Stable Population Structure Research Articles

Evaluating sustainability of Thalictrum petaloideum L., a peripheral population in Korea

Conservation of rare plants, both at the national level and the regional level is important to maintain and conserve plant diversity. This study focused on Thalictrum petaloideum L., an endangered species, for which the Korean peninsula represents the rear edge of the global distribution. T. petaloideum is distributed in isolated populations across four regions. Yeongwol, in Gangwon, had the largest extent of distribution (27,663 m2), the highest number of sub-populations (204), and the highest total population size (87,681), followed by Danyang, in Chungbuk (3970 m2/28/10,285), Samcheok, in Gangwon (3390 m2/13/3871), and Yeosu, in Jeolanam (800 m2/10/816), in descending order. The most stable population structure was found in Yeongwol. Yeosu was found to have the most unstable population structure and the highest risk of extinction. To ensure the sustainability of the population in Yeosu, artificial management of climbing plants, such as Pueraria lobata, is recommended to maintain spaces suitable for regeneration. In Yeongwol, the population is likely to be sustained over a long period. The maintenance of traditional graveyards is necessary to ensure the population’s sustainability. Further studies should assess the genetic characteristics of each regional population for an in-depth characterization of plant distribution on the Korean peninsula.

Stable population structure in Europe since the Iron Age, despite high mobility.

Ancient DNA research in the past decade has revealed that European population structure changed dramatically in the prehistoric period (14,000-3000 years before present, YBP), reflecting the widespread introduction of Neolithic farmer and Bronze Age Steppe ancestries. However, little is known about how population structure changed from the historical period onward (3000 YBP - present). To address this, we collected whole genomes from 204 individuals from Europe and the Mediterranean, many of which are the first historical period genomes from their region (e.g. Armenia and France). We found that most regions show remarkable inter-individual heterogeneity. At least 7% of historical individuals carry ancestry uncommon in the region where they were sampled, some indicating cross-Mediterranean contacts. Despite this high level of mobility, overall population structure across western Eurasia is relatively stable through the historical period up to the present, mirroring geography. We show that, under standard population genetics models with local panmixia, the observed level of dispersal would lead to a collapse of population structure. Persistent population structure thus suggests a lower effective migration rate than indicated by the observed dispersal. We hypothesize that this phenomenon can be explained by extensive transient dispersal arising from drastically improved transportation networks and the Roman Empire's mobilization of people for trade, labor, and military. This work highlights the utility of ancient DNA in elucidating finer scale human population dynamics in recent history.

Continuous Reproduction Causes Stable Population Structure of Antipatharian-Associated Shrimp Sandyella tricornuta (Decapoda: Palaemonidae)

Sandyella tricornuta (Hendrickx, 1990) is a small (<13 mm total length), obligate and highly specific ectosymbiont of the black coral Antipathes galapagensis Deichmann, 1941 with a remarkable morphology and body coloration that resembles black coral polyps. Sandyella tricornuta population structure was investigated to infer the reproductive periods evidenced with ovigerous females from monthly collection at Espíritu Santo Island (April 2009–March 2010) and along a latitudinal gradient of six islands (24–30° N, July 2009) located along the west coast of the Gulf of California, Mexico. A total of 2,899 S. tricornuta individuals were collected from 70 colonies of A. galapagensis with a mean density of 210 inds./m3 per black coral colony. Sea floor temperature of S. tricornuta/A. galapagensis habitat seasonally ranged between 21 and 30°C. Females constituted >60% of the entire S. tricornuta population and >59% of the collected females were ovigerous females, suggesting active reproduction throughout the year and along the latitudinal gradient investigated. Sandyella tricornuta population density and sex ratio was similar throughout the year indicating a seasonally stable population size. Total abundance of S. tricornuta was density independent of black coral colony size and weight indicating that S. tricornuta depends on A. galapagensis, but the black coral colony can grow and develop without S. tricornuta characteristic of a commensalism ectosymbiotic association.

