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Understanding population genetics, genetic diversity and the migration pattern of ecologically important species is crucial for effective conservation plans. We studied mitochondrial cytochrome c oxidase subunit-I (COI) gene variation in painted lady butterfly (Vanessa cardui) from different altitudinal gradients of Uttarakhand (Western Himalayas), India. We sequenced COI) gene of 91 samples and 22 COI sequences retrieved from GenBank as representatives of different localities for comparative analysis. We observed a total of 16 haplotypes, of which seven haplotypes were observed in Uttarakhand with intra-species sequence divergence ranges from 0.001 to 0.009. Haplotype (Hd) and nucleotide diversity (π) were comparatively low and averaging 0.635 and 0.002, respectively. The neutrality test, mismatch distribution graph and observed pattern of diversity indices (Hd and π) revealed population expansion. It was further confirmed by the Median Joining Network, which exhibited a star-like topology from the core haplotype, while the Bayesian phylogenetic tree displayed a mixing of haplotypes from different localities to an identical clade. Haplotype organization in the Bayesian tree and Median Joining Network was not clustered as per their topographical affinity, indicating incomplete lineage sorting and late species population development or colonization in the novel area.

Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus

Rosa roxburghii Tratt. is a well-known commercial horticultural crop in China with nutritional and medicinal value. Wild germplasms of this species are mainly distributed in Southwest China but the population is decreasing due to continuous exploitation, habitat destruction, and fragmentation. Therefore, assessing the genetic diversity and phylogeography is essential for efficient conservation. Herein, two chloroplast intergenic spacers (trnL-trnF and accD-psaI) were investigated in 255 individuals from 29 R. roxburghii populations and 18 haplotypes (H1–H18) were identified. High levels of haplotype diversity (Hd = 0.829) and nucleotide diversity (π = 1.3 × 10−3) were detected in these populations. Also, the genetic variation representing 86.4% of the total variation was detected by an analysis of molecular variance. A significant correlation was established between genetic divergence and geographic distance by the Mantel test (r = 0.204, P = 0.04, 9 999 permutations), suggesting the isolation-by-distance model. A significantly higher Nst than Gst (Nst = 0.257, Gst = 0.136, P < 0.05) indicated the phylogeographic structure of R. roxburghii. Further phylogeographic analysis revealed rapid range expansion in the population, probably between 647 073 and 217 848 years ago. The primary processes shaping the genetic patterns of the R. roxburghii populations included restricted gene flow with isolation distance within clades 1-8, 2-3, and overall, contiguous expansion within clades 1-3 and 3-2, past fragmentation, and/or long-distance colonization within clades 1-9 and 2-2. Conservation priority should be given to the core populations GZ, FQ, DF, DS, xy, AL, LC, PB, and XY in the Yunnan-Guizhou Plateau, NZ and MX in the Qingling-Bashan mountains, and MN in the Hengduan mountains, where an in situ preservation and management strategy should be applied.

Our study investigates the genetic and phenotypic variability of two populations of shrimps of the Macrobrachium amazonicum complex from two rivers of the same hydrographic basin in southeastern Brazil. We tested the hypothesis that the two hololimnetic populations are composed of different species from M. amazonicum complex. We identified, sexed, measured the specimens, and collected the genetic material for molecular analysis. We realized a meta-analyzes with other populations data from a bibliographic survey based on compilation of sex ratio and carapace length from 22 populations. Considering the molecular phylogenetic analysis, COI DNA fragments were used to generate a phylogenetic tree and haplotype network. A total of 703 individuals was sampled in the Araguari River and 808 individuals in the Grande River. In the Araguari River population, females were larger than males and no male morphotypes observed. While in the Grande River population, no differences in body size between sexes were observed, but the male morphotypes were present. Our results showed that the shrimps sampled in Araguari River belong to the species M. pantanalense, based in molecular, morphological and population evidences. In turn, the population of shrimps sampled in Grande River presents similar characteristics to M. amazonicum. Our findings contribute to the knowledge of phylogeography of the species of M. amazonicum complex and to expand the distribution range of M. pantanalense in Parana Hydrographic Basin.

Trichaptum abietinum and Trichaptum fuscoviolaceum (Hymenochaetales, Basidiomycota) are closely related saprotrophic fungi, widely distributed on coniferous wood in temperate regions worldwide. Three intersterility groups have previously been detected in T. abietinum, while no prezygotic barriers have been proven within T. fuscoviolaceum. The aim of this study was to reveal the phylogeography and genetic relationship between these two closely related species and to explore whether the previously observed intersterility groups in T. abietinum are reflected in the genetic data. We assembled worldwide fruit body collections of both species (N = 314) and generated DNA sequences from three nuclear (ITS2, LSU, IGS) and one mitochondrial rDNA region (mtLSU). The two species are genetically well separated in all analyses. In correspondence with observations from earlier mating studies, our results revealed that T. fuscoviolaceum is genetically more uniform than T. abietinum. Multiple genetic sub-groups exist in T. abietinum that may correspond to the previously observed intersterility groups. However, there is low consistency across the investigated loci in delimiting the different sub-groups, except for a consistent North American group. As for many other widespread fungi, a complex phylogeographic pattern is found in T. abietinum which may have been formed by geographic, as well as multiple genetic intersterility barriers.

Climatic oscillation often have influenced the present distribution and intraspecific genetic diversity Oecophylla smaragdina through its wide range of geographical distribution. Previous phylogeographic study of Asian weaver ant population denotes the evidence of distribution of Indian types in Indian, Sri Lanka and SE Asian types in South Asian countries including Bangladesh. However, recent phylogenetic analysis reveals the overlapping distribution of the Indian and South East Asian clades of O. smaragdina in Bangladesh. The present study aims to identify the haplotypes and it’s networking in Bangladesh based on extensive materials. Sampling was executed according to zonation of 5 areas, demarcated by 3 main rivers during the years 2013 to 2018. Adult O. smaragadina workers were collected from 71 colonies of 67 localities belonging to 47 districts of Bangladesh. A total of 25 haplotypes were identified in Bangladesh comprises 13 and 12 of Indian and SE Asian types, respectively from 93 sequences of Cytochrome c oxidase subunit I (COI) gene of 639 bp. The geographical distribution of this haplotype reveals that the Indian haplotypes are mostly located at the western part of Bangladesh while SE Asian haplotypes were dominated in the Eastern part of the country. Central part of Bangladesh has overlapped with the mixture of both Indian and SE Asian haplotypes. The results of the haplotype network give the evidence of recent expansion of O. smaragdina population in Bangladesh and clarify the evidence of presence of many missing haplotypes in refugee.

Studying dipterans at the scene of a death can provide essential information for interpreting the evidence and help to reconstruct the events happened to a corpse in the past. Molecular tools have been employed for identification at specific levels in the cases of cryptic species or poorly conserved specimens. Identification of specimens is essential in forensic entomology since each species has a specific growth rate, which determines the calculation of the minimum post mortem interval (minPMI). In addition, phylogeographic reconstruction within a species can help to differentiate the haplotypes from a geographic area, thereby helping to clarify the possible relocation of a corpse. The morphological identification of Sarcophagidae species is often difficult, especially for the females. This is an important Diptera family since some of its species are among the first to reach a corpse, especially in warm areas. In this study, we compared the sarcophagids found in human corpses in forensic cases in Alicante (southeast of Spain) with specimens collected from baited traps in the same area and surrounding provinces. In total, 189 specimens were collected, comprising 72 from forensic cases and 117 from baited traps. Molecular identification was conducted by sequencing the cox1 mitochondrial gene and analyzing the sequences using ABGD, GMYC, and BIN species delimitation methods. The median joining algorithm in the PopART program was used to construct phylogeographic networks. Eight species in the family Sarcophagidae were identified. The most widely collected species were Sarcophaga argyrostoma and Sarcophaga tibialis. The haplotype networks obtained for these species did not indicate a clear geographic distribution of haplotypes. The S. argyrostoma samples from Alcoy were clearly isolated. The results demonstrated that this method is useful for identifying Sarcophagidae samples in forensic investigations and it can be employed for minPMI estimation.

