Conservation Status and Historical Relatedness of South African Communal Indigenous Goat Populations Using Genome-Wide Snp Marker

Abstract Background: Indigenous goats forms the majority of populations in smallholder; low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support communal farming. Effective population size (Ne), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Results: Across populations, the current Ne of Gauteng was the lowest at 371 animals, while the historical Ne across populations suggests that the ancestor Ne has decreased by 53.86%, 44.58%, 42.16% and 41.16% in Free State (FS), North West (NW), Limpopo (LP) and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship (FROH >5Mb) was highest in FS (0.08±0.09) and lowest for Eastern Cape (EC) (0.02±0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR and MAPK3 were identified (occurring in over 20% of the samples) in FS (n = 37), GP (n = 42), NW (n = 2) populations only. The mean length of ROH across populations was 7.76Mb and ranged from 1.61Mb KwaZulu-Natal (KZN) to 98.05Mb (GP and NW). Distribution of ROH according to their size showed that the majority (n = 1949) of the detected ROH were >5Mb in length than the other categories. Assuming two hypothetical ancestral populations, the population from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP shared an origin but have substantial admixture from the EC and NW populations.Conclusions: These findings indicated a greater negative impact of inbreeding in recent times which is important for planning conservation strategies. It was revealed that the occurrence of high Ne and autozygosity varied largely across breeds in communal indigenous goat populations at different recent and ancient events when a genome-wide SNP marker was used.

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A fully integrated machine learning scan of selection in the chimpanzee genome

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqaa061 ◽

2020 ◽

Vol 2 (3) ◽

Author(s):

Jessica Nye ◽

Mayukh Mondal ◽

Jaume Bertranpetit ◽

Hafid Laayouni

Keyword(s):

Machine Learning ◽

Positive Selection ◽

Demographic History ◽

Effective Population ◽

Fully Integrated ◽

Genome Wide ◽

A Genome ◽

Machine Learning Approach ◽

History Of ◽

The Impact

Abstract After diverging, each chimpanzee subspecies has been the target of unique selective pressures. Here, we employ a machine learning approach to classify regions as under positive selection or neutrality genome-wide. The regions determined to be under selection reflect the unique demographic and adaptive history of each subspecies. The results indicate that effective population size is important for determining the proportion of the genome under positive selection. The chimpanzee subspecies share signals of selection in genes associated with immunity and gene regulation. With these results, we have created a selection map for each population that can be displayed in a genome browser (www.hsb.upf.edu/chimp_browser). This study is the first to use a detailed demographic history and machine learning to map selection genome-wide in chimpanzee. The chimpanzee selection map will improve our understanding of the impact of selection on closely related subspecies and will empower future studies of chimpanzee.

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A genome-wide transcriptomic analysis of embryos fathered by obese males in a murine model of diet-induced obesity

Scientific Reports ◽

10.1038/s41598-021-81226-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Laura Bernhardt ◽

Marcus Dittrich ◽

Rabih El-Merahbi ◽

Antoine-Emmanuel Saliba ◽

Tobias Müller ◽

...

Keyword(s):

Gene Expression ◽

Negative Impact ◽

Preimplantation Embryos ◽

High Fat ◽

Cell Stage ◽

Genetic Transmission ◽

Diet Induced Obesity ◽

Genome Wide ◽

A Genome ◽

Paternal Obesity

AbstractPaternal obesity is known to have a negative impact on the male’s reproductive health as well as the health of his offspring. Although epigenetic mechanisms have been implicated in the non-genetic transmission of acquired traits, the effect of paternal obesity on gene expression in the preimplantation embryo has not been fully studied. To this end, we investigated whether paternal obesity is associated with gene expression changes in eight-cell stage embryos fathered by males on a high-fat diet. We used single embryo RNA-seq to compare the gene expression profile of embryos generated by males on a high fat (HFD) versus control (CD) diet. This analysis revealed significant upregulation of the Samd4b and Gata6 gene in embryos in response to a paternal HFD. Furthermore, we could show a significant increase in expression of both Gata6 and Samd4b during differentiation of stromal vascular cells into mature adipocytes. These findings suggest that paternal obesity may induce changes in the male germ cells which are associated with the gene expression changes in the resulting preimplantation embryos.

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Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching

10.1101/867754 ◽

2019 ◽

Cited By ~ 7

Author(s):

Zachary L. Fuller ◽

Veronique J.L. Mocellin ◽

Luke Morris ◽

Neal Cantin ◽

Jihanne Shepherd ◽

...