Measuring forest health at stand level: A multi-indicator evaluation for use in adaptive management and policy

Assessments of forest ecosystem health for use in adaptive management need an integrative multi-indicator examination at the stand scale. To assess forest health, we exained multiple forest indicators including diversity, age structure, regeneration, and edaphic factors of the dominant and associated tree species in their natural forest habitats. A stratified random cluster sampling strategy was used to gather vegetation samples from the five main forest types in the Zabarwan Mountain Range—Acacia forest (ACFT), Broad leaved forest (BLFT), Oak forest (OKFT), Pinus wallichiana forest (PWFT), and Scrub forest (SRFT). The Pearson method and canonical correspondence analysis (CCA) were used to investigate the relationship between tree species and edaphic factors. A total of 22 tree species were found, of which 13 were exotic and 9 were native. The proportion of exotic species was highest in OKFT (85%), followed by BLFT (75%), and the least (50%) SRFT. The BLFT forest type had the highest Shannon diversity while the lowest was the SRFT. ACFT and BLFT forest types have significantly higher Shannon diversity indexes than other forest types. Based on the density-girth class distribution, ACFT & SRFT forest types showed an Inverse-J distribution pattern, indicating a stable population structure. The dominant tree species, such as Populus alba in BLFT, demonstrated comparatively no regeneration, whereas Parrotiopsis jacquemontiana in SRFT, Pinus wallichiana in PWFT, Quercus robur in OKFT, and Robinia pseudoacacia demonstrated adequate regeneration performance. Overall exotic tree species such as Robinia pseudoacacia, Prunus cerasifera, Celtis australis, and Ailanthus altissima showed high/sufficient regeneration performance. The average seedling/tree value for all forest types in the area was 2.14, with the highest value at BLFT (3.61) and the lowest value at SRFT (0.71). In the CCA it showed that SRFT forests were greatly influenced by salinity and organic carbon, whereas ACFT and OKFT forests had comparable habitat preferences and were mutually influenced by electrical conductance and phosphorus availability. Prunus cerasifera was the only species positively associated with available calcium. By combining the data of numerous field-based indicators into a single integrated study, our research will give decision-makers an update on a forest's current and anticipated health.

Stable dingo population structure and purity over 11 years of lethal management

Context Interaction between predators and humans is a key driver of human–wildlife conflicts, and can underpin management of predator populations. Management of the impacts of dingoes on livestock and native species is a prime example of a persistent and contentious predator management issue with potential impacts on the integrity of dingo populations. To manage the potential impacts of dingoes and their control, it is imperative to understand the effects of control approaches on their populations in the short and long term. Hybridisation of dingoes with domestic dogs also threatens the genetic integrity of pure dingoes. It has been hypothesised that lethal control of dingoes can facilitate hybridisation through disrupting pack social structures leading to increased dingo–domestic dog interactions. Aims We aimed to to investigate how dingo population structure and genetic purity have changed, assessing dingo purity, individual relatedness, population clustering and gene flow, particularly across land use types and barrier fences, in the context of ongoing lethal control within the Murchison Regional Vermin Cell area in Western Australia (WA). Methods We tested dingo genetic samples from three distinct sampling periods (2009, 2014 and 2020) for changes in population summary statistics and dingo ancestry. Barriers and corridors to gene flow were also examined. Key results We identified three genetically distinct populations in the study area, consistent with previous genetic studies in WA. We did not find any evidence of change in dingo purity or population characteristics; however, barrier fencing may be influencing recent gene flow. Conclusions The metapopulation of dingoes in the southern rangelands of WA appears to be stable over the 11 years assessed. Implications Because we were unable to demonstrate that lethal control has accelerated hybridisation between dingoes and domestic dogs in the study area over the last 11 years, we have no evidence that lethal control to reduce losses to livestock production and for conservation of native wildlife in the southern rangelands of WA is putting dingo purity at risk. Fencing appears to be an effective management tool because there is some evidence it is congruent with reduced gene flow in areas where the fences are well maintained.

