Subspecies Differentiation Research Articles

Subspecies-specific sequence detection for differentiation of Mycobacterium abscessus complex

Mycobacterium abscessus complex (MABC) is a taxonomic group of rapidly growing, nontuberculous mycobacteria that are found as etiologic agents of various types of infections. They are considered as emerging human pathogens. MABC consists of 3 subspecies—M. abscessus subsp. bolletti, M. abscessus subsp. massiliense and M. abscessus subsp. abscessus. Here we present a novel method for subspecies differentiation of M. abscessus named Subspecies-Specific Sequence Detection (SSSD). This method is based on the presence of signature sequences present within the genomes of each subspecies of MABC. We tested this method against a virtual database of 1505 genome sequences of MABC. Further, we detected signature sequences of MABC in 45 microbiological samples through DNA hybridization. SSSD showed high levels of sensitivity and specificity for differentiation of subspecies of MABC, comparable to those obtained by rpoB sequence typing.

Did genetic lineage divergence or spatial environmental variance lead to global subspecies differentiation of northern goshawk (Accipiter gentilis)?

Abstract When a widely distributed species undergoes ecological or geological isolation, it tends to divide into subspecies. In general, subspecies differentiation is affected by environmental variance and genetic divergence. But the extent to which these two factors influence subspecies differentiation in species with different distribution ranges and modes of living, might be different. Despite having high breeding habitat fidelity, northern goshawk is a forest raptor that is widely dispersed. We investigated morphological traits in combination with the genetic background of northern goshawk individuals at a large global scale. We also collected genetic, palynological and climatic data to reveal what caused global subspecies differentiation in northern goshawk. Eurasian and North American subspecies populations are thought to have diverged approximately 660 000 years ago to undergo different evolutionary routes, which remarkably facilitated intercontinental subspecies differentiation through genetic lineage divergence. During the last glacial period (18 000 years ago) the different isolation levels of northern goshawk refugia on the continents caused genetic lineage divergences, which, however, are unlikely to have led to subspecies differentiation directly. Spatial environmental variance due to the wide distribution of northern goshawks made an important contribution to subspecies differentiation throughout continents.

Subspecies differentiation in an enigmatic chaparral shrub species.

Delimiting biodiversity units is difficult in organisms in which differentiation is obscured by hybridization, plasticity, and other factors that blur phenotypic boundaries. Such work is more complicated when the focal units are subspecies, the definition of which has not been broadly explored in the era of modern genetic methods. Eastwood manzanita (Arctostaphylos glandulosa Eastw.) is a widely distributed and morphologically complex chaparral shrub species with much subspecific variation, which has proven challenging to categorize. Currently 10 subspecies are recognized, however, many of them are not geographically segregated, and morphological intermediates are common. Subspecies delimitation is of particular importance in this species because two of the subspecies are rare. The goal of this study was to apply an evolutionary definition of "subspecies" to characterize structure within Eastwood manzanita. We used publicly available geospatial environmental data and reduced-representation genome sequencing to characterize environmental and genetic differentiation among subspecies. In addition, we tested whether subspecies could be differentiated by environmentally associated genetic variation. Our analyses do not show genetic differentiation among subspecies of Eastwood manzanita, with the exception of one of the two rare subspecies. In addition, our environmental analyses did not show ecological differentiation, though limitations of the analysis prevent strong conclusions. Genetic structure within Eastwood manzanita does not correspond to current subspecies circumscriptions, but rather reflects geographic distribution. Our study suggests that subspecies concepts need to be reconsidered in long-lived plant species, especially in the age of next-generation sequencing.

