Low Levels Of Genetic Diversity Research Articles

Genetic diversity and population structure of a rare and endangered freshwater macrophyte <i>Potamogeton rutilus</i> Wolfg.

Comprehending genetic variation and population structure is paramount for devising optimal management strategies and conservation efforts. In this study, we employed amplified fragment length polymorphism (AFLP) analysis to assess the distribution of genetic variation within and among populations of the rare macrophyte <i>Potamogeton rutilus</i> Wolfg. This species has experienced habitat alterations leading to its disappearance from numerous previously known European locations. Our analysis encompassed eight populations collected from Poland, Lithuania, and Estonia, situated within the central region of <i>P. rutilus</i> distribution. The results of our study indicate that the analyzed populations are characterized by relatively low levels of genetic diversity (the mean of Nei’s gene diversity was 0.031±0.003 and the Shannon’s information index 0.049± 0.004), and intermediate gene flow (Nm = 0.289). Analysis of molecular variance (AMOVA) revealed higher levels of variation among populations (63%) than within populations (37%); PhiPT = 0.634, <i>p</i> < 0.001, which might be attributed to the founder effect, frequent vegetative propagation, and limited seedling recruitment. The results of STRUCTURE, PCoA and NeighbourNet analyses suggest that the genetic structure of the studied populations falls into three main clusters not fully corresponding to geographical regions. The Mantel test did not show a significant correlation between genetic distance and geographical distance among populations. The most geographically isolated population sampled in Poland (ROT) is genetically close to the Estonian population VAL and VIT, although it is located far closer to the stations in Lithuania. Implications of acquired data for the genetic management of the species are discussed.

Microsatellite (SSR) Analysis of Dolichos Lablab (Lablab purpureus (L.) Sweet) Germplasm in Namibia

Dolichos lablab (Lablab purpureus (L.) Sweet)) is a multipurpose drought tolerant protein-rich legume crop native to Africa and grown in warm temperate to tropical climates for its edible seeds and manure. Literature informs that Lablab purpureus holds significant benefits to subsistence farmers and offers a great promise for sustainable crop productivity, especially in marginalised areas. Its uses range from human consumption as a vegetable to improving soil fertility, and as forage. Not with standing Lablab purpureus crucial potential functions in Namibia, there is currently limited information regarding the plant’s genetic diversity. This study followed a descriptive quantitative research approach where the data collected was used to describe the samples collected. The study aimed at evaluating the genetic diversity among 26 accessions of Lablab purpureus. The plant’s genetic diversity was determined by PCR amplification of three SSR markers namely VM38, AGB8 and GATS911. The SSR markers had PIC values of 0.452663 for marker VM38, 0.473373 for marker AGB8 and 0.260355 for marker GATS911. The Shannon Index of diversity gave a value of 1.25 meaning low levels of genetic diversity among the accessions. The study was the first report of Lablab purpureus’s genetic diversity in Namibia.

Population Structure and Genetic Diversity Analyses Provide New Insight into the Endemic Species Aster spathulifolius Maxim. and Its Evolutionary History.

Aster spathulifolius, an ecologically significant plant species native to the coastal regions of Korea and Japan, remains understudied in terms of its genetic structure and evolutionary history. In this study, we employed four chloroplast markers and the nuclear ITS region from 15 populations of A. spathulifolius from both Korea and Japan, including their islands, to unravel the spatial genetic structure, differentiation, gene flow, phylogenetic, and biogeographical relationships. Analysis based on multiple methods identified a low level of genetic diversity, genetic differentiation and gene flow among A. spathulifolius populations. Network analysis and principal coordinates analysis showed that 15 populations could be divided into two groups: mainland and island. Furthermore, UPGMA, neighbor-net, maximum-likelihood and Bayesian inference-based phylogenetic tree confirmed that these populations formed two distinct clades. Therefore, the island populations might be treated as A. spathulifolius populations rather than A. oharai populations. Divergence time analysis estimated the divergence of A. spathulifolius lineages approximately 23.09 million years ago, while ancestral area reconstruction analysis suggested Korea as the potential origin, conflicting with alternative scenarios. These findings contribute to a comprehensive understanding of the evolutionary history, genetic structure, and adaptive strategies of A. spathulifolius in coastal environments. Our study challenges previous assumptions and underscores the necessity for further population studies to elucidate the intricate dynamics of this distinctive plant species.

