Genetic Founder Effects Research Articles

Fragile X syndrome in the largest world clustering. I. Genetic epidemiology and founder effect outline.

The FMR1 5' regulation gene region harbors a CGG trinucleotide repeat expansion (CGG-TRE) that causes Fragile X syndrome (FXS) when it expands to more than 200 repetitions. Ricaurte is a small village in southwestern Colombia, with an FXS prevalence of 1 in 38 men and 1 in 100 women (~100 times higher than the worldwide reported prevalence), defining Ricaurte as the largest FXS cluster in the world. In the present study, using next-generation sequencing of whole exome capture, we genotype 55 individuals from Ricaurte (49 with either full mutation or with premutation), four individuals from neighboring villages (with either the full mutation or with the premutation), and one unaffected woman, native of Ricaurte, who did not belong to any of the affected families. With advanced clustering and haplotype reconstruction, we modeled a common haplotype of 33 SNPs spanning 83,567,899 bp and harboring the FMR1 gene. This reconstructed haplotype was found in all the men from Ricaurte who carried the expansion, demonstrating that the genetic conglomerate of FXS in this population is due to a founder effect. The definition of this founder effect and its population outlining will allow a better prediction, follow-up, precise and personalized characterization of epidemiological parameters, better knowledge of the disease's natural history, and confident improvement of the clinical attention, life quality, and health interventions for this community.

HOW THE PAST SHAPES CURRENT STORIES: (EPI)GENETIC EPIDEMIOLOGICAL PROFILES OF METABOLIC SYNDROME IN BRAZILIAN MENNONITES

Mennonites present cc. 500 years genetic isolation and three bottleneck events that reducedtheir genetic diversity. In order to identify (epi)genetic markers for metabolic syndrome (MS),we used a modified version of the Brazilian National Health Survey to interview 762Mennonites from three settlements, between 2016-2023. We compared 63 vs. 127 exomes(Illumina HiSeq) from Mennonites with/without metabolic syndrome (MS) and genotypedcandidate variants in regulatory regions with mass spectrometry (iPLEX) and sequence-specific amplification (PCR-SSP). We also evaluated DNA methylation of the NR3C1 andFKBP5 genes in peripheral blood mononuclear cells (PBMCs) of up to 66 and 141 individualswith/without MS. MS prevalence was 14.02%, less than half the one reported forNeobrazilians (34.8%, P<0.00001), being paralleled by a three times lower prevalence ofacute myocardial infarction (AMI). Among independent MS risk factors, we found lowermaternal warmth in infancy (OR=1.59, P=0.019) and a higher susceptibility to AMI with theharshest migratory route to Brazil (OR=1.57, P=0.001). Thirty-nine variants of 34 genes wereassociated with MS (p<0.02), 41% create/disrupt CpG sites and 12 were associated withvisceral adipose and/or cardiovascular tissue expression. There were no methylationdifferences between individuals with and without MS in PBMCs with the NR3C1 and FKBP5genes, pointing to other epigenetic causal effects. In conclusion, Mennonites have a peculiarepidemiological profile marked by (epi)genetic founder effects that also affect theirmetabolism, calling for urgent action for prevention and to alleviate the burden ofcomorbidities due to late diagnosis.

Invasion potential of hornets (Hymenoptera: Vespidae: Vespa spp.).

Hornets are large, predatory wasps that have the potential to alter biotic communities and harm honey bee colonies once established in non-native locations. Mated, diapausing females (gynes) can easily be transported to new habitats, where their behavioral flexibility allows them to found colonies using local food and nest materials. Of the 22 species in the genus Vespa, five species are now naturalized far from their endemic populations and another four have been detected either in nature or during inspections at borders of other countries. By far the most likely pathway of long-distance dispersal is the transport of gynes in transoceanic shipments of goods. Thereafter, natural dispersal of gynes in spring and accidental local transport by humans cause shorter-range expansions and contribute to the invasion process. Propagule pressure of hornets is unquantified, although it is likely low but unrelenting. The success of introduced populations is limited by low propagule size and the consequences of genetic founder effects, including the extinction vortex linked to single-locus, complementary sex determination of most hymenopterans. Invasion success is enhanced by climatic similarity between source locality and introduction site, as well as genetic diversity conferred by polyandry in some species. These and other factors that may have influenced the successful establishment of invasive populations of V. velutina, V. tropica, V. bicolor, V. orientalis, and V. crabro are discussed. The highly publicized detections of V. mandarinia in North America and research into its status provide a real-time example of an unfolding hornet invasion.