ГЕНОТИПІЧНА ТА ФЕНОТИПІЧНА ХАРАКТЕРИСТИКА СТІЙКОСТІ ДО АНТИМІКОБАКТЕРІАЛЬНИХ ПРЕПАРАТІВ 8 ШТАМІВ M. TUBERCULOSIS, ВИДІЛЕНИХ ВІД ХВОРИХ З ВПЕРШЕ ДІАГНОСТОВАНИМ ТУБЕРКУЛЬОЗОМ ЛЕГЕНЬ

The article presents the experience of whole-genome sequencing of M. tuberculosis (MBT) strains. Materials and methods. 8 MBT isolates were tested. The strains were obtained from patients with newly detected pulmonary tuberculosis (NDPTB). Critical concentrations of anti-mycobacterial drugs (AMBD): H; R; E; Z; Lfx; Mfx; Am; cm; Lzd; Bdq; Dlm and Cfz were determined using the BACTEC MGIT system. Sequencing of MBT strains was performed on Illumina MiSeq equipment at the laboratory of microbiology and biochemistry of the National Institute of phthisiology and pulmonology (NIPP). The obtained whole-genome sequences of MBT strains were deposited in fastq files and analyzed using the PhyResSE program (https://bioinf.fz-borstel.de/mchips/phyresse/) with the bioanalytical solution package. The panel of this package includes gene targets involved in the development of MBT to AMBP. Phylogenetic information and a certain spoligotype make it possible to obtain neutral single nucleotide polymorphisms. The genetic profile of the drug was performed according to the WHO mutation catalog (https://www.who.int/publications/i/item/9789240028173). The results. The dominant in Ukraine Beijing genotype was represented by 7 strains. The non-beijing group included 1 strain: Ural. 7 MBT strains belonged to the Beijing family, Lineage 2 phylogenetic line with the same spoligotype indices. The analysis of mutations according to the “Catalogue of mutations of the M. tuberculosis complex and their association with drug resistance”, WHO, 2021, allowed all detected mutations to be divided into categories - associated with resistance, associated with resistance - intermediate, not associated with resistance, with uncertain significance. Comparison of the resistance profile with the corresponding genotype showed that isolates, belonging to the Beijing genotype, usually carried MDR/pre-XDR mutations. Comparison of the resistance profile with the corresponding genotype showed that isolates belonging to the Beijing genotype usually carried MDR/pre-XDR mutations. All MBT strains with resistance to R had mutations found in the rpoB gene. The canonical amino acid substitution of rpoB S450L, associated with a high level of resistance to R with a non-significant decrease in the viability of the strains, was identified in 6 isolates. Another clinically significant mutation in rpoB (S435Y) was found in 2 cases and only in representatives of the Beijing family. Mutations of the categories: not associated with resistance (rpoC (E1092D)) and of uncertain significance: rpoC (I491V), rpoB (H674N), rpoB (V496A), were detected only in combination with “strictly associated” positions in phenotypic-resistant isolates of the genotype Beijing. The canonical single amino acid substitution katG S315T was detected in all isolates selected for sequencing. All 8 strains resistant to H showed mutations in genes associated with resistance to the drug. Mutations in the key Bdq resistance genes - atpE and mmpR - were not detected in any genome. In 1 strain of MBT, a C154R mutation associated with Lzd resistance was detected in the rplC gene. Similarly, in 1 strain of MBT, a mutation in ddn (D30S0) was detected with an as yet undetermined significance of association with resistance to Dlm. Conclusions. The study provided information on the genetic diversity of modern MBT isolates in TB patients. The predominance of the Beijing genotype testified to the stable population structure of the TB pathogen and the preservation of trends of high levels of the spread of TB forms of infection on the territory of the country. The combination of phenotype and molecular genetic data made it possible to give a more complete assessment of DR isolates. A large share of MDR was caused by mutations that did not have a negative effect on the viability and transmissibility of the pathogen, indicating a large epidemic reservoir of MBT strains with MDR/pre-XDR. The highly transmissible strains of Beijing carried mostly single uncombined R and H mutations, which were associated with a high level of resistance. Key words: genetic diagnostics, sequencing, pulmonary tuberculosis.