Optimization of Conditions for The Multiplex PCR for Diagnostics of Horse Strangles with Subspecies Differentiation of Streptococcus Equi Subsp Equi

As a result of the work performed, the conditions for setting up multiplex PCR with electrophoretic detection for the diagnosis of horse strangles were determined, allowing the identification and differentiation of S. equi subsp. equi in one reaction. It was found that the developed PCR protocol for the detection and species differentiation of S. equi subsp. equi with electrophoretic detection in a “multiplex” format has a high specificity and does not lead to amplification of PCR products with DNA of closely related microorganisms, saprophytic microflora, and bacterial pathogens. The sensitivity of the protocols for the detection and species differentiation of S. equi subsp. equi with electrophoretic detection was assessed. Diluted DNA samples of two S. equi subspecies were used as objects of research: S. equi subsp. equi and S. equi subsp. zooepidemicus. DNA samples were diluted by two-fold dilutions, starting from a concentration of 5 ng (which corresponds to 2 million 170 thousand copies in the genomic equivalent) to 1.19 * 10-6 ng (which corresponds to 0.71 copies in the genomic equivalent). DNA detection limit for S. equi subsp. equi was 66 copies in genomic equivalent or 152 fg, DNA of S. equi subsp. zooepidemicus – 132 copies in genomic equivalent or 305 fg.

Did genetic lineage divergence or spatial environmental variance lead to global subspecies differentiation of northern goshawk (Accipiter gentilis)

When a widely distributed species undergoes ecological or geological isolation, it tends to divide into subspecies. In general, subspecies differentiation is affected by environmental variance and genetic divergence. But the extent to which these two factors influence subspecies differentiation in species with different distribution ranges and modes of living, might be different. Despite having high breeding habitat fidelity, northern goshawk is a forest raptor that is widely dispersed. We investigated morphological traits in combination with the genetic background of northern goshawk individuals at a large global scale. We also collected genetic, palynological and climatic data to reveal what caused global subspecies differentiation in northern goshawk. Eurasian and North American subspecies populations are thought to have diverged approximately 660,000 years ago to undergo different evolutionary routes, which remarkably facilitated intercontinental subspecies differentiation through genetic lineage divergence. During the last glacial period (18,000 years ago) the different isolation levels of northern goshawk refugia on the continents caused genetic lineage divergences, which, however, are unlikely to have led to subspecies differentiation directly. Spatial environmental variance due to the wide distribution of northern goshawks made an important contribution to subspecies differentiation throughout continents.

Discrimination of Iranian honeybee populations (Apis mellifera meda) from commercial subspecies of Apis mellifera L. using morphometric and genetic methods

Abstract The morphological characters of honeybees have an important role for discriminating honeybee subspecies. In the present research, Iranian populations of honeybee (Apis mellifera) were collected from 19 areas in Iran. The samples were collected from stationary beekeeping sites. Moreover, pictures of honeybee forewings held in the Bee Data Bank in Oberursel were compared with Iranian honeybee populations. 19 morphological characters were measured for each forewing of worker honeybee to evaluate differentiation of Iranian honeybee populations from the commercial honeybee subspecies A. m. mellifera, A. m. carnica, A. m. caucasica and A. m. ligustica. Additionally, part of the tRNAleu gene, an intergenic region and part of COII was used to confirm differentiation of the commercial subspecies from Iranian honeybee populations. Results of the cluster analyses showed that 19 morphological characters of forewings differentiated Iranian populations from the commercial subspecies. Moreover, the phylogenetic tree of part of the tRNAleu gene, an intergenic region and part of COII differentiated the commercial subspecies from Iranian honeybee populations. Results of the discriminant function analyses (DFA) indicated that the references samples of A. m. meda overlapped with Iranian populations.

