Intraspecific Genetic Structure Research Articles

Ecological characteristics explain neutral genetic variation of three coastal sparrow species.

Eco-phylogeographic approaches to comparative population genetic analyses allow for the inclusion of intrinsic influences as drivers of intraspecific genetic structure. This insight into microevolutionary processes, including changes within a species or lineage, provides better mechanistic understanding of species-specific interactions and enables predictions of evolutionary responses to environmental change. In this study, we used single nucleotide polymorphisms (SNPs) identified from reduced representation sequencing to compare neutral population structure, isolation by distance (IBD), genetic diversity and effective population size (Ne) across three closely related and co-distributed saltmarsh sparrow species differing along a specialization gradient-Nelson's (Ammospiza nelsoni subvirgata), saltmarsh (A. caudacuta) and seaside sparrows (A. maritima maritima). Using an eco-phylogeographic lens within a conservation management context, we tested predictions about species' degree of evolutionary history and ecological specialization to tidal marshes, habitat, current distribution and population status on population genetic metrics. Population structure differed among the species consistent with their current distribution and habitat factors, rather than degree of ecological specialization: seaside sparrows were panmictic, saltmarsh sparrows showed hierarchical structure and Nelson's sparrows were differentiated into multiple, genetically distinct populations. Neutral population genetic theory and demographic/evolutionary history predicted patterns of genetic diversity and Ne rather than degree of ecological specialization. Patterns of population variation and evolutionary distinctiveness (Shapely metric) suggest different conservation measures for long-term persistence and evolutionary potential in each species. Our findings contribute to a broader understanding of the complex factors influencing genetic variation, beyond specialist-generalist status and support the role of an eco-phylogeographic approach in population and conservation genetics.

Comparative landscape genomics has arrived with a splash.

Comparative methods are central for understanding the distribution of biodiversity. Assessing spatial variation of multiple species can identify biodiversity drivers across landscapes, including on the genetic level. Molecular ecology approaches have expanded in spatial precision, from phylogeography to landscape genetics, as have molecular tools that now allow genome-scale inferences for virtually any organism. These welcome increases in genomic data richness, however, have not been matched by growth in the multispecies dimension, and empirical studies continue to focus predominantly on single species. In this issue of Molecular Ecology, Zbinden etal. (Molecular Ecology, 2022, 32) present a landmark achievement for comparative landscape genomics, surveying an impressive 31 species of fishes, sampled from 75 locations in the White River Basin and genotyping each species for thousands of SNPs. Zbinden etal. (Molecular Ecology, 2022, 32) draw upon the statistical tools of landscape genetics to comprehensively interrogate four hypotheses-that populations of multiple freshwater fish species are isolated by river distance, barriers to dispersal, stream hierarchy or environment. Stream hierarchy overwhelmingly predicts population structure within co-distributed fish species pointing to commonalities among species at the large landscape scale (100s of km). The tight alignment between intraspecific genetic spatial structure and stream hierarchies, moreover, provides clear validation for conservation and fisheries management to use watershed divisions as distinct management units.

