scholarly journals VolcanoFinder: genomic scans for adaptive introgression

2019 ◽  
Author(s):  
Derek Setter ◽  
Sylvain Mousset ◽  
Xiaoheng Cheng ◽  
Rasmus Nielsen ◽  
Michael DeGiorgio ◽  
...  
Keyword(s):  
Related Species ◽  
Genomic Data ◽  
Composite Likelihood ◽  
Genomic Variation ◽  
Human Populations ◽  
Closely Related Species ◽  
Adaptive Introgression ◽  
A Genome ◽  
Wide Range ◽  
Donor Species

AbstractRecent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method—VolcanoFinder—to detect recent events of adaptive introgression using polymorphism data from the recipient species only.VolcanoFinder detects adaptive introgression sweeps from the pattern of excess intermediate-frequency polymorphism they produce in the flanking region of the genome, a pattern which appears as a volcano-shape in pairwise genetic diversity.Using coalescent theory, we derive analytical predictions for these patterns. Based on these results, we develop a composite-likelihood test to detect signatures of adaptive introgression relative to the genomic background. Simulation results show that VolcanoFinder has high statistical power to detect these signatures, even for older sweeps and for soft sweeps initiated by multiple migrant haplotypes. Finally, we implement VolcanoFinder to detect archaic introgression in European and sub-Saharan African human populations, and uncovered interesting candidates in both populations, such as TSHR in Europeans and TCHH-RPTN in Africans. We discuss their biological implications and provide guidelines for identifying and circumventing artifactual signals during empirical applications of VolcanoFinder.Author summaryThe process by which beneficial alleles are introduced into a species from a closely-related species is termed adaptive introgression. We present an analytically-tractable model for the effects of adaptive introgression on non-adaptive genetic variation in the genomic region surrounding the beneficial allele. The result we describe is a characteristic volcano-shaped pattern of increased variability that arises around the positively-selected site, and we introduce an open-source method VolcanoFinder to detect this signal in genomic data. Importantly, VolcanoFinder is a population-genetic likelihood-based approach, rather than a comparative-genomic approach, and can therefore probe genomic variation data from a single population for footprints of adaptive introgression, even from a priori unknown and possibly extinct donor species.

Revision of Coronostrongylus (Nematoda : Strongyloidea) parasitic in the stomachs of macropodid marsupials

2002 ◽  
Vol 16 (6) ◽  
pp. 893 ◽  
Author(s):  
I. Beveridge
Keyword(s):  
Papua New Guinea ◽  
Host Species ◽  
Related Species ◽  
New Guinea ◽  
Nematode Species ◽  
Closely Related Species ◽  
Nematode Genus ◽  
Eastern Australia ◽  
Wide Range ◽  
Species Occurrences

The monotypic nematode genus Coronostrongylus Johnston & Mawson, 1939 from the stomachs of macropodid marsupials was reviewed and was found to consist of a least seven closely related species. Coronostrongylus coronatus Johnston & Mawson, 1939 is found most commonly in Macropus rufogriseus, but occurs occasionally in M. dorsalis, M. parryi and Petrogale inornata. Coronostrongylus johnsoni, sp. nov. is most commonly found in M. dorsalis, but occurs also in M. rufogriseus, M. parma, Thylogale stigmatica, Petrogale godmani and P. brachyotis. Coronostrongylus barkeri, sp. nov. is most prevalent in Onychogalea unguifera, but occurs also in M. rufus, M. robustus and P. brachyotis. Coronostrongylus closei, sp. nov. is restricted to Petrogale persephone. Coronostrongylus sharmani, sp. nov. occurs only in rock wallabies from eastern Australia: P.�coenensis, P. godmani and P. mareeba; C. spratti, sp. nov. occurs in P. inornata and P. assimilis. Coronostrongylus spearei, sp. nov. is restricted to Papua New Guinea where it is found in Dorcopsulus vanhearni, Dorcopsis hageni and D. muelleri. Although all of the nematode species occur in one principal host species or a series of closely related host species, occurrences in geographically disjunct areas and in phylogenetically distant hosts are features of C. coronatus, C. barkeri, sp. nov. and C. johnsoni, sp. nov. The occurrence of seven closely related nematode species found in a wide range of macropodid host species is more readily accounted for by a hypothesis involving multiple colonisations of hosts than by the hypothesis of co-speciation.

scholarly journals Recessive deleterious variation has a limited impact on signals of adaptive introgression in human populations

2020 ◽  
Author(s):  
Xinjun Zhang ◽  
Bernard Kim ◽  
Kirk E. Lohmueller ◽  
Emilia Huerta-Sánchez
Keyword(s):  
False Positive ◽  
False Positive Rate ◽  
Genomic Variation ◽  
Human Populations ◽  
Deleterious Mutations ◽  
Modern Humans ◽  
Recombination Rates ◽  
Limited Impact ◽  
Adaptive Mutations ◽  
Adaptive Introgression