Development and application of indica\u2013japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding

Molecular markers are efficient and essential genotyping tools for molecular breeding and genetic analysis of rice. We developed two 96-plex indica–japonica single nucleotide polymorphism (SNP) genotyping sets for genetic analysis and molecular breeding in rice using the Fluidigm platform. Informative SNPs between indica and japonica were selected from SNP data of the Rice Diversity database, HapRice world SNP data of the Q-TARO database, and our 40 rice cultivar resequencing dataset. SNPs in set 1 were evenly distributed across all 12 rice chromosomes at a spacing of 4–5 Mb between adjacent SNPs. SNPs in set 2 mapped to the long genetic intervals in set 1 and included 14 functional or linked SNPs in genes previously cloned and associated with agronomic traits. Additionally, we used the SNP sets developed in this study to perform genetic diversity analysis of various cultivated and wild rice accessions, construction and validation of a subspecies diagnostic subset, linkage map construction and quantitative trait locus (QTL) analysis of a japonica × indica F2 population, and background profiling during marker-assisted backcrossing. Furthermore, we identified subspecies-specific SNPs and discuss their distribution and association with agronomic traits and subspecies differentiation. Our results indicate that these subspecies-specific SNPs were present in wild rice prior to domestication. This genotyping system will serve as an efficient and quick tool for genetic analysis and molecular breeding in rice.

Diversity of Pectobacterium strains by biochemical, physiological, and molecular characterization

Pectobacterium is a complex taxon of strains with diverse characteristics. It comprises several genera, including Erwinia, Brenneria, Pectobacterium, Dickeya, and Pantoea. Pectobacterium and Dickeya cause diseases in a wide range of plants, including potatoes, where they are causative agents of soft rot in tubers and blackleg in field-grown plants. Characterizing Pectobacterium species allows for the analysis of the diversity of pectinolytic bacteria, which may support control strategies for plant bacterial diseases. The aim of this study was to perform biochemical, physiological, and molecular characterizations of Pectobacterium spp. from different sites and host plants. The isolated strains were characterized by the glucose fermentation test, Gram staining, catalase activity, oxidase activity, growth at 37 ºC, reducing substances from sucrose, phosphatase activity, indole production, acid production from different sources (sorbitol, melibiose, citrate, and lactose), pathogenicity in potato, and hypersensitivity reactions. Molecular characterization was performed with species-specific primers ECA1f/ECA2r and EXPCCF/EXPCCR, which identify P. atrosepticum and P. carotovorum subsp. carotovorum (Pcc), respectively, and with primers 1491f/L1RA/L1RG and Br1f/L1RA/L1RG that differentiate Pcc from Dickeya chrysanthemi and from P. carotovorum subsp. brasiliensis. The strains were identified as belonging to the genus Pectobacterium, though they did not fit the biochemical nor the molecular classification standards for subspecies differentiation, indicating significant diversity among the strains.

The impact of genetic adaptation on chimpanzee subspecies differentiation.

Chimpanzees, humans' closest relatives, are in danger of extinction. Aside from direct human impacts such as hunting and habitat destruction, a key threat is transmissible disease. As humans continue to encroach upon their habitats, which shrink in size and grow in density, the risk of inter-population and cross-species viral transmission increases, a point dramatically made in the reverse with the global HIV/AIDS pandemic. Inhabiting central Africa, the four subspecies of chimpanzees differ in demographic history and geographical range, and are likely differentially adapted to their particular local environments. To quantitatively explore genetic adaptation, we investigated the genic enrichment for SNPs highly differentiated between chimpanzee subspecies. Previous analyses of such patterns in human populations exhibited limited evidence of adaptation. In contrast, chimpanzees show evidence of recent positive selection, with differences among subspecies. Specifically, we observe strong evidence of recent selection in eastern chimpanzees, with highly differentiated SNPs being uniquely enriched in genic sites in a way that is expected under recent adaptation but not under neutral evolution or background selection. These sites are enriched for genes involved in immune responses to pathogens, and for genes inferred to differentiate the immune response to infection by simian immunodeficiency virus (SIV) in natural vs. non-natural host species. Conversely, central chimpanzees exhibit an enrichment of signatures of positive selection only at cytokine receptors, due to selective sweeps in CCR3, CCR9 and CXCR6 -paralogs of CCR5 and CXCR4, the two major receptors utilized by HIV to enter human cells. Thus, our results suggest that positive selection has contributed to the genetic and phenotypic differentiation of chimpanzee subspecies, and that viruses likely play a predominate role in this differentiation, with SIV being a likely selective agent. Interestingly, our results suggest that SIV has elicited distinctive adaptive responses in these two chimpanzee subspecies.

