scholarly journals The Y-chromosome clarifies the evolutionary history of Sus scrofa by large-scale deep genome sequencing

2017 ◽  
Author(s):  
Huashui Ai ◽  
Jun Ren ◽  
Junwu Ma ◽  
Zhiyan Zhang ◽  
Wanbo Li ◽  
...  
Keyword(s):  
Gene Flow ◽  
Y Chromosome ◽  
Sus Scrofa ◽  
Evolutionary History ◽  
Large Scale ◽  
Divergence Time ◽  
Chromosome Y ◽  
Wild Boars ◽  
History Of ◽  
Ancient Gene

AbstractThe genetics and evolution of sex chromosomes are largely distinct from autosomes and mitochondrial DNA (mtDNA). The Y chromosome offers unique genetic perspective on male-line inheritance. Here, we uncover novel evolutionary history of Sus scrofa based on 205 high-quality genomes from worldwide-distributed different wild boars and domestic pig breeds. We find that only two haplotypes exist in the distal and proximal blocks of at least 7.7 Mb on chromosome Y in pigs across European and Asian continents. And the times of most recent common ancestors (TMRCA) within both haplotypes, approximately 0.14 and 0.10 million years, are far smaller than their divergence time of around 1.07 million years. What’s more, the relationship between Sumatran and Eurasian continent Sus scrofa is much closer than that we knew before. And surprisingly, European pigs share the same haplotype with many Chinese pigs, which is not consistent with their deep splitting status on autosome and mtDNA. Further analyses show that the haplotype in Chinese pigs was likely introduced from European wild boars via ancient gene flow before pig domestication about 24k years ago. Low mutation rates and no recombination in the distal and proximal blocks on chromosome Y help us detect this male-driven ancient gene flow. Taken together, our results update the knowledge of pig demography and evolution, and might shed insight into the genetics and evolution studies on chromosome Y in other mammals.

scholarly journals Recombination-aware phylogenomics unravels the complex divergence of hybridizing species.

2018 ◽  
Author(s):  
Gang Li ◽  
Henrique V. Figueiro ◽  
Eduardo Eizirik ◽  
William J. Murphy
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Selective Sweeps ◽  
A Genome ◽  
Chromosome Recombination ◽  
History Of ◽  
Lineage Divergence ◽  
Recurrent Patterns ◽  
Ancient Gene

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of gene flow that result in a mosaic of phylogenetic signals that interact with recombinational variation. Here we tested the validity of this assumption with a recombination-aware analysis of whole genome sequences from 27 species of the cat family. We found that the prevailing phylogenetic signal within the autosomes is not always representative of speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within large, conserved X-chromosome recombination deserts that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ~40%. We conclude that standard phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic partitioning of phylogenetic signal relative to recombination rate, and its interplay with historical hybridization.

scholarly journals Inversions shape the divergence of Drosophila pseudoobscura and D. persimilis on multiple timescales

2019 ◽  
Author(s):  
Katharine L Korunes ◽  
Carlos A Machado ◽  
Mohamed AF Noor
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Whole Genome Sequence ◽  
Drosophila Pseudoobscura ◽  
Ancestral Polymorphism ◽  
Chromosomal Inversions ◽  
History Of ◽  
Ancient Gene

AbstractBy shaping meiotic recombination, chromosomal inversions can influence genetic exchange between hybridizing species. Despite the recognized importance of inversions in evolutionary processes such as divergence and speciation, teasing apart the effects of inversions over time remains challenging. For example, are their effects on sequence divergence primarily generated through creating blocks of linkage-disequilibrium pre-speciation or through preventing gene flux after speciation? We provide a comprehensive look into the influence of chromosomal inversions on gene flow throughout the evolutionary history of a classic system: Drosophila pseudoobscura and D. persimilis. We use extensive whole-genome sequence data to report patterns of introgression and divergence with respect to chromosomal arrangements. Overall, we find evidence that inversions have contributed to divergence patterns between Drosophila pseudoobscura and D. persimilis over three distinct timescales: 1) pre-speciation segregation of ancestral polymorphism, 2) post-speciation ancient gene flow, and 3) recent gene flow. We discuss these results in terms of our understanding of evolution in this classic system and provide cautions for interpreting divergence measures in similar datasets in other systems.

scholarly journals Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective

PeerJ ◽  
2015 ◽  
Vol 4 ◽  
pp. e1556 ◽  
Author(s):  
Rosa Alicia Jiménez ◽  
Juan Francisco Ornelas
Keyword(s):  
Gene Flow ◽  
Species Complex ◽  
Evolutionary History ◽  
Divergence Time ◽  
Haplotype Network ◽  
Genetic Admixture ◽  
Isolation With Migration ◽  
History Of ◽  
Isthmus Of Tehuantepec ◽  
Assignment Analysis

