The conundrum of species delimitation: a genomic perspective on a mitogenetically super-variable butterfly

The Palaearctic butterfly Melitaea didyma stands out as one of the most striking cases of intraspecific genetic differentiation detected in Lepidoptera: 11 partially sympatric mitochondrial lineages have been reported, displaying levels of divergence of up to 7.4%. To better understand the evolutionary processes underlying the diversity observed in mtDNA, we compared mtDNA and genome-wide SNP data using double-digest restriction site-associated DNA sequencing (ddRADseq) results from 93 specimens of M. didyma ranging from Morocco to eastern Kazakhstan. We found that, between ddRADseq and mtDNA results, there is a match only in populations that probably remained allopatric for long periods of time. Other mtDNA lineages may have resulted from introgression events and were probably affected by Wolbachia infection. The five main ddRADseq clades supported by STRUCTURE were parapatric or allopatric and showed high pairwise F ST values, but some were also estimated to display various levels of gene flow. Melitaea didyma represents one of the first cases of deep mtDNA splits among European butterflies assessed by a genome-wide DNA analysis and reveals that the interpretation of patterns remains challenging even when a high amount of genomic data is available. These findings actualize the ongoing debate of species delimitation in allopatry, an issue probably of relevance to a significant proportion of global biodiversity.

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Genetic analysis of sucrose concentration in soybean seeds using a historical soybean genomic panel

10.21203/rs.3.rs-158915/v1 ◽

2021 ◽

Author(s):

Alexandra Ficht ◽

Robert W. Bruce ◽

Davoud Torkamaneh ◽

Christopher Grainger ◽

Milad Eskandari ◽

...

Keyword(s):

Genetic Variability ◽

Genome Wide Association Study ◽

Sucrose Concentration ◽

Soybean Seed ◽

Breeding Programs ◽

Snp Data ◽

Genome Wide ◽

A Genome ◽

Important Trait ◽

Genotype By Sequencing

Abstract Soybean (Glycine max (L.) Merr) is a crop of global importance for both human and animal consumption, which was domesticated in China more than 6000 years ago. A concern about losing genetic diversity as a result of decades of breeding has been expressed by soybean researchers. In order to develop new cultivars, it is critical for breeders to understand the genetic variability present for traits of interest in their program germplasm. Sucrose concentration is becoming an increasingly important trait for the production of soy-food products. The objective of this study was to use a genome-wide association study (GWAS) to identify putative QTL for sucrose concentration in soybean seed. A GWAS panel consisting of 266 historic and current soybean accessions was genotyped with 76k genotype-by-sequencing (GBS) SNP data and phenotyped in four field locations in Ontario (Canada) from 2015 to 2017. Seven putative QTL were identified on chromosomes 1, 6, 8, 9, 10, 13 and 14. A key gene related to sucrose synthase (Glyma.06g182700) was found to be associated with the QTL found on chromosome 6. This information will facilitate efforts to increase the available genetic variability for sucrose concentration in soybean breeding programs and develop new and improved high-sucrose soybean cultivars suitable for the soy-food industry.

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Species Delimitation using Genome-Wide SNP Data

10.1101/001172 ◽

2013 ◽

Author(s):

Adam Leache ◽

Matthew Fujita ◽

Vladimir Minin ◽

Remco Bouckaert

Keyword(s):

Species Delimitation ◽

Dynamic Programming Algorithm ◽

Common Denominator ◽

Gene Trees ◽

Species Trees ◽

Competing Species ◽

Marginal Likelihoods ◽

Snp Data ◽

Genome Wide ◽

True Model

The multi-species coalescent has provided important progress for evolutionary inferences, including increasing the statistical rigor and objectivity of comparisons among competing species delimitation models. However, Bayesian species delimitation methods typically require brute force integration over gene trees via Markov chain Monte Carlo (MCMC), which introduces a large computation burden and precludes their application to genomic-scale data. Here we combine a recently introduced dynamic programming algorithm for estimating species trees that bypasses MCMC integration over gene trees with sophisticated methods for estimating marginal likelihoods, needed for Bayesian model selection, to provide a rigorous and computationally tractable technique for genome-wide species delimitation. We provide a critical yet simple correction that brings the likelihoods of different species trees, and more importantly their corresponding marginal likelihoods, to the same common denominator, which enables direct and accurate comparisons of competing species delimitation models using Bayes factors. We test this approach, which we call Bayes factor delimitation (*with genomic data; BFD*), using common species delimitation scenarios with computer simulations. Varying the numbers of loci and the number of samples suggest that the approach can distinguish the true model even with few loci and limited samples per species. Misspecification of the prior for population size θ has little impact on support for the true model. We apply the approach to West African forest geckos (Hemidactylus fasciatus complex) using genome-wide SNP data data. This new Bayesian method for species delimitation builds on a growing trend for objective species delimitation methods with explicit model assumptions that are easily tested.

