Levels Of Gene Flow Research Articles

Monitoring spatiotemporal patterns in the genetic diversity of a European butterfly species

Abstract The importance of genetic diversity has been recognised by the Convention on Biological Diversity but attempts at monitoring or improving the genetic diversity of populations have been minimal. Here, we investigate changes over time in the genetic diversity of a wild insect species, Maniola jurtina (Lepidoptera: Nymphalidae) and present a large‐scale investigation into contemporary spatial genetic diversity. Using microsatellite markers, we calculate multiple measures of genetic diversity and divergence for M. jurtina populations over 8 years in the UK and compare these findings with long‐term abundance trends. We also conduct a large‐scale spatial analysis into the genetic diversity and population structuring of M. jurtina across Europe. All UK populations sampled have high levels of gene flow and genetic diversity, with genetic diversity stable over time. Across Europe, we find some population structuring between populations in the UK and the European mainland, suggesting restricted geneflow between the two regions. The monitoring of a wild species' genetic diversity is an achievable aim, and one that could be carried out for many species, particularly Lepidoptera. Future approaches may aim to develop higher resolution genetic markers and cover a wider range of species. The use of abundance data offers additional insight, and we find that concurrent, dedicated genetic monitoring can provide effective tracking of biodiversity trends.

Small-scale geographic differences in multiple-driver environmental variability can modulate contrasting phenotypic plasticity despite high levels of gene flow

Climate change is altering not only the mean conditions of marine environments, but also their temporal variability and predictability. As these alterations are not uniform across seascapes, their biological effects are expected to accentuate intra-specific differences in the adaptive capacity (e.g., plasticity and evolutionary potential) of natural populations. To test this theoretical framework, we assessed the phenotypic and genetic profiles of mussel from three study sites across a multi-driver heterogeneous environmental mosaic in Chilean Patagonia. Our study reveals that temporal variability, predictability, and exposure to extreme events (low pH/low salinity), collectively, can modulate the plasticity and optimal conditions of mussels. Despite these phenotypic differences, we observed low genetic differentiation, likely resulting from significant gene flow induced by aquaculture, ultimately diminishing variation among individuals from different geographic areas. Our findings underscore how variability and predictability are essential factors shaping phenotypic diversity, even at small spatial scales. Balancing these factors could enhance species resilience and ecological success, crucial for biodiversity conservation amidst climate change.

Phenotypic divergence of Glossina morsitans (Diptera: Glossinidae) populations in Zambia: Application of landmark-based wing geometric morphometrics to discriminate population-level variation.

An important consequence of the discontinuous distribution of insect populations within their geographic range is phenotypic divergence. Detection of this divergence can be challenging when it occurs through subtle shifts in morphological traits with complex geometries, such as insect wing venation. Here, we used landmark-based wing geometric morphometrics to investigate the population-level phenotypic variation of the two subspecies of Glossina morsitans, G. m. centralis Machado and G. m. morsitans Westwood that occur in Zambia. Twelve homologous landmarks digitised on the right wings of 720 specimens collected from four and five sites (80 per site with 1:1 sex ratio) within the G. m. centralis and G. m. morsitans range respectively, were subjected to generalised Procrustes analysis to obtain wing centroid size (CS) and wing shape variables. Linear permutation models and redundancy analysis were then used to compare CS and wing shape between male and female G. morsitans, the two subspecies G. m. centralis and G. m. morsitans, the sexes of each subspecies and between sample locations within each subspecies range, respectively. Significant differences in CS and wing shape were observed between G. morsitans sexes, subspecies and sample locations within each subspecies range. A neighbour-joining cladogram derived from the analysis of Procrustes distances showed that tsetse within each subspecies range were highly divergent. We conclude that G. morsitans populations in Zambia exhibit significant population-level variation in fly size and wing shape which suggests high levels of population structuring. The main drivers of this structuring could be random genetic drift in G. m. centralis demes and local adaptation to environmental conditions in G. m. morsitans populations. We therefore recommend molecular studies to estimate the levels of gene flow between these populations and identify possible barriers to genetic flow.

