Genetic Subdivision Research Articles

Population genomics informs the management of harvested snappers across north-western Australia

Failure to consider population structure when managing harvested fishes increases the risk of stock depletion, yet empirical estimates of population structure are often lacking for important fishery species. In this study, we characterise genetic variation in single nucleotide polymorphisms (SNPs) to assess population structure for three harvested species of tropical snappers across the broad (up to 300 km wide) and extensive (~ 4000 km) continental shelf of north-western Australia. Comparisons across ~ 300 individuals per species, showed remarkably similar patterns of genetic structure among Lutjanus sebae (red emperor), L. malabaricus (saddletail snapper) and Pristipomoides multidens (goldband snapper) despite subtle differences in biological and ecological traits. Low levels of genetic subdivision were reflected in an isolation by distance relationship where genetic connectivity increased with geographic proximity. This indicates extensive but not unlimited dispersal across the north-western Australian shelf. Our findings provide evidence of connectivity between current management areas, violating the assumption of multiple independent stocks. Spatial stock assessment models may be more suitable for the management of these species however demographic connectivity rates cannot be accurately estimated from the conventional population genetic approaches applied in this study. We recommend that managers aim to maintain adequate spawning biomass across current management areas, and assess stocks at finer scales, where practical.

Population genetic structure of the endemic sponge Lubomirskia baikalensis in Lake Baikal in the light of mass disease and mortality events

Abstract The study of the state of Baikal endemic sponge populations is of great interest because of the occurrence of mass mortalities and disease in recent decades. To identify possible signs of species vulnerability to extinction, it is crucial to develop appropriate genetic markers that help developing measures for conservation. In this paper, we describe the population genetic structure of the Baikal endemic sponge Lubomirskia baikalensis examined with the set of microsatellite markers we developed. We analysed 251 samples from eight locations that cover all three basins of Lake Baikal. A genetic subdivision into three clusters was revealed. Such a structure can be explained mainly by the low ability of larvae to disperse. Despite the presence of dead and diseased individuals in all studied locations, all populations were in Hardy–Weinberg equilibrium and no bottleneck effect was found at all. This is the first time that a genetic connectivity study has been performed for L. baikalensis, a species endemic of Lake Baikal. Reconstruction of the changes in the effective population size agrees with the results obtained during drill sample analysis and it demonstrates that the effective population size was 55.5 times lower about 24,000 years ago, which indicates that apparently there is no threat of extinction of the Baikal endemic sponges at present.

Genetic Diversity of Trypanosoma cruzi in the United States of America: The Least Endemic Country for Chagas Disease.

Chagas disease (CD), caused by Trypanosoma cruzi and endemic in Latin America, has become an emergent health problem in non-endemic countries due to human migration. The United States (US) is the non-Latin American country with the highest CD burden and cannot be considered as non-endemic, since triatomine vectors and reservoir animals have been found. Populations of T. cruzi are divided into genetic subdivisions, which are known as discrete typing units (DTUs): TcI to TcVI and TcBat. Autochthonous human T. cruzi infection in the US is sporadic, but it may change due to environmental factors affecting the geographic distribution of triatomines. We aimed to perform a literature review of the genetic diversity of T. cruzi in triatomine vectors and mammalian hosts, including human cases, in the US. The 34 analyzed studies revealed the presence of T. cruzi in 18 states, which was mainly concentrated in Texas, Louisiana and New Mexico. TcI and TcIV were the principal DTUs identified, being TcI the most genotyped (42.4%; 917/2164). This study represents a first attempt to compile the molecular epidemiology of T. cruzi in the US, which is fundamental for predicting the progression of the infection in the country and could be of great help in its future management.

