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Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a serious invasive crop pest native to Asia and currently widespread in many parts of the globe. However, little information is available on its seasonal abundance in southern Italian fruit crops, including Mount Etna (Sicily, Italy). Here, we aimed at investigating i) the pest seasonal flight activity, ii) its population genetics, and iii) the potential occurrence of associated parasitoids. To this end, traps were deployed in five locations of strawberry and cherry districts of East and North-West sides of the Mount Etna for one year. In addition, host-parasitoid interactions with wasp species sampled by sentinel fruit trapping were investigated under laboratory conditions. The East locations were warmer than the North-West ones, and flies were captured all year except in August. In the North-West locations no flies were caught during the winter. Fly captures peaked in late spring and autumn in all locations. Sequencing of a portion of the mithocondrial cytochrome oxidase I (COI) from individuals of D. suzukii indicated a population genetic identity suggesting a single source of invasion. The field trapping revealed the occurrence of one larval parasitoid, Leptopilina boulardi (Barbotin, Carton and Kelner-Pillault) (Hymenoptera: Figitidae), and two pupal parasitoids, Pachycrepoideus vindemiae (Rondani) (Hymenoptera: Pteromalidae) and Trichopria drosophilae Perkins (Hymenoptera: Diapriidae). Nevertheless, only the pupal parasitoids were able to successfully develop on D. suzukii in laboratory bioassays. While obtained results indicate that climatic conditions strongly affect the local fly population and represent the bases for developing sustainable D. suzukii management programs, native parasitoid impact on pest population dynamic should be further investigated in this region-specific context. [ABSTRACT FROM AUTHOR]

The first data on the population genetic structure of the Daphnia cristata Sars, 1862 and D. longiremis Sars, 1862 species (Anomopoda: Daphniidae) from the water bodies of Northern Eurasia are presented. The variability of the fragment of the 12S gene of the mtDNA for these taxa belonging to subgenus Daphnia (Daphnia) O.F. Müller, 1776 (Crustacea: Cladocera) in this region is studied, and a phylogenetic analysis performed. The genealogical relationships between haplotypes of the Daphnia cristata and D. longiremis species and their geographical distribution are shown. Our new data allow us to suggest a recent rapid spatial expansion for D. cristata during the Late Pleistocene and Early–Middle Holocene periods. According to the results of the study, the distribution of D. cristata and D. longiremis species are separated in the latitudinal direction with the zone of their contact in Central Yakutia. Our results provide convincing evidence for the influence of the Ice Ages and interglacials on the formation of modern genetic diversity and the phylogeographic structure of D. cristata and D. longiremis. [ABSTRACT FROM AUTHOR]

The blackbuck (Antilope cervicapra) is endemic to the Indian subcontinent. It occurs in a wide variety of habitats that range from open plains, grasslands, scrublands, and lightly forested areas. The current study provides insights into the existing genetic variation in blackbuck populations, which is crucial for enhancing population fitness and long-term survival. To understand the phylogeny and genetic diversity of blackbuck, we processed the pellet samples (n = 233) from 18 locations across their distribution range in India for MtDNACytb and control region. High haplotype (0.991) and nucleotide diversity (0.033) were observed in the populations. The mtDNA-based AMOVA indicated 41.73% genetic variations among the blackbuck populations of India. The results confirmed that the blackbuck has a unique haplotype in different locations that is not shared by other populations. Geographically, our results identified four genetically distinct clusters: Northern, Southern East, Southern West and Eastern central regions of India. The study reveals that an ancestral population initially separated into two groups, leading to the formation of the North and South clusters. Subsequently, the South population diverged further into three clusters: Southeast, Southwest, and Eastern-central populations. Neighbor-joining analysis suggested the Eastern-central region as part of the Southern East region, while Bayesian phylogeny indicated a separate clade emerging from the Eastern-central region at a later time. Bayesian skyline plots revealed a history of population equilibrium in the Northern region followed by a recent population expansion in Southern East, Southern West and Eastern-central regional populations. Demographic analysis suggests that blackbucks have effectively adapted to their respective landscapes. [ABSTRACT FROM AUTHOR]

Early orogeny and historical climate change strongly influenced the evolution and geological distribution of flora. To further understand the effects of the uplift of the Qinghai-Tibet Plateau (QTP) and Quaternary climatic oscillations on the evolution of modern alpine plants, we conducted a phylogeographic study on Semenovia malcolmii, which is distributed on the QTP and in adjacent areas. We sampled a total of 337 individuals from 45 populations and used a combination of two nuclear fragments (ITS and ETS) and three chloroplast fragments (rps16, trnL-trnT, and ndhF-rpl32) to analyze the genetic diversity and differentiation of the species and evaluated the impact of early climatic and geological events on the genetic structure of the populations. Thirty-four nuclear rDNA haplotypes and 33 plastid haplotypes were identified and they formed three branches in the phylogenetic tree. This important phylogenetic structure suggested that S. malcolmii may have experienced long periods of geographic isolation. Based on molecular clock analysis, two divergence events occurred within the species, at approximately 3.34 Ma and 2.57 Ma, leading to the formation of the three major lineages. The populations of S. malcolmii exhibited relatively high genetic diversity and haplotype diversity throughout its entire distribution range. Therefore, we propose that S. malcolmii had multiple refugia across the QTP during the Quaternary glaciation. [ABSTRACT FROM AUTHOR]

Genetic connectivity and historical population expansion are characteristics that have largely been studied and observed in several members of the Lutjanidae family throughout the Western South Atlantic, particularly in Brazilian waters. In this study, the population genetic structure of Lutjanus jocu was investigated using four genomic regions: two from mitochondrial DNA (Control Region and Cytochrome B) and two nuclear genes (Delta 6 desaturase—intron 8 and Ribosomal Protein S7—intron 1), in 144 specimens distributed in six locations on the Atlantic coast of Brazil. The results revealed high levels of genetic diversity for both mtDNA and nuDNA markers, and intense gene flow, indicating, consistent with other studies, that this species is represented by a single genetic stock along the Brazilian coast. This is likely due to the high dispersal capacity of L. jocu larvae, driven by the main equatorial currents, as well as biological and ecological factors, contributing to a genetically homogeneous population. Historical demographic analysis and neutrality tests suggest that the species experienced population expansion, possibly during the Pleistocene. Information regarding the genetic structure of populations is extremely important, especially for species of high economic and fishing importance, and can be very useful in guiding stock management and management measures. [ABSTRACT FROM AUTHOR]

The hydrozoan Blackfordia virginica Mayer (1910), recognized as a successful invader, has been identified in brackish waters globally, posing a growing threat to ocean biodiversity. The species was discovered at Sihwa Lake in the western region of Korea in 2013, where the jellyfish blooms almost every year. However, there was a sudden bloom in 2021 at the Seomjin River estuary in the southern region of Korea. This study investigated the population genetic structure of B. virginica using mitochondrial DNA cytochrome c oxidase I (COI) from the samples collected from Sihwa Lake (SWL) and Seomjin River Estuary (SRE). We found high COI haplotype diversity within the Korean population, comprising 16 unique haplotypes that were highly differentiated based on geographical locations. Analysis of molecular variance (AMOVA) indicates significant genetic variation (FST = 0.6), which suggests multiple introduction events. Furthermore, a comparison of B. virginica COI data from Korea with GenBank records from the USA, China, India, and the Baltic Sea uncovers a global genetic structure within the species. Notably, the Korean population exhibited significant genetic differences from other populations, further making it challenging to determine the haplotype source origin. Nevertheless, the emergence of high genetic diversity and considerable genetic distance between the Korean population and other populations poses an intriguing puzzle, warranting further investigations. [ABSTRACT FROM AUTHOR]

