Genetic Diversity In Space Research Articles

Deep genetic substructure within bonobos.

Establishing the genetic and geographic structure of populations is fundamental, both to understand their evolutionary past and preserve their future. Nevertheless, the patterns of genetic population structure are unknown for most endangered species. This is the case for bonobos (Pan paniscus), which, together with chimpanzees (Pan troglodytes), are humans' closest living relatives. Chimpanzees live across equatorial Africa and are classified into four subspecies,1 with some genetic population substructure even within subspecies. Conversely, bonobos live exclusively in the Democratic Republic of Congo and are considered a homogeneous group with low genetic diversity,2 despite some population structure inferred from mtDNA. Nevertheless, mtDNA aside, their genetic structure remains unknown, hampering our understanding of the species and conservation efforts. Mapping bonobo genetic diversity in space is, however, challenging because, being endangered, only non-invasive sampling is possible for wild individuals. Here, we jointly analyze the exomes and mtDNA from 20 wild-born bonobos, the whole genomes of 10 captive bonobos, and the mtDNA of 136 wild individuals. We identify three genetically distinct bonobo groups of inferred Central, Western, and Far-Western geographic origin within the bonobo range. We estimate the split time between the central and western populations to be ∼145,000 years ago and genetic differentiation to be in the order of that of the closest chimpanzee subspecies. Furthermore, our estimated long-term Ne for Far-West (∼3,000) is among the lowest estimated for any great ape lineage. Our results highlight the need to attend to the bonobo substructure, both in terms of research and conservation.

A validated protocol for eDNA-based monitoring of within-species genetic diversity in a pond-breeding amphibian

In light of the dramatic decline in amphibian biodiversity, new cost-efficient tools to rapidly monitor species abundance and population genetic diversity in space and time are urgently needed. It has been amply demonstrated that the use of environmental DNA (eDNA) for single-species detection and characterization of community composition can increase the precision of amphibian monitoring compared to traditional (observational) approaches. However, it has been suggested that the efficiency and accuracy of the eDNA approach could be further improved by more timely sampling; in addition, the quality of genetic diversity data derived from the same DNA has been confirmed in other vertebrate taxa, but not amphibians. Given the availability of previous tissue-based genetic data, here we use the common frog Rana temporaria Linnaeus, 1758 as our target species and an improved eDNA protocol to: (i) investigate differences in species detection between three developmental stages in various freshwater environments; and (ii) study the diversity of mitochondrial DNA (mtDNA) haplotypes detected in eDNA (water) samples, by amplifying a specific fragment of the COI gene (331 base pairs, bp) commonly used as a barcode. Our protocol proved to be a reliable tool for monitoring population genetic diversity of this species, and could be a valuable addition to amphibian conservation and wetland management.

The effects of drift and selection on latitudinal genetic variation in Scandinavian common toads (Bufo bufo) following postglacial recolonisation

Clinal variation is paramount for understanding the factors shaping genetic diversity in space and time. During the last glacial maximum, northern Europe was covered by glacial ice that rendered the region uninhabitable for most taxa. Different evolutionary processes during and after the recolonisation of this area from different glacial refugia have affected the genetic landscape of the present day European flora and fauna. In this study, we focus on the common toad (Bufo bufo) in Sweden and present evidence suggesting that these processes have resulted in two separate lineages of common toad, which colonised Sweden from two directions. Using ddRAD sequencing data for demographic modelling, structure analyses, and analysis of molecular variance (AMOVA), we provide evidence of a contact zone located between Uppland and Västerbotten in central Sweden. Genetic diversity was significantly higher in southern Sweden compared to the north, in accordance with a pattern of decreased genetic diversity with increasing distance from glacial refugia. Candidate genes under putative selection are identified through outlier detection and gene–environment association methods. We provide evidence of divergent selection related to stress response and developmental processes in these candidate genes. The colonisation of Sweden by two separate lineages may have implications for how future conservation efforts should be directed by identifying management units and putative local adaptations.