Molecular epidemiology of the Old World screwworm fly (OWSF) in Iraq, and the genetic structure of various OWSF populations worldwide

Despite being endemic in Iraq, no reports have been published in the past 10 years to update the molecular epidemiology of the Old World screwworm fly (OWSF), Chrysomya bezziana, in this country. In the present study, 130 sheep from 10 Iraqi governorates were found infected with C. bezziana larvae, whose identities were PCR-confirmed based on the cytochrome b (Cytb) gene, and 23 isolates from various tested governorates were successfully sequenced. Although most isolates (n = 20) belonged to the common haplotype circulating in Iraq, two new haplotypes were detected. Significant changes in OWSF epidemiology in Iraq were also suggested, since infestations were detected, for the first time, in Nineveh governorate. Isolates of the present study were combined to those previously published from Iraq and worldwide, collected after searching the GenBank, and various genetic and population structure analyses were conducted. These isolates displayed a great statistically significant value when tested for the purifying (negative) selection, suggesting the limited occurrence of genetic variations, which was evidenced by the high sequence conservation (C = 0.937) value detected. A few isolates from Africa were revealed during our search, and clustered in a separate lineage other than that of the Asian isolates. The latter displayed different genetic variation patterns when compared. For example, isolates from geographically separate regions, e.g., the Gulf Arab countries and South-Eastern Asia had marked genetic differences. On the other hand, isolates from regions with close geographic proximity (the Gulf Arab countries and Iran) had limited genetic subdivision. This is not the case when comparing isolates from 10 islands in the Indonesian Archipelago. Populations from Sumatra and Sumba were isolated and displayed high genetic variations toward the other populations. On the contrary, populations from Sulawesi, Lombok and Sumbawa displayed limited genetic variations. This is particularly important, since it can help detecting the dynamics of establishing the sterile insect technique over various regions as an effective control strategy against the OWSFs.

Phylogenetic, phylogeographic and divergence time analysis of Anopheles subpictus species complex using ITS2 and COI sequences

Objective: To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles (An.) subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2 (ITS2) and cytochrome C oxidase I (COI) sequences deposited at the GenBank. Methods: Seventy-five ITS2, 210 COI and 26 concatenated sequences available in the NCBI database were used. Phylogenetic analysis was performed using Bayesian likelihood trees, whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic analysis. Genetic diversity indices and genetic differentiation were also calculated. Results: Two genetically divergent molecular forms of An. subpictus species complex corresponding to sibling species A and B are established. Species A evolved around 37-82 million years ago in Sri Lanka, India, and the Netherlands, and species B evolved around 22-79 million years ago in Sri Lanka, India, and Myanmar. Vietnam, Thailand, and Cambodia have two molecular forms: one is phylogenetically similar to species B. Other forms differ from species A and B and evolved recently in the above mentioned countries, Indonesia and the Philippines. Genetic subdivision among Sri Lanka, India, and the Netherlands is almost absent. A substantial genetic differentiation was obtained for some populations due to isolation by large geographical distances. Genetic diversity indices reveal the presence of a long-established stable mosquito population, at mutation-drift equilibrium, regardless of population fluctuations. Conclusions: An. subpictus species complex consists of more than two genetically divergent molecular forms. Species A is highly divergent from the rest. Sri Lanka and India contain only species A and B.

SSR Marker–Based Genetic Diversity and Relationship Analyses of Stephania tetrandra S. Moore