Relevance of molecular systematics in insect pest management

Insects (Insecta, Arthropoda), undeniably represent the most triumphant group of living organisms, in terms of evolutionary achievement, existing on earth. With over one million described species, they account for more than 75 percent of all known species, and it is estimated that at least 4-5 million insect species still remain undiscovered and undescribed (Stork, 2018). They represent one of the largest components of biodiversity in the world, closely associated with human's wellbeing in different forms like pests, natural enemies, producers of economic products and facilitators of pollination. In contemporary times, despite notable progress in agricultural output and economic prosperity in many regions, the problem of food insecurity persists as a significant concern affecting substantial segments of the global population (Palli, 2022). To cater the food demand of the fast expanding global population, intensive agricultural practices like extensive use of chemical fertilizers and insecticides, greater tillage and irrigation, as well as heavy mechanization are followed. The result is frequent outbreak of phytophagous insect pests along with a rapid decline in the biodiversity of beneficial insects including natural enemies and pollinators. It is estimated that crop losses caused by insects are a major problem in both developed and developing countries, destroying 18 to 20 per cent of the annual crop production globally, having worth over US$ 470 billion (Srivastava and Chakravarty, 2021). Initially, when pesticides were used to control or prevent insect pest outbreaks, the chemicals were often applied as soon as a problem was perceived, without accurate identification of the insect's identity or discovery of why the problem had developed in the first place. This lack of understanding of the cause of outbreak meant that the same problem could reoccur. Sustainable pest management requires a more scientific approach. The first step in this direction is the correct identification of the insect species. Accurate species identification, whether of the pest or its associated natural enemy along with their biological systematic studies provide backbone information for the success of any integrated pest management programme (Chakravarty et al., 2022). Traditional systematics or taxonomy was primarily reliant on morphology-based taxon identification systems. However, the process of morphological identification poses significant challenges in numerous insect taxa, mostly attributable to the absence of dependable diagnostic traits or the presence of cryptic species complexes (Shashank et al., 2022). Moreover, due to a decrease in the number of proficient morpho-taxonomists, specifically those specializing in lesser-known insect groups, there is a need for alternate approaches to species identification. Presently, entomologists are leveraging a wide array of molecular techniques that were previously untapped, while also embracing novel technologies under the paradigm of a "technology-driven revolution" in the field of systematics (Srivastava et al., 2019). Molecular techniques present a highly advantageous strategy for the identification and classification of insects, offering distinct benefits when compared to traditional morphological methods. Over the past twenty years, DNA barcoding has emerged as a swift and dependable technique for the identification of species, thereby revitalizing the field of taxonomic study. It refers to the technique, where short fragment of the conserved mitochondrial cytochrome c oxidase subunit I (COI) gene, the “DNA barcode,” is sequenced from a taxonomically undesignated specimen and comparisons are made with the DNA sequence of species of known origin for establishing a species level identification (Hebert et al., 2003). This approach has been frequently employed in various studies focusing on insects (and other arthropods in general), leading to the identification of previously unknown or cryptic species. Additionally, it has helped identify species complexes and evolutionary significant units, thereby establishing a basis for further comprehensive integrative taxonomic research (Firake and Behere, 2021). DNA barcoding considerably facilitates the monitoring of invasive species, vectors, and economically important endangered and/or endemic arthropod species. Furthermore, the utilization of DNA metabarcoding in ecological and surveillance initiatives has become increasingly prevalent. This approach enables the rapid evaluation of biodiversity in certain geographical regions, as well as the study of arthropod biosystems and communities that would otherwise be inaccessible. In recent times, entomologists in India have efficiently identified various invasive insect pest species, such as the elephant beetle, tomato pinworm, rugose spiralling whitefly, coconut case caterpillar, fall armyworm, and cassava mealy bug, by incorporating molecular systematics either as the sole method or in conjunction with traditional taxonomical tools (Srivastava and Chakravarty, 2021). In addition, there have been endeavours to offer extensive data through molecular characterization and/or DNA barcoding of indigenous organisms that serve as natural enemies and pollinators within diverse agricultural systems of India (Srivastava et al., 2019). A good number of insect genomes, particularly the mitochondrial genome have also been wholly sequenced in the country, including