The variability of the cytochrome b gene in 11 individuals of Korean field mouse from the Ussuri Nature Reserve located on the southern spurs of the Sikhote-Alin in the Przewalski Mountains has been analyzed. In the population, a high level of genetic diversity was identified owing to the discovery of individuals with haplotypes of three phylogenetic lineages, i.e., Amur, Korea, and Manchuria. The majority of individuals (72.73%) in the population had Amur haplotypes. A significantly lower frequency of occurrence of individuals with Korea haplotypes in the Ussuri Nature Reserve (9.09%) compared to the previously analyzed population of the Khasansky district (38.46%) located in the very south of the Primorsky krai was noted. In the Ussuri Nature Reserve, for the first time in the Russian Far East, two individuals with Manchuria haplotypes were discovered. Previously, only one finding of an individual with a similar haplotype was noted in the literature in the Heilongjiang province of Northeast China. It was suggested that individuals with haplotypes of the Korea phylogroup penetrate into the south of Sikhote-Alin from South Korea and with haplotypes of the Manchuria phylogroup from Northeast China. [ABSTRACT FROM AUTHOR]

The burrowing scorpions of the genus Scorpio Linnaeus, 1758 were considered to be a single polymorphic species, Scorpio maurus Linnaeus, 1758, distributed from West Africa across the Sahel and the Saharan highlands through the Maghreb and the Middle East, to Iran. After various revisions, the complex was treated as including 18 species and seven subspecies. Five additional new Scorpio species were recently described. However, doubts remain regarding the validity of these taxa due to the lack of reliable characters and the lack of genetic data for many species. The aim of the present study was to analyze the phylogenetic relationships and the evolutionary events that promoted diversification within the genus. Phylogenetic analyses were performed using 633 base pairs of the mitochondrial COI gene from 51 individuals collected in Tunisia, Morocco, and Egypt, combined with 74 previously published sequence data. Phylogenetic analyses revealed twenty distinct lineages forming two geographically separate clades, a Maghrebian clade and a Middle Eastern clade. Although most named species formed distinct lineages, various additional lineages were identified, highlighting potential unnamed species. Divergence time estimates indicate that the division within the genus Scorpio began during the Mid-Miocene, a period characterized by tectonic events coupled with climatic oscillations. Further differentiation occurred during the Miocene-Pliocene transition when climatic fluctuations resumed and the Mediterranean became increasingly arid. Speciation within the genus Scorpio may have been driven by the expansion of the savannas and Sahara Desert, the associated reduction of a once widespread rainforest into numerous micro-refugia in the mountains of the Mediterranean region, and by adaptation to these new habitats. [ABSTRACT FROM AUTHOR]

The Antarctic benthos is rich in biodiversity, with many species being endemic to the Southern Ocean. Multiple factors such as oceanic currents, glacial cycles and reproductive life stages have been attributed to the distribution of benthic dwelling invertebrates around the continent. The sea spider (Pycnogonida) Nymphon australe is a paternal brooder, which lacks a pelagic planktonic life stage. Typically brooding is assumed to suggest limited dispersal capabilities. Here we investigated the genetic structure of N. australe, a highly abundant pycnogonid species in the Southern Ocean to test assumptions of a documented circumpolar distribution. Previous studies with mitochondrial data have revealed that N. australe has high genetic diversity, limited gene flow, as well as distinct geographic structure. To resolve the phylogeographic structure of the circumpolar N. australe from the Antarctic continental shelf, we used 3RAD single nucleotide polymorphism (SNP) data from 111 individuals sampled from ten different, circumpolar geographic regions including the Western Antarctic Peninsula, Ross Sea, Weddell Sea, and Eastern Antarctica. Analyses revealed populations to have distinct regional populations with strong geographic structuring observed by locality and suggest the possibility that N. australe may be a species complex in the Southern Ocean. [ABSTRACT FROM AUTHOR]

The heteroplasmic mitogenome of the stingless bee Tetragonula laeviceps from Peninsular Malaysia consists of two variants (TL1-1 and TL1-2), both with 29,084 bp consisting of two segments: the “canonical” segment contains 36 genes—13 protein-coding genes (PCGs), 2 rRNA, and 21 tRNA genes; and the inverted repeat segment consists of 31 genes (11 PCGs, 2 rRNAs, and 18 tRNAs). In the TL1-2 variant, the (nad4-nad4L-trnP-trnS1) gene segment in the “canonical” genome of the TL1-1 variant was inverted to (trnS1-trnP-nad4-nad4L). Phylogenetic analyses based on 13 PCGs and 15 mt-genes reveal that T. laeviceps from Peninsular Malaysia and China form a lineage in the subclade consisting also of the Tetragonula lineage of T. mellipes, T. davenporti, T. carbonaria, and T. hockingsi. The genetic distances of 13 PCGs and 15 mt-genes between T. laeviceps of Peninsular Malaysia and China (p = over 10%) and between the taxa of China (p = about or over 10%) indicate that these three taxa are genetically distinct, reflecting the presence of a species complex. The large genetic distances, based on COX1 sequences, of p = over 10% among the taxa of T. laeviceps of China, Peninsular Malaysia, Sabah, Indonesia, and India indicate beyond reasonable doubt that they are not conspecific. Assuming that the Peninsular Malaysian taxon is T. laeviceps s.str., the taxa of China, Sabah, Indonesia, and India (as well as Thailand based on the 16S rRNA gene) warrant to be accorded as distinct cryptic species. Likewise, the taxonomic status of some taxa (e.g., Tetragonula fuscobalteata of Sabah and Sulawesi) needs clarification. [ABSTRACT FROM AUTHOR]

Prosorhochmidae, known as smiling worms, are hoplonemerteans of great interest to nemertologists, since some species display viviparity and hermaphroditism, both rare traits in this phylum, and can be found in terrestrial and marine environments. Prosorhochmus is a predominantly marine genus and was never recorded on the Brazilian coast. The present study documents the first record of the oviparous Prosorhochmus belizeanus, along with population genetic diversity analyses. Here, we sequenced cytochrome c oxidase subunit 1 (COI) and 16S ribosomal RNA (16SrRNA) regions from individuals of three localities along the Brazilian Northeast coast. From these analyses, we found moderate genetic diversity, no genetic structuring, and no clear geographical pattern. In addition, migration analysis evidenced some influence of the Brazilian Current in the species’ dispersion. Those findings indicate colonization by a small number of mtDNA lineages followed by population stability and shed light into the importance of deepening the knowledge about those organisms to elucidate genetic and dispersion patterns of oviparous invertebrates of rocky shores. [ABSTRACT FROM AUTHOR]

Coastal dunes are unique habitats, threatened by human activities. In biogeographical terms, coastal dunes are habitat islands, being discrete and distinct patches of similar habitat among themselves, separated from each other by a different type of habitat. Furthermore, coastal dunes harbor endemic species, adapted to living solely in the habitats found on specific dune systems. For example, the honeypot ant Myrmecocystus baja is endemic and restricted to coastal dunes of Mexico's Baja California Pacific coast. This ecological and biogeographical scenario led to the questions whether their geographical isolation is reflected in their genetic diversity and structuring, and how their demographic history is related with the formation of the dune system habitats. To answer these questions, population genetic, isolation-with-migration, and phylogeographical analyses were carried out, based on mitochondrial and five nuclear intronic markers. Minimal gene flow was detected only between two of the dune systems sampled; otherwise, the M. baja populations were found to be isolated and genetically structured, and their divergence generally pre-dated the modern-day dune systems. It is therefore highly likely that these ants were already present in paleodunes and that each of the populations was established from founder populations as the dunes formed. These findings highlight the importance of coastal dunes for species such as the honeypot ant from Baja California, in promoting genetic differentiation. [ABSTRACT FROM AUTHOR]

