scholarly journals The Timing and Direction of Introgression Under the Multispecies Network Coalescent

Genetics ◽  
2019 ◽  
Vol 211 (3) ◽  
pp. 1059-1073 ◽  
Author(s):  
Mark S. Hibbins ◽  
Matthew W. Hahn
Keyword(s):  
Statistical Methods ◽  
Biological Process ◽  
Genomic Data ◽  
Hybrid Speciation ◽  
Saccharomyces Paradoxus ◽  
Genomic Signatures ◽  
Wild Yeast ◽  
Other Information ◽  
Homoploid Hybrid ◽  
New Statistics

Introgression is a pervasive biological process, and many statistical methods have been developed to infer its presence from genomic data. However, many of the consequences and genomic signatures of introgression remain unexplored from a methodological standpoint. Here, we develop a model for the timing and direction of introgression based on the multispecies network coalescent, and from it suggest new approaches for testing introgression hypotheses. We suggest two new statistics, D1 and D2, which can be used in conjunction with other information to test hypotheses relating to the timing and direction of introgression, respectively. D1 may find use in evaluating cases of homoploid hybrid speciation (HHS), while D2 provides a four-taxon test for polarizing introgression. Although analytical expectations for our statistics require a number of assumptions to be met, we show how simulations can be used to test hypotheses about introgression when these assumptions are violated. We apply the D1 statistic to genomic data from the wild yeast Saccharomyces paradoxus—a proposed example of HHS—demonstrating its use as a test of this model. These methods provide new and powerful ways to address questions relating to the timing and direction of introgression.

scholarly journals The timing and direction of introgression under the multispecies network coalescent

2018 ◽  
Author(s):  
Mark S. Hibbins ◽  
Matthew W. Hahn
Keyword(s):  
Statistical Methods ◽  
Biological Process ◽  
Genomic Data ◽  
Hybrid Speciation ◽  
Saccharomyces Paradoxus ◽  
Genomic Signatures ◽  
Wild Yeast ◽  
Other Information ◽  
Homoploid Hybrid ◽  
New Statistics

AbstractIntrogression is a pervasive biological process, and many statistical methods have been developed to infer its presence from genomic data. However, many of the consequences and genomic signatures of introgression remain unexplored from a methodological standpoint. Here, we develop a model for the timing and direction of introgression based on the multispecies network coalescent, and from it suggest new approaches for testing introgression hypotheses. We suggest two new statistics, D1 and D2, which can be used in conjunction with other information to test hypotheses relating to the timing and direction of introgression, respectively. D1 may find use in evaluating cases of homoploid hybrid speciation, while D2 provides a four-taxon test for polarizing introgression. Although analytical expectations for our statistics require a number of assumptions to be met, we show how simulations can be used to test hypotheses about introgression when these assumptions are violated. We apply the D1 statistic to genomic data from the wild yeast Saccharomyces paradoxus, a proposed example of homoploid hybrid speciation, demonstrating its use as a test of this model. These methods provide new and powerful ways to address questions relating to the timing and direction of introgression.

scholarly journals Speciation driven by hybridization and chromosomal plasticity in a wild yeast

2015 ◽  
Author(s):  
Jean-Baptiste Leducq ◽  
Lou Nielly-Thibault ◽  
Guillaume Charron ◽  
Chris Eberlein ◽  
Jukka-Pekka Verta ◽  
...  
Keyword(s):  
Rapid Evolution ◽  
Natural Populations ◽  
Secondary Contact ◽  
Hybrid Speciation ◽  
Hybrid Species ◽  
Chromosome Architecture ◽  
The North ◽  
Wild Yeast ◽  
Homoploid Hybrid ◽  
Powerful Mechanism

Hybridization is recognized as a powerful mechanism of speciation and a driving force in generating biodiversity. However, only few multicellular species, limited to a handful of plants and animals, have been shown to fulfill all the criteria of homoploid hybrid speciation. This lack of evidence could lead to the misconception that speciation by hybridization has a limited role in eukaryotes, particularly in single-celled organisms. Laboratory experiments have revealed that fungi such as budding yeasts can rapidly develop reproductive isolation and novel phenotypes through hybridization, showing that in principle homoploid speciation could occur in nature. Here we report a case of homoploid hybrid speciation in natural populations of the budding yeast Saccharomyces paradoxus inhabiting the North American forests. We show that the rapid evolution of chromosome architecture and an ecological context that led to secondary contact between nascent species drove the formation of an incipient hybrid species with a potentially unique ecological niche.

scholarly journals Detection and evaluation of selection signatures in sheep

2018 ◽  
Vol 53 (5) ◽  
pp. 527-539 ◽  
Author(s):  
Tiago do Prado Paim ◽  
Patrícia Ianella ◽  
Samuel Rezende Paiva ◽  
Alexandre Rodrigues Caetano ◽  
Concepta Margaret McManus Pimentel
Keyword(s):  
Statistical Methods ◽  
Phenotypic Diversity ◽  
Selection Process ◽  
Genomic Data ◽  
Research Field ◽  
Economic Traits ◽  
Selection Signatures ◽  
Important Species ◽  
Challenges And Opportunities ◽  
Genomic Regions