International audience; Rice yellow mottle virus (RYMV) has persisted as a major biotic constraint to rice production in Africa. However, no data on RYMV epidemics were available in Ghana, although it is an intensive rice-producing country. Surveys were performed from 2010 to 2020 in eleven rice-growing regions of Ghana. Symptom observations and serological detections confirmed that RYMV is circulating in most of these regions. Coat protein gene and complete genome sequencings revealed that RYMV in Ghana almost exclusively belongs to the strain S2, one of the strains covering the largest area in West Africa. We also detected the presence of the S1ca strain which is being reported for the first time outside its area of origin. These results suggested a complex This preprint research paper has not been peer reviewed.

Although the Holarctic fauna has been explored for centuries, many questions on its formation are still unanswered. For example, i) what was the impact of the uplift of the Himalaya and Tibetan Plateau?, ii) what were the timings and climate of the faunal bridges connecting the Nearctic and Palearctic regions?, and iii) how did insect lineages respond to the late Paleogene global cooling and regional aridification? To answer these, we developed a phylogenetic dataset of 1229 nuclear loci for a total of 222 species of rove beetles (Staphylinidae) with emphasis in the tribe Quediini, especially Quedius-lineage and its subclade Quedius sensu stricto. Using eight fossils for calibrating molecular clock, we estimated divergence times and then analysed in BioGeoBEARS paleodistributions of the most recent common ancestor for each target lineage. For each species we generated climatic envelopes of the temperature and precipitation and mapped them across the phylogeny to explore evolutionary shifts. Our results suggest that the warm and humid Himalaya and Tibetan Plateau acted as an evolutionary cradle for the Quedius-lineage originating during the Oligocene from where, in the Early Miocene, the ancestor of the Quedius s. str. dispersed into the West Palearctic. With the climate cooling from the Mid Miocene onwards, new lineages within Quedius s. str. emerged and gradually expanded distributions across the Palearctic. In Late Miocene, a member of the group dispersed to the Nearctic region via Beringia before the closure of this land bridge 5.3 Ma. Paleogene global cooling and regional aridification largely shaped the current biogeographic pattern for Quedius s. str. species, many of them originating during the Pliocene and shifting or contracting their ranges during Pleistocene.

Tomato mosaic virus (ToMV) is a tobamovirus affecting solanaceous crops worldwide. The process of its emergence, however, is poorly understood. Here, Bayesian phylogenetic framework was employed to reconstruct the phylogeography of ToMV in Eurasia. The results showed that the ToMV in Europe, Middle East and East Asia has been evolving at a rate of 4.05 × 10−4 substitutions/site/year (95% credibility interval 2.43 × 10−4 – 5.62 × 10−4). Their most recent common ancestor (MRCA), most probably first appeared in Europe, was dated to around 1757 Common Era. The first introduction of ToMV into Middle East occurred in 1920s, with Europe as the source, while the first introduction of ToMV into East Asia occurred shortly afterwards, with Middle East as the source. From about 1950 onwards, inter-regional migrations of ToMV between Europe, Middle East and East Asia have been common. Overall, these data provide a glimpse into the phylogeographic history of ToMV in Eurasia.

Polygalacturonase (PG) is a hydrolase that participates in pectin degradation, pod shattering and fruit softening. Here, we identified 2786 PG genes across 54 plants, which could be divided into three groups. Evolutionary analysis suggested that PG family originated from the charophyte green algae, and Subgroups A2-A4 evolved from the Subgroup A1 after the tracheophyte-angiosperm split. Whole-genome duplication was the major force leading to PG gene expansion. Interestingly, the PG genes continuously expanded in eudicots, whereas it contracted in monocots after the eudicot-monocot split. PG genes in Group A are expressed at high levels in floral organs, whereas genes in Groups B and C are expressed at high levels in various tissues. Moreover, three BnaPG15 members were found for their potential possibility in pod shattering in Brassica napus. Our results provide new insight into the evolutionary history of PG family, and their potentially functional role in plants.

Strong genetic incompatibilities exist between two primary rice subspecies, indica and japonica. However, the wild ancestors of rice, O. nivara Sharma et Shastry and O. rufipogon Griff., are genetically compatible. How this genetic incompatibility became established has not been clearly elucidated. To provide insights into the process, we analyzed a pair of hybrid sterility genes in rice, DOPPELGANGER 1 (DPL1) and DOPPELGANGER 2 (DPL2). Either of the two loci can have one defective allele (DPL1- and DPL2-). Hybrid pollen carrying both DPL1- and DPL2- alleles is sterile. To explore the origination of DPL1- and DPL2-, we sequenced the DPL1 and DPL2 genes of 811 individual plants, including Oryza sativa (132), O. nivara (296) and O. rufipogon (383). We then obtained 20 DPL1 and 34 DPL2 sequences of O. sativa from online databases. Using these sequences, we analyzed the genetic and geographic distribution patterns of DPL genes in modern rice and its wild ancestors. Compared with the ancestral populations, DPL1- and DPL2- showed reduced diversity but increased frequency in modern rice. We speculated that the diversity reduction was due to a historic genetic bottleneck, and the frequency had likely increased because the defective alleles were preferred following this artificial selection. Such results indicated that standing variances in ancestral lines can lead to severe incompatibilities among descendants. Haplotype analysis indicated that the DPL1- haplotype of rice emerged from an O. nivara population in India, whereas the DPL2- haplotype emerged from O. rufipogon in South China. Hence, the evolutionary history of DPLs conforms to the presumed multiple domestication events of modern rice.

The Central Ryukyus, a group of islands in southwestern Japan, harbor many endemic reptiles and amphibians, and the geographic ranges of the endemics are limited to south of the Tokara Gap, an old sea strait. Ateuchosaurus pellopleurus is a lizard with an exceptionally wide geographic range that encompasses the Central Ryukyus and north of the Tokara Gap. The intraspecific geographic variation of this species and the divergence time between A. pellopleurus and its sister species in southern China, Ateuchosaurus chinensis, were assessed by molecular phylogeographic analyses. The results indicated that the populations north of the gap were established by recent northward dispersal, prior to which the distribution of this species was limited to the Central Ryukyus. The estimated divergence time between A. pellopleurus and A. chinensis was in the Oligocene or Miocene, which was concordant with the divergence times of most Central Ryukyu endemics. These results demonstrated that A. pellopleurus is essentially a Central Ryukyu endemic that shares a common biogeographic history with other endemics. The common divergence times suggested that isolation of the endemics from their sister species in surrounding areas are attributable to geographic isolation by a tectonic event in the Miocene. In addition, A. pellopleurus showed distinct divergence between the populations in the northern and southern parts of the Central Ryukyus, and further diversification within and between islands in the southern part. Comparison of the phylogeographic patterns between this species and other endemics revealed that the present diversity in the Central Ryukyu endemics was formed by a complex history that involved occasional dispersal rather than simple vicariance events.

Tibetan foxes (Vulpes ferrilata) have been confirmed as the main wild definitive hosts in echinococcosis transmission in the eastern Tibetan Plateau. However, little information is available about the epidemiology in wildlife from the perspective of the Taeniidae family, which is essential knowledge in understanding the epidemiology and phylogeography of cestode species in the Tibetan plateau. Therefore, in this study, we used copro-PCR techniques, by amplifying nad1 and cox1 gene fragments, to detect the taeniid species from Tibetan fox feces collected in Shiqu County, (Sichuan Province, China), eastern Tibetan Plateau. Phylogenetic relationships between amplified sequences and existed Taenia species genotypes were evaluated. Then, the maximum prevalence (positive PCR results from at least one primer pair) and the conservative prevalence (positive PCR results from at least two primer pairs) were calculated. Thirty-six Tibetan fox feces were analyzed. Echinococcus multilocularis (conservative prevalence ± 95% CI: 22.2% ± 13.6%; maximum prevalence ± 95% CI: 33.3% ± 15.4%) and E. shiquicus (2.8 ± 5.4%; 8.3 ± 9.0%) was detected. Meanwhile, DNA fragments of T. polyacantha were detected with high similarity to NCBI sequences (cox1, 94.0%) and to the larva sample DNA sequenced in this study (93.4%), and were supported by phylogenetic analysis. Thus, T. polyacantha might infect Tibetan foxes (5.6% ± 7.5%, 11.1% ± 10.3%). Our limited findings in the epidemiology of parasitic Taenia species suggest that sylvatic transmission cycles for a more species-rich Taeniid community must be established between wild canids and small mammals than just for the two Echinococcus species. Besides, discrepancies in different primer pairs in detecting the taeniid species were evaluated. The sensitivity of some widely used universal primer pairs was poor in detecting Taenia species from canid copro-DNA samples. It is still challenging to the development of effective taeniid species-specific molecular markers especially for non-zoonotic species.