Abstract IA35: Follicular lymphoma dynamics through single-cell analysis

Abstract Follicular lymphoma (FL) is the second most common non-Hodgkin lymphoma in the Western world, generally characterized by a disseminated disease at diagnosis, an indolent clinical course, and recurrent, increasingly chemoresistant relapses. Overt FL is preceded by an insidious phase of asymptomatic growth and might emerge from common precursor clones, evolving over decades, and which might participate in subsequent relapses. Consequently, the cell of origin remains ambiguous. Although FL results from the malignant transformation of germinal center B cells, FL precursors emerge much earlier in B-cell ontogeny with the hallmark t(14;18) translocation and ensuing constitutive expression of BCL2 in bone marrow pre-B cells. While t(14;18) is considered the necessary early first hit to transformation, BCL2 as such is a very weak driver, as evidenced by the detection of t(14;18) in peripheral blood from a large fraction of the adult healthy population and the long latency and low penetrance observed in various BCL2 mouse models. Recent data of clonal dynamics in human and mouse models strongly suggest that additional illegitimate events likely accumulate over iterative GC passages, generating a highly mutagenic dynamics linked with slow oncogenic progression. Combined with the power of next-generation sequencing, molecular interrogations of t(14;18)+ clones in healthy individuals and FL patients recently provided the extent of FL genetic diversity in space (distinct tissues) and time (diagnosis vs. relapse). Thus, the path to transformation appears as a complex multi-hit process occurring along B-cell ontogeny, escalating along successive derailments of B-cell receptor diversification mechanisms, and subversion of specific immunologic properties of B cells. This protracted clonal evolution generates a massive accumulation of subclones and an associated complex overall genetic heterogeneity. This raises several questions. While FL originate from germinal center B cells, it is unclear to what extent overt lymphoma B cells retain GC B-cell functional dynamics or are blocked in a particular stage of the GC reaction. Furthermore, although one might intuitively assume that distinct subclones likely have a different gene expression profile associated to specific functions (and potentially driving distinct capacity to respond to therapy), it is still unclear to which extent subclonal genetic heterogeneity imprints functional heterogeneity. Because subclonal heterogeneity is hidden in bulk, where all distinct subclones are mixed and averaged, we recently used integrative single-cell analysis of phenotype, gene expression, and IGH sequence to track the characteristic human GC B-cell program in FL B cells. We used pseudo-time approaches to model the cyclic continuum of GC B-cell transitional states and identified characteristic patterns of synchronously expressed gene clusters in GC B cells. Strikingly this GC-specific gene expression synchrony was lost in single lymphoma B cells. Yet, distinct and conserved FL-specific cell states co-existed within single patient biopsies. Our data show that lymphoma B cells are not blocked in a GC B-cell state but may adopt new dynamic modes of functional diversity, opening novel definitions of lymphoma identity. Citation Format: Bertrand Nadel. Follicular lymphoma dynamics through single-cell analysis [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr IA35.

Secondary contact, hybridization and polyploidization add to the biodiversity in the Hengduan Mountains, exemplified by the widespread Corallodiscus lanuginosus (Gesneriaceae)

Corallodiscus lanuginosus is distributed 12,000 km across its northeast–southwest boundaries, showing its highest morphological diversity in the Hengduan Mountains, Southwest China. We investigated the mechanisms behind the high diversity in this species. We acquired ITS sequence data across the distribution range of the genus, reconstructed dated phylogenies, projected the resulting clades onto geographic maps and linked the results with inferred ploidy levels of the populations. We found strong geographic patterns for the ITS clades but with extensively overlapping ranges, particularly in the Hengduan Mountains area. We deduced an origin of C. lanuginosus in the mid-Oligocene. We used the presence of ITS polymorphisms to infer a high level of hybridization events mainly in areas of clade overlap, where we also inferred repeated tetraploidization events to have taken place. Pre- and post-Quaternary climate oscillation-driven expansions and contractions of distribution ranges have allowed secondary contacts, hybridization and introgression that shaped the current patchy distribution of morphological diversity in the species. Polyploidization as a reinforcing genetic barrier added to the genetic diversity in space and time particularly in the Hengduan Mountains.