The lipid profile of three Malassezia species assessed by Raman spectroscopy and discriminant analysis

Malassezia yeasts constitute the major eukaryotic cutaneous flora of homoeothermic vertebrates. These lipophilic yeasts are able to cause, trigger, or aggravate common skin diseases under favorable conditions. Species identification and subspecies differentiation is currently based on morphological characteristics, lipid assimilation profile, and molecular tests. Mass spectrometry has been also reported as a reliable, yet costly and labor-intensive, method to classify Malassezia yeasts. Here, we introduce Raman spectroscopy as a new molecular technique able to differentiate three phylogenetically close Malassezia species (M.globosa, M.pachydermatis, and M.sympodialis) by examining their lipid metabolic profile. Using Raman spectroscopy, lipid fingerprints of Malassezia cultures on Leeming-Notman agar, were analyzed by spectral bands assignment and partial least squares discriminant analysis. Our results demonstrate differential utilization of lipid supplements among these three species and the ability of Raman spectroscopy to rapidly and accurately discriminate them by predictive modelling.

Comparative analysis of mitochondrial genomes of the honey bee subspecies A. m. caucasica and A. m. carpathica and refinement of their evolutionary lineages

The complete mitochondrial genome sequences of the honey bee subspecies Apis mellifera caucasica and Apis mellifera carpathica were analyzed for the first time. The length of the mitochondrial DNA (mtDNA) sequences of A. m. caucasica and A. m. carpathica are 16,341 and 16,336 bps, respectively. Both sequences contain 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 AT-rich region. The overall composition of the nucleotides in the mtDNA of A. m. caucasica/A. m. carpathica is as follows: A (43.2/43.3%), C (9.5/9.6%), G (5.6/5.5%), and T (41.6/41.6%). Most of the mtDNA genes of both subspecies (ND2, COX1, COX2, ATP8, ATP6, COX3, ND3, ND6, CYTB, and 14 tRNA genes) are located on the heavy strand, and less (ND1, ND4, ND4L, ND5, SrRNA, LrRNA, and 8 tRNA genes) are located on the light strand. Phylogenetic analysis based on the complete mtDNA showed that both subspecies A. m. caucasica and A. m. carpathica are representatives of the C lineage. Thirty-five unique markers (ND5/XbaI and 34 SNPs) were found which enable the differentiation of the honey bee subspecies A. m. caucasica and A. m. carpathica. These genetic markers can contribute to purebred beekeeping and will help to prevent hybridization between these endangered honey bee subspecies in Europe.

Phylogeography and Population Genetics of Vicugna vicugna: Evolution in the Arid Andean High Plateau.

The vicuña (Vicugna vicugna) is the most representative wild ungulate of the high Andes of South America with two recognized morphological subspecies, V. v. mensalis in the north and V. v. vicugna in the south of its distribution. Current vicuña population size (460,000–520,000 animals) is the result of population recovery programs established in response to 500 years of overexploitation. Despite the vicuña’s ecosystemic, economic and social importance, studies about their genetic variation and history are limited and geographically restricted. Here, we present a comprehensive assessment of the genetic diversity of vicuña based on samples collected throughout its distribution range corresponding to eleven localities in Peru and five in Chile representing V. v. mensalis, plus four localities each in Argentina and Chile representing V. v. vicugna. Analysis of mitochondrial DNA and microsatellite markers show contrasting results regarding differentiation between the two vicuña types with mitochondrial haplotypes supporting subspecies differentiation, albeit with only a few mutational steps separating the two subspecies. In contrast, microsatellite markers show that vicuña genetic variation is best explained as an isolation by distance pattern where populations on opposite ends of the distribution present different allelic compositions, but the intermediate populations present a variety of alleles shared by both extreme forms. Demographic characterization of the species evidenced a simultaneous and strong reduction in the effective population size in all localities supporting the existence of a unique, large ancestral population (effective size ∼50,000 individuals) as recently as the mid-Holocene. Furthermore, the genetic variation observed across all localities is better explained by a model of gene flow interconnecting them rather than only by genetic drift. Consequently, we propose space “continuous” Management Units for vicuña as populations exhibit differentiation by distance and spatial autocorrelation linked to sex biased dispersal instead of population fragmentation or geographical barriers across the distribution.