Wind is expected to be one of the main vectors of passive dispersal for small zooplankters between discrete, unconnected habitats. However, little is known about the differences in the dispersal capacity of species in relation to their propagule traits. Here we assessed the effect of volume and weight of diapausing eggs and substrate granulometry on the dispersal departure propensity of two differently body-sized rotifer species belonging to the Brachionus plicatilis complex using a wind tunnel experiment. Diapausing eggs of the larger species were also larger but, counterintuitively, were lifted by the wind to a greater extent than those of the smaller one. Further, diapausing eggs on the finer substrate were more exposed to the wind than those over the coarser one, and therefore higher departure rates were observed in the former. Overall, results show that wind is a relevant dispersal vector for the rotifers of the B. plicatilis species complex, with egg morphological traits and substrate granulometry being important factors modulating their dispersal. This study is a proof of concept for the departure phase of dispersal. Further studies on transfer and settlement phases are needed to get a complete picture of the dispersal potential of these organisms. [ABSTRACT FROM AUTHOR]

Wyeomyia smithii, the pitcher-plant mosquito, has evolved from south to north and from low to high elevations in eastern North America. Along this seasonal gradient, critical photoperiod has increased while apparent involvement of the circadian clock has declined in concert with the evolutionary divergence of populations. Response to classical experiments used to test for a circadian basis of photoperiodism varies as much within and among populations of W. smithii as have been found in the majority of all other insects and mites. The micro-evolutionary processes revealed within and among populations of W. smithii, programmed by a complex underlying genetic architecture, illustrate a gateway to the macro-evolutionary divergence of biological timing among species and higher taxa in general. [ABSTRACT FROM AUTHOR]

The Eurasian subspecies of the Goosander Mergus merganser consists of three subclades (Fennoscandian–British, E European–N Asian, and Alpine). Recently, this species expressed a rapid expansion in the Carpathians. In this study, we used mitochondrial DNA to track the origins of this population. Sequencing revealed that the majority of the Carpathian birds are related to the N Polish and Russian populations, whereas one sample has a haplotype known from the Alps. This mixed ancestry was probably caused by an outbreeding enhancement and/or enlarged habitat requirements that allowed the birds to settle in the mountain rivers of the Carpathians. [ABSTRACT FROM AUTHOR]

Three sardine species of Harengula and one of Opisthonema (Clupeiformes, Clupeidae) are known in the Western Atlantic, where the Amazon-Orinoco plume has been recognized as a major biogeographic barrier, albeit permeable to larger and generalist species. Here we used mitochondrial cox1 gene DNA sequences to check the lineage delimitation of both genera, testing the influence of the Amazon-Orinoco barrier (AOB) and marine provinces on their phylogeographic structure. Results indicate that the two genera are differently affected by the AOB, including cryptic speciation in Harengula and population structure in Opisthonema. Harengula show a broad distribution in the Brazilian Province (BRA) distinct from H. clupeola and H. jaguana from the Greater Caribbean Region (GCR). Divergence time between Harengula from the GCR vs. BRA was estimated as about 2.4 Mya, which coincides with the period of increasing sediment and freshwater discharge of the Amazon River in the Atlantic. Results also indicate the existence of a single species of Opisthonema, albeit with population structuring related to the marine provinces. Since species of both genera are relevant to artisanal fisheries and the maintenance of oceanic ecosystems, these results may help in fisheries management of these important marine resources. [ABSTRACT FROM AUTHOR]

El'gygytgyn is the only ancient lake in the Arctic that avoided continental-scale glaciations. This lake is located on an arid mountain plateau, far from the main routes of post-glacial freshwater fish dispersal, and it is therefore challenging to consider the local fauna in a historical context. Here we present a study of the ecology and evolutionary history of the local charr complex (genus Salvelinus). We found that the endemic charrs exhibit extreme longevity, contrasting lifestyles and phenotypes. Salvelinus svetovidovi is a relic benthivorous species. The remaining charrs are descendants of Salvelinus taranetzi. Mitochondrial and microsatellite DNA polymorphisms analyzed in them and in charrs from surrounding basins indicate that S. taranetzi invaded the lake from Arctic Chukotka in the late Pleistocene as two distinct, previously diverged lineages. Descendants of both lineages occupied the pelagic food chain. The first lineage has flourished as a monomorphic planktivorous population since colonization. The second represents an example of a recent in-lake adaptive divergence, in which a deepwater piscivore specialist formed a new epilimnetic ecomorph of an impressive size (up to 9.0 kg). We suggest that this diversification was triggered by modern warming in the Arctic, which led to the formation of a productive littoral ecosystem. [ABSTRACT FROM AUTHOR]

Anthropogenic activities such as mining pose a putative threat to deep-sea ecosystems and baseline studies of key indicator species are required to assess future loss of biodiversity. We examined population genetic structure, connectivity, cryptic diversity and phylogeography of the deep-sea scavenging amphipod, Abyssorchomene distinctus, using DNA sequence data (mitochondrial COI and nuclear 28S genes) from 373 specimens collected from six abyssal basins. We observed a striking absence of cryptic diversity, suggesting a single, widely distributed species in the Pacific and Indian Ocean. A single event of population expansion across distances up to 24,000 km is further supported by a main ancestral haplotype in the star-like shaped COI haplotype network, a skewed nucleotide mismatch distribution and deviations from evolutionary neutrality tests. In the Pacific, A. distinctus showed weak genetic population structure and low differentiation between the basins of the Clarion-Clipperton Zone and the DISCOL Experimental Area, suggesting a possible higher chance of recovery from deep-sea mining impacts. However, since our data indicate a single recent historic population expansion event, A. distinctus populations will likely be affected to unknown extents, as the exact drivers shaping distribution and dispersion of A. distinctus are still unclear. [ABSTRACT FROM AUTHOR]

One of the most important steps in identifying priority areas for conservation is the assessment of species richness and their extinction risks. While most species remain undescribed, the identification of cryptic lineages is frequent in phylogenetic and phylogeographic studies. This is particularly common in troglobites, exclusively subterranean organisms. The Jandaíra Formation, in the Brazilian semiarid, combines the occurrence of extensive karstic areas with hundreds of caves and subterranean aquifers in a region with intense paleoclimatic changes. This region is recognized for the richness of troglobitic species, some of which are widely distributed in heterogeneous areas. This suggests cryptic lineages that can be differentially exposed to anthropogenic threats, with distinct extinction risks regarding the nominal taxa of which they putatively belong. To test it, a large sampling was conducted and, by means of lineage delimitation analyses, the genetic structure of four troglobitic taxa, three aquatic and one terrestrial, was evaluated. In addition, the extinction risk of these lineages was assessed and priority areas for conservation were identified. The results indicated that while Cirolanidae sp. 1 (Isopoda) is a single species widely distributed, Cirolanidae sp. 2, Potiberaba porakuara (Amphipoda) and Kinnapotiguara troglobia (Hemiptera) present an extensive diversity of cryptic and endemic lineages, most of which are likely new threatened species. Furthermore, two priority areas for conservation of these lineages were identified. Thus, comparative phylogeography may represent a first step in the conservation of subterranean taxa, indicating areas that should be prioritized in a context of increasing threats and dwindling conservation resources. [ABSTRACT FROM AUTHOR]

Cetaceans and pinnipeds are lineages of mammals that have independently returned to the aquatic environment, acquiring varying degrees of dependence on it while sharing adaptations for underwater living. Here, we focused on one critical adaptation from both groups, their ability to withstand the ischemia and reperfusion experienced during apnea diving, which can lead to the production of reactive oxygen species (ROS) and subsequent oxidative damage. Previous studies have shown that cetaceans and pinnipeds possess efficient antioxidant enzymes that protect against ROS. In this study, we investigated the molecular evolution of key antioxidant enzyme genes (CAT, GPX3, GSR, PRDX1, PRDX3, and SOD1) and the ROS-producing gene XDH, in cetaceans and pinnipeds lineages. We used the ratio of non-synonymous (dN) to synonymous (dS) substitutions as a measure to identify signatures of adaptive molecular evolution in these genes within and between the two lineages. Additionally, we performed protein modeling and variant impact analyzes to assess the functional consequences of observed mutations. Our findings revealed distinct selective regimes between aquatic and terrestrial mammals in five of the examined genes, including divergences within cetacean and pinniped lineages, between ancestral and recent lineages and between crowns groups. We identified specific sites under positive selection unique to Cetacea and Pinnipedia, with one site showing evidence of convergent evolution in species known for their long and deep-diving capacities. Notably, many sites under adaptive selection exhibited radical changes in amino acid properties, with some being damaging mutations in human variations, but with no apparent detrimental impacts on aquatic mammals. In conclusion, our study provides insights into the adaptive changes that have occurred in the antioxidant systems of aquatic mammals throughout their evolutionary history. We observed both distinctive features within each group of Cetacea and Pinnipedia and instances of convergence. These findings highlight the dynamic nature of the antioxidant system in response to challenges of the aquatic environment and provide a foundation for further investigations into the molecular mechanisms underlying these adaptations. [ABSTRACT FROM AUTHOR]