both crop pests and beneficial insects (Firake and Behere, 2021). However, our nation renowned for its exceptional biodiversity, exhibits a mere 3.73% coverage of DNA barcodes for its documented insect species. Notably, the orders Lepidoptera and Hemiptera are the most extensively represented in this limited dataset (Shashank et al., 2022). Such a delay in developing DNA barcode reference libraries for insects will set us back in our efforts to effectively document and preserve our rich biodiversity. The introduction of molecular systematics has also precipitated a revolution in our understanding of intraspecific genetic diversity and population genetic structure of several key insect pest species of agricultural importance in the country, helpful to detect the changes they adapt to overcome hurdles of various selection pressures including insecticides (Chakravarty et al., 2020). A necessity for the development of effective and safe management techniques for a target pest is the acquisition of comprehensive knowledge pertaining to its population structure and dynamics. Despite the emergence of inconsistencies between morphological and molecular phylogenies, as well as conflicting results from different molecular research, the utilization of phylogenomic analysis has proved helpful in resolving numerous controversial connections within insects. Over the past decade, our working group has devoted its research efforts entirely to this particular issue. Based on the molecular characterization with RAPD markers (Deepa and Srivastava, 2011) and COI gene (Chakravarty et al., 2021), phenotyping of immature and adult stages (Chakravarty and Srivastava, 2020; Chakravarty et al., 2023b), and other biological traits (Chakravarty et al., 2019 and 2023a), existence of sub-specific level variations among Helicoverpa armigera populations from diverse agro-ecologies of India has been deciphered. Similar studies for Leucinodes orbonalis (Padwal et al., 2022), Spodoptera litura (Ganguly et al., 2023) and Maruca vitrata (Mahalle et al., 2022) revealed genetic homogeneity for these pest species in the country. Further, Mahalle et al. (2023) have also screened publically accessible expressed sequence tag resources to identify microsatellites and evaluate their suitability as DNA markers for investigating gene flow patterns among populations of M. vitrata from pigeonpea fields throughout India. Molecular systematics has also proven to be a valuable tool in the identification of convergent evolution phenomena, such as the emergence of eusocial behaviours and caste systems among Hymenoptera (Berens et al., 2015); comprehending predator-prey dynamics within trophic food web investigations (Novotny and Miller, 2014), as well as resolving challenges associated with limited specimen availability or local species populations (Deng et al., 2019). Nevertheless, it is important to note that relying solely on molecular analyses to determine the identity of a species or assess population diversity can be precarious. This is due to potential biases introduced by the improper utilization of neighbor-joining trees, fixed distance thresholds, bootstrap resampling, interpretation of the barcoding gap, as well as limitations associated with DNA barcode repositories such as the Barcode of Life Data Systems (BOLD) and the National Centre for Biotechnology Information (NCBI). For instance, in a study conducted by Kvist (2013), it was found that 42% of invasive insects were not included in the BOLD database. Furthermore, the outcomes of phylogenetic analyses can be affected by various factors, such as the occurrence of recent speciation events, the presence of paraphyly, inadequate taxonomy, interspecific hybridization, and the high prevalence of endosymbiotic bacteria like Wolbachia, that hinders the replication or detection of the target sequence from insect specimens during the polymerase chain reaction, as highlighted by Shashank et al. (2022). Therefore, it is recommended that molecular methodologies should be utilized in conjunction with, rather than in lieu of, morphological identification in order to achieve optimal outcomes (Chakravarty et al., 2023b). Last but not the least, a note of appreciation for the “Journal of Environmental Biology” is also appropriate at this juncture. We are pleased to share our research experience and expertise through this editorial in the aforementioned journal, with which we have been affiliated for several years in various roles such as author, reviewer, and editor. This open access journal is notable for its comparatively modest processing charges, which enable researchers to publish their original work at an affordable cost. The enduring anticipation for highly critical reviews has contributed to the continued prominence of this journal within the realm of environmental science and related disciplines. We appreciate the visions of late Professor R.C. Dalela and his dedicated team, who have worked tirelessly over the years to make this journal a valuable resource for the global environmental outlook, with the ultimate aim of promoting societal well-being. Currently, the responsibility of overseeing this journal rests with Dr. Divakar Dalela, the Executive Editor, and Dr. Sumati Gaumat, the Editor, together with their dedicated publication team. They are diligently working towards upholding the international standards of this esteemed journal. We extend our best wishes for the continued success of the journal in the years to come.