Genomic diversity and population structure of Carniolan honey bee in its native habitat

BackgroundResearch into the genetic diversity of honey bee (Apis melliferaL.) populations has become increasingly significant in recent decades, primarily due to population declines attributed to human activities and climate change. As a species of great importance, breeding programs that leverage understanding of genomic diversity could offer solutions to mitigate these challenges. The objective of this study was to examine the genomic diversity and population structure of Carniolan honey bees (Apis mellifera carnica) using the Illumina SNP chip on a large honey bee sample collected from Central and South-Eastern European countries. The study also aims to offer recommendations for future breeding programs.ResultsOur analysis involved Discriminant Analysis of Principal Components (DAPC), heterozygosity, admixture analysis, fixation indices (FST), Neighbour-Joining tree, gene flow and Isolation-by-distance analysis. DAPC indicated distinct separation between the Carniolan and Italian honey bee (Apis mellifera ligustica) populations, whereas the admixture analysis revealed varying levels of gene flow and genetic admixture within the Carniolan honey bee populations, demonstrating closer relationships between specific geographic regions (confirmed by Isolation-by-distance analysis). Furthermore, the research of heterozygosity, genomic inbreeding, pairwise FST values, and Neighbour-Joining tree provided insights into the patterns of genetic differentiation and similarity among the populations of Carniolan honey bee within its natural habitat. We have observed genetic homogeneity of the Carniolan honey bee population when considered in a broader genetic/geographical context. However, the Carniolan honey bee has sufficient genetic diversity in its geographical home range that needs to be carefully monitored and maintained.ConclusionsThis study provides important insights into the genetic composition, differentiation, and relationships among Carniolan honey bee populations in Central and South-Eastern European countries. The findings are crucial for conservation efforts, breeding programs, and sustainable beekeeping practices. They emphasise the importance of considering genetic factors and population structure in the breeding and management of honey bees. By understanding these genetic relationships, we can develop strategies to preserve genetic diversity, improve breeding outcomes, and ensure the resilience of honey bee populations in the face of environmental changes and challenges. This knowledge can also inform policy makers and stakeholders on best practices to maintain healthy bee populations, which are vital for ecosystem services and agricultural productivity.

Does rafting promote contemporary gene flow? Global and regional patterns of population genetic diversity and structure on the false limpet Siphonaria lateralis in the Southern Ocean

Rafting has been proposed as an effective mechanism for species without free-living pelagic larvae to achieve long-distance dispersal, theoretically preventing population differentiation over wide distributional ranges. Moreover, rafting has been advocated as a main dispersal mechanism for marine invertebrates with sub-Antarctic distributions, because of abundant buoyant kelps, driven by the Antarctic Circumpolar Current. Nonetheless, little attention has been given to the role of rafting to establish regular gene flow across the sub-Antarctic, and the geographic and temporal scales at which it occurs. Aiming to unravel these major questions about the extent of genetic connectivity across the Southern Ocean (SO), we studied the pulmonate limpet Siphonaria lateralis, a benthic species with encapsulated larvae, found on the rocky intertidal of sub-Antarctic islands and southern South America. Since S. lateralis is closely associated with D. antarctica, dispersal by rafting is plausible, as revealed by the absence of phylogeographic structure across the sub-Antarctic. We sampled 116 individuals from eight localities across the SO, and used 5,515 SNPs obtained through Genotyping-by-Sequencing, to determine contemporary genetic diversity, structure, and gene flow at two spatial scales; global, across the SO, and regional, within Kerguelen. Results identified substantial genetic structure, differentiating Patagonia, Falklands/Malvinas Islands, South Georgia and the Kerguelen archipelago, and low levels of contemporary gene flow. The most notable genetic differentiation was found between Patagonia/Falklands and South Georgia/Kerguelen. Structure was also significant between Patagonia and the Falkland/Malvinas Islands. Conversely, South Georgia and Kerguelen exhibited closer genetic affinity, and indications of recent but limited gene flow. Moreover, historical gene flow estimates between the four populations were low. At regional scale, noteworthy genetic structure persisted, and gene flow was insufficient to prevent genetic differentiation within Kerguelen. Consequently, rafting’s potential may be overestimated as a contemporary mechanism promoting gene flow across the SO, as these events may be sporadic, irregular, and unpredictable for marine invertebrates lacking a larval dispersal stage, since contemporary dispersal events don’t seem to facilitate high gene flow at both scales. Accordingly, other oceanographic factors or processes may hinder the establishment of species associated with macroalgae, and as consequence, contemporary genetic connectivity in the sub-Antarctic.