The widespread occurrence of the wild boar Sus scrofa, its controversial role in natural communities, and its close relationship with humans make this animal an important and convenient subject for studying the history and evolution of natural communities. The territory of Central Asia has been poorly represented in mammalian phylogeographic studies, namely in the case of wild boars and domestic pigs. In this study, we provide new information on wild boar genetic diversity in Central Asia in terms of mitochondrial and Y-chromosome markers and compare the set of haplotypes observed in Uzbekistan and Kazakhstan with those from other parts of the species' range. The wild boar population in Central Asia is characterized by high uniqueness of mitochondrial and Y-chromosome markers and high haplotype diversity (as compared to other Asian regions). A maternal lineage marker (mitochondrial-DNA control region) clearly places this species in the Asian clade, whereas a paternal lineage markers (AMELY + USP9) positions it closer to wild boars from the western clade. Thus, the molecular genetic data supported the existence of a regionally specific subspecies of the wild boar: S. s. nigripes Blanford, 1875. Median-joining network analysis showed that Central Asia may be a center of dispersal and formation of S. scrofa genetic lineages in North Asia. [ABSTRACT FROM AUTHOR]

In IUFRO experimental plots of 1969–1970, two 'Italian' provenances, I11 and I15, of unknown genetic origins, have consistently exhibited remarkable performance and stability over time and space in previous studies. It was deemed essential to acquire knowledge about the genetic origin area and conduct a genetic characterization of these two Italian provenances for their formal registration. Considering the observed intraspecific genetic variation across the American geographic cline, it was imperative to ensure that the selected provenances adequately represented diverse eco-physiological regions within the species range. To achieve this, most likely American provenances were selected, building upon historical document hypotheses and aiming to cover various geo-climatic areas. Specifically, five coastal variety and three interior variety provenances were chosen, two for each major geo-climatic region. The results obtained, using seven microsatellites, through four genetic structure analysis methods, predominantly attributed I11 to the area around 1080 origin, Washington Cascades region and 1094, Oregon Coast area. Similarly, I15 was primarily attributed to the area around the 1096 provenances, the Oregon Cascades region, compared to other coastal areas it appeared to differ. Among the three interior origins, 1162 from Arizona, Interior South area, exhibited intermediate genetic characteristics between the two varieties, despite its geographical location falling within the range of the interior variety. Similar to our expectations, comparing the distinct characteristics of the origin areas for each Italian provenance, it becomes feasible to complete their certification as 'seed stands' and to plan an appropriate management strategy for the species' diffusion. [ABSTRACT FROM AUTHOR]

In this study, the influence of geographic isolation on the levels of morphological and genetic differentiation among populations of the karst forest-adapted Pilea pteridophylla (Urticaceae) was evaluated. Based on our results, there is a strong morphological differentiation among the only two know populations of Pilea pteridophylla. Both populations can be clearly differentiated based on vegetative and reproductive characters, and the observed variation is geographically structured. Moreover, our genetic data from the chloroplast genome show strong levels of population differentiation and no shared haplotypes were observed between populations. Also, our estimation of divergence times supports a long-term isolation hypothesis between populations. Based on our results, dispersal seed limitation, long-term forest isolation and topographic heterogeneity (local adaptation) are related to high levels of endemism and species turnover in the mountain karst forests of Mexico. [ABSTRACT FROM AUTHOR]

Corsica and Sardinia are amongst the largest islands of the Western Mediterranean. Their complex geological history included belonging to the European–Iberian continental margin (close to current-day Catalonia and Provence) and varying degrees of isolation for the last 30 million years, leading to peculiar, highly endemic faunas and floras. This is especially true for their earthworm faunas, which include endemic species of several Lumbricoidea genera and the endemic family (or subfamily) Diporodrilidae. Only three species have been described for the morphologically unique Diporodrilus, but there exists evidence for wide morphological variability within them and the existence of several species-level genetic lineages within Corsica. This work aimed to investigate the genetic diversity and phylogenetic relationships between the genetic lineages of Diporodrilus from Corsica and Sardinia (based on the sequences of 5 mito-nuclear markers), to perform an integrative systematics revision combining species delimitation techniques and morphological data, and to obtain a time-calibrated phylogeny of Diporodrilus and other Corso-Sardinian Lumbricoidea. Within 15 populations of the morphospecies Diporodrilus omodeoi and Diporodrilus pilosus across Corsica and Sardinia, 10 species-level genetic lineages were detected. Phylogenetic independence, high genetic divergence and morphological differences provided the support for the description of five new pseudocryptic species: Diporodrilus rotundus sp. nov., Di. jorgei sp. nov., Di. minor sp. nov., Di. meridionalis sp. nov. and Di. telti sp. nov. Time-calibrated phylogenetic inference estimated the age for genus Diporodrilus at 65.9 Mya; even if other Corso-Sardinian genera were significantly younger, all of them presented deep divergences predating the break-off of the microplate from the continent. The almost threefold increase in the known diversity of Diporodrilus stresses the need for comprehensive earthworm diversity inventories in both Sardinia and Corsica, and for studies on their ecological role and conservation status. The close correspondence between some geological and cladogenetic events suggest that the distribution of Corso-Sardinian earthworms could be used to inform standing geological controversies. [ABSTRACT FROM AUTHOR]

The genus Gracilinanus ranges from savannas to dense forests in South America, yet its systematics have never been thoroughly investigated across its wide distributional range. We assessed Gracilinanus phylogenetic relationships, species boundaries, and geographical limits using mtDNA sequences. Our analysis confirmed the distinctiveness of the six recognized species (G. aceramarcae, G. agilis, G. emiliae, G. marica, G. microtarsus, and G. peruanus), with a mean p-distance for interspecific nucleotide sequence divergences ranging from 13–16.2% and robust phylogenetic support (BPP > 0.95; BS > 75%). Refined species delimitation approaches (GMYC, PTP, ASAP) revealed potential cryptic diversity, suggesting up to 20 candidate species. Three geographically structured and divergent lineages (4.1–4.8% sequence divergence) were identified within G. agilis, extending its Cerrado range. Within G. emiliae, we found divergence values ranging from 4.7–5.7% and the first known record for the northeastern Atlantic Forest. Three divergent clades were recovered within G. microtarsus (9.0–9.8% sequence divergence), including a new lineage for the northern Atlantic Forest. For G. peruanus, we found two divergent lineages (7.2%) and the first documented occurrence for Amazonian lowland forest. This comprehensive sampling revealed greater genetic diversity in Gracilinanus, extending its geographic limits. Here we propose nine putative new species, emphasizing a hidden diversity that warrants formal description and further increases the taxonomic diversity of this genus. These newly identified lineages underscore the urgency of inventorying and conserving the threatened ecosystems of the Cerrado and Atlantic Forest hotspots. [ABSTRACT FROM AUTHOR]