AbstractAdmixture with archaic hominins has altered the landscape of genomic variation in modern human populations. Several gene regions have been previously identified as candidates of adaptive introgression (AI) that facilitated human adaptation to specific environments. However, simulation-based studies have suggested that population genetics processes other than adaptive mutations, such as heterosis from recessive deleterious variants private to populations before admixture, can also lead to patterns in genomic data that resemble adaptive introgression. The extent to which the presence of deleterious variants affect the false-positive rate and the power of current methods to detect AI has not been fully assessed. Here, we used extensive simulations to show that recessive deleterious mutations can increase the false positive rates of tests for AI compared to models without deleterious variants. We further examined candidates of AI in modern humans identified from previous studies and show that, although deleterious variants may hinder the performance of AI detection in modern humans, most signals remained robust when deleterious variants are included in the null model. While deleterious variants may have a limited impact on detecting signals of adaptive introgression in humans, we found that at least two AI candidate genes, HYAL2 and HLA, are particularly susceptible to high false positive rates due to the recessive deleterious mutations. By quantifying parameters that affect heterosis, we show that the high false positives are largely attributed to the high exon densities together with low recombination rates in the genomic regions, which can further be exaggerated by the population growth in recent human evolution. Although the combination of such parameters is rare in the human genome, caution is still warranted in other species with different genomic composition and demographic histories.

Are polymorphic species of Uropodina (Acari: Mesostigmata) more successful evolutionarily?—A case study of closely related species from the genus Oodinychus Berlese, 1917 based on DNA sequences

2019 ◽  
Vol 24 (5) ◽  
pp. 866
Author(s):  
Jerzy Błoszyk ◽  
Katarzyna Buczkowska ◽  
Anna Maria Bobowicz ◽  
Alina Bączkiewicz ◽  
Zbigniew Adamski ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Related Species ◽  
Habitat Preferences ◽  
Abundant Species ◽  
Systematic Position ◽  
Genetic Differences ◽  
Similar Species ◽  
Closely Related Species ◽  
Wide Range

The study presented in this research paper is the first taxonomic investigation focusing on Uropodina (Acari: Mesostigmata) mites with a brief discussion of the genetic differences of two very closely related species from the genus Oodinychus Berlese, 1917, i.e. O. ovalis (C.L. Koch, 1839) and O. karawaiewi (Berlese, 1903). These two morphologically similar species are quite common and they have a wide range of occurrence in Europe. They also live in almost the same types of habitat. However, O. ovalis usually exhibits higher abundance and frequency of occurrence. The major aim of the study was to carry out a comparative analysis of the systematic position, morphological and biological differences, as well as habitat preferences and distribution of O. ovalis and O. karawaiewi. The next aim was to ascertain whether the differences in number and frequency of these species may stem from the genetic differences at the molecular level (16S rDNA and COI). The study shows that O. ovalis, which is a more abundant species than O. karawaiewi, turned out to be genetically more polymorphic.

scholarly journals Evolutionary Patterns in the Genus Homo

2021 ◽  
Vol 21 (01) ◽  
Author(s):  
Nisar A. Shar
Keyword(s):  
Related Species ◽  
Homo Sapiens ◽  
Demographic History ◽  
Human Intelligence ◽  
Evolutionary Patterns ◽  
Closely Related Species ◽  
Genus Homo ◽  
Wide Range ◽  
History Of

ABSTRACT The demographic history of Homo sapiens is complex; it involves a wide range of migrations and genetic adaptations. One of the closely related species to Homo sapiens is Neanderthals, which became extinct about 30,000 years ago. The aim of this research is to compare Homo sapiens with Neanderthals and chimpanzees to understand the patterns of inheritance and survival instincts of Homo sapiens. Results show that out of all selected groups of genes in this study, metabolism, and language genes are found to be the most evolving group of genes. This shows that these most evolving genes are contributing to the advancement of Homo sapiens. However, after comparing human intelligence genes with the primates, it is found that exonic regions are contributing more to the evolution of human intelligence hence, making Homo sapiens unique in terms of intelligence.

scholarly journals Genomic compatibility occurs over a wide range of parental genetic similarity in an outcrossing plant

2005 ◽  
Vol 272 (1570) ◽  
pp. 1333-1338 ◽  
Author(s):  
Yvonne Willi ◽  
Josh Van Buskirk
Keyword(s):  
Mate Choice ◽  
Inbreeding Depression ◽  
Related Species ◽  
Genetic Similarity ◽  
Mating Systems ◽  
Hybrid Breakdown ◽  
Offspring Performance ◽  
Closely Related Species ◽  
Wide Range ◽  
Broad Scale

The theory of inbreeding and outbreeding suggests that there is a hump-shaped relationship between the genetic similarity of sexually reproducing parents and the performance of their offspring. Inbreeding depression occurs when genetic similarity is high, whereas hybrid breakdown is expected when genetic similarity is low. Between these extremes, the effect of genetic similarity on fitness is unclear. We studied the shape of this relationship by crossing 65 target genotypes of the clonal, self-incompatible Ranunculus reptans with partner genotypes spanning a broad scale of genetic similarity, ranging from crosses within populations to between-population crosses and hybridisation with a closely related species. Offspring were raised in outdoor tubs. Results revealed a quadratic relationship between parental genetic distance and offspring performance, with the clonal component of fitness more strongly hump-shaped than the sexual component. Optimal genetic similarity encompassed a broad range of within-population and between-population crosses. This pattern of genomic compatibility has important implications for the evolution of mating systems and mate choice.

