Population genomics in two cave-obligate invertebrates confirms extremely limited dispersal between caves

Abstract Caves offer selective pressures that are distinct from the surface. Organisms that have evolved to exist under these pressures typically exhibit a suite of convergent characteristics, including a loss or reduction of eyes and pigmentation. As a result, cave-obligate taxa, termed troglobionts, are no longer viable on the surface. This circumstance has led to an understanding of highly constrained dispersal capabilities, and the prediction that, in the absence of subterranean connections, extreme genetic divergence between cave populations. An effective test of this model would involve (1) common troglobionts from (2) nearby caves in a cave-dense region, (3) good sample sizes per cave, (4) multiple taxa, and (5) genome-wide characterization. With these criteria in mind, we used RAD-seq to genotype an average of ten individuals of the troglobiotic spider Nesticus barri and the troglobiotic beetle Ptomaphagus hatchi, each from four closely located caves (ranging from 3 to 13 km apart) in the cave-rich southern Cumberland Plateau of Tennessee, USA. Consistent with the hypothesis of highly restricted dispersal, we find that populations from separate caves are indeed highly genetically isolated. Our results support the idea of caves as natural laboratories for the study of parallel evolutionary processes.

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Testing the ‘caves as islands’ model in two cave-obligate invertebrates with a genomic approach

10.1101/2020.04.08.032789 ◽

2020 ◽

Author(s):

Andras Balogh ◽

Lam Ngo ◽

Kirk S. Zigler ◽

Groves Dixon

Keyword(s):

Genetic Diversity ◽

Genetic Divergence ◽

Nucleotide Diversity ◽

Dense Region ◽

Cumberland Plateau ◽

Small Areas ◽

Selective Pressures ◽

Genome Wide ◽

Genomic Approach ◽

Good Sample

AbstractCaves offer selective pressures that are distinct from the surface. Organisms that have evolved to exist under these pressures typically exhibit a suite of convergent characteristics, including a loss or reduction of eyes and pigmentation. As a result, cave-obligate taxa, termed troglobionts, are no longer viable on the surface. This circumstance has led to a “caves as islands” model of troglobiont evolution that predicts extreme genetic divergence between cave populations even across relatively small areas. An effective test of this model would involve (1) common troglobionts from (2) nearby caves in a cave-dense region, (3) good sample sizes per cave, (4) multiple taxa, and (5) genome-wide characterization. With these criteria in mind, we used RAD-seq to genotype an average of ten individuals of the troglobiotic spider Nesticus barri and the troglobiotic beetle Ptomaphagus hatchi, each from four closely located caves (ranging from 3-13 km apart) in the cave-rich southern Cumberland Plateau of Tennessee, USA. Consistent with the caves as islands model, we find that populations from separate caves are indeed highly genetically isolated. In addition, nucleotide diversity was correlated to cave length, suggesting that cave size is a dominant force shaping troglobiont population size and genetic diversity. Our results support the idea of caves as natural laboratories for the study of parallel evolutionary processes.

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Natural selection and neutral evolutionary processes contribute to genetic divergence in leaf traits across a precipitation gradient in the tropical oakQuercus oleoides

Molecular Ecology ◽

10.1111/mec.14566 ◽

2018 ◽

Vol 27 (9) ◽

pp. 2176-2192 ◽

Cited By ~ 24

Author(s):

José A. Ramírez-Valiente ◽

Nicholas J. Deacon ◽

Julie Etterson ◽

Alyson Center ◽

Jed P. Sparks ◽

...

Keyword(s):

Natural Selection ◽

Genetic Divergence ◽

Leaf Traits ◽

Precipitation Gradient ◽

Evolutionary Processes

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Estimating Effect Sizes and Expected Replication Probabilities from GWAS Summary Statistics

10.1101/032474 ◽

2015 ◽

Author(s):

Dominic Holland ◽

Yunpeng Wang ◽

Wesley K Thompson ◽

Andrew Schork ◽

Chi-Hua Chen ◽

...