Lomami Buffer Zone (DRC): Forest composition, structure, and the sustainability of its use by local communities

AbstractThe recently created Lomami National Park has an extensive Buffer Zone where local communities are allowed to use forest products sustainably. However, the management of this Buffer Zone is hampered by inadequate understanding of the floristic composition and the impacts of harvesting certain plant products. To fill in this data gap, we established and sampled 30 vegetation plots of 40 × 40 m, and investigated the population structure of 11 useful tree species preferred by local communities. We found that the Buffer Zone is mostly composed of mixed‐species undisturbed old growth forest. It contains nine tree species of international conservation concern (listed in the IUCN Red list and/or apart from the Red list, Gibourtia demeusei, not been assessed by IUCN Red list, is listed in CITES Appendix II since January 2017; UNEP‐WCMC, Review of selected Dalbergia species and Guibourtia demeusei, UNEP‐WCMC, 2017). The floristic diversity of the Buffer Zone, which requires further investigation as some species remained unidentified. Most preferred tree species (including Garcinia kola and Milicia excelsa) are abundant and showed a reverse‐J size distribution, indicating a relatively stable population structure. For these species, current levels of exploitation seem sustainable. Further research is needed for two nonabundant species of conservation concern (Autranella congolensis and Michelsonia microphylla). Although timber/firewood commercial harvesting is currently limited in the study area, the management plan of the Buffer Zone should consider these risks given increasing commercial hunting. Surveys and permanent plots provide essential information to guide the management of newly formed protected areas.Abstract in French is available with online material.

Population Ecology and Genetic Diversity of the Invasive Alien Species Procambarus clarkii in Lake Trasimeno (Italy).

Simple SummaryThe population of Procambarus clarkii was surveyed twenty years after its introduction into Lake Trasimeno (Central Italy), investigating both ecological and genetic aspects. Our results confirmed that P. clarkii is well acclimatized with a stable population structure, mainly characterized by a unique mitochondrial lineage, suggesting that a single introduction event may have occurred in the lake, complemented by secondary events.The deliberate or accidental introduction of invasive alien species (IAS) causes negative ecological and economic impacts altering ecosystem processes, imperiling native species and causing damage to human endeavors. A monthly monitoring program was performed in Lake Trasimeno (Central Italy) from July 2018 to July 2019 in order to provide an upgrade of the population ecology of Procambarus clarkii and to assess the genetic diversity by analyzing the relationships among mitochondrial DNA diversity. Our results confirmed that P. clarkii is well acclimatized in the lake, revealing a stable population structure favored by the resources and conditions typical of this ecosystem, which seem to be optimal for the maintenance of the species. Four distinct mitochondrial haplotypes were detected, but one of them was clearly overrepresented (76%), suggesting that a single predominant introduction event may have occurred in this area, likely followed by secondary events. The identification of the typical genetic variants provides a better understanding of the evolutionary scenarios of P. clarkii in this biotope and it can be helpful in management plans concerning the expanding populations of this invasive alien species.

Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK

BackgroundThe incidence of Gram-negative bloodstream infections (BSIs), predominantly caused by Escherichia coli and Klebsiella species, continues to increase; however, the causes of this are unclear and effective interventions are therefore hard to design.MethodsIn this study, we sequenced 3468 unselected isolates over a decade in Oxfordshire (UK) and linked this data to routinely collected electronic healthcare records and mandatory surveillance reports. We annotated genomes for clinically relevant genes, contrasting the distribution of these within and between species, and compared incidence trends over time using stacked negative binomial regression.ResultsWe demonstrate that the observed increases in E. coli incidence were not driven by the success of one or more sequence types (STs); instead, four STs continue to dominate a stable population structure, with no evidence of adaptation to hospital/community settings. Conversely in Klebsiella spp., most infections are caused by sporadic STs with the exception of a local drug-resistant outbreak strain (ST490). Virulence elements are highly structured by ST in E. coli but not Klebsiella spp. where they occur in a diverse spectrum of STs and equally across healthcare and community settings. Most clinically hypervirulent (i.e. community-onset) Klebsiella BSIs have no known acquired virulence loci. Finally, we demonstrate a diverse but largely genus-restricted mobilome with close associations between antimicrobial resistance (AMR) genes and insertion sequences but not typically specific plasmid replicon types, consistent with the dissemination of AMR genes being highly contingent on smaller mobile genetic elements (MGEs).ConclusionsOur large genomic study highlights distinct differences in the molecular epidemiology of E. coli and Klebsiella BSIs and suggests that no single specific pathogen genetic factors (e.g. AMR/virulence genes/sequence type) are likely contributing to the increasing incidence of BSI overall, that association with AMR genes in E. coli is a contributor to the increasing number of E. coli BSIs, and that more attention should be given to AMR gene associations with non-plasmid MGEs to try and understand horizontal gene transfer networks.