Phylogeography, genetic diversity, and intraspecific genetic structure of the black-horned capuchin (Sapajus nigritus).

Recent molecular studies have clarified the overarching taxonomy of capuchin monkeys, but intraspecific genetic diversity remains unexplored for most capuchin species. One example is Sapajus nigritus, the southernmost capuchin monkey, found in Brazil and Argentina; its phenotypic diversity has been recognized as two geographic subspecies, but the intraspecific genetic structure of this taxon is poorly known. Here, we sampled across most of this species' geographic distribution, producing a newly sequenced data set for genetic analyses that included 78 individuals from 14 populations. We investigated the intraspecific diversity, genetic structure, and evolutionary history using three mitochondrial markers. Our results indicated that S. nigritus populations exhibited high levels of genetic structure. We found strong support for two monophyletic clades within this species with a deep phylogenetic split, and clear separation from other related taxa. Vicariance events seem to have played a prevalent role in shaping S. nigritus genetic differentiation. The Paraíba do Sul River may have driven the deep divergence between southern and northern clades, whereas the Tietê River may have had a weaker, more recent effect on the divergence of populations within the southern clade.

Phylogeography of two codistributed terrestrial snails in the Maputaland–Pondoland–Albany biodiversity hotspot, South Africa

Abstract We investigated the evolutionary patterns of two forest-dwelling endemic terrestrial snails (Gittenedouardia spadicea and Maizania wahlbergi) in the Maputaland–Pondoland–Albany biodiversity hotspot in South Africa to examine the degree of phylogeographical congruence between the two species. Phylogenetic relationships and divergence time estimations within each species were inferred using the combined mitochondrial DNA (mtDNA) sequence dataset for the cytochrome c oxidase subunit I (COI) and large subunit ribosomal RNA (16S rRNA). In addition, the rapidly evolving COI datasets were used to infer intraspecific genetic structure and population differentiation within both species. Phylogeographical concordance factor (PCF) analysis was used to statistically estimate the degree of congruence between the two species at localities where both species were sampled. Phylogenetically, G. spadicea exhibited two clades that diverged during the Plio/Pleistocene, while M. wahlbergi formed a single shallow clade that showed Pleistocene divergence. The haplotype networks for the COI locus demonstrated evidence of geographical and genetic isolation within both species. PCF analysis demonstrated partial phylogeographical concordance, suggesting that the two species may have been affected by similar ancient climatic events. Traits other than poor dispersal capabilities and limited gene flow may also influence how a species responds to fluctuating climate change.

Applying molecular genetic data at different scales to support conservation assessment of European Habitats Directive listed species: A case study of Eurasian otter in Austria.

Evaluating intraspecific genetic structure and diversity is fundamental to assessing a species' conservation status, but direct incorporation of such information into legal frameworks such as the EU's Habitats Directive is surprisingly rare. How genetic structure aligns with EU member state boundaries or biogeographic regions may be very important in designing management plans or achieving legislative goals. The Eurasian fish otter experienced a sharp population decline during the 20th century but is currently re-expanding in several countries. The species is listed under Annex II and IV of the European Habitats Directive, and member states are obliged to assess the species separately across different biogeographic regions. We genotyped 2492 otter spraints across four provinces in Austria, collected between 2017 and 2021. A total of 384 different genotypes were identified, supporting densities along river habitats from 0.1 to 0.47 otters per river km (mean: 0.306), with a resampling-based simulation supporting limited density overestimation at survey lengths of 20 km or more. Three distinct genetic clusters were revealed, two of them presumably reflecting two relict populations whereas the source of the third cluster is unknown. The geographic extent of the three clusters does not coincide with provincial or biogeographic boundaries, both relevant for assessment and management within existing national or European legislative frameworks. We advocate more consideration of genetic structure in the assessment and conservation management planning of species listed in the European Habitats Directive.

Demographic history and conservation aspects of two relict shrubs (Daphnimorpha spp., Thymelaeaceae) showing disjunct and restricted distribution in the southern part of Japan

Climate relicts are of particular importance in evolutionary biology because of the strategies they may adopt for long-term survival despite climatic oscillations. However, because their current distribution is usually restricted and fragmented, many climatic relicts are at risk of extinction. Daphnimorpha (Thymelaeaceae) is a genus endemic to Japan that comprises two species (D. capitellata and D. kudoi) with a disjunct distribution in southern Japan. These two shrub species are endemic to a single mountain range. In this study, we conducted population genetic analyses using genome-wide single nucleotide polymorphisms obtained from multiplexed inter-simple sequence repeats genotyping by sequencing to reveal the phylogeographic history and obtain conservation implications for the two species. The results showed that these two species may have been isolated since the Tertiary period, supporting their status as climate relicts. In addition, D. kudoi showed clear genetic differentiation between the two mountains where it occurred (Mt. Nagata and Mt. Kuromi), with a decline in the effective population sizes inferred during the last glacial period. In contrast, D. capitellata showed no clear intraspecific genetic structure, and its effective population size was relatively stable. These differences could result in contrasting light tolerance between species. For conservation, we recommend managing these species as three evolutionarily significant units (ESUs): D. capitellata, D. kudoi population on Mt. Nagata, and D. kudoi population on Mt. Kuromi. Considering the limited gene flow among subpopulations and small population census, all ESUs require conservation attention to maintain or increase their effective population sizes.