AbstractStephania tetrandra S. Moore (family: Menispermaceae), a dioecious herbaceous vine and the only species in the subgenus Botryodiscia of the genus Stephania of the family Menispermaceae, is mainly distributed in hilly areas south of the Huaihe River in China and found in many provinces of China, showing a high genetic diversity. This paper aimed to study genetic diversity of and genetic relationship among individuals of S. tetrandra within China to provide a basis for evaluation, exploitation, and utilization of S. tetrandra by using simple sequence repeat (SSR) molecular markers. Our results show that effective products were amplified from the 26 screened SSR gene loci, a total of 183 alleles amplified (2–16 alleles amplified by each pair of primers). Among the 26 loci, 16 had a PIC value higher than 0.5, indicating a high level of polymorphism. For most of the loci, the number of effective alleles was lower than that of the observed alleles, and the observed heterozygosity was lower than the expected heterozygosity. The genetic differentiation coefficient (0.021–0.547) was lower than 0.05 (low level of genetic differentiation) for 7 loci and higher than 0.25 (very high level of genetic differentiation) for 2 loci, and had a value representing a medium level of genetic differentiation for the remaining 17 loci. The intra-population inbreeding coefficient had a positive value for 21 loci, suggesting the presence of inbreeding and homozygous excess. The gene flow value was bigger than 1, indicating that genetic drift and natural selection played an unimportant role in population genetic differentiation of S. tetrandra. Based on discriminant analysis of principal components and Bayesian Information Criterion, K-means clustering was performed on 620 samples. These samples were divided into 9 genetic clusters, whose similarity coefficients and genetic distances were 0.755–0.918 and 0.067–0.280, respectively, indicating that these clusters were highly similar and short-distanced. The Bayesian clustering analysis was implemented in the STRUCTURE software to analyze the genetic structure of S. tetrandra and it was found that the 620 samples could be clustered into 5 ancestor groups; the 9 clusters and 40 natural populations inherited genes from the 5 groups to varying degrees, but the proportion of genes inherited from the 5 groups by each cluster and natural population differed. S. tetrandra was characterized by the presence of population structure and pronounced genetic subdivision, which, together with the presence of gene flow, may indicate a relatively stable recent state of these populations.

Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent.

Due to their limited dispersal ability, fossorial species with predominantly belowground activity usually show increased levels of population subdivision across relatively small spatial scales. This may be exacerbated in harsh mountain ecosystems, where landscape geomorphology limits species' dispersal ability and leads to small effective population sizes, making species relatively vulnerable to environmental change. To better understand the environmental drivers of species' population subdivision in remote mountain ecosystems, particularly in understudied high-elevation systems in Africa, we studied the giant root-rat (Tachyoryctes macrocephalus), a fossorial rodent confined to the afro-alpine ecosystem of the Bale Mountains in Ethiopia. Using mitochondrial and low-coverage nuclear genomes, we investigated 77 giant root-rat individuals sampled from nine localities across its entire ~1000 km2 range. Our data revealed a distinct division into a northern and southern group, with no signs of gene flow, and higher nuclear genetic diversity in the south. Landscape genetic analyses of the mitochondrial and nuclear genomes indicated that population subdivision was driven by slope and elevation differences of up to 500 m across escarpments separating the north and south, potentially reinforced by glaciation of the south during the Late Pleistocene (~42,000-16,000 years ago). Despite this landscape-scale subdivision between the north and south, weak geographic structuring of sampling localities within regions indicated gene flow across distances of at least 16 km at the local scale, suggesting high, aboveground mobility for relatively long distances. Our study highlights that despite the potential for local-scale gene flow in fossorial species, topographic barriers can result in pronounced genetic subdivision. These factors can reduce genetic variability, which should be considered when developing conservation strategies.

Disease-driven top predator decline affects mesopredator population genomic structure.

Top predator declines are pervasive and often have dramatic effects on ecological communities via changes in food web dynamics, but their evolutionary consequences are virtually unknown. Tasmania's top terrestrial predator, the Tasmanian devil, is declining due to a lethal transmissible cancer. Spotted-tailed quolls benefit via mesopredator release, and they alter their behaviour and resource use concomitant with devil declines and increased disease duration. Here, using a landscape community genomics framework to identify environmental drivers of population genomic structure and signatures of selection, we show that these biotic factors are consistently among the top variables explaining genomic structure of the quoll. Landscape resistance negatively correlates with devil density, suggesting that devil declines will increase quoll genetic subdivision over time, despite no change in quoll densities detected by camera trap studies. Devil density also contributes to signatures of selection in the quoll genome, including genes associated with muscle development and locomotion. Our results provide some of the first evidence of the evolutionary impacts of competition between a top predator and a mesopredator species in the context of a trophic cascade. As top predator declines are increasing globally, our framework can serve as a model for future studies of evolutionary impacts of altered ecological interactions.