Analysis of the genetic diversity and population structure of Tilia amurensis from China using SSR markers: Implications for conservation

Tilia amurensis is a deciduous broad-leaved tree in the Malvaceae family. It is one of the second-class key protected wild plants in China. The evaluation of genetic polymorphisms of crucial protected species is necessary for conserving germplasm resources. In this study, 15 pairs of highly polymorphic SSR primers were used to analyse the genetic diversity of eight T. amurensis populations and the population structure of nine Tilia populations distributed in China. At the population level (Na = 6.050, Ne = 2.930, I = 1.123, HO = 0.485, HE = 0.523), there was a high level of genetic diversity. The AMOVA results showed that 12 % and 88 % of the total variation occurred among and within populations, respectively. The degree of genetic differentiation was moderate (FST = 0.124), and the level of gene flow was high (Nm = 1.763). The results of UPGMA cluster analysis, PCoA and structure analysis (ΔK = 2) revealed different degrees of gene introgression between the eight T. amurensis populations and Tilia japonica as the outgroup. These findings have important implications for formulating appropriate conservation strategies.

The Migration, Diversity, and Evolution of Puccinia triticina in China.

Wheat leaf rust, caused by Puccinia triticina, is one of the most common fungal diseases of wheat in China and occurs widely in various wheat-growing regions. To clarify the epidemic, spread rules, and population structure of P. triticina among different regions, 217 isolates of P. triticina collected from Hebei, Shandong, Sichuan, and Xinjiang in China were tested by 34 Thatcher near-isogenic lines and 21 pairs of EST-SSR primers. A total of 83 races were identified, and THTT, PHTT, THTS, and PHJT were the most predominant races in the four provinces in 2009. We found enriched virulence and genetic diversity in the four P. triticina populations and a significant correlation between genetic polymorphism and geographic regions. However, no significant correlation was found between virulence phenotypes and molecular genotypes. Moreover, a notable high level of gene flow (Nm = 2.82 > 1) among four P. triticina populations was detected. The genetic relationship among Hebei, Shandong, and Sichuan populations was close, possibly due to the spread of P. triticina from Sichuan to Shandong and then to Hebei. In contrast, the Xinjiang population was relatively independent. Genetic differentiation analysis showed some level of differentiation among or within populations of P. triticina in the four provinces, and the genetic variation within populations (74.97%) was higher than across populations (25.03%). Our study provides a basis for a better understanding of the regional migration, epidemic, and population structure of P. triticina in China.

Integrating genetic assortment and molecular insights for climate-resilient breeding to unravel drought tolerance in cotton

This study addresses the challenges posed by rainfall variability, leading to water deficits during critical stages of crop growth, resulting in a drastic reduction of cotton yield. In a comprehensive evaluation, thirty cotton genotypes, including five Gossypium arboreum (wild) and twenty-five Gossypium hirsutum (cultivated), were grown under rainfed and irrigated conditions. Drought tolerance indices (DTI) were evaluated, categorizing genotypes based on their resilience. Further, in-vitro screening at the seedling stage (20 days) under PEG-induced drought identified tolerant genotypes exhibiting elevated levels of free proline (19.07±5.31 mg.g−100fr.wt.), amino acids (34.59±6.51 mg.g−100fr.wt.), soluble proteins (13.73±2.65 mg.g−1fr.wt.), and glycine betaine (10.95±3.62 mg.g−100fr.wt.), in their leaves, positively correlating (p<0.001) with relative water content (87.70±3.45 %). Molecular analysis using drought-specific simple sequence repeats (SSR) markers revealed significant genetic variability in a cotton genotypes, with lower observed and higher expected heterozygosity. F statistics exposed a higher level of gene flow corresponding to low differentiation among populations. Among the genotypes group, wild GAM-67 and cultivated Deviraj emerged as the most potent, exhibiting the higher DTI and diverse gene pools. Study exhibited higher total gene diversity in drought-tolerant wild GAM-67 (0.8501) and greater expected heterozygosity (0.626) and gene flow (0.6731) in cultivated Deviraj, underlining their robust genetic adaptability to drought conditions. The integrated approach of field evaluations, in-vitro screening, and molecular analyses explained substantial genetic diversity, with the identification of promising genotypes displaying higher drought tolerance indices, elevated levels of stress-related biochemical osmolytes, and pronounced genetic adaptability, thereby contributing to the advancement of breeding initiatives for enhanced drought resilience in cotton.