Clonal evolution of Candida albicans, Candida glabrata and Candida dubliniensis at oral niche level in health and disease

ABSTRACT Background: Candida species have long been recognised as aetiological agents of opportunistic infections of the oral mucosa, and more recently, as players of polymicrobial interactions driving caries, periodontitis and oral carcinogenesis. Methods: We studied the clonal structure of Candida spp. at oral niche resolution in patients (n = 20) with a range of oral health profiles over 22 months. Colonies from oral micro-environments were examined with multilocus sequencing typing. Results: Candida spp. identified were C. albicans, C. glabrata and C. dubliniensis. Increased propensity for micro-variations giving rise to multiple diploid strain types (DST), as a result of loss of heterozygosity, was observed among C. albicans clade 1 isolates compared to other clades. Micro-variations among isolates were also observed in C. dubliniensis contra to expectations of stable population structures for this species. Multiple sequence types were retrieved from patients without clinical evidence of oral candidosis, while single sequence types were isolated from oral candidosis patients. Conclusion: This is the first study to describe the clonal population structure, persistence and stability of Candida spp. at oral niche level. Future research investigating links between Candida spp. clonality and oral disease should recognise the propensity to micro-variations amongst oral niches in C. albicans and C. dubliniensis identified here.

Composition and Structure of Woody Vegetation in Community Compared to State Forests in Tehuledere District, South Wollo, Ethiopia

ABSTRACT Restoring the degraded areas with vegetation cover is an optimal strategy to mitigate land degradation. The objective of this study was to examine the composition and structure of woody vegetation in community and state forests in Tehuledere District, South Wollo, Ethiopia. The vegetation data were collected by sampling a total of 40 systematically laid sample plots (i.e. 20 samples in each forest type) and analyzed to determine woody species composition (i.e. number of species, frequency, density, dominance, and importance value index) and forest structure (i.e. diameter distribution, basal area, and biodiversity index). The vegetation structure was described by diameter class using inverse J-shaped as this type of distribution considered being indicative of a stable population structure or good regeneration status. The results revealed that significantly greater densities of seedlings and saplings were found in the community forest than that of the state forest. Moreover, a total of 45 woody species, representing 29 families were recorded in this forest. However, 29 woody species, representing 25 families were only found in the state forest, suggesting that 25 woody species were common in both forest types. However, 20 woody species were found only in the community forest, whereas only three species were exclusively obtained in the state forest. Woody plant densities were 10,881 and 9,501 individuals’ ha−1 in community and state forests, respectively. The result suggested that Juniperus procera was the most dominant species in both forest types. The community forest had a diversity value of 2.26, while the corresponding value for the state forest was only 2.07. Overall, as compared to the state forest, the community forest had a better status in several biological parameters. Generally, the results emphasize the importance of the relative advantage of the community forestry approach to restore, enhance, and maintain (e.g. enrichment planting, pruning, and selective cutting) the forest resources over the conventional or protectionist way of the state forest management. Therefore, intervention for legal framework and institutional development particularly through formal recognition of people’s ownership and right over the conservation management of forests is essential toward sustainable forestry.

The first rapid forest inventory and resource use assessment of Dashtijum Nature Reserve, Tajikistan: a mixed methods approach

AbstractThere is critical need for more information on the status of forests in Central Asia, to inform conservation management. Here we assess the status and use of the globally important, threatened walnut–fruit forests of Dashtijum Nature Reserve, Tajikistan. We use a mixed methods approach combining a semi-structured interview based socio-economic survey with statistical analysis. Thirty-three tree species were recorded, with Rosaceae the most common family. The mean basal area of the forest was 20.8 m2 per ha and most tree species exhibited stable population structures. Resource use was prevalent throughout the community; most households harvested at least one fruit or nut species (78%), firewood (88%) and grazed livestock (85%). Most respondents noted declines in availability of fruits, nuts and firewood and reported a decrease in the overall area and quality of grazing. Statistical analysis and machine learning identified that distance to nearest settlement significantly affected forest total basal area, tree species richness and the Shannon index, a metric of diversity sensitive to rare species. Our results suggest that conservation management by the government and NGOs is partly effective but there is a need for increased enforcement of grazing restrictions, to prevent further forest degradation.