Genetic Structure and Diversity of Dalbergia nigra from Brazilian Atlantic Forest Fragments

Dalbergia nigra is a long-living tree endemic to the Atlantic Rain Forest. Due to its high commercial value, this species has been widely exploited for timber production and is now endangered. It is widely known that understanding patterns of genetic structure is paramount for conserving threatened species. We analyzed the genetic diversity of 140 individuals from four different forest fragments in the southern region of Bahia, Brazil, to verify the possible effects of fragmentation on these populations and provide information for conservation initiatives. High polymorphism levels were detected from the genotyping of nine microsatellite loci (mean HE = 0.733). All populations showed high genetic diversity; however, a reduction of genetic diversity was detected in each population (HO < HE). The average fixation index was high and significant (f = 0.167), which could be due to the occurrence of inbreeding, the Wahlund effect, reproductive system, or from null alleles. Genetic differentiation among populations was high (mean θP = 0.118), suggesting strong isolation, a pattern consistent with historically low gene flow. The Bayesian analysis revealed five different genetic groups, among which three groups correspond to three different forest fragments, and two groups showed the genetic subdivision of individuals from the other forest fragment. Based on our results, the suggested conservation strategy for D. nigra populations in the southern region of Bahia, Brazil, involves high environmental investments to protect all sampled forest fragments and individuals. Another strategy would be to collect seeds from all individuals from the sampled fragments and start a new population with human interference in its evolutive history inside a protection unit.

Temporal population genetic structure of Phormia regina (Diptera: Calliphoridae).

The genetic structure of forensically important blow fly (Brauer & Bergenstamm) (Diptera: Calliphoridae) populations has remained elusive despite high relatedness within wild-caught samples. This research aimed to determine if the implementation of a high-resolution spatiotemporal sampling design would reveal latent genetic structure among blow fly populations and to elucidate any environmental impacts on observed patterns of genetic structure. Adult females of the black blow fly, Phormia regina (Meigen) (Diptera: Calliphoridae), were collected from 9 urban parks in Indiana, USA over 3 yr and genotyped at 6 polymorphic microsatellite loci. The data analysis involved 3 clustering methods: principal coordinate analysis (PCoA), discriminant analysis of principal components (DAPC), and STRUCTURE. While the PCoA did not uncover any discernible clustering patterns, the DAPC and STRUCTURE analyses yielded significant results, with 9 and 4 genetic clusters, respectively. Visualization of the STRUCTURE bar plot revealed N = 11 temporal demarcations indicating barriers to gene flow. An analysis of molecular variance of these STRUCTURE-inferred populations supported strong temporally driven genetic differentiation (FST = 0.048, F'ST = 0.664) relative to geographic differentiation (FST = 0.009, F'ST = 0.241). Integrated Nested Laplace Approximation and Boosted Regression Tree analyses revealed that collection timepoint and 4 main abiotic factors (temperature, humidity, precipitation, and wind speed) were associated with the genetic subdivisions observed for P. regina. A complex interplay between environmental conditions, the unique reproductive strategies of the blow fly, and the extensive dispersal abilities of these organisms likely drives the strong genetic structure of P. regina in the Midwestern US.

DNA Identification of Parasitic Copepods <i>Salmincola</i> (Copepoda, Siphonostomatoida, Lernaeopodidae): Variability and Rate of Evolution of the Mitochondrial Cytochrome c Oxidase Subunit I Gene