Genetic structure of Aedes albopictus (Diptera: Culicidae) populations in China and relationship with the knockdown resistance mutations

BackgroundMosquito control is needed to prevent dengue fever, which is mainly spread by Aedes albopictus in China. Application of insecticides is one of the main mosquito control methods; however, this approach can fail due to the knockdown resistance (kdr) gene mutation that causes decreased sensitivity to insecticides in Ae. albopictus. The kdr mutation patterns among different regions in China differ significantly. However, the underlying mechanism and factors that influence kdr mutation remain unclear. To explore the potential influence of genetic background on the development of insecticide resistance in Ae. albopictus, we analyzed the genetic structure of Ae. albopictus populations in China and its correlation with major kdr mutations.MethodsWe collected Ae. albopictus from 17 sites in 11 provinces (municipalities) across China from 2016 to 2021 and extracted the genomic DNA from individual adult mosquitoes. We selected eight microsatellite loci for genotyping, and based on microsatellite scores, we estimated intraspecific genetic diversity, population structure, and effective population size. The association between the intrapopulation genetic variation and F1534 mutation rate was evaluated by the Pearson correlation coefficient.ResultsBased on variation analysis of the microsatellite loci of 453 mosquitoes representing 17 populations throughout China, more than 90% of the variation occurred within individuals, whereas only about 9% of the variation occurred among populations, indicating that field populations of Ae. albopictus are highly polymorphic. The northern populations tended to belong to gene pool I (BJFT 60.4%, SXXA 58.4%, SDJN 56.1%, SXYC 46.8%), the eastern populations tended to belong to pool III (SH 49.5%, JZHZ 48.1%), and the southern populations tended to belong to three different gene pools. Moreover, we observed that the greater the fixation index (FST), the lower the wild-type frequency of F1534 of VSGC.ConclusionsThe degree of genetic differentiation among Ae. albopictus populations in China was low. These populations were divided into three gene pools, in which the northern and eastern pools are relatively homogeneous, while the southern gene pool is heterogeneous. The possible correlation between its genetic variations and kdr mutations is also noteworthy.Graphical

Intraspecific Genetic Structure of the Gray Wolf, Canis lupus, Linnaeus, 1758—Current State of Knowledge

Intraspecific Genetic Structure of the Gray Wolf, Canis lupus, Linnaeus, 1758—Current State of Knowledge

The importance of considering the evolutionary history of polyploids when assessing climatic niche evolution

AbstractAimAlthough whole‐genome duplication (WGD) is an important speciation force, we still lack a consensus on the role of niche differentiation in polyploid evolution. In addition, the role of genome doubling per se vs. later divergence on polyploid niche evolution remains obscure. One reason for this might be that the intraspecific genetic structure of polyploid complexes and interploidy gene flow is often neglected in ecological studies. Here, we aim to investigate to which extent these evolutionary processes impact our inference on niche differentiation of autopolyploids.LocationEurope.TaxonArabidopsis arenosa (Brassicaceae).MethodsLeveraging a total of 352 cytotyped populations of diploid‐autotetraploid A. arenosa, we examined differences among climatic niches of diploid and tetraploid lineages both globally, and independently for each tetraploid lineage with respect to the niche of its evolutionary closest relative. Then, we tested whether there was an effect of additional interploidy introgression from other sympatric but ancestrally divergent diploid lineages of A. arenosa on climatic niches of tetraploids.ResultsEcological niche shift of tetraploids is only detected when the assignment of populations to intraspecific genetic lineages is considered. We found different patterns of climatic niche evolution (i.e. niche conservatism, contraction or expansion) in each tetraploid lineage when compared to its evolutionary closest relatives. We observed an effect of interploidy gene flow in patterns of climatic niche evolution of the tetraploid ruderal lineage of A. arenosa.Main conclusionsThe niche shift of tetraploids in A. arenosa is not driven by WGD per se but rather reflects dynamic post‐WGD evolution in the species, involving tetraploid migration out of their ancestral area and interploidy introgression with other diploid lineages. Our study supports that evolutionary processes following WGD—which usually remain undetected by studies neglecting evolutionary history of polyploids—may play a key role in the adaptation of polyploids to challenging environments.

Development and characterization of microsatellite markers in the African timber tree species Cylicodiscus gabunensis (Fabaceae).