Keyword(s):

Association Studies ◽

Significant Snps ◽

Effect Sizes ◽

Genome Wide Association Studies ◽

Summary Statistics ◽

Sample Sizes ◽

Genetic Components ◽

Complex Phenotypes ◽

Genome Wide ◽

Z Scores

Genome-wide Association Studies (GWAS) result in millions of summary statistics (``z-scores'') for single nucleotide polymorphism (SNP) associations with phenotypes. These rich datasets afford deep insights into the nature and extent of genetic contributions to complex phenotypes such as psychiatric disorders, which are understood to have substantial genetic components that arise from very large numbers of SNPs. The complexity of the datasets, however, poses a significant challenge to maximizing their utility. This is reflected in a need for better understanding the landscape of z-scores, as such knowledge would enhance causal SNP and gene discovery, help elucidate mechanistic pathways, and inform future study design. Here we present a parsimonious methodology for modeling effect sizes and replication probabilities that does not require raw genotype data, relying only on summary statistics from GWAS substudies, and a scheme allowing for direct empirical validation. We show that modeling z-scores as a mixture of Gaussians is conceptually appropriate, in particular taking into account ubiquitous non-null effects that are likely in the datasets due to weak linkage disequilibrium with causal SNPs. The four-parameter model allows for estimating the degree of polygenicity of the phenotype -- the proportion of SNPs (after uniform pruning, so that large LD blocks are not over-represented) likely to be in strong LD with causal/mechanistically associated SNPs -- and predicting the proportion of chip heritability explainable by genome wide significant SNPs in future studies with larger sample sizes. We apply the model to recent GWAS of schizophrenia (N=82,315) and additionally, for purposes of illustration, putamen volume (N=12,596), with approximately 9.3 million SNP z-scores in both cases. We show that, over a broad range of z-scores and sample sizes, the model accurately predicts expectation estimates of true effect sizes and replication probabilities in multistage GWAS designs. We estimate the degree to which effect sizes are over-estimated when based on linear regression association coefficients. We estimate the polygenicity of schizophrenia to be 0.037 and the putamen to be 0.001, while the respective sample sizes required to approach fully explaining the chip heritability are 106and 105. The model can be extended to incorporate prior knowledge such as pleiotropy and SNP annotation. The current findings suggest that the model is applicable to a broad array of complex phenotypes and will enhance understanding of their genetic architectures.

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Genome-wide characterization of genetic diversity and population structure of Valeriana officinalis L.

10.21203/rs.2.10069/v1 ◽

2019 ◽

Author(s):

Maja Boczkowska ◽

Katarzyna Bączek ◽

Olga Kosakowska ◽

Anna Rucińska ◽

Wiesław Podyma ◽

...

Keyword(s):

Population Structure ◽

Population Genomics ◽

Natural Populations ◽

Valeriana Officinalis ◽

Wild Populations ◽

Genetic Fingerprint ◽

Genome Wide ◽

Species Population ◽

Outcrossing Species

Abstract Background: Valeriana officinalis L. is one of the most important medicinal plant with a mild sedative, nervine, antispasmodic and relaxant effect. Despite a substantial number of studies on this species, population genomics has not yet been analyzed. The main aim of this study was: characterization of genetic variation of natural populations of V. officinalis in Poland and comparison of variation of wild populations and the cultivated form using Next Generation Sequencing based DArTseq technique. We also would like to establish foundations for genetic monitoring of the species in the future and to develop genetic fingerprint profile for samples deposited in gene bank and in natural sites in order to assess the degree of their genetic integrity and population structure preservation in the future.Results: The major and also the most astounding result of our work is the low level of observed heterozygosity of individual plants from natural populations despite the fact that the species is widespread in the studied area. Inbreeding, in naturally outcrossing species such as valerian, decreases the reproductive success. The analysis of the population structure indicated the potential presence of metapopulation in a broad area of Poland and the formation of a distinct gene pool in Bieszczady Mountains. The results also indicate the presence of individuals of the cultivated form in natural populations in the region where the species is cultivated for the needs of the pharmaceutical industry and this could lead to structural and genetic imbalance in wild populations.Conclusions: The DArTseq technology can be applied effectively in genetic studies of V. officinalis. The genetic variability of wild populations is in fact significantly lower than assumed. Individuals from the cultivated population are found in the natural environment and their impact on wild populations should be monitored.