Genetic footprints of Quaternary climatic fluctuations on the endangered Tuco-tuco-das-dunas (Ctenomys flamarioni)

Abstract The biogeographic history of a species results from responses to past and current processes, and understanding those responses at both temporal scales is essential. We explored phylogeographic and current genetic variation structure in Ctenomys flamarioni—a subterranean rodent that inhabits a small region of the coastal plain of Brazil—and contrasted the roles of “present-day niche suitability” versus “historical climate stability” to understand current and past intraspecific genetic diversity. We used both mitochondrial DNA sequences (concatenated Cytb and D-loop, n = 78) and nuclear DNA (9 microsatellites loci, n = 154) molecular markers for individuals across the entire distribution of the species. We used phylogeographic trees, Bayesian clustering, and haplotype networks to explore genetic variation and diversity. We correlated genetic diversity with measures of current niche suitability and potential areas of Late Quaternary paleostability. Phylogeographic patterns confirmed low levels of genetic diversity structured at different hierarchical levels. We also found a weak but significant pattern of isolation by distance, indicating that geographical distance partially modulates genetic differences among populations. We also observed a positive correlation between genetic diversity and climate paleostability for microsatellites at local and regional scales. However, we found no significant association between genetic diversity and niche suitability for microsatellites at local or regional scales. We observed several signatures of bottleneck and population expansion at different geographic scales. Our results suggest that Quaternary climatic fluctuations—acting together with habitat suitability and other contemporary factors—played a fundamental role in elucidating the evolutionary history of the species—including patterns of historical dispersal, and current patterns of habitat occupation and genetic structure. In addition, based on our molecular and environmental data sets from the across the range of the species and considering the restricted endemism of C. flamarioni, we emphasize the urgency of conservation actions to protect this endangered species.

What happens in ice age, does not stay in ice age: Phylogeography of Bombus terrestris revealed a low genetic diversity amongst the Eurasian populations

The objective of this research was to assess the genetic diversity and phylogeography of Bombus terrestris and examine the historical events that shaped its contemporary genetic structures using the COI mitochondrial marker. Specimens of the species were collected from its distribution range alongside the Alborz Mountain range, and GenBank sequences from the Eurasian distribution range were incorporated into the dataset. The COI sequences were employed in Bayesian and Maximum Likelihood analyses to generate phylogenetic trees for the species populations and to investigate the evolutionary history of the species. Additionally, species occurrence points and climate data were utilized in Species Distribution Modeling (SDM) analyses to reconstruct the species range under past, present, and future climate conditions. The ML and BI trees yielded similar topologies, indicating extremely low genetic diversity and a homogeneous structure in the species population distribution range in Eurasia. Demographic analyses suggested that the species may have experienced a bottleneck during the last glacial maximum in Eurasia, followed by a recent expansion. The SDM analyses revealed significant fluctuations in the species range in the past and expansion under present conditions. Given the high dispersal ability of the species, the population expansion rate has surpassed the rate of developing new genetic diversity, and the estimated polymorphic sites for the species are likely relatively recent. This low level of genetic variation can also be attributed to the absence of geographical barriers and the excellent flying ability of the queen bee, leading to sustained gene flow throughout the entire continent. Despite the general correlation between larger populations and higher genetic diversity, bumblebees can expand their population size without increasing genetic diversity when residing in resourceful habitats.