Does divergent selection predict the evolution of mate preference and reproductive isolation in the tropical butterfly genus Melinaea (Nymphalidae: Ithomiini)?

Many studies have shown that speciation can be facilitated when a trait under divergent selection also causes assortative mating. In Müllerian mimetic butterflies, a change in wing colour pattern can cause reproductive isolation. However, colour pattern divergence does not always lead to reproductive isolation. Understanding how divergent selection affects speciation requires identifying the mechanisms that promote mate preference and/or choosiness. This study addresses whether shifts in wing colour pattern drives mate preference and reproductive isolation in the tropical butterfly genus Melinaea (Nymphalidae: Ithomiini), and focuses on five taxa that form a speciation continuum, from subspecies to fully recognized species. Using genetic markers, wing colour pattern quantification, male pheromone characterization and behavioural assays of mating preference, we characterize the extent of genetic and phenotypic differentiation between taxa and compare it to the level of reproductive isolation. We show strong premating isolation between the closely related species M.satevis and M.marsaeus, in addition to genetic and phenotypic (colour pattern and pheromones) differentiation. By contrast, M.menophilus and M.marsaeus consist of pairs of subspecies that differ for colour pattern but that cannot be differentiated genetically. Pheromonal differentiation of subspecies was significant only for M.marsaeus, although most individuals were indistinguishable. Melinaea menophilus and M.marsaeus also differ in the strength of assortative mating, suggesting that mate preference has evolved only in M.marsaeus, consistent with selection against maladaptive offspring, as subspecific 'hybrids' of M.marsaeus have intermediate, non-mimetic colour patterns, unlike those of M.menophilus which display either parental phenotypes. We conclude that a shift in colour pattern per se is not sufficient for reproductive isolation, but rather, the evolution of assortative mating may be caused by selection against maladaptive intermediate phenotypes. This study suggests that mate preference and assortative mating evolve when adaptive, and that even in the early stages of divergence, reproductive isolation can be nearly complete due to mating preferences.

Towards honey authentication: Differentiation of Apis mellifera subspecies in European honeys based on mitochondrial DNA markers

Honey is the natural sweet substance produced by Apis mellifera honeybees in Europe. Depending on the country/region, the A. mellifera subspecies native to Europe belong to three different lineages: A (A. m. iberiensis), M (A. m. iberiensis and A. m. mellifera) and C (A. m. ligustica and A. m. carnica). In this work, two DNA-based approaches were developed with the aim of entomological authentication of European honeys. A cytb specific PCR assay was proposed to identify A-lineage honeybees, while a second method based on real-time PCR coupled to high resolution melting analysis targeting the COI gene was developed to differentiate C- and M-lineages honeybees. The proposed methodologies were validated successfully with honeys of known origin and applied to the entomological authentication of 20 commercial samples from different European countries. The results highlight the predominance of honeys from C-lineage honeybees in Europe, except in Iberian Peninsula countries (honey from A-lineage honeybees).

Правовая помощь: опыт систематизации универсального уровня

We present the results of a legal study which devote to the identification of provisions regulating legal assistance in the international law norms. Based on the variability associated with some political and legal trends, we identify and characterize three groups of international treaties on legal assistance, to which the Russian Federation is a party (multidimensional, sectoral and special-military). It is emphasized that, in addition to the designated classification, it is necessary to point to international agreements on legal assistance, divided depending on the subject of their conclusion: between sovereign states; between sovereign states law enforcement agencies; between other authorities of sovereign states. We reveal the international treaties specialization tendency on legal assistance in relation to situationally relevant international relations, which form the basis of the subject of regulation. The conclusion is made about a certain typicity of international acts on legal assistance, based on their construction of the content and compositional aspect. We come to the conclusion that the category “assistance” is very popular at the international level, which confirms the relevance of the stated research topic. Moreover, at the international level, the key subject of regulation is legal assistance and its subspecies differentiation is carried out in the future.

