Intraspecific Genetic Variation Research Articles

The Sela macaque (Macaca selai) is a distinct phylogenetic species that evolved from the Arunachal macaque following allopatric speciation

Arunachal macaque (M. munzala) is an endangered and recently discovered cercopithecine primate from Western Arunachal Pradesh, India. On genetic analyses of Arunachal macaques, we observed spatially distributed substantial inter-species genetic divergence among the samples collected from Arunachal Pradesh. The results suggested that Arunachal macaque evolved into two phylogenetic species about 1.96 mya following allopatric speciation by means of Sela mountain pass in Arunachal Pradesh, India. We describe - Sela macaque (M. selai) as a new macaque species that interestingly exhibited high intra-specific genetic variation and also harbors at least two conservation units. Further, we report the past demographic trajectories and quantify genetic variation required for taxonomic clarification. The present study also identifies gap areas for undertaking surveys to document the relic and unknown trans-boundary populations of macaques through multinational, multi-lateral cross border collaboration.

Integrative taxonomy of coastal Cafiusbistriatus (Erichson) species complex (Coleoptera, Staphylinidae).

A systematic review of the marine littoral Cafiusbistriatus (Erichson) along the eastern Pacific and the western Atlantic coasts including the Caribbean Sea is presented based on morphological and molecular (COI and 28S) characters. Specimens of the Cafiusbistriatus species complex [C.bistriatus, C.rufifrons Bierig, and C.sulcicollis (LeConte)] are similar to each other, including the form and structure of the aedeagus, and they can be treated as cryptic species. Detailed micromorphological characters (SEM) and molecular analyses support the validity of these three species. Intraspecific genetic divergence of COI using uncorrected p-distance among individuals of Cafiusbistriatus ranged from 0% to 1.56%, while interspecific divergence among three species ranged from 4.90% to 14.59%. All three species were each supported as a single lineage using COI and 28S on both parsimony and maximum likelihood trees. Morphological characters among C.bistriatus, C.rufifrons, and C.sulcicollis are compared. Cafiusbistriatusfulgens Frank is synonymized under C.bistriatus and Cafiusbistriatus is redescribed with illustrations of diagnostic characters.

Exploring Large-Scale Patterns of Genetic Variation in the COI Gene among Insecta: Implications for DNA Barcoding and Threshold-Based Species Delimitation Studies.

Simple SummaryInsecta is the most diverse group in the kingdom Animalia, and it accounts for approximately two-thirds of all animals. The most commonly used gene for species delimitation in animals is cytochrome c oxidase subunit 1 (COI). We calculated the genetic distance of 64,414 insect species, downloaded from BOLD, and found that approximately one-quarter of the species of Insecta showed high intraspecific genetic variation (>3%). Owing to the high intraspecific genetic variation in insects, false positives may easily occur in threshold-based species delimitation based on the COI gene. Compared to the fixed thresholds, the thresholds that were calculated from the “threshOpt” and “localMinima” algorithms that are embedded in the Spider package are recommended in threshold-based species delimitation studies.The genetic variation in the COI gene has had a great effect on the final results of species delimitation studies. However, little research has comprehensively investigated the genetic divergence in COI among Insecta. The fast-growing COI data in BOLD provide an opportunity for the comprehensive appraisal of the genetic variation in COI among Insecta. We calculated the K2P distance of 64,414 insect species downloaded from BOLD. The match ratios of the clustering analysis, based on different thresholds, were also compared among 4288 genera (35,068 species). The results indicate that approximately one-quarter of the species of Insecta showed high intraspecific genetic variation (>3%), and a conservative estimate of this proportion ranges from 12.05% to 22.58%. The application of empirical thresholds (e.g., 2% and 3%) in the clustering analysis may result in the overestimation of the species diversity. If the minimum interspecific genetic distance of the congeneric species is greater than or equal to 2%, it is possible to avoid overestimating the species diversity on the basis of the empirical thresholds. In comparison to the fixed thresholds, the “threshOpt” and “localMinima” algorithms are recommended for the provision of a reference threshold for threshold-based species delimitation studies.

