scholarly journals Evolutionary implications of recombination differences across diverging populations of Anopheles

2021 ◽  
Author(s):  
Joel T. Nelson ◽  
Omar E. Cornejo ◽  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Rate Variation ◽  
Anopheles Coluzzii ◽  
Fine Scale ◽  
Recombination Rates ◽  
Population Genetic Differentiation ◽  
Recombination Hotspots

AbstractRecombination is one of the main evolutionary mechanisms responsible for changing the genomic architecture of populations; and in essence, it is the main mechanism by which novel combinations of alleles, haplotypes, are formed. A clear picture that has emerged across study systems is that recombination is highly variable, even among closely related species. However, it is only until very recently that we have started to understand how recombination variation between populations of the same species impact genetic diversity and divergence. Here, we used whole-genome sequence data to build fine-scale recombination maps for nine populations within two species of Anopheles, Anopheles gambiae and Anopheles coluzzii. The genome-wide recombination averages were on the same order of magnitude for all populations except one. Yet, we identified significant differences in fine-scale recombination rates among all population comparisons. We report that effective population sizes, and presence of a chromosomal inversion has major contribution to recombination rate variation along the genome and across populations. We identified over 400 highly variable recombination hotspots across all populations, where only 9.6% are shared between two or more populations. Additionally, our results are consistent with recombination hotspots contributing to both genetic diversity and absolute divergence (dxy) between populations and species of Anopheles. However, we also show that recombination has a small impact on population genetic differentiation as estimated with FST. The minimal impact that recombination has on genetic differentiation across populations represents the first empirical evidence against recent theoretical work suggesting that variation in recombination along the genome can mask or impair our ability to detect signatures of selection. Our findings add new understanding to how recombination rates vary within species, and how this major evolutionary mechanism can maintain and contribute to genetic variation and divergence within a prominent malaria vector.

scholarly journals Effect of Heterogeneity in Recombination Rate on Variation in Realised Relationship

2018 ◽  
Author(s):  
Ian M.S. White ◽  
William G. Hill
Keyword(s):  
Recombination Rate ◽  
Genetic Information ◽  
Fine Scale ◽  
Recombination Rates ◽  
Recombination Hotspots ◽  
Identical By Descent ◽  
Small Influence ◽  
Scale Levels ◽  
Pedigree Relationship ◽  
Actual Relationship

ABSTRACTIndividuals of specified pedigree relationship vary in the proportion of the genome they share identical by descent, i.e. in their realised or actual relationship. Basing predictions of the variance in realised relationship solely on the proportion of the map length shared implicitly assumes that both recombination rate and genetic information are uniformly distributed along the genome, ignoring the possible existence of recombination hotspots, and failing to distinguish between coding and non-coding sequences. In this paper we quantify the effects of heterogeneity in recombination rate at broad and fine scale levels on the variation in realised relationship. A chromosome with variable recombination rate usually shows more variance in realised relationship than does one having the same map length with constant recombination rate, especially if recombination rates are higher towards chromosome ends. Reductions in variance can also be found, and the overall pattern of change is quite complex. In general, local (fine-scale) variation in recombination rate, e.g. hotspots, has a small influence on the variance in realised relationship. Differences in rates across longer regions and between chromosome ends can increase or decrease the variance in realised relationship, depending on the genomic architecture.

scholarly journals Population genomics of East Asian ethnic groups

Hereditas ◽  
2020 ◽  
Vol 157 (1) ◽  
Author(s):  
Ziqing Pan ◽  
Shuhua Xu
Keyword(s):  
Genetic Diversity ◽  
East Asia ◽  
Ethnic Groups ◽  
Population Genomics ◽  
Sequence Data ◽  
East Asian ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Evolutionary Forces ◽  
Asian Populations