DNA barcoding of Tribolium castaneum (Coleoptera: Tenebrionidae) from selected states in Nigeria based on mitochondrial DNA sequences

Tribolium castaneum also known as red flour beetle is one of the most important pests of stored grain product with a cosmopolitan distribution in Nigeria and all over the world contributing to food spoilage. The aim of this study was to characterize the T. castaneum by morphometric and molecular analyses. Samples of yam flour with evidence of the red flour beetles present inside were obtained from four locations in Kwara, Kogi, Oyo and Ekiti states in Nigeria. Morphological and molecular identifications of T. castaneum were carried out using standard methods. A dissecting microscope was used to identify the beetles and measurements were taken using ImageJ. Genomic DNA was extracted and checked on 1.5% agarose gel to confirm the presence of DNA. Species-specific primers were used to amplify mitochondrial cytochrome oxidase I (COI) gene of T. castaneum and the PCR amplicon size was also checked on 1.5% agarose. Morphometric measurements showed that the highest mean number (33.00±4.24 mm) of T. castaneum larvae observed was recorded on day 61 in Ilorin and the lowest was in Iwo, Osun state (4.00±0.00 mm) on the same day. The mean of the total body length of larvae from sampling sites was (1.31±0.37 mm) with minimum and (1.63±1.14 mm) maximum lengths respectively. There was no significant difference (p>0.05) between the mean length of the larvae collected from the study locations. Aligned cytochrome oxidase subunit 1 (COI) sequences of 313bp were analyzed. Phylogenetic analysis inferred by maximum likelihood method showed that the T. castaneum sequences analyzed for this study and sequences obtained from GenBank formed a monophyletic group. The molecular and phylogenetic analyses confirmed the presence of a single species of T. castaneum. The results from this study showed low levels of genetic diversity and variability in the studied T. castaneum populations. The observed genetic similarity in T. castaneum could be due to the fact that they were probably from similar origin when compared with those in the GenBank database. However, further studies are needed with more samples to characterize T. castaneum species from stored food grains across Nigeria.

The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification.

Chloroplast genomes are a source of information successfully used in various fields of plant genetics, including molecular species identification. However, recent studies indicate an extremely low level of interspecific variability in the plastomes of some taxonomic groups of plants, including the genus Stipa L., which is a representative of the grass family. In this study we aimed to analyze the level of chloroplast genome diversity within particular genera as well as the effectiveness of identifying plant species in the Poaceae family and the other representatives of Poales order. Analysis of complete plastid genome alignments created for 96 genera comprising 793 species and 1707 specimens obtained from the GenBank database allowed defining and categorizing molecular diagnostic characters distinguishing the analyzed species from the other representatives of the genus. The results also demonstrate which species do not have any species-specific mutations, thereby they cannot be identified on the basis of differences between the complete chloroplast genomes. Our research showed a huge diversity of the analyzed species in terms of the number of molecular diagnostic characters and indicated which genera pose a particular challenge in terms of molecular species identification. The results show that a very low level of genetic diversity between plastomes is not uncommon in Poales. This is the first extensive research on super-barcoding that tests this method on a large data set and illustrates its effectiveness against the background of phylogenetic relationships.

Analysis of Genetic Variation of MatK Gene Sequences in Ammothamnus lehmannii NCBI Popset 2440747918 Using In Silico RFLP

Genetic diversity or genetic variation is variation that occurs in an organism due to differences in the sequence of nucleotide bases (adenine, thymine, guanine and cytosine) that form DNA in cells. Variation genetics can be studied in silico using available gene sequences in the NCBI genbank database. This study used the MatK (Maturase-K) gene sequence with the identity number Popset 2440747918 which was downloaded in fasta format from NCBI . Then screening of restriction enzyme candidates was carried out to determine the restriction enzymes prior to in silico RFLP. The restriction enzyme selected from the screening was the restriction enzyme HindIII which has the recognition site A'AGC_T. The results obtained from 79 samples of DNA sequences, 76 samples were cut and 3 samples were not. And found three allele variations with the percentage of the presence of fragments A1 (86.07%), A2 (10.12%) and A3 (3.79%). The percentage values and frequencies of these A1, A2 and A3 alleles indicate a low level of genetic variation.