Identification of TARDBP Gly298Ser as a founder mutation for amyotrophic lateral sclerosis in Southern China

BackgroundAmyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterized by predominant impairment of upper and lower motor neurons. Over 50 TARDBP mutations have been reported in both familial (FALS) and sporadic ALS (SALS). Some mutations in TARDBP, e.g. A382T and G294V, have genetic founder effects in certain geographic regions. However, such prevalence and founder effect have not been reported in Chinese.MethodsWhole-exome sequencing (WES) was performed in 16 Chinese FALS patients, followed by Sanger sequencing for the TARDBP p.Gly298Ser mutation (G298S) in 798 SALS patients and 1,325 controls. Haplotype analysis using microsatellites flanking TARDBP was conducted in the G298S-carrying patients and noncarriers. The geographic distribution and phenotypic correlation of the TARDBP mutations reported worldwide were reviewed.ResultsWES detected the TARDBP G298S mutation in 8 FALS patients, and Sanger sequencing found additional 8 SALS cases, but no controls, carrying this mutation. All the 16 cases came from Southern China, and 7 of these patients shared the 117-286-257-145-246-270 allele for the D1S2736-D1S1151-D1S2667-D1S489-D1S434-D1S2697 markers, which was not found in the 92 non-carrier patients (0/92) (p < 0.0001) and 65 age-matched and neurologically normal individuals (0/65) (p < 0.0001). The A382T and G298S mutations were prevalent in Europeans and Eastern Asians, respectively. Additionally, carriers for the M337V mutation are dominated by bulbar onset with a long survival, whereas those for G298S are dominated by limb onset with a short survival.ConclusionsSome prevalent TARDBP mutations are distributed in a geographic pattern and related to clinical profiles. TARDBP G298S mutation is a founder mutation in the Southern Chinese ALS population.

Genetic spectrum and founder effect of non-dystrophic myotonia: a Japanese case series study.

Non-dystrophic myotonias (NDM) are rare skeletal muscle channelopathies, mainly linked to two voltage-gated ion channel genes, CLCN1 and SCN4A. The aim of this study is to identify the clinical and genetic features of patients with NDM in Japan. We collected a Japanese nationwide case series of patients with clinical diagnosis of NDM (1999-2021). Among 71 out of 88 pedigrees, using Sanger and next-generation sequencing targeting both CLCN1 and SCN4A genes, variants classified as pathogenic/likely pathogenic/unknown significance were detected from CLCN1 (31 probands), SCN4A (36 probands), or both genes (4 probands), and 11 of them were novel. Pedigrees carrying mono-allelic CLCN1 variants were more commonly seen than that with bi-allelic/double variants (24:7). Compared to patients with CLCN1 variants, patients harboring SCN4A variants showed younger onset age (5.64 ± 4.70years vs. 9.23 ± 5.21years), fewer warm-up phenomenon, but more paramyotonia, hyperCKemia, transient muscle weakness, and cold-induced myotonia. Haplotype analysis verified founder effects of the hot spot variants in both CLCN1 (p.T539A) and SCN4A (p.T1313M). This study reveals variants in CLCN1 and SCN4A from 80.7% of our case series, extending genetic spectrum of NDM, and would further our understanding of clinical similarity/diversity between CLCN1- and SCN4A-related NDM, as well as the genetic racial differences.

Mutation Analysis of The Phenylalanine Hydroxylase Gene in Phenylketonuria Patients from Different Regions of Azerbaijan