Life history characteristics of cryptobenthic reef fishes (CRFs), such as their fast growth and reproductive rates, near-shore larval retention and high turnover, predispose these species to rapid diversification and cryptic speciation. This may be particularly true for isolated CRF populations. The sailfin blenny, Emblemaria pandionis, is widespread throughout the Caribbean and is found on the reefs of the Flower Garden Banks, an isolated reef system in the NW Gulf of Mexico. Using DNA barcoding and multi-locus delimitation, we show that E. pandionis is a species complex comprised of at least four distinct taxonomic units in the Caribbean, one at the Flower Garden Banks, a second in eastern Florida, a third in the central Caribbean and a fourth in Curaçao. The phylogenetic relationships within the E. pandionis species complex are defined by well-established phylogeographic barriers to gene flow in the Caribbean. Populations of E. pandionis from eastern Florida are genetically distinct from populations found in the Bahamas, highlighting the role of the Florida Strait as a strong barrier to gene flow and populations in Curaçao are deeply divergent from all other populations sampled in the Caribbean. Results from this study highlight the roles of isolated reefs and ocean currents in the speciation of cryptobenthic reef fishes. [ABSTRACT FROM AUTHOR]

Despite the current disjoint distribution of Amazonian and Atlantic forests, evidence suggests past historical connections. Here we investigated the historical connections between three didelphid mammal species from Amazonian and Atlantic forests (Caluromys philander, Marmosa demerarae, and M. murina) using comparative phylogeography and paleodistribution models. We generated ecological niche models from the present until the Pliocene to evaluate changes in distributions over time, focusing on the previously suggested connection routes. We inferred divergence times between populations of each species using the mitochondrial Cytochrome b, estimated the phylogeographic relationships with haplotype networks, and calculated the genetic distances. All species exhibited populations that were separated between the Amazonian and Atlantic forests around 1–2 million years ago, while some populations showed more recent divergences. Paleodistributions were more extensive for periods predating the estimated times of divergence for all species, becoming narrower after this period. We suggest that the climatic oscillations during the onset of the Pleistocene largely influenced the phylogenetic structuring of these forest-dwelling species. This led to the separation of populations currently restricted to Amazonian or Atlantic forests. Our findings also point to repeated connections over time, with both North- and South-Eastern routes compatible with ancient connections. This represents the first simultaneous evaluation of past connections between Amazonian and Atlantic forests combining phylogeographic inferences with paleodistribution models for didelphid marsupials. We suggested the relation of the responses to past climate change, such as increases in the paleodistribution, and species resilience. [ABSTRACT FROM AUTHOR]

Foot-and-mouth disease is a highly contagious disease affecting cloven-hoofed animals, resulting in considerable economic losses. Its causal agent is foot-and-mouth disease virus (FMDV), a picornavirus. Due to its error-prone replication and rapid evolution, the transmission and evolutionary dynamics of FMDV can be studied using genomic epidemiological approaches. To analyze FMDV evolution and identify possible transmission routes in an Argentinean region, field samples that tested positive for FMDV by PCR were obtained from 21 farms located in the Mar Chiquita district. Whole FMDV genome sequences were obtained by PCR amplification in seven fragments and sequencing using the Sanger technique. The genome sequences obtained from these samples were then analyzed using phylogenetic, phylogeographic, and evolutionary approaches. Three local transmission clusters were detected among the sampled viruses. The dataset was analyzed using Bayesian phylodynamic methods with appropriate coalescent and relaxed molecular clock models. The estimated mean viral evolutionary rate was 1.17 × 10− 2 substitutions/site/year. No significant differences in the rate of viral evolution were observed between farms with vaccinated animals and those with unvaccinated animals. The most recent common ancestor of the sampled sequences was dated to approximately one month before the first reported case in the outbreak. Virus transmission started in the south of the district and later dispersed to the west, and finally arrived in the east. Different transmission routes among the studied herds, such as non-replicating vectors and close contact contagion (i.e., aerosols), may be responsible for viral spread. [ABSTRACT FROM AUTHOR]

An analysis of the genetic diversity of the field vole was carried out with the inclusion of new data on the complete sequences of the cytochrome b gene from the least studied area of the range of the species—the central part of Northern Eurasia (20 localities of the East European Plain, the Urals, Western and Eastern Siberia). The obtained results are generally consistent with modern view on the phylogeography of the species, but indicate the previously not investigated genetic heterogeneity of the Eastern clade, which occupies the entire Asian part of the range of the species and its European part to Northern and Eastern Europe. A comparison of the results of analysis of genetic diversity with the age of paleontological findings carried out using the Urals as an example allows one to assume that climatic changes in the Late Pleistocene and Holocene could not have led to the complete extinction of the species in the region, but to the spatial redistribution of its populations and to the complete or partial replacement of some genetic groups by others. [ABSTRACT FROM AUTHOR]

Context: Understanding genetic structure at multiple spatial scales and identifying drivers of genetic isolation are important for developing comprehensive conservation plans including for grassland conservation efforts. However, few studies account for multiple genetic isolation processes nor partition genetic variance among these processes. Objectives: We assess key processes that can create spatial genetic patterns including isolation by barrier (IBB), isolation by distance (IBD), and isolation by environment (IBE) for a widespread pocket gopher species (Geomys bursarius) and a spatially restricted subspecies (Geomys bursarius illinoensis). We further partition genetic variation to each isolating effect and identify genetic variation that was shared between processes. Methods: We used seven microsatellites to determine spatial genetic clustering and identify environmental factors impacting genetic similarities. Then, we used redundancy analysis to partition variance explained by IBB, IBD, and IBE. Results: Major rivers including the Mississippi River acted as barriers and explained the most genetic variation across the species. In contrast, IBD explained the most genetic variation for G. b. illinoensis. Gophers had genetic associations to soil sand percent and soil color, but IBE uniquely explained a small amount of genetic structure for G. bursarius, with additional variation shared with other isolating processes. Conclusions: Gopher genetic structure resulted from barriers, distance, and environmental factors at the species range as well as for a subspecies' region, but the relative amount of genetic variance assigned to unique isolating processes differed between scales. Delineation of conservation units should consider major rivers as natural boundaries, and finer-scale management should identify and protect areas close to source populations with similar soil friability. Our study exemplifies how analyzing gene flow at rangewide and regional scales can aid managers in developing localized strategies that fit within broader conservation units. [ABSTRACT FROM AUTHOR]

Speciation processes in the marine environment are often directly associated with vicariant events. In the case of loliginid squids (Cephalopoda: Loliginidae), these processes have been increasingly elucidated in recent years with the development of molecular technologies and increased sampling in poorly studied geographical regions, revealing a high incidence of cryptic speciation. Doryteuthis pealeii is a commercially important squid species for North Atlantic fisheries and has the second broadest geographic distribution in this genus. This study aimed to investigate the evolutionary history of this species and which biogeographic events may have influenced its diversification by assessing mitochondrial and nuclear markers. Our findings indicate that two previously detected lineages diverged from one another ~ 8 million years, compatible with the formation of the Caribbean and the establishment of the Amazon plume. Furthermore, separation between a North Atlantic and a Gulf of Mexico lineage during the Pleistocene period was noted. The inadequate classification of this cryptic diversity may have negative implications for the development of effective conservation and fisheries measures. [ABSTRACT FROM AUTHOR]

Here we report the first thorough genetic characterization of the long-understudied red deer population of Belarus in regards to its ancestry according to mtDNA sequence analysis. Employing a 346 base pair segment of the mitochondrial control region (d-loop) from 36 deer specimens of either sex recently harvested across the country, we have discovered 10 haplotypes belonging to 3 of the widely described European red deer lineages, or haplogroups: Iberian (A), Tyrrhenian (B), and Maraloid (E), clarifying the range limits of those lineages in the region. Combining this data with a comparative analysis of genetic diversity and historical records, we conclude that the Belarusian population of red deer has an artificially mixed origin, though it remains unclear how desirable such a state is, in terms of sustainable management, use, and conservation. Inquiries into ancient DNA are required to recognize the lineages closest to the autochthonous deer population of Belarus. [ABSTRACT FROM AUTHOR]

