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Malécot's theory of isolation by distance under 'continuous' migration is shown to fit acceptably to various human populations. Although it provides a less complete and reliable prediction of population structure than migration matrices, it is applicable to a greater range of structures and data.
Lalouel's assertion that I misinterpreted Malécot's work on isolation by distance may or may not be correct. If so, my assertions of error in Malécot's derivation are wrong, although they do apply to others who have used models involving a spatial continuum. Lalouel's other claims of error in my derivations of the consequences of a spatially continuous model of population reproduction and migration are incorrect, with the exception of one isolated misprint.
Bacterial species within the mammalian gut microbiota exhibit considerable strain diversity associated with both geography and host genetic ancestry. However, because geography and host ancestry are typically confounded, disentangling their contributions to the diversification of gut bacterial strains has remained challenging. Here, we show through joint profiling of gut bacterial and mitochondrial genomes from wild-living populations of deer mice (Peromyscus maniculatus) sampled across the United States that isolation by distance (IBD) drives gut bacterial strain diversification independently of the effects of host ancestry. Analyses revealed significant IBD in 27 predominant gut bacterial species, including members of the Muribaculaceae and Lachnospiraceae, but limited evidence for co-inheritance of gut bacterial genomes with mitochondria during the diversification of extant mouse populations. Gut bacterial species capable of forming spores exhibited reduced IBD independently of phylogenetic history, indicating that adaptations facilitating bacterial dispersal can mitigate the geographic structuring of strain diversity. These results show that the diversification of gut bacterial strains within rodent species has been mediated by geographic separation of host populations rather than host genealogical divergence.
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Azadirachta indica (A. indica) A. Juss., commonly known as Neem, is a valuable multipurpose tree with profound medicinal properties and socioeconomic importance, widely recognized since ancient Ayurvedic times. Despite its prominence, knowledge about its genetic diversity within the metropolitan area of Ahmedabad is limited. This study marks the first in-depth exploration of the genetic diversity and population structure of A. indica in Ahmedabad. The authenticity of the species was validated through DNA barcoding, and a Geographical Information System (GIS) was used to collect the samples. A total of 35 A. indica accessions were analyzed using five Inter Simple Sequence Repeat (ISSR) primers. Genetic diversity and population structure were evaluated using Inter Simple Sequence Repeat (ISSR) markers through polymorphism assessment, clustering, ordination, and Bayesian population structure analyses. ISSRs revealed a high level of polymorphism (75.66%), indicating substantial genetic variability among accessions. An analysis of genetic diversity indices revealed low to moderate diversity (Hs = 0.14, Ht = 0.217, I = 0.217). Analysis of Molecular Variance (AMOVA) analysis depicted 81% variation within the population and 19% among the population. Low to moderate genetic differentiation (Gst = 0.319) and moderate gene flow (Nm = 1.06) indicated that urban development has not hindered gene flow among populations. Mantel's test revealed a weak but significant correlation between genetic and geographic distances, suggesting limited isolation by distance. The estimated ΔK using STRUCTURE exhibited two subpopulations, representing two gene pools for A. indica accessions (K = 2). Collectively, these patterns indicate that urbanization has not severely disrupted genetic connectivity in A. indica, reflecting its resilience and adaptive potential in a metropolitan environment. These findings provide pivotal knowledge for further understanding the genetic diversity and population structure of A. indica in one of the fastest-growing cities in India, which can be utilized for new breeding programmes, sustainable development and future conservation strategies around the globe.
The blue structural coloration of male Polyommatus icarus butterflies functions as a sexual signaling trait and exhibits remarkable spectral stability within populations despite being generated by highly complex photonic nanoarchitectures. The correlation of the blue sexual signaling color and population genetic variation of the butterflies was investigated across the Western and Central Palearctic regions. Dorsal wing reflectance spectra was measured for 95 male specimens and compared with the population genetic structure revealed in 99 specimens by 18 recently developed microsatellites. Reflectance measurements indicated a clear separation between the European and Central Asian populations, consistent with our previous findings, while the intermediate populations near the Ural Mountains exhibited distinct European spectral characteristics. In contrast, genetic variation showed limited structuring and correlated primarily with geographic distance, as indicated by a significant isolation-by-distance pattern. Thus, although both reflectance and genetic variations are geographically structured, spectral properties are only weakly correlated with genetic differentiation. Populations near the Ural Mountains exhibited genetic ancestry linked to Central Palearctic groups, while displaying distinct Western Palearctic coloration, suggesting that the focal species' sexual signaling is strongly influenced by local factors. These findings suggest that sexual signaling coloration may evolve at least partially independently of the neutral genetic background, offering additional insight into evolutionary divergence across broad geographic scales.
