Utilisation de la PCR-RFLP sur de l'ADN chloro-plastique pour l'étude des relations phylogénétiques au sein du genre Phaseolus

Phylogenetic relationships among 74 accessions belonging to six species of Phaseolus are investigated using variation in chloroplast DNA assessed according to a PCR-RFLP protocol. Three fragments of chloroplast DNA are amplified using universal primers, and then digested with 10 restriction enzymes. Thirty-six haplotypes are identified on the basis of the polymorphism in fragment number and size. Three main phylogenetic groups, strongly supported through bootstrap analysis, are identified: (1) accessions from Phaseolus lunatus and Phaseolus xolocotzii; (2) accessions from Phaseolus glabellus; (3) accessions from Phaseolus vulgaris, Phaseolus polyanthus and Phaseolus coccineus. Within the third group, accessions of Phaseolus coccineus are scattered along the phylogenetic tree, which provides some evidence that coccineus accessions are paraphyletic with respect to Phaseolus vulgaris and Phaseolus polyanthus. An analysis of molecular variance applied on four species show that they are significantly differentiated with 79% of molecular variance among species and 21% within species. The results agree with previous investigations on chloroplast DNA variation in the genus Phaseolus, and suggest that PCRRFLP methods, which are technically less labour-intensive than previous methods, are of great value for phylogenetic investigations at the generic level

Whole‐genome sequencing and genome regions of special interest : lessons from major histocompatibility complex, sex determination, and plant self‐incompatibility

Whole-genome sequencing of non-model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. However, some genomic regions that are of high biological interest remain problematic for assembly and data-handling. Three such regions are the major histocompatibility complex (MHC), sex-determining regions (SDRs) and the plant self-incompatibility locus (S-locus). Using these as examples, we illustrate the challenges of both assembling and resequencing these highly polymorphic regions and how bioinformatic and technological developments are enabling new approaches to their study. Mapping short-read sequences against multiple alternative references improves genotyping comprehensiveness at the S-locus thereby contributing to more accurate assessments of allelic frequencies. Long-read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S-locus haplotypes. These advances are adding value to short-read genome resequencing approaches by allowing, for example, more accurate haplotype phasing across longer regions. Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches

Diversification dynamics of freshwater bivalves (Unionidae: Parreysiinae: Coelaturini) indicate historic hydrographic connections throughout the East African Rift System

Invertebrates are exceptionally diverse, but many are in decline because of anthropogenic changes to their habitat. This situation is particularly problematic for taxa that are not well monitored or taxonomically poorly understood, because the lack of knowledge hampers conservation. Despite their important functional role in freshwater ecosystems, African bivalves of the family Unionidae remain poorly studied compared to their highly threatened relatives in Europe, the U.S.A. and Canada. To resolve relationships and to study diversification dynamics in space and time, we performed time-calibrated phylogenetic studies and biogeographical modeling on the unionids from the East African Rift System and surroundings, including representatives of all currently recognized Afrotropical genera except for Brazzaea (and Unio from southern Africa). Our analyses indicate that all sampled Afrotropical unionids belong to the tribe Coelaturini (subfamily Parreysiinae), as does the genus Moncetia from Lake Tanganyika, which is currently attributed to the family Iridinidae. Colonization of Africa from Eurasia by Parreysiinae occurred ~17 Ma ago, and the subsequent diversification of Coelaturini in Africa continued at a steady pace, although net diversification decreased over time as more niches and ecoregions became occupied. Clades in Coelaturini largely reflect drainage basins, with the oldest lineages and highest regional diversity occurring in Lake Tanganyika, followed by the Congo Basin watershed in general. The species assemblage of Lake Tanganyika reflects multiple independent events of colonization and intralacustrine diversification since the Late Miocene or Early Pliocene. The clades of other regions, including that containing the species from Lake Malawi, are comparatively young. Biogeographical analyses indicate that the colonization history was mainly driven by cladogenesis in sympatry, whereas few anagenetic events contributed to the modern distribution of Coelaturini. Ancestral range estimations demonstrate that Coelaturini originated in the Victoria and/or Tanganyika ecoregions, and that the Congo Basin played an essential role in the colonization of Africa by Coelaturini.The attached document is the authors’ final accepted/submitted version of the journal article. You are advised to consult the publisher’s version if you wish to cite from it

Expression and trans-specific polymorphism of self-incompatibility RNases in Coffea (Rubiaceae)