Development and Application of Potentially Universal Microsatellite Markers for Pheasant Species

Pheasants are widely distributed in the southwest of China, but many of them are endangered due to habitat fragmentation and environmental changes. Genetic diversity is crucial for species to maintain their evolutionary potential, and thus it is important to develop universal genetic markers for facilitating the assessment of genetic diversity and planning effective conservation actions in these endangered species. In this study, 471 microsatellite loci which are common among eight pheasant species were screened based on genome data, and 119 loci were selected to develop microsatellite markers. After PCR amplifications and reaction condition optimizations, and validation of microsatellite loci in 14 species of 11 genera within Phasianidae. Finally, 49 potentially universal microsatellite markers in pheasant species were obtained. These microsatellite markers were successfully applied to assess the genetic diversity of 3 pheasant species. The Sichuan hill partridge (Arborophila rufipectus), blood pheasant (Ithaginis cruentus), buff-throated partridge (Tetraophasis szechenyii) and Sichuan hill partridge had a relatively low genetic diversity level. These 49 microsatellite loci are potentially universal microsatellite loci for pheasants and are of great significance to establish a shared platform in population genetics study of pheasants.

Whole-genome resequencing confirms the genetic effects of dams on an endangered fish Hemibagrus guttatus (Siluriformes: Bagridae): A case study in a tributary of the Pearl River

Dam construction in riverine ecosystems has fragmented natural aquatic habitats and has altered environmental conditions. As a result, damming has been demonstrated to threaten aquatic biodiversity by reducing species distribution ranges and hindering gene exchange, leading to the inability to adapt to environmental changes. Knowledge of the contemporary genetic diversity and genetic structure of fish populations that are separated by dams is vital to developing effective conservation strategies, particularly for endangered fish species. We chose the Lianjiang River, a tributary of the Pearl River, as a case study to assess the effects of dams on the genetic diversity and genetic structure of an endangered fish species, Hemibagrus guttatus, using whole-genome resequencing data from 63 fish samples. The results indicated low levels of genetic diversity, high levels of inbreeding and decreasing trend of effective population size in fragmented H. guttatus populations. In addition, there were significant genetic structure and genetic differentiation among populations, suggesting that the dams might have affected H. guttatus populations. Our findings may benefit management and conservation practices for this endangered species that is currently suffering from the effects of dam construction.

Range wide genetic differentiation in the bull kelp Nereocystis luetkeana with a seascape genetic focus on the Salish Sea

IntroductionIn temperate regions, one of the most critical determinants of present range-wide genetic diversity was the Pleistocene climate oscillations, the most recent one created by the last glacial maximum (LGM). This study aimed to describe N. luetkeana genetic structure across its entire range (Alaska to California) and test different models of population connectivity within the Salish Sea. This region was colonized after the LGM and has been under increased disturbance in recent decades.MethodsWe utilized microsatellite markers to study N. luetkeana genetic diversity at 53 sites across its range. Using higher sampling density in the Salish Sea, we employed a seascape genetics approach and tested isolation by hydrodynamic transport and environment models.ResultsAt the species distribution scale, we found four main groups of genetic co-ancestry, Alaska; Washington with Vancouver Island’s outer coast and Juan de Fuca Strait; Washington’s inner Salish Sea; and Oregon with California. The highest allelic richness (AR) levels were found in California, near the trailing range edge, although AR was also high in Alaska. The inner Salish Sea region had the poorest diversity across the species distribution. Nevertheless, a pattern of isolation by hydrodynamic transport and environment was supported in this region.DiscussionThe levels of allelic, private allele richness and genetic differentiation suggest that during the LGM, bull kelp had both northern and southern glacial refugia in the Prince of Wales Island-Haida Gwaii region and Central California, respectively. Genetic diversity in Northern California sites seems resilient to recent disturbances, whereas the low levels of genetic diversity in the inner Salish Sea are concerning.

Genetic diversity and population structure of Mastacembelus armatus in the river systems of southern China revealed by microsatellites