The fungus Ophiocordyceps sinensis is endemic to the vast region of the Qinghai-Tibetan plateau (QTP). The unique and complex geographical environmental conditions have led to the “sky island” distribution structure of O. sinensis. Due to limited and unbalanced sample collections, the previous data on O. sinensis regarding its genetic diversity and spatial structure have been deemed insufficient. In this study, we analyzed the diversity and phylogeographic structures of O. sinensis using internally transcribed spacer region (ITS) and 5-locus datasets by a large-scale sampling. A total of 111 haplotypes of ITS sequences were identified from 948 samples data of the fungus O. sinensis, with representing high genetic diversity, and 8 phylogenetic clades were recognized in O. sinensis. Both the southeastern Tibet and the northwestern Yunnan were the centers of genetic diversity and genetic differentiation of the fungus, and they were inferred as the glacial refugia in the Quaternary. Three distribution patterns were identified to correspond to the 8 clades, including but not limited to the coexistence of widely and specific local distributive structures. It also revealed that the differentiation pattern of O. sinensis did not fit for the isolation-by-distance model. The differentiation into the 8 clades occurred between 1.56 Myr and 6.62 Myr. The ancestor of O. sinensis most likely originated in the late Miocene (6.62 Myr) in the northwestern Yunnan, and the Scene A–C of the Qinghai–Tibetan movements may have played an important role in the differentiation of O. sinensis during the late Miocene–Pliocene periods. Our current results provide a much clearer and detailed understanding of the genetic diversity and geographical spatial distribution of the endemic alpine fungus O. sinensis. It also revealed that the geochronology resulting from paleogeology could be cross-examined with biomolecular clock at a finer scale. Keywords: Large-scale sampling, Phylogeographic structure, Molecular clock, Correlation, Qinghai–Tibetan plateau

Phellinus noxius is a root-decay pathogen with a pan-tropical/subtropical distribution that attacks a wide range of tree hosts. For this study, genomic sequencing was conducted on P. noxius isolate P919-02W.7 from Federated States of Micronesia (Pohnpei), and its gene expression profile was analyzed using different host wood (Acer, Pinus, Prunus, and Salix) substrates. The assembled genome was 33.92 Mbp with 2954 contigs and 9389 predicted genes. Only small differences were observed in size and gene content in comparison with two other P. noxius genome assemblies (isolates OVT-YTM/97 from Hong Kong, China and FFPRI411160 from Japan, respectively). Genome analysis of P. noxius isolate P919-02W.7 revealed 488 genes encoding proteins related to carbohydrate and lignin metabolism, many of these enzymes are associated with degradation of plant cell wall components. Most of the transcripts expressed by P. noxius isolate P919-02W.7 were similar regardless of wood substrates. This study highlights the vast suite of decomposing enzymes produced by P. noxius, which suggests potential for degrading diverse wood substrates, even from temperate host trees. This information contributes to our understanding of pathogen ecology, mechanisms of wood decomposition, and pathogenic/saprophytic lifestyle.

As global climate change is altering the distribution range of macroalgae across the globe, it is critical to assess its impact on species range shifts to inform the biodiversity conservation of macroalgae. Latitude/environmental gradients could cause intraspecific variability, which may result in distinct responses to climate change. It remains unclear whether geographical variation occurs in the response of species' populations to climate change. We tested this assumption using the brown alga Sargassum thunbergii, a habitat-forming macroalgae encompassing multiple divergent lineages along the Northwest Pacific. Previous studies revealed a distinct lineage of S. thunbergii in rear-edge populations. Given the phylogeographic structure and temperature gradients, we divided these populations into the southern and northern groups. We assessed the physiological responses of the two groups to temperature changes and estimated their niche differences using n-dimensional hypervolumes. A higher photosynthetic rate and antioxidative abilities were detected in the southern group of S. thunbergii than in the northern group. In addition, significant niche differentiation was detected between the two groups, suggesting the possibility for local adaptation. Given these results, we inferred that the southern group (rear-edge populations) may be more resilient to climate change. To examine climate-driven range shifts of S. thunbergii, we constructed species- and lineage-level species distribution models (SDMs). Predictions of both levels showed considerable distribution contracts along the Chinese coasts in the future. For the southern group, the lineage-level model predicted less habitat loss than the species-level model. Our results highlight the importance of considering intraspecific variation in climate change vulnerability assessments for coastal species.

Population divergence leading to speciation is often explained by physical barriers causing allopatric distributions of historically connected populations. Environmental barriers have increasingly been shown to cause population divergence through local adaptation to distinct ecological characteristics. In this study, we evaluate population structuring and phylogeographic history within the Yucatán banded gecko Coleonyx elegans Gray 1845 to assess the role of both physical and environmental barriers in shaping the spatio-genetic distribution of a Mesoamerican tropical forest taxon. We generated RADseq and multi-locus Sanger datasets that included sampling across the entire species' range. Results find support for two distinct evolutionary lineages that diverged during the late Pliocene and show recent population expansions. Furthermore, these genetic lineages largely align with subspecies boundaries defined by morphology. Several mountain ranges identified as phylogeographic barriers in other taxa act as physical barriers to gene flow between the two clades. Despite the absence of a physical barrier between lineages across the lowland Isthmus of Tehuantepec, no introgression was observed. Here, a steep environmental cline associated with seasonality of precipitation corresponds exactly with the distributional limits of the lineages, whose closest samples are only 30 km apart. The combination of molecular and environmental evidence, and in conjunction with previous morphological evidence, allows us to reassess the current taxonomy in an integrative framework. Based on our findings, we elevate the previously recognized subspecies from the Pacific versant, the Colima banded gecko C. nemoralis Klauber 1945, to full species status and comment on conservation implications.

The preference of certain plant species for gypsum soils with a patchy distribution leads to disjunct population structures that are thought to generate island-like dynamics potentially influencing biogeographic patterns at multiple evolutionary scales. Here, we study the evolutionary and biogeographic history of Nepeta hispanica, a western Mediterranean plant associated with gypsum soils and displaying a patchy distribution with populations very distant from each other. Three approaches were used: (a) interspecific phylogenetic analyses based on nuclear DNA sequences of the ITS region to unveil the relationships and times of divergence between N. hispanica and its closest relatives; (b) phylogeographic analyses using plastid DNA regions trnS-trnG and psbJ-petA to evaluate the degree of genetic isolation between populations of N. hispanica, their relationships and their genetic diversity; and (c) ecological niche modelling to evaluate historical distributional changes. Results reveal that N. hispanica belongs to an eastern Mediterranean and Asian (Irano-Turanian) clade diversified in arid environments since the Miocene-Pliocene. This species represents the only lineage of this clade that colonised the western Mediterranean, probably through the northern Mediterranean coast (southern Europe). Present Iberian populations display a high plastid genetic diversity and, even if geographically distant from each other, they are highly connected according to the distribution of plastid haplotypes and lineages. This can be explained by a scenario involving a complex history of back-and-forth colonisation events, facilitated by a relative stability of suitable conditions for the species across the western Mediterranean throughout the Quaternary, This work would not have been possible without the support of Julian ´ García, Rub´en de Pablo, Jesús del Río, Leonardo Guti´errez, Javier Puente, Javier Pavon ´ and Luis M. Medrano, who helped us with field sample collection; Leopoldo Medina, Cyrille Chatelain, Jesús Riera and Javier Hernandez, ´ who granted us permission to use specimens from the MA, G, VAL and SALA herbaria respectively; and Emilio Cano, who provided his invaluable help in the RJB-CSIC molecular systematics laboratory. Fieldwork was financed by the Universidad Autonoma ´ de Madrid with a grant to IRG’s Master thesis. Laboratory work was funded by a Juan de la Cierva fellowship to MF-M (Spanish Ministry of Economy and Competitiveness, reference IJCI-2015–23459)