The Finnish gene pool derives primarily from a relatively homogeneous Finno-Ugric population established during the Iron Age (100 B.C.-800 A.D.) in the southwest and southeast of Finland. Gene flow from Sweden to the southwest coastal areas, dating from prehistoric times, as well as the patterns of settlement and migration throughout Finland during the past 1000 years, appear to have been the major biosocial factors underlying the genetic structure of the contemporary population. Analysis of genetic variation and covariation at nine polymorphic loci in a large random sample of rural Finns, partitioned into either 8 countries or 27 geographic districts, showed that all of the essential features of the genetic structure suggested by the archaeological and historical data could be distinguished. Procedures for obtaining inference on the genetic structure of such a population are reviewed, including coefficients of similarity and (genetic) distance among subpopulations, the relation between linear or planar geographic structure and genetic covariation, and the methods for describing allelic differentiation. Bias resulting from the inappropriate assumption of a simple phylogenetic model can be substantial, expecially for the analysis of isolation by distance; procedures for avoiding misleading inference on the genetic structure are demonstrated.
Mountains are important centers of biodiversity and studies of speciation. In particular, the north-south linear orientation of the Andes allows examination of how geographic isolation, elevation, and latitude influence divergence in closely related species such as Myioborus warblers (Parulidae), the focal taxa of this study. Traditional models of Andean speciation have emphasized allopatric divergence due to geographic barriers, but thanks to the limited sampling of hybrid zones and lack of genome-wide datasets in tropical taxa, we may have underestimated of the role of gene flow in shaping patterns of divergence in the region. Using ddRAD-seq genomic data, Céspedes Arias et al. (2026) demonstrated that geographic isolation and hybridization both contribute to the generation and maintenance of Andean warbler lineages. Their results revealed how complex patterns of genetic divergence, introgression, and isolation-by-distance contribute to the historical buildup of biodiversity in the Andes, challenging strictly isolationist models of mountain evolution.
Habitat fragmentation is widely expected to reduce population connectivity and increase genetic differentiation, although the strength of these effects depends on species-specific traits such as dispersal ability. Here, we investigated the population genetic structure of the cosmopolitan butterfly, Pieris rapae L. (Lepidoptera: Pieridae), across western Germany using genome-wide single-nucleotide polymorphism (SNP) data. To analyze the effects of landscape structure on genetic connectivity, we applied a paired study design comprising four landscape pairs, each consisting of a highly intensified, modern agricultural landscape and a more heterogeneous, traditional landscape. Our results revealed no evidence of genetic differentiation. Pairwise FST values were close to zero; we detected no isolation by distance, and clustering analyses supported a single genetic population. No meaningful associations between genetic variation and environmental variables were detected, with landscape effects explaining less than 0.4% of genomic variation. Consequently, we found no evidence for stronger genetic structuring in modern compared to more connected traditional landscapes. Our results suggest that extensive habitat fragmentation does not necessarily translate into reduced genetic connectivity in highly mobile, generalist species. In P. rapae , high dispersal ability and ecological generalism appear to buffer against the genetic consequences of landscape modification, resulting in panmictic population structure even across strongly contrasting agricultural landscapes.