The present study aimed to determine frequencies of mutations in the phenylalanine hydroxylase gene (PAH) in 30 patients diagnosed with phenylketonuria, from 633 person who presented to Scientific Research Pediatric Institute of the Ministry of Health of Azerbaijan and hospitals of different regions of Azerbaijan over the period from 2016 to 2020. More than 600 mutations in the PAH gene in exons 6, 7, 8, 11 and 12 have been detected in various countries around the world. Among them, 18 different mutations were found in Azerbaijani patients (V245V, R261Q, Q232Q, V245V, P281L, R241C, L385L, V399V, E280K, R261X, A434D, R176X, Ex6-96A&gt; G, R241C, R243Q, R256Q). The R261Q mutation in exon 7 was observed in seven patients from 30 patients. In this study, we identified mutations in the PAH gene and to evaluate the genetic heterogeneity of PKU disease in 30 Azerbaijanian patients who had been referred to Lankaran, Masalli (Southern region of Azerbaijan), Qabala, Oguz, Zagatala, Balakan (North-western region of Azerbaijan), Guba, Gusar, Khachmaz and Khudat (Northern region of Azerbaijan) regions. From this experiment, 7 of 30 PKU patients had the same mutation. Our analysis of the R261Q mutations was nearly similar to that observed in Southern region of Azerbaijan. The R261Q mutation in exon 7 with a relative frequency of 23.3 % is G → A substitution leads to conservation of arginine amino acid to glutamine amino acid at codon 782 of PAH. The another major mutation in our study was R241C (10%), which is similar to the data obtained in population of Northern region of Azerbaijan, R243Q (6.6%) and R252Q (6.6%). Studies have shown that this mutation is most common in the Azerbaijani population. Genetic drift and founder effect may have also played a role in the mutation spectrum we observed. The data obtained in our study can also be used in the development of genetic tests for phenylketonuria. Phenylketonuria (PKU) is an autosomal recessive genetic disease, caused by the phenylalanine hydroxylase (PAH) deficiency in the metabolic pathway, which prevents phenylalanine from being converted into tyrosine, leading to a large amount of phenylalanine discharged from the urine. Therefore, it is necessary to establish a simple, fast, accurate and reliable PKU molecular diagnostic method for clinical diagnosis.

Population Structure of the South West Indian Ocean Islands: Implications for Precision Medicine.

Precision medicine has brought new hopes for patients around the world with the applications of novel technologies for understanding genetics of complex diseases and their translation into clinical services. Such applications however require a foundation of skills, knowledge and infrastructure to translate genetics for health care. The crucial element is no doubt the availability of genomics data for the target populations, which is seriously lacking for most parts of Africa. We discuss here why it is vital to prioritize genomics data for the South West Indian Ocean region where a mosaic of ethnicities co-exist. The islands of the SWIO, which comprise Madagascar, La Reunion, Mauritius, Seychelles and Comoros, have been the scene for major explorations and trade since the 17th century being on the route to Asia. This part of the world has lived through active passage of slaves from East Africa to Arabia and further. Today’s demography of the islands is a diverse mix of ancestries including European, African and Asian. The extent of admixtures has yet to be resolved. Except for a few studies in Madagascar, there is very little published data on human genetics for these countries. Isolation and small population sizes have likely resulted in reduced genetic variation and possible founder effects. There is a significant prevalence of diabetes, particularly in individuals of Indian descent, while breast and prostate cancers are on the rise. The island of La Reunion is a French overseas territory with a high standard of health care and close ties to Mauritius. Its demography is comparable to that of Mauritius but with a predominantly mixed population and a smaller proportion of people of Indian descent. On the other hand, Madagascar’s African descendants inhabit mostly the lower coastal zones of the West and South regions, while the upper highlands are occupied by peoples of mixed African-Indonesian ancestries. Historical records confirm the Austronesian contribution to the Madagascar genomes. With the rapid progress in genomic medicine, there is a growing demand for sequencing services in the clinical settings to explore the incidence of variants in candidate disease genes and other markers. Genome sequence data has become a priority in order to understand the population sub-structures and to identify specific pathogenic variants among the different groups of inhabitants on the islands. Genomic data is increasingly being used to advise families at risk and propose diagnostic screening measures to enhance the success of therapies. This paper discusses the complexity of the islands’ populations and argues for the needs for genotyping and understanding the genetic factors associated with disease risks. The benefits to patients and improvement in health services through a concerted regional effort are depicted. Some private patients are having recourse to external facilities for molecular profiling with no return of data for research. Evidence of disease variants through sequencing represents a valuable source of medical data that can guide policy decisions at the national level. There are presently no such records for future implementation of strategies for genomic medicine.