The Zig-zag eel (Mastacembelus armatus) is an economically important species in southern China. Its natural resources have declined year by year due to overfishing. Understanding its genetic diversity and population structure is very important for resource conservations. Here, we first successfully developed 28 polymorphic microsatellite markers for zig-zag eels and ten of them were used to examine the genetic diversity and differentiation of 7 populations collected from the major river systems of south China. In total, 224 alleles were found with the 10 microsatellite loci in 7 populations, ranging from 4.6 (Nandujiang: NDJ) to 11.1 (Xijiang, XJ), with an average of 8.871 alleles. The average observed and expected heterozygosity ranged from 0.550 (NDJ) to 0.964 (Yuangjiang, YJ) and from 0.537 (NDJ) to 0.775 (Tanjiang, TJ), respectively. The average polymorphism-information content ranged from 0.472 (NDJ) to 0.757 (TJ). Hardy–Weinberg equilibrium test results revealed the loci showed differing deviation in different populations. In total, low level of genetic diversity was only found in HJ (Hanjiang) and NDJ populations. Besides, evidence of recent bottleneck was found in the HJ populations. Analysis of molecular variation showed that the percent variation within individuals (75.00%) was higher than that among populations (25%). In addition, population structure and the pairwise FST revealed that there was low differentiation among XJ, TJ and YJ populations. These data provide important genetic resources for understanding the population differentiation and facilitating genetic conservation and utilization of this species.

Morphological Traits and Nuclear Genetic Diversity of Coptis sp. in Hoang Lien National Park, Lao Cai Province, Vietnam

Coptis is a medicinal plant genus in the Ranunculaceae family, and is also known as “Hoang Lien” in Vietnamese. It is a perennial herb that grows in some regions of the world. However, Coptis is endangered and faces global threats. This study aimed to characterize some main morphological characteristics and performed a phylogenetic analysis of 11 samples of Coptis sp. collected from Hoang Lien National Park using nuclear DNA sequence analyses. All sample species have unique morphological traits with distinct yellow rhizomes and basal leaves with five segments. The petiole measures 13-25 cm and is smooth, while the leaf blade is ovate, ranging from 7 to 15.5 cm in length and 5.5 to 14 cm in width. The leaves are subleathery, glabrous on the underside, and sparsely puberulous on the veins on the upper side. The molecular characterization of Coptis sp. genotypes was determined by ITS markers. The length of the ITS1-ITS2 sequences varied from 363 to 371 nucleotides. The average nucleotide composition was 17.11% A, 31.25% C, 32.247% G and 19.41% T, respectively. The comparison with the GenBank database showed that the samples had 95.71- 96.37% similarity with the species Coptis quinquesecta. The genetic distance among the 11 Coptis samples fluctuated from 0.00 to 0.017. A neighbor-joining tree was constructed to show the genetic relationships among Coptis samples. The results indicated that this endangered species had low levels of genetic diversity. The study has provided valuable information for genetic-based conservation of this rare endemic species and suggested some conservation strategies.

High connectivity among Vesicomyid bivalves from cold seeps and deep-sea fans of Congo

Chemosynthetic ecosystems are scattered in the deep ocean, harbouring highly specialized communities, among which the degree of connectivity and dispersal is scarcely studied. This gap is largely due to limited range distribution, either real or due to highly partial exploration, preventing the availability of a sufficient number of samples for population genetic analysis. For the few species that escaped this gap, large-scale panmixia was often reported, raising wonders as to the evolutionary mechanisms involved in the first steps of speciation. Vesicomyid bivalves are one of the most abundant groups of chemosynthetic fauna, for which depth was proposed as an essential driver of differentiation. Early stages of speciation are thus expected to involve genetic differentiation along depth gradients. The vesicomyid bivalve Christineconcha regab was studied across widely separated localities along the Western African margin, from the cold-seeps of Regab pockmarks located at 3150 m depth on the Congo margin to the turbiditic lobes of the Congo deep-sea fan located at 5000 m depth, using mitochondrial (COI) sequences and eight microsatellite loci. Despite rather high density in relation to high organic matter availability, results obtained showed rather low levels of genetic diversity at both mtDNA and microsatellites. The main consistent pattern of differentiation was observed across depths from Regab pockmark (South-Western part) and lobe areas (Lobe B and C). This is likely due to the largest sample sizes characterizing Regab_SW and Lobe C allowing the detection of faint genetic differentiation, and possibly to a stronger signature in the demographically declining (thus acknowledgedly under sampled) Lobe B. Other significant results were not congruent among markers, suggesting low statistical power due to limited sample size or the occurrence of chaotic genetic patchiness. Altogether, the results suggest the occurrence of effective gene flow at regional scale, and departure from equilibrium in the recently discovered lobes of the Congo River, possibly resulting from unstable environmental conditions and recurrent events of extinction recolonization.