High-density SNP arrays are increasingly used in ecological and evolutionary studies, yet their application in wild species remains challenging. In this study, we evaluated the performance of the Affymetrix Axiom Mouse HD array, originally developed for Mus musculus, in two wild small mammals, Apodemus flavicollis and Apodemus sylvaticus, with particular focus on genetic diversity and population connectivity across seven sampling sites within a fragmented landscape. A total of 96 individuals (43 A. flavicollis and 53 A. sylvaticus) were genotyped using a 616K SNP array. After quality control filtering for missingness and minor allele frequency, more than 160,000 high-quality autosomal SNPs were retained for each species. Despite being designed for a different species, the array effectively discriminated between A. flavicollis and A. sylvaticus, with principal component analysis clearly separating the two species. Levels of genetic diversity were comparable across sites, with mean observed heterozygosity around 0.33 and consistently negative F IS values, indicating a slight excess of heterozygotes. Population structure analyses revealed extremely weak spatial genetic differentiation. ADMIXTURE supported a single genetic cluster (K = 1) within each species, while analysis of molecular variance attributed more than 99% of genetic variation to within-individual components. Pairwise relationship analyses showed that related individuals were not confined to single sites but occurred across sampling locations, supporting ongoing gene flow even across the fragmented landscape. No significant isolation-by-distance pattern was detected. Overall, our results indicate high population connectivity and limited spatial genetic structuring in both species across the study area, consistent with the documented dispersal capacity of these species at the spatial scale investigated. Moreover, this study demonstrates that high-density SNP arrays can provide powerful genomic tools for investigating dispersal dynamics and population structure in closely related wildlife species under habitat fragmentation, where subtle genetic patterns may otherwise remain undetected.
Information about biological traits essential for pest management, such as species identity, diet and movement often require laborious and time-intensive studies on pest natural history, in both laboratory and field settings. However, new agricultural pest threats are continually emerging, often requiring prompt responses with limited information. Using a combination of molecular gut content analysis and RAD-seq, we examined the species identities, plant diet composition, and population genetic structure of an emerging and important agricultural pest in the US, the peanut burrower bug, Pangaeus bilineatus Say (Hemiptera, Cydnidae). We found that two, morphologically similar, burrowing bug species (including P. bilineatus) were commonly caught in light traps near peanut fields, one of which (Dallasiellus lugubris) was not previously considered a pest of peanut. Molecular gut content analysis revealed a wide, but somewhat distinct, variety of plants among the diets of both bug species. Surprisingly, peanut was a rare part of the diet of either species. RAD-seq analysis revealed evidence consistent with weak isolation-by-distance and modest spatial genetic differentiation for both species. Together, these results suggest a potential pest complex where previously only one species was in focus. Moreover, their broad diets and spatially restricted population dispersal patterns may also explain the sporadic nature of damage that has been recorded for this potential pest complex. Responses to emerging pest challenges can benefit from insights generated by population genomics techniques, opening up new avenues for research and supporting efforts to quickly tailor management strategies for novel pests.
Nucella lapillus is an important player in rocky shore food chains and has been a focal organism of ecological and evolutionary studies for decades. Despite poor dispersal, they have a broad geographic range, which makes them an ideal species to examine isolation by distance and selection across environmental gradients. Here we present the fully annotated genome of N. lapillus generated with Oxford Nanopore Techonology sequencing at ∼37× coverage. The genome assembly is 2.32 Gbp and consists of 2,525 contigs, with an N50 length of 2 Mbp. Repeat annotation identified 2,491 families that cover 67.56% of the genome, which is similar to other gastropods. Despite its large size and high proportion of repeats, the genome is of high quality. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis revealed a score of 96.8%. Functional annotation of the genome produced 45,848 protein-coding genes with a 96.6% BUSCO score. Genomic resources for mollusks lag behind that of other phyla, perhaps because many of their innate characteristics complicate DNA extraction, sequencing, and assembly. This new N. lapillus genome will increase our genomic understanding of the second largest phylum (and the most diverse class within said phylum) and serve as a key resource to advance studies on the organismal biology and population genetics of this iconic species as well as the connection between genomic variation and community-level processes.
Archaeological and palaeogenomic data show that dogs were the only domestic animals introduced during the early peopling of the Americas. Hunter-gatherer groups spread quickly towards the south of the continent, but it is unclear when dogs reached Central and South America. To address this issue, we generated and analysed 70 complete mitochondrial genomes from archaeological and modern dogs ranging from Central Mexico to Central Chile and Argentina, revealing the dynamics of dog populations. Our results demonstrate that pre-contact Central and South American dogs are all assigned to a specific clade that diverged after dogs entered North America. Specifically, the divergence time between North, Central and South American dog clades is consistent with the spread of agriculture and the adoption of maize in South America between 7000 and 5000 years ago. An isolation-by-distance best characterizes how dogs expanded into South America. We identify the arrival of new lineages of dogs in post-contact South America, likely of European origin, and their legacy in modern village dogs. Interestingly, the pre-contact Mesoamerican maternal origin of the Chihuahua has persisted in some modern individuals.