BackgroundThe Mesoamerican dominion is a biogeographic area of great interest due to its complex topography and distinctive climatic history. This area has a large diversity of habitats, including tropical deciduous forests, which house a large number of endemic species. Here, we assess phylogeographic pattern, genetic and morphometric variation in the Cinnamon Hummingbird complexAmazilia rutila, which prefers habitats in this region. This resident species is distributed along the Pacific coast from Sinaloa—including the Tres Marías Islands in Mexico to Costa Rica, and from the coastal plain of the Yucatán Peninsula of Mexico south to Belize.MethodsWe obtained genetic data from 85 samples ofA. rutila, using 4 different molecular markers (mtDNA: ND2, COI; nDNA: ODC, MUSK) on which we performed analyses of population structure (median-joining network, STRUCTURE,FST, AMOVA), Bayesian and Maximum Likelihood phylogenetic analyses, and divergence time estimates. In order to evaluate the historic suitability of environmental conditions, we constructed projection models using past scenarios (Pleistocene periods), and conducted Bayesian Skyline Plots (BSP) to visualize changes in population sizes over time. To analyze morphometric variation, we took measurements of 5 morphological traits from 210 study skins. We tested for differences between sexes, differences among geographic groups (defined based on genetic results), and used PCA to examine the variation in multivariate space.ResultsUsing mtDNA, we recovered four main geographic groups: the Pacific coast, the Tres Marías Islands, the Chiapas region, and the Yucatán Peninsula together with Central America. These same groups were recovered by the phylogenetic results based on the multilocus dataset. Demography based on BSP results showed constant population size over time throughout theA. rutilacomplex and within each geographic group. Ecological niche model projections onto past scenarios revealed no drastic changes in suitable conditions, but revealed some possible refuges. Morphometric results showed minor sexual dimorphism in this species and statistically significant differences between geographic groups. The Tres Marías Islands population was the most differentiated, having larger body size than the remaining groups.ConclusionsThe best supported evolutionary hypothesis of diversification within this group corresponds to geographic isolation (limited gene flow), differences in current environmental conditions, and historical habitat fragmentation promoted by past events (Pleistocene refugia). Four well-defined clades comprise theA. rutilacomplex, and we assess the importance of a taxonomic reevaluation. Our data suggest that both ofA. r. graysoni(Tres Marías Islands) andA. r. rutila(Pacific coast) should be considered full species. The other two strongly supported clades are: (a) the Chiapas group (southern Mexico), and (b) the populations from Yucatán Peninsula and Central America. These clades belong to thecorallirostristaxon, which needs to be split and properly named.

The distribution and species/lineage diversity of freshwater invertebrate zooplankton remains understudied in China. Here, we explored the species/lineage diversity and phylogeography of Ceriodaphnia species across China. The taxonomy of this genus is under-explored. Seven morphospecies of Ceriodaphnia (C. cornuta, C. laticaudata, C. megops, C. pulchella, C. quadrangula, C. rotunda and C. spinata) were identified across 45 of 422 water bodies examined. Rather little morphological variation was observed within any single morphospecies regardless of country of origin. Nevertheless, we recognized that some or all of these morphospecies might represent species complexes. To investigate this, phylogenetic relationships within and among these morphospecies were investigated based on mitochondrial (partial cytochrome c oxidase subunit I gene) and nuclear (partial 28S rRNA gene) markers. The mitochondrial marker placed these populations in nine lineages corresponding to the morphospecies: C. laticaudata and C. pulchella were each represented by two lineages, suggesting that both are species complexes. The remaining five morphospecies were each represented by a single mtDNA lineage. Three of the nine mitochondrial lineages (belonging to C. pulchella, C. rotunda and C. megops) are newly reported and exhibited a restricted distribution within China. The nuclear-DNA phylogeny also recognized seven Ceriodaphnia taxa within China. We detected occasional mito-nuclear discordances in Ceriodaphnia taxa across China, suggesting interspecific introgression and hybridization. Our study contributes to an understanding of the species/lineage diversity of Ceriodaphnia, a genus with understudied taxonomy.

Climate change and geological events have long been known to shape biodiversity, implying that these can likewise be viewed from a biological perspective. To study whether plants can shed light on this, and how they responded to climate change there, we examined Oreocnide, a genus widely distributed in SE Asia. Based on broad geographic sampling with genomic data, we employed an integrative approach of phylogenomics, molecular dating, historical biogeography, and ecological analyses. We found that Oreocnide originated in mainland East Asia and began to diversify ~6.06 Ma, probably in response to a distinct geographic and climatic transition in East Asia at around that time, implying that the last important geological change in mainland SE Asia might be 1 Ma older than previously suggested. Around four immigration events to the islands of Malesia followed, indicating that immigration from the mainland could be an underestimated factor in the assembly of biotic communities in the region. Two detected increases of diversification rate occurred 3.13 and 1.19 Ma, which strongly implicated climatic rather than geological changes as likely drivers of diversification, with candidates being the Pliocene intensification of the East Asian monsoons, and Pleistocene climate and sea level fluctuations. Distribution modelling indicated that Pleistocene sea level and climate fluctuations were inferred to enable inter-island dispersal followed by allopatric separation, underpinning radiation in the genus. Overall, our study, based on multiple lines of evidence, linked plant diversification to the most recent climatic and geological events in SE Asia. We highlight the importance of immigration in the assembly and diversification of the SE Asian flora, and underscore the utility of plant clades, as independent lines of evidence, for reconstructing recent climatic and geological events in the SE Asian region.

The genus Rhabdias StilesHassall, 1905 comprises lung parasites of amphibians and reptiles worldwide. In Japan, 9 species have been recorded, including Rhabdias incerta Wilkie, 1930 which has been reported only in Bufo species. In this study, to assess the diversity of R. incerta, we performed molecular analyses of Rhabdias species sampled from three species/subspecies of Japanese toads namely Bufo japonicus, B. japonicus formosus, and B. torrenticola, collected in various regions of Honshu, Shikoku, and Kyushu, Japan. DNA sequence divergence was compared using mtDNA (COI) and nuclear DNA (28S) to identify possible cryptic species. Morphological analysis was performed through light microscopy and scanning electron microscopy (SEM). The results revealed that Bufo spp. serve as hosts for at least three Rhabdias species. Morphologically, most samples were identified as R. incerta but with a longer body and larger buccal cavity than originally described. Rhabdias incerta appears to be specific to the genus Bufo and is further subdivided into two or three phylogroups based on subspecies divisions and biogeography of their host. Some Rhabdias specimens collected in this study resemble R. tokyoensis Wilkie, 1930, parasitic in hosts from the order Caudata, which suggests host switching. Both molecular and morphological analyses suggested the presence of undescribed and cryptic Rhabdias species within toads collected in Japan. This study was the first to molecularly characterize Rhabdias species in Japan, including novel sequences of R. incerta and two undescribed species.