Riverscape genomics of the endangered freshwater mussel Lampsilis rafinesqueana

Abstract Historical periods of rapid climate change and associated direct and indirect impacts such as glaciation and restructuring of drainage systems are important in shaping biodiversity, lineage divergence, and contemporary genetic variation amongst many aquatic taxa. Through an understanding of the impacts of these ancient changes in land‐ and waterscapes on current diversity, practitioners can account for a species' unique evolutionary history when developing conservation strategies. We investigated intraspecific genetic diversity of the critically endangered freshwater mussel, Lampsilis rafinesqueana, endemic to the interior region of the U.S.A. Our study (1) characterises genetic variation within and amongst populations to infer biogeographic history and (2) applies genetic information to potential conservation strategies. We applied restriction‐site associated DNA sequencing and mitochondrial DNA sequencing to investigate genetic diversity within and amongst populations of L. rafinesqueana from across the species' distribution. We then considered this information in the context of historical riverscape processes and applicability to conservation. Variation within rivers was similar, but we found different genetic populations associated with two major ecoregions, the Central Interior Highlands and Osage Plains. The plains population displayed an Ne value approximately 10‐fold lower than the highlands population. Historical demographic modelling suggests the two populations diverged approximately 1.2 million years ago and then both populations underwent a substantial decrease in population size around 19,700 years ago. These two major events are each correlated with known periods of historic rapid climate change. We identified two distinct populations of a federally endangered mussel, L. rafinesqueana. Contemporary genetic diversity of this species was strongly influenced by direct and indirect impacts of rapid historic shifts in climate. The highlands population has undergone a recent expansion, typical of post‐Pleistocene climate change, while also having a much larger Ne value than the plains population. Our results suggest low levels of gene flow amongst the two distinct populations across generations. We recommend that conservation managers for this species take into account relative difference in diversity between populations when developing management strategies. In many species, assisted gene flow amongst genetically unique populations should only be considered in extreme circumstances; however, in L. rafinesqueana, low levels of assisted migration amongst populations may be a valuable tactic to maintain natural levels of genetic variation. Our study shows that biogeographical frameworks can be useful for developing conservation strategies that serve to retain important genomic variation that represents the evolutionary potential of target freshwater species.

Genetic Features of the Bream Abramis brama Population from the Lake System of Sebezhsky National Park

The genetic variability of microsatellite DNA has been studied for the first time for five loci in the common bream Abramis brama (L.) from lakes Sebezhskoye and Necheritsa of the Sebezhsky National Park lake system (Pskov oblast). The results demonstrate the uniformity of estimates of the genetic variability of the bream in the lake system. Estimates of the allelic diversity of microsatellite loci and the expected heterozygosity of local bream groups do not differ significantly. The total genetic differentiation of bream is θ = 0.004, 95% CI (–0.01; 0.01), and is statistically insignificant. The Bayesian analysis of the studied multilocus genotypes has not revealed any population–genetic structure. The results indicate a high level of gene flow between local bream groupings and make it possible to assume the presence of a genetically unified panmixed population in the Sebezhsky National Park lake system.