Understanding crop genetic diversity under modern plant breeding.

Key messageMaximizing crop yield while at the same time minimizing crop failure for sustainable agriculture requires a better understanding of the impacts of plant breeding on crop genetic diversity. This review identifies knowledge gaps and shows the need for more research into genetic diversity changes under plant breeding.Modern plant breeding has made a profound impact on food production and will continue to play a vital role in world food security. For sustainable agriculture, a compromise should be sought between maximizing crop yield under changing climate and minimizing crop failure under unfavorable conditions. Such a compromise requires better understanding of the impacts of plant breeding on crop genetic diversity. Efforts have been made over the last three decades to assess crop genetic diversity using molecular marker technologies. However, these assessments have revealed some temporal diversity patterns that are largely inconsistent with our perception that modern plant breeding reduces crop genetic diversity. An attempt was made in this review to explain such discrepancies by examining empirical assessments of crop genetic diversity and theoretical investigations of genetic diversity changes over time under artificial selection. It was found that many crop genetic diversity assessments were not designed to assess diversity impacts from specific plant breeding programs, while others were experimentally inadequate and contained technical biases from the sampling of cultivars and genomes. Little attention has been paid to theoretical investigations on crop genetic diversity changes from plant breeding. A computer simulation of five simplified breeding schemes showed the substantial effects of plant breeding on the retention of heterozygosity over generations. It is clear that more efforts are needed to investigate crop genetic diversity in space and time under plant breeding to achieve sustainable crop production.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-015-2585-y) contains supplementary material, which is available to authorized users.

Population structure of the invasive forest pathogen Hymenoscyphus pseudoalbidus.

Understanding the genetic diversity and structure of invasive pathogens in source and in introduced areas is crucial to the revelation of hidden biological features of an organism, to the reconstruction of the course of invasions and to the establishment of effective control measures. Hymenoscyphus pseudoalbidus (anamorph: Chalara fraxinea) is an invasive and highly destructive fungal pathogen found on common ash Fraxinus excelsior in Europe and is native to East Asia. To gain insights into its dispersal mechanisms and history of invasion, we used microsatellite markers and characterized the genetic structure and diversity of H. pseudoalbidus populations at three spatial levels: (i) between Europe and Japan, (ii) in Europe and (iii) at the epidemic's front in Switzerland. Phylogenetic and network analysis demonstrated that individuals from both regions are conspecific. However, populations from Japan harboured a higher genetic diversity and were genetically differentiated from European ones. No evident population structure was found among the 1208 European strains using Bayesian and multivariate clustering analysis. Only the distribution of genetic diversity in space, pairwise population differentiation (GST) and the spatial analysis of principal components revealed a faint geographical pattern around Europe. A significant allele deficiency in most European populations pointed to a recent genetic bottleneck, whereas no pattern of isolation by distance was found. Our data suggest that H. pseudoalbidus was introduced just once by at least two individuals. The potential source region of H. pseudoalbidus is vast, and further investigations are required for a more accurate localization of the source population.

Inter-specific relationships and hierarchical spatial genetic structuring in Nervilia nipponica, an endangered orchid in Japan

An understanding of the extent to which reproductive strategy and seed dispersal lead to the structuring of genetic diversity in space is required when planning measures towards the conservation of endangered plant species. In this study, genetic structure in the endangered terrestrial orchid Nervilia nipponica was investigated using amplified fragment length polymorphisms following extensive sampling throughout the species' range in Japan and intensive sampling at a single population. Limited diversity was found within the species as a whole, but significant structuring was detected between populations. One genotype was common to two widely separated sites, possibly indicative of long-range dispersal. Significant structure was also detected at the intensively sampled site, as a result of the presence of two distinct putative clones. These findings are consistent with observations of the species' ability to set seed autogamously and propagate vegetatively. Given the strong colonising capability inferred for the species, attention should focus on identifying and securing habitat conditions conducive to seed germination and seedling establishment in the development of a conservation strategy. As presently circumscribed, N. nipponica is shown to comprise two polyphyletic taxa, both endemic to Japan, and both distinct from N. taiwaniana, a species that some authors have considered conspecific.