AbstractEast Asia constitutes one-fifth of the global population and exhibits substantial genetic diversity. However, genetic investigations on populations in this region have been largely under-represented compared with European populations. Nonetheless, the last decade has seen considerable efforts and progress in genome-wide genotyping and whole-genome sequencing of the East-Asian ethnic groups. Here, we review the recent studies in terms of ancestral origin, population relationship, genetic differentiation, and admixture of major East- Asian groups, such as the Chinese, Korean, and Japanese populations. We mainly focus on insights from the whole-genome sequence data and also include the recent progress based on mitochondrial DNA (mtDNA) and Y chromosome data. We further discuss the evolutionary forces driving genetic diversity in East-Asian populations, and provide our perspectives for future directions on population genetics studies, particularly on underrepresented indigenous groups in East Asia.

scholarly journals Brown banded bamboo shark (Chiloscyllium punctatum) shows high genetic diversity and differentiation in Malaysian waters

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kean Chong Lim ◽  
Amy Yee-Hui Then ◽  
Alison Kim Shan Wee ◽  
Ahemad Sade ◽  
Richard Rumpet ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Population Structure ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Fishery Management ◽  
Peninsular Malaysia ◽  
Fine Scale ◽  
Nadh Dehydrogenase Subunit 2 ◽  
Bamboo Shark

AbstractThe demersal brown banded bamboo shark Chiloscyllium punctatum is a major component of sharks landed in Malaysia. However, little is known about their population structure and the effect of high fishing pressure on these weak swimming sharks. Both mitochondrial DNA control region (1072 bp) and NADH dehydrogenase subunit 2 (1044 bp) were used to elucidate the genetic structure and connectivity of C. punctatum among five major areas within the Sundaland region. Our findings revealed (i) strong genetic structure with little present day mixing between the major areas, (ii) high intra-population genetic diversity with unique haplotypes, (iii) significant correlation between genetic differentiation and geographical distance coupled with detectable presence of fine scale geographical barriers (i.e. the South China Sea), (iv) historical directional gene flow from the east coast of Peninsular Malaysia towards the west coast and Borneo, and (v) no detectable genetic differentiation along the coastline of east Peninsular Malaysia. Genetic patterns inferred from the mitochondrial DNA loci were consistent with the strong coastal shelf association in this species, the presence of contemporary barriers shaped by benthic features, and limited current-driven egg dispersal. Fine scale population structure of C. punctatum highlights the need to improve genetic understanding for fishery management and conservation of other small-sized sharks.

scholarly journals Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations

2018 ◽  
Author(s):  
Enrique J. Schwarzkopf ◽  
Juan C. Motamayor ◽  
Omar E. Cornejo
Keyword(s):  
Genetic Differentiation ◽  
Recombination Rate ◽  
Plant Domestication ◽  
Population Divergence ◽  
Sequence Motifs ◽  
Recombination Rates ◽  
Genomic Features ◽  
Recombination Hotspots ◽  
Genomic Locations ◽  
Dna Sequence Motifs

AbstractOur study investigates the possible drivers of recombination hotspots in Theobroma cacao using ten genetically differentiated populations. By comparing recombination patterns between multiple populations, we obtain a novel view of recombination at the population-divergence timescale. For each population, a fine-scale recombination map was generated using the coalescent with a standard method based on linkage disequilibrium (LD). These maps revealed higher recombination rates in a domesticated population and a population that has undergone a recent bottleneck. We inferred hotspots of recombination for each population and find that the genomic locations of hotspots correlate with genetic differentiation between populations (FST). We used randomization approaches to generate appropriate null models to understand the association between hotspots of recombination and both DNA sequence motifs and genomic features. We found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. Our findings indicate that recombination hotspots are evolving in a way that is consistent with genetic differentiation but are also preferentially driven to near coding regions. We illustrate that, consistent with predictions in plant domestication, the recombination rate of the domesticated population is orders of magnitude higher than that of other populations. More importantly, we find two fixed mutations in the domesticated population’s FIGL1 protein. FIGL1 has been shown to increase recombination rates in Arabidopsis by several orders of magnitude, suggesting a possible mechanism for the observed increased recombination rate in the domesticated population.