Analysis of the genetic structure of populations of the terrestrial mollusk &lt;i&gt;Caucasotachea vindobonensis&lt;/i&gt; (Helicidae) in conditions at the eastern border of the range using microsatellite markers

BACKGROUND: Assessing the genetic structure of populations of rare and vulnerable species provides useful information for developing conservation strategies. AIM: The aim of the study was to study the genetic structure of Caucasotachea vindobonensis populations in the south of the Central Russian Upland using SSR markers. MATERIALS AND METHODS: Genetic structure of the populations was studied using eight microsatellite markers, first identified by the authors for the species under study. Fragment analysis of PCR products was carried out on an automatic capillary DNA sequencer Nanophore 05 (Russia). A total of 498 individuals from 24 populations were studied. RESULTS: A total of 59 alleles were isolated in the eight studied SSR loci, of which 21 (36%) turned out to be private. At the same time, private alleles were found in eleven studied populations, which is 46% of their total number. According to the data obtained, the effective number of alleles (Ae) averaged 1.6 ± 0.06, the Shannon index (I) was 0.45 ± 0.03, and the level of expected heterozygosity (He) was 0.27 ± 0.021. A high level of spatial subdivision of population gene pools was noted (Fst = 0.47 ± 0.08) with a fairly low level of gene flow (Nm = 1.15 ± 0.91). PCA analysis showed that the populations of the central and eastern parts of the south of the Central Russian Upland form a closely related group, different from other populations of the region. Calculation of the effective abundance using the LD method showed that Ne varies in different groups of snails from 0.6 to infinity. CONCLUSIONS: Populations of C. vindobonensis in the south of the Central Russian Upland live in conditions of significant isolation, as evidenced by the high degree of differentiation of the studied groups. The analysis of principal components based on genetic distances according to Nei and Wright’s F-statistics indicate a pronounced division of populations in the study area into two clusters, which is probably associated with the historical features of landscape formation. Calculation of effective numbers indicates the high viability of the majority of the studied populations. At the same time, some groups of snails are clearly in a depressed state, which is reflected in low levels of genetic diversity and their effective size.

Historical and contemporary processes driving the origin and structure of an admixed population within a contact zone between subspecies of a north temperate diadromous fish.

Hybridization between divergent lineages can result in losses of distinct evolutionary taxa. Alternatively, hybridization can lead to increased genetic variability that may fuel local adaptation and the generation of novel traits and/or taxa. Here, we examined single-nucleotide polymorphisms generated using genotyping-by-sequencing in a population of Dolly Varden char (Pisces: Salmonidae) that is highly admixed within a contact zone between two subspecies (Salvelinus malma malma, Northern Dolly Varden [NDV] and S. m. lordi, Southern Dolly Varden [SDV]) in southwestern Alaska to assess the spatial distribution of hybrids and to test hypotheses on the origin of the admixed population. Ancestry analysis revealed that this admixed population is composed of advanced generation hybrids between NDV and SDV or advanced backcrosses to SDV; no F1 hybrids were detected. Coalescent-based demographic modelling supported the origin of this population about 55,000 years ago by secondary contact between NDV and SDV with low levels of contemporary gene flow. Ancestry in NDV and SDV varies within the watershed and ancestry in NDV was positively associated with distance upstream from the sea, contingent on habitat-type sampled, and negatively associated with the number of migrations that individual fish made to the sea. Our results suggest that divergence between subspecies over hundreds of thousands of years may not be associated with significant reproductive isolation, but that elevated diversity owing to hybridization may have contributed to adaptive divergence in habitat use and life history.

Contrasting patterns of spatial genetic structure in endangered southern damselfly (Coenagrion mercuriale) populations facing habitat fragmentation and urbanisation