The known terrestrial vertebrate fauna of the New Hebrides consists of 16 species of mammals (excluding feral domestic stock), 61 species of resident land- and freshwater birds, 20 species of reptiles and one amphibian. Of these, three, five, four and one species respectively have apparently been introduced by man. The non-introduced fauna is clearly Indo-Australian in origin, but some species have an exclusively Pacific island distribution and others (two bats, seven birds, and four lizards) are endemic. On the six islands visited 95 out of the possible 98 vertebrate species occur. Santo, the largest and most northerly island, supports the richest fauna. The comparative impoverishment of more southerly islands is not directly attributable to the progressive increase in isolation and distance from presumptive source area, nor to decrease in island area or maximum height.
INTRODUCTION: Leptospirosis is a complex zoonotic disease requiring high-resolution surveillance. A systems-thinking framework was used to connect genomic and ecological data and map the geographic and host-based structuring of co-circulating pathogenic Leptospira lineages in Puerto Rico. METHODS: Forty-four core genomes of L. interrogans, L. borgpetersenii, and L. kirschneri from human, domestic, and wildlife hosts were analyzed. Spatiotemporal and landscape metadata were integrated using root-to-tip regression, isolation-by-distance profiling and calibrated single-nucleotide polymorphism (SNP) thresholds (≤1, ≤5, and ≤10 SNPs) to define transmission clusters. RESULTS: Leptospira species exhibited distinct ecological pathways partitioned by geography, explaining 56% of genomic variance for L. interrogans and 91% for L. borgpetersenii (PERMANOVA). L. interrogans displayed high landscape connectivity across multiple hosts, forming localized networks (≤1 to ≤10 SNPs) that capture active spillovers (human-to-rat linkages at ≤1 SNP) and resolved into rodent host-specific lineages (R2 = 0.34). Conversely, L. borgpetersenii showed spatial and temporal genomic homogeneity and a lack of host-associated structure within an unpartitioned transmission pool dominated by Mus musculus. As a result, fixed genomic thresholds yielded disparate outcomes: L. interrogans resolved into 4 to 5 discrete, expanding clusters, whereas L. borgpetersenii grouped into a single uniform population at the ≤10-SNP threshold. CONCLUSION: Co-circulating pathogenic leptospires occupy distinct ecological niches shaped by varying host restriction and environmental persistence. Fixed genomic thresholds lack universal applicability; effective genomic epidemiological surveillance must employ species-specific threshold calibration to accurately map transmission pathways.
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Theoretical distributions of genetic distance between reproductively isolated taxa are derived by means of computer simulation, taking into account mutation and random genetic drift. The distributions obtained are in good agreement with the observed distributions of interracial and interspecific genetic distances for enzymes loci in Drosophila. This indicates that the gene substitution at enzyme loci can be explained by the neutral mutation theory.
Pathogens rarely mix freely throughout host populations, and the presence of barriers to transmission can be detected as patterns of increased genetic isolation among pathogen isolates. Despite the importance of transmission patterns in host societies, and the risk of epizootics from wildlife disease systems, barriers to open pathogen transmission are poorly understood in wild hosts. We tested the influence of host kinship and social structure on genetic divergence among strains of Mycobacterium bovis, the causative agent of bovine tuberculosis (bTB), in a wild badger population. We measured genetic distances between M. bovis isolates from badger hosts that varied in their own genetic similarity (a proxy for kinship) and in their social group affiliations. Using jack-knifing analyses to control for pseudoreplication, we found that genetic distances between pathogen isolates decreased with increasing kinship of host dyads, but only when hosts shared the same social group. Our findings suggest that the open transmission of bTB in wild hosts is constrained by a combination of social and kin structure, in particular the sharing of similar pathogen strains among kin within social groups. We discuss the implications of these transmission structures for the understanding and management of wildlife diseases.