scholarly journals Genome-scale rates of evolutionary change in bacteria

2016 ◽  
Author(s):  
Sebastian Duchêne ◽  
Kathryn E. Holt ◽  
François-Xavier Weill ◽  
Simon Le Hello ◽  
Jane Hawkey ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Sequence Data ◽  
Temporal Structure ◽  
Evolutionary Rates ◽  
Whole Genome Sequence ◽  
Rate Variation ◽  
Data Sets ◽  
Inverse Association ◽  
Nucleotide Substitutions ◽  
Ecological Processes

ABSTRACTEstimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host-pathogen associations, and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with “ancient DNA” data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from 10−6 to 10−8 nucleotide substitutions site-1 year-1. This variation was largely attributable to sampling time, which was strongly negatively associated with estimated evolutionary rates, with this relationship best described by an exponential decay curve. To avoid potential estimation biases such time-dependency should be considered when inferring evolutionary time-scales in bacteria.

scholarly journals Fine-scale crossover rate variation on the C. elegans X chromosome

2016 ◽  
Author(s):  
Max R. Bernstein ◽  
Matthew V. Rockman
Keyword(s):  
X Chromosome ◽  
Nucleosome Occupancy ◽  
Gc Content ◽  
Genotypic Diversity ◽  
Rate Variation ◽  
Open Chromatin ◽  
Fine Scale ◽  
Recombination Rates ◽  
Crossover Rate ◽  
Scale Variation

AbstractMeiotic recombination creates genotypic diversity within species. Recombination rates vary substantially across taxa and the distribution of crossovers can differ significantly among populations and between sexes. Crossover locations within species have been found to vary by chromosome and by position within chromosomes, where most crossover events occur in small regions known as recombination hotspots. However, several species appear to lack hotspots despite significant crossover heterogeneity. The nematode Caenorhabditis elegans was previously found to have the least fine-scale variation in crossover distribution among organisms studied to date. It is unclear whether this pattern extends to the X chromosome given its unique compaction through the pachytene stage of meiotic prophase in hermaphrodites. We generated 798 recombinant nested near-isogenic lines (NILs) with crossovers in a 1.41 Mb region on the left arm of the X chromosome to determine if its recombination landscape is similar to that of the autosomes. We find that the fine-scale variation in crossover rate is lower than that of other model species and is inconsistent with hotspots. The relationship of genomic features to crossover rate is dependent on scale, with GC content, histone modifications, and nucleosome occupancy being negatively associated with crossovers. We also find that the abundances of 4-6 base pair DNA motifs significantly explain crossover density. These results are consistent with recombination occurring at unevenly distributed sites of open chromatin.

scholarly journals Homogeneity of Arabian Peninsula dromedary camel populations with signals of geographic distinction based on whole genome sequence data

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Hussain Bahbahani ◽  
Faisal Almathen
Keyword(s):  
Genetic Diversity ◽  
Genome Sequence ◽  
Arabian Peninsula ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Dromedary Camels ◽  
Genome Sequence Data ◽  
Similarity Indices ◽  
Bactrian Camels

AbstractDromedary camels in the Arabian Peninsula distribute along different geographical and ecological locations, e.g. desert, mountains and coasts. Here, we are aiming to explore the whole genome sequence data of ten dromedary populations from the Arabian Peninsula to assess their genetic structure, admixture levels, diversity and similarity indices. Upon including reference dromedary and Bactrian camel populations from Iran and Kazakhstan, we characterise inter-species and geographic genetic distinction between the dromedary and the Bactrian camels. Individual-based alpha genetic diversity profiles are found to be generally higher in Bactrian camels than dromedary populations, with the exception of five autosomes (NC_044525.1, NC_044534.1, NC_044540.1, NC_044542.1, NC_044544.1) at diversity orders (q ≥ 2). The Arabian Peninsula camels are generally homogenous, with a small degree of genetic distinction correlating with three geographic groups: North, Central and West; Southwest; and Southeast of the Arabian Peninsula. No significant variation in diversity or similarity indices are observed among the different Arabian Peninsula dromedary populations. This study contributes to our understanding of the genetic diversity of Arabian Peninsula dromedary camels. It will help conserve the genetic stock of this species and support the design of breeding programmes for genetic improvement of favorable traits.