Keyword(s):

Genome Wide Association Study ◽

Balancing Selection ◽

Genome Wide Association ◽

Conservation Strategies ◽

Genome Sequences ◽

Acropora Millepora ◽

Genome Wide ◽

A Genome ◽

In The Wild

AbstractAlthough reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

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Coalescence times, life history traits and conservation concerns: an example from four coastal shark species from the Indo-Pacific

10.22541/au.161963333.37636342/v2 ◽

2021 ◽

Author(s):

Pierre Lesturgie ◽

Serge Planes ◽

Stefano Mona

Keyword(s):

Population Structure ◽

Life History ◽

Life History Traits ◽

New Caledonia ◽

Demographic History ◽

Conservation Strategies ◽

Shark Species ◽

Effective Population ◽

Demographic Models ◽

Mobile Species

Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographic ranges and less mobile ones organized in meta-populations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (meta-population) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.

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Genome-wide diversity and global migration patterns in dromedaries follow ancient caravan routes

Communications Biology ◽

10.1038/s42003-020-1098-7 ◽

2020 ◽

Vol 3 (1) ◽

Cited By ~ 2

Author(s):

Sara Lado ◽

Jean Pierre Elbers ◽

Angela Doskocil ◽

Davide Scaglione ◽

Emiliano Trucchi ◽

...

Keyword(s):

Demographic History ◽

Genomic Diversity ◽

Phylogeographic Structure ◽

Arid Environments ◽

Migration Patterns ◽

Migration Rates ◽

Global Migration ◽

Genome Wide ◽

A Genome ◽

Scale Population

AbstractDromedaries have been essential for the prosperity of civilizations in arid environments and the dispersal of humans, goods and cultures along ancient, cross-continental trading routes. With increasing desertification their importance as livestock species is rising rapidly, but little is known about their genome-wide diversity and demographic history. As previous studies using few nuclear markers found weak phylogeographic structure, here we detected fine-scale population differentiation in dromedaries across Asia and Africa by adopting a genome-wide approach. Global patterns of effective migration rates revealed pathways of dispersal after domestication, following historic caravan routes like the Silk and Incense Roads. Our results show that a Pleistocene bottleneck and Medieval expansions during the rise of the Ottoman empire have shaped genome-wide diversity in modern dromedaries. By understanding subtle population structure we recognize the value of small, locally adapted populations and appeal for securing genomic diversity for a sustainable utilization of this key desert species.

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A globally threatened shark, Carcharias taurus, shows no population decline in South Africa

Scientific Reports ◽

10.1038/s41598-020-75044-2 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Juliana D. Klein ◽

Aletta E. Bester-van der Merwe ◽

Matthew L. Dicken ◽

Arsalan Emami-Khoyi ◽

Kolobe L. Mmonwa ◽

...

Keyword(s):

South Africa ◽

Census Data ◽

Demographic History ◽

Conservation Status ◽

Population Decline ◽

Multilocus Genotype ◽

Population Declines ◽

Effective Population ◽

Anthropogenic Pressures ◽

Carcharias Taurus

Abstract Knowledge about the demographic histories of natural populations helps to evaluate their conservation status, and potential impacts of natural and anthropogenic pressures. In particular, estimates of effective population size obtained through molecular data can provide useful information to guide management decisions for vulnerable populations. The spotted ragged-tooth shark, Carcharias taurus (also known as the sandtiger or grey nurse shark), is widely distributed in warm-temperate and subtropical waters, but has suffered severe population declines across much of its range as a result of overexploitation. Here, we used multilocus genotype data to investigate the demographic history of the South African C. taurus population. Using approximate Bayesian computation and likelihood-based importance sampling, we found that the population underwent a historical range expansion that may have been linked to climatic changes during the late Pleistocene. There was no evidence for a recent anthropogenic decline. Together with census data suggesting a stable population, these results support the idea that fishing pressure and other threats have so far not been detrimental to the local C. taurus population. The results reported here indicate that South Africa could possibly harbour the last remaining, relatively pristine population of this widespread but vulnerable top predator.

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Chromosome-level assembly of the Atlantic silverside genome reveals extreme levels of sequence diversity and structural genetic variation

10.1101/2020.10.27.357293 ◽

2020 ◽

Author(s):

Anna Tigano ◽

Arne Jacobs ◽

Aryn P. Wilder ◽

Ankita Nand ◽

Ye Zhan ◽

...

Keyword(s):

Genetic Variation ◽

Structural Variation ◽

Demographic History ◽

Genome Structure ◽

Genomic Variation ◽

Adaptive Divergence ◽

Effective Population ◽

Atlantic Silverside ◽

A Genome ◽

Chromosome Level

AbstractThe levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10X Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia) - an established ecological model for studying the phenotypic effects of natural and artificial selection - and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is the highest reported for a fish, or any vertebrate, to date (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ~23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.

