Phylogeography

We examined the contact zone of two parapatric species of grass snake (Natrix astreptophora and Natrix helvetica) in southern France. To this end, we used comprehensive sampling, analysed mtDNA sequences and microsatellite loci, and built Species Distribution Models for current and past climatic conditions. The contact zone had established by the mid-Holocene during range expansions from glacial refuges in the Iberian Peninsula (N. astreptophora) and southern or western France (N. helvetica). The contact zone represents a narrow bimodal hybrid zone, with steep genetic transition from one taxon to the other and rare hybridization, supporting species status for N. astreptophora and N. helvetica. Our results suggest that the steepness of the clines is a more robust tool for species delimitation than cline width. In addition, we discovered in western France, beyond the hybrid zone, a remote population of N. helvetica with genetic signatures of hybridization with N. astreptophora, most l...

Because it is indicative of reproductive isolation, the amount of genetic introgression across secondary contact zones is increasingly considered in species delimitation. However, patterns of admixture at range margins can be skewed by the regional dynamics of hybrid zones. In this context, we posit an important role for phylogeographic history: hybrid zones located within glacial refugia (putatively formed during the Late-Pleistocene) should be better defined than those located in post-glacial or introduced ranges (putatively formed during the Holocene and the Anthropocene). We test this hypothesis in a speciation continuum of tree frogs from the Western Palearctic (Hyla), featuring ten identified contacts between species spanning Plio-Pleistocene to Miocene divergences. We review the rich phylogeographic literature of this group and examine the overlooked transition between H. arborea and H. molleri in Western France using a multilocus dataset. Our comparative analysis supports a ...

Life history plays a critical role in governing microevolutionary processes such as gene flow and adaptation, as well as macroevolutionary processes such speciation. Here, we use multilocus phylogeographic analyses to examine a speciation event involving spectacular life-history differences between sister species of sea stars. Cryptasterina hystera has evolved a suite of derived life-history traits (including internal self-fertilization and brood protection) that differ from its sister species Cryptasterina pentagona , a gonochoric broadcast spawner . We show that these species have only been reproductively isolated for approximately 6000 years (95% highest posterior density of 905–22 628), and that this life-history change may be responsible for dramatic genetic consequences, including low nucleotide diversity, zero heterozygosity and no gene flow. The rapid divergence of these species rules out some mechanisms of isolation such as adaptation to microhabitats in sympatry, or slow d...

There is an ongoing debate on the scale of pelagic larval dispersal in promoting connectivity among populations of shallow, benthic marine organisms. The linearly arranged Hawaiian Islands are uniquely suited to study scales of population connectivity and have been used extensively as a natural laboratory in terrestrial systems. Here, we focus on Hawaiian populations of the lobe coral Porites lobata, an ecosystem engineer of shallow reefs throughout the Pacific. Patterns of recent gene flow and population structure in P. lobata samples (n = 318) from two regions, the Hawaiian Islands (n = 10 sites) and from their nearest neighbour Johnston Atoll, were analysed with nine microsatellite loci. Despite its massive growth form, ∼ 6% of the samples from both regions were the product of asexual reproduction via fragmentation. Cluster analysis and measures of genetic differentiation indicated that P. lobata from the Hawaiian Islands are strongly isolated from those on Johnston Atoll (F(ST) ...

Plankton communities often consist of cosmopolitan species with an extensive gene flow between populations. Nevertheless, populations of some plankton species are genetically structured, owing to various barriers such as ocean currents, hydrological fronts, and continents. Drivers that could explain the genetic structures of most mesopelagic species remain unknown on an ocean-basin scale, and our study aims to analyze the genetic and morphological differences between populations of a cosmopolitan mesopelagic shrimp, Systellaspis debilis, from the Southern and Northern Atlantic Ocean, and the Southwest Indian Ocean. We analyzed the ITS-1 and COI markers of 75 specimens and assessed the genetic integrity and within-species variability of these genes. We also coded 32 morphological characteristics in 73 specimens, analyzed their variability, and assessed the correlation between morphological and genetic characteristics using a Redundancy analysis and Mantel test. Systellaspis debilis w...