Clan Networks and Enterprise Innovation：Synergy and Balance of Prior Experience of Rural Entrepreneurs

Over the past 40 years of reform and opening up, China’s sustained rapid economic growth is closely related to the effective solution of the three rural issues. Compared with cities, China’s rural areas have relatively low level of economic development, relatively closed information, narrow financing channels, weak infrastructure conditions, and a lack of human capital and professional knowledge. At the same time, the relatively stable population structure, genetic relationship and intergenerational inheritance make the rural areas have closer clan relations. In this situation, how rural entrepreneurs seek advantages and avoid disadvantages, and obtain resources needed for enterprise development is not only related to the quality of their innovation and entrepreneurship, but also of great significance to the revitalization of rural economy.Existing research has recognized the important role of clan networks and other social capital, but it has not explained clearly what factors in clan networks are the key factors affecting the innovation of rural enterprises, and it has not recognized the moderating effect and inter-regional differences of prior experience of rural entrepreneurs.This paper empirically tests the influence of clan networks on enterprise innovation based on the micro data of the survey on thousand villages”, including the coordination and balance of prior experience of entrepreneurs. This paper finds that clan intensity reflects the relationship and cognitive characteristics of social capital, and the supply of resource capital and normative capital can promote the innovation level of rural entrepreneurial enterprises. In regions with high level of economic development or strong clan culture, clan scale has a more significant negative impact on the enterprise innovation level. That is to say, clan scale reflects more network characteristics of social capital and inhibits enterprise innovation by excluding outsiders and restricting the flow of personnel and knowledge. At the same time, the competence view based on the social capital theory finds that the accumulation of prior experience can improve the knowledge, resource, cognitive level or personal ability of entrepreneurs, making rural entrepreneurs better play the positive role of clan strength in innovation and reduce the potential negative impact of the clan scale on innovation. That is to say, the prior experience of entrepreneurs plays a balance and synergy role between clan networks and enterprise innovation.This paper contributes to the following four aspects: Firstly, it enriches the existing literature’s understanding of the influencing factors of enterprise innovation, focuses on the unique social situation in China, and studies the internal mechanism of clan networks and enterprise innovation. Secondly, we divide clan networks into two levels: scale and intensity, to conduct a more comprehensive and detailed study, and find that the clan strength reflecting clan cohesion has a more positive impact on the level of enterprise innovation. Thirdly, we analyze how the prior experience of entrepreneurs moderates the impact of clan networks. Fourthly, we take 3311 Chinese rural entrepreneurs as samples to reveal the impact mechanism of regional clan networks on the enterprise innovation level in rural areas of China.

The Anatolian Diagonal and Paleoclimatic Changes Shaped the Phylogeography of Cynips quercus (Hymenoptera, Cynipidae)

Cynips quercus is a with widespread oak-gall wasp species distributed across the Western Palearctic from Europe, the northern Caucasus and North Africa to Iran. In this study, we used 175 asexual-generation individuals of C. quercus collected from 30 localities in Turkey to investigate the effects of topography and climatic factors on the phylogeographic structure of the species. Sequence analysis of the mitochondrial cytochrome-b gene (MT-CYB) and the nuclear ITS2 region supported a genetic break between the eastern and the western sides of the Anatolian Diagonal. The ITS2 results indicated that the populations underwent expansion, while in contrast the MT-CYB data implied a stable population structure for C. quercus. Molecular clock applied to the MT-CYB data suggested that the climatic and environmental changes during the Pliocene and Pleistocene had a profound effect on the phylogeography of the species.

