scholarly journals Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two sexual species

2018 ◽  
Author(s):  
Robert D. Denton ◽  
Ariadna E. Morales ◽  
H. Lisle Gibbs
Keyword(s):  
Genetic Variation ◽  
Evolutionary History ◽  
Parental Species ◽  
Extended Period ◽  
Reproductive Mode ◽  
Mapping Method ◽  
Genetic Introgression ◽  
Sexual Species ◽  
History Of ◽  
Genomic Material

AbstractQuantifying genetic introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what factors drive the longevity of putatively asexual groups. However, the presence of multiple distinct subgenomes within a single lineage provides a significant logistical challenge to evaluating the origin of genetic variation in most polyploids. Here, we capitalize on three recent innovations—variation generated from ultraconserved elements (UCEs), bioinformatic techniques for assessing variation in polyploids, and model-based methods for evaluating historical gene flow—to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all-female salamanders and two ancestral sexual species. We first analyzed variation from more than a thousand UCEs using a reference mapping method developed for polyploids to infer subgenome specific patterns of variation in the all-female lineage. We then used PHRAPL to choose between sets of historical models that reflected different patterns of introgression and divergence between the genomes of the parental species and the same genomes found within the polyploids. Our analyses support a scenario in which the genomes sampled in unisexuals salamanders were present in the lineage ∼3.4 million years ago, followed by an extended period of divergence from their parental species. Recent secondary introgression has occurred at different times between each sexual species and their representative genomes within the unisexuals during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage has been the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have also undergone long periods of divergence without introgression. Unlike other unisexual, sperm-dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could reveal the scenarios in which the influx of novel genomic material is favored and potentially explain why these salamanders are among the oldest described unisexual animals.

scholarly journals Approximating the coalescent under facultative sex

2019 ◽  
Author(s):  
Matthew Hartfield
Keyword(s):  
Population Size ◽  
Evolutionary History ◽  
Sampling Strategies ◽  
Effective Population ◽  
Sexual Species ◽  
History Of ◽  
Mitotic Gene Conversion ◽  
Evolutionary Consequences ◽  
Insight Into ◽  
Coalescent Time

AbstractGenome studies of facultative sexual species, which can either reproduce sexually or asexually, are providing insight into the evolutionary consequences of mixed reproductive modes. It is currently unclear to what extent the evolutionary history of facultative sexuals’ genomes can be approximated by the standard coalescent, and if a coalescent effective population size Ne exists. Here, I determine if and when these approximations can be made. When sex is frequent (occurring at a frequency much greater than 1/N per reproduction per generation, for N the actual population size), the underlying genealogy can be approximated by the standard coalescent, with a coalescent Ne ≈ N. When sex is very rare (at frequency much lower than 1/N), approximations for the pairwise coalescent time can be obtained, which is strongly influenced by the frequencies of sex and mitotic gene conversion, rather than N. However, these terms do not translate into a coalescent Ne. These results are used to discuss the best sampling strategies for investigating the evolutionary history of facultative sexual species.

scholarly journals Genetic variation and evolutionary history of a mycorrhizal fungus regulate the currency of exchange in symbiosis with the food security crop cassava

2020 ◽  
Vol 14 (6) ◽  
pp. 1333-1344
Author(s):  
Romain Savary ◽  
Cindy Dupuis ◽  
Frédéric G. Masclaux ◽  
Ivan D. Mateus ◽  
Edward C. Rojas ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Food Security ◽  
Evolutionary History ◽  
Mycorrhizal Fungus ◽  
History Of

scholarly journals Evidence for Genetic Hitchhiking Effect Associated With Insecticide Resistance in Aedes aegypti

Genetics ◽  
1998 ◽  
Vol 148 (2) ◽  
pp. 793-800
Author(s):  
Guiyun Yan ◽  
Dave D Chadee ◽  
David W Severson
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Aedes Aegypti ◽  
Evolutionary History ◽  
Large Fraction ◽  
Target Site ◽  
Chromosome 1 ◽  
Disease Epidemiology ◽  
Length Polymorphisms ◽  
History Of

