shared alleles
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2021 ◽  
Vol 25 (03) ◽  
pp. 757-762
Author(s):  
Anderson Vilasboa de Vasconcellos ◽  
◽  
Livia Bonetti Villela ◽  
Denise Borges dos Santos Dias ◽  
Karina Alessandra Morelli ◽  
...  

We analyzed the genetic connectivity between mullets (Mugil liza) captured around the protected Natural Monument of Cagarras Islands (MoNa Cagarras) and inside Rodrigo de Freitas Lagoon, using microsatellite markers polymorphisms. Our data revealed the occurrence of 31 shared alleles (from 41 sampled), a high similarity in both allelic frequencies and genetic diversity and lack of differentiation between collection points (FST = 0.000, p > 0.05, STRUCTURE best estimative K = 1), results which, analyzed together, are strongly indicative of panmixia. We conclude that individuals collected inside the Rodrigo de Freitas Lagoon are genetically similar to those individuals collected around MoNa Cagarras. Given the importance of estuaries for the reproduction and development of individuals of M. liza, it is recommended that the Rodrigo de Freitas Lagoon to be managed in order to maintain genetic connectivity and diversity between the two ecosystems.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Veronika Konečná ◽  
Sian Bray ◽  
Jakub Vlček ◽  
Magdalena Bohutínská ◽  
Doubravka Požárová ◽  
...  

AbstractRelative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated serpentine invasion, we assess selection on SNPs and structural variants (TEs) in 78 resequenced individuals and discover significant parallelism in candidate genes involved in ion homeostasis. We further model parallel selection and infer repeated sweeps on a shared pool of variants in nearly all these loci, supporting theoretical expectations. A single striking exception is represented by TWO PORE CHANNEL 1, which exhibits convergent evolution from independent de novo mutations at an identical, otherwise conserved site at the calcium channel selectivity gate. Taken together, this suggests that polyploid populations can rapidly adapt to environmental extremes, calling on both pre-existing variation and novel polymorphisms.


2021 ◽  
Author(s):  
Carlos G. Boluda ◽  
Víctor J. Rico ◽  
Yamama Naciri ◽  
David L. Hawksworth ◽  
Christoph Scheidegger
Keyword(s):  

2021 ◽  
Author(s):  
Mengge Wang ◽  
Weian Du ◽  
Renkuan Tang ◽  
Yan Liu ◽  
Xing Zou ◽  
...  

Sherpa people, one of the high-altitude hypoxic adaptive populations, mainly reside in Nepal and the southern Tibet Autonomous Region. The genetic origin and detailed evolutionary profiles of Sherpas remain to be further explored and comprehensively characterized. Here we analyzed the newly-generated InDel genotype data from 628 Dingjie Sherpa people by merging with 4222 worldwide InDel profiles and collected genome-wide SNP data (approximately 600K SNPs) from 3324 individuals in 382 modern and ancient populations to explore and reconstruct the fine-scale genetic structure of Sherpas and their relationships with nearby modern and ancient East Asians based on the shared alleles and haplotypes. The forensic parameters of 57 autosomal InDels (A-InDels) included in our used new-generation InDel amplification system showed that this updated InDel panel is informative and polymorphic in Sherpas, suggesting that it can be used as the supplementary tool for forensic personal identification and parentage testing in the highland East Asians. Descriptive findings from the PCA, ADMIXTURE and TreeMix-based phylogeny suggested that Sherpas showed excess allele sharing with neighboring Tibeto-Burman Tibetans. Furthermore, patterns of allele sharing in f-statistics demonstrated that Sherpa people had a different evolutionary history compared with their neighbors from Nepal (Newar and Gurung) but showed genetic similarity with 2700-year-old Chokhopani and modern Tibet Tibetans. QpAdm/qpGraph-based admixture sources and models further showed that Sherpa, core Tibetans and Chokhopani formed one clade which could be fitted as having the main ancestry from late Neolithic Qijia millet farmers and other deep ancestries from early Asians. Chromosome painting profiles and shared IBD fragments inferred from FineStructure and ChromoPainter not only confirmed the abovementioned genomic affinity patterns but also revealed the fine-scale microstructures among Sino-Tibetan speakers. Finally, natural-selection signals revealed via iHS, nSL, and iHH12 showed signatures associated with disease susceptibility in Sherpa people. Generally, we provided the comprehensive landscape of admixture and evolutionary history of Sherpa people based on the shared alleles and haplotypes from the low-density forensic markers and high-density genome-wide SNP data. The more detailed genetic landscape of Sherpa people should be further confirmed and characterized via ancient genomes or single-molecule real-time sequencing technology.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sunčica Stipoljev ◽  
Toni Safner ◽  
Pavao Gančević ◽  
Ana Galov ◽  
Tina Stuhne ◽  
...  