Germany: Lanxess – iron oxide pigments

Six subspecies are currently recognized in the wild olive (Olea europaea L.): cuspidata, europaea, laperrinei, maroccana, cerasiformis, and guanchica. These occur in different natural distribution ranges in Europe, Africa, and Asia. Here we present an overview and summary of the accumulated information on the molecular diversity and gene flow in the species. Past climatic oscillations and geographical barriers have been identified to govern the pattern of genetic diversity and gene movement within and between taxa. Seed dispersal by animals and cultivar transport over vast geographical distances by man are important factors which have prevented the complete differentiation of subspecies. Available evidence has shown that subsp. cuspidata is the early diverging taxon of the olive complex. However, results were not fully consistent concerning the relationships between the other subspecies. Molecular studies using nuclear and cytoplasmic markers show that the oleasters (subsp. europaea var. sylvestris) are ancestors to the cultivated forms (subsp. europaea var. europaea). However, due to hybridization in geographical proximate regions sometimes other subspecies also have influenced the cultivars. This complex process has blurred the domestication history of the species. The wild relatives of the cultivated olive are endangered in many parts of their range, albeit being important for forest restoration. Overall, molecular studies have answered a number of important questions, but most of the genetic studies so far focused on the Mediterranean oleasters, while the widespread cuspidata has not been sufficiently investigated. Using genomic approaches to understand the pattern of genetic variation will be helpful to solve open questions. Moreover, future genetic studies should focus on quantifying the local effects of disturbance factors on genetic diversity and mating system parameters of wild olive.

Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle

BackgroundPectobacterium spp. are necrotrophic bacterial plant pathogens of the family Pectobacteriaceae, responsible for a wide spectrum of diseases of important crops and ornamental plants including soft rot, blackleg, and stem wilt. P. carotovorum is a genetically heterogeneous species consisting of three valid subspecies, P. carotovorum subsp. brasiliense (Pcb), P. carotovorum subsp. carotovorum (Pcc), and P. carotovorum subsp. odoriferum (Pco).ResultsThirty-two P. carotovorum strains had their whole genomes sequenced, including the first complete genome of Pco and another circular genome of Pcb, as well as the high-coverage genome sequences for 30 additional strains covering Pcc, Pcb, and Pco. In combination with 52 other publicly available genome sequences, the comparative genomics study of P. carotovorum and other four closely related species P. polaris, P. parmentieri, P. atrosepticum, and Candidatus P. maceratum was conducted focusing on CRISPR-Cas defense systems and pathogenicity determinants. Our analysis identified two CRISPR-Cas types (I-F and I-E) in Pectobacterium, as well as another I-C type in Dickeya that is not found in Pectobacterium. The core pathogenicity factors (e.g., plant cell wall-degrading enzymes) were highly conserved, whereas some factors (e.g., flagellin, siderophores, polysaccharides, protein secretion systems, and regulatory factors) were varied among these species and/or subspecies. Notably, a novel type of T6SS as well as the sorbitol metabolizing srl operon was identified to be specific to Pco in Pectobacterium.ConclusionsThis study not only advances the available knowledge about the genetic differentiation of individual subspecies of P. carotovorum, but also delineates the general genetic features of P. carotovorum by comparison with its four closely related species, thereby substantially enriching the extent of information now available for functional genomic investigations about Pectobacterium.

Subspecies differentiation and genotyping of Francisella tularensis strains isolated from clinical and environmental samples.