Self-incompatibility (SI) is widespread in the angiosperms, but identifying the biochemical components of SI mechanisms has proven to be difficult in most lineages. Coffea (coffee; Rubiaceae) is a genus of old-world tropical understory trees in which the vast majority of diploid species utilize a mechanism of gametophytic self-incompatibility (GSI). The S-RNase GSI system was one of the first SI mechanisms to be biochemically characterized, and likely represents the ancestral Eudicot condition as evidenced by its functional characterization in both asterid (Solanaceae, Plantaginaceae) and rosid (Rosaceae) lineages. The S-RNase GSI mechanism employs the activity of class III RNase T2 proteins to terminate the growth of "self" pollen tubes. Here, we investigate the mechanism of Coffea GSI and specifically examine the potential for homology to S-RNase GSI by sequencing class III RNase T2 genes in populations of 14 African and Madagascan Coffea species and the closely related self-compatible species Psilanthus ebracteolatus. Phylogenetic analyses of these sequences aligned to a diverse sample of plant RNase T2 genes show that the Coffea genome contains at least three class III RNase T2 genes. Patterns of tissue-specific gene expression identify one of these RNase T2 genes as the putative Coffea S-RNase gene. We show that populations of SI Coffea are remarkably polymorphic for putative S-RNase alleles, and exhibit a persistent pattern of trans-specific polymorphism characteristic of all S-RNase genes previously isolated from GSI Eudicot lineages. We thus conclude that Coffea GSI is most likely homologous to the classic Eudicot S-RNase system, which was retained since the divergence of the Rubiaceae lineage from an ancient SI Eudicot ancestor, nearly 90 million years ago.United States National Science Foundation [0849186]; Society of Systematic Biologists; American Society of Plant Taxonomists; Duke University Graduate Schoolinfo:eu-repo/semantics/publishedVersio

Population Genetic Diversity and Structure of a Naturally Isolated Plant Species, Rhodiola dumulosa (Crassulaceae)

Aims: Rhodiola dumulosa (Crassulaceae) is a perennial diploid species found in high-montane areas. It is distributed in fragmented populations across northern, central and northwestern China. In this study, we aimed to (i) measure the genetic diversity of this species and that of its populations; (ii) describe the genetic structure of these populations across the entire distribution range in China; and (iii) evaluate the extent of gene flow among the naturally fragmented populations. Methods: Samples from 1089 individuals within 35 populations of R. dumulosa were collected, covering as much of the entire distribution range of this species within China as possible. Population genetic diversity and structure were analyzed using AFLP molecular markers. Gene flow among populations was estimated according to the level of population differentiation. Important Findings: The total genetic diversity of R. dumulosa was high but decreased with increasing altitude. Populationstructure analysis indicated that the most closely related populations were geographically restricted and occurred in close proximity to each other. A significant isolation-by-distance pattern, caused by the naturally fragmented population distribution, was observed. At least two distinct gene pools were found in the 35 sampled populations, one composed of populations in northern China and the other composed of populations in central and northwestern China. The calculation of Nei’s gene diversity index revealed that the genetic diversity in the northern China pool (0.1972) was lower than that in th

Mannose-Binding Lectin 2 Polymorphisms Do Not Influence Frequency or Type of Infection in Adults with Chemotherapy Induced Neutropaenia

BACKGROUND: Mannose-binding Lectin protein (MBL) has been suggested to be relevant in the defence against infections in immunosuppressed individuals. In a Swedish adult cohort immunosuppressed from both the underlying disease and from iatrogenic treatments for their underlying disease we investigated the role of MBL in susceptibility to infection. METHODS: In this cross sectional, prospective study, blood samples obtained from 96 neutropaenic febrile episodes, representing 82 individuals were analysed for single nucleotide polymorphism (SNP) in the MBL2 gene. Concurrent measurement of plasma MBL protein concentrations was also performed for observation of acute response during febrile episodes. FINDINGS: No association was observed between MBL2 genotype or plasma MBL concentrations, and the type or frequency of infection. Adding to the literature, we found no evidence that viral infections or co-infections with virus and bacteria would be predisposed by MBL deficiency. We further saw no correlation between MBL2 genotype and the risk of fever. However, fever duration in febrile neutropaenic episodes was negatively associated with MBL2 SNP mutations (p<0.05). Patients with MBL2 SNP mutations presented a median febrile duration of 1.8 days compared with 3 days amongst patients with wildtype MBL2 genotype. INTERPRETATION: We found no clear association between infection, or infection type to MBL2 genotypes or plasma MBL concentration, and add to the reports casting doubts on the benefit of recombinant MBL replacement therapy use during iatrogenic neutropaenia

Homoplasy corrected estimation of genetic similarity from AFLP bands, and the effect of the number of bands on the precision of estimation

