 (12% had measurable ctDNA despite uMRD by FCM and 12% lacked ctDNA despite having measurable MRD by FCM). FCM and Ig-HTS concordantly defined the MRD status in 67% of cases with κ=0.40 (33% had measurable MRD by Ig-HTS despite uMRD by FCM). All patients, who had measurable MRD by FCM and/or CAPP-seq, had measurable MRD by Ig-HTS, which instead detected measurable MRD in 11% of patients who scored negative by both FCM and CAPP-seq (κ=0.77). By CAPP-seq of gDNA from purified CLL cells collected before therapy, the most frequently mutated genes were TP53, IGLL5, BRAF, SF3B1, NXF1, and ZMYM3. At baseline the concordance in mutation recovery by CAPP-seq of gDNA from purified CLL and ctDNA from plasma was high (73%). Before therapy, BCL2 mutations were never detected in either gDNA from purified CLL cells, or in ctDNA. To overcome the limitations imposed to genomic profiling by the small size of MRD under Ven or VenR treatment, we leveraged ctDNA for tracking the acquisition of BCL2 mutations. A total of 5 longitudinal, post-treatment timepoints spanning up to two years of therapy were analyzed. No patients who had measurable ctDNA at the one-year landmark (n=16) acquired BCL2 mutations. Conclusions The rate of uMRD achievable by venetoclax-based therapy in RR-CLL as measured in this real-world prospective study is congruent with the rate observed in the randomized clinical study MURANO. Ig-HTS has the best diagnostic performance for MRD detection. BCL2 mutations are not detectable in ctDNA after one year of venetoclax-based treatment, confirming that time limited therapy has low risk of selecting resistance. 1.) Kater AP. et al. Fixed Duration of Venetoclax-Rituximab in Relapsed/Refractory Chronic Lymphocytic Leukemia Eradicates Minimal Residual Disease and Prolongs Survival: Post-Treatment Follow-Up of the MURANO Phase III Study. JCO 2019, 7(4):269-277

Locomotor play behavior evolves by random genetic drift but not as a correlated response to selective breeding for high voluntary wheel-running behavior

Locomotor play is vigorous and seemingly purposeless behavior, commonly observed in young mammals. It can be costly in terms of energy expenditure, increased injury risk, and predator exposure. The main hypothesized benefit of locomotor play is enhancement of neuromuscular development, with effects persisting into adulthood. We hypothesized that levels of locomotor play would have evolved as a correlated response to artificial selection for increased voluntary exercise behavior. We studied mice from 4 replicate lines bred for voluntary wheel running (High Runner or HR) at 6–8 weeks of age and four non-selected Control (C) lines. Mice were weaned at 21 days of age and play behavior was observed for generations 20 (22–24 days old), 68 (22–23 days old), and 93 (15 days old). We quantified locomotor play as (1) rapid, horizontally directed jerk-run sequences and (2) vertical "bouncing." We used focal sampling to continuously record behavior in cages containing 4–6 individuals during the first 2–3 h of the dark cycle. Observations were significantly repeatable between observers and days. A two-way, mixed-model simultaneously tested effects of linetype (HR vs. C), sex, and their interaction. Contrary to our hypothesis, HR and C lines did not differ in any generation, nor did we find sex differences. However, differences among the replicate HR lines and among the replicate C lines were detected, and may be attributed to the effects of random genetic drift (and possibly founder effects). Thus, play behavior did evolve in this selection experiment, but not as a correlated response to selection for voluntary exercise.

Frequent asymmetric migrations suppress natural selection in spatially structured populations.

Natural microbial populations often have complex spatial structures. This can impact their evolution, in particular the ability of mutants to take over. While mutant fixation probabilities are known to be unaffected by sufficiently symmetric structures, evolutionary graph theory has shown that some graphs can amplify or suppress natural selection, in a way that depends on microscopic update rules. We propose a model of spatially structured populations on graphs directly inspired by batch culture experiments, alternating within-deme growth on nodes and migration-dilution steps, and yielding successive bottlenecks. This setting bridges models from evolutionary graph theory with Wright-Fisher models. Using a branching process approach, we show that spatial structure with frequent migrations can only yield suppression of natural selection. More precisely, in this regime, circulation graphs, where the total incoming migration flow equals the total outgoing one in each deme, do not impact fixation probability, while all other graphs strictly suppress selection. Suppression becomes stronger as the asymmetry between incoming and outgoing migrations grows. Amplification of natural selection can nevertheless exist in a restricted regime of rare migrations and very small fitness advantages, where we recover the predictions of evolutionary graph theory for the star graph.

Neutralization of African enterovirus A71 genogroups by antibodies to canonical genogroups.