Survival profiles from linear models versus Weibull models: Estimating stable and stationary population structures for Pleistocene large mammals

Survival and mortality profiles of mammalian species can provide information on the environmental context of Pleistocene archaeopaleontological localities as well as on the agents involved in the site formation process (e.g., the role played by the bone-accumulating agents, including their patterns of food procurement and carcass consumption, or the strategies of space use by carnivores and humans). Environmental context (i.e., climate and vegetation cover) and meat availability were both relevant factors for determining human settlements in Europe during the Pleistocene. For this reason, to gain deeper insights on the paleoecology of the large mammal communities can provide key information on human evolution and dispersal patterns. In this study we compare two mathematical approaches that allow reconstructing survival and mortality profiles of large mammals and their age-structured populations: the linear model and the Weibull model. Both approaches provide similar results for all species of large mammals analyzed. The lowest correlation coefficient was for Bison bison (0.789), but the difference in biomass estimates between the models decreases to <2%. When both methodologies were compared at the community level in the Orce sites, the ecological indexes used to compare paleocommunities showed also differences of <2%. Given the similarities in the output data derived from both models, we suggest a preferential use of the Weibull model due to its strength of results and easier computation compared to the linear model. Moreover, α and β parameters of the Weibull model supply information on the fertility and maturity of the age-structured populations, which are useful for differentiating among the reproductive strategies of the species compared. Therefore, our results suggest that the Weibull model is a valuable tool for investigating the availability of meat resources and the level of competition among carnivores in the Pleistocene communities of large mammals that inhabited Europe during the Pleistocene.

Genomic analysis of the emergence of drug-resistant strains of Mycobacterium tuberculosis in the Middle East

Tuberculosis (TB) represents a significant challenge to public health authorities, especially with the emergence of drug-resistant (DR) and multidrug-resistant (MDR) isolates of Mycobacterium tuberculosis. We sought to examine the genomic variations among recently isolated strains of M. tuberculosis in two closely related countries with different population demography in the Middle East. Clinical isolates of M. tuberculosis from both Egypt and Saudi Arabia were subjected to phenotypic and genotypic analysis on gene and genome-wide levels. Isolates with MDR phenotypes were highly prevalent in Egypt (up to 35%) despite its relatively stable population structure (sympatric pattern). MDR-TB isolates were not identified in the isolates from Saudi Arabia despite its active guest worker program (allopatric pattern). However, tuberculosis isolates from Saudi Arabia, where lineage 4 was more prevalent (>65%), showed more diversity than isolates from Egypt, where lineage 3 was the most prevalent (>75%). Phylogenetic and molecular dating analyses indicated that lineages from Egypt were recently diverged (~78 years), whereas those from Saudi Arabia were diverged by over 200 years. Interestingly, DR isolates did not appear to cluster together or spread more widely than drug-sensitive isolates, suggesting poor treatment as the main cause for emergence of drug resistance rather than more virulence or more capacity to persist.

Diversity, population structure, and regeneration potential of tree species in five sacred forests of western Odisha, India

ABSTRACTFrom September 2015 to February 2016, we collected field data to study the tree species diversity, population structure and regeneration potential of five sacred forests of western Odisha, India, that differ in size, associated deities, and local communities. The close association of sacred forests with local people represents a community-based, participatory approach to conservation. Our quantitative analysis in five sites documented 78 tree species of 66 genera and 33 families. Tree density and species diversity were higher than previously reported for the forests of the Eastern Ghats, India. Population structure and regeneration potential in four out of five study sites showed a higher percentage of density in the seedling and sapling layers, demonstrating that these sites are regenerating. However, in the Gugarpat sacred forest, the population structure revealed large numbers of mature trees with a stable population structure. In our study, large proportions of species had either poor regeneration potential or were not regenerating. Hence, management strategies are needed to conserve these species. Our study documents the diversity, population patterns, and regeneration of the tree species of five sacred forests, which may help in further management and conservation of the biodiversity of sacred forests in India and globally.