scholarly journals Development and Validation of Polymorphic Microsatellite Loci for the NA2 Lineage of Phytophthora ramorum from Whole Genome Sequence Data

Plant Disease ◽  
2017 ◽  
Vol 101 (5) ◽  
pp. 666-673 ◽  
Author(s):  
Marie-Claude Gagnon ◽  
Nicolas Feau ◽  
Angela L. Dale ◽  
Braham Dhillon ◽  
Richard C. Hamelin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genome Sequence ◽  
Sequence Data ◽  
Ornamental Plants ◽  
Phytophthora Ramorum ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
And Migration

Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only two markers are polymorphic in the NA2 lineage, which is predominant in Canadian nurseries. Microsatellite motifs were mined from whole-genome sequence data of six P. ramorum NA2 isolates. Of the 43 microsatellite primer pairs selected, 13 loci displayed different allele sizes among the four P. ramorum lineages, 10 loci displayed intralineage variation in the EU1, EU2, and/or NA1 lineages, and 12 microsatellites displayed polymorphism in the NA2 lineage. Genotyping of 272 P. ramorum NA2 isolates collected in nurseries in British Columbia, Canada, from 2004 to 2013 revealed 12 multilocus genotypes (MLGs). One MLG was dominant when examined over time and across sampling locations, and only a few mutations separated the 12 MLGs. The NA2 population observed in Canadian nurseries also showed no signs of sexual recombination, similar to what has been observed in previous studies. The markers developed in this study can be used to assess P. ramorum inter- and intralineage genetic diversity and generate a better understanding of the population structure and migration patterns of this important plant pathogen, especially for the lesser-characterized NA2 lineage.

scholarly journals Simulation of African and non-African low and high coverage whole genome sequence data to assess variant calling approaches

2020 ◽  
Author(s):  
Shatha Alosaimi ◽  
Noëlle van Biljon ◽  
Denis Awany ◽  
Prisca K Thami ◽  
Joel Defo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
False Positive ◽  
Sequence Data ◽  
False Negative ◽  
Variant Calling ◽  
High Rate ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequence Coverage ◽  
High Coverage

Abstract Current variant calling (VC) approaches have been designed to leverage populations of long-range haplotypes and were benchmarked using populations of European descent, whereas most genetic diversity is found in non-European such as Africa populations. Working with these genetically diverse populations, VC tools may produce false positive and false negative results, which may produce misleading conclusions in prioritization of mutations, clinical relevancy and actionability of genes. The most prominent question is which tool or pipeline has a high rate of sensitivity and precision when analysing African data with either low or high sequence coverage, given the high genetic diversity and heterogeneity of this data. Here, a total of 100 synthetic Whole Genome Sequencing (WGS) samples, mimicking the genetics profile of African and European subjects for different specific coverage levels (high/low), have been generated to assess the performance of nine different VC tools on these contrasting datasets. The performances of these tools were assessed in false positive and false negative call rates by comparing the simulated golden variants to the variants identified by each VC tool. Combining our results on sensitivity and positive predictive value (PPV), VarDict [PPV = 0.999 and Matthews correlation coefficient (MCC) = 0.832] and BCFtools (PPV = 0.999 and MCC = 0.813) perform best when using African population data on high and low coverage data. Overall, current VC tools produce high false positive and false negative rates when analysing African compared with European data. This highlights the need for development of VC approaches with high sensitivity and precision tailored for populations characterized by high genetic variations and low linkage disequilibrium.

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