Genetic structure of the Maximowicz's vole Alexandromys maximowiczii was assessed using data on the mtDNA control region variability, and the high level of genetic variability was revealed for the species as a whole. Three phylogenetic groups ("east," "west," and "south") were distinguished, and within the "east" group, three subclades ("Chit," "Amur," and "Khab") were identified. All phylogenetic groups and subclades were characterized by mainly allopatric geographical distribution across the species range with one "hybrid" sampling found in the vicinity of the settlement of Savvo-Borzya (Zabaykalsky krai), the individuals of which had different variants of the mt genotype. One individual carried the "west" variant, and the second one—the "east"/"Amur" variant. The revealed phylogeographic structure was generally congruent with the differentiation pattern as revealed by the chromosomal forms, but did not agree with the previously accepted subspecies system. Complex intraspecific subdivision of the Maximowicz's vole, revealed at different organization levels (molecular genetic, as well as chromosomal), reflects not only complex geography of the study area, but also the history of dynamic changes in the natural environment. [ABSTRACT FROM AUTHOR]

Coastal wetland ecosystems support unique biodiversity and are imminently threatened by climate change-driven sea level rise. However, the impact of climate change on their demographic and evolutionary histories is poorly understood. To improve our understanding, we examined how past climatic events have shaped the evolutionary history of the salt marsh harvest mouse (Reithrodontomys raviventris), an endangered species and a salt marsh habitat specialist, completely restricted to coastal wetlands in the San Francisco Estuary (SFE). We used whole mitochondrial genome sequences of 102 salt marsh harvest mice to characterize phylogeography and demographic history. Then, we predicted the ancient distribution of salt marsh habitat and examined correspondence between divergence, demographic history, and changes in ancient marsh habitat caused by sea level rise. A Bayesian Skyline Plot revealed demographic expansions during periods of sea level rise, particularly during the formation of the modern SFE (~ 10 kya), and rapid decline consistent with recent anthropogenic landscape change. Bayesian estimates of divergence time were consistent with subspecies divergence ~ 10 kya, and subpopulation divergence ~ 5 kya, consistent with multiple episodes of vicariance caused by Holocene sea level rise. Spatial Analysis of Molecular Variance and ΦST revealed a mismatch between the morphological and molecular subspecies assignment of two populations. Our study implicates sea level rise as a force of demographic change and evolutionary divergence in coastal marsh ecosystems. Our study also aids conservation of an endangered species by clarifying genetic subspecies boundaries and highlighting the unique nature of isolated populations that are increasingly threatened by modern sea level rise. [ABSTRACT FROM AUTHOR]

The intricate river systems forming various drainages play a crucial role as natural barriers, impeding the gene flow of extensively distributed taxa. However, there have been limited studies focused on examining the impact of river barriers on the phylogeography of plant lineages with restricted distributions. Cycas chenii X. Gong & W. Zhou, an endemic plant species found alongside rivers in the Yunnan region of China, possesses considerable research significance. By utilizing double digest restriction site associated DNA sequencing, we investigated the genetic diversity, genetic structure, and population historical dynamics for C. chenii to explore the influence of rivers on this species. We found C. chenii displayed greater genetic diversity in comparison to other Cycas species, with the HB population, a sole population situated in southwest Red River Region, exhibiting the highest genetic diversity at the population level. The AMOVA results revealed that the predominant genetic variations existed within populations (84.46%). Mantel test revealed a significant positive correlation between genetic differentiation and geographic distance in C. chenii. Both genetic structure and phylogenetic analyses strongly corroborate the categorization of the ten populations of C. chenii into three distinct clusters, aligning with their respective rivers and geographic distributions. Furthermore, the populations of C. chenii experienced three bottlenecks within the last five million years, which could be correlated with geological events. Based on these findings, specific conservation strategies were proposed for the three evolutionary significant units (ESUs) of C. chenii, each of which encounters distinct conservation challenges. [ABSTRACT FROM AUTHOR]

Human-mediated introductions of non-native species are expected to increase globally and threaten native biodiversity. Lepomis auritus (Redbreast Sunfish), a carnivorous freshwater fish native to rivers in eastern North America, has been introduced far outside of its native range due to its popularity in recreational fisheries. However, poor documentation of introductions and lack of thorough ichthyofaunal surveys before the mid-20th century have complicated our understanding of the establishment and spread of non-native L. auritus over the past 90 years, precluding effective management. We conducted phylogenomic analyses using ddRAD data from 197 specimens of L. auritus collected throughout the known geographic range of the species to reconstruct the introduction history of the species. Our protocols allow for the reconstruction of complicated introduction routes and reveal that L. auritus in Texas is the result of a single-source introduction from the Suwannee River, the population in the upper Tennessee River has two sources of introduction from the Savannah River and the northeastern rivers that drain into the Atlantic Ocean, and the populations in the middle Tennessee River and the Mobile River Basin have sources from the upper Tennessee River system and the Apalachicola River Basin. Ecological and evolutionary investigations of the non-native populations of L. auritus will broaden the understanding of invasion dynamics in species of Lepomis and other non-native freshwater fishes in North America. Our study provides critical information for the conservation of native populations and invasive management of non-native populations of L. auritus. [ABSTRACT FROM AUTHOR]

Candidia barbata is a primary freshwater fish distributed in the western portion of Taiwan Island, but this species has also been found in southern and eastern Taiwan. Previous studies have documented that human-intervention populations of freshwater fishes exist not only in eastern Taiwan but also widely. To investigate the native population genetic diversity and structure and evaluate the sources of human-intervention populations of C. barbata, the sequences from the mitochondrial DNA cytochrome b gene and d-loop region were analyzed. These results indicated that (1) the native populations were distributed in northern, northwestern, western and southwestern Taiwan; (2) the human-intervention populations originated from multiple sources, including native populations and aquarium stocks; (3) most aquarium stocks originated from the northwestern and western populations; (4) the geological history of Taiwan Island shaped the native distribution range and population genetic structure; (5) the effective size of the populations declined greatly; and (6) the native populations could be assorted into three distinct management significant units (α − γ). Finally, the human-mediated dispersal of freshwater species in Taiwan was more severe than expected and should be evaluated and monitored carefully. [ABSTRACT FROM AUTHOR]

Significant progress in our knowledge of Beringian biodiversity and in the technologies available for biodiversity research has been made in the several decades since a comprehensive biogeographic synthesis of Beringian freshwater fishes was compiled and published in 1986. Further, the fish fauna of Beringia and, more broadly, of high latitude freshwater systems of the northern hemisphere face some of the most intense well documented effects of global climate change. Here we synthesize current understanding of how the dynamic spatial and ecological landscapes of Pleistocene glaciations have shaped the distribution of taxonomic and genetic diversity in fish faunas of Beringia. Through a more complete integration of knowledge obtained in studies of fishes in Russian drainages, we aimed to identify promising strategies to test alternative biogeographic hypotheses on the roles played by the Bering land bridge, paleorivers and glacial history in intercontinental faunal movement. We focus on freshwater fishes of the Bering Strait region, which live in an environment that is premised on extreme instability and profound changes in long-term connectivity for fishes and offers opportunities to assess long-term evolutionary trends in both speciation and life history variation. Such information is critical for both our scientific understanding of evolutionary processes in fishes and valuable for those tasked with the challenges of management and conservation of natural resources in this expansive, dynamic and remote region. We provide an overview of Beringian freshwater ichthyofauna and examine genetic differentiation among population units within these lineages. We also examine evidence for how long population units have been separated based on historic glacially-related separations and the more recent marine barrier of the Bering Strait that constrains freshwater or diadromous species based on their ability to disperse in salt water. Our review concludes on how Arctic and sub-Arctic fishes may adapt and persist in their dynamic environment considering low genetic diversity, the role of adaptive introgression, and epigenetic variation. We find that Beringian fishes may poorly fit traditional taxonomic categories and the designation of conservation units below the species level may be of great practical application. Furthermore, as hybridization is documented to increase in the Arctic, the use of this process for ecological monitoring may also be of high utility with Beringian fishes. [ABSTRACT FROM AUTHOR]