Enterovirus 71 (EV-A71) is a major public health problem, causing a range of illnesses from hand-foot-and-mouth disease to severe neurological manifestations. EV-A71 strains have been phylogenetically classified into eight genogroups (A to H), based on their capsid-coding genomic region. Genogroups B and C have caused large outbreaks worldwide and represent the two canonical circulating EV-A71 subtypes. Little is known about the antigenic diversity of new genogroups as compared to the canonical ones. Here, we compared the antigenic features of EV-A71 strains that belong to the canonical B and C genogroups and to genogroups E and F, which circulate in Africa. Analysis of the peptide sequences of EV-A71 strains belonging to different genogroups revealed a high level of conservation of the capsid residues involved in known linear and conformational neutralization antigenic sites. Using a published crystal structure of the EV-A71 capsid as a model, we found that most of the residues that are seemingly specific to some genogroups were mapped outside known antigenic sites or external loops. These observations suggest a cross-neutralization activity of anti-genogroup B or C antibodies against strains of genogroups E and F. Neutralization assays were performed with diverse rabbit and mouse anti-EV-A71 sera, anti-EV-A71 human standards and a monoclonal neutralizing antibody. All the batches of antibodies that were tested successfully neutralized all available isolates, indicating an overall broad cross-neutralization between the canonical genogroups B and C and genogroups E and F. A panel constituted of more than 80 individual human serum samples from Cambodia with neutralizing antibodies against EV-A71 subgenogroup C4 showed quite similar cross-neutralization activities between isolates of genogroups C4, E and F. Our results thus indicate that the genetic drift underlying the separation of EV-A71 strains into genogroups A, B, C, E and F does not correlate with the emergence of antigenically distinct variants.

Partitioning variance in reproductive success, within years and across lifetimes.

Variance in reproductive success (, with k = number of offspring) plays a large role in determining the rate of genetic drift and the scope within which selection acts. Various frameworks have been proposed to parse factors that contribute to , but none has focused on age-specific values of , which indicate the degree to which reproductive skew is overdispersed (compared to the random Poisson expectation) among individuals of the same age and sex. Instead, within-age effects are generally lumped with residual variance and treated as "noise." Here, an ANOVA sums-of-squares framework is used to partition variance in annual and lifetime reproductive success into between-group and within-group components. For annual reproduction, the between-age effect depends on age-specific fecundity (b x), but relatively few empirical data are available on the within-age effect, which depends on ϕ x. By defining groups by age-at-death rather than age, the same ANOVA framework can be used to partition variance in lifetime reproductive success (LRS) into between-group and within-group components. Analytical methods are used to develop null-model expectations for random contributions to within-group and between-group components. For analysis of LRS, random variation in longevity appears as part of the between-group variance, and effects (if any) of skip breeding and persistent individual differences contribute to the within-group variance. Simulations are used to show that the methods for variance partitioning are asymptotically unbiased. Practical application is illustrated with empirical data for annual reproduction in American black bears and lifetime reproduction in Dutch great tits. Results show that overdispersed within-age variance (1) dominates annual in both male and female black bears, (2) is the primary factor that reduces annual effective size to a fraction of the number of adults, and (3) represents most of the opportunity for selection. In contrast, about a quarter of the variance in LRSin great tits can be attributed to random variation in longevity, and most of the rest is due to modest differences in fecundity with age estimated for a single cohort of females. R code is provided that reads generic input files for annual and lifetime reproductive success and allows users to conduct variance partitioning with their own data.

Mitogenomics clarifies the position of the Nearctic magpies (Pica hudsonia and Pica nuttalli) within the Holarctic magpie radiation.

Partial separation of a peripheral population may lead to its divergence and, potentially, speciation due to genetic drift followed by selection and geographic isolation. This process may cause taxonomic uncertainty because reproductive isolation in allopatry cannot be verified directly. The two Nearctic allopatric species of magpies (Aves, Corvidae: Pica) serve as a good example of these problems. The Black-billed magpie Pica hudsonia is widely distributed in North America, whereas the Yellow-billed Magpie Pica nuttalli is endemic to a restricted range in California. Their relationships with Palearctic species have been little studied. We obtained complete mitochondrial genomes of both Nearctic magpie species, along with the Eurasian Magpie (Pica pica) and the Oriental Magpie (Pica serica), 20 mitogenomes in total. Phylogenetic analysis reveals a basal position of P. serica, and P. pica as a sister clade to the two Nearctic species. P. hudsonia and P. nuttalli form reciprocal monophyletic subclades, showing recent divergence between and within them. Our data show that the Nearctic magpie lineage diverged from the common ancestor with P. pica, with a single migration wave via the Beringia. Within the Nearctic, we hypothesize a peripatric mode of speciation among Pica taxa due to the divergence and separation of the small marginal population in California below the Sierra-Nevada mountains. Diversifying amino acid substitutions in ND4-ND5-ND6 genes along the branch leading to the New World clade may indicate selection for heat-tolerance. Considering the clear phenotypic differences between P. hudsonia and P. nuttalli, our data, showing their reciprocal monophylies and genetic distinctness, is consistent with the two-species taxonomy.

Reliable detection and quantification of selective forces in language change

AbstractLanguage change is a cultural evolutionary process in which variants of linguistic variables change in frequency through processes analogous to mutation, selection and genetic drift. In this work, we apply a recently-introduced method to corpus data to quantify the strength of selection in specific instances of historical language change. We first demonstrate, in the context of English irregular verbs, that this method is more reliable and interpretable than similar methods that have previously been applied. We further extend this study to demonstrate that a bias towards phonological simplicity overrides that favouring grammatical simplicity when these are in conflict. Finally, with reference to Spanish spelling reforms, we show that the method can also detect points in time at which selection strengths change, a feature that is generically expected for socially-motivated language change. Together, these results indicate how hypotheses for mechanisms of language change can be tested quantitatively using historical corpus data.