The barcode fragment of the COI gene was sequenced in 91 specimens of five species of parasitic Salmincola copepods, sampled from salmonids mainly from the Russian Far East: S. californiensis (mykiss and masu salmon) and S. edwardsii (various species of chars, sockeye salmon from Lake Kronotskoe), S. carpionis (various species of chars), S. markewitschi (whitespotted char), S. stellata (Sakhalin taimen). A total of 41 haplotypes were found with a maximum level of differences of 0.183 nucleotide substitutions per position. The distance between species varied from 0.139 ± 0.014 in the S. markewitschi–S. carpionis pair to 0.179 ± 0.015 in the S. stellata–S. californiensis pair. The intraspecific nucleotide diversity of the COI gene fragment is much lower: for S. californiensis and S. edwardsii, inhabiting the gill cavity and fins of the host – 0.013 ± 0.003 and 0.015 ± 0.003, and for S. stellata, S. markewitschi, and S. carpionis, localized in the buccal cavity of the hosts – 0.002 ± 0.001, 0.004 ± 0.001, and 0.005 ± 0.001, respectively. A comparison of samples of three Salmincola copepod species from different regions of the Russian Far East revealed a significant (Fst = 0.28–0.42, P \( \ll \) 0.001) genetic subdivision. Three subclades of edwardsii-like copepods – S. edwardsii from the Russian Far East, S. edwardsii from the American brook char of eastern North America, and S. siscowet from the lake char of Michigan (COI sequences of copepods from the last two groups are taken from genetic databases) – differed from each other by an average of 9.3–10.9% nucleotide positions, which means the need for a taxonomic revision of S. edwardsii. According to the molecular dating carried out, the divergence of Salmincola lineages started in the Miocene and ended in the early Pliocene. The phylogenetic substitution rate was 0.0228 (95% interval: 0.0132–0.033) nucleotide substitutions/position/million years/lineage. The rate of nucleotide substitutions at the population level is 3.7 times higher – 0.0849 (0.0212–0.170). The high level of variability of the COI gene fragment makes this marker a useful tool both for developing the taxonomy and phylogeny of Salmincola and Lernaeopodidae copepods at the species and genus levels, and for analyzing the differentiation of their populations.

Genetic Uniqueness and Genetic Structure of Populations of Picea obovata Ledeb. and Larix sibirica Ledeb. in the Northern and Middle Urals

Establishing sustainable plantations with genetic diversity equivalent to that of natural populations is vital for successful reforestation efforts. In this study, we present an innovative approach for selecting populations suitable for reforestation, taking into account their genetic uniqueness using Inter Simple Sequence Repeats (ISSR) markers. Our investigation focused on six populations of Picea obovata Ledeb and six populations of Larix sibirica Ledeb, collected from the Northern and Middle Urals. We found that the indicators of genetic diversity were significantly higher in L. sibirica compared to P. obovata, while the number of rare alleles was greater in Siberian spruce (R = 19). Among the P. obovata populations, the Cherdyn’s forestry exhibited notably high genetic diversity, and for L. sibirica, the Gainy’s forestry stood out in this regard. Moreover, the genetic subdivision of the six P. obovata populations (GST = 0.331) was higher than that of the six L. sibirica populations (GST = 0.177). To ensure optimal seed selection considering the genetic originality coefficient (GOC) and population differentiation, we recommend utilizing the P. obovata population from Gainy’s forestry with a GOC of 0.554 and the L. sibirica population from Cherdyn’s forestry with a GOC of 0.372. These populations harbor typical alleles characteristic of the research region, making them ideal candidates for seed selection. Furthermore, the specific alleles identified can serve as valuable markers for determining the geographic origin of P. obovata and L. sibirica wood, aiding in efforts to trace the sources of these species in forestry and trade practices.

Domestication in dry-cured meat Penicillium fungi: Convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision.