Semicassis globosum (Mollusca: Gastropoda: Cassidae) from the upper Eocene Ocala Limestone of Florida with redescription and discussion of its extreme morphological variability

ABSTRACT This study aimed to resolve the taxonomy of cassid gastropods from the upper Eocene Ocala Limestone based on specimens collected from Florida Museum of Natural History locality AL004. In 1890, Dall described a specimen from this formation, collected in a nearby county as Phalium globosum (subfamily Phaliinae). However, further collection of cassids from AL004 suggested the presence of more than one morphologically distinct taxon. Eocene cassids are particularly interesting because that is presumably the time when cassids experienced rapid diversification, which has implications for the evolutionary history of echinoid-cassid predator–prey interactions. Based on 75 specimens from AL004, it appears that the specimens interpreted as belonging to two or more morphologically distinct taxa are more likely members of a single species with extreme morphological variability, redescribed here as Semicassis globosum. Results of morphometric analyses using nine qualitatively defined cassid morphotaxa (subfamily Phaliinae) suggest that S. globosum is characterised by high intraspecific variability in shell morphology that may reflect high ecophenotypic variability or elevated intraspecific genetic variability. This study highlights the challenges associated with delineating species status using low numbers of specimens, as a dearth of diagnostic material may lead to taxonomic “over-splitting,” thereby resulting in an inflated estimate of biodiversity.

Comparative phylogeography in a marine biodiversity hotspot provides novel insights into evolutionary processes across the Atlantic‐Indian Ocean transition

AbstractAimIntraspecific genetic variation is a key component of biodiversity, with higher diversity indicating greater resilience and population substructuring suggesting unique evolutionary histories. Comparative approaches, in which intraspecific genetic variation is assessed across multiple species, are powerful tools to identify evolutionary hotspots, but are still rarely applied at spatial scales relevant to conservation planning. Here, we use comparative phylogeography to understand patterns and potential drivers of genetic variation within a biodiversity and ocean warming hotspot.LocationThe South African coastline, Indian/Atlantic Oceans.MethodsA literature search was conducted to obtain mitochondrial DNA cytochrome oxidasecsubunit I and cytochromebsequence data for 17 marine fish and invertebrate species. From these data, we compared averages of haplotype and nucleotide diversity, and within‐region ΦSTbetween four biogeographic provinces in the region. Mixed linear models tested whether environmental variability, habitat preference, or geographic location significantly influence genetic variation.ResultsAverage diversity values differed between haplotype and nucleotide diversity, but both broadly displayed highest diversity levels within the South‐West bioregion, which is also a region of high levels of within‐region ΦST. Range in sea surface temperatures (SSTs) was the only significant fixed‐effect term in the haplotype diversity mixed linear models. Mean SST, stability in SSTs since the Mid‐Holocene and position within the species' geographic distribution all had no significant effect on genetic variation.Main conclusionsAlong this coastline characterized by high environmental heterogeneity, we find that variation in temperature is a prominent source of intraspecific variation. Genetic diversity differs between bioregions, but does not display higher levels within the core of each species’ range when assessed across multiple species. With elevated levels of genetic diversity, the South‐West region of the South African coast is highlighted as a conservation priority area, representing both high genetic diversity and differentiation across taxa.

Determinants of Genetic Structure in a Highly Heterogeneous Landscape in Southwest China.