AbstractAimHuman‐induced environmental changes result in habitat loss and fragmentation, impacting wildlife population genetic structure and evolution. Urbanised and geographically peripheral areas often represent unfavourable environments, reducing connectivity among populations and causing higher population genetic differentiation and lower intra‐population genetic diversity. We examined how geographic peripherality and anthropogenic pressures affect genetic diversity and genetic differentiation in the protected southern damselfly (Coenagrion mercuriale, Odonata), which has low dispersal capabilities and specific habitat requirements and whose populations are declining.LocationWe studied two areas: one in semi‐natural habitats at the periphery of the species geographic range (northern France) and the other more central to the species' range, in an urbanised area surrounding the city of Strasbourg (Alsace, eastern France).MethodsWe genotyped 2743 individuals from 128 populations using 11 microsatellite loci. We analysed the spatial distribution of neutral genetic diversity (allelic richness, heterozygosity, levels of inbreeding and genetic relatedness), the extent of genetic differentiation and population affiliations (sPCAs) within the two areas. We also examined fine‐scale patterns of gene flow in the urbanised area of Alsace by investigating patterns of isolation by distance and estimating effective migration surfaces (EEMS) method.ResultsNorthern peripheral populations showed lower levels of genetic diversity and higher levels of genetic differentiation than central Alsacian populations. Although located in anthropised habitats, geographically central Alsacian populations showed high levels of gene flow, with dispersal events mainly occurring overland and not restricted to watercourses. However, the highly urbanised city of Strasbourg negatively impacted nearby populations by reducing levels of genetic diversity and increasing population genetic differentiation.Main ConclusionsThese results showed the need for management action by restoring breeding sites and creating migratory corridors for peripheral southern damselfly populations. However, our results also highlighted the resilience of southern damselfly in central range populations facing strong urbanisation pressures.

Molecular identification and genetic diversity of biting midges (Diptera: Ceratopogonidae) in the tropical environment on Hainan Island, China.

Biting midges are hematophagous arthropods responsible for zoonotic infectious diseases and have a wide distribution in temperate and tropical latitudes of the world. The genomic DNA of midge samples was extracted using the Chelex method and the ITS1gene was amplified by PCR to identify the midge species via BLAST. The sequence characteristics and the genetic diversity were analyzed using ClustalOmega, DnaSP, Arlequin, PopART, and TCS software tool. The validity of the ITS1 gene as a DNA barcode marker was evaluated using DAMBE. The phylogenetic relationship was established in the MEGA software. The ABGD web determined the species boundary and the SDT software visualized the pairwise sequence comparisons. A total of 39 midge samples possessed the range from 364 to 429 bp of the ITS1 sequences. The midge samples were identified as Culicoides imicola, Culicoides oxystoma, Culicoides peregrinus, Culicoides jacobsoni, Forcipomyia peregrinator, and Culicoides fulvus, respectively. The ITS1 sequences had 288 conserved sites (60.25%), 167 variable sites (34.94%), 141 parsimony-informative sites (29.50%), and 26 singleton sites (5.44%), with a considerable sequence variation with a high haplotype diversity. Populations in Lingao, Haikou, Tunchang were relatively independent, with a low level of gene flow. A separate population of Forcipomyia genus in Danzhou was observed. The biting midges in Hainan, a tropical island, had abundant genetic diversity. Timely surveillance is a crucial control measure for the spread of midge-borne diseases.

Invasion away from roadsides was not driven by adaptation to grassland habitats in Dittrichia graveolens (stinkwort)

Invasive plants along transportation corridors can significantly threaten ecosystems and biodiversity if they spread beyond anthropogenic environments. Rapid evolution may increase the ability of invading plant populations to establish in resident plant communities over time, posing a challenge to invasion risk assessment. We tested for adaptive differentiation in Dittrichia graveolens (stinkwort), an invasive species of ruderal habitat in California that is increasingly spreading away from roadsides into more established vegetation. We collected seeds from eight pairs of vegetated sites and their nearest (presumed progenitor) roadside population. We assessed differentiation between populations in roadside and vegetated habitat for germination behavior and for response to competition in a greenhouse experiment. We also tested for increased performance in vegetated habitat with a grassland field experiment including a neighbor removal treatment. Germination rates were slightly reduced in seeds from vegetated sites, which may indicate lower seed viability. Otherwise, plants did not show consistent differences between the two habitat types. Competition strongly reduced performance of D. graveolens in both the greenhouse and in the field, but plants originating from vegetated sites did not show enhanced competitive ability. Our findings show no evidence of adaptive differentiation between D. graveolens populations from roadside and vegetated habitats to date, suggesting that invasiveness in grasslands has not been enhanced by rapid evolution in the 40 + years since this species was introduced to California. Evolutionary constraints or potentially high levels of gene flow at this small scale may limit adaptation to novel habitats along roadsides.