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Post-Genotyping Optimization of Dataset Formation Could Affect Genetic Diversity Parameters: An Example of Analyses with Alpine Goat Breeds

10.21203/rs.3.rs-133590/v1 ◽

2020 ◽

Author(s):

Neža Pogorevc ◽

Mojca Simčič ◽

Negar Khayatzadeh ◽

Johann Soelkner ◽

Beate Berger ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Genetic Distances ◽

Phylogenetic Study ◽

European Alps ◽

Global Context ◽

Outlier Test ◽

Snp Data ◽

Genome Wide ◽

A Genome

Abstract BackgroundLocal breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. One objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters.ResultsDistinct genetic origin of the Drežnica goat was demonstrated having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Drežnica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning.ConclusionsGenetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of the breeding and management programs and therefore important for preserving genetic variability and uniqueness of local rare breeds.

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Mapping of genome-wide copy number variations in the Iranian indigenous cattle using a dense SNP data set

Animal Production Science ◽

10.1071/an16384 ◽

2018 ◽

Vol 58 (7) ◽

pp. 1192 ◽

Cited By ~ 3

Author(s):

K. Karimi ◽

A. Esmailizadeh ◽

D. D. Wu ◽

C. Gondro

Keyword(s):

Copy Number ◽

Copy Number Variations ◽

Indigenous Cattle ◽

Data Set ◽

Single Nucleotide ◽

Snp Data ◽

Genome Wide ◽

A Genome ◽

Wide Range ◽

Environmental Responses

The objective of this study was to present the first map of the copy number variations (CNVs) in Iranian indigenous cattle based on a high-density single nucleotide polymorphism (SNP) dataset. A total of 90 individuals were genotyped using the Illumina BovineHD BeadChip containing 777 962 SNPs. The QuantiSNP algorithm was used to perform a genome-wide CNV detection across autosomal genome. After merging the overlapping CNV, a total of 221 CNV regions were identified encompassing 36.4 Mb or 1.44% of the bovine autosomal genome. The length of the CNV regions ranged from 3.5 to 2252.8 Kb with an average of 163.8 Kb. These regions included 147 loss (66.52%) and 74 gain (33.48%) events containing a total of 637 annotated Ensembl genes. Gene ontology analysis revealed that most of genes in the CNV regions were involved in environmental responses, disease susceptibility and immune system functions. Furthermore, 543 of these genes corresponded to the human orthologous genes, which involved in a wide range of biological functions. Altogether, 73% of the 221 CNV regions overlapped either completely or partially with those previously reported in other cattle studies. Moreover, novel CNV regions involved several quantitative trait loci (QTL)-related to adaptative traits of Iranian indigenous cattle. These results provided a basis to conduct future studies on association between CNV regions and phenotypic variations in the Iranian indigenous cattle.

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Species Delimitation using Genome-Wide SNP Data

Systematic Biology ◽

10.1093/sysbio/syu018 ◽

2014 ◽

Vol 63 (4) ◽

pp. 534-542 ◽

Cited By ~ 216

Author(s):

Adam D. Leaché ◽

Matthew K. Fujita ◽

Vladimir N. Minin ◽

Remco R. Bouckaert

Keyword(s):

Species Delimitation ◽

Snp Data ◽

Genome Wide

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Estimating the heritability of reporting stressful life events captured by common genetic variants

Psychological Medicine ◽

10.1017/s0033291712002589 ◽

2012 ◽

Vol 43 (9) ◽

pp. 1965-1971 ◽

Cited By ~ 32

Author(s):

R. A. Power ◽

T. Wingenbach ◽

S. Cohen-Woods ◽

R. Uher ◽

M. Y. Ng ◽

...

Keyword(s):

Life Events ◽

Genetic Variants ◽

Stressful Life Events ◽

Genome Wide Association Study ◽

Significant Proportion ◽

Stressful Life ◽

Phenotypic Variance ◽

Genome Wide ◽

Common Genetic Variants ◽

A Genome

BackgroundAlthough usually thought of as external environmental stressors, a significant heritable component has been reported for measures of stressful life events (SLEs) in twin studies.MethodWe examined the variance in SLEs captured by common genetic variants from a genome-wide association study (GWAS) of 2578 individuals. Genome-wide complex trait analysis (GCTA) was used to estimate the phenotypic variance tagged by single nucleotide polymorphisms (SNPs). We also performed a GWAS on the number of SLEs, and looked at correlations between siblings.ResultsA significant proportion of variance in SLEs was captured by SNPs (30%, p = 0.04). When events were divided into those considered to be dependent or independent, an equal amount of variance was explained for both. This ‘heritability’ was in part confounded by personality measures of neuroticism and psychoticism. A GWAS for the total number of SLEs revealed one SNP that reached genome-wide significance (p = 4 × 10−8), although this association was not replicated in separate samples. Using available sibling data for 744 individuals, we also found a significant positive correlation of R2 = 0.08 in SLEs (p = 0.03).ConclusionsThese results provide independent validation from molecular data for the heritability of reporting environmental measures, and show that this heritability is in part due to both common variants and the confounding effect of personality.