Intra-specific genetic diversity is a fundamental component of biodiversity, and is key to species adaptation and persistence. However, significant knowledge gaps still exist in our understanding of the patterns of genetic diversity and their key determinants. Most previous investigations mainly utilized single-species and/or a limited number of explanatory variables; so here we mapped the patterns of plastid genetic diversity within 15 plant species, and explored the key determinants shaping these patterns using a wide range of variables. Population-level cpDNA sequence data for 15 plant species from the Longitudinal Range Gorge Region (LRGR), southwest China, were retrieved from literature and used to estimate haplotype diversity (HD) and population pairwise genetic differentiation (FST) indices. Genetic diversity and divergence landscape surfaces were then generated based on the HD and FST, respectively, to clarify the patterns of genetic structure in the region. Subsequently, we analyzed the relationships between plastid genetic diversity and 16 explanatory variables (classified as anthropogenic, climatic, and topographic). We found that the highest genetic diversity occurred in the Yulong Mountain region, with a significant proportion (~74.81%) of the high diversity land area being located outside of protected areas. The highest genetic divergence was observed approximately along the 25°N latitudinal line, with notable peaks in the western and eastern edges of the LRGR. Genetic diversity (HD) was weakly but significantly positively correlated with both Latitude (lat) and Annual Mean Wet Day Frequency (wet), yet significantly negatively correlated with all of Longitude (long), Annual Mean Cloud Cover Percent (cld), Annual Mean Anthropogenic Flux (ahf), and Human Footprint Index (hfp). A combination of climatic, topographic, and anthropogenic factors explained a significant proportion (78%) of genetic variation, with topographic factors (lat and long) being the best predictors. Our analysis identified areas of high genetic diversity (genetic diversity “hotspots”) and divergence in the region, and these should be prioritized for conservation. This study contributes to a better understanding of the features that shape the distribution of plastid genetic diversity in the LRGR and thus would inform conservation management efforts in this species-rich, but vulnerable region.

DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera).

BackgroundThe hemi-metabolous aquatic order Plecoptera (stoneflies) constitutes an indispensable part of terrestrial and aquatic food webs due to their specific life cycle and habitat requirements. Stoneflies are considered one of the most sensitive groups to environmental changes in freshwater ecosystems and anthropogenic changes have caused range contraction of many species. Given the critical threat to stoneflies, the study of their distribution, morphological variability and genetic diversity should be one of the priorities in conservation biology. However, some aspects about stoneflies, especially a fully resolved phylogeny and their patterns of distribution are not well known. A study that includes comprehensive field research and combines morphological and molecular identification of stoneflies has not been conducted in Croatia so far. Thus, the major aim of this study was to regenerate a comprehensive and taxonomically well-curated DNA barcode database for Croatian stoneflies, to highlight the morphological variability obtained for several species and to elucidate results in light of recent taxonomy.MethodsA morphological examination of adult specimens was made using basic characteristics for distinguishing species: terminalia in males and females, head and pronotum patterns, penial morphology, and egg structures. DNA barcoding was applied to many specimens to help circumscribe known species, identify cryptic or yet undescribed species, and to construct a preliminary phylogeny for Croatian stoneflies.ResultsSequences (658 bp in length) of 74 morphospecies from all families present in Croatia were recovered from 87% of the analysed specimens (355 of 410), with one partial sequence of 605 bp in length for Capnopsis schilleri balcanica Zwick, 1984. A total of 84% morphological species could be unambiguously identified using COI sequences. Species delineation methods confirmed the existence of five deeply divergent genetic lineages, with monophyletic origin, which also differ morphologically from their congeners and represent distinct entities. BIN (Barcode Index Number) assignment and species delineation methods clustered COI sequences into different numbers of operational taxonomic units (OTUs). ASAP delimited 76 putative species and achieved a maximum match score with morphology (97%). ABGD resulted in 62 and mPTP in 61 OTUs, indicating a more conservative approach. Most BINs were congruent with traditionally recognized species. Deep intraspecific genetic divergences in some clades highlighted the need for taxonomic revision in several species-complexes and species-groups. Research has yielded the first molecular characterization of nine species, with most having restricted distributions and confirmed the existence of several species which had been declared extinct regionally.

Molecular Evolutionary Rate Predicts Intraspecific Genetic Polymorphism and Species-Specific Selection.

It is unknown what determines genetic diversity and how genetic diversity is associated with various biological traits. In this work, we provide insight into these issues. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual human, chimpanzee, gorilla, mouse, and dog/wolf genomes, we found that intraspecific genetic diversity can be predicted by long-term molecular evolutionary rates rather than de novo mutation rates. This relationship was established during the early stage of mammalian evolution. Moreover, we developed a method to detect fluctuations of species-specific selection on genes based on the deviations of intraspecific genetic diversity predicted from long-term rates. We showed that the evolution of epithelial cells, rather than connective tissue, mainly contributed to morphological evolution of different species. For humans, evolution of the immune system and selective sweeps caused by infectious diseases are the most representative examples of adaptive evolution.