Abstract: The recent development of genome-wide single nucleotide polymorphism (SNP) arrays made it possible to carry out several studies with different species. The selection process can increase or reduce allelic (or genic) frequencies at specific loci in the genome, besides dragging neighboring alleles in the chromosome. This way, genomic regions with increased frequencies of specific alleles are formed, caracterizing selection signatures or selective sweeps. The detection of these signatures is important to characterize genetic resources, as well as to identify genes or regions involved in the control and expression of important production and economic traits. Sheep are an important species for theses studies as they are dispersed worldwide and have great phenotypic diversity. Due to the large amounts of genomic data generated, specific statistical methods and softwares are necessary for the detection of selection signatures. Therefore, the objectives of this review are to address the main statistical methods and softwares currently used for the analysis of genomic data and the identification of selection signatures; to describe the results of recent works published on selection signatures in sheep; and to discuss some challenges and opportunities in this research field.

scholarly journals Transient hybridization, not homoploid hybrid speciation, between ancient and deeply divergent conifers

2016 ◽  
Vol 103 (2) ◽  
pp. 246-259 ◽  
Author(s):  
J. R. P. Worth ◽  
M. J. Larcombe ◽  
S. Sakaguchi ◽  
J. R. Marthick ◽  
D. M. J. S. Bowman ◽  
...  
Keyword(s):  
Hybrid Speciation ◽  
Homoploid Hybrid

Homoploid hybrid speciation in action

Taxon ◽  
2010 ◽  
Vol 59 (5) ◽  
pp. 1375-1386 ◽  
Author(s):  
Richard J. Abbott ◽  
Matthew J. Hegarty ◽  
Simon J. Hiscock ◽  
Adrian C. Brennan
Keyword(s):  
Hybrid Speciation ◽  
Homoploid Hybrid

scholarly journals Behavioural isolation may facilitate homoploid hybrid speciation in cichlid fish

2013 ◽  
Vol 27 (2) ◽  
pp. 275-289 ◽  
Author(s):  
O. M. Selz ◽  
R. Thommen ◽  
M. E. Maan ◽  
O. Seehausen
Keyword(s):  
Cichlid Fish ◽  
Hybrid Speciation ◽  
Homoploid Hybrid

scholarly journals Homoploid hybrid speciation and genome evolution via chromosome sorting

2015 ◽  
Vol 282 (1807) ◽  
pp. 20150157 ◽  
Author(s):  
Vladimir A. Lukhtanov ◽  
Nazar A. Shapoval ◽  
Boris A. Anokhin ◽  
Alsu F. Saifitdinova ◽  
Valentina G. Kuznetsova
Keyword(s):  
Reproductive Isolation ◽  
Direct Consequence ◽  
Convincing Evidence ◽  
Interspecific Crosses ◽  
Parental Origin ◽  
Hybrid Speciation ◽  
Species Formation ◽  
Homoploid Hybrid ◽  
Creative Role

Genomes of numerous diploid plant and animal species possess traces of interspecific crosses, and many researches consider them as support for homoploid hybrid speciation (HHS), a process by which a new reproductively isolated species arises through hybridization and combination of parts of the parental genomes, but without an increase in ploidy. However, convincing evidence for a creative role of hybridization in the origin of reproductive isolation between hybrid and parental forms is extremely limited. Here, through studying Agrodiaetus butterflies, we provide proof of a previously unknown mode of HHS based on the formation of post-zygotic reproductive isolation via hybridization of chromosomally divergent parental species and subsequent fixation of a novel combination of chromosome fusions/fissions in hybrid descendants. We show that meiotic segregation, operating in the hybrid lineage, resulted in the formation of a new diploid genome, drastically rearranged in terms of chromosome number. We also demonstrate that during the heterozygous stage of the hybrid species formation, recombination was limited between rearranged chromosomes of different parental origin, representing evidence that the reproductive isolation was a direct consequence of hybridization.

scholarly journals The spatial scale of genetic differentiation in a model organism: the wild yeast Saccharomyces paradoxus

2006 ◽  
Vol 361 (1475) ◽  
pp. 1941-1946 ◽  
Author(s):  
Vassiliki Koufopanou ◽  
Joseph Hughes ◽  
Graham Bell ◽  
Austin Burt
Keyword(s):  
Genetic Differentiation ◽  
Population Genomics ◽  
Model Organism ◽  
Physical Distance ◽  
Saccharomyces Paradoxus ◽  
Population Genetic Differentiation ◽  
Wild Yeast ◽  
Oak Trees ◽  
Eukaryotic Microbes ◽  
Well Differentiated

Little information is presently available on the factors promoting genetic divergence in eukaryotic microbes. We studied the spatial distribution of genetic variation in Saccharomyces paradoxus , the wild relative of Saccharomyces cerevisiae , from the scale of a few centimetres on individual oak trees to thousands of kilometres across different continents. Genealogical analysis of six loci shows that isolates from Europe form a single recombining population, and within this population genetic differentiation increases with physical distance. Between different continents, strains are more divergent and genealogically independent, indicating well-differentiated lineages that may be in the process of speciation. Such replicated populations will be useful for studies in population genomics.

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