Improved awareness of the hepatitis C virus (HCV) transmission has contributed to the overall decline in the HCV infection rate in some developing countries including Thailand. Chronic HCV infection in some rural Thai communities, however, presents a challenge in the efforts to treat and manage HCV-related diseases. Published and unpublished studies have suggested an unusually high incidence of HCV infection in a Thai province of Phetchabun compared to elsewhere in Thailand. To determine the magnitude of HCV infection and identify potential factors contributing to the higher rate of HCV infection in this province, we performed a population-based study in Phetchabun (n = 1667) and the neighboring Khon Kaen province (n = 1410) where HCV prevalence is much lower. Individuals between 30 and 64 years old completed detailed questionnaires designed to identify HCV risk factors and provided blood samples for anti-HCV antibody screening. The anti-HCV seropositive rates were 15.5% (259/1667) ...

The hermaphroditic nematode Pristionchus pacificus is an established model system for comparative studies with Caenorhabditis elegans in developmental biology, ecology, and population genetics. In this study, we present whole-genome sequencing data of 104 P. pacificus strains and the draft assembly of the obligate outcrossing sister species P. exspectatus. We characterize genetic diversity within P. pacificus and investigate the population genetic processes shaping this diversity. P. pacificus is 10 times more diverse than C. elegans and exhibits substantial population structure that allows us to probe its evolution on multiple timescales. Consistent with reduced effective recombination in this self-fertilizing species, we find haplotype blocks that span several megabases. Using the P. exspectatus genome as an outgroup, we polarized variation in P. pacificus and found a site frequency spectrum (SFS) that decays more rapidly than expected in neutral models. The SFS at putatively neut...

Background Urbanization will increase in the next decades, causing the loss of green areas and bird diversity within cities. There is a lack of studies at a continental scale analyzing the relationship between urban green areas, such as parks and cemeteries, and bird species richness in the Neotropical region. Bird diversity-environment relationships in urban parks and cemeteries may be influenced by latitudinal gradients or species-area relationships. However, the seasonal variation of species diversity- environment has not been analyzed at a continental scale in the Neotropics. Methods Bird surveys were conducted in 36 cemeteries and 37 parks within 18 Neotropical cities during non-breeding and breeding seasons. Bird diversity was assessed through Hill numbers, focusing on species richness, the effective number of species derived from Shannon index and the Simpson index. Environmental variables included latitude, altitude, and local scale variables such as area size, habitat diver...

Non-native species threaten native ecosystems and species, particularly on islands where rates of endemism and vulnerability to threats are high. Understanding species invasion will aid in providing insights into ecological and evolutionary processes. To identify the non-native sika deer (Cervus nippon) population in Jeju, South Korea, and their phylogenetic affinities, we collected tissue samples from roadkill and the World Natural Heritage Headquarters in Jeju. Mitochondrial DNA cytochrome B (CytB) gene sequences were analyzed to determine two distinct CytB haplotypes. Phylogenetic analysis using maximum likelihood tree revealed two haplotypes of CytB clustered into two different groups representing two subspecies: C. n. yakushimae, native to Japan, and C. n. taiouanus, native to Taiwan. The tentative divergence time between the two subspecies was estimated at 1.81 million years. Our study confirmed that the two subspecies of sika deer are sympatric in the natural ecosystem of Jej...