New species, redescriptions and new records of deep-sea brittle stars (Echinodermata: Ophiuroidea) from the South China Sea, an integrated morphological and molecular approach

Deep-sea ophiuroids were collected by the manned submersible ‘Shenhaiyongshi’ from the South China Sea at depths of 500–3550 m, in 2017 to 2020. A total of 18 species were identified, including three new species and eight new records, increasing the total number of species known from the South China Sea to 304. Most of the ophiuroids recorded from the South China Sea were found in shallow waters (77.9%) and a few of them occurred only in deep water (20.4%). Three new species are described as Ophiacantha aster sp. nov., Ophiomoeris petalis sp. nov. and Ophiopristis shenhaiyongshii sp. nov. We provide comprehensive descriptions of morphological features, including characteristics of the arm skeletons, and a phylogenetic analysis based on COI and 16S sequences. Overall intraspecific and interspecific genetic distance variations among the families found in this study were 0.5% to 2.47% and 1.16% to 44.16%, respectively, along the South Pacific region to the South China Sea. Our phylogenetic analysis suggested that COI partial genes resolved the interspecies complexity in the class Ophiuroidea better than 16S partial genes. The order Euryalida had low interspecies genetic distance variation within the class Ophiuroidea. The present study suggests a high probability that species of Asteroschema and Gorgonocephalus are more widely spread around the Indo-Pacific region than previously expected.

Morphology, genetic characterization and molecular phylogeny of the poorly known nematode parasite Cissophyllus leytensis Tubangui & Villaamil, 1933 (Nematoda: Ascaridida) from the Philippine sailfin lizard Hydrosaurus pustulatus (Eschscholtz, 1829) (Reptilia: Squamata)

BackgroundThe genus Cissophyllus (Cosmocercoidea: Kathlaniidae) is a rare group of nematodes parasitic in turtles and lizards. To date, only four species have been reported in Asia and North America. However, most of them are inadequately described. The species Cissophyllus leytensis has never been reported since it was originally described by Tubangui and Villaamil in 1933 from the Philippine sailfin lizard Hydrosaurus pustulatus (Eschscholtz, 1829) (Reptilia: Squamata). Furthermore, the systematic status of Cissophyllus/Cissophyllinae in the family Kathlaniidae of the superfamily Cosmocercoidea remains under debate.MethodsThe detailed morphology of C. leytensis was studied using light microscopy (LM) and, for the first time, scanning electron microscopy (SEM), based on newly collected specimens from the type host H. pustulatus. Six different genetic markers, including nuclear sequences [small ribosomal subunit (18S), internal transcribed spacer (ITS) and large ribosomal subunit (28S)], plus mitochondrial genes [cytochrome c oxidase subunit 1 (cox1), cytochrome c oxidase subunit 2 (cox2) and 12S small subunit ribosomal RNA gene] of C. leytensis were sequenced. Additionally, in order to test the validity of the subfamily Cissophyllinae and clarify the phylogenetic relationships of Cissophyllus and the other genera in the family Kathlaniidae, phylogenetic analyses based on 18S + 28S and ITS sequence data were performed using maximum likelihood (ML) and Bayesian inference (BI) analyses, respectively.ResultsOur observations using LM and SEM revealed some previously unreported morphological features, necessitating the redescription of this poorly known species. The presence of remarkable morphological variation in the isthmus and the position of excretory pore among different individuals was found. Molecular analysis showed no intraspecific nucleotide divergence detected in the 18S, ITS, 28S, cox2 and 12S regions among different individuals of C. leytensis, but a low level of intraspecific genetic variation was found in the cox1 (0.52%). Our phylogenetic results showed the representatives of the Cosmocercoidea divided into four large clades (Cosmocerca + Aplectana + Cosmocercoides representing the family Cosmocercidae, Cruzia representing the subfamily Cruzinae of Kathlaniidae, Falcaustra + Cissophyllus + Megalobatrachonema representing the subfamily Kathlaniinae of Kathlaniidae, and Orientatractis + Rondonia representing the family Atractidae). The genus Cissophyllus clustered together with the genus Megalobatrachonema in both the ML and BI trees using ITS sequence data, but displayed a sister relationship to the genus Falcaustra in the ML tree and to the genera Falcaustra + Megalobatrachonema in the BI tree using 18S + 28S sequence data.ConclusionsMolecular phylogenetic results further confirmed that the family Kathlaniidae is not a monophyletic group. The subfamily Cruziinae should be moved from the hitherto-defined family Kathlaniidae and elevated as a separate family Cruziidae. The present phylogenetic results also negated the validity of the subfamily Cissophyllinae and supported the genus Cissophyllus assigned in the subfamily Kathlaniinae. Molecular analysis indicated that the morphological variation in the isthmus and position of excretory pore among different individuals should be considered as intraspecific variation. Moreover, some characters important for the specific diagnosis of C. leytensis are reported for the first time: the number of acuminate denticles (lamellae) on each lip, the chitinized pharynx with three flabellate pharyngeal plates, the presence of single medioventral precloacal papilla and the detailed morphology of caudal papillae. The present study is only the second record of C. leytensis.Graphical

