scholarly journals Evidence for extensive hybridisation and past introgression events in feather grasses using genome-wide SNP genotyping

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Evgenii Baiakhmetov ◽  
Daria Ryzhakova ◽  
Polina D. Gudkova ◽  
Marcin Nobis
Keyword(s):  
Large Scale ◽  
Phenotypic Variability ◽  
Distinct Species ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
Grass Species ◽  
Hybrid Zones ◽  
Genetic Population ◽  
Contemporary Gene Flow ◽  
Genome Wide

Abstract Background The proper identification of feather grasses in nature is often limited due to phenotypic variability and high morphological similarity between many species. Among plausible factors influencing this issue are hybridisation and introgression recently detected in the genus. Nonetheless, to date, only a bounded set of taxa have been investigated using integrative taxonomy combining morphological and molecular data. Here, we report the first large-scale study on five feather grass species across several hybrid zones in Russia and Central Asia. In total, 302 specimens were sampled in the field and classified based on the current descriptions of these taxa. They were then genotyped with high density genome-wide markers and measured based on a set of morphological characters to delimitate species and assess levels of hybridisation and introgression. Moreover, we tested species for past introgression and estimated divergence times between them. Results Our findings demonstrated that 250 specimens represent five distinct species: S. baicalensis, S. capillata, S. glareosa, S. grandis and S. krylovii. The remaining 52 individuals provided evidence for extensive hybridisation between S. capillata and S. baicalensis, S. capillata and S. krylovii, S. baicalensis and S. krylovii, as well as to a lesser extent between S. grandis and S. krylovii, S. grandis and S. baicalensis. We detected past reticulation events between S. baicalensis, S. krylovii, S. grandis and inferred that diversification within species S. capillata, S. baicalensis, S. krylovii and S. grandis started ca. 130–96 kya. In addition, the assessment of genetic population structure revealed signs of contemporary gene flow between populations across species from the section Leiostipa, despite significant geographical distances between some of them. Lastly, we concluded that only 5 out of 52 hybrid taxa were properly identified solely based on morphology. Conclusions Our results support the hypothesis that hybridisation is an important mechanism driving evolution in Stipa. As an outcome, this phenomenon complicates identification of hybrid taxa in the field using morphological characters alone. Thus, integrative taxonomy seems to be the only reliable way to properly resolve the phylogenetic issue of Stipa. Moreover, we believe that feather grasses may be a suitable genus to study hybridisation and introgression events in nature.

scholarly journals Integrative taxonomy confirms the species status of the Himalayan langurs, Semnopithecus schistaceus Hodgson 1840

2019 ◽  
Author(s):  
Kunal Arekar ◽  
S. Sathyakumar ◽  
K. Praveen Karanth
Keyword(s):  
Taxonomic Status ◽  
Single Species ◽  
Distinct Species ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
Multiple Sources ◽  
Species Status ◽  
Species Identity ◽  
Hanuman Langur ◽  
As Species

AbstractTaxonomy is replete with groups where the species identity and classification remain unresolved. One such group is the widely distributed Hanuman langur (Colobinae: Semnopithecus). For most part of the last century, Hanuman langur was considered to be a single species with multiple subspecies. Nevertheless, recent studies using an integrative taxonomy approach suggested that this taxon is a complex, with at least three species. However, these studies did not include the Himalayan population of the Hanuman langur whose taxonomic status remains unresolved. The Himalayan population of Hanuman langurs have been classified as a distinct species with multiple subspecies or have been subsumed into other species. These classification schemes are wholly based on morphological characters and which are sometimes insufficient to delimit different species. Here, we have integrated data from multiple sources viz. morphology, DNA, and ecology to resolve the taxonomy of the Himalayan langur and to understand its distribution limit. Our results with three lines of evidence corresponding to three different species concepts show that Himalayan langur is a distinct species from S. entellus of the plains. Additionally, these results did not show any support for splitting of the Himalayan langur into multiple subspecies. Our study supports the classification proposed by Hill (1939) and we recommend Semnopithecus schistaceus, Hodgson 1840 as species name for the Himalayan langur and subsume all the known subspecies into it.

Genome-wide association study of rice grain width variation

Genome ◽  
2018 ◽  
Vol 61 (4) ◽  
pp. 233-240 ◽  
Author(s):  
Xiao-Ming Zheng ◽  
Tingting Gong ◽  
Hong-Ling Ou ◽  
Dayuan Xue ◽  
Weihua Qiao ◽  
...  
Keyword(s):  
Association Study ◽  
Seed Size ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Rice Variety ◽  
Genome Wide Association ◽  
Grass Species ◽  
Rice Grain ◽  
Genome Wide ◽  
Grain Width

Seed size is variable within many plant species, and understanding the underlying genetic factors can provide insights into mechanisms of local environmental adaptation. Here we make use of the abundant genomic and germplasm resources available for rice (Oryza sativa) to perform a large-scale genome-wide association study (GWAS) of grain width. Grain width varies widely within the crop and is also known to show climate-associated variation across populations of its wild progenitor. Using a filtered dataset of >1.9 million genome-wide SNPs in a sample of 570 cultivated and wild rice accessions, we performed GWAS with two complementary models, GLM and MLM. The models yielded 10 and 33 significant associations, respectively, and jointly yielded seven candidate locus regions, two of which have been previously identified. Analyses of nucleotide diversity and haplotype distributions at these loci revealed signatures of selection and patterns consistent with adaptive introgression of grain width alleles across rice variety groups. The results provide a 50% increase in the total number of rice grain width loci mapped to date and support a polygenic model whereby grain width is shaped by gene-by-environment interactions. These loci can potentially serve as candidates for studies of adaptive seed size variation in wild grass species.