The Japanese beetle, Popillia japonica, is a highly polyphagous Scarabaeidae native to Japan that colonized North America and Azores in the last century and has recently invaded Italy and Switzerland. Considering its economic impact on the horticulture and turfgrass industries, this species was ranked within the EU priority pests list in 2019. According to the EU Convention on Biological Diversity, the identification of invasion routes is a pivotal aspect in an effective management program aimed at controlling invasive alien species. To reconstruct the source of introductions of this pest, we investigated the genetic variability of P. japonica in its native and invaded areas worldwide by analyzing 9 microsatellite loci and two mitochondrial genes, COX I and CytB. In its native area, P. japonica is structured into two populations: one in the southern and another in the northern-central region of Japan. A limited area within central Japan was identified as the putative source of the North American outbreak. Moreover, the ABC inference and phylogeographic reconstruction suggest that two European populations originated from two independent introductions. The Azores Islands outbreak occurred approximately 50 years ago and originated from the southeastern region of North America (For simplicity, in this paper North America refers to Canada and the USA), while the second introduction, more recently, occurred in Italy and Switzerland and originated from northeastern region of North America. [ABSTRACT FROM AUTHOR]

Loaches of the genus Lepidocephalichthys are ubiquitous in Peninsular India and the nearby continental-shelf island of Sri Lanka. Four valid species are reported from this region: L. thermalis, a species reported from across this region; L. jonklaasi, confined to rainforests in southern Sri Lanka; L. coromandelensis, from the Eastern Ghats and L. guntea, from the northern Western Ghats of the Indian peninsula. Here, based on collections from 25 locations in 13 river basins in Sri Lanka and 20 locations across India, including a dataset downloaded from GenBank, we present a molecular phylogeny constructed from the mitochondrial cytochrome b (cytb) and cytochrome c oxidase subunit 1 (cox1) sequences. We show that ancestral Lepidocephalichthys colonized Sri Lanka in the late Miocene. Multiple back-migrations to India, as well as colonizations from the mainland, took place in the Plio-Pleistocene. The persistence on the island of L. jonklaasi, an obligatory rainforest associate, suggests that perhumid refugia existed in Sri Lanka throughout this time. Lepidocephalichthys thermalis appears to have colonized the Sri Lankan highlands as recently as the Pleistocene. The data suggest that Lepidocephalichthys thermalis is a species complex in which multiple species remain to be investigated and described, both in India and Sri Lanka. [ABSTRACT FROM AUTHOR]

Potamothrix hammoniensis (Michaelsen, 1901) is one of the freshwater Clitellata species of Ponto-Caspian origin. Nearly 30 distinct morphological taxonomic characters are used for identification at the species level within the phylum Annelida. It is predicted that this species will show patterns of speciation dependent on allopatric isolation in relation to distribution barriers in the phylogeographic history of the species. The geography of Türkiye has many barriers capable of isolating aquatic organisms regardless of whether their active distribution is limited or not. In this study, P. hammoniensis (Oligochaeta) samples were collected in eight natural lakes (Lakes Gala, Büyük Akgöl, Sapanca, Eğirdir, Mogan, Cernek, Gölbaşı, and Nemrut) located in different geographical regions from the west to east of Türkiye between 2010 and 2013. These lakes have geographically isolation barriers among them and are thought to best reflect allopatric isolation. The samples were described based on both morphological differentiation and molecular characterisation using the data of COI and ITS2 fragments. According to the obtained results, the species of interest is not represented by a single species in the distribution area of Türkiye. The samples determined from Lake Gala may represent a new species. The samples obtained from Lakes Sapanca and Eğirdir show differentiation, but this differentiation is not as high as that observed for the Lake Gala samples. The Lake Nemrut samples also had a high rate of differentiation with an isolation process and mechanism that differed from those of the samples of all other investigated lakes. [ABSTRACT FROM AUTHOR]

Understanding how natural populations will respond to contemporary changes in climate is becoming increasingly urgent and of fundamental importance for the preservation of future biodiversity. Among vertebrates, amphibians and reptiles are more sensitive to environmental perturbations than endotherms and ectotherm diversity will likely be disproportionally impacted by climate change. Notwithstanding concerns surrounding the climate change resilience of ectotherm populations, accurately predicting future population trajectories based on contemporary ecological and physiological data alone remains challenging and much can be learnt by studying how populations have responded to climate change in the past. Genomic approaches can now assay the genetic diversity of contemporary population at an unprecedented scale but to date have been relatively underutilised when studying the demographic history of amphibians and reptiles. In this review, we first summarise how changing climatic conditions may influence the ectotherm phenotype and how this can translate to changes in fitness and population dynamics. We then discuss how the relative role of past climate in shaping ectotherm diversity has traditionally been approached in a phylogeographic context and how expanding genomic resources for ectotherm species can be leveraged to improve the study of past demography for many amphibian and reptilian groups. An integrative approach that links known proximate effects on phenotype due to climate change, with past changes in demographic trajectories will ultimately enable us to generate more accurate models of future population change and improve our ability to assess climate change resilience for many ectotherm groups. [ABSTRACT FROM AUTHOR]

Populations of species fluctuate through time and across geographic space. Identifying the potential drivers of temporal variability in population dynamics is a fundamental aim of population ecology, with clear implications to understanding population extinction risk, the influence of diversity on composite community scale variability, and the extent to which temporal variability is driven by exogenous (e.g., climate) or endogenous (e.g., life history) factors. We used data from the National Ecological Observatory Network (NEON) consisting of over 750 carabid beetle species systematically sampled between 2013 and 2021 across 47 terrestrial sites in the USA to examine the relative roles of geographic location, environmental gradients, and species identity on temporal variability. We find an effect of species taxonomic identity on resulting temporal variability in abundance both at site-level and taxonomy-level scales. Environmental variables (mean annual temperature and precipitation and seasonality in temperature and precipitation) and geographic position (latitude and longitude) were not strongly related to temporal variability, and there was no spatial signal in site-level mean temporal variability. The importance of species to temporal variability highlights the role of life history differences across species, resulting in a mean shift in population growth rate, as a potentially more important driver than aspects of site and environment that may relate more to temporal changes in population growth rates. [ABSTRACT FROM AUTHOR]

Available knowledge on the European white oaks (Quercus, sect. Quercus) plastome still exhibits large gaps, mostly in respect of detailed phylogeny and information from southern Europe and adjacent Near East. We investigated DNA sequence polymorphism at two plastid loci on 270 individuals representing 13 white oak species/taxa and retrieved several hundred sequences of the same two DNA regions from GenBank to fill the above gaps, and contribute to a better understanding of white oak diversity and evolution. The modern European sect. Quercus species exhibits a poorly differentiated plastid DNA, despite its current highly diversified taxonomy. Twenty-nine haplotypes were identified across the Euro-Mediterranean and Near East regions, including two ancestral variants that are westerly and south-easterly partitioned. Other high- and low-frequency haplotypes also showed a well-structured geographic distribution consistent with the current phytogeographic framework of the European continent. The climatic and geological events that characterized the end of the Tertiary and Quaternary periods played a crucial role in triggering haplotype mixing, isolation, and in offering niche opportunities for more recent diversification. Euro-Mediterranean southern territories host a high and as yet poorly studied genetic variation; the role of the Italian Peninsula as a crossroad and threshold for haplotype diversity and distribution clearly emerges from this study. [ABSTRACT FROM AUTHOR]

