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

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

Scientific Reports ◽

10.1038/s41598-020-74508-9 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Andras Balogh ◽

Lam Ngo ◽

Kirk S. Zigler ◽

Groves Dixon

Keyword(s):

Genetic Divergence ◽

Population Genomics ◽

Sample Sizes ◽

Dense Region ◽

Evolutionary Processes ◽

Cumberland Plateau ◽

Selective Pressures ◽

Genome Wide ◽

Good Sample ◽

Limited Dispersal

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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Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species

Genome Biology and Evolution ◽

10.1093/gbe/evz212 ◽

2019 ◽

Vol 11 (10) ◽

pp. 2875-2886 ◽

Cited By ~ 1

Author(s):

Venkat Talla ◽

Lucile Soler ◽

Takeshi Kawakami ◽

Vlad Dincă ◽

Roger Vila ◽

...

Keyword(s):

Genetic Diversity ◽

Natural Selection ◽

Nucleotide Diversity ◽

Gene Annotation ◽

Rate Variation ◽

Butterfly Species ◽

Relative Role ◽

Effective Population ◽

Genome Wide ◽

Population Sizes

Abstract The relative role of natural selection and genetic drift in evolution is a major topic of debate in evolutionary biology. Most knowledge spring from a small group of organisms and originate from before it was possible to generate genome-wide data on genetic variation. Hence, it is necessary to extend to a larger number of taxonomic groups, descriptive and hypothesis-based research aiming at understanding the proximate and ultimate mechanisms underlying both levels of genetic polymorphism and the efficiency of natural selection. In this study, we used data from 60 whole-genome resequenced individuals of three cryptic butterfly species (Leptidea sp.), together with novel gene annotation information and population recombination data. We characterized the overall prevalence of natural selection and investigated the effects of mutation and linked selection on regional variation in nucleotide diversity. Our analyses showed that genome-wide diversity and rate of adaptive substitutions were comparatively low, whereas nonsynonymous to synonymous polymorphism and substitution levels were comparatively high in Leptidea, suggesting small long-term effective population sizes. Still, negative selection on linked sites (background selection) has resulted in reduced nucleotide diversity in regions with relatively high gene density and low recombination rate. We also found a significant effect of mutation rate variation on levels of polymorphism. Finally, there were considerable population differences in levels of genetic diversity and pervasiveness of selection against slightly deleterious alleles, in line with expectations from differences in estimated effective population sizes.

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The genetic basis of cis-regulatory divergence between the subspecies of cultivated rice (Oryza sativa)

10.1101/511550 ◽

2019 ◽

Cited By ~ 2

Author(s):

Malachy T Campbell ◽

Qian Du ◽

Kan Liu ◽

Sandeep Sharma ◽

Chi Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Phenotypic Variability ◽

Cultivated Rice ◽

Regulatory Variation ◽

Selective Pressures ◽

Regulatory Variants ◽

Genome Wide ◽

Comprehensive Characterization ◽

Transcriptome Level

AbstractCultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1). The transcriptomes of the two subspecies of rice are highly divergent. The expression and genetic diversity was significantly lower within Japonica relative to Indica, which is consistent with the known population bottleneck during Japonica domestication. Moreover, 1,860 and 1,325 genes showed differences in heritability in the broad and narrow sense respectively, between the subspecies, which was driven largely by environmental and genetic effects rather than differences in phenotypic variability. We leveraged high-density genotypic data and transcript levels to identify cis-regulatory variants that may explain the genetic divergence between the subspecies. We identified significantly more eQTL that were specific to the Indica subspecies compared to Japonica, suggesting that the observed differences in expression and genetic variability also extends to cis-regulatory variation. We next explored the potential causes of this cis-regulatory divergence by assessing local genetic diversity for cis-eQTL. Local genetic diversity around subspecies-specific cis-eQTL was significantly lower than genome-wide averages in subspecies lacking the eQTL, suggesting that selective pressures may have shaped regulatory variation in each subspecies. This study provides the first comprehensive characterization of transcriptional and cis-regulatory variation in cultivated rice, and could be an important resource for future studies.

