Native drivers of fish life history traits are lost during the invasion process

Rapid adaptation to global change can counter vulnerability of species to population declines and extinction. Theoretically, under such circumstances both genetic variation and phenotypic plasticity can maintain population fitness, but empirical support for this is currently limited. Here, we aim to characterize the role of environmental and genetic diversity, and their prior evolutionary history (via haplogroup profiles) in shaping patterns of life history traits during biological invasion. Data were derived from both genetic and life history traits including a morphological analysis of 29 native and invasive populations of topmouth gudgeon Pseudorasbora parva coupled with climatic variables from each location. General additive models were constructed to explain distribution of somatic growth rate (SGR) data across native and invasive ranges, with model selection performed using Akaike's information criteria. Genetic and environmental drivers that structured the life history of populations in their native range were less influential in their invasive populations. For some vertebrates at least, fitness-related trait shifts do not seem to be dependent on the level of genetic diversity or haplogroup makeup of the initial introduced propagule, nor of the availability of local environmental conditions being similar to those experienced in their native range. As long as local conditions are not beyond the species physiological threshold, its local establishment and invasive potential are likely to be determined by local drivers, such as density-dependent effects linked to resource availability or to local biotic resistance

What about Current Diversity of Mycolactone-Producing Mycobacteria? Implication for the Diagnosis and Treatment of Buruli Ulcer

The identification of an emerging pathogen in humans can remain difficult by conventional methods such as enrichment culture assays that remain highly selective, require appropriate medium and cannot avoid misidentifications, or serological tests that use surrogate antigens and are often hampered by the level of detectable antibodies. Although not originally designed for this purpose, the implementation of polymerase-chain-reaction (PCR) has resulted in an increasing number of diagnostic tests for many diseases. However, the design of specific molecular assays relies on the availability and reliability of published genetic sequences for the target pathogens as well as enough knowledge on the genetic diversity of species and/or variants giving rise to the same disease symptoms. Usually designed for clinical isolates, molecular tests are often not suitable for environmental samples in which the target DNA is mixed with a mixture of environmental DNA. A key challenge of such molecular assays is thus to ensure high specificity of the target genetic markers when focusing on clinical and environmental samples in order to follow the dynamics of disease transmission and emergence in humans. Here we focus on the Buruli ulcer (BU), a human necrotizing skin disease mainly affecting tropical and subtropical areas, commonly admitted to be caused by Mycobacterium ulcerans worldwide although other mycolactone-producing mycobacteria and even mycobacterium species were found associated with BU or BU-like cases. By revisiting the literature, we show that many studies have used non-specific molecular markers (IS2404, IS2606, KR-B) to identify M. ulcerans from clinical and environmental samples and propose that all mycolactone-producing mycobacteria should be definitively considered as variants from the same group rather than different species. Importantly, we provide evidence that the diversity of mycolactone-producing mycobacteria variants as well as mycobacterium species potentially involved in BU or BU-like skin ulcerations might have been underestimated. We also suggest that the specific variants/species involved in each BU or BU-like case should be carefully identified during the diagnosis phase, either via the key to genetic identification proposed here or by broader metabarcoding approaches, in order to guide the medical community in the choice for the most appropriate antibiotic therapy

Variant calling pipeline designed for the Bioinformatics Learning Lab (BILL: release_2023.1)

Bioinformatics_Learning_la

Origins and insights into the historic Judean date palm based on genetic analysis of germinated ancient seeds and morphometric studies

Germination of 2000-year-old seeds of Phoenix dactylifera from Judean desert archaeological sites provides a unique opportunity to study the Judean date palm, described in antiquity for the quality, size, and medicinal properties of its fruit, but lost for centuries. Microsatellite genotyping of germinated seeds indicates that exchanges of genetic material occurred between the Middle East (eastern) and North Africa (western) date palm gene pools, with older seeds exhibiting a more eastern nuclear genome on a gradient from east to west of genetic contributions. Ancient seeds were significantly longer and wider than modern varieties, supporting historical records of the large size of the Judean date. These findings, in accord with the region’s location between east and west date palm gene pools, suggest that sophisticated agricultural practices may have contributed to the Judean date’s historical reputation. Given its exceptional storage potentialities, the date palm is a remarkable model for seed longevity research

Génotypage d’une collection tunisienne de palmier dattier par les marqueurs microsatellites

Introduction Les oasis tunisiennes sont caractérisées par une richesse génétique considérable comme en témoigne la présence d’au moins 250 cultivars répertoriés (Rhouma, 1994). Cependant, avec l’évolution économique et sociale du pays, les palmeraies de Djérid et de Nefzaoua sont réorganisées pour satisfaire une demande sans cesse croissante en dattes de qualité supérieure à l’instar du cultivar « élite » Deglet Nour. Cette réorganisation a fait que la phoéniciculture est passée d’un système ..