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Coupling Wright-Fisher and coalescent dynamics for realistic simulation of population-scale datasets

10.1101/674440 ◽

2019 ◽

Author(s):

Dominic Nelson ◽

Jerome Kelleher ◽

Aaron P. Ragsdale ◽

Gil McVean ◽

Simon Gravel

Keyword(s):

State Of The Art ◽

Demographic History ◽

Recent Past ◽

Computationally Efficient ◽

Effective Population ◽

Genome Data ◽

Coalescent Simulations ◽

Genome Wide ◽

Fisher Model ◽

Ancestry Proportions

1AbstractCoalescent simulations are widely used to examine the effects of evolution and demographic history on the genetic makeup of populations. Thanks to recent progress in algorithms and data structures, simulators such as the widely-used msprime [1] now provide genome-wide simulations for millions of individuals. However, this software relies on classic coalescent theory and the corresponding assumptions that sample sizes are small relative to effective population size and that the region being simulated is short. Here we show that coalescent simulations of long regions of the genome exhibit large biases in identity-by-descent (IBD), long-range linkage disequilibrium (LD), and ancestry patterns, particularly when sample size is large. We present a Wright-Fisher extension to msprime, and show that it produces more realistic distributions of IBD, LD, and ancestry proportions, while also addressing more subtle biases of the coalescent. Further, these extensions are more computationally efficient than state-of-the-art coalescent simulations when simulating long regions, including whole-genome data. For shorter regions, efficiency and accuracy can be maintained via a flexible hybrid model which simulates the recent past under the Wright-Fisher model and uses coalescent simulations in the distant past.

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The genomic impact of European colonization of the Americas

10.1101/676437 ◽

2019 ◽

Cited By ~ 1

Author(s):

Linda Ongaro ◽

Marilia O. Scliar ◽

Rodrigo Flores ◽

Alessandro Raveane ◽

Davide Marnetto ◽

...

Keyword(s):

Gene Flow ◽

Demographic History ◽

Colonial Era ◽

Genome Wide ◽

A Genome ◽

European Colonization ◽

High Degree ◽

The Impact ◽

North And South America ◽

North And South

AbstractThe human genetic diversity of the Americas has been shaped by several events of gene flow that have continued since the Colonial Era and the Atlantic slave trade. Moreover, multiple waves of migration followed by local admixture occurred in the last two centuries, the impact of which has been largely unexplored.Here we compiled a genome-wide dataset of ∼12,000 individuals from twelve American countries and ∼6,000 individuals from worldwide populations and applied haplotype-based methods to investigate how historical movements from outside the New World affected i) the genetic structure, ii) the admixture profile, iii) the demographic history and iv) sex-biased gene-flow dynamics, of the Americas.We revealed a high degree of complexity underlying the genetic contribution of European and African populations in North and South America, from both geographic and temporal perspectives, identifying previously unreported sources related to Italy, the Middle East and to specific regions of Africa.

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Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper

Horticulture Research ◽

10.1038/s41438-020-00376-z ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Shijing Feng ◽

Zhenshan Liu ◽

Yang Hu ◽

Jieyun Tian ◽

Tuxi Yang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Demographic History ◽

Genomic Analysis ◽

Genotyping By Sequencing ◽

Gansu Province ◽

Climatic Oscillations ◽

Genome Wide ◽

A Genome ◽

Wild Accessions

Abstract Chinese pepper, mainly including Zanthoxylum bungeanum and Zanthoxylum armatum, is an economically important crop popular in Asian countries due to its unique taste characteristics and potential medical uses. Numerous cultivars of Chinese pepper have been developed in China through long-term domestication. To better understand the population structure, demographic history, and speciation of Chinese pepper, we performed a comprehensive analysis at a genome-wide level by analyzing 38,395 genomic SNPs that were identified in 112 cultivated and wild accessions using a high-throughput genome-wide genotyping-by-sequencing (GBS) approach. Our analysis provides genetic evidence of multiple splitting events occurring between and within species, resulting in at least four clades in Z. bungeanum and two clades in Z. armatum. Despite no evidence of recent admixture between species, we detected substantial gene flow within species. Estimates of demographic dynamics and species distribution modeling suggest that climatic oscillations during the Pleistocene (including the Penultimate Glaciation and the Last Glacial Maximum) and recent domestication events together shaped the demography and evolution of Chinese pepper. Our analyses also suggest that southeastern Gansu province is the most likely origin of Z. bungeanum in China. These findings provide comprehensive insights into genetic diversity, population structure, demography, and adaptation in Zanthoxylum.

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