scholarly journals Two new hybrid zones expand the swordtail hybridization model system

2020 ◽  
Author(s):  
Daniel L. Powell ◽  
Ben Moran ◽  
Bernard Kim ◽  
Shreya M. Banerjee ◽  
Stepfanie M. Aguillon ◽  
...  
Keyword(s):  
Distinct Species ◽  
Model System ◽  
Natural Hybridization ◽  
Hybrid Zones ◽  
Local Ancestry ◽  
Swordtail Fish ◽  
Contemporary Gene Flow ◽  
Species Pairs ◽  
Low Coverage ◽  
Hybridization Model

AbstractNatural hybridization events provide unique windows into the barriers that keep species apart as well as the consequences of their breakdown. Here we characterize hybrid populations formed between the northern swordtail fish Xiphophorus cortezi and X. birchmanni from collection sites on two rivers. We develop sensitive and accurate local ancestry calling for this system based on low coverage whole genome sequencing. Strikingly, we find that hybrid populations on both rivers consist of two genetically distinct subpopulations: a cluster of nearly pure X. birchmanni individuals and one of phenotypically intermediate hybrids that derive ~85-90% of their genome from X. cortezi. Simulations and empirical data suggest that at both sites initial hybridization occurred ~150 generations ago, with little evidence for contemporary gene flow between subpopulations, likely due to strong assortative mating. The patterns of population structure uncovered here mirror those seen in hybridization between X. birchmanni and its sister species, X. malinche. Future comparisons will provide a window into the repeatability of the outcomes of hybridization not only across independent hybridization events between the same species but also across distinct species pairs.

scholarly journals BiPSim: a flexible and generic stochastic simulator for polymerization processes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Stephan Fischer ◽  
Marc Dinh ◽  
Vincent Henry ◽  
Philippe Robert ◽  
Anne Goelzer ◽  
...  
Keyword(s):  
Large Scale ◽  
Stochastic Simulation Algorithm ◽  
Specific Information ◽  
Whole Cell ◽  
Simulation Speed ◽  
Genome Wide ◽  
Cell Simulation ◽  
Stochastic Simulator ◽  
Modeling Formalisms ◽  
Stochastic Phenomena

AbstractDetailed whole-cell modeling requires an integration of heterogeneous cell processes having different modeling formalisms, for which whole-cell simulation could remain tractable. Here, we introduce BiPSim, an open-source stochastic simulator of template-based polymerization processes, such as replication, transcription and translation. BiPSim combines an efficient abstract representation of reactions and a constant-time implementation of the Gillespie’s Stochastic Simulation Algorithm (SSA) with respect to reactions, which makes it highly efficient to simulate large-scale polymerization processes stochastically. Moreover, multi-level descriptions of polymerization processes can be handled simultaneously, allowing the user to tune a trade-off between simulation speed and model granularity. We evaluated the performance of BiPSim by simulating genome-wide gene expression in bacteria for multiple levels of granularity. Finally, since no cell-type specific information is hard-coded in the simulator, models can easily be adapted to other organismal species. We expect that BiPSim should open new perspectives for the genome-wide simulation of stochastic phenomena in biology.

scholarly journals Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

2021 ◽  
Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Species Complex ◽  
Large Scale ◽  
Genomic Sequence ◽  
Bacterial Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
The Novel ◽  
Staphylococcus Cohnii ◽  
Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

scholarly journals Cerebrospinal fluid metabolomics identifies 19 brain-related phenotype associations

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Daniel J. Panyard ◽  
Kyeong Mo Kim ◽  
Burcu F. Darst ◽  
Yuetiva K. Deming ◽  
Xiaoyuan Zhong ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Drug Targets ◽  
Large Scale ◽  
Prediction Models ◽  
Genome Wide Association ◽  
Large Samples ◽  
Genome Wide ◽  
Metabolomic Data ◽  
Related Phenotype ◽  
Omic Data

AbstractThe study of metabolomics and disease has enabled the discovery of new risk factors, diagnostic markers, and drug targets. For neurological and psychiatric phenotypes, the cerebrospinal fluid (CSF) is of particular importance. However, the CSF metabolome is difficult to study on a large scale due to the relative complexity of the procedure needed to collect the fluid. Here, we present a metabolome-wide association study (MWAS), which uses genetic and metabolomic data to impute metabolites into large samples with genome-wide association summary statistics. We conduct a metabolome-wide, genome-wide association analysis with 338 CSF metabolites, identifying 16 genotype-metabolite associations (metabolite quantitative trait loci, or mQTLs). We then build prediction models for all available CSF metabolites and test for associations with 27 neurological and psychiatric phenotypes, identifying 19 significant CSF metabolite-phenotype associations. Our results demonstrate the feasibility of MWAS to study omic data in scarce sample types.

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