Fisheries damage caused by Chattonella red tide has been recorded in Southeast Asia. Molecular studies have clarified the presence of two species, Chattonella marina complex and Chattonella subsalsa in the region, unlike East Asia that had only C. marina complex. To elucidate the phylogeography of Chattonella in Asia, further phylogenetic and morphological examinations were carried out with 33 additional culture strains, including the strains isolated during a bloom of Chattonella sp. (up to 142 cells mL

The Brazilian Atlantic Forest has long been considered a global biodiversity hotspot. In the last decade, the phylogeographic patterns of endemic taxa have been unraveling the biogeographic history of the biome. However, highly diverse invertebrate species have still been poorly studied. Sodreana harvestmen (Gonyleptidae) are distributed in most of the humid coastal forests in the southern portion of the Atlantic Forest, a region that has experienced complex topographic evolution and differing climatic conditions since the Early Cretaceous, which likely affected the geographic distribution and diversification of the group. In this study, we investigated the molecular phylogeny and phylogeography of Sodreana to clarify the species relationships and to make inferences about the historical biogeography of the southern Atlantic Forest. We applied coalescent-based phylogenetic analyses using one mitochondrial and three nuclear markers coupled with an ecological niche modeling approach to verify relationships among species, date the main divergence events in the genus, and make inferences concerning possible changes in the geographical distribution and population dynamics from the past. Our results supported the validity of most Sodreana species and suggested that Paleogene-Neogene geomorphologic processes such as the formation of rivers systems, uplift of mountain ranges and related environmental changes have profoundly affected the evolutionary history of Sodreana. The ecological niche models showed that the areas potentially occupied by the species were greatly reduced during Quaternary glacial periods but no recent lineage divergences or genetic bottlenecks were detected, suggesting that climatically stable micro-habitats could have helped maintain populations during drier periods. Our study highlights the importance of humidity-dependent and poor-dispersal taxa in understanding the effects of ancient geological and climate processes on the Atlantic Forest biota.

Guangdong Province is one of the most developed and populous provinces in southern China. The subtype situation of hepatitis C virus (HCV) in Guangdong remains unknown. The aim of this study was to investigate and estimate the HCV subtypes in drug users (DU) using a city-based sampling strategy to better understand the characteristics of HCV transmission in Guangdong. Archived plasma samples (n = 1074) from DU who were anti-HCV positive in 2014 were selected randomly from 20 cities in Guangdong Province. Subtypes were determined based on core and/or E1 sequences using phylogenetic analysis. The distributions of HCV subtypes in DU and different regions were analyzed. A total of 8 genotypes were identified. The three main HCV subtypes in DU in Guangdong were 6a (63.0%), 3a (15.2%), and 3b (11.8%). Significant differences were discovered among different registered residency and regions but not among genders, marital status, education level, or drug use patterns. HCV subtype 3b was significantly higher in Guangdong residents than in non-Guangdong residents. In contrast, HCV subtype 6a was significantly lower in Guangdong residents than in non-Guangdong residents. Subtype 1b in eastern Guangdong (eastern) was significantly lower, while 6a was significantly higher when compared with other regions. Subtype 3a in the Pearl River Delta (PRD) region was significantly higher, while 3b was significantly lower when compared with other regions. In western Guangdong, HCV subtype 3a was significantly lower when compared with other regions. Additionally, in northern Guangdong subtypes 1b and 3b were significantly higher, while 6a was significantly lower when compared with other regions. Our study revealed the diversity and distribution of HCV subtypes in DU in nearly all the cities in Guangdong. The results provide essential information that will allow the establishment of specific intervention strategies that may help prevent HCV transmission.

The Tropical Andes contains exceptionally high diversity, much of it arising within the Quaternary period. The complex geology of the Andes and paleoclimate fluctuations within the Quaternary suggest complex speciation scenarios. This, in turn, has contributed to idiosyncratic speciation modes among shallowly diverged Amazonian taxa. Many relationships among these taxa remain poorly resolved. Here we use a sequence capture approach, ultraconserved elements (UCEs), to address the phylogenetic relationships among three recently diverged Peruvian Ameerega poison frog species (A. cainarachi, A. petersi, and A. smaragdina; family Dendrobatidae) and explore a possible mode of speciation in this group. We assess concordance among concatenated phylogenetic tree inference, gene-tree based species tree inference, SNP-based species tree inference, and Bayes factor lineage delimitation to resolve species boundaries. We complement these analyses with assessments of call divergence to address the presence of a prezygotic reproductive barrier. Additionally, we further explore the phylogeographic history of these species of Ameerega with demographic inference, considering evidence for admixture and population expansions. Our results support the synonymy of A. smaragdina as a junior synonym of A. petersi and we find that speciation in this group is characterized by admixture and signatures of a population bottleneck followed by expansion. We invoke the disturbance-vicariance hypothesis to explain the observed patterns and call for more, detailed investigations of in-situ speciation in the Tropical Andes.

The biogeographical history of Mesoamerican cloud forests is complex, encompassing a diverse and heterogeneous mixture of species with temperate and tropical origins. The dynamic geological landscape and climate change from the Miocene to the Pleistocene affected the distributions and composition of cloud forests in the region, and contributed to divergence events at different time scales. We assessed genetic variation of 29 populations of P. matudae, and closely related P. guatemalensis and P. oleifolius (Podocarpaceae) by sequencing 255 samples of the psbA-trnH and trnL-F intergenic spacer regions across the species ranges. We conducted phylogenetic, population and spatial genetic analyses as well as divergence time estimation and ecological niche modelling (ENM) to test the generality of demographic and genetic scenarios for cloud forest-adapted species. The results revealed genetic differentiation among species, with some individuals of P. oleifolius and P. guatemalensis placed in the P. matudae group and some P. oleifolius in the P. guatemalensis group. Predictions of ENMs under past climatic conditions and a strong signal of spatial expansion suggest that the highland P. matudae and P. oleifolius populations experienced expansions into lower elevation during the Last Glacial Maximum (LGM). Contrary to predictions by the two precipitation models and elevational ups and downs for cloud forest taxa during the LGM, genetic differentiation and predicted distribution of suitable habitat support the hypotheses that P. matudae and P. oleifolius remained in situ during the LGM primarily within the current fragmented distribution of the cloud forest and spread into the lowlands during the LGM, whereas the distribution of suitable habitat for P. guatemalensis had no major changes upwards from the Last Inter Glacial (LIG) to current conditions.

International audience; The cyst nematode Heterodera carotae, which parasitizes carrot roots, has been recorded in many countries in Europe (Italy, The Netherlands, Switzerland, France, Denmark, …), in South Africa and in North America (Canada, USA). To date, there is a lack of knowledge about the genetic structure of the populations of this economically important nematode. The aim of this work was to study the structuration of the genetic diversity of the carrot cyst nematode at the European scale. We have developed a set of thirteen polymorphic microsatellite markers and used it to genotype seventeen European populations of H. carotae coming from France, Switzerland, Italy, Denmark and one non-European population from Canada. As previously showed for other cyst nematode species, the H. carotae populations were characterised by a strong heterozygote deficit. A Bayesian clustering analysis revealed two distinct genetic clusters, with one group located in the north of Europe and a second one located in the south of Europe. Moreover, our results highlighted rather limited gene flow at small spatial scale and some events of long distance migration. This first investigation of the genetic diversity of H. carotae populations would be useful to develop sustainable control strategies.

The evolutionary history of taxa with limited overseas dispersal abilities is considered to be majorly influenced by vicariant events constituting them as model organisms for the interpretation of evolutionary processes. An excellent candidate are the wall lizards of the genus Podarcis exhibiting an impressive level of genetic and morphological diversification and harboring several cases of recently discovered cryptic diversity. In this study, we investigated the effect of palaeogeographic events on the wall lizards’ biodiversity patterns in the Aegean (Greece) as well as the evolutionary processes that acted both in space and time. To accomplish that we studied a group of three endemic Podarcis species (i.e., P. cretensis, P. levendis, and P. peloponnesiacus) both at the intra and interspecific levels employing mitochondrial and nuclear DNA sequence data as well as microsatellites. Furthermore, presence information coupled with bioclimatic data (i.e., species distribution modeling, and niche similarity analyses) shed light on the necessary ecological factors for the species’ occurrence. These approaches revealed yet another case of cryptic diversity for this group of lizards, with the existence of two slightly overlapping lineages within P. peloponnesiacus and highly structured populations within P. cretensis. Species diversification occurred during the Pliocene with P. peloponnesiacus divergence into the two lineages dating back to 1.86 Mya. Furthermore, temperature and precipitation related environmental parameters were the most important ones regarding the current distribution of the studied species. Based on the results, we propose a more detailed phylogeographic scenario where both the paleogeography of the area and several environmental parameters have shaped the genetic diversity and the current distribution pattern of this species group.