Molecular polymorphism and genetic relationships in date palm (Phoenix dactylifera L.): The utility of nuclear microsatellite markers

Due to the economic importance of the date palm in Tunisia, we attempt to develop microsatellite markers for the genetic characterisation and identification of cultivars. This characterisation will enable us to obtain an extensive understanding of the local genetic diversity and its distribution. Fourteen microsatellite loci of Phoenix dactylifera L. were tested to examine the genetic diversity in the Tunisian date palm germplasm: 74 female and 27 male cultivars were represented. A total of 136 alleles and 311 genotypes were detected based on 14 loci microsatellite. A high level of polymorphism was detected at the DNA level. The 101 date palms from three main oases exhibited a high degree of generic diversity and were structured independently of their geographical origin and sex. All the local date palm accessions were successfully fingerprinted and easily distinguished based on only five loci. The possibility of using microsatellites in the large-scale molecular labelling of offshoots and in vitro plantlets and in the certification of plant material is discussed

Contribution à l’étude transcriptomique de la maladie des feuilles cassantes chez le palmier dattier en Tunisie (Phoenix dactylifera L.)

Introduction Le palmier dattier (Phœnix dactylifera L.) est considéré comme étant l’arbre de vie dans les régions sahariennes des pays de l’Afrique du Nord et du Moyen-Orient. En effet, cette plante dioïque et pérenne, constitue l’axe principal de l’agro-système oasien. A ce sujet, le palmier dattier joue un important rôle socioéconomique en Tunisie. En outre, il constitue la base de la production agricole ainsi que la principale source financière et alimentaire des oasiens. Cependant, en dép..

Origins and insights into the historic Judean date palm based on genetic analysis of germinated ancient seeds and morphometric studies

Germination of 2000-year-old seeds of Phoenix dactylifera from Judean desert archaeological sites provides a unique opportunity to study the Judean date palm, described in antiquity for the quality, size, and medicinal properties of its fruit, but lost for centuries. Microsatellite genotyping of germinated seeds indicates that exchanges of genetic material occurred between the Middle East (eastern) and North Africa (western) date palm gene pools, with older seeds exhibiting a more eastern nuclear genome on a gradient from east to west of genetic contributions. Ancient seeds were significantly longer and wider than modern varieties, supporting historical records of the large size of the Judean date. These findings, in accord with the region's location between east and west date palm gene pools, suggest that sophisticated agricultural practices may have contributed to the Judean date's historical reputation. Given its exceptional storage potentialities, the date palm is a remarkable model for seed longevity research

The influence of native populations' genetic history on the reconstruction of invasion routes: the case of a highly invasive aquatic species

International audienceInsufficient data on the origins of the first introduced propagule and the initial stages of invasion complicate the reconstruction of a species' invasion history. Phylogeography of the native area profoundly shapes the genomic patterns of the propagules on which subsequent demographic processes of the invasion are based. Thus, a better understanding of this aspect helps to disentangle native and invasive histories. Here, we used genomic data together with clustering methods, explicit admixture tests combined with ABC models and Machine Learning algorithms, to compare patterns of genetic structure and gene flow of native and introduced populations, and infer the most likely invasion pathways of the highly invasive freshwater fish Pseudorasbora parva. This species is the vector of a novel lethal fungal-like pathogen (Sphaerothecum destruens) that is responsible for the decline of several fish species in Europe. We found that the current genetic structuring in the native range of P. parva has been shaped by waves of gene flow from populations in southern and northern China. Furthermore, our results strongly suggest that the genetic diversity of invasive populations results from recurrent global invasion pathways of admixed native populations. Our study also illustrates how the combination of admixture tests, ABC and Machine Learning can be used to detect high-resolution demographic signatures and reconstruct an integrative biological invasion history

Genetic diversity of Southeastern Nigerien date palms reveals a secondary structure within Western populations

International audienceDate palm (Phoenix dactylifera L.) is mainly cultivated for its edible fruit and is of great socio-economic importance for the populations of arid zones. Analysis of the date palm genetic diversity in the Old World had revealed a strong genetic structure with the existence of two gene pools, one Eastern comprising Asia and Djibouti, and one Western, consisting of North African accessions. So far, mainly date palm populations from countries within the Maghreb and the Middle East were characterized, but no information from the Sahel was included. Here, we present the genetic diversity of date palms from Southeastern Niger. The DNA of 113 date palm accessions were analyzed and compared with a database containing the genetic information of 248 accessions from the Old World. The diversity generated from microsatellite markers was compared to that of the same loci of both the Eastern and Western genetic pools. Our results show that date palms from Southeastern Niger constitute a unique group with a high level of genetic diversity. Moreover, even though this group is included in the Western genetic pool, it shows a specific originality which differentiates it from other Western populations. It also shows one of the lowest admixture levels of the Western pool. Global analysis showed a secondary genetic structure within the Western pool highlighting a new genetic group located in Southeastern Niger that distinguishes itself from the North African group