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Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds

10.21203/rs.2.21585/v4 ◽

2020 ◽

Author(s):

Xunhe Huang ◽

Newton O. Otecko ◽

Minsheng Peng ◽

Zhuoxian Weng ◽

Weina Li ◽

...

Keyword(s):

Genetic Structure ◽

Population Genomics ◽

Biochemical Properties ◽

Conservation Strategies ◽

Potential Candidate ◽

Solute Carrier Family ◽

Indigenous Chicken ◽

Genome Wide ◽

Yellow Color ◽

Solute Carrier

Abstract Background: Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these iconic chickens. This study aimed to uncover the genetic structure and the molecular underpinnings of the YFCs trademark coloration. Results: The whole-genomes of 100 YFCs from 10 major traditional breeds and 10 Huaibei partridge chickens from China were re-sequenced. Comparative population genomics based on autosomal single nucleotide polymorphisms (SNPs) revealed three geographically based clusters among the YFCs. Compared to other Chinese indigenous chicken genomes incorporated from previous studies, a closer genetic proximity within YFC breeds than between YFC breeds and other chicken populations is evident. Through genome-wide scans for selective sweeps, we identified RALY heterogeneous nuclear ribonucleoprotein (RALY), leucine rich repeat containing G protein-coupled receptor 4 ( LGR4 ), solute carrier family 23 member 2 ( SLC23A2 ), and solute carrier family 2 member 14 ( SLC2A14 ), besides the classical beta-carotene dioxygenase 2 ( BCDO2 ), as major candidates pigment determining genes in the YFCs. Conclusion: We provide the first comprehensive genomic data of the YFCs. Our analyses show phylogeographical patterns among the YFCs and potential candidate genes giving rise to the yellow color trait of the YFCs. This study lays the foundation for further research on the genome-phenotype cross-talks that define important poultry traits and for formulating genetic breeding and conservation strategies for the YFCs.

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Increased antibiotic susceptibility in Neisseria gonorrhoeae through adaptation to the cervical environment

10.1101/2020.01.07.896696 ◽

2020 ◽

Cited By ~ 6

Author(s):

Kevin C Ma ◽

Tatum D Mortimer ◽

Allison L Hicks ◽

Nicole E Wheeler ◽

Leonor Sánchez-Busó ◽

...

Keyword(s):

Neisseria Gonorrhoeae ◽

Antibiotic Susceptibility ◽

Microbial Population ◽

Population Genomics ◽

Efflux Pump ◽

Loss Of Function ◽

Environmental Pressures ◽

Genome Wide ◽

A Subunit ◽

The Impact

AbstractNeisseria gonorrhoeae is an urgent public health threat due to rapidly increasing incidence and antibiotic resistance. In contrast with the trend of increasing resistance, clinical isolates that have reverted to susceptibility regularly appear, prompting questions about which pressures compete with antibiotics to shape gonococcal evolution. Here, we used genome-wide association on the largest collection of N. gonorrhoeae isolates to date (n=4852) to identify loss-of-function (LOF) mutations in the efflux pump mtrCDE operon as a mechanism of increased antibiotic susceptibility and demonstrate that these mutations are overrepresented in cervical isolates relative to urethral isolates (odds ratio (OR) = 3.74, 95% CI [1.98-6.70]). In support of a model in which pump expression incurs a fitness cost in this niche, cervical isolates were also enriched relative to urethral isolates in LOF mutations in the mtrCDE activator mtrA (OR = 8.60, 95% CI [4.96-14.57]) and in farA, a subunit of the FarAB efflux pump (OR = 6.25, 95% CI [3.90-9.83]). In total, approximately 2 in 5 cervical isolates (42.6%) contained a LOF mutation in either the efflux pump components mtrC or farA or the activator mtrA. Our findings extend beyond N. gonorrhoeae to other Neisseria: mtrC LOF mutations are rare (<1%) in the primarily nasopharyngeal-colonizing N. meningitidis in a collection of 14,798 genomes but enriched in a heterosexual urethritis-associated lineage (8.6%, p = 9.90×10−5), indicating that efflux pump downregulation contributes broadly to the adaptation of pathogenic Neisseria to the female urogenital tract. Overall, our findings highlight the impact of integrating microbial population genomics with host metadata and demonstrate how host environmental pressures can lead to increased antibiotic susceptibility.

