ResearchPad - phylogeography https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Local and landscape-level diversity effects on forest functioning]]> https://www.researchpad.co/article/elastic_article_14584 Research of the past decades has shown that biodiversity is a fundamental driver of ecosystem functioning. However, most of this biodiversity–ecosystem functioning (BEF) research focused on experimental communities on small areas where environmental context was held constant. Whether the established BEF relationships also apply to natural or managed ecosystems that are embedded in variable landscape contexts remains unclear. In this study, we therefore investigated biodiversity effects on ecosystem functions in 36 forest stands that were located across a vast range of environmental conditions in managed landscapes of Central Europe (Switzerland). Specifically, we approximated forest productivity by leaf area index and forest phenology by growing-season length and tested effects of tree species richness and land-cover richness on these variables. We then examined the correlation and the confounding of these local and landscape-level diversity effects with environmental context variables related to forest stand structure (number of trees), landscape structure (land-cover edge density), climate (annual precipitation) and topography (mean altitude). We found that of all tested variables tree species richness was among the most important determinants of forest leaf area index and growing-season length. The positive effects of tree species richness on these two ecosystem variables were remarkably consistent across the different environmental conditions we investigated and we found little evidence of a context-dependent change in these biodiversity effects. Land-cover richness was not directly related to local forest functions but could nevertheless play a role via a positive effect on tree species richness.

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<![CDATA[Large-scale metabarcoding analysis of epipelagic and mesopelagic copepods in the Pacific]]> https://www.researchpad.co/article/elastic_article_14565 A clear insight into the large-scale community structure of planktonic copepods is critical to understanding the mechanisms controlling diversity and biogeography of marine taxa in terms of their high abundance, ubiquity, and sensitivity to environmental changes. Here, we applied a 28S metabarcoding approach to large-scale communities of epipelagic and mesopelagic copepods at 70 stations across the Pacific Ocean and three stations in the Arctic Ocean. Major patterns of community structure and diversity, influenced by water mass structures, agreed with results from previous morphology-based studies. However, a large-scale metabarcoding approach could detect community changes even under stable environmental conditions, including changes in the north/south subtropical gyres and east/west areas within each subtropical gyre. There were strong effects of the epipelagic environment on mesopelagic communities, and community subdivisions were observed in the environmentally stable mesopelagic layer. In each sampling station, higher operational taxonomic unit (OTU) numbers and lower phylogenetic diversity were observed in the mesopelagic layer than in the epipelagic layer, indicating a recent rapid increase in species numbers in the mesopelagic layer. The phylogenetic analysis utilizing representative sequences of OTUs revealed trends of recent emergence of cold-water OTUs, which are mainly distributed at high latitudes with low water temperatures. Conversely, the high diversity of copepods at low latitudes was suggested to have been formed through long evolution under high water temperature conditions. The metabarcoding results suggest that evolutionary processes have strong impacts on current patterns of copepod diversity, and support the “out of the tropics” theory explaining latitudinal diversity gradients of copepods. Diversity patterns in both epipelagic and mesopelagic copepods was highly correlated to sea surface temperature; thus, predicted global warming may have a significant impact on copepod diversity in both layers.

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<![CDATA[Genetic variation and phylogeographic structure of <i>Spodoptera exigua</i> in western China based on mitochondrial DNA and microsatellite markers]]> https://www.researchpad.co/article/elastic_article_14552 The beet armyworm, Spodoptera exigua, is a significant agricultural pest of numerous crops and has caused serious economic losses in China. To effectively control this pest, we analyzed its genetic variation, population genetic structure and demographic history. We used mitochondrial DNA (mtDNA) fragments of the cytochrome oxidase subunit I (COI) and eight nuclear microsatellite loci to investigate genetic diversity and population genetic structure of S. exigua populations at 14 sampling sites in western China. Both mtDNA and microsatellite data indicated low levels of genetic diversity among all populations. A moderate genetic differentiation among some S. exigua populations was detected. Neighbor-joining dendrograms, STRUCTURE, and principal coordinate analysis (PCoA) revealed two genetically distinct groups: the KEL group and the remaining population group. Isolation by distance (IBD) results showed a weak significant correlation between geographic distance and genetic differentiation. Haplotype networks, neutrality testing, and mismatch distribution analysis indicated that the beet armyworm experienced a recent rapid expansion without a recent genetic bottleneck in western China. Thus, the results of this population genetic study can help with the development of strategies for managing this highly migratory pest.