Migrations of cancer cells through the lens of phylogenetic biogeography

Malignant cells leave their initial tumor of growth and disperse to other tissues to form metastases. Dispersals also occur in nature when individuals in a population migrate from their area of origin to colonize other habitats. In cancer, phylogenetic biogeography is concerned with the source and trajectory of cell movements. We examine the suitability of primary features of organismal biogeography, including genetic diversification, dispersal, extinction, vicariance, and founder effects, to describe and reconstruct clone migration events among tumors. We used computer-simulated data to compare fits of seven biogeographic models and evaluate models’ performance in clone migration reconstruction. Models considering founder effects and dispersals were often better fit for the clone phylogenetic patterns, especially for polyclonal seeding and reseeding of metastases. However, simpler biogeographic models produced more accurate estimates of cell migration histories. Analyses of empirical datasets of basal-like breast cancer had model fits consistent with the patterns seen in the analysis of computer-simulated datasets. Our analyses reveal the powers and pitfalls of biogeographic models for modeling and inferring clone migration histories using tumor genome variation data. We conclude that the principles of molecular evolution and organismal biogeography are useful in these endeavors but that the available models and methods need to be applied judiciously.

Associations between population epigenetic differentiation and environmental factors in the exotic weed mile-a-minute (Mikania micrantha)

AbstractInvasive species face new selective pressures and low genetic variation caused by genetic bottlenecks and founder effects when they are introduced into novel environments. Epigenetic variation may help them to cope with these problems. Mile-a-minute (Mikania micranthaKunth) is a highly invasive exotic weed that has seriously damaged biodiversity and agricultural ecosystems. We first adopted methylation-sensitive amplified polymorphism (MSAP) markers to investigate epigenetic variation of 21M. micranthapopulations in southern China, and further explored the effects of environmental factors on population epigenetic differentiation by correlating epigenetic and climate and soil data. Adaptive epiloci positively correlated with climate/soil variables were identified. Minimum temperature of the coldest month and mean temperature of the coldest quarter were considered as decisive factors for its distribution. Climate is presumed to play a relatively more important role than soil in shaping the adaptive epigenetic differentiation inM. micrantha. Under ongoing global warming, populations ofM. micranthaare predicted to expand northward. In addition, the weed also presented higher epigenetic variation compared with genetic variation. Leaf shape variation was detected related to methylation-state change at the population level.

Genetic diversity in seedling populations of Dipterocarpus gracilis in Kecubung Ulolanang Nature Conservation Reserve, Indonesia

Abstract. Romadini NP, Indrioko S, Widiyatno, Faridah E, Ratnaningrum YWN. 2021. Genetic diversity in seedling populations of Dipterocarpus gracilis in Kecubung Ulolanang Nature Conservation Reserve, Indonesia. Biodiversitas 22: 1138-1145. Dipterocarpus gracilis Blume is one of the native Dipterocarpus species in Java Island, Indonesia. It has commercial value as timber (wood) and non-timber forest products (oleoresin). This species has been considered vulnerable following the Red List of Threatened Species criteria by The International Union for Conservation of Nature (IUCN). We aimed to study the genetic diversity and genetic structure of seedlings as the natural regenerating population of Dipterocarpus gracilis Blume in The Kecubung Ulolanang Nature Conservation Reserve, Batang District, Central Java Province, Indonesia. The D. gracilis population in this area is distributed in four zones. We observed a total of 137 juvenile seedlings representing all the zones. Isozyme markers detected the genetic diversity of D. gracilis by peroxidase (PRX), esterase (EST), and acid phosphatase (ACP) enzymes. The mean observed heterozygosity of all the zones was lower (HO=0.078) than expected heterozygosity (HE=0.203). Genetic depletion occurred because of genetic drifts and founder effects due to low parental diversity. The genetic structure of seedlings is similar to the consequence of inbreeding. We conclude that the genetic diversity of D. gracilis decreases when mature trees are reduced. This population has essential values ​​in Java Island and should be a priority evaluation in the in-situ and ex-situ conservation of genetic resources.

Hermansky-Pudlak syndrome pulmonary fibrosis: a rare inherited interstitial lung disease.

Pulmonary fibrosis is a progressive interstitial lung disease of unknown aetiology with a poor prognosis. Studying genetic diseases associated with pulmonary fibrosis provides insights into the pathogenesis of the disease. Hermansky-Pudlak syndrome (HPS), a rare autosomal recessive disorder characterised by abnormal biogenesis of lysosome-related organelles, manifests with oculocutaneous albinism and excessive bleeding of variable severity. Pulmonary fibrosis is highly prevalent in three out of 10 genetic types of HPS (HPS-1, HPS-2 and HPS-4). Thus, genotyping of individuals with HPS is clinically relevant. HPS-1 tends to affect Puerto Rican individuals due to a genetic founder effect. HPS pulmonary fibrosis shares some clinical features with idiopathic pulmonary fibrosis (IPF), including dyspnoea, cough, restrictive lung physiology and computed tomography (CT) findings of fibrosis. In contrast to IPF, HPS pulmonary fibrosis generally affects children (HPS-2) or middle-aged adults (HPS-1 or HPS-4) and may be associated with ground-glass opacification in CT scans. Histopathology of HPS pulmonary fibrosis, and not IPF, shows vacuolated hyperplastic type II cells with enlarged lamellar bodies and alveolar macrophages with lipofuscin-like deposits. Antifibrotic drugs approved as treatment for IPF are not approved for HPS pulmonary fibrosis. However, lung transplantation has been performed in patients with severe HPS pulmonary fibrosis. HPS pulmonary fibrosis serves as a model for studying fibrotic lung disease and fibrosis in general.