Background The gamma-aminobutyric acid (GABA) receptor-chloride channel complex is known to be the target site of dieldrin, a cyclodiene insecticide. GABA-receptors, with a naturally occurring amino acid substitution, A302S/G in the putative ion-channel lining region, confer resistance to cyclodiene insecticides that includes aldrin, chlordane, dieldrin, heptachlor, endrin and endosulphan. Methods A total of 154 mosquito samples from 10 provinces of malaria-endemic areas across Indonesia (Aceh, North Sumatra, Bangka Belitung, Lampung, Central Java, East Nusa Tenggara, West Nusa Tenggara, West Sulawesi, Molucca and North Molucca) were obtained and identified by species, using morphological characteristic. The DNA was individually extracted using chelex-ion exchanger and the DNA obtained was used for analyses using sequencing method. Results Molecular analysis indicated 11% of the total 154 Anopheles samples examined, carried Rdl mutant alleles. All of the alleles were found in homozy...

We investigated the population structure of Grosmannia clavigera (Gc), a fungal symbiont of the mountain pine beetle (MPB) that plays a crucial role in the establishment and reproductive success of this pathogen. This insect–fungal complex has destroyed over 16 million ha of lodgepole pine forests in Canada, the largest MPB epidemic in recorded history. During this current epidemic, MPB has expanded its range beyond historically recorded boundaries, both northward and eastward, and has now reached the jack pine of Alberta, potentially threatening the Canadian boreal forest. To better understand the dynamics between the beetle and its fungal symbiont, we sampled 19 populations in western North America and genotyped individuals from these populations with eight microsatellite markers. The fungus displayed high haplotype diversity, with over 250 unique haplotypes observed in 335 single spore isolates. Linkage equilibria in 13 of the 19 populations suggested that the fungus reproduces s...

Background and AimQuaternary glaciations strongly affected the distribution of species from arid and semi-arid environments, as temperature drops were accompanied by strong fluctuations in rainfall. In this study, we examined the response of xerophytic species to glacial cycles, determining the genetic patterns and climatic niche of Echinopsis chiloensis var. chiloensis, an endemic columnar cactus of arid and semi-arid regions of Chile.MethodsWe analysed 11 polymorphic microsatellites for 130 individuals from 13 populations distributed across the entire distribution of the species. We examined genetic diversity and structure, identified possible patterns of isolation by distance (IBD) and tested two competing population history scenarios using Approximate Bayesian Computation. The first scenario assumes a constant population size while the second includes a bottleneck in the southern population. The latter scenario assumed that the southernmost populations experienced a strong contr...

Several European freshwater crayfish species are currently included in one of the IUCN Red list categories. In the Iberian Peninsula, the native Austropotamobius pallipes species complex (the white clawed crayfish, WCC) has experienced a drastic decline since 1973. Implementing conservation management strategies for this species requires a better understanding of the patterns and structure of its genetic diversity. In this study, we assessed the levels and patterns of genetic variation in 71 populations along the whole distributional range of the WCC in the Iberian Peninsula. The two mitochondrial markers analyzed (Cytochrome Oxidase subunit I and 16S rRNA genes) indicated high levels of genetic diversity, which are significantly geographically structured in three main genetic groups, two corresponding to Northern and one to Central-Eastern and the westernmost Iberian Peninsula. The diversity found included new private haplotypes, and revealed the potential effect of paleogeographic...

The islands of Sardinia, Crete, and Cyprus are hosting the last native insular griffon populations in the Mediterranean basin. Their states have been evaluated from “vulnerable” to “critically endangered”. The sequence analysis of molecular markers, particularly the mtDNA D-loop region, provides useful information in studying the evolution of closely related taxa and the conservation of endangered species. Therefore, a study of D-loop region sequence was carried out to estimate the genetic diversity and phylogenetic relationship within and among these three populations. Among 84 griffon specimens (44 Sardinian, 33 Cretan, and 7 Cypriot), we detected four haplotypes including a novel haplotype (HPT-D) that was exclusively found in the Cretan population with a frequency of 6.1%. When considered as a unique population, haplotype diversity (Hd) and nucleotide diversity (π) were high at 0.474 and 0.00176, respectively. A similar level of Hd and π was found in Sardinian and Cretan populat...