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<![CDATA[An Out-of-Patagonia migration explains the worldwide diversity and distribution of <i>Saccharomyces eubayanus</i> lineages]]> https://www.researchpad.co/article/elastic_article_14503 Lager yeast history has intrigued scientists for decades. The recent isolation of S. eubayanus, the lager yeast ancestor, represents an unprecedented opportunity to extend our knowledge on yeast phylogeography and the origins of the S. pastorianus lager hybrid. However, the genetic, phenotypic and evolutionary history of this species remains poorly known. Our work demonstrates that S. eubayanus isolates from Patagonia have the greatest genetic diversity, comprising the largest number of lineages within a single geographic region and experienced ancestral and recent admixture between lineages, likely suggesting co-occurrence in Patagonia. Importantly, some isolates exhibited significant phenotypic differences for traits such as high temperature and ethanol tolerance, together with fermentation performance, demonstrating their potential in the brewing industry for the generation of new styles of lager beers. Furthermore, our results support the idea of colonization from peripheral glacial refugia from the South, as responsible for the high genetic diversity observed in southern Chilean Patagonia. Our results allow hypothesizing a successful physiological adjustment of the species to the local conditions in Patagonia, explaining its wide distribution in the southern hemisphere.

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<![CDATA[An explicit test of Pleistocene survival in peripheral versus nunatak refugia in two high mountain plant species]]> https://www.researchpad.co/article/N8e97a9dd-ab9d-4a03-a0fa-4f65a81dc6df

Abstract

Pleistocene climate fluctuations had profound influence on the biogeographical history of many biota. As large areas in high mountain ranges were covered by glaciers, biota were forced either to peripheral refugia (and possibly beyond to lowland refugia) or to interior refugia (nunataks). However, nunatak survival remains controversial as it relies solely on correlative genetic evidence. Here, we test hypotheses of glacial survival using two high alpine plant species (the insect‐pollinated Pedicularis asplenifolia and wind‐pollinated Carex fuliginosa) in the European Alps. Employing the iDDC (integrative Distributional, Demographic and Coalescent) approach, which couples species distribution modelling, spatial and temporal demographic simulation and Approximate Bayesian Computation, we explicitly test three hypotheses of glacial survival: (a) peripheral survival only, (b) nunatak survival only and (c) peripheral plus nunatak survival. In P. asplenifolia the peripheral plus nunatak survival hypothesis was supported by Bayes factors (BF> 100), whereas in C. fuliginosa the peripheral survival only hypothesis, although best supported, could not be unambiguously distinguished from the peripheral plus nunatak survival hypothesis (BF = 5.58). These results are consistent with current habitat preferences (P. asplenifolia extends to higher elevations) and the potential for genetic swamping (i.e., replacement of local genotypes via hybridization with immigrating genotypes [expected to be higher in the wind‐pollinated C. fuliginosa]). Although the persistence of plants on nunataks during glacial periods has been debated and studied over decades, this is one of the first studies to explicitly test the hypothesis instead of solely using correlative evidence.

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<![CDATA[The genetic diversity and population structure of Sophora alopecuroides (Faboideae) as determined by microsatellite markers developed from transcriptome]]> https://www.researchpad.co/article/N8ed88142-6689-430c-b82a-b033b4ff58ac

Sophora alopecuroides (Faboideae) is an endemic species, mainly distributed in northwest China. However, the limited molecular markers range for this species hinders breeding and genetic studies. A total of 20,324 simple sequence repeat (SSR) markers were identified from 118,197 assembled transcripts and 18 highly polymorphic SSR markers were used to explore the genetic diversity and population structure of S. alopecuroides from 23 different geographical populations. A relatively low genetic diversity was found in S. alopecuroides based on mean values of the number of effective alleles (Ne = 1.81), expected heterozygosity (He = 0.39) and observed heterozygosity (Ho = 0.55). The results of AMOVA indicated higher levels of variation within populations than between populations. Bayesian-based cluster analysis, principal coordinates analysis and Neighbor-Joining phylogeny analysis roughly divided all genotypes into four major groups with some admixtures. Meanwhile, geographic barriers would have restricted gene flow between the northern and southern regions (separated by Tianshan Mountains), wherein the two relatively ancestral and independent clusters of S. alopecuroides occur. History trade and migration along the Silk Road would together have promoted the spread of S. alopecuroides from the western to the eastern regions of the northwest plateau in China, resulting in the current genetic diversity and population structure. The transcriptomic SSR markers provide a valuable resource for understanding the genetic diversity and population structure of S. alopecuroides, and will assist effective conservation management.