Abstract Information on genetic variation within and between populations is critical for understanding the evolutionary history of mosquito populations and disease epidemiology. Previous studies with Drosophila suggest that genetic variation of selectively neutral loci in a large fraction of genome may be constrained by fixation of advantageous mutations associated with hitchhiking effect. This study examined restriction fragment length polymorphisms of four natural Aedes aegypti mosquito populations from Trinidad and Tobago, at 16 loci. These populations have been subjected to organophosphate (OP) insecticide treatments for more than two decades, while dichlor-diphenyltrichlor (DDT) was the insecticide of choice prior to this period. We predicted that genes closely linked to the OP target loci would exhibit reduced genetic variation as a result of the hitchhiking effect associated with intensive OP insecticide selection. We also predicted that genetic variability of the genes conferring resistance to DDT and loci near the target site would be similar to other unlinked loci. As predicted, reduced genetic variation was found for loci in the general chromosomal region of a putative OP target site, and these loci generally exhibited larger FST values than other random loci. In contrast, the gene conferring resistance to DDT and its linked loci show polymorphisms and genetic differentiation similar to other random loci. The reduced genetic variability and apparent gene deletion in some regions of chromosome 1 likely reflect the hitchhiking effect associated with OP insecticide selection.

scholarly journals The eastern migratory caribou: the role of genetic introgression in ecotype evolution

2016 ◽  
Vol 3 (2) ◽  
pp. 150469 ◽  
Author(s):  
Cornelya F. C. Klütsch ◽  
Micheline Manseau ◽  
Vicki Trim ◽  
Jean Polfus ◽  
Paul J. Wilson
Keyword(s):  
Evolutionary History ◽  
Rangifer Tarandus ◽  
Genetic Introgression ◽  
Conservation Unit ◽  
Woodland Caribou ◽  
Barren Ground ◽  
Specific Contact ◽  
History Of ◽  
Species At Risk Act

Understanding the evolutionary history of contemporary animal groups is essential for conservation and management of endangered species like caribou ( Rangifer tarandus ). In central Canada, the ranges of two caribou subspecies (barren-ground/woodland caribou) and two woodland caribou ecotypes (boreal/eastern migratory) overlap. Our objectives were to reconstruct the evolutionary history of the eastern migratory ecotype and to assess the potential role of introgression in ecotype evolution. STRUCTURE analyses identified five higher order groups (i.e. three boreal caribou populations, eastern migratory ecotype and barren-ground). The evolutionary history of the eastern migratory ecotype was best explained by an early genetic introgression from barren-ground into a woodland caribou lineage during the Late Pleistocene and subsequent divergence of the eastern migratory ecotype during the Holocene. These results are consistent with the retreat of the Laurentide ice sheet and the colonization of the Hudson Bay coastal areas subsequent to the establishment of forest tundra vegetation approximately 7000 years ago. This historical reconstruction of the eastern migratory ecotype further supports its current classification as a conservation unit, specifically a Designatable Unit, under Canada’s Species at Risk Act. These findings have implications for other sub-specific contact zones for caribou and other North American species in conservation unit delineation.

Gender dependent and independent morphological dimorphism in sexual and apomictic Antennaria monocephala sensu lato

1991 ◽  
Vol 69 (7) ◽  
pp. 1433-1448 ◽  
Author(s):  
J. G. Chmielewski ◽  
C. C. Chinnappa
Keyword(s):  
Chromosome Number ◽  
Key Words ◽  
Reproductive Biology ◽  
Chromosome Numbers ◽  
Evolutionary History ◽  
Multivariate Analyses ◽  
Reproductive Mode ◽  
Polyploid Complex ◽  
Adaxial Surface ◽  
History Of

Taxa included in the Antennaria monocephala DC. polyploid complex were previously circumscribed at the specific, subspecific, or varietal levels without concensus. The purpose of this phenetic study was to construct a taxonomy that not only reflects the presumed evolutionary history of the complex but also presents a taxonomy that is both functional and informative, regardless of an individual's gender or more importantly, the reproductive mode of the population. The rank of subspecies (A. monocephala ssp. monocephala and A. monocephala ssp. angustata (Green) Hultén) was accepted as the most appropriate level of gender independent circumscription that satisfied the purpose of the phenetic study. These subspecies differ with respect to tomentum, chromosome number, reproductive biology, and (in part) provenance. The former taxon, A. monocephala ssp. monocephala, is a sexual diploid (2n = 28); the latter taxon, A. monocephala ssp. augustata, is an apomictic polyploid, with chromosome numbers ranging from tetraploid (2n = 56) to octoploid (2n = 112). In A. monocephala ssp. monocephala the adaxial surface of the basal and cauline leaves is glabrous-strigose, as is the stem. In A. monocephala ssp. angustata the adaxial surface of both basal and cauline leaves is floccose-tomentose, as is the surface of the stem. Key words: Antennaria monocephala polyploid complex, multivariate analyses.