Whole genome sequence analysis of the Mycobacterium tuberculosis (Mtb) isolates show correlation to their drug resistance phenotype which may also reflect in their global metabolome. In this report, clinical Mtb isolates (S1, S4, S5, S6, S7, S10) harvested from the sputum of tuberculosis patients were characterized using drug sensitive test (DST), electron microscope, whole genome sequencing (WGS) and metabolomics. Majority of these Mtb isolates showed similar size to the H37Rv Mtb strain whereas significant variations were observed in their growth kinetics, WGS and metabolome profiles. In-silico drug resistance prediction, from the WGS data (single-nulceotide polymorphisms (SNP) pattern) of these Mtb isolates showed resistance to tuberculosis drugs and matched with DST results. Differences in the genes involved in stress response, pathogenicity, drug efflux pumps were observed between isolates but genes of the central carbon metabolic pathways and amino acid metabolism were conserv...

Recent extensive field prospecting conducted in the Upper Miocene of Lebanon resulted in the discovery of several new fossiliferous localities. One of these, situated in the Zahleh area (Bekaa Valley, central Lebanon) has yielded a particularly diverse vertebrate fauna. Micromammals constitute an important part of this assemblage because not only do they represent the first Neogene rodents and insectivores from Lebanon, but they are also the only ones from the early Late Miocene of the Arabian Peninsula and circumambient areas. Analyses of the murines from Zahleh reveal that they belong to a small-sized early Progonomys, which cannot be assigned to any of the species of the genus hitherto described. They are, thereby, shown to represent a new species: Progonomys manolo. Morphometric analyses of the outline of the first upper molars of this species suggest a generalist and omnivorous diet. This record sheds new light onto a major phenomenon in the evolutionary history of rodents, whi...

There are volumes of patient reports generated in any healthcare organization daily. The reports can be very lengthy or of few pages. Maintaining records of patients is essential for ensuring quality medical care. Doctors, apart from their routine activities, are also responsible to sort, examine and archive the generated reports. However, this process consumes doctors’ time, who are already hard-pressed for time. The objective of this study is to search for a method that can assign reports to doctors to ensure equitable and fair distribution of the overall workload. As a part of the solution, a mathematical model will be proposed to perform different developed heuristics. An experimental evaluation using different classes with a total of 2,450 different instances will be tested to measure the performance of the developed heuristics in terms of, elapsed time and gap value calculations. The clustering heuristics which is based on two groups is the best heuristic with 96.1% for the sm...

Hybridization is an important evolutionary process, with ecological and behavioural factors influencing gene exchange between hybrids and parent species. Patterns of hybridization in anemonefishes may result from living in highly specialized habitats and breeding status regulated by size-based hierarchal social groups. Here, morphological, ecological and genetic analyses in Kimbe Bay, Papua New Guinea, examine the hybrid status of Amphiprion leucokranos, a nominal species and presumed hybrid between Amphiprion sandaracinos and Amphiprion chrysopterus. We test the hypothesis that habitat use and relative size differences of the parent species and hybrids determine the patterns of gene exchange. There is strong evidence that A. leucokranos is a hybrid of smaller A. sandaracinos and larger A. chrysopterus, where A. chrysopterus is exclusively the mother to each hybrid, based on mtDNA cytochrome b and multiple nDNA microsatellite loci. Overlap in habitat, depth and host anemone use was ...

Divergence time estimation from multilocus genetic data has become common in population genetics and phylogenetics. We present a new Bayes inference method that treats the divergence time as a random variable. The divergence time is calculated from an assembly of splitting events on individual lineages in a genealogy. The waiting time for such a splitting event is drawn from a hazard function of the truncated normal distribution. This allows easy integration into the standard coalescence framework used in programs such as MIGRATE. We explore the accuracy of the new inference method with simulated population splittings over a wide range of divergence time values and with a dataset of the Zika virus; the geographic analyses of the expansion of the pathogen follows a trajectory from Africa to Asia to America, corroborating analyses based only on the dates of incidences. Evaluations of simple divergence models show high accuracy, whereas the accuracy of the results of isolation with mig...