Morphological and molecular characterization of Paraleptus chiloscyllii Yin & Zhang, 1983 (Nematoda: Physalopteridae) from the brownbanded bambooshark Chiloscyllium punctatum Müller & Henle (Elasmobranchii: Orectolobiformes).

Paraleptus (Spirurida: Physalopteridae) is a small genus of nematodes, parasitic in fishes, most species of which are inadequately described. Genetic data for these congeners have not been reported. The detailed morphology of P. chiloscyllii was studied using light and scanning electron microscopy, based on newly collected specimens from the brownbanded bambooshark C. punctatum Müller & Henle (Elasmobranchii: Orectolobiformes) in the Taiwan Strait. Some previously unreported morphological features of taxonomic significance were observed, i.e., pseudolabium with two sublateral rows of 6-7 small spines, 7-8 small spines on each lower rim between pseudolabia, deirids not distally bifurcated, vulva with remarkable protruding lip, presence of 1 pair medio-ventral precloacal papillae and 1 pair of discoid protrusions of postcloacal lip in male. The specimens described by González-Solís & Ali's (2015) as P. chiloscyllii from the Arabian carpetshark C. arabicum off Iraq are considered a new species, for which the name P. moraveci n. sp. is proposed. The genetic characterization of the partial small (18S) and large (28S) ribosomal DNA, and the partial mitochondrial cytochrome c oxidase subunit 1 (cox1) of P. chiloscyllii are provided for the first time. There was no intraspecific nucleotide divergence detected in the 18S and 28S regions among different individuals of P. chiloscyllii, but a low level of intraspecific genetic variation was found in the cox1 (0.62-0.92%). The present genetic data is very important for molecular identification, and will be valuable for further invertigantions on the population genetics and phylogeny of this group.

Assessment of iPBS Primers Potential to Be Used in Genetic Diversity Studies of Wild Cloudberry (Rubus Chamaemorus L.) Populations

Abstract Inter-primer binding site (iPBS) molecular retrotransposon-based markers are a universal and simple tool to estimate genetic diversity. The goal of this study was to select highly informative iPBS primers to be used in studies of intraspecific genetic diversity of cloudberry (Rubus chamaemorus L.), a common plant species of the boreal zone, associated with raised bog habitats and transitional bogs. Initially, 75 iPBS primers were screened and three of the most informative primers (indicated by numbers 2298, 2277, and 2229) were selected based on the highest number of polymorphic bands and PIC (polymorphic information content) values. Electrophoretic analysis revealed 34 bands amplified with primer 2229, 25 bands with primer 2298, and 22 bands with primer 2277. The percentage of polymorphic loci ranged from 90.9 to 97.1% and PIC values ranged from 0.4885 to 0.4965, indicating potential of the selected primers to be applied in population genetic studies of R. chamaemorus.