The evolution of Peninsular Indian biodiversity has been a fascinating topic of research due to historical connections of this region to the ancient Gondwanaland. We investigated the phylogeny and historical biogeography of nearly all extant species of the genus Piper reported from the region to assess the biogeographical origins and test mechanisms of lineage diversification (dispersal, vicariance and in situ radiation) of this highly diverse genus of angiosperms commonly found in the understory of evergreen forests. The phylogeny of 21 species of Piper reported from Peninsular India was reconstructed for the first time, which included three new putative species from the Western Ghats. We used BEAST for the divergence time estimations (using three constraints), and ancestral range estimations were performed with the dated phylogenetic tree using BIOGEOBEARS. Divergence dating analysis revealed that the genus Piper originated during lower Cretaceous around 110 Ma [95% highest posterior density (HPD): 116–105 Ma] and colonized Peninsular India five times independently, from Southeast Asia starting from the Oligocene. The two major dispersals into India occurred during the periods of 27.3 Ma (95% HPD: 35.8–19.9.) and 15.5 Ma (95% HPD: 24.9–7.11). This was followed by rapid radiations in some lineages with subsequent back dispersals to Southeast Asia. Our study indicates that dispersals from Southeast Asia led to the arrival of Piper to Indian subcontinent following the Indo-Eurasian collision. Members of Piper have colonized and diversified within the climatically stable habitats of Peninsular India. Furthermore, the present study provides evidence for the Miocene overland dispersal of Piper species to Africa from South Asia.

Zika virus (ZIKV), a vector-borne infectious agent that has recently been associated with neurological diseases and congenital microcephaly, was first reported in the Western hemisphere in early 2015. A number of authors have reconstructed its epidemiological history using advanced phylogenetic approaches, and the majority of Zika phylogeography studies have used discrete diffusion models. Continuous space diffusion models make it possible to infer the possible origin of the virus in real space by reconstructing its ancestral location on the basis of geographical coordinates deduced from the latitude and longitude of the sampling locations. We analysed all the ZIKV complete genome isolates whose sampling times and localities were available in public databases at the time the study began, using a Bayesian approach for discrete and continuous phylogeographic reconstruction. The discrete phylogeographic analysis suggested that ZIKV emerged to become endemic/epidemic in the first decade of the 1900s in the Ugandan rainforests, and then reached Western Africa and Asia between the 1930s and 1950s. After a long period of about 40 years, it spread to the Pacific islands and reached Brazil from French Polynesia. Continuous phylogeography of the American epidemic showed that the virus entered in north-eastern Brazil in late 2012 and started to spread in early 2013 from two high probability regions: one corresponding to the entire north-east Brazil and the second surrounding the city of Rio de Janeiro, in a mainly northwesterly direction to Central America, the north-western countries of south America and the Caribbean islands. Our data suggest its cryptic circulation in both French Polynesia and Brazil, thus raising questions about the mechanisms underlying its undetected persistence in the absence of a known animal reservoir, and underline the importance of continuous diffusion models in making more reliable phylogeographic reconstructions of emerging viruses.

The tribe Urticeae (Urticaceae), popularly known as Nettles, include 12 genera and ca. 200 species, constituting a diverse and cosmopolitan plant clade centered in tropical Asia, Africa, and South America. The global distribution of this clade makes it an excellent group to test hypotheses regarding the processes underlying tropical intercontinental disjunctions. More specifically, it allows us to test whether current distribution patterns resulted from recent transoceanic long-distance dispersal or ancient vicariance after boreotropical migration. We reconstructed the phylogeny of Nettles with the nuclear ITS and four plastid DNA regions (rbcL, trnL-F, matK and rpl14-rpl36) using Bayesian inference and maximum parsimony approaches. We inferred divergence times using a Bayesian uncorrelated lognormal relaxed molecular clock model and ancestral areas using the divergence-extinction-cladogenesis (DEC) model. Our results indicate a tropical Asian origin for the tribe during the late Paleocene. Migration events to Eurasia, South America and Africa occurred mainly during the Oligocene and Miocene. However, several long-distance dispersal events, including dispersals from Asia to Hawaii or Australasia, were inferred to have occurred from the Miocene onwards. The fleshy fruits and winged diaspores of several taxa are suited for long-distance dispersal.

A group of seven endemic Polystichum species inhabit Patagonia, the southern region of South America. To date, evolutionary relationships of these Austral South American Polystichum remain unknown. The biota of the Southern Andes appears to be more closely related to the temperate Australasian species than to northern South American ones. Differences in morphological characters suggested that Austral South American Polystichum follows that biogeographical pattern, not being closely related to their congeners in the Northern and Central Andes. We sought to reveal the evolutionary relationships, estimate the divergence times and reconstruct both ancestral areas and ancestral ploidy levels of Austral South America Polystichum. Phylogenetic relationships were estimated using maximum likelihood and Bayesian approaches. The seven Austral South American species plus 31 Polystichum species spanning all other major biogeographic regions were sampled for three DNA markers. Divergence times were estimated in BEAST and Bayesian binary Markov chain Monte Carlo reconstruction was applied in order to infer ancestral areas. The evolution of ploidy was reconstructed on the maximum clade credibility tree, using stochastic character mapping. Austral South American Polystichum was recovered as monophyletic. The earliest divergence reconstructed within the Austral South American Clade was that of Polystichum andinum; subsequently two other lineages diverged comprising the remaining Austral South American species. The Austral South American lineage is not closely allied to North and Central Andes congeners. Long-distance dispersal of an ancestral tetraploid from Australasia during the late Miocene is the most likely explanation for the origin of Patagonian Polystichum. Then, Pliocene and Pleistocene orogenic and climatic changes may have shaped its diversification in Patagonia. Fil: Morero, Rita Ema. Universidad Nacional de Córdoba; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina Fil: Deanna, Rocío. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina. Universidad Nacional de Córdoba; Argentina Fil: Barboza, Gloria Estela. Universidad Nacional de Córdoba; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina Fil: Barrington, David S.. University of Vermont; Estados Unidos

Astragalus, a highly diverse genus of flowering plants with its highest center of diversity in West Asia, is a classic example of rapid species-level radiation and adaptation to a diversity of habitats throughout the world. We examined the historical biogeography of Astragalus using molecular dating and ancestral area reconstruction to understand how past climate changes, geographical patterns and transition in life history have provoked diversification of Astragalus. Our results suggest that Astragalus probably originated during the middle Miocene in West Asia, underwent rapid diversification, subsequently and repeatedly expanded its range in the Mediterranean region, and later to North America through West Europe. This distribution range was also extended toward central and eastern Asia from the Middle Miocene to Pleistocene. Several climatic and geological processes during the Miocene-Pliocene may be implicated in the diversification of the major Astragalus clades. In particular, the annual lineages, which are important elements in the Mediterranean flora of Africa and Europe and in the deserts of southwest to central Asia, have arisen in response to progressing aridity from the late Miocene onwards (between 8.6 Ma and 2.98 Ma). Diversification rate analyses indicate three rapid and recent diversification events, one at c. 11 Ma in the clade that groups most of the Astragalus s.s. (all except the Ophiocarpus sister lineage), one at c. 5 Ma in the crown group of the Hypoglottis clade, including herbaceous annual and perennial species, and the most recent one at c. 3 Ma in the spiny cushion forming Astracantha clade. Our study highlights the complexity of processes and factors shaping diversifications in Astragalus; a complex interaction among climatic modifications providing opportunities for diversification and likely coincident with the evolution of key morphological and physiological adaptations.