Genetic Diversity and Population Structure in Captive Populations of Formosan Sambar Deer (Rusa unicolor swinhoei).

Formosan sambar deer (Rusa unicolor swinhoei) are of great economic significance in Taiwan, resulting in a substantial increase in deer farming to meet the high demand for velvet antlers. Inbreeding depression and reduced genetic variability can lead to the deterioration of captive populations. In this study, 239 Formosan sambar deer were genotyped using 13 microsatellites to analyze their genetic diversity and population genetic structure. Our results indicate a high-resolution power of these microsatellites in individual discrimination and parentage analysis. However, captive populations exhibit a low level of genetic diversity, likely because of inbreeding and bottleneck effects. Both principal coordinate analysis (PCoA) and STRUCTURE analyses revealed two distinct and segregated genetic groups within the captive populations and indicated no clear population genetic structure among the captive populations. Introducing new genetic material from the wild through translocation offers a potential solution for mitigating the impact of inbreeding and enhancing genetic diversity. The comprehensive information obtained from these genetic analyses is crucial for the development of effective breeding strategies aimed at preserving and enhancing Formosan sambar deer populations.

Genetic and Ecological Approaches to Introduced Populations of Pumpkinseed Sunfish (Lepomis gibbosus) in Southwestern Europe

Freshwater systems are among the most affected by the introduction of exotic species. The pumpkinseed sunfish Lepomis gibbosus, a centrarchid native to eastern North America, is listed among the top ten introduced freshwater fishes with the greatest ecological impact globally. Despite this, genetic and evolutionary studies of the species are still scarce. Here, we analyzed the genetic variability of introduced populations of L. gibbosus using three mitochondrial genes (COI, d-loop, and ND1). In addition, we used species distribution modeling to compare the niche of introduced versus native populations to assess the present and potential future distribution of the species under different climate change scenarios. Compared with the native populations, introduced ones present a lower level of genetic variability, indicating these populations originated from a small number of individuals from the native (Atlantic) population in the USA and Canada. The low variability was likely driven by a founder effect and subsequent bottleneck, as often occurs in invasive species. Our modeling results suggest not only that L. gibbosus modified its niche during the invasion process in Europe but also the possible global expansion of the species under future climatic conditions, which could facilitate its establishment in almost all continents.

Are rare plant species less resistant than common ones to herbivores? A multi-plant species study using above- and below-ground generalist herbivores.

Rare plant species are suggested to be less resistant to herbivores than common species. Their lower apparency and the fact that they often live in isolated populations, resulting in fewer herbivore encounters, might have led to the evolution of reduced defences. Moreover, their frequent lower levels of genetic diversity compared with common species could negatively affect their resistance against enemies. However, the hypothesis that plant resistance depends on plant regional and local rarity, independently of habitat and competitive and growth strategy, lacks evidence. To test this hypothesis, we assessed the performance and preference of one belowground and three aboveground generalist invertebrate herbivores from different taxonomic groups as indicators of plant resistance. Herbivores were fed a total of 62 regionally and locally rare and common plant species from Switzerland. We accounted for differences in a plant's growth and competitive strategy and habitat resource availability. We found that regionally and locally rare and common plant species did not generally differ in their resistance to most generalist herbivores. However, one herbivore species even performed better and preferred locally and regionally common plant species over rarer ones, indicating that common species are not more resistant, but tend to be less resistant. We also found that all herbivore species consistently performed better on competitive and large plant species, although different herbivore species generally preferred and performed better on different plant species. The latter indicates that the use of generalist herbivores as indicators of plant-resistance levels can be misleading. Synthesis: Our results show that rare plant species are not inherently less resistant than common ones to herbivores. Instead, our results suggest that the ability of plants to allocate resources away from defence towards enhancing their competitive ability might have allowed plants to tolerate herbivory, and to become locally and regionally common.

Guidelines and quantitative standards for improved cetacean taxonomy using full mitochondrial genomes.