AFLP is a DNA fingerprinting technique, resulting in binary band presence–absence patterns, called profiles, with known or unknown band positions. We model AFLP as a sampling procedure of fragments, with lengths sampled from a distribution. Bands represent fragments of specific lengths. We focus on estimation of pairwise genetic similarity, defined as average fraction of common fragments, by AFLP. Usual estimators are Dice (D) or Jaccard coefficients. D overestimates genetic similarity, since identical bands in profile pairs may correspond to different fragments (homoplasy). Another complicating factor is the occurrence of different fragments of equal length within a profile, appearing as a single band, which we call collision. The bias of D increases with larger numbers of bands, and lower genetic similarity. We propose two homoplasy- and collision-corrected estimators of genetic similarity. The first is a modification of D, replacing band counts by estimated fragment counts. The second is a maximum likelihood estimator, only applicable if band positions are available. Properties of the estimators are studied by simulation. Standard errors and confidence intervals for the first are obtained by bootstrapping, and for the second by likelihood theory. The estimators are nearly unbiased, and have for most practical cases smaller standard error than D. The likelihood-based estimator generally gives the highest precision. The relationship between fragment counts and precision is studied using simulation. The usual range of band counts (50–100) appears nearly optimal. The methodology is illustrated using data from a phylogenetic study on lettuce

Unexpected Fine-Scale Population Structure in a Broadcast-Spawning Antarctic Marine Mollusc

Several recent empirical studies have challenged the prevailing dogma that broadcast-spawning species exhibit little or no population genetic structure by documenting genetic discontinuities associated with large-scale oceanographic features. However, relatively few studies have explored patterns of genetic differentiation over fine spatial scales. Consequently, we used a hierarchical sampling design to investigate the basis of a weak but significant genetic difference previously reported between Antarctic limpets (Nacella concinna) sampled from Adelaide and Galindez Islands near the base of the Antarctic Peninsula. Three sites within Ryder Bay, Adelaide Island (Rothera Point, Leonie and Anchorage Islands) were each sub-sampled three times, yielding a total of 405 samples that were genotyped at 155 informative Amplified Fragment Length Polymorphisms (AFLPs). Contrary to our initial expectations, limpets from Anchorage Island were found to be subtly, but significantly distinct from those sampled from the other sites. This suggests that local processes may play an important role in generating fine-scale population structure even in species with excellent dispersal capabilities, and highlights the importance of sampling at multiple spatial scales in population genetic surveys

On the Evolutionary Modification of Self-Incompatibility: Implications of Partial Clonality for Allelic Diversity and Genealogical Structure

Experimental investigations of homomorphic self-incompatibility (SI) have revealed an unanticipated level of complexity in its expression, permitting fine regulation over the course of a lifetime or a range of environmental conditions. Many flowering plants express some level of clonal reproduction, and phylogenetic analyses suggest that clonality evolves in a correlated fashion with SI in Solanum (Solanaceae). Here, we use a diffusion approximation to explore the effects on the evolutionary dynamics of SI of vegetative propagation with SI restricted to reproduction through seed. While clonality reduces the strength of frequency-dependent selection maintaining S-allele diversity, much of the great depth typical of S-allele genealogies is preserved. Our results suggest that clonality can play an important role in the evolution of SI systems, and may afford insight into unexplained features of allele genealogies in the Solanaceae

Genetic Diversity and Ecological Niche Modelling of Wild Barley:Refugia, Large-Scale Post-LGM Range Expansion and Limited Mid-Future Climate Threats?

Describing genetic diversity in wild barley (Hordeum vulgare ssp. spontaneum) in geographic and environmental space in the context of current, past and potential future climates is important for conservation and for breeding the domesticated crop (Hordeum vulgare ssp. vulgare). Spatial genetic diversity in wild barley was revealed by both nuclear- (2,505 SNP, 24 nSSR) and chloroplast-derived (5 cpSSR) markers in 256 widely-sampled geo-referenced accessions. Results were compared with MaxEnt-modelled geographic distributions under current, past (Last Glacial Maximum, LGM) and mid-term future (anthropogenic scenario A2, the 2080s) climates. Comparisons suggest large-scale post-LGM range expansion in Central Asia and relatively small, but statistically significant, reductions in range-wide genetic diversity under future climate. Our analyses support the utility of ecological niche modelling for locating genetic diversity hotspots and determine priority geographic areas for wild barley conservation under anthropogenic climate change. Similar research on other cereal crop progenitors could play an important role in tailoring conservation and crop improvement strategies to support future human food security