Current knowledge about the performance of floating seaweeds as dispersal vectors comes mostly from mid latitudes (30°-40°), but phylogeographic studies suggest that long-distance dispersal (LDD) is more common at high latitudes (50°-60°). To test this hypothesis, long-term field experiments with floating southern bull kelp Durvillaea antarctica were conducted along a latitudinal gradient (30°S, 37°S and 54°S) in austral winter and summer. Floating time exceeded 200d in winter at the high latitudes but in summer it dropped to 90d, being still higher than at low latitudes (45d). Biomass variations were due to loss of buoyant fronds. Reproductive activity diminished during long floating times. Physiological changes included mainly a reduction in photosynthetic (F

The lacertid lizards of the genus Mesalina inhabit the arid regions of the Old World, from North Africa to NW India. Of the 19 recognized species within the genus, eleven occur in Arabia. In this study, we explore the genetic variability and phylogeographic patterns of the less studied M. adramitana group from southern Arabia and the Socotra Archipelago within the phylogenetic and biogeographic context of the entire genus. Our unprecedented sampling extends the distribution ranges of most Mesalina species and, for the first time, sequences of M. ayunensis are included in a phylogenetic analysis. We perform analyses of concatenated multilocus datasets and species trees, conduct species delimitation analyses, and estimate divergence times within a biogeographic framework. Additionally, we inferred the environmental suitability and identified dispersal corridors through which gene flow is enabled within M. adramitana. Our results show that the Socotra Archipelago was colonized approximately 7 Mya by a single oversea colonization from mainland Arabia. Then, an intra-archipelago dispersal event that occurred approximately 5 Mya resulted in the speciation between M. balfouri, endemic to Socotra, Samha and Darsa Islands, and M. kuri, endemic to Abd al Kuri Island. Similar to previous studies, we uncovered high levels of genetic diversity within the M. adramitana species-group, with two highly divergent lineages of M. adramitana living in allopatry and adapted to locally specific climatic conditions that necessitate further investigation., All efforts were made to minimize animal suffering. All collecting and export permits were issued by the Nature Conservation Department of the Ministry of Environment and Climate Affairs, Oman (Refs: 08/2005; 16/2008; 38/2010; 12/2011; 13/2013; 21/2013; 37/2014; 31/2016). This work was supported by the Ministerio de Economía y Competitividad, Spain (co-funded by FEDER) under grant numbers CGL2012-36970 and CGL2015-70390-P; Ministry of Environment and Climate Affairs under Grant number 22412027; Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya under grant number 2017-SGR-00991. MSR was funded by an FPI grant from the Ministerio de Economía y Competitividad, Spain (BES-2013-064248). JS was funded by the Czech Science Foundation (GACR, project number 18-15286Y) and the Ministry of Culture of the Czech Republic (DKRVO 2019–2023/6.VII.a, 00023272).

To investigate the past spatial dynamics of Atlantic Forest (AF) ‘island-like’ enclaves in northeastern Brazil, we employed ecological niche modeling (ENM) using a set of georeferenced records of 13 woody plant species. ENMs were constructed using the Ensemble forecasting approach and were projected into past climatic conditions for the last interglacial period (LIG, 120 kyr), last glacial maximum (LGM, 21 kyr), and the Middle Holocene (MH, 6 kyr). Our results suggest an expansion of wetter forests during the LGM into areas currently covered by the Caatinga seasonally dry woodlands, with recent retraction to the current distribution. Central AF islands located south of the Sao Francisco River underwent a different history compared to Northern AF islands north of this river: the former were mostly connected to coastal AF since the LIG (with a very recent separation), whereas the latter presented a more dynamic historical distribution. Results reveal contrasting spatiotemporal histories of forest instability and isolation across the various enclaves, supporting three main biogeographic hypotheses: i) moderate connectivity with coastal AF and a recent population bottleneck in the Araripe and Pernambuco/Paraiba enclaves, ii) low connectivity to, and long-term isolation from, other enclaves, as well as recent population bottleneck, in the northernmost North Ceara enclaves; and iii) high connectivity with coastal AF and recent population expansion in the southernmost Chapada Diamantina enclaves. Future comparative phylogeography studies will largely aid in assessing the herein proposed biogeographic scenarios during the highly dynamic recent history of the AF enclaves.

In order to provide a global overview of genotypic, epidemiologic, demographic, phylogeographical, and drug resistance characteristics related to the prevailing tuberculosis (TB) epidemic, we hereby report an update of the 6th version of the international genotyping database SITVIT2. We also make all the available information accessible through a dedicated website (available at http://www.pasteur-guadeloupe.fr:8081/SITVIT2). Thanks to the public release of SITVIT2 which is currently the largest international multimarker genotyping database with a compilation of 111,635 clinical isolates from 169 countries of patient origin (131 countries of isolation, representing 1032 cities), our major aim is to highlight macro- and micro-geographical cleavages and phylogeographical specificities of circulating Mycobacterium tuberculosis complex (MTBC) clones worldwide. For this purpose, we retained strains typed by the most commonly used PCR-based methodology for TB genotyping, i.e., spoligotyping based on the polymorphism of the direct repeat (DR) locus, 5-loci Exact Tandem Repeats (ETRs), and MIRU-VNTR minisatellites used in 12-, 15-, or 24-loci formats. We describe the SITVIT2 database and integrated online applications that permit to interrogate the database using easy drop-down menus to draw maps, graphics and tables versus a long list of parameters and variables available for individual clinical isolates (year and place of isolation, origin, sex, and age of patient, drug-resistance, etc.). Available tools further allow to generate phylogenetical snapshot of circulating strains as Lineage-specific WebLogos, as well as minimum spanning trees of their genotypes in conjunction with their geographical distribution, drug-resistance, demographic, and epidemiologic characteristics instantaneously; whereas online statistical analyses let a user to pinpoint phylogeographical specificities of circulating MTBC lineages and conclude on actual demographic trends. Available associated information on gender (n = 18,944), age (n = 16,968), drug resistance (n = 19,606), and HIV serology (n = 2673), allowed to draw some important conclusions on TB geo-epidemiology; e.g. a positive correlation exists between certain Mycobacterium tuberculosis lineages (such as CAS and Beijing) and drug resistance (p-value.001), while other lineages (such as LAM, X, and BOV) are more frequently associated with HIV-positive serology (p-value.001). Besides, availability of information on the year of isolation of strains (range 1759-2012), also allowed to make tentative correlations between drug resistance information and lineages - portraying probable evolution trends over time and space. To conclude, the present approach of geographical mapping of predominant clinical isolates of tubercle bacilli causing the bulk of the disease both at country and regional level in conjunction with epidemiologic and demographic characteristics allows to shed new light on TB geo-epidemiology in relation with the continued waves of peopling and human migration.

Since late 2011, outbreaks of pseudorabies virus (PRV) have occurred in southern China causing major economic losses to the pig industry. We previously reported that variant PRV forms and recombination in China could be the source of continued epidemics. Here, we analyzed samples from intensive pig farms in eastern China between 2017 and 2019, and sequenced the main glycoproteins (gB, gC, gD, and gE) to study the evolution characteristics of PRV. Based on the gC gene, we found that PRV variants belong to clade 2 and detected a founder effect during by the PRV epidemic. In addition, we detected inter- and intra-clade recombination; in particular, inter-clade recombination in the gB genes of strains FJ-ZXF and FJ-W2, which were recombinant with clade 1 strains. We also found specific amino-acid changes and positively selected sites, possibly associated with functional changes. This analysis of the emergence of PRV in China illustrates the need for continuous monitoring and the development of vaccines against specific variants of PRV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12250-019-00140-1) contains supplementary material, which is available to authorized users.

Hepatitis B virus (HBV) infection is a leading cause of severe chronic liver disease worldwide. The HBV epidemiology in Latin American countries is complex and the data is still scanty and fragmentary. The aim of this study was to investigate the distribution of HBV genotypes in Paraguay and to estimate the viral population dynamic and spread pattern of the main phylogenetic group. To this end, partial and complete genome sequences were obtained from 60 blood donor candidates and analysed by phylogenetic and Bayesian phylodynamic approaches. The phylogenetic analysis based on sequences of partial Polymerase/Pre-S1 overlapping region showed a predominance of the Native American subgenotype F4 (81.7%), the presence of the European subgenotypes A2 (1.7%) and D3 (8.3%), the African subgenotype A1 (3, 5%) and the Asian subgenotypes B2 (1.7%) and C2 (1.7%). The distribution of HBV genotypes was in accordance with the ethnic composition of the population. The phylogeographic analysis of subgenotype F4 complete genomes suggests that this lineage emerged and spread in the last 300 years. Paraguay was the most probable location of the common ancestor. The lineage diverged into two main clades and spread to neighbor regions, mainly Bolivia and Northwest Argentina, and Buenos Aires. The phylogeny showed a scanty geographical structure and a complex migratory pattern. In conclusion, the HBV genotypes circulating in Paraguay reflect the ethnic origin of the population. The distribution of genotypes and the phylogeographic reconstruction showed the impact of both global and local migrations in shaping the HBV molecular epidemiology in the region.