Some fungi have been domesticated for food production, with genetic differentiation between populations from food and wild environments, and food populations often acquiring beneficial traits through horizontal gene transfers (HGTs). Studying their adaptation to human-made substrates is of fundamental and applied importance for understanding adaptation processes and for further strain improvement. We studied here the population structures and phenotypes of two distantly related Penicillium species used for dry-cured meat production, P. nalgiovense, the most common species in the dry-cured meat food industry, and P. salamii, used locally by farms. Both species displayed low genetic diversity, lacking differentiation between strains isolated from dry-cured meat and those from other environments. Nevertheless, the strains collected from dry-cured meat within each species displayed slower proteolysis and lipolysis than their wild conspecifics, and those of P. nalgiovense were whiter. Phenotypically, the non-dry-cured meat strains were more similar to their sister species than to their conspecific dry-cured meat strains, indicating an evolution of specific phenotypes in dry-cured meat strains. A comparison of available Penicillium genomes from various environments revealed HGTs, particularly between P. nalgiovense and P. salamii (representing almost 1.5 Mb of cumulative length). HGTs additionally involved P. biforme, also found in dry-cured meat products. We further detected positive selection based on amino acid changes. Our findings suggest that selection by humans has shaped the P. salamii and P. nalgiovense populations used for dry-cured meat production, which constitutes domestication. Several genetic and phenotypic changes were similar in P. salamii, P. nalgiovense and P. biforme, indicating convergent adaptation to the same human-made environment. Our findings have implications for fundamental knowledge on adaptation and for the food industry: the discovery of different phenotypes and of two mating types paves the way for strain improvement by conventional breeding, to elucidate the genomic bases of beneficial phenotypes and to generate diversity.

Genetic and morphological diversity in populations of Annona senegalensis Pers. occurring in Western (Benin) and Southern (Mozambique) Africa.

Understanding morpho-genetic diversity and differentiation of species with relatively large distributions is crucial for the conservation and sustainable management of their genetic resources. The present study focused on Annona senegalensis Pers., an important multipurpose wild plant, distributed exclusively in natural ecosystems but facing several threats. The study assessed the genetic and morphological diversity, structure, and differentiation of the species in populations from Western (Benin) and Southern (Mozambique) Africa. The material was evaluated to ascertain the environmental (climatic) determinants of the variation within this species. Four sub-populations comprised of 154 individuals were phenotyped based on nineteen plant, fruit, and leaf morphological traits and further genotyped using ten polymorphic nuclear microsatellite (nSSR) markers. The results indicated strong differences in plant, fruit, and leaf morphological traits between Western and Southern populations. Furthermore, the studied populations were characterized by high genetic diversity, with an average genetic diversity index of 1.02. Western populations showed higher heterozygosity values (0.61-0.71) than Southern populations (0.41-0.49). Western and Southern populations were clearly differentiated into two different genetic groups, with further genetic subdivisions reflecting four sub-populations. Genetic variation between regions (populations) was higher (69.1%) than among (21.3%) and within (9.6%) sub-populations. Four distinct morphological clusters were obtained, which were strongly associated with the four genetic groups representing each sub-population. Climate, mainly precipitation and temperature indexes, explained the relatively higher variation found in morphological traits from Western (40.47%) in relation to Southern (27.98%) populations. Our study suggests that both environmental and genetic dynamics play an important role in the development of morphological variation in A. senegalensis.

Evaluation of Stagonospora Nodorum Blotch Severity and Parastagonospora nodorum Population Structure and Genetic Diversity Across Multiple Locations and Wheat Varieties in Virginia.

Parastagonospora nodorum is a necrotrophic pathogen that causes Stagonospora nodorum blotch (SNB) in wheat. Wheat varieties grown in Virginia vary in susceptibility to SNB, and the severity of SNB varies across locations and years. However, the impacts of wheat genetic backgrounds and environments on SNB severity and the structure of P. nodorum populations in the region have not been well studied. Thus, a population genetic study was conducted utilizing P. nodorum isolates collected from different wheat varieties and locations in Virginia. A total of 320 isolates were collected at seven locations over 2 years from five wheat varieties. Isolates were genotyped using multilocus simple sequence repeat markers, and necrotrophic effector (NE) and mating type genes were amplified using gene-specific primers. Wheat varieties varied in susceptibility to SNB, but site-specific environmental conditions were the primary drivers of disease severity. Fungal populations were genetically diverse, but no genetic subdivision was observed among locations or varieties. The ratio of the two mating type idiomorphs was not significantly different from 1:1, consistent with the P. nodorum population undergoing sexual reproduction. Three major NE genes were detected within the P. nodorum population, but not with equal frequency. However, NE gene profiles were similar for groups of isolates originating from different varieties, suggesting that wheat genetic backgrounds do not differentially select for NEs. There was no evidence of population structure among P. nodorum populations in Virginia and, thus, no support for wheat genetic backgrounds shaping these populations. Finally, although varieties only exhibited moderate resistance to SNB, current levels of resistance are likely to be durable over time and remain a useful tool for integrated management of SNB in the region. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genomic Insights Into the Evolution and Demographic History of the SARS-CoV-2 Omicron Variant: Population Genomics Approach.