Cylicodiscus gabunensis (Fabaceae) or 'Okan' is a Central African multipurpose timber species that is used for heavy construction and traditional medicine. Despite being currently heavily exploited, the species shows a low population density and a natural regeneration deficit in dense forest. We aimed to characterize polymorphic microsatellite markers that can be used to study patterns of genetic structure and gene flow (mating system, pollen and seed dispersal and inbreeding depression) and ultimately, help to develop sustainable forest management practices. We developed 24 polymorphic markers that can be amplified in three PCR multiplexes that were tested in 647 individuals of C. gabunensis from three populations. The number of alleles ranged from 4 to 27 and the average observed and expected heterozygosity across loci and populations were Ho = 0.585 (0.081-0.936) and He = 0.510 (0.076-0.914), respectively. This set of markers is a useful tool for exploring intra-specific diversity, genetic structure and gene flow of C. gabunensis.

A new set of microsatellite markers for Phoxinus lumaireul senso lato, Phoxinus marsilii and Phoxinus krkae for population and molecular taxonomic studies.

Minnows of the genus Phoxinus are common and an often highly abundant fish species in Palearctic freshwater habitats. Phoxinus species have a complex evolutionary history, phylogenetic relationships are not well understood and there are a number of unresolved taxonomic problems. There are currently 23 different mitochondrial genetic lineages identified in the genus Phoxinus, 13 of which are recognized as valid species. The taxonomic status of these lineages requires resolution, including the degree to which they can interbreed. Suitable nuclear molecular markers for studies of population divergence and interbreeding between morphotypes and mitochondrial lineages are lacking for Phoxinus species. Therefore, the authors developed a set of microsatellite markers using genomic information from Phoxinus lumaireul and tested their suitability for this and two related species, Phoxinus krkae and Phoxinus marsilii. Out of 16 microsatellite candidate loci isolated, 12 were found to be in Hardy-Weinberg equilibrium when tested on two P. lumaireul senso lato populations. Seven loci amplified across the three species, enabling the study of intraspecific genetic diversity and population structure within P. marsilii and P. krkae. The markers were able to clearly resolve differences among the three tested species, including the recently described P. krkae, and are therefore suitable for the detection of introgression and hybridization among populations consisting of mixtures of two or more of P. lumaireul s. l., P. marsilii and P. krkae.

Historical persistence and isolation by distance of

Context Empirical studies of intraspecific genetic diversity and population structure can inform the evolutionary and demographic history of individual species and of landscapes at the bioregional level. Aims We aimed to assess intraspecific genetic variation at macroevolutionary and microevolutionary temporal scales for Mirbelia viminalis, a key species present on the Hamersley Range in the ancient and highly diverse landscape of the Pilbara bioregion of northwest Western Australia. Methods We sampled extant populations and assessed diversity and structure using sequences (chloroplast DNA, 1759 base pairs) and microsatellite markers (nuclear DNA, 15 loci) data. Key results Significant phylogeographic structure and a lack of historical demographic signals of population contraction or expansion suggest historical population persistence. Moderate chloroplast haplotype diversity (h = 15) and moderate divergence among extant haplotypes indicates a degree of historical connectivity via seed dispersal across central populations on the Hamersley Range. Levels of nuclear genetic diversity were low to moderate (allelic richness = 3.554, expected heterozygosity = 0.489, observed heterozygosity = 0.462) and depauperate compared to another member of the Mirbelia genus present further south in the Midwest region. Nuclear diversity revealed a strong signal of isolation by distance with localised admixture among populations and some contemporary genetic clustering along a north-west to south-east transect of the Hamersley Range. Conclusions Low nuclear genetic diversity may be related to recent reductions in population size for M. viminalis. Historical population persistence with few barriers to dispersal other than geographic distance may be common for members of the Fabaceae across the Hamersley Range.

One Species, Hundreds of Subspecies? New Insight into the Intraspecific Classification of the Old World Swallowtail (Papilio machaon Linnaeus, 1758) Based on Two Mitochondrial DNA Markers.