This study assesses the genetic structure and gene flow of the salt marsh species Salicornia tegetaria between estuaries and tests three hypotheses: (1) that the relocation of estuaries on a shallow continental shelf during the last glacial maximum created a historical biogeographic barrier, the exact location of which we attempt to pin-point, (2) that there is connectivity and thus gene flow at present between estuaries, and (3) that some estuaries have higher genetic diversity and are therefore of higher conservation priority. DNA samples were collected from 17 estuaries and used to create haplotype networks. Analyses of molecular variance, isolation by distance, selective neutrality and genetic distance between estuaries were also conducted. Eleven ITS ribotypes, one found exclusively between Olifants and Breede Estuaries, and eight rpS16 haplotypes were recovered with a dominant haplotype occurring in most estuaries. The remaining ribotypes and haplotypes from ITS and rpS16 sequences were unique, predominantly on the South and East Coast. A high amount of gene flow and an increase in genetic differentiation from west to east was found. The topography of the continental shelf and diverging ocean currents did provide a historical geographic barrier during the last glacial maximum approximately 18,000 years ago. A high degree of connectivity between estuaries allows for the exchange of genetic material in the direction of the ocean current, but long distance dispersal is also suggested. Repeated habitat fragmentation, most likely due to fluctuating sea levels, contributed to a higher amount of rare haplotypes on the South and East Coast. This study provides baseline information on a salt marsh species for which there is a paucity of data that is widely distributed in an ecosystem that is likely to be heavily impacted by climate change.

Natural history collections are increasingly valued as genomic resources. Their specimens reflect the combined efforts of collectors and curators over hundreds of years. For many rare or endangered species, specimens are the only readily available source of DNA. We leveraged specimens from a historical collection to study the evolutionary history of wood-partridges in the genus Dendrortyx. The three Dendrortyx species are found in the highlands of central Mexico and Central America south to Costa Rica. One of these species is endangered, and in general, Dendrortyx are secretive and poorly represented in tissue collections. We extracted DNA from historical museum specimens and sequenced ultraconserved elements (UCEs) and mitochondrial DNA (mtDNA) to assess their phylogeny and divergence times. Phylogenies built from hundreds to thousands of nuclear markers were well resolved and largely congruent with an mtDNA phylogeny. The divergence times revealed an unusually old avian divergence across the Isthmus of Tehuantepec in the Pliocene around 3.6 million years ago. Combined with other recent studies, our results challenge the general pattern that highland bird divergences in Mesoamerica are relatively young and influenced by the Pleistocene glacial cycles compared to the older divergences of reptiles and plants, which are thought to overlap more with periods of mountain formation. We also found evidence for monophyletic genetic lineages in mountain ranges within the widespread D. macroura, which should be investigated further with integrative taxonomic methods. Our study demonstrates the power of museum genomics to provide insight into the evolutionary histories of groups where modern samples are lacking.

The large diversity of new tick-borne phleboviruses, and the negative impacts of the virulent viruses on human/animal health have led to a growing interest in their analysis. In this report, new insights are brought out into the diversity of putative phleboviruses circulating in Portugal (both the continental territory and the islands of Sao Miguel, in the Azores, and Madeira), as well as in the Spanish western regions of Extremadura and Castilla and Leon. Phlebovirus sequences were frequently detected (L-segment) from both questing and feeding ticks, but especially in Rhipicephalus sanguineus sensu lato (s.l.) specimens. These sequences were detected in adult ticks, as well as nymphs and eggs, supporting the hypothesis of viral maintenance by vertical transmission. Though multiple genetic groups could be identified in phylogenetic trees (AnLuc, KarMa, RiPar virus 1, and Spanish group 1 and 2), all the sequences from Portugal and Spain shared common ancestry with other viral sequence obtained from samples collected over a large geographic coverage. Spatiotemporal analysis placed Middle-East as the geographic origin of the most recent common ancestor (MRCA) of all phleboviruses analysed in the present study. More recent viral transitions might include migrations from Spain to continental Portugal, and from there to the Portuguese Islands. Our findings suggest that the time of the MRCA of phleboviruses was dated around 225 years ago [95% HPD: 124–387 year before the last sampling date].

Lyngbya majuscula is a marine filamentous cyanobacteria belonging to the family Oscillatoriaceae. Recent phylogenetic analyses of L. majuscula have reclassified a subset of this species into various genera such as Moorea, Okeania and Dapis. From the genus Moorea, Moorea producens is a toxic invasive cyanobacterium that produces bioactive secondary metabolites that can cause severe inflammation and blistering. Despite the global distribution of M. producens, little information is available on their origin, patterns of dispersal and population structure. In this study, the spatial population structure of M. producens was investigated using near-complete 16S rRNA sequences. Analysis of the global population of M. producens by Isolation by Distance and STRUCTURE revealed two significantly distinct cosmopolitan populations that were separated by a genetic break. Lineage-specific divergence estimates of 147 cyanobacterial taxa, based on a relaxed molecular clock indicated the first global emergence of M. producens during the Mesoarchean and a subsequent global recolonization during the Mesoproterozoic period. We conclude that the genetic discontinuity between both cosmopolitan populations is attributed to refugia associated with Proterozoic glacial cycles.

Mutual dependence and shared geographic distributions of ectomycorrhizal fungi and their hosts suggest that comigration has had an influential role in the evolution of the ectomycorrhizal symbiosis. To test the hypothesis of comigration of ectomycorrhizal symbionts we conducted a phylogeographic analysis of host specific ectomycorrhizal fungi in genus Rhizopogon sampled throughout the natural range of their Pseudotsuga (Douglas fir) hosts. Low coverage genome assemblies were sequenced for all Rhizopogon species-level clades and a novel data mining method, genome-scale sequence typing, was developed to produce a genome-scale phylogenetic dataset. Phylogenetic and phylogeographic analyses support a single evolutionary origin of the Rhizopogon-Pseudotsuga ectomycorrhizal symbiosis in coastal western North America with a single migration into Asia and two independent migrations east into the North American Intermountain West. Our results suggest that the Rhizopogon-Pseudotsuga ectomycorrhizal symbiosis predates species radiation in Pseudotsuga and that these genera have undergone processes of comigration and codiversification.

Over time, mountain biota has undergone complex evolutionary histories that have left imprints on its genomic arrangement, geographical distribution and diversity of contemporary lineages. Knowledge on these biogeographical aspects still lags behind for invertebrates inhabiting the Alpine region. In the present study, we examined three scorpion species of the subgenus Euscorpius (Alpiscorpius) from the European Alps using cytogenetic and molecular phylogenetic approaches to determine the variation and population structure of extant lineages at both chromosome and genetic level, and to provide an insight into the species diversification histories. We detected considerable intraspecific variability in chromosome complements and localization of the 18S rDNA loci in all studied species. Such chromosome differences were noticeable as the existence of three [in E. (A.) alpha and E. (A.) germanus] or four [in E. (A.) gamma] range-restricted karyotypic races. These races differed from one another either by 2n [in E. (A.) alpha 2n = 54, 60, 90; in E. (A.) gamma 2n = 58, 60, 88, 86–92], or by the karyotypic formula [in E. (A.) germanus 2n = 34m + 12sm; 36m + 10sm; 42m + 4sm]. Using mitochondrial (16S rRNA, COI) and nuclear (28S rDNA) genetic markers, we examined genetic variation and reconstructed phylogenetic relationships among the karyotypic races. Both approaches provided evidence for the existence of ten deeply divergent lineages exhibiting the features of local endemics and indicating the presence of cryptic species. Molecular dating analyses suggest that these lineages diversified during the Plio-Pleistocene and this process was presumably accompanied by dynamic structural changes in the genome organization.