Phytophthora spp. Associated with Appalachian Oak Forests and Waterways in Pennsylvania, with P. abietivora as a Pathogen of Five Native Woody Plant Species.

To document the distribution of potentially harmful Phytophthora spp. within Pennsylvania, the Pennsylvania Department of Agriculture collected 89 plant, 137 soil, and 48 water samples from 64 forested sites during 2018 to 2020. In total, 231 Phytophthora strains were isolated using baiting assays and identified based on morphological characteristics and sequences of nuclear and mitochondrial loci. Twenty-one Phytophthora spp. in nine clades and one unidentified species were present. Phytophthora abietivora, a recently described clade 7a species, was recovered from diseased tissue of 10 native broadleaved plants and twice from soil from 12 locations. P. abietivora is most likely endemic to Pennsylvania based on pathogenicity tests on six native plant species, intraspecific genetic diversity, wide distribution, and recoveries from Abies Mill. and Tsuga Carrière plantations dating back to 1989. Cardinal temperatures and morphological traits are provided for this species. Other taxa, in decreasing order of frequency, include P. chlamydospora, P. plurivora, P. pini, P. cinnamomi, P. xcambivora, P. irrigata, P. gonapodyides, P. cactorum, P. pseudosyringae, P. hydropathica, P. stricta, P. xstagnum, P. caryae, P. intercalaris, P. 'bitahaiensis', P. heveae, P. citrophthora, P. macilentosa, P. cryptogea, and P. riparia. Twelve species were associated with diseased plant tissues. This survey documented 53 new plant-Phytophthora associations and expanded the known distribution of some species.

Symbiont-conferred immunity interacts with effects of parasitoid genotype and intraguild predation to affect aphid immunity in a clone-specific fashion

BackgroundHost-parasite interactions represent complex co-evolving systems in which genetic and associated phenotypic variation within a species can significantly affect selective pressures on traits, such as host immunity, in the other. While often modelled as a two-species interaction between host and parasite, some systems are more complex due to effects of host enemies, intraguild predation, and endosymbionts, all of which affect host immunity. However, it remains unclear how these factors, combined with genetic variation in the host and the parasitoid, affect host immunity. We address this question in an important agricultural pest system, the pea aphid Acyrthosiphon pisum, which shows significant intraspecific variability in immunity to the parasitoid wasp Aphidius ervi. In a complex experiment, we use a quantitative genetic design in the parasitoid, two ecologically different aphid lineages and the aphid lion Chrysoperla carnea as an intraguild predator to unravel the complex interdependencies.ResultsWe demonstrate that aphid immunity as a key trait of this complex host-parasite system is affected by intraspecific genetic variation in the parasitoid and the aphid, the interaction of intraspecific genetic variation with intraguild predation, and differences in defensive endosymbionts between aphid lineages. Further, aphid lineages differ in their altruistic behaviour whereby infested aphids move away from the clonal colony to facilitate predation.ConclusionsOur findings provide new insights into the influence of endosymbiosis and genetic variability in an important host-parasitoid system which is influenced by natural enemies of the parasitoid and the aphid, including its endosymbiont communities. We show that endosymbiosis can mediate or influence the evolutionary arms race between aphids and their natural enemies. The outcome of these complex interactions between species has significant implications for understanding the evolution of multitrophic systems, including eco-agricultural settings.