Simple SummaryThe Old World swallowtail Papilio machaon Linnaeus, 1758 is one of the most iconic butterflies, and like many butterflies, it was, and still is, a popular collecting item. P. machaon is characterised by a very high individual variability, which, combined with the great interest of collectors and amateur entomologists, has been converted into the descriptions of over 100 colour forms, aberrations and subspecies. The present study examines two mitochondrial DNA sequences (mtDNA) of 16S rDNA, and cytochrome b of 87 specimens of P. machaon collected in the entire Palearctic Region and their correlation with intraspecific classification. The results of our research showed that the proposed intraspecific classification by different authors does not correlate with the variability in mitochondrial DNA sequences.The Old World swallowtail Papilio machaon Linnaeus, 1758 is one of the most well-known and most characteristic members of the family Papilionidae. Over the past two centuries, the butterfly has been the subject of many studies. P. machaon is characterised by a tendency to change the wing colour pattern. In turn, due to the great interest of collectors and amateur entomologists, these studies have been converted into the description of over 100 colour forms, aberrations and subspecies. In this study, mitochondrial DNA (mtDNA), 16S rDNA and cytochrome b sequences were used to examine the correlation between the intraspecific classification and genetic structure of P. machaon. The study used 87 specimens from 59 different localities covering the geographic distribution of this species in the Palaearctic. The phylogenetic relationships within and between the Old World swallowtail subspecies showed that the intraspecific classification proposed by various authors does not correlate with the variability in mitochondrial DNA sequences. In addition, populations occurring at the species distribution borders in the Palaearctic Region (i.e., Japan, Kamchatka, Morocco and Sakhalin) are genetically distinct from other species.

Intra- and interspecific comparison of protein polymorphism to establish genetic differentiation in two sympatric species of Drosophila: D. bipectinata and D. malerkotliana.

Drosophila bipectinata species complex includes four monophyletic closely related sympatric species with perfect reproductive isolation in natural conditions. Among these, two species, i.e., D. bipectinata and D. malerkotliana are known to be more prevalent in their occurrence all along their distribution area of Oriental-Australian regions. Genetic characteristics of these two species have been studied by earlier researchers mainly by focusing on their chromosomal polymorphism to gain knowledge pertaining to their evolutionary trend. The present work is one step farther, as we considered isozyme variants of three polymorphic enzymes to envisage genetic differentiation among the different natural populations of these two species, along with, a comparative perusal of their certain population genetic parameters. Natural populations of these two species were sampled from eight places aligned on the north-south axis of India and were subjected to isozyme analysis. The collection of both species and the geographical locations were kept same to avoid the effect of temporal or seasonal factors on the distribution of their allelic frequency. The results of this study clearly indicate that there is intraspecific genetic structuring among the populations of both the species with a distinct steady increase in the level of heterozygosity from north to south. The evolutionary tree in the form of dendrogram depicts two genetically differentiated groups of natural populations, one for north and other for South India. Most essential aspect that has been noticed through this study is the evolutionary trend of these two sympatric species being largely similar all along the north-south axis of India.

Evidence for Genetic Hybridization between Released and Wild Game Birds: Phylogeography and Genetic Structure of Chukar Partridge, Alectoris chukar, in Turkey

The Chukar Partridge (Alectoris chukar, Galliformes) is one of the most important game birds in its native range, spanning from the Balkans to eastern Asia, and the regions of Europe, North America and New Zealand where it was introduced. Previous studies found two main genetic lineages of the species forming an eastern and a western clade. Chukar Partridges are raised in game farms and released to supplement natural populations for shooting in the USA, Canada, Greece, and Turkey. To explore intraspecific genetic structure, phylogeography, and possible genetic admixture events of A. chukar in Turkey, we genotyped individuals from fourteen wild and five captive populations at two mitochondrial and ten microsatellite DNA loci in. Wild and farmed Chukar Partridge samples were analyzed together to investigate possible influences of intraspecific hybridizations. We found that the farmed chukars, which mainly (85%) cluster into the eastern clade, and wild ones were genetically distinct. The latter could be separated into six management units (MUs), with partridges from Gökçeada Island in the Aegean Sea forming the most divergent population. Intraspecific hybridization was detected between wild and captive populations. This phenomenon causes rampant introgression and homogenization. The phylogeographic analysis revealed admixture among wild populations; nevertheless, this did not impair pointing to Anatolia as likely having a “refugia-within-refugia” structure. We recommend that the genetic structure of Chukar Partridge and its MUs be taken into account when developing the policy of hunting, production, and release to preserve the genetic integrity of this species.

Lack of genetic structure suggests high connectivity of Parnassius phoebus between nearby valleys in the Alps

The spatial scale of intraspecific genetic connectivity and population structure are important aspects of conservation genetics. However, for many species these properties are unknown. Here we used genomic data to assess the genetic structure of the small Apollo butterfly (Parnassius phoebus Fabricius, 1793; Lepidoptera: Papilionidae) across three nearby valleys in the Central Swiss Alps. One of the valleys is currently used for hydropower production with future plans to raise the existing dam wall further. We found no significant genetic structure, suggesting a currently high connectivity of this species in our studied region.