AbstractThe aoudad (Ammotragus lervia Pallas 1777) is an ungulate species, native to the mountain ranges of North Africa. In the second half of the twentieth century, it was successfully introduced in some European countries, mainly for hunting purposes, i.e. in Croatia, the Czech Republic, Italy, and Spain. We used neutral genetic markers, the mitochondrial DNA control region sequence and microsatellite loci, to characterize and compare genetic diversity and spatial pattern of genetic structure on different timeframes among all European aoudad populations. Four distinct control region haplotypes found in European aoudad populations indicate that the aoudad has been introduced in Europe from multiple genetic sources, with the population in the Sierra Espuña as the only population in which more than one haplotype was detected. The number of detected microsatellite alleles within all populations (< 3.61) and mean proportion of shared alleles within all analysed populations (< 0.55) indicates relatively low genetic variability, as expected for new populations funded by a small number of individuals. In STRUCTURE results with K = 2–4, Croatian and Czech populations cluster in the same genetic cluster, indicating joined origin. Among three populations from Spain, Almeria population shows as genetically distinct from others in results, while other Spanish populations diverge at K = 4. Maintenance of genetic diversity should be included in the management of populations to sustain their viability, specially for small Czech population with high proportion of shared alleles (0.85) and Croatian population that had the smallest estimated effective population size (Ne = 5.4).


2021 ◽  
Author(s):  
Sonia Kakkar ◽  
Phulen Sarma ◽  
Inusha Pannigrihi ◽  
S. P. Mandal ◽  
R. K. Kumawat ◽  
...  

Abstract kinship analysis in forensic is based on calculation of respective kinship indices. But calculation of the same is possible only when the subject under identification has been associated to a particular population whose gene frequency data is available for the particular set of markers used in forensic practices. In case of the mass disasters where a huge number of individuals are to be identified, gathering the population frequency data and calculating the kinship indices can be an intricate progression requiring a lot of time and huge resources. The present study is based on allele matching score values which doesn’t require the use of allele frequency data to establish kinship. This method is based on the allele sharing approach which simply refers to the number of shared alleles (1 or 2) between two individuals; also known as identical by state (IBS) alleles which might have been inherited from a recent common ancestor in which the alleles are identical by descendent (IBD). In case of mass disasters this method can be used to narrow down the investigation by screening the number of related individuals which can further be confirmed with other tests if required. This method has been tested for various statistical parameters and has shown promising values which suggests the potential use of this method in forensic practice. This method has been tested on siblings and grandparent-grandchildren by using autosomal and X-STR markers both as the reference samples from parents can’t always be available. The present study also compares the results shown by autosomal and X-STR markers in siblings and grandparent-grandchildren identification, thereby suggesting the better set of markers for siblings and grandparent-grandchildren identification.


2021 ◽  
Author(s):  
Matthew R Lincoln ◽  
Noah Connally ◽  
Pierre-Paul Axisa ◽  
Christiane Gasperi ◽  
Mitja Mitrovic ◽  
...  