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<![CDATA[Biogeography of the endosymbiotic dinoflagellates (Symbiodiniaceae) community associated with the brooding coral Favia gravida in the Atlantic Ocean]]> https://www.researchpad.co/article/5c8c1937d5eed0c484b4d1a6

Zooxanthellate corals live in symbiosis with phototrophic dinoflagellates of the family Symbiodiniaceae, enabling the host coral to dwell in shallow, nutrient-poor marine waters. The South Atlantic Ocean is characterized by low coral diversity with high levels of endemism. However, little is known about coral–dinoflagellate associations in the region. This study examined the diversity of Symbiodiniaceae associated with the scleractinian coral Favia gravida across its distributional range using the ITS-2 marker. This brooding coral endemic to the South Atlantic can be found across a wide range of latitudes and longitudes, including the Mid-Atlantic islands. Even though it occurs primarily in shallower environments, F. gravida is among the few coral species that live in habitats with extreme environmental conditions (high irradiance, temperature, and turbidity) such as very shallow tide pools. In the present study, we show that F. gravida exhibits some degree of flexibility in its symbiotic association with zooxanthellae across its range. F. gravida associates predominantly with Cladocopium C3 (ITS2 type Symbiodinium C3) but also with Symbiodinium A3, Symbiodinium linucheae (ITS2 type A4), Cladocopium C1, Cladocopium C130, and Fugacium F3. Symbiont diversity varied across biogeographic regions (Symbiodinium A3 and S. linucheae were found in the Tropical Eastern Atlantic, Cladocopium C1 in the Mid-Atlantic, and other subtypes in the Southwestern Atlantic) and was affected by local environmental conditions. In addition, Symbiodiniaceae diversity was highest in a southwestern Atlantic oceanic island (Rocas Atoll). Understanding the relationship between corals and their algal symbionts is critical in determining the factors that control the ecological niches of zooxanthellate corals and their symbionts, and identifying host-symbiont pairs that may be more resistant to environmental changes.

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<![CDATA[Phylogeographic investigation of 2014 porcine epidemic diarrhea virus (PEDV) transmission in Taiwan]]> https://www.researchpad.co/article/5c89779dd5eed0c4847d319c

The porcine epidemic diarrhea virus (PEDV) that emerged and spread throughout Taiwan in 2014 triggered significant concern in the country’s swine industry. Acknowledging the absence of a thorough investigation at the geographic level, we used 2014 outbreak sequence information from the Taiwan government’s open access databases plus GenBank records to analyze PEDV dissemination among Taiwanese pig farms. Genetic sequences, locations, and dates of identified PEDV-positive cases were used to assess spatial, temporal, clustering, GIS, and phylogeographic factors affecting PEDV dissemination. Our conclusion is that S gene sequences from 2014 PEDV-positive clinical samples collected in Taiwan were part of the same Genogroup 2 identified in the US in 2013. According to phylogenetic and phylogeographic data, viral strains collected in different areas were generally independent of each other, with certain clusters identified across different communities. Data from GIS and multiple potential infection factors were used to pinpoint cluster dissemination in areas with large numbers of swine farms in southern Taiwan. The data indicate that the 2014 Taiwan PEDV epidemic resulted from the spread of multiple strains, with strong correlations identified with pig farm numbers and sizes (measured as animal concentrations), feed mill numbers, and the number of slaughterhouses in a specifically defined geographic area.

