Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic patterning in Central Eurasia: population history and pigmentation

Central-western Asia has often been underrepresented in population genetic studies, but it is important for the clarification of the peopling of Eurasia and the relationship between its western and eastern extremities. We genotyped individuals from over 40 population groups, mostly central Eurasian, for mitochondrial HVR1, CCR5del32 and five functional MC1R variants (p.Val60Leu, p.Val92Met, p.Arg151Cys, p.Arg160Trp, p.Arg163Gln), and collected published genotype data for comparison. Mitochondrial profiles confirm both the higher heterozygosity in Central Asia than in surrounding areas, and the broadly northern European distribution of CCR5del32. The MC1R variants profile alone is a good determinant of the longitudinal position of a population group, and combined FST values divide Eurasia into seven broad geographic divisions. We can conclude that Central Asia shares genetic features with both eastern and western Eurasia, compatible with both a scenario where the former acted as a source for the latter two’s genetic diversity, or one where Central Asia is a ‘hybrid zone’ where eastern and western peoples met. Furthermore, the overall high FST values for functional MC1R variants combined with presumed selection pressures on skin pigmentation in low-UV areas lead us to conclude that different variants were selected for in east and west Eurasia, an example of convergent evolution.
H2AFX and MDC1 Protect Genomic Integrity in Male Germ Cells by Promoting Recombination and Activation of the Recombination-Dependent Checkpoint

In somatic cells, H2afx and Mdc1 are close functional partners in DNA repair and damage response. However, it is not known whether they are also involved in the maintenance of genome integrity in meiosis. By analyzing chromosome dynamics in H2afx-/- spermatocytes, we found that synapsis of the autosomes and X-Y chromosomes were impaired in a relevant fraction of cells. Such defect correlated with an abnormal recombination profile. Conversely, Mdc1 was dispensable for the synapsis of the autosomes, and only played a minor role in X-Y synapsis, relatively to H2afx. This suggested that those genes have non-overlapping functions in chromosome synapsis. However, we observed that both genes play a similar role in the assembly of MLH3 onto chromosomes, a key step in crossover formation. Moreover, we showed that H2afx and Mdc1 cooperate in promoting the activation of the recombination-dependent checkpoint, a mechanism that restrains the differentiation of cells with unrepaired DSBs. This occurs by a mechanism that involves P53. Overall, our data showed that, in male germ cells, H2afx and Mdc1 promote the maintenance of genome integrity.
Synopsis and taxonomic revision of three genera in the snake tribe Sonorini

ABSTRACT Delimiting species is a crucial goal of integrative biology, and yet can be misled by homoplasy and high levels of morphological variation. The snake tribe Sonorini contains three genera that have long confounded taxonomists: Chilomeniscus, Chionactis and Sonora. Dynamic colour evolution in this group, including rampant geographic variation in colour and colour polymorphism, has led to a chaotic taxonomy. We used mitochondrial and high-throughput nuclear data (ddRADseq) and complete taxonomic sampling of each genus to reconstruct phylogenetic relationships and systematically revise the genus. Our research revealed that Sonora is paraphyletic with regards to Chilomeniscus and Chionactis and that at least one species (S. semiannulata) is paraphyletic with respect to at least one other recognized species. Additionally, we found substantial undescribed genetic diversity within multiple species which is incongruent with morphological variation in coloration. Accordingly, we proposed synonymizing Chionactis and Chilomeniscus with Sonora, which has taxonomic priority over both genera. As we found genetic evidence that supported some of the historically delimited diversity within multiple taxa, we revised species-level taxonomy accordingly. This new taxonomy recognizes a revised genus of Sonora that contains 15 species of diminutive and often brightly coloured snakes that are distributed from central Mexico to north-western USA. http://www.zoobank.org/urn:lsid:zoobank.org:pub:45A553D8-6435-4E0A-84ED-DF31E2CCD872
Investigating the Role of Genetic Background and Niche of Origin in the Adaptation of Pseudomonas aeruginosa