Population genetic analysis of the Humboldt’s flying squirrel using high-throughput sequencing

Abstract The San Bernardino flying squirrel (Glaucomys oregonensis californicus) is thought to be the southernmost population of the Humboldt’s flying squirrel (G. oregonensis) and is restricted to the San Bernardino and San Jacinto Mountains in California. However, recent surveys indicate they have been extirpated from the latter locality. In this study, we characterized the intraspecific genetic structure and diversity of G. oregonensis. We amplified and sequenced at least 300 bp of the mitochondrial cytochrome-b gene and 11 nuclear microsatellites to provide baseline genetic data for this species and subspecies, investigate G. oregonensis genetic structure with a focus on the subspecies distributed in California, and finally evaluate the genetic diversity within G. o. californicus. Population and phylogenetic analyses were performed on a total of 147 samples (tissue, hair, and museum specimen) using the Illumina high-throughput sequencing (HTS) platform, thereby bioinformatically coding microsatellite alleles using established pipelines. Our results indicate reduced genetic diversity in G. o. californicus and highlight genetic distinctiveness of the San Jacinto population. In addition, the differences in genetic diversity between the mitochondrial and nuclear markers suggest sex-biased dispersal and historic separation of the species in multiple refugia followed by more recent gene flow among subpopulations in northern California. This study contributes valuable information toward understanding the genetic variation within G. oregonensis, provides information for future conservation decisions for G. o. californicus, and has novel implications for HTS genotyping-by-sequencing.

Next-generation phylogeography of the banded newts (Ommatotriton): A phylogenetic hypothesis for three ancient species with geographically restricted interspecific gene flow and deep intraspecific genetic structure

Technological developments now make it possible to employ many markers for many individuals in a phylogeographic setting, even for taxa with large and complex genomes such as salamanders. The banded newt (genus Ommatotriton) from the Near East has been proposed to contain three species (O. nesterovi, O. ophryticus and O. vittatus) with unclear phylogenetic relationships, apparently limited interspecific gene flow and deep intraspecific geographic mtDNA structure. We use parallel tagged amplicon sequencing to obtain 177 nuclear DNA markers for 35 banded newts sampled throughout the range. We determine population structure (with Bayesian clustering and principal component analysis), interspecific gene flow (by determining the distribution of species-diagnostic alleles) and phylogenetic relationships (by maximum likelihood inference of concatenated sequence data and based on a summary-coalescent approach). We confirm that the three proposed species are genetically distinct. A sister relationship between O. nesterovi and O. ophryticus is suggested. We find evidence for introgression between O. nesterovi and O. ophryticus, but this is geographically limited. Intraspecific structuring is extensive, with the only recognized banded newt subspecies, O. vittatus cilicensis, representing the most distinct lineage below the species level. While mtDNA mostly mirrors the pattern observed in nuclear DNA, all banded newt species show mito-nuclear discordance as well.

Evidence of dispersal between the Yenisei and the Lena river basins during the late Pleistocene within the whitefish (Coregonus lavaretus pidschian) complex

The Coregonus lavaretus (Linnaeus, 1758) complex is a morphologically and genetically diverse group of whitefish. Its taxonomic structure has been controversial for almost a century. At least 25 forms of C. lavaretus have been described in Siberia, but there is still no consensus on their intraspecific structure and taxonomy. Coregonus lavaretus pidschian (Gmelin, 1789) was described as a subspecies of C. lavaretus. Recently, it was assumed that this subspecies is also a complex. The purpose of this study was to compare the distributions of pidschian-like whitefish haplotypes in two basins of large Siberian rivers, Yenisei and Lena, and to assess the gene flow between basins of these rivers, which were connected after the last glaciation. The sequence of the following mitochondrial DNA genes, 16S rRNA (partial), tRNA-Leu (full), NADH dehydrogenase subunit 1 (full), tRNA-Ile (full), and tRNA-Gln (partial), were used for the inference of intraspecific genetic structure of C. l. pidschian. Whitefish haplotypes were clustered into two groups according to their distribution between two large Siberian river basins; however, there were shared haplotypes indicating events of migration and hybridization, which could occur when Bolshoi Yenisei and Lena river systems were connected after the last glaciation (the Late Pleistocene).