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<![CDATA[Origins and geographic diversification of African rice (Oryza glaberrima)]]> https://www.researchpad.co/article/5c897765d5eed0c4847d2be9

Rice is a staple food for the majority of the world’s population. Whereas Asian rice (Oryza sativa) has been extensively studied, the exact origins of African rice (Oryza glaberrima) are still contested. Previous studies have supported either a centric or a non-centric geographic origin of African rice domestication. Here we review the evidence for both scenarios through a critical reassessment of 206 whole genome sequences of domesticated and wild African rice. While genetic diversity analyses support a severe bottleneck caused by domestication, signatures of recent and strong positive selection do not unequivocally point to candidate domestication genes, suggesting that domestication proceeded differently than in Asian rice–either by selection on different alleles, or different modes of selection. Population structure analysis revealed five genetic clusters localising to different geographic regions. Isolation by distance was identified in the coastal populations, which could account for parallel adaptation in geographically separated demes. Although genome-wide phylogenetic relationships support an origin in the eastern cultivation range followed by diversification along the Atlantic coast, further analysis of domestication genes shows distinct haplotypes in the southwest—suggesting that at least one of several key domestication traits might have originated there. These findings shed new light on an old controversy concerning plant domestication in Africa by highlighting the divergent roots of African rice cultivation, including a separate centre of domestication activity in the Guinea Highlands. We thus suggest that the commonly accepted centric origin of African rice must be reconsidered in favour of a non-centric or polycentric view.

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<![CDATA[Rectifying long-standing misconceptions about the ρ statistic for molecular dating]]> https://www.researchpad.co/article/5c75ac76d5eed0c484d08825

When divided by a given mutation rate, the ρ (rho) statistic provides a simple estimator of the age of a clade within a phylogenetic tree by averaging the number of mutations from each sample in the clade to its root. However, a long-standing critique of the use of ρ in genetic dating has been quite often cited. Here we show that the critique is unfounded. We demonstrate by a formal mathematical argument and illustrate with a simulation study that ρ estimates are unbiased and also that ρ and maximum likelihood estimates do not differ in any systematic fashion. We also demonstrate that the claim that the associated confidence intervals commonly estimate the uncertainty inappropriately is flawed since it relies on a means of calculating standard errors that is not used by any other researchers, whereas an established expression for the standard error is largely unproblematic. We conclude that ρ dating, alongside approaches such as maximum likelihood (ML) and Bayesian inference, remains a useful tool for genetic dating.

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<![CDATA[Secondary contact between diverged host lineages entails ecological speciation in a European hantavirus]]> https://www.researchpad.co/article/5c76fdefd5eed0c484e5b0f1

The diversity of viruses probably exceeds biodiversity of eukaryotes, but little is known about the origin and emergence of novel virus species. Experimentation and disease outbreak investigations have allowed the characterization of rapid molecular virus adaptation. However, the processes leading to the establishment of functionally distinct virus taxa in nature remain obscure. Here, we demonstrate that incipient speciation in a natural host species has generated distinct ecological niches leading to adaptive isolation in an RNA virus. We found a very strong association between the distributions of two major phylogenetic clades in Tula orthohantavirus (TULV) and the rodent host lineages in a natural hybrid zone of the European common vole (Microtus arvalis). The spatial transition between the virus clades in replicated geographic clines is at least eight times narrower than between the hybridizing host lineages. This suggests a strong barrier for effective virus transmission despite frequent dispersal and gene flow among local host populations, and translates to a complete turnover of the adaptive background of TULV within a few hundred meters in the open, unobstructed landscape. Genetic differences between TULV clades are homogenously distributed in the genomes and mostly synonymous (93.1%), except for a cluster of nonsynonymous changes in the 5′ region of the viral envelope glycoprotein gene, potentially involved in host-driven isolation. Evolutionary relationships between TULV clades indicate an emergence of these viruses through rapid differential adaptation to the previously diverged host lineages that resulted in levels of ecological isolation exceeding the progress of speciation in their vertebrate hosts.