Prolonged respiratory infection by the opportunistic pathogen, Pseudomonas aeruginosa, is the major contributor to early mortality in individuals with cystic fibrosis (CF). Patients often acquire their infections from the environment, however it is unknown whether all genotypes are capable of causing infection. To investigate this, we experimentally evolved 18 environmental and CF-clinical genotypes within synthetic CF lung sputum (SCFM), to identify any genotypic and/or prior niche constraints on trait evolution and pathoadaptation. We found that genotype significantly constrained evolution within SCFM, which was evidenced through phylogenetic signal in the change of both traits and fitness. We also found that environmental strains evolve differently in SCFM compared to their CF-clinical counterparts. Altogether our results suggest there is widespread variation in the adaptation of P. aeruginosa, which is in part constrained by both genetic background, and niche of origin.
The Major Histocompatibility Complex in Song Sparrows: Immunity, Signals, and Mate Choice

In recent years, sexual selection theory has redefined genetic quality to consider not only additive genetic effects on fitness but also non-additive genetic effects, such as heterozygote advantage or disadvantage. In jawed vertebrates, the major histocompatibility complex (MHC) gene family has been shown to exhibit both additive and non-additive genetic effects on fitness. MHC gene products are involved in initiating adaptive immune responses, and MHC genotype determines the range of pathogens to which an individual can respond. Therefore, parasite-mediated selection at MHC may favour locally-adapted, rare, or particular combination of alleles. Because heterozygote advantage at MHC is widespread, sexual selection should favour mechanisms by which individuals assess the MHC genotypes of potential mates, and mate non-randomly. Studies exploring the role of MHC in immunity and sexual selection are widespread amongst mammals and fish, but in birds (especially songbirds) there is relatively scant evidence for MHC-mediated mating and the mechanism by which this might be accomplished remains unknown. First, I assessed differentiation at MHC class I and II that might underlie locally-good gene effects in two populations of song sparrows (Melospiza melodia) previously shown to exhibit higher resistance to sympatric malaria (Plasmodium) strains. I found no population differentiation, suggesting no locally-good gene effects at MHC, but individuals with higher class I diversity were less likely to be infected when experimentally inoculated with Plasmodium. Second, I explored whether song sparrows convey information on MHC class II genotype through chemical (preen oil) or auditory (birdsong) cues. Pairwise similarity at MHC was related to pairwise similarity of preen oil chemical composition, but not to pairwise similarity in song repertoire content. Song repertoire size, a sexually selected trait in this species, was nonlinearly related to MHC diversity, such that males with intermediate MHC diversity sang the most songs. Finally, to investigate MHCmediated mate choice, I compared MHC similarity of socially mated pairs of free-living song sparrows to random expectations. Contrary to my prediction of MHC-disassortative mating, social pairs were more similar at MHC than expected by chance. This work
Neo-formation of chromosomes in bacteria

Although the bacterial secondary chromosomes/megaplasmids/chromids, first noticed about forty years ago, are commonly held to originate from stabilized plasmids, their true nature and definition are yet to be resolved. On the premise that the integration of a replicon within the cell cycle is key to deciphering its essential nature, we show that the content in genes involved in the replication, partition and segregation of the replicons and in the cell cycle discriminates the bacterial replicons into chromosomes, plasmids, and another class of essential genomic elements that function as chromosomes. These latter do not derive directly from plasmids. Rather, they arise from the fission of a multi-replicon molecule corresponding to the co-integrated and rearranged ancestral chromosome and plasmid. All essential replicons in a distributed genome are thus neochromosomes. Having a distributed genome appears to extend and accelerate the exploration of the bacterial genome evolutionary landscape, producing complex regulation and leading to novel eco-phenotypes and species diversification.
Complete chloroplast genome of glyphosate resistant Sonchus oleraceus L. from Australia, with notes on the small single copy (SSC) region orientation