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Construction and Genetic Analysis of a Worldwide Core Collection of Rapeseed

10.21203/rs.3.rs-1059860/v1 ◽

2021 ◽

Author(s):

Yiyi Guo ◽

Ying Xu ◽

Tao Yan ◽

Lixi Jiang ◽

Jie Dong ◽

...

Keyword(s):

Genetic Diversity ◽

Flowering Time ◽

Core Collection ◽

Nucleotide Diversity ◽

Selective Sweep ◽

Oilseed Crop ◽

Genome Resequencing ◽

Genetic Studies ◽

Genome Wide ◽

Whole Genome Resequencing

Abstract Rapeseed (Brassica napus) is an important oilseed crop, which is widely planted in the world. In a previous study, we collected 991 accessions of rapeseed from the worldwide germplasm and revealed genetic polymorphisms within these germplasm by whole-genome resequencing. However, management of such a large amount of accessions is time-consuming, laborious and costly. Therefore, we constructed a core collection of rapeseed consisting of 300 worldwide accessions based on their genetic diversity. Compared with 991 accessions, the worldwide core collection showed similar geographic distribution, the proportion of three ecotypes, nucleotide diversity and the associated SNPs of flowering time. Besides, we identified FT ortholog (BnaA02g12130D) and FLC ortholog (BnaA10g22080D) responsible for flowering time and ecotype differentiation through selective sweep analysis and genome-wide association analysis (GWAS) of flowering time using the rapeseed core collection. FT and FLC are two well-known genes regulating flowering time in Arabidopsis. These results indicate that the worldwide core collection can represent the genetic diversity of 991 worldwide accessions, which could be more efficiently used for phenotypic and genetic studies in rapeseed.

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The Molecular Evolution of terminal ear1, a Regulatory Gene in the Genus Zea

Genetics ◽

10.1093/genetics/153.3.1455 ◽

1999 ◽

Vol 153 (3) ◽

pp. 1455-1462 ◽

Cited By ~ 8

Author(s):

Shawn E White ◽

John F Doebley

Keyword(s):

Genetic Diversity ◽

Nucleotide Diversity ◽

Morphological Evolution ◽

Regulatory Gene ◽

Synonymous Substitution ◽

Synonymous Substitution Rate ◽

Nucleotide Polymorphism ◽

Genome Wide ◽

A Genome ◽

Maize Gene

Abstract Nucleotide diversity in the terminal ear1 (te1) gene, a regulatory locus hypothesized to be involved in the morphological evolution of maize (Zea mays ssp. mays), was investigated for evidence of past selection. Nucleotide polymorphism in a 1.4-kb region of te1 was analyzed for a sample of 26 sequences isolated from 12 maize lines, five populations of the maize progenitor, Z. mays ssp. parviglumis, six other Zea populations, and two Tripsacum species. Although nucleotide diversity in te1 in maize is reduced relative to ssp. parviglumis, phylogenetic and statistical analyses of the pattern of polymorphism among these sequences provided no evidence of past selection, indicating that the region of the gene studied was probably not involved in maize evolution. The level of reduction in genetic diversity in te1 in maize relative to its progenitor is comparable to that found in previous reports for isozymes and other neutrally evolving maize genes and is consistent with a genome-wide reduction of genetic diversity resulting from a domestication bottleneck. An estimate of the age (1.2–1.4 million yr) of the maize gene pool based on te1 is roughly consistent with previous estimates based on other neutral genes, but may be biased by the apparently slow synonymous substitution rate at te1.

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Genetic diversity and population structure of popcorn germplasm resources using genome-wide SNPs through genotyping-by-sequencing

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01137-0 ◽

2021 ◽

Author(s):

Diansi Yu ◽

Hui Wang ◽

Wei Gu ◽

Tao Qin ◽

Pingdong Sun ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genotyping By Sequencing ◽

Germplasm Resources ◽

Genome Wide

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On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Genetics Selection Evolution ◽

10.1186/s12711-021-00639-w ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Gabriele Senczuk ◽

Salvatore Mastrangelo ◽

Paolo Ajmone-Marsan ◽

Zsolt Becskei ◽

Paolo Colangelo ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Indices ◽

Melting Pot ◽

Cattle Breeds ◽

Snp Data ◽

Early Migration ◽

Genome Wide ◽

European Colonization ◽

Approximate Bayesian ◽

European Cattle

Abstract Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

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