Autoimmune and inflammatory diseases are polygenic disorders of the immune system. Many genomic loci harbor risk alleles for several diseases, but the limited resolution of genetic mapping prevents deter- mining if the same allele is responsible, indicating a shared underlying mechanism. Using a collection of 129,058 cases and controls across six diseases, we show that ~40% of overlapping associations are due to the same allele. We improve fine-mapping resolution for shared alleles two-fold by combining cases and controls across diseases, allowing us to identify more eQTLs driven by the shared alleles. The patterns of sharing indicate widespread shared mechanisms, but not a single global autoimmune mecha- nism. Our approach can be applied to any set of traits, and is particularly valuable as sample collections become depleted.


Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 429
Author(s):  
Grażyna Polak ◽  
Artur Gurgul ◽  
Igor Jasielczuk ◽  
Tomasz Szmatoła ◽  
Jędrzej Krupiński ◽  
...  

Traditionally, pedigree-based relationship coefficients were used to manage inbreeding and control inbreeding depression that occurs within populations. The extensive incorporation of genomic data in livestock breeding creates the opportunity to develop and implement methods to manage populations at the genomic level. Consequently, the realized proportion of the genome that two individuals share can be more accurately estimated instead of using pedigree information to estimate the expected proportion of shared alleles. To make use of this improvement, in this study we evaluated the genomic inbreeding measures in the Polish conserved cold-blooded horse population and compared the data with the traditional measures of inbreeding. Additionally, an ancestry fractions/proportions from Admixture software were tested as an estimate of lineage (ancestry coefficient) used for horses qualifying for the conservation program. The highest correlation of pedigree-based (FPED) and genomic inbreeding estimates was found for FROH (runs of homozygosity-based F coefficient) and FUNI (F coefficient based on the correlation between uniting gametes). FROH correlation with FPED tended to increase as the number of generations registered as pedigree increased. While lineage and gene contributions (Q) from Admixture software correlated, they showed poor direct compliance; hence, Q-value cannot be recommended as the estimate of pedigree-based lineage. All these findings suggest that the methods of genomics should be considered as an alternative or support in the analysis of population structure in conservative breeding that can help control inbreeding in rare horse populations.


2021 ◽  
Vol 17 (3) ◽  
Author(s):  
Yesbol Manat ◽  
Katrine K. Lund-Hansen ◽  
Georgios Katsianis ◽  
Jessica K. Abbott

Intralocus sexual conflict arises when the expression of shared alleles at a single locus generates opposite fitness effects in each sex (i.e. sexually antagonistic alleles), preventing each sex from reaching its sex-specific optimum. Despite its importance to reproductive success, the relative contribution of intralocus sexual conflict to male pre- and post-copulatory success is not well-understood. Here, we used a female-limited X-chromosome (FLX) evolution experiment in Drosophila melanogaster to limit the inheritance of the X-chromosome to the matriline, eliminating possible counter-selection in males and allowing the X-chromosome to accumulate female-benefit alleles. After more than 100 generations of FLX evolution, we studied the effect of the evolved X-chromosome on male attractiveness and sperm competitiveness. We found a non-significant increase in attractiveness and decrease in sperm offence ability in males expressing the evolved X-chromosomes, but a significant increase in their ability to avoid displacement by other males' sperm. This is consistent with a trade-off between these traits, perhaps mediated by differences in body size, causing a small net reduction in overall male fitness in the FLX lines. These results indicate that the X-chromosome in D. melanogaster is subject to selection via intralocus sexual conflict in males.


2021 ◽  
Author(s):  
Veronika Konečná ◽  
Sian Bray ◽  
Jakub Vlček ◽  
Magdalena Bohutínská ◽  
Doubravka Požárová ◽  
...  

AbstractRelative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms, which maintain increased variation. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated serpentine invasion, we assess selection on SNPs and structural variants (TEs) in 78 resequenced individuals and discovered substantial parallelism in candidate genes involved in ion homeostasis. We further modelled parallel selection and inferred repeated sweeps on a shared pool of variants in nearly all these loci, supporting theoretical expectations. A single, striking exception is represented by TWO PORE CHANNEL 1, which exhibits convergent evolution from independent de novo mutations at an identical, otherwise conserved site at the calcium channel selectivity gate. Taken together, this suggests that polyploid populations can rapidly adapt to environmental extremes, calling on both pre-existing variation and novel polymorphisms.


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