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<![CDATA[Pathogen diversity drives the evolution of generalist MHC-II alleles in human populations]]> https://www.researchpad.co/article/5c5ca310d5eed0c48441f094

Central players of the adaptive immune system are the groups of proteins encoded in the major histocompatibility complex (MHC), which shape the immune response against pathogens and tolerance to self-peptides. The corresponding genomic region is of particular interest, as it harbors more disease associations than any other region in the human genome, including associations with infectious diseases, autoimmune disorders, cancers, and neuropsychiatric diseases. Certain MHC molecules can bind to a much wider range of epitopes than others, but the functional implication of such an elevated epitope-binding repertoire has remained largely unclear. It has been suggested that by recognizing more peptide segments, such promiscuous MHC molecules promote immune response against a broader range of pathogens. If so, the geographical distribution of MHC promiscuity level should be shaped by pathogen diversity. Three lines of evidence support the hypothesis. First, we found that in pathogen-rich geographical regions, humans are more likely to carry highly promiscuous MHC class II DRB1 alleles. Second, the switch between specialist and generalist antigen presentation has occurred repeatedly and in a rapid manner during human evolution. Third, molecular positions that define promiscuity level of MHC class II molecules are especially diverse and are under positive selection in human populations. Taken together, our work indicates that pathogen load maintains generalist adaptive immune recognition, with implications for medical genetics and epidemiology.

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<![CDATA[Ecological niche modeling the potential geographic distribution of four Culicoides species of veterinary significance in Florida, USA]]> https://www.researchpad.co/article/5c7067aad5eed0c4847c7470

Epizootic hemorrhagic disease (EHD) is a viral arthropod-borne disease affecting wild and domestic ruminants, caused by infection with epizootic hemorrhagic disease virus (EHDV). EHDV is transmitted to vertebrate animal hosts by biting midges in the genus Culicoides Latreille (Diptera: Ceratopogonidae). Culicoides sonorensis Wirth and Jones is the only confirmed vector of EHDV in the United States but is considered rare in Florida and not sufficiently abundant to support EHDV transmission. This study used ecological niche modeling to map the potential geographical distributions and associated ecological variable space of four Culicoides species suspected of transmitting EHDV in Florida, including Culicoides insignis Lutz, Culicoides stellifer (Coquillett), Culicoides debilipalpis Hoffman and Culicoides venustus Lutz. Models were developed with the Genetic Algorithm for Rule Set Production in DesktopGARP v1.1.3 using species occurrence data from field sampling along with environmental variables from WorldClim and Trypanosomiasis and Land use in Africa. For three Culicoides species (C. insignis, C. stellifer and C. debilipalpis) 96–98% of the presence points were predicted across the Florida landscape (63.8% - 72.5%). For C. venustus, models predicted 98.00% of presence points across 27.4% of Florida. Geographic variations were detected between species. Culicoides insignis was predicted to be restricted to peninsular Florida, and in contrast, C. venustus was predicted to be primarily in north Florida and the panhandle region. Culicoides stellifer and C. debilipalpis were predicted nearly statewide. Environmental conditions also differed by species, with some species’ ranges predicted by more narrow ranges of variables than others. The Normalized Difference Vegetation Index (NDVI) was a major predictor of C. venustus and C. insignis presence. For C. stellifer, Land Surface Temperature, Middle Infrared were the most limiting predictors of presence. The limiting variables for C. debilipalpis were NDVI Bi-Annual Amplitude and NDVI Annual Amplitude at 22.5% and 28.1%, respectively. The model outputs, including maps and environmental variable range predictions generated from these experiments provide an important first pass at predicting species of veterinary importance in Florida. Because EHDV cannot exist in the environment without the vector, model outputs can be used to estimate the potential risk of disease for animal hosts across Florida. Results also provide distribution and habitat information useful for integrated pest management practices.

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<![CDATA[Population genetic structure and geographical variation in Neotricula aperta (Gastropoda: Pomatiopsidae), the snail intermediate host of Schistosoma mekongi (Digenea: Schistosomatidae)]]> https://www.researchpad.co/article/5c58d632d5eed0c48403188e

Background

Neotricula aperta is the snail-intermediate host of the parasitic blood-fluke Schistosoma mekongi which causes Mekong schistosomiasis in Cambodia and the Lao PDR. Despite numerous phylogenetic studies only one DNA-sequence based population-genetic study of N. aperta had been published, and the origin, structure and persistence of N. aperta were poorly understood. Consequently, a phylogenetic and population genetic study was performed, with addition of new data to pre-existing DNA-sequences for N. aperta from remote and inaccessible habitats, including one new taxon from Laos and 505 bp of additional DNA-sequence for all sampled taxa,.