Evaluation of genetic diversity of Cantaloupe landraces based on the internal transcriptional spacer regions (ITS1, 4)

ABSTRACT Cantaloupe (Cucumis melo L.) landraces have highly genetic diversity so that it is important to evaluate such distances for future breeding projects. Internal transcribed spacer regions (ITS1 and ITS4 regions) capability was used to evaluate genetic diversity of cantaloupe landraces and to identity genetic diversity among cantaloupe landraces. After DNA extraction from leaf tissue at the 4-true leaf stage and DNA quantification and qualification based on spectrophotometer and agarose gel electrophoresis, electrophoretic bands were sequenced. The sequence quality was assessed and compared with the ClustalW method. Phylogenetic relationship dendrograms were plotted based on genetic distance. Melon landraces could not be separated based on geographical location. The ITS1 region was more separable and diverse than the ITS4 region and was able to differentiate landraces related to the Hirmand region in a separate dendrogram. The numerical value (dN/dS) in ITS1 and ITS4 were 0.658 and 0.450, respectively, indicating pure selection had occurred in the gene and did not cause any important changes. The ITS region is not suitable to investigate intraspecific genetic diversity.

Demographic history shapes genomic variation in an intracellular parasite with a wide geographical distribution.

Analysing variation in a species' genomic diversity can provide insights into its historical demography, biogeography and population structure, and thus its ecology and evolution. Although such studies are rarely undertaken for parasites, they can be highly revealing because of the parasite's co-evolutionary relationships with hosts. Modes of reproduction and transmission are thought to be strong determinants of genomic diversity for parasites and vary widely among microsporidia (fungal-related intracellular parasites), which are known to have high intraspecific genetic diversity and interspecific variation in genome architecture. Here we explore genomic variation in the microsporidium Hamiltosporidium, a parasite of the freshwater crustacean Daphnia magna, looking especially at which factors contribute to nucleotide variation. Genomic samples from 18 Eurasian populations and a new, long-read-based reference genome were used to determine the roles that reproduction mode, transmission mode and geography play in determining population structure and demographic history. We demonstrate two main Hamiltosporidium tvaerminnensis lineages and a pattern of isolation-by-distance, but note an absence of congruence between these two parasite lineages and the two Eurasian host lineages. We suggest a comparatively recent parasite spread through Northern Eurasian host populations after a change from vertical to mixed-mode transmission and the loss of sexual reproduction. While gaining knowledge about the ecology and evolution of this focal parasite, we also identify common features that shape variation in genomic diversity for many parasites, such as distinct modes of reproduction and the intertwining of host-parasite demographies.

Anthropocene refugia in Patagonia: A macrogenetic approach to safeguarding the biodiversity of flowering plants

Intraspecific genetic diversity (IGD), the fundamental dimension of biodiversity, is scarcely considered in the context of anthropogenic impact at regional and global scales. Here, encouraged by the knowledge about the effect of past climate changes that shaped IGD at the community level, we evaluated how current land use and future climate changes may erode mechanisms underlying genetic diversity and species richness of the native flora of the Patagonian steppe, a cold desert that covers 827,446 km2 in the southern cone of South America. About 36% of the Patagonian steppe could serve as Anthropocene refugia, with only 1.8% being protected areas at present. Moreover, 63% of the areas with the highest species richness and endemism, and 37% with the highest genetic diversity are outside the refugia areas. Human-driven changes threaten plant biodiversity mainly in northern Patagonia. We provide the first broad assessment of climate change and land-use effects on IGD for the Patagonian steppe. The conservation of the detected high genetic diversity and species-rich areas with moderate land use and projected low climate anomaly should be prioritized, whereas high-risk areas, those for which a high climatic anomaly is projected, deserve monitoring and mitigation policies. This approach which includes IGD as a biodiversity metric may be useful for other endangered ecoregions in the world, with promising results for biodiversity conservation.