Genetic analysis of Carasobarbus Karaman, 1971 (Actinopterygii Cyprinidae) in Anatolia

We sequenced the complete mitochondrial cytochrome b gene (1141 bp) of 70 individuals from ten populations of three Carasobarbus species in Anatolia. Totally eight haplotypes were identified. The intraspecies genetic distance ranged from 0.00% to 0.21%, while it varied from 2.6% to 9.0% for interspecies. Except for Gaziantep samples with low sample size, high haplotype diversity (Hd= 0,590-0,833) and low nucleotide diversity (Pi= 0,05-0,65) values can be explained by the presence of small populations sensitive to genetic drift and founder effects. Phylogenetic analyses constructed with neihgbour joining, maximum likelihood and maximum parsimony generated similar topologies supported by high bootstrap values. Phylogenetic tree topologies showed that the C. apoensis haplotype was located in the C. luteus species. Therefore, the validity of species status of C. apoensis should be checked morphologically. On the other hand, since the Kahta population in C. luteus has a remarkably high genetic diversity, it must be re-evaluated morphologically. The tectonic uplift of the Anatolian Plateau between the African and European plates during the Pliocene period may have probably prevented the presence of Carasobarbus in the west of the Anatolian diagonal.

Mapping of Diabetes Susceptibility Loci in a Domestic Cat Breed with an Unusually High Incidence of Diabetes Mellitus.

Genetic variants that are associated with susceptibility to type 2 diabetes (T2D) are important for identification of individuals at risk and can provide insights into the molecular basis of disease. Analysis of T2D in domestic animals provides both the opportunity to improve veterinary management and breeding programs as well as to identify novel T2D risk genes. Australian-bred Burmese (ABB) cats have a 4-fold increased incidence of type 2 diabetes (T2D) compared to Burmese cats bred in the United States. This is likely attributable to a genetic founder effect. We investigated this by performing a genome-wide association scan on ABB cats. Four SNPs were associated with the ABB T2D phenotype with p values <0.005. All exons and splice junctions of candidate genes near significant single-nucleotide polymorphisms (SNPs) were sequenced, including the genes DGKG, IFG2BP2, SLC8A1, E2F6, ETV5, TRA2B and LIPH. Six candidate polymorphisms were followed up in a larger cohort of ABB cats with or without T2D and also in Burmese cats bred in America, which exhibit low T2D incidence. The original SNPs were confirmed in this cohort as associated with the T2D phenotype, although no novel coding SNPs in any of the seven candidate genes showed association with T2D. The identification of genetic markers associated with T2D susceptibility in ABB cats will enable preventative health strategies and guide breeding programs to reduce the prevalence of T2D in these cats.

The Eskimo-Aleut Dentition: Crown and Root Morphology.

Objective of workThis paper provides an overview of crown and root morphology in Eskimo-Aleut populations of the American Arctic. For context, Eskimo-Aleut dental variation is compared to closely related American Indians and distantly related Europeans.Material and methodsThe characterization of dental trait frequency variation is based on observations made on approximately 10,000 dentitions scored by the late Christy G. Turner II and the author. Sixteen crown and five root traits were scored following the conventions outlined in the Arizona State University Dental Anthropology System.ResultsOf the 21 dental traits considered, only three showed slight differences among Eskimo-Aleuts, American Indians, and Europeans (UM1 cusp 5, LM2 groove pattern, LM2 root number). For the remaining traits, there was typically a dramatic contrast between the two New World populations and Europeans. While generally similar, Eskimo-Aleuts and American Indians showed differences in UI1 winging, shoveling, and double shoveling, UM1 Carabelli trait, 2-cusped UM2, 3-rooted UM2, and especially 3-rooted LM1.ConclusionThe differences between the three groups are likely a product of genetic drift and founder effect although recent work on the EDAR V370A allele suggests some dental variables like shoveling and lower molar cusp number may indirectly reflect natural selection operating on other variables influenced by this allele.Key wordsTooth Crown; Tooth Root; Alaska Natives; North American Indians; European Continental Ancestry Group

Can polyploidy confer invasive plants with a wider climatic tolerance? A test using Solidago canadensis.