Abstract Sonchus oleraceus, common sowthistle, is an asteraceous weed in Australian agricultural systems and has recently developed resistance to glyphosate. We present the complete chloroplast sequence of S. oleracueus reconstructed from Illumina whole genome shotgun sequencing. This is the first complete chloroplast genome available for the genus Sonchus. The complete chloroplast sequence is 151,808 bp long. A Bayesian phylogeny of the chloroplast coding regions of the tribe Cichorieae (Asteraceae) is presented. The S. oleraceus chloroplast genome is deposited at GenBank under accession number MG878405.
Anthropogenic cause of range shifts and gene flow between two grasshopper species revealed by environmental modelling, geometric morphometrics and population genetics

The range of a species is controlled by biotic and abiotic factors; both could have changed recently due to human activity. We used environmental modelling, morphometric and genetic data to interpret ecological responses at the species boundary of a pair of New Zealand grasshoppers with very different ranges; one widespread (Phaulacridium marginale) and one restricted to semi‐arid central/southern South Island (Phaulacridium otagoense). Climate‐ and habitat‐based distribution models for grasshoppers in the past (last glacial maximum), present and future (2070), in concert with modelling of vegetation patterns imply range and demographic expansion of P. marginale and stability of P. otagoense. mtDNA sequence revealed four main lineages with pronounced differences in genetic diversity and geographical range. The widespread lineage associated with P. marginale revealed a signature of range expansion but regionally restricted lineages were geographically structured at a fine scale. Within the narrow geographical range of P. otagoense, three mtDNA lineages resulted in high diversity, more typical of large stable populations. Geometric analysis of pronotum shape identified individuals from a region of sympatry with mixed characteristics. Mismatch of phenotype, mtDNA lineage and nuclear DNA sequence indicates introgression between grasshopper species now in contact. This appears to be accompanied by P. otagoense range reduction through ecological competition. Deforestation by people starting ∼800 years ago best explains range change and resulting hybridisation of these grasshoppers. Anthropogenic habitat modification can have indirect consequences on insect biodiversity and conservation by enabling introgression between formerly separate populations and species.
Weed control in sesame with pre-emergence herbicides

Pendimethalin, imazethapyr, metribuzin, oxyfluorfen, imezemox were evaluated as pre-emergence herbicides in sesame during summer season of 2013 and 2014 at ICAR-Directorate of Weed Research, Jabalpur. All the herbicides reduced the weed population significantly as compared with weedy check but delayed the germination of sesame and caused sesame injury. Among all the herbicides, pendimethalin alone and in combination with lower dose of imazethapyr caused less injury to the sesame and produced higher sesame yield. None of the herbicides surpassed the yield what was achieved with 2 HW.
Macronutrient signature of dietary generalism in an ecologically diverse primate in the wild

Theory predicts that animals with a broad diet should be capable of using macronutrients (protein, fats, and carbohydrates) flexibly, such that a shortfall in one can be made up by additional intake of another. We used Rhesus macaques, a highly generalist primate, to test this in the wild. Our results strongly support the theory, and raise the question of why the same does not apply to the most generalist primate of all, humans.
MiRNA expression profiles of serum exosomes derived from individuals with latent and active tuberculosis