Genetic variation and relationships in the mitochondrial DNA D-loop region of Qinghai indigenous and commercial pig breeds

BackgroundBamei pigs are special germplasm resources in Qinghai. In the specific environment of the Qinghai plateau, local breeds, through long-term natural and artificial selection, have acquired a relatively stable population structure and genetic diversity. This study revealed Bamei pigs’ genetic diversity at the molecular level and the degree of introgression of commercial breeds into Bamei pigs.MethodsThe mitochondrial DNA D-loop region was amplified and sequenced using the ABI 3130 DNA sequencer. Sequences were collected, edited and aligned using the MEGA 5.0, DNASTAR and ClustalX 1.81 software. Haplotypes of all sequences and genetic diversity were analyzed by DnaSP 5.0 software.Results and conclusionsWe identified a total of 73 polymorphic sites in our 489 novel sequences, including 1 single variable site and 72 parsimony informative sites.Genetic diversity was analyzed in this study. The results showed that haplotype diversity, nucleotide diversity and the average number of nucleotide differences of Bamei pigs were lower than those of commercial pigs. Synthetic evaluation of genetic diversity through principal component analysis indicated that Bamei pigs also showed low genetic diversity. In summary, the results of sequence analysis showed that Bamei pigs were low in genetic diversity, and the introgression of commercial pigs into Bamei pigs was serious.

Orchid colonization: multiple parallel dispersal events and mosaic genetic structure in Dactylorhiza majalis ssp. lapponica on the Baltic island of Gotland.

The island of Gotland in the Baltic Sea has had no contact with surrounding continental areas since the withdrawal of the Weichselian ice sheet at approx. 17 ka BP. Plants present on Gotland must have arrived by long-distance dispersal, so populations are expected to exhibit reduced levels of genetic diversity compared with populations on surrounding mainlands. However, orchids have very small seeds, which appear well adapted to long-distance dispersal, and they should therefore be less affected than other plant species by colonization bottlenecks. The aim of this study was to analyse the genetic structure of orchids colonizing isolated islands, using the marsh orchid Dactylorhiza majalis ssp. lapponica as a case study. More than 500 samples from 27 populations were analysed for 15 plastid and eight nuclear marker loci. Population diversity and differentiation patterns were compared for nuclear and plastid marker systems and analysed in relation to geographical location. We found high genetic diversity but no clear geographical structure of genetic differentiation between populations on Gotland. However, the between-population differentiation in plastid and nuclear markers were correlated and the greatest diversity was found at sites at comparatively high elevations, which were the first to emerge above the water after the Ice Age. The regional population on Gotland has been established by a minimum of four dispersal events from continental regions. Subsequent gene flow between sites has not yet homogenized the differentiation pattern originating from initial colonization. We conclude that long-distance seed dispersal in orchids has a strong impact on structuring genetic diversity during periods of expansion and colonization, but contributes less to gene flow between populations once a stable population structure has been achieved.

Stable genetic structure andconnectivity in pollution-adapted and nearby pollution-sensitive populations of Fundulus heteroclitus.

Populations of the non-migratory estuarine fish Fundulus heteroclitus inhabiting the heavily polluted New Bedford Harbour (NBH) estuary have shown inherited tolerance to local pollutants introduced to their habitats in the past 100 years. Here we examine two questions: (i) Is there pollution-driven selection on the mitochondrial genome across a fine geographical scale? and (ii) What is the pattern of migration among sites spanning a strong pollution gradient? Whole mitochondrial genomes were analysed for 133 F. heteroclitus from seven nearby collection sites: four sites along the NBH pollution cline (approx. 5 km distance), which had pollution-adapted fish, as well as one site adjacent to the pollution cline and two relatively unpolluted sites about 30 km away, which had pollution-sensitive fish. Additionally, we used microsatellite analyses to quantify genetic variation over three F. heteroclitus generations in both pollution-adapted and sensitive individuals collected from two sites at two different time points (1999/2000 and 2007/2008). Our results show no evidence for a selective sweep of mtDNA in the polluted sites. Moreover, mtDNA analyses revealed that both pollution-adapted and sensitive populations harbour similar levels of genetic diversity. We observed a high level of non-synonymous mutations in the most polluted site. This is probably associated with a reduction in Ne and concomitant weakening of purifying selection, a demographic expansion following a pollution-related bottleneck or increased mutation rates. Our demographic analyses suggest that isolation by distance influences the distribution of mtDNA genetic variation between the pollution cline and the clean populations at broad spatial scales. At finer scales, population structure is patchy, and neither spatial distance, pollution concentration or pollution tolerance is a good predictor of mtDNA variation. Lastly, microsatellite analyses revealed stable population structure over the last decade.