Генетична структура української популяції водяних буйволів за ISSR-PCR маркерами

The study of intraspecific genetic diversity of cattle, including species of the genus Bubalus from the subfamily Bull, is important because of the reduction of biodiversity of farm animals. The basis of genetic diversity is its genetic component. The loss of native species and breeds of cattle is a real threat to the biosphere, as the resilience of natural ecosystems and agroecosystems is directly linked to their genetic ability to adapt to environmental conditions. Polymorphism of ISSR-markers of the Ukrainian population of water buffaloes (Bubalus bubalis) from the farm of “TASBIO” LLC (Chernihiv region) was analyzed in 66 animals selected for the study. Genomic DNA samples were isolated from venous blood with a standard set of reagents. Genotyping was performed using specific ISSR primers: (ACC)6G, (GAG)6C, (AG)9C, (CTC)6C, (AG)8CA, (AG)8CGand (GA)6CC. We determined the difference in spectra both by the number of amplicons, their lengths (number of nucleotides) and by their polymorphism. As a result of the study, all primers showed polymorphism of buffalo DNA regions. Amplicons were defined in the range from 200 bp up to 4000 bp. Analysis of ISSR spectra revealed 87 loci, of which 71 were polymorphic. (AG)8CA-marker was the least polymorphic (PIC=0.234), (CTC)6C the most polymorphic (PIC=0.389). Conservative loci were found in four ISSR markers: 6 in (AG)8CA marker, 5 in (AG)8CG, 4 in (GA)6CC, and 1 in (AG)9C. 67 species-specific loci were identified for the Ukrainian water buffalo population: 10 for (AG)9C, 3 loci for (ACC)6G, 4 for (GAG)6C, 7 for (CTC)6C, 15 for (AG)8CA, and 14 in (AG)8CG and (GA)6CC. The ISSR primers used are recommended for molecular genetic analysis of buffalo DNA polymorphism.

Gated Communities: Inter- and Intraspecific Diversity of Endosymbionts Across Four Sympatric Aphid Species

Aphids have evolved tight relationships with heritable endosymbionts, i.e., bacteria hosted within their tissues. Besides the primary endosymbiont Buchnera aphidicola, aphids host many facultative secondary endosymbionts with functions they may or may not benefit from. The different phenologies, lifestyles, and natural enemies of aphid species are predicted to favor the selection for distinct endosymbiont assemblages, as well as the emergence of intra-specific genetic diversity in the symbiotic bacteria. In this study, we (1) investigated the diversity of endosymbionts associated with four species from the genus Aphis in the field, and (2) we characterized the genetic diversity of Hamiltonella defensa, an endosymbiont that protects aphids against parasitoid wasps. We observed strong differences in the composition of endosymbiont communities among the four aphid species. H. defensa was clearly the dominant symbiont, although its abundance in each species varied from 25 to 96%. Using a multilocus sequence-typing approach, we found limited strain diversity in H. defensa. Each aphid species harbored two major strains, and none appeared shared between species. Symbiont phylogenies can thus help to understand the (seemingly limited) mobility of endosymbionts in aphid communities and the selection forces driving strain diversification.

Population Analysis of Diospyros lotus in the Northwestern Caucasus Based on Leaf Morphology and Multilocus DNA Markers.

Diospyros lotus is the one of the most frost-tolerant species in the Diospyros genera, used as a rootstock for colder regions. Natural populations of D. lotus have a fragmented character of distribution in the Northwestern Caucasus, one of the coldest regions of Diospyros cultivation. To predict the behavior of D. lotus populations in an extreme environment, it is necessary to investigate the intraspecific genetic diversity and phenotypic variability of populations in the colder regions. In this study, we analyzed five geographically distant populations of D. lotus according to 33 morphological leaf traits, and the most informative traits were established, namely, leaf length, leaf width, leaf index (leaf to length ratio) and the length of the fourth veins. Additionally, we evaluated the intraspecific genetic diversity of D. lotus using ISSR and SCoT markers and proposed a new parameter for the evaluation of genetic polymorphism among populations, in order to eliminate the effect of sample number. This new parameter is the relative genetic polymorphism, which is the ratio of polymorphism to the number of samples. Based on morphological and genetic data, the northernmost population from Shkhafit was phenotypically and genetically distant from the other populations. The correspondence between several morphological traits (leaf width, leaf length and first to fifth right vein angles) and several marker bands (SCoT5, SCoT7, SCoT30: 800–1500 bp; ISSR13, ISSR14, ISSR880: 500–1000 bp) were observed for the Shkhafit population. Unique SCoT and ISSR fragments can be used as markers for breeding purposes. The results provide a better understanding of adaptive mechanisms in D. lotus in extreme environments and will be important for the further expansion of the cultivation area for persimmon in colder regions.