Reassessing the evolutionary history of ass-like equids: Insights from patterns of genetic variation in contemporary extant populations

2015 ◽  
Vol 85 ◽  
pp. 88-96 ◽  
Author(s):  
Sónia Rosenbom ◽  
Vânia Costa ◽  
Shanyuan Chen ◽  
Leili Khalatbari ◽  
Gholam Hosein Yusefi ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Evolutionary History ◽  
History Of

Unveiling patterns of genetic variation in parasite–host associations: an example with pinworms and Neotropical primates

Parasitology ◽  
2018 ◽  
Vol 146 (3) ◽  
pp. 356-362 ◽  
Author(s):  
Brenda Solórzano García ◽  
Amanda D. Melin ◽  
Filippo Aureli ◽  
Gerardo Pérez Ponce de León
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Central America ◽  
Genetic Divergence ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Spider Monkey ◽  
Neotropical Primates ◽  
Genetic Patterns ◽  
History Of

AbstractPatterns of genetic variation among populations can reveal the evolutionary history of species. Pinworm parasites are highly host specific and form strong co-evolutionary associations with their primate hosts. Here, we describe the genetic variation observed in four Trypanoxyuris species infecting different howler and spider monkey subspecies in Central America to determine if historical dispersal processes and speciation in the host could explain the genetic patterns observed in the parasites. Mitochondrial (cox1) and ribosomal (28S) DNA were analysed to assess genetic divergence and phylogenetic history of these parasites. Sequences of the 28S gene were identical within pinworms species regardless of host subspecies. However, phylogenetic analyses, haplotype relationships and genetic divergence with cox1 showed differentiation between pinworm populations according to host subspecies in three of the four Trypanoxyuris species analysed. Haplotype separation between host subspecies was not observed in Trypanoxyuris minutus, nor in Trypanoxyuris atelis from Ateles geoffoyi vellerosus and Ateles geoffoyi yucatanensis. Levels of genetic diversity and divergence in these parasites relate with such estimates reported for their hosts. This study shows how genetic patterns uncovered in parasitic organisms can reflect the host phylogenetic and biogeographic histories.

scholarly journals Ancient Hybridization with an Unknown Population Facilitated High-Altitude Adaptation of Canids

2020 ◽  
Vol 37 (9) ◽  
pp. 2616-2629 ◽  
Author(s):  
Ming-Shan Wang ◽  
Sheng Wang ◽  
Yan Li ◽  
Yadvendradev Jhala ◽  
Mukesh Thakur ◽  
...  
Keyword(s):  
High Altitude ◽  
Evolutionary History ◽  
Nuclear Genome ◽  
Genetic Introgression ◽  
Data Set ◽  
Whole Genomes ◽  
Ancient Lineage ◽  
History Of ◽  
Evolutionary Trajectories ◽  
Altitude Adaptation

Abstract Genetic introgression not only provides material for adaptive evolution but also confounds our understanding of evolutionary history. This is particularly true for canids, a species complex in which genome sequencing and analysis has revealed a complex history of admixture and introgression. Here, we sequence 19 new whole genomes from high-altitude Tibetan and Himalayan wolves and dogs and combine these into a larger data set of 166 whole canid genomes. Using these data, we explore the evolutionary history and adaptation of these and other canid lineages. We find that Tibetan and Himalayan wolves are closely related to each other, and that ∼39% of their nuclear genome is derived from an as-yet-unrecognized wolf-like lineage that is deeply diverged from living Holarctic wolves and dogs. The EPAS1 haplotype, which is present at high frequencies in Tibetan dog breeds and wolves and confers an adaptive advantage to animals living at high altitudes, was probably derived from this ancient lineage. Our study underscores the complexity of canid evolution and demonstrates how admixture and introgression can shape the evolutionary trajectories of species.

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