Principal findings

Spatial Principal Component Analysis revealed the presence of significant spatial-genetic clustering. Genetic-distance-based clustering indicated four populations with near perfect match to a priori defined ecogeographical regions. Spring-dwelling taxa were found to form an ecological isolate relative to other N. aperta. The poor dispersal capabilities suggested by spatial-genetic analyses were confirmed by Bayesian inference of migration rates. Population divergence time estimation implied a mid-Miocene colonisation of the present range, with immediate and rapid radiation in each ecogeographical region. Estimated effective population sizes were large (120–310 thousand).

Conclusions

The strong spatial-genetic structure confirmed the poor dispersal capabilities of N. aperta—suggesting human-mediated reintroduction of disease to controlled areas as the primary reason for control failure. The isolation of the spring-dwelling taxa and ecogeographical structure suggests adaptation of sub-populations to different habitats; the epidemiological significance of this needs investigation. The large effective population sizes indicate that the high population densities observed in surveyed habitats are also present in inaccessible areas; affording great potential for recrudescence driven by animal-reservoir transmission in remote streams. Mid-Miocene colonisation implies heterochronous evolution of these snails and associated schistosomes and suggests against coevolution of snail and parasite. Heterochronicity favours ecological factors as shapers of host-parasite specificity and greater potential for escape from schistosomiasis control through host-switching.

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<![CDATA[Phylogenetic analysis of hepatitis C virus among HIV/ HCV co-infected patients in Nigeria]]> https://www.researchpad.co/article/5c648d10d5eed0c484c81eb5

Hepatitis C virus (HCV) infection has been associated with liver disease including liver cirrhosis and hepatocellular carcinoma (HCC) in chronically-infected persons. However, in HIV/HCV co-infected patients, increased rate of progression to cirrhosis and HCC has been reported. Limited information exists regarding genetic variants of HCV circulating among co-infected patients, which could be important in the design of broadly protective vaccine and management of the disease. Here, we determined the genotypes of HCV isolates circulating among HIV/HCV co-infected patients in Ibadan, southwestern Nigeria. One hundred and twenty-five HIV/HCV IgM positive samples obtained from HIV laboratory, University of Ibadan were used for this study. HCV NS5B gene was amplified using polymerase chain reaction (PCR). The amplified NS5B gene was sequenced using gene specific primers. Twenty isolates were amplified, out of which 13 were successfully sequenced. Phylogenetic analysis of the 13 sequenced isolates showed three HCV subtypes 1a, 3a and 5a belonging to genotypes 1, 3 and 5 respectively. Ten isolates (77%) belong to subtype 5a, followed by 2 isolates (15%) subtype 1a and 1 isolate (8%) was subtype 3a. The predominant HCV genotype was 5, followed by genotype 1 (subtype 1a). The findings, as well as the observed mutations in NS5B gene, indicate the need for screening and monitoring of HIV/HCV co-infected patients. Further study to determine the phylogeny of isolates circulating in other parts of Nigeria will be carried out.

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<![CDATA[Regional and global shifts in crop diversity through the Anthropocene]]> https://www.researchpad.co/article/5c648ceed5eed0c484c81b0f

The Anthropocene epoch is partly defined by anthropogenic spread of crops beyond their centres of origin. At global scales, evidence indicates that species-level taxonomic diversity of crops being cultivated on large-scale agricultural lands has increased linearly over the past 50 years. Yet environmental and socio-economic differences support expectations that temporal changes in crop diversity vary across regions. Ecological theory also suggests that changes in crop taxonomic diversity may not necessarily reflect changes in the evolutionary diversity of crops. We used data from the Food and Agricultural Organization (FAO) of the United Nations to assess changes in crop taxonomic- and phylogenetic diversity across 22 subcontinental-scale regions from 1961–2014. We document certain broad consistencies across nearly all regions: i) little change in crop diversity from 1961 through to the late 1970s; followed by ii) a 10-year period of sharp diversification through the early 1980s; followed by iii) a “levelling-off” of crop diversification beginning in the early 1990s. However, the specific onset and duration of these distinct periods differs significantly across regions and are unrelated to agricultural expansion, indicating that unique policy or environmental conditions influence the crops being grown within a given region. Additionally, while the 1970s and 1980s are defined by region-scale increases in crop diversity this period marks the increasing dominance of a small number of crop species and lineages; a trend resulting in detectable increases in the similarity of crops being grown across regions. Broad similarities in the species-level taxonomic and phylogenetic diversity of crops being grown across regions, primarily at large industrial scales captured by FAO data, represent a unique feature of the Anthropocene epoch. Yet nuanced asymmetries in regional-scale trends suggest that environmental and socio-economic factors play a key role in shaping observed macro-ecological changes in the plant diversity on agricultural lands.