A thorough understanding of the patterns of genetic subdivision in a pathogen can provide crucial information that is necessary to prevent disease spread. For SARS-CoV-2, the availability of millions of genomes makes this task analytically challenging, and traditional methods for understanding genetic subdivision often fail. The aim of our study was to use population genomics methods to identify the subtle subdivisions and demographic history of the Omicron variant, in addition to those captured by the Pango lineage. We used a combination of an evolutionary network approach and multivariate statistical protocols to understand the subdivision and spread of the Omicron variant. We identified subdivisions within the BA.1 and BA.2 lineages and further identified the mutations associated with each cluster. We further characterized the overall genomic diversity of the Omicron variant and assessed the selection pressure for each of the genetic clusters identified. We observed concordant results, using two different methods to understand genetic subdivision. The overall pattern of subdivision in the Omicron variant was in broad agreement with the Pango lineage definition. Further, 1 cluster of the BA.1 lineage and 3 clusters of the BA.2 lineage revealed statistically significant signatures of selection or demographic expansion (Tajima's D<-2), suggesting the role of microevolutionary processes in the spread of the virus. We provide an easy framework for assessing the genetic structure and demographic history of SARS-CoV-2, which can be particularly useful for understanding the local history of the virus. We identified important mutations that are advantageous to some lineages of Omicron and aid in the transmission of the virus. This is crucial information for policy makers, as preventive measures can be designed to mitigate further spread based on a holistic understanding of the variability of the virus and the evolutionary processes aiding its spread.

Identification by High-Throughput Real-Time PCR of 30 Major Circulating Listeria monocytogenes Clonal Complexes in Europe.

Listeria monocytogenes is a ubiquitous bacterium that causes a foodborne illness, listeriosis. Most strains can be classified into major clonal complexes (CCs) that account for the majority of outbreaks and sporadic cases in Europe. In addition to the 20 CCs known to account for the majority of human and animal clinical cases, 10 CCs are frequently reported in food production, thereby posing a serious challenge for the agrifood industry. Therefore, there is a need for a rapid and reliable method to identify these 30 major CCs. The high-throughput real-time PCR assay presented here provides accurate identification of these 30 CCs and eight genetic subdivisions within four CCs, splitting each CC into two distinct subpopulations, along with the molecular serogroup of a strain. Based on the BioMark high-throughput real-time PCR system, our assay analyzes 46 strains against 40 real-time PCR arrays in a single experiment. This European study (i) designed the assay from a broad panel of 3,342 L. monocytogenes genomes, (ii) tested its sensitivity and specificity on 597 sequenced strains collected from 24 European countries, and (iii) evaluated its performance in the typing of 526 strains collected during surveillance activities. The assay was then optimized for conventional multiplex real-time PCR for easy implementation in food laboratories. It has already been used for outbreak investigations. It represents a key tool for assisting food laboratories to establish strain relatedness with human clinical strains during outbreak investigations and for helping food business operators by improving their microbiological management plans. IMPORTANCE Multilocus sequence typing (MLST) is the reference method for Listeria monocytogenes typing but is expensive and takes time to perform, from 3 to 5 days for laboratories that outsource sequencing. Thirty major MLST clonal complexes (CCs) are circulating in the food chain and are currently identifiable only by sequencing. Therefore, there is a need for a rapid and reliable method to identify these CCs. The method presented here enables the rapid identification, by real-time PCR, of 30 CCs and eight genetic subdivisions within four CCs, splitting each CC into two distinct subpopulations. The assay was then optimized on different conventional multiplex real-time PCR systems for easy implementation in food laboratories. The two assays will be used for frontline identification of L. monocytogenes isolates prior to whole-genome sequencing. Such assays are of great interest for all food industry stakeholders and public agencies for tracking L. monocytogenes food contamination.