Context: Processes that shape genomic and ecological divergence can reveal important evolutionary dynamics to inform the conservation of threatened species. Fontainea is a genus of rainforest shrubs and small trees including critically endangered and threatened species restricted to narrow, but complex geographic and ecological regions. Several species of Fontainea are subject to spatially explicit conditions and experience limited intra-specific gene flow, likely generating genetic differentiation and local adaptation. Objectives: Here, we explored the genetic and ecological mechanisms underlying patterns of diversification in two, closely related threatened Fontainea species. Our aim was to compare spatial patterns of genetic variation between the vulnerable Fontainea australis (Southern Fontainea) and critically endangered F. oraria (Coastal Fontainea), endemic to the heterogeneous subtropical region of central, eastern Australia, where large-scale clearing has severely reduced rainforest habitat to a fraction (< 1%) of its pre-European settlement extent. Methods: We used a set of 10,000 reduced-representation markers to infer genetic relationships and the drivers of spatial genetic variation across the two species. In addition, we employed a combination of univariate and multivariate genome-environment association analysis using a set of topo-climatic variables to explore potential patterns of local adaptation as a factor impacting genomic divergence. Results: Our study revealed that Coastal Fontainea have a close genetic relationship with Southern Fontainea. We showed that isolation by distance has played a key role in their genetic variation, indicating that vicariance can explain the spatial genetic distribution of the two species. Genotype-environment analyses showed a strong association with temperature and topographic features, suggesting adaptation to localised thermal environments. We used a multivariate redundancy analysis to identify a range of putatively adapted loci associated with local environmental conditions. Conclusions: Divergent selection at the local-habitat scale as a result of dispersal limitations and environmental heterogeneity (including physical barriers) are likely contributors to adaptive divergence between the two Fontainea species. Our findings have presented evidence to indicate that Southern and Coastal Fontainea were comprised of distinct genetic groups and ecotypes, that together may form a single species continuum, with further phenotype research suggested to confirm the current species boundaries. Proactive conservation actions, including assisted migration to enhance the resilience of populations lacking stress-tolerant single nucleotide polymorphisms (SNPs) may be required to secure the long-term future of both taxa. This is especially vital for the critically endangered Coastal Fontainea given projections of habitat decline for the species under future climate scenarios. [ABSTRACT FROM AUTHOR]

Forests are considered as one of the most complex terrestrial ecosystems due to their high level of biodiversity, including genetic diversity. Understanding the genetic diversity of keystone species at a population level is vital to forest managers and policymakers for the conservation and sustainable utilization of forest genetic resources. Quercus semecarpifolia, commonly known as brown oak, is a keystone species of climax community thriving in the alpine zone of the Himalayas, which is presently experiencing population decline and range shift under the changing climate. In the present study, a landscape genetic approach was employed for deciphering the population genetic structure of Q. semecarpifolia in the western Himalayas using nuclear simple sequence repeat (SSR) markers. By analysing 718 individuals of 24 populations at 10 SSR loci, a high gene diversity (expected heterozygosity, He = 0.72; Allelic richness, Ar = 8.37) was recorded with a moderate genetic differentiation (FST = 0.16; P < 0.001). Genetic clustering and STRUCTURE analysis have displayed two major gene pools which appear to be primarily differentiated by the landscape and ecological constraints rather than the linear geographical distances. The hierarchical AMOVA analysis further supports the regional genetic divergence with a substantial proportion of genetic variation detected among the regions. Diversity maps generated by spatial interpolation elucidated the distribution pattern of genetic diversity and structure across the range, and aid in the demarcation of the diversity hotspots for conservation implications. To the best of our knowledge, this is the first comprehensive genetic study carried out in any Himalayan oaks, and the information generated herein is novel and of paramount importance in guiding conservation decisions. [ABSTRACT FROM AUTHOR]

Assessing genetic diversity, population connectivity, demographic patterns, and phylogeographic relationships is vital for understanding the evolutionary history of species and thus aid in conservation management decisions. Indian wolves (currently, Canis lupus pallipes and Canis lupus chanco) are considered ancient, unique and divergent lineages among grey wolves, yet their population genetics are poorly understood. To void this knowledge gap, we collected samples from Indian peninsular (n = 77) and Himalayan wolves (n = 24) and used a combination of maternal (mtDNA CR and Cyt b) and bi-parental (nuclear microsatellites) markers to estimate levels of genetic diversity, examine the patterns of genetic structuring between them and within their distribution range, and assess their demographic histories. Both the wolf populations showed moderate levels of genetic variability, comparable to other grey wolves. Low levels of genetic differentiation were observed within both the Indian peninsular and Himalayan wolves indicating high levels of gene flow within their populations. On the other hand, high levels of genetic differentiation were observed between the two wolves indicating absence of gene flow. Molecular analysis highlighted the uniqueness of both the Indian wolves which was further supported by the presence of unique haplotypes indicating no admixture between them. Demographic analysis using both mtDNA and microsatellites revealed decline in population sizes of both the wolf lineages and both have undergone bottlenecks. Estimates of past effective population size revealed recent population declines of both lineages of Indian wolves at around 25–50 generations corresponding to about 100–200 years ago. Our results further support the designation of both lineages of Indian wolves as two distinct species Canis pallipes and Canis himalayensis and suggest increasing conservation efforts to save the unique and ancient wolf species from extinction. [ABSTRACT FROM AUTHOR]

The aoudad (Ammotragus lervia) is a Vulnerable bovid endemic of North Africa. Although legally protected in almost every country of its native distribution, the aoudad continues to be hunted for meat and trophy in both North Africa and the countries where it has been introduced. The species was subject to past translocations planned irrespectively of the genetic diversity and local adaptations of source and receiving populations, and no management or conservation units have ever been designed. We aim to provide here important insights on the taxonomy of the aoudad subspecies and the genetic diversity of most of its wild and captive populations. We collected 127 invasive and non-invasive samples from five of the six subspecies of aoudad recognized to date. We could successfully retrieve genetic data for 74 samples. Of those, 36 provided both nuclear (11 microsatellites) and mitochondrial (Cyt-b) data, 31 just nuclear data, and six just mitochondrial data. We implement Bayesian approaches to infer the population structure and phylogenetic relationships between the different populations/subspecies and backtrack the maternal lineages of introduced individuals in European populations. Our results support the presence of four genetically different wild populations, corresponding to three distinct mitochondrial lineages plus a fourth group restricted to Egypt identified by the nuclear markers. We also provide genetic evidence on the affiliation of some introduced European populations with respect to the native ones. The genetic diversity instead of variation within all wild populations was low. This might be a consequence of small effective population size and/or high inbreeding degree, probably related to hunting, decline in habitat availability and quality (i.e. overgrazing, and frequent drought), and high inbreeding degree. Our results provide important information for the aoudad conservation, including reintroductions and reinforcement actions of wild populations, and the exchange of individuals among captive stocks. [ABSTRACT FROM AUTHOR]

Understanding how, and from where, invasive species were introduced is critical for revealing the invasive mechanism, explaining the invasion success, and providing crucial insights for effective management. Here, we combined a phylogeographic approach with ecological niche modeling comparisons to elucidate the introduction mode and source of Nicotiana glauca, a native South American species that is now invasive worldwide. We tested three different scenarios based on the invasion source—random native, restricted native, and bridgehead invasive—considering genetic diversity and climatic niche comparisons among native and invaded areas. We found three genetic lineages geographically and climatically differentiated within the native range. Only one of these genetic groups contained the invasive haplotypes, but showed no climatic niche overlap with any invaded area. Conversely, one invaded area located in western South America, with more genetic diversity than other invaded areas but less than the native range, showed climatic niche overlap with almost all other invaded areas worldwide. These findings indicate that N. glauca first likely invaded the southernmost areas beyond its native range, forming a bridgehead invasive source, from which the species subsequently invaded other regions around the world. Invasiveness would have been fostered by changes in the environmental preferences of the species in the bridgehead area, towards drier, colder and less seasonal climates, becoming the actual source of invasion to areas climatically similar throughout the world. The fine scale resolution analyses combining genetic and climatic approaches within the native range were essential to illuminating the introduction scenario of this invasive species. [ABSTRACT FROM AUTHOR]