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<![CDATA[Genetic variation and phylogeography of the Triatoma dimidiata complex evidence a potential center of origin and recent divergence of haplogroups having differential Trypanosoma cruzi and DTU infections]]> https://www.researchpad.co/article/5c58d62ed5eed0c48403184e

The population genetics of Triatoma dimidiata haplogroups was analyzed at landscape and sub-regional scales in Chiapas and regional level across the Mexican Neotropics, and phylogeography of the complex was re-analyzed across its complete geographic range. Two contiguous fragments of the ND4 gene were analyzed due to bias from differential haplogroup specificity using a previously designed sequence. At both landscape (anthropic modification gradient) and regional (demographic, fragmentation, biogeographic, climate) scales, lowest T. dimidiata genetic diversity occurs where there is greatest historical anthropic modification, and where T. cruzi infection prevalence is significantly highest. Trypanosoma cruzi prevalence was significantly higher than expected in haplogroups 1 and 3, while lower than expected in haplogroup 2. There was also a significant difference of DTUI and DTUVI infection frequencies in both haplogroups 1 and 3, while no difference of either in haplogroup 2. All haplogroups from the Mexican Neotropics had moderate to high haplotype diversity, while greatest genetic differentiation was between haplogroups 1 and 3 (above FST = 0.868, p < 0.0001). Divergence of the complex from the MRCA was estimated between 0.97 MYA (95% HPD interval = 0.55–1.53 MYA) and 0.85 MYA (95% HPD interval = 0.42–1.5 MYA) for ND4A and both concatenated fragments, respectively, with primary divergence from the MRCA of haplogroups 2 and 3. Effective population size for Mexican haplogroups 1 and 2 increased between 0.02 and 0.03 MYA. This study supports previous ecological niche evidence for the complex´s origin surrounding the Tehuantepec Isthmus, and provides evidence for recent divergence of three primary dimidiata haplogroups, with differential T. cruzi infection frequency and DTU specificity, important components of vector capacity.

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<![CDATA[Genetic diversity and population structure of Miscanthus lutarioriparius, an endemic plant of China]]> https://www.researchpad.co/article/5c5df329d5eed0c484580de8

Miscanthus lutarioriparius is a native perennial Miscanthus species of China, which is currently used as raw material of papermaking and bioenergy crop. It also has been considered as a promising eco-bioindustrial plant, which can offer raw material and gene for the biomass industry. However, lack of germplasm resources and genetic diversity information of M. lutarioriparius have become the bottleneck that prevents the stable and further development of the biomass industry. In the present study, genetic diversity of 153 M. lutarioriparius individuals nine populations was studied using 27 Start Codon Targeted (SCoT) markers. High polymorphic bands (97.67%), polymorphic information content (0.26) and allele number (1.88) showed SCoT as a reliable marker system for genetic analysis in M. lutarioriparius. At the species, the percentage of polymorphic loci [PPL] was 97.2%, Nei’s gene diversity [H] was 0.36, Shannon index [I] was 0.54 and Expected Heterozygosity [He] was 0.56. Genetic variation within populations (84.91%) was higher than among populations (15.09%) based on analysis of molecular variance (AMOVA). Moderate level of genetic differentiation was found in M. lutarioriparius populations (Fst = 0.15), which is further confirmed by STRUCTURE, principal coordinates analysis (PCoA) and an unweighted pair group method with arithmetic mean (UPGMA) analysis that could reveal a clear separation between groups of the north and south of Yangtze River. The gene flow of the populations within the respective south and north of Yangtze River area was higher, but lower between the areas. There was no obvious correlation between genetic distance and geographic distance. The breeding systems, geographical isolation and fragmented habitat of M. lutarioriparius may be due to the high level of genetic diversity, moderate genetic differentiation, and the population, structure. The study further suggests some measure for conservation of genetic resources and provides the genetic basis for improving the efficiency of breeding based on the results of diversity analysis.