Genetic subdivisions of follicular lymphoma defined by distinct coding and noncoding mutation patterns

AbstractFollicular lymphoma (FL) accounts for ∼20% of all new lymphoma cases. Increases in cytological grade are a feature of the clinical progression of this malignancy, and eventual histologic transformation (HT) to the aggressive diffuse large B-cell lymphoma (DLBCL) occurs in up to 15% of patients. Clinical or genetic features to predict the risk and timing of HT have not been described comprehensively. In this study, we analyzed whole-genome sequencing data from 423 patients to compare the protein coding and noncoding mutation landscapes of untransformed FL, transformed FL, and de novo DLBCL. This revealed 2 genetically distinct subgroups of FL, which we have named DLBCL-like (dFL) and constrained FL (cFL). Each subgroup has distinguishing mutational patterns, aberrant somatic hypermutation rates, and biological and clinical characteristics. We implemented a machine learning–derived classification approach to stratify patients with FL into cFL and dFL subgroups based on their genomic features. Using separate validation cohorts, we demonstrate that cFL status, whether assigned with this full classifier or a single-gene approximation, is associated with a reduced rate of HT. This implies distinct biological features of cFL that constrain its evolution, and we highlight the potential for this classification to predict HT from genetic features present at diagnosis.

Evolution of the rice blast pathogen on spatially structured rice landraces maintains multiple generalist fungal lineages.

Traditional agrosystems, where humans, crops and microbes have coevolved over long periods, can serve as models to understand the ecoevolutionary determinants of disease dynamics and help the engineering of durably resistant agrosystems. Here, we investigated the genetic and phenotypic relationship between rice (Oryza sativa) landraces and their rice blast pathogen (Pyricularia oryzae) in the traditional Yuanyang terraces of flooded rice paddies in China, where rice landraces have been grown and bred over centuries without significant disease outbreaks. Analyses of genetic subdivision revealed that indica rice plants clustered according to landrace names. Three new diverse lineages of rice blast specific to the Yuanyang terraces coexisted with lineages previously detected at the worldwide scale. Population subdivision in the pathogen population did not mirror pattern of population subdivision in the host. Measuring the pathogenicity of rice blast isolates on landraces revealed generalist life history traits. Our results suggest that the implementation of disease control strategies based on the emergence or maintenance of a generalist lifestyle in pathogens may sustainably reduce the burden of disease in crops.

Population genetics of Glossina fuscipes fuscipes from southern Chad

In Subsaharan Africa, tsetse flies (genus Glossina) are vectors of trypanosomes causing Human African Trypanosomiasis (HAT) and Animal African Trypanosomosis (AAT). Some foci of HAT persist in Southern Chad, where a program of tsetse control was started against the local vector Glossina fuscipes fuscipes in the Mandoul focus in 2014, and in Maro in 2018. Flies were also sampled in 2018 in Timbéri and Dokoutou. We analyzed the population genetics of G. fuscipes fuscipes from the four tsetse-infested zones. The trapping samples were characterized by a strong female biased sex-ratio, except in Timbéri and Dokoutou that had high tsetse densities. Apparent density and effective population density appeared smaller in the main foci of Mandoul and Maro and the average dispersal distance (within the spatial scale of each zone) was as large as or larger than the total length of each respective zone. The genetic signature of a population bottleneck was found in the Mandoul and Timbéri area, suggesting a large ancient interconnected metapopulation that underwent genetic subdivision into small, isolated pockets due to adverse environmental conditions. The long-range dispersal and the existence of genetic outliers suggest a possibility of migration from remote sites such as the Central African Republic in the south (although the fly situation remains unknown there) and/or a genetic signature of recent exchanges. Due to likely isolation, an eradication strategy may be considered for sustainable HAT control in Mandoul focus. Another strategy will probably be required in Maro focus, which probably experiences much more exchanges with its neighbors.