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Genetic Architecture of Early Vigor Traits in Wild Soybean

International Journal of Molecular Sciences ◽

10.3390/ijms21093105 ◽

2020 ◽

Vol 21 (9) ◽

pp. 3105

Author(s):

Janice Kofsky ◽

Hengyou Zhang ◽

Bao-Hua Song

Keyword(s):

Genome Wide Association Study ◽

Agronomic Traits ◽

Glycine Soja ◽

Wild Soybean ◽

Current Increase ◽

Snp Data ◽

Genome Wide ◽

A Genome ◽

Cultivated Soybean ◽

Early Vigor

A worldwide food shortage has been projected as a result of the current increase in global population and climate change. In order to provide sufficient food to feed more people, we must develop crops that can produce higher yields. Plant early vigor traits, early growth rate (EGR), early plant height (EPH), inter-node length, and node count are important traits that are related to crop yield. Glycine soja, the wild counterpart to cultivated soybean, Glycine max, harbors much higher genetic diversity and can grow in diverse environments. It can also cross easily with cultivated soybean. Thus, it holds a great potential in developing soybean cultivars with beneficial agronomic traits. In this study, we used 225 wild soybean accessions originally from diverse environments across its geographic distribution in East Asia. We quantified the natural variation of several early vigor traits, investigated the relationships among them, and dissected the genetic basis of these traits by applying a Genome-Wide Association Study (GWAS) with genome-wide single nucleotide polymorphism (SNP) data. Our results showed positive correlation between all early vigor traits studied. A total of 12 SNPs significantly associated with EPH were identified with 4 shared with EGR. We also identified two candidate genes, Glyma.07G055800.1 and Glyma.07G055900.1, playing important roles in influencing trait variation in both EGR and EPH in G. soja.

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Signatures of selection in the genome of Swedish warmblood horses selected for sport performance

BMC Genomics ◽

10.1186/s12864-019-6079-1 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 15

Author(s):

Michela Ablondi ◽

Åsa Viklund ◽

Gabriella Lindgren ◽

Susanne Eriksson ◽

Sofia Mikko

Keyword(s):

Complex Traits ◽

Sport Performance ◽

Functional Studies ◽

Snp Data ◽

Genome Wide ◽

A Genome ◽

Physical Abilities ◽

Signatures Of Selection ◽

Selection For ◽

Genomic Regions

Abstract Background A growing demand for improved physical skills and mental attitude in modern sport horses has led to strong selection for performance in many warmblood studbooks. The aim of this study was to detect genomic regions with low diversity, and therefore potentially under selection, in Swedish Warmblood horses (SWB) by analysing high-density SNP data. To investigate if such signatures could be the result of selection for equestrian sport performance, we compared our SWB SNP data with those from Exmoor ponies, a horse breed not selected for sport performance traits. Results The genomic scan for homozygous regions identified long runs of homozygosity (ROH) shared by more than 85% of the genotyped SWB individuals. Such ROH were located on ECA4, ECA6, ECA7, ECA10 and ECA17. Long ROH were instead distributed evenly across the genome of Exmoor ponies in 77% of the chromosomes. Two population differentiation tests (FST and XP-EHH) revealed signatures of selection on ECA1, ECA4, and ECA6 in SWB horses. Conclusions Genes related to behaviour, physical abilities and fertility, appear to be targets of selection in the SWB breed. This study provides a genome-wide map of selection signatures in SWB horses, and ground for further functional studies to unravel the biological mechanisms behind complex traits in horses.

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Heritability And Genetic Correlations For Hormone-Sensitive Cancers In The UK Biobank: A Molecular Evidence of Shared Aetiology

10.21203/rs.3.rs-926833/v1 ◽

2021 ◽

Author(s):

Muktar Ahmed ◽

Ville-Petteri Mäkinen ◽

Anwar Mulugeta ◽

Jisu Shin ◽

Terry Boyle ◽

...

Keyword(s):

Genome Wide Association Study ◽

Genetic Correlations ◽

Significant Proportion ◽

Molecular Evidence ◽

Nucleotide Polymorphisms ◽

Uk Biobank ◽

Genome Wide ◽

A Genome ◽

Hormone Sensitive ◽

The Uk

Abstract Hormone-related cancers, including cancers of the breast, prostate, ovaries, uterine, and thyroid, globally contribute to the majority of cancer incidence. We hypothesize that hormone-sensitive cancers share common genetic risk factors that have rarely been investigated by previous genomic studies of site-specific cancers. To test this hypothesis, we analysed five hormone-sensitive cancers in the UK Biobank as a single disease. We observed that a significant proportion of variance in disease liability was explained by the genome-wide single nucleotide polymorphisms (SNPs), i.e., SNP-based heritability on the liability scale was estimated as 10.06% (SE 0.70%) for the disease. Moreover, we found 55 genome-wide significant SNPs for the disease, using a genome-wide association study. Our finding suggests that heritable genetic factors may be a key driver in the mechanism of carcinogenesis shared by hormone-sensitive cancers.

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