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<![CDATA[Environmental heterogeneity explains coarse–scale β–diversity of terrestrial vertebrates in Mexico]]> https://www.researchpad.co/article/5c57e6f3d5eed0c484ef453e

We explored the hypothesis that high β–diversity of terrestrial vertebrates of Mexico is associated with a high environmental heterogeneity (HEH) and identify the drivers of β–diversity at different spatial scales. We used distribution range maps of 2,513 species of amphibians, reptiles, mammals, and birds occurring in Mexico. We estimated β–diversity for each taxon at four spatial scales (grid cells of 2°, 1°, 0.5° and 0.25°) using the multiplicative formula of Whittaker βw. For each spatial scale, we derived 10 variables of environmental heterogeneity among cells based on raw data of temperature, precipitation, elevation, vegetation and soil. We applied conditional autoregressive models (CAR) to identify the drivers of β–diversity for each taxon at each spatial scale. CARs increased in explanatory power from fine–to–coarse spatial scales in amphibians, reptiles and mammals. The heterogeneity in precipitation including both, coefficient of variation (CV) and range of values (ROV), resulted in the most important drivers of β–diversity of amphibians; the heterogeneity in temperature (CV) and elevation (ROV) were the most important drivers of β–diversity for reptiles; the heterogeneity in temperature (ROV) resulted in the most important driver in β–diversity for mammals. For birds, CARs resulted significant at fine scales (grid cells of 0.5° and 0.25°), and the precipitation (ROV and CV), temperature (ROV), and vegetation (H) and soil (H) were heterogeneity variables retained in the model. We found support for the hypothesis of environmental heterogeneity (HEH) for terrestrial vertebrates at coarse scales (grid cell of 2°). Different variables of heterogeneity, mainly abiotic, were significant for each taxon, reflecting physiological differences among terrestrial vertebrate groups. Our study revealed the importance of mountain areas in the geographic patterns of β–diversity of terrestrial vertebrates in Mexico. At a coarse scale, specific variables of heterogeneity can be used as a proxy of β–diversity for amphibians and reptiles.

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<![CDATA[Phylogeographic analysis of human influenza A and B viruses in Myanmar, 2010–2015]]> https://www.researchpad.co/article/5c40f7c1d5eed0c48438683f

We investigated the circulation patterns of human influenza A and B viruses in Myanmar between 2010 and 2015 by analyzing full HA genes. Upper respiratory tract specimens were collected from patients with symptoms of influenza-like illness. A total of 2,860 respiratory samples were screened by influenza rapid diagnostic test, of which 1,577 (55.1%) and 810 (28.3%) were positive for influenza A and B, respectively. Of the 1,010 specimens that were positive for virus isolation, 370 (36.6%) were A(H1N1)pdm09, 327 (32.4%) were A(H3N2), 130 (12.9%) B(Victoria), and 183 (18.1%) were B(Yamagata) viruses. Our data showed that influenza epidemics mainly occurred during the rainy season in Myanmar. Our three study sites, Yangon, Pyinmana, and Pyin Oo Lwin had similar seasonality and circulating type and subtype of influenza in a given year. Moreover, viruses circulating in Myanmar during the study period were closely related genetically to those detected in Thailand, India, and China. Phylogeographic analysis showed that A(H1N1)pdm09 viruses in Myanmar originated from Europe and migrated to other countries via Japan. Similarly, A(H3N2) viruses in Myanmar originated from Europe, and disseminated to the various countries via Australia. In addition, Myanmar plays a key role in reseeding of influenza B viruses to Southeast Asia and East Asia as well as Europe and Africa. Thus, we concluded that influenza virus in Myanmar has a strong link to neighboring Asian countries, Europe and Oceania.

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