The effects of grassland degradation on the genetic structure of a small mammal.

Grassland degradation is challenging the health of grassland ecosystems globally and causing biodiversity decline. Previous studies have demonstrated the impact of grassland degradation on the abundance and behavior of small mammals. Little is known about how it affects the genetic structure of gregarious mammals in the wild. This study explores the effects of grassland degradation on the genetic structure of a small burrowing mammal, plateau pika (Ochotona curzoniae). We used nine microsatellite loci to analyze the genetic diversity and genetic differentiation between colonies and genetic relatedness between individuals within the colony. We found that pikas in severely degraded grasslands had a significantly higher genetic diversity within colonies, a higher level of gene flow between colonies, and a lower genetic differentiation between colonies compared to pikas in less degraded grasslands. Individuals within colonies had a significantly lower genetic relatedness in severely degraded grasslands than in less degraded grasslands. This study has provided potential evidence of a significant impact of grassland degradation on the genetic structure of pikas, which has caused a breakdown of their kin-selected colony structure.

Evaluating the impact of historical climate and early human groups in the Araucaria Forest of eastern South America

It has been hypothesized that the Araucaria Forest in southern Brazil underwent expansions in the past, driven either by human groups or by climate fluctuations of the Holocene and Pleistocene. Fossil pollen records of the Paraná pine Araucaria angustifolia, a dominant tree in that forest, provide some insights into when those may have occurred. Still, the timing of those expansions has never been estimated. To infer past range shifts and shed light on their main drivers, we employed next‐generation DNA sequencing (ddRADseq), machine learning, and a comprehensive database of fossil pollen records into a study of historical demographic inference and paleo‐distribution modeling of the Paraná pine. We found that A. angustifolia comprises two populations expanding at different times: one in the Mantiqueira mountain chain, the other in the southern Brazilian plateau. The southern population began to expand during the Last Glacial Period ~ 70 kya, long before human arrival in South America. Still, genetic analyses support that humans later impacted this population, resulting in lower genetic diversity, higher inbreeding, and high levels of gene flow over large distances with a weak pattern of isolation‐by‐distance. It is possible this resulted from human influence on seed dispersal and germination on the southern Brazilian plateau. The Mantiqueira population, in contrast, expanded only recently (~ 3 kya). This timing coincides with Holocene climatic changes and human settlements established further south, although, to date, there is little archeological evidence of human impact in the Mantiqueira. In addition, multitemporal species distribution models built from a combination of present‐day and pollen records infer a range expansion of the Araucaria Forest during glacial times until the cold humid HS1 event (~ 16 kya), when the forest was most widespread, with no evidence of glacial refugia. The combination of genomic and spatial analyses suggests that both human and climatic controls played a role in the dynamics of the Araucaria Forest.

Thymus algeriensis Boiss. et Reut., a north African endemic plant species: genetic diversity and population structure as assessed by molecular markers, a pioneer step for conservation implications.

Thymus algeriensis Boiss. et Reut. is one of the most widespread North African species of the genus Thymus L. The species is subshrub growing primarily in subtropical biome of Morocco, Algeria, Tunisia and Libya. In Tunisia, the plant species is under high pressure of anthropogenic activities including over-collecting. The assessment of genetic diversity and population structure of T. algeriensis is a pioneer step to retrace its evolutionary history and to perform appropriate conservation strategies of the plant species. Seven wild populations growing, widely, in different bioclimatic zones were selected and analysed using two molecular markers systems. Fifteen Simple Sequence Repeats (SSRs) and fifteen Inter-Simple Sequence Repeats (ISSRs) were used to characterize genetically 140 different genotypes. The results showed a high molecular variation within populations and among the studied genotypes. The intra-populations genetic diversity revealed by SSRs was higher (P = 80.95%, Na = 2.143 and He = 0.364) than that based on ISSRs (P = 78.12%, Na = 1.632, He = 0.265 and I = 0.398). As demonstrated by inbreeding coefficients, a significant level of differentiation and a low level of gene flow were detected among studied populations (FST = 0.161 for SSRs and ΦST = 0.197 for ISSRs). Furthermore, the results of ISSRs marker suggest land strips as barriers in population genetic structure. While SSRs marker reflects a relatively structured bioclimatic patterns of studied populations. The Bayesian analysis showed a specific adaptation of populations to local environments. The used molecular markers (ISSRs and SSRs) seem to be effective in deciphering genetic polymorphism of Tunisian genotypes of T. algeriensis. Therefore, the genetic structure of the studied genotypes could constitute a starting point for further conservation, characterization and breeding programs.