Tuberculosis (TB) has become a leading cause of death worldwide, which is largely attributed to the difficulties in diagnosis and treatment of TB patients. Exosomes carrying RNA, particularly miRNA, have been indicated their functional and diagnostic potential in diseases, including tuberculosis (TB). In the present study, we performed RNA-seq based analysis on exosomal miRNA profiles for clinical specimens of healthy controls (HC), active tuberculosis (TB) and latent tuberculosis infection (LTBI). We identified many distinct up-regulated and down-regulated differentially expressed miRNA and further screened top 20 in each compared groups which might provide a potential panel for differentiation of HC, LTBI, and TB. We classified all the differentially expressed miRNAs into six expression patterns and identified three persistently up-regulated miRNA (hsa-miR-140-3p, hsa-miR-3184-5p and hsa-miR-423-3p) as potential markers during TB progression. Combined with our previously detected exsomal mRNA, we screened the genes overlapped with predicted mRNA targets of differentially expressed miRNA and analyzed their involvement in Biological Process, indicating a decreased signaling transduction and increased cell death in LTBI and TB. Our results indicate the selective packaging of RNA cargoes into exosomes under different stages of Mycobacterium tuberculosis infection and facilitate further study of TB pathogenesis and development. IMPORTANCE The main reason for failure to eliminate TB is lack of understanding molecular mechanism of TB pathogenesis and difficulties in TB diagnosis and treatment. Exosomes provide a promising research tool because they are released from various cells containing valuable biochemical information related to diseases. We reveale distinct miRNA expression profile of the exosomes, which indicates selective packaging of RNA cargoes into exosomes under different stages of Mycobacterium tuberculosis infection. Further, we also provide evidence of related miRNA candidates potentially involving in TB progression and facilitating discovery of TB biomarkers.
Aggressive or moderate drug therapy for infectious diseases? Trade-offs between different treatment goals at the individual and population levels

Antimicrobial resistance is one of the major public health threats of the 21st century. There is a pressing need to adopt more efficient treatment strategies in order to prevent the emergence and spread of resistant strains. The common approach is to treat patients with high drug doses, both to clear the infection quickly and to reduce the risk of de novo resistance. Recently, several studies have argued that, at least in some cases, low-dose treatments could be more suitable to reduce the within-host emergence of antimicrobial resistance. However, the choice of a drug dose may have consequences at the population level, which has received little attention so far. Here, we study the influence of the drug dose on resistance and disease management at the host and population levels. We develop a nested two-strain model and unravel trade-offs in treatment benefits between an individual and the community. We use several measures to evaluate the benefits of any dose choice. Two measures focus on the emergence of resistance, at the host level and at the population level. The other two focus on the overall treatment success: the outbreak probability and the disease burden. We find that different measures can suggest different dosing strategies. In particular, we identify situations where low doses minimize the risk of emergence of resistance at the individual level, while high or intermediate doses prove most beneficial to improve the treatment efficiency or even to reduce the risk of resistance in the population. Author summary The obvious goals of antimicrobial drug therapy are rapid patient recovery and low disease prevalence in the population. However, achieving these goals is complicated by the rapid evolution and spread of antimicrobial resistance. A sustainable treatment strategy needs to account for the risk of resistance and keep it in check. One parameter of treatment is the drug dosage, which can vary within certain limits. It has been proposed that lower doses may, in some cases, be more suitable than higher doses to reduce the risk of resistance evolution in any one patient. However, if lower doses prolong the period of infectiousness, such a strategy has consequences for the pathogen dynamics of both strains at the population level. Here, we set up a nested model of within-host and between-host dynamics for an acute self-limiting infection. We explore the consequences of drug dosing on several measures of treatment success: the risk of resistance at the individual and population levels and the outbreak probability and the disease burden of an epidemic. Our analysis shows that trade-offs may exist between optimal treatments under these various criteria. The criterion given most weight in the decision process ultimately depends on the disease and population under consideration.
Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections

Abstract Global herbarium collections house a vast number of plant specimens stretching back over centuries. They include rare and extinct species, important historical collections, and valuable type specimens that could help to resolve long-standing taxonomic issues. Historical plant collections also provide unique windows into past evolutionary processes and population histories that do not exist with modern data alone. However, because the DNA in such specimens is often degraded and scarce, manipulation and analysis of their genetic material can be challenging. Recent developments in non-destructive genetic sampling and working with very small quantities of genomic DNA, especially in next-generation sequencing and bioinformatic analysis of ancient DNA, now make the majority of herbarium specimens potentially accessible to phylogenetic, population genetic, and barcoding studies. For example, studies of DNA from long time series of Ipomoea batatas and Anacamptis palustris collections revealed linkages between anthropogenic activity and changes in haplotype distribution. These time series also enable the identification of genes under recent selection in the genomes of both the plants and their pathogens, as was shown for Phytophthora infestans, a microbial pathogen of Solanum tuberosum. Here, we summarize the major challenges in using historical plant DNA in evolutionary studies and review genetic studies integrating herbarium specimens. We expect future genetic studies of historical herbarium specimens to use genomic, metagenomic, and population genetic approaches to: investigate how plant populations respond to environmental change; infer temporal changes in genetic diversity; identify genes under recent selection; and investigate past plant pathogen epidemics.
Prediction of macrophyte distribution: The role of natural versus anthropogenic physical disturbances

Co-ordinating Editor: Hannes Feilhauer Abstract Questions: Do natural and anthropogenic physical disturbances equally affect the distribution of aquatic plant communities? Can hydrodynamic and geomorphological features be used to predict the establishment of macrophyte communities at the shoreline scale? Locations: Two large, shallow lakes, southwest France. Methods: Based on field observations (vegetation occurrence and anthropogenic modifications of the shore) and data generated by a geographic information system (wave exposure, waveinduced sediment resuspension, slope and land cover), we defined sites and community groups using cluster and indicator species analyses. The groups were then analysed by means of a statistical classifier (Random Forest). These different steps in data treatment enabled us to characterize the importance of each physical factor in determining macrophyte occurrence and distribution. As a result, a predictive map to forecast aquatic plant distribution at the shoreline scale was obtained. Results: Anthropogenic disturbances were less important parameters than natural physical variables in structuring the distribution of lakeshore macrophytes. Within natural factors, waveinduced sediment resuspension and slope had the most impact; nevertheless, the presence of swimming areas seemed to have a strong impact on aquatic habitats, being correlated with the total absence of aquatic vegetation. The predictive map obtained through the model spatially defined the position and occurrence of suitable sites for the settlement of both invasive and rare and endangered species. Conclusions: In this study, natural disturbances play a major role in structuring aquatic plant distribution over physical anthropogenic factors. The model contributes to improving knowledge on plant communities with respect to local hydrodynamic and morphological features of lakeshores. Furthermore, the model provides a predictive map as a useful tool for the management of aquatic vegetation in temperate shallow lakes.
Strong pair bonds and high site fidelity in a subarctic-breeding migratory shorebird

ABSTRACT Interannual mate and site fidelity is common in migratory shorebirds with monogamous mating systems. After long-distance migrations and separation during the winter, birds often relocate their former mate at their previous breeding territory. Although pairs frequently reunite, new pairs are also formed. Why birds change mates is still not completely understood. Mate change can involve active decisions, in which one or both mates actively chooses to divorce from a previous mate, but can also be related to arrival timing or mate availability at the breeding grounds. We explored possible causes of mate change in the Pacific subspecies of the migratory shorebird Dunlin (Calidris alpina pacifica) breeding at the subarctic Yukon-Kuskokwim Delta, Alaska, USA (61°36′N, 165°12′W). Interannual return rates of Dunlin to their breeding grounds were higher for males (74%) than for females (54%) and were 14% higher for birds with high previous breeding success. Mate change was rare if both birds returned to the breeding grounds in a consecutive breeding season: only 8% of all pairs divorced when previous mates were available. When former mates failed to return or returned late, however, many individuals formed new pairs (45% of males and 53% of females). Nest initiation dates were not delayed for new pairs compared to reuniting pairs, and nest survival did not differ between new and reuniting pairs; however, renesting after nest failure within a season was faster for reuniting pairs. We conclude that avoiding delayed nesting is a strong determinant of breeding decisions in Pacific Dunlin nesting in the short subarctic summer.