Polyploidy can cause variation in plant functional traits and thereby generate individuals that can adapt to fluctuating environments and exploit new environments. However, few empirical studies have tested for an association between ploidy level and climatic tolerance of invasive cytotypes relative to conspecific native‐range cytotypes. Here, we used an invasive plant Solidago canadensis to test whether invasive populations had a higher proportion of polyploids, greater height and stem‐base diameter, and occupied a wider range of climatic conditions than conspecific native‐range populations. We also tested whether the invasive populations had overcome genetic founder effects. We sampled a total of 80 populations in parts of the invaded range in China and native range in North America for in situ measurements of plant height and stem‐base diameter in the field and for population genetic and cytotype analyses. To examine climatic correlates, we augmented our field‐sampled data with occurrence records obtained from Global Biodiversity Information Facility. All, except one, of the populations that we sampled in China occurred in a humid subtropical climate. In contrast, the North American populations occurred in humid continental, humid subtropical, and semi‐arid climatic zones. All populations of S. canadensis in China were purely hexaploid, while the North American populations were diploid, tetraploid, and hexaploid. The invasive hexaploids were significantly taller and had a larger stem‐base diameter than native hexaploids. Native hexaploids were significantly taller and had larger stem‐base diameter than native diploids. Climatic correlate assessment found that invasive and native populations occupied different climatic envelopes, with invasive populations occurring in warmer and less seasonal climates than native populations. However, there was no significant correlation between ploidy level and climatic envelope of S. canadensis. Molecular phylogeography data suggest reduced genetic founder effects in the invaded range. Overall, these results suggest that polyploidy does not influence S. canadensis climatic tolerance.

\u2018Mainland-island\u2019 population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation

Adaptation to different ecological environments can, through divergent selection, generate phenotypic and genetic differences between populations, and eventually give rise to new species. The fire salamander (Salamandra salamandra) has been proposed to represent an early stage of ecological speciation, driven by differential habitat adaptation through the deposition and development of larvae in streams versus ponds in the Kottenforst near Bonn (Germany). We set out to test this hypothesis of ecological speciation in an area different from the one where it was raised and we took the opportunity to explore for drivers of genetic differentiation at a landscape scale. A survey over 640 localities demonstrated the species’ presence in ponds and streams across forests, hilly terrain and areas with hedgerows (‘bocage’). Genetic variation at 14 microsatellite loci across 41 localities in and around two small deciduous forests showed that salamander effective population sizes were higher in forests than in the bocage, with panmixia in the forests (Fst < 0.010) versus genetic drift or founder effects in several of the small and more or less isolated bocage populations (Fst > 0.025). The system fits the ‘mainland-island’ metapopulation model rather than indicating adaptive genetic divergence in pond versus stream larval habitats. A reanalysis of the Kottenforst data indicated that microsatellite genetic variation fitted a geographical rather than an environmental axis, with a sharp transition from a western pond-breeding to an eastern, more frequently stream-breeding group of populations. A parallel changeover in mitochondrial DNA exists but remains to be well documented. The data support the existence of a hybrid zone following secondary contact of differentiated lineages, more so than speciation in situ.

The GenomeAsia 100K Project enables genetic discoveries across Asia

The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world’s population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue. Here we describe the pilot phase of the GenomeAsia 100K Project. This includes a whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups and 64 countries across Asia. We catalogue genetic variation, population structure, disease associations and founder effects. We also explore the use of this dataset in imputation, to facilitate genetic studies in populations across Asia and worldwide.