In many organisms, especially those of conservation concern, traditional lines of evidence for taxonomic delineation, such as morphological data, are often difficult to obtain. In these cases, genetic data are often the only source of information available for taxonomic studies. In particular, population surveys of mitochondrial genomes offer increased resolution and precision in support of taxonomic decisions relative to conventional use of the control region or other gene fragments of the mitochondrial genome. To improve quantitative guidelines for taxonomic decisions in cetaceans, we build on a previous effort targeting the control region and evaluate, for whole mitogenome sequences, a suite of divergence and diagnosability estimates for pairs of recognized cetacean populations, subspecies, and species. From this overview, we recommend new guidelines based on complete mitogenomes, combined with other types of evidence for isolation and divergence, which will improve resolution for taxonomic decisions, especially in the face of small sample sizes or low levels of genetic diversity. We further use simulated data to assist interpretations of divergence in the context of varying forms of historical demography, culture, and ecology.

Genomic analyses indicate the North American Ap-ha variant of the tick-vectored bacterium Anaplasma phagocytophilum was introduced from Europe

BackgroundAnaplasma phagocytophilum is a tick-vectored, obligately intracellular bacterium that infects a diversity of vertebrate hosts. In North America, the Ap-ha variant of A. phagocytophilum can cause dangerous infections in humans, whereas symptomatic human infections in Europe are rare. Conversely, the European host-generalist ecotype of A. phagocytophilum frequently causes illness in domestic ruminants while no comparable infections have been recorded from North America. Despite these differences in pathogenicity, the Ap-ha variant is closely aligned phylogenetically with the European host-generalist ecotype. Furthermore, North American populations of A. phagocytophilum are less genetically diverse than those in Europe. Taken together, these observations suggest that the North American Ap-ha variant may represent an introduced population of this bacterium.Methods Data from publicly available whole genomes of A. phagocytophilum were used to compare phylogeographic patterns and the extent of genetic divergence between the North American Ap-ha variant and the European host-generalist ecotype.ResultsThe results confirm that North American Ap-ha samples are phylogenetically nested within the diversity of the European host-generalist ecotype, and that Ap-ha likely radiated within the last 100 years. As expected, the Ap-ha variant also exhibited relatively low genetic diversity levels compared to the European host-generalist ecotype. Finally, North American Ap-ha harbored significantly more derived alleles than the European host-generalist A. phagocytophilum population.ConclusionsCollectively, these results support the hypothesis that the Ap-ha variant was recently introduced to North America from Europe and underwent a strong genetic bottleneck during this process (i.e. a ‘founder event’). Adaptation to novel vectors may have also played a role in shaping genetic diversity and divergence patterns in these pathogenic bacteria. These findings have implications for future studies aimed at understanding evolutionary patterns and pathogenicity variation within A. phagocytophilum.Graphical

Open areas associated with traditional agriculture promote functional connectivity among amphibian demes in Mediterranean agrosystems

ContextFunctional connectivity across fragmented habitat patches is essential for the conservation of animal populations in humanized landscapes. Given their low dispersal capacity, amphibians in the Mediterranean region are threatened by habitat fragmentation and loss due to changes in land use, including agricultural intensification.ObjectivesWe assessed patterns of functional connectivity of a Near Threatened Mediterranean amphibian, the sharp ribbed newt (Pleurodeles waltl), in an agricultural landscape matrix in NW Spain subject to different intensification regimes.MethodsWe sampled newts in 17 ponds embedded in a terrestrial habitat matrix dominated by agricultural land uses. Genome-wide molecular markers (1390 SNPs) were used to assess patterns of genetic diversity and gene flow among ponds. We tested the role of landscape features on functional connectivity using isolation by resistance models incorporating information on Normalized Difference Vegetation Index (NDVI) data.ResultsWe found low levels of genetic diversity in all sampled populations. Global FST estimates and cluster analyses revealed shallow but significant genetic structure in the study area, with NDVI-based resistance models showing that open areas (rainfed crops and grasslands) offer lower resistance to gene flow and thus promote functional connectivity among demes.ConclusionsOur study highlights the important role of landscape features, such as open areas resulting from traditional rainfed agriculture, in promoting functional connectivity between amphibian populations in Mediterranean agrosystems. Conservation policies must adopt a functional network strategy and protect groups of inter-connected temporary ponds across the traditional agricultural matrix to efficiently preserve their associated biotic communities.