scholarly journals A Revision of the Ant Genus Rhytidoponera (Hymenoptera: Formicidae) in New Caledonia

1984 ◽  
Vol 32 (1) ◽  
pp. 131 ◽  
Author(s):  
PS Ward
Keyword(s):  
New Species ◽  
Related Species ◽  
New Caledonia ◽  
Morphological Differentiation ◽  
Forest Edge ◽  
Nest Architecture ◽  
Closely Related Species ◽  
Wide Range ◽  
Species Groups ◽  
Group Species

In this revision of the genus Rhytidoponera on the island of New Caledonia, 18 species are recognized: seven previously described taxa (acanthoponeroides Viehmeyer, atropurpurea Emery, fulgens Emery, numeensis Andre, pulchella Emery, versicolor Brown, and wilsoni Brown) and 11 new species (aquila sp.nov., arborea sp.nov., depilis sp.nov., insularis sp.nov., koumensis sp.nov., litoralis sp.nov., luteipes sp.nov., mimica sp.nov., nitidiventris sp.nov., opaciventris sp.nov., and terrestris sp.nov.). All of these species are endemic (except perhaps terrestris, for which there is a questionable record from Vanuatu), and they segregate into four species-groups: acanthoponeroides group (one species), fulgens group (four species), numeensis group (three species) and pulchella group (ten species). Alate queens have not been found in any species, suggesting that colonies are entirely worker-reproductive. The behaviour and nest architecture of species in the pulchella group indicates specialization as foliage-foragers on understorey and forest edge vegetation, in contrast to the ground-foraging tendencies of the remaining species. Some pulchella-group species are involved in mimicry complexes with other ants and other foliage- frequenting arthropods. Closely related species of New Caledonian Rhytidoponera are usually distributed allopatrically, and conspecific populations exhibit a wide range of morphological differentiation.

scholarly journals ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Angel Ruiz-Reche ◽  
Akanksha Srivastava ◽  
Joel A. Indi ◽  
Ivan de la Rubia ◽  
Eduardo Eyras
Keyword(s):  
Deep Learning ◽  
Related Species ◽  
Model Organisms ◽  
Closely Related Species ◽  
Link Type ◽  
A Genome ◽  
Long Read

AbstractWe describe ReorientExpress, a method to perform reference-free orientation of transcriptomic long sequencing reads. ReorientExpress uses deep learning to correctly predict the orientation of the majority of reads, and in particular when trained on a closely related species or in combination with read clustering. ReorientExpress enables long-read transcriptomics in non-model organisms and samples without a genome reference without using additional technologies and is available at https://github.com/comprna/reorientexpress.

scholarly journals The Impact of Recessive Deleterious Variation on Signals of Adaptive Introgression in Human Populations

Genetics ◽  
2020 ◽  
Vol 215 (3) ◽  
pp. 799-812 ◽  
Author(s):  
Xinjun Zhang ◽  
Bernard Kim ◽  
Kirk E. Lohmueller ◽  
Emilia Huerta-Sánchez
Keyword(s):  
Human Genome ◽  
False Positive ◽  
False Positive Rate ◽  
Genomic Variation ◽  
Human Populations ◽  
Deleterious Mutations ◽  
Recombination Rates ◽  
Adaptive Mutations ◽  
Adaptive Introgression ◽  
The Impact

Admixture with archaic hominins has altered the landscape of genomic variation in modern human populations. Several gene regions have been identified previously as candidates of adaptive introgression (AI) that facilitated human adaptation to specific environments. However, simulation-based studies have suggested that population genetic processes other than adaptive mutations, such as heterosis from recessive deleterious variants private to populations before admixture, can also lead to patterns in genomic data that resemble AI. The extent to which the presence of deleterious variants affect the false-positive rate and the power of current methods to detect AI has not been fully assessed. Here, we used extensive simulations under parameters relevant for human evolution to show that recessive deleterious mutations can increase the false positive rates of tests for AI compared to models without deleterious variants, especially when the recombination rates are low. We next examined candidates of AI in modern humans identified from previous studies, and show that 24 out of 26 candidate regions remain significant, even when deleterious variants are included in the null model. However, two AI candidate genes, HYAL2 and HLA, are particularly susceptible to high false positive signals of AI due to recessive deleterious mutations. These genes are located in regions of the human genome with high exon density together with low recombination rate, factors that we show increase the rate of false-positives due to recessive deleterious mutations. Although the combination of such parameters is rare in the human genome, caution is warranted in such regions, as well as in other species with more compact genomes and/or lower recombination rates. In sum, our results suggest that recessive deleterious mutations cannot account for the signals of AI in most, but not all, of the top candidates for AI in humans, suggesting they may be genuine signals of adaptation.

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