Population genomics of Tillandsia landbeckii reveals unbalanced genetic diversity and founder effects in the Atacama Desert

Abstract In hyper-arid habitats vegetation tends to be highly patchy with individual plant populations set widely apart from each other. In the Atacama Desert of northern Chile, rainfall is essentially absent, but fog occurring both at the coast and sometimes reaching inland areas supports patches of vegetation in an otherwise barren environment. Tillandsia landbeckii (Bromeliaceae), a epiarenic plant without functional roots, completely depends on fog as source for water, therefore it is found only in fog corridors. Here, we investigate the genetic connectivity within and between populations of T. landbeckii, using genome-wide single-nucleotide-polymorphisms (SNP) obtained through genotyping-by-sequencing (GBS). The 21 sampled populations from the Chilean Atacama Desert are distributed in three geographically ordered south to north clusters, with the southern cluster containing only one population that is genetically very distant from the others. From our study we obtained three genetic groups that corresponded to these three geographical clusters, with the exception of the two populations 16 and 18, where genetic affiliation lies at least in part with the central cluster. Further, our results show uneven distribution of genetic diversity among the populations with highest diversity in the central cluster. We found large amounts of shared heterozygous SNPs as well as negative values for the inbreeding coefficient FIS in the populations of the north and south. They indicate that these populations are strongly affected by clonal reproduction, while the populations in the center are mostly reproducing sexually. We interpret these data as the result of genetic bottlenecks due to founder events involving few dispersing genotypes combined with strong geographical isolation for the northern and southern populations, following stepping stone dispersal of Tillandsia during more climatically favorable episodes.

Founder effects and species introductions: A host versus parasite perspective.

Species colonizations (both natural and anthropogenic) can be associated with genetic founder effects, where founding populations demonstrate significant genetic bottlenecks compared to native populations. Yet, many successfully established free‐living species exhibit little reduction in genetic diversity—possibly due to multiple founding events and/or high propagule pressure during introductions. Less clear, however, is whether parasites may show differential signatures to their free‐living hosts. Parasites with indirect life cycles may particularly be more prone to founder effects (i.e., more genetically depauperate) because of inherently smaller founding populations and complex life cycles. We investigated this question in native (east coast) and introduced (west coast) North American populations of a host snail Tritia obsoleta (formerly Ilyanassa obsoleta, the eastern mudsnail) and four trematode parasite species that obligately infect it. We examined genetic diversity, gene flow, and population structure using two molecular markers (mitochondrial and nuclear) for the host and the parasites. In the host snail, we found little to no evidence of genetic founder effects, while the trematode parasites showed significantly lower genetic diversity in the introduced versus native ranges. Moreover, the parasite's final host influenced infection prevalence and genetic diversity: Trematode species that utilized fish as final hosts demonstrated lower parasite diversity and heightened founder effects in the introduced range than those trematodes using birds as final hosts. In addition, inter‐regional gene flow was strongest for comparisons that included the putative historical source region (mid‐Atlantic populations of the US east coast). Overall, our results broaden understanding of the role that colonization events (including recent anthropogenic introductions) have on genetic diversity in non‐native organisms by also evaluating less studied groups like parasites.

Why are tall-statured energy grasses of polyploid species complexes potentially invasive? A review of their genetic variation patterns and evolutionary plasticity

Perennial tall-statured grasses are regarded as a sustainable source of renewable energy for their high yields of lignocellulosic biomass, low resource input, wide ecological tolerance and capacity for storing large amounts of atmospheric CO2 in their perennial underground rhizome systems. These same traits, that make such crops agronomically attractive and sustainable, make these species highly competitive and potentially invasive. Several perennial energy crop grasses are outbreeding species that belong to cosmopolitan polyploid species complexes, i.e. groups of interbreeding species with ploidy variation. The cultivation of such highly productive and genetically diverse crops can have unwanted consequences through the evolution of invasive species. The goal of this review is to provide the scientific community, including agronomists, breeders, users and nature managers, with an introduction to the genetic dynamics occurring within the polyploid species complexes of the emerging energy species Arundo donax, Miscanthus × giganteus, Panicum virgatum, Phalaris arundinacea and Phragmites australis, and the broad biogeographical extent of their gene flow impact. Such aspects are difficult to predict, and are not captured by invasion risk assessments and by the sustainability certifications of the bioenergy supply chain. The review integrates literature from the phylogenetic, cytology, population ecology and agronomic research and focuses on the evolutionary processes that shape invasiveness that can be activated post-introduction by the dispersal of pollen, seeds and plant fragments from the energy crops to the environment. Due to the high genetic diversity of the crops, the adverse effects that genetic drift and founder effect can have on the establishment of small populations are very unlikely. On the contrary the data collected suggests that the risk of fostering panmictic continental invasive populations is high. Agronomic measures, regulations and genetic improvements that can contain dispersal from crops are discussed, as well as urgent research needs.