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Exploring the industrial potential of Lactobacillus delbrueckii ssp. bulgaricus by population genomics and genome-wide association study analysis

Journal of Dairy Science ◽

10.3168/jds.2020-19467 ◽

2021 ◽

Vol 104 (4) ◽

pp. 4044-4055

Author(s):

Yuqin Song ◽

Jie Zhao ◽

Wenjun Liu ◽

Weicheng Li ◽

Zhihong Sun ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Population Genomics ◽

Lactobacillus Delbrueckii ◽

Genome Wide Association ◽

Study Analysis ◽

Genome Wide

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A Whole Genome Re-Sequencing Based GWA Analysis Reveals Candidate Genes Associated with Ivermectin Resistance in Haemonchus contortus

Genes ◽

10.3390/genes11040367 ◽

2020 ◽

Vol 11 (4) ◽

pp. 367 ◽

Cited By ~ 4

Author(s):

Sawar Khan ◽

Ayesha Nisar ◽

Jianqi Yuan ◽

Xiaoping Luo ◽

Xueqin Dou ◽

...

Keyword(s):

Candidate Genes ◽

Haemonchus Contortus ◽

Population Genomics ◽

Small Ruminants ◽

Track Record ◽

Genome Wide ◽

Signatures Of Selection ◽

Parasitic Worms ◽

Important Parasite

The most important and broad-spectrum drug used to control the parasitic worms to date is ivermectin (IVM). Resistance against IVM has emerged in parasites, and preserving its efficacy is now becoming a serious issue. The parasitic nematode Haemonchus contortus (Rudolphi, 1803) is economically an important parasite of small ruminants across the globe, which has a successful track record in IVM resistance. There are growing evidences regarding the multigenic nature of IVM resistance, and although some genes have been proposed as candidates of IVM resistance using lower magnification of genome, the genetic basis of IVM resistance still remains poorly resolved. Using the full magnification of genome, we herein applied a population genomics approach to characterize genome-wide signatures of selection among pooled worms from two susceptible and six ivermectin-resistant isolates of H. contortus, and revealed candidate genes under selection in relation to IVM resistance. These candidates also included a previously known IVM-resistance-associated candidate gene HCON_00148840, glc-3. Finally, an RNA-interference-based functional validation assay revealed the HCON_00143950 as IVM-tolerance-associated gene in H. contortus. The possible role of this gene in IVM resistance could be detoxification of xenobiotic in phase I of xenobiotic metabolism. The results of this study further enhance our understanding on the IVM resistance and continue to provide further evidence in favor of multigenic nature of IVM resistance.

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Current State and Perspectives in Population Genomics of the Common Bean

Plants ◽

10.3390/plants9030330 ◽

2020 ◽

Vol 9 (3) ◽

pp. 330 ◽

Cited By ~ 3

Author(s):

Gaia Cortinovis ◽

Giulia Frascarelli ◽

Valerio Di Vittori ◽

Roberto Papa

Keyword(s):

Common Bean ◽

Population Genomics ◽

Crop Evolution ◽

Entire Genome ◽

Sequencing Technologies ◽

Specific Effects ◽

Current State ◽

Genome Wide ◽

History Of ◽

Genomic Basis

Population genomics integrates advances in sequencing technologies, bioinformatics tools, statistical methods and software into research on evolutionary and population genetics. Its application has provided novel approaches that have significantly advanced our understanding of new and long-standing questions in evolutionary processes. This has allowed the disentangling of locus-specific effects from genome-wide effects and has shed light on the genomic basis of fitness, local adaptation and phenotypes. “-Omics” tools have provided a comprehensive genome-wide view of the action of evolution. The specific features of the Phaseolus genus have made it a unique example for the study of crop evolution. The well-documented history of multiple domestications in Phaseolus vulgaris L. (common bean) and its further adaptation to different environments have provided the opportunity to investigate evolutionary issues, such as convergent evolution in the same species across different domestication events. Moreover, the availability of the P. vulgaris reference genome now allows adaptive variations to be easily mapped across the entire genome. Here, we provide an overview of the most significant outcomes obtained in common bean through the use of different computational tools for analysis of population genomics data.

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