Assessment of genetic diversity in space by superimposition of a distorted geographic map with a spatial population clustering. Application to GM haplotypes of native Amerindian tribes.

The GM immunoglobulin (Ig) allotype distributions of 49 native Amerindian populations from North to South America were analysed by a new technique called 'Mobile Sites Method' (MSM). This allows the global interpretation of genetic diversity in space by means of a distorted geographic map called a 'genetic similarity map'. This approach has been improved by superimposing in the distorted geographic map both the haplotype set (represented by hypothetical populations having a 100% frequency of the haplotype considered) and the 'geography-genetics discontinuities' (i.e. the zones between homogeneous population clusters). This bidimensional representation completes the interpretation of the genetic distances between populations in terms of local genetic diversity and possible migrations. Our results concerning the spatial distribution of the Amerindian populations show: (i) a great interdependence of the geographic locations and the GM haplotype distributions (the importance of the geographic factor was checked with the usual technique of 'random sampling' and the percentage of explained distance variability decreases from 78% with the observed data to a level less than 67% with the random data); (ii) a parallelism between genetics and linguistics groups as indicated by the population clusters in the similarity map, and (iii) a complex distorted map revealing the presence of multiple population migrations and admixtures in the course of time. A particular distortion of South America suggests possible migrations by sea along the western and eastern coasts of Central America, or multiple migration waves without population admixture across Central America.

Assessment of genetic diversity in space by superimposition of a distorted geographic map with a spatial population clustering. Application to GM haplotypes of native Amerindian tribes

Assessment of genetic diversity in space by superimposition of a distorted geographic map with a spatial population clustering. Application to GM haplotypes of native Amerindian tribes

A new approach for interpreting the genetic diversity in space: ‘Mobile Site Method’. Application to Gm haplotype distribution of twenty‐seven Amerindian tribes from North and Central America

We present a new approach, called 'Mobile Site Method' (MSM), to the construction of 'genetic similarity maps' more efficient than that described in a preceding paper (Hazout et al. 1991). After building a triangular mesh between the geographical sites, the method consists of moving these locations at each iteration to reduce the overall differences between the geographic and genetic distances. The genetic similarity map, i.e. the final distorted map, allows the interpretation of the genetic diversity of a population set. We have applied this method to the study of Gm immunoglobulin allotypes of twenty-seven Amerindian groups from North and Central America. By a local weighted linear regression, we have reconstituted the distorted contour of America. This representation completes the observations of the sites during the map distortion. In this study, we have defined a large geographical factor in the genetic data (84% of the variability explained), related to a linguistic factor.

Enzyme polymorphism, morphometric variation and population structure in a restricted endemic, Silene diclinis (Caryophyllaceae)

Silene diclinis is a dioecious perennial herb, restricted to a small area of the SE Spanish province of Valencia. Polyacrylamide gel electrophoresis and morphometric analysis were carried out on cultivated material derived from seed collected from the main population of S. diclinis at Játiva. Only two out of 26 inferred enzyme loci showed substantial variation. There was some indication of population subdivision in both. The esterase locus also showed homozygote excess within the population as a whole and within one subpopulation. Morphological characters showed significant differentiation between subpopulations. Low allozyme variability characterizes populations of most endemic species that have been investigated. Isolation and historical events may have been as important as population size or edaphic specialization in causing this low variability. But S. diclinis resembles other outbreeding plants in showing population structure and homozygote excess, suggesting restricted within-population gene flow. Mechanisms that may restrict gene flow in S. diclinis include environmentally-induced differences in flowering time, poor seed dispersal and possibly short pollinator foraging distances. Morphological variability and the incidence of developmental abnormalities are speculatively linked with homozygosity. Storage of genetic diversity in space can occur in restricted as well as widespread species and sampling for gene banking should then be spatially representative. Silene diclinis is threatened by continued habitat loss and consequent genetic erosion; its long-term future may depend on the gene bank and the botanic garden.