GENETIC CHARACTERIZATION OF RELICT ENDEMIC LIQUIDAMBAR ORIENTALIS (ALTINGIACEAE) POPULATIONS

Liquidambar orientalis, a relict endemic species, is distributed in the south-west of Turkey. The natural spread areas of the species have been decreasing since the early 1900s. This poses a great threat to the future and genetic diversity of the species. In this study, the genetic diversity of a total of 190 individuals in ten populations was examined with ten polymorphic ISSR primers. Data analysis was performed using POPGENE ver. 1.32 and GenAlEx 6.503 softwares. According to the results of the analysis, a total of 271 loci were identified. For the ten populations, the rate of polymorphic loci ranged from 21.03% to 34.69%. The mean number of observed alleles (Na) and mean number of effective alleles (Ne) were found as 1.98 ± 0.13 and 1.47 ± 24 0.37, respectively. Nei's genetic diversity values (h) ranged from 0.07 ± 0.15 to 0.12 ± 0.18. According to the results of Molecular Analysis of Variance (AMOVA) and POPGENE ver. 1.32 analysis, it was determined that the main contribution to the genetic variance originated from among the populations. In addition, the gene flow level (NM) was found to be low with a value of 0.27 per generation.

Pan-azole- and multi-fungicide-resistant Aspergillus fumigatus is widespread in the United States.

Aspergillus fumigatus is an important global fungal pathogen of humans. Azole drugs are among the most effective treatments for A. fumigatus infection. Azoles are also widely used in agriculture as fungicides against fungal pathogens of crops. Azole-resistant A. fumigatus has been increasing in Europe and Asia for two decades where clinical resistance is thought to be driven by agricultural use of azole fungicides. The most prevalent mechanisms of azole resistance in A. fumigatus are tandem repeats (TR) in the cyp51A promoter coupled with mutations in the coding region which result in resistance to multiple azole drugs (pan-azole resistance). Azole-resistant A. fumigatus has been isolated from patients in the United States (U.S.), but little is known about its environmental distribution. To better understand the distribution of azole-resistant A. fumigatus in the U.S., we collected isolates from agricultural sites in eight states and tested 202 isolates for sensitivity to azoles. We found azole-resistant A. fumigatus in agricultural environments in seven states showing that it is widespread in the U.S. We sequenced environmental isolates representing the range of U.S. sample sites and compared them with publicly available environmental worldwide isolates in phylogenetic, principal component, and ADMIXTURE analyses. We found worldwide isolates fell into three clades, and TR-based pan-azole resistance was largely in a single clade that was strongly associated with resistance to multiple agricultural fungicides. We also found high levels of gene flow indicating recombination between clades highlighting the potential for azole-resistance to continue spreading in the U.S.IMPORTANCEAspergillus fumigatus is a fungal pathogen of humans that causes over 250,000 invasive infections each year. It is found in soils, plant debris, and compost. Azoles are the first line of defense antifungal drugs against A. fumigatus. Azoles are also used as agricultural fungicides to combat other fungi that attack plants. Azole-resistant A. fumigatus has been a problem in Europe and Asia for 20 years and has recently been reported in patients in the United States (U.S.). Until this study, we did not know much about azole-resistant A. fumigatus in agricultural settings in the U.S. In this study, we isolated azole-resistant A. fumigatus from multiple states and compared it to isolates from around the world. We show that A. fumigatus which is resistant to azoles and to other strictly agricultural fungicides is widespread in the U.S.