Molecular epidemiology is one of the most rapidly developing research area. In the light of past and modern technologies it has gained number of typing methods based on molecular biology techniques. In this report, the subspecies differentiation of Francisella tularensis and genotyping of strains isolated in Poland and other geographic locations were investigated using real-time PCR and multispacer typing (MST) methods respectively. In total, 49 strains of F.tularensis included 15 strains from Poland, for subspecies differentiation the real-time PCR method was applied. For molecular typing using MST method four intergenic spacers (IS) were sequenced and compared with those previously described and deposited in GenBank (NCBI). Phylogenetic testing was performed using with the UPGMA model using MEGA6 software. The real-time PCR enables to distinguish five strains belonged to type A and 44 to type B among deposited F.tularensis strains. The MST revealed previously described genotypes, as well as 23 new genotypes were detected. The use of real-time PCR and MST method are valuable in the analysis of F.tularensis. SIGNIFICANCE AND IMPACT OF THE STUDY: This study demonstrate convenient molecular tools (real-time PCR and multispacer typing) for Francisella tularensis detection, differentiation and genotyping which can be applied for molecular epidemiological studies and providing useful information for scientific research and during natural tularaemia outbreaks.

Population and Subspecies Differentiation in a High Latitude Breeding Wader, the Common Ringed Plover Charadrius hiaticula

Exploring the patterns of genetic structure in the context of geographical and phenotypic variation is important to understand the evolutionary processes involved in speciation. We investigated population and subspecies differentiation in the Common Ringed Plover Charadrius hiaticula, a high latitude wader that breeds in arctic and temperate zones from northeast Canada across Eurasia to the Russian Far East. Three subspecies, hiaticula, tundrae and psammodromus, are currently widely recognised, whereas a fourth subspecies, kolymensis, has been proposed based on geographic isolation and phenotypic differences. We genotyped 173 samples from eleven Common Ringed Plover breeding sites, representing all four putative subspecies, at eight polymorphic microsatellite loci to examine the patterns of population and subspecies differentiation. Bayesian clustering identified three genetic clusters among samples, corresponding to the breeding sites of the three currently recognised subspecies. The existence of the subspecies kolymensis was not supported. We also detected the presence of a previously unknown hybridisation zone extending from Northern Scandinavia to Belarus. Differentiation of the subspecies tundrae and hiaticula most likely occurred in allopatry on the Eurasian continent during past glaciation events, followed by population expansion leading to colonisation of Iceland and Greenland. The lack of genetic differentiation within the tundrae subspecies is consistent with ongoing range expansion and high gene flow maintained through migratory behaviour. We discuss the importance of historic climate changes, migratory behaviour and mating system on shaping the observed pattern of genetic differentiation.

Demographic inference in barn swallows using whole‐genome data shows signal for bottleneck and subspecies differentiation during the Holocene

Accounting for historical demographic features is vital for many types of evolutionary inferences, including the estimation of divergence times between closely related populations. In barn swallow, Hirundo rustica, inferring historical population sizes and subspecies divergence times can shed light on the recent co-evolution of this species with humans. Pairwise sequentially Markovian coalescent uncovered population growth beginning on the order of one million years ago-which may reflect the radiation of the broader Hirundo genus-and a more recent population decline. Additionally, we used approximate Bayesian computation to evaluate hypotheses about recent timescale barn swallow demography, including population growth due to human commensalism, and a potential founder event associated with the onset of nesting on human structures. We found signal for a bottleneck event approximately 7,700years ago, near the time that humans began building substantial structures, although there was considerable uncertainty associated with this estimate. Subspecies differentiation and subsequent growth occurred after the bottleneck in the best-supported model, an order of magnitude more recently than previous estimates in this system. We also compared results obtained from whole-genome sequencing versus reduced representation sequencing, finding many similar results despite substantial allelic dropout in the reduced representation data, which may have affected estimates of some parameters. This study presents the first genetic evidence of a potential barn swallow founder effect and subspecies divergence coinciding with the Holocene, which is an important step in analysing the biogeographical history of a well-known human commensal species.