The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds,Amazilia beryllina,Amazilia cyanuraandAmazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA) sequence data and microsatellite loci scores for populations throughout the range of the threeAmaziliaspecies, as well as morphological and ecological data. Haplotype network, Bayesian phylogenetic and divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of thisAmaziliaspecies complex. An isolation-with-migration coalescent model and Bayesian assignment analysis were assessed to determine historical introgression and current genetic admixture. mtDNA haplotypes were geographically unstructured, with haplotypes from disparate areas interdispersed on a shallow tree and an unresolved haplotype network. Assignment analysis of the nuclear genome (nuDNA) supported three genetic groups with signs of genetic admixture, corresponding to: (1)A. beryllinapopulations located west of the Isthmus of Tehuantepec; (2)A. cyanurapopulations between the Isthmus of Tehuantepec and the Nicaraguan Depression (Nuclear Central America); and (3)A. saucerotteipopulations southeast of the Nicaraguan Depression. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns suggest an evolutionary history of introgression mediated by Quaternary climatic fluctuations. High levels of gene flow were indicated by mtDNA and asymmetrical isolation-with-migration, whereas the microsatellite analyses found evidence for three genetic clusters with distributions corresponding to isolation by the Isthmus of Tehuantepec and the Nicaraguan Depression and signs of admixture. Historical levels of migration between genetically distinct groups estimated using microsatellites were higher than contemporary levels of migration. These results support the scenario of secondary contact and range contact during the glacial periods of the Pleistocene and strongly imply that the high levels of structure currently observed are a consequence of the limited dispersal of these hummingbirds across the isthmus and depression barriers.

scholarly journals Out of the Qinghai-Tibetan Plateau (QTP) and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae)

AoB Plants ◽  
2021 ◽  
Author(s):  
Min-Jie Li ◽  
Huan-Xi Yu ◽  
Xian-Lin Guo ◽  
Xing-Jin He
Keyword(s):  
Evolutionary History ◽  
Divergence Time ◽  
Time Estimation ◽  
Adjacent Region ◽  
Rapid Radiation ◽  
Divergence Time Estimation ◽  
Species Diversification ◽  
The Third ◽  
Evolutionary Line ◽  
History Of

Abstract The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of the modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidate the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the QTP and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 Mya. Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.

A new endemic family of New Zealand passerine birds: adding heat to a biodiversity hotspot

2007 ◽  
Vol 55 (2) ◽  
pp. 73 ◽  
Author(s):  
Amy Driskell ◽  
Les Christidis ◽  
B. J. Gill ◽  
Walter E. Boles ◽  
F. Keith Barker ◽  
...  
Keyword(s):  
New Zealand ◽  
Evolutionary History ◽  
Divergence Time ◽  
Biodiversity Hotspot ◽  
Passerine Birds ◽  
New Family ◽  
Close Relationship ◽  
History Of ◽  
Anthornis Melanura ◽  
Notiomystis Cincta

The results of phylogenetic analysis of two molecular datasets sampling all three endemic New Zealand ‘honeyeaters’ (Prosthemadera novaeseelandiae, Anthornis melanura and Notiomystis cincta) are reported. The undisputed relatedness of the first two species to other honeyeaters (Meliphagidae), and a close relationship between them, are demonstrated. However, our results confirm that Notiomystis is not a honeyeater, but is instead most closely related to the Callaeidae (New Zealand wattlebirds) represented by Philesturnus carunculatus in our study. An estimated divergence time for Notiomystis and Philesturnus of 33.8 mya (Oligocene) suggests a very long evolutionary history of this clade in New Zealand. As a taxonomic interpretation of these data we place Notiomystis in a new family of its own which takes the name Notiomystidae. We expect this new phylogenetic and taxonomic information to assist policy decisions for the conservation of this rare bird.

scholarly journals Chromosomal dynamics in space and time: evolutionary history of Mycetophylax ants across past climatic changes in the Brazilian Atlantic coast

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ricardo Micolino ◽  
Maykon Passos Cristiano ◽  
Natália Martins Travenzoli ◽  
Denilce Meneses Lopes ◽  
Danon Clemes Cardoso
Keyword(s):  
Evolutionary History ◽  
Chromosomal Rearrangements ◽  
Atlantic Coast ◽  
Ecological Impact ◽  
Divergence Time ◽  
Molecular Data ◽  
Recent Common Ancestor ◽  
Integrative Approach ◽  
Most Recent Common Ancestor ◽  
History Of

AbstractFungus-farming ants of the genus Mycetophylax exhibit intra and interspecific chromosome variability, which makes them suitable for testing hypotheses about possible chromosomal rearrangements that endure lineage diversification. We combined cytogenetic and molecular data from Mycetophylax populations from coastal environments to trace the evolutionary history of the clade in light of chromosomal changes under a historical and geographic context. Our cytogenetic analyses revealed chromosomal differences within and among species. M. morschi exhibited three distinct karyotypes and considerable variability in the localization of 45S rDNA clusters. The molecular phylogeny was congruent with our cytogenetic findings. Biogeographical and divergence time dating analyses estimated that the most recent common ancestor of Mycetophylax would have originated at about 30 Ma in an area including the Amazon and Southern Grasslands, and several dispersion and vicariance events may have occurred before the colonization of the Brazilian Atlantic coast. Diversification of the psammophilous Mycetophylax first took place in the Middle Miocene (ca. 18–10 Ma) in the South Atlantic coast, while “M. morschi” lineages diversified during the Pliocene-Pleistocene transition (ca. 3–2 Ma) through founder-event dispersal for the Northern coastal regions. Psammophilous Mycetophylax diversification fits into the major global climatic events that have had a direct impact on the changes in sea level as well as deep ecological impact throughout South America. We assume therefore that putative chromosomal rearrangements correlated with increased ecological stress during the past climatic transitions could have intensified and/or accompanied the divergence of the psammophilous Mycetophylax. We further reiterate that “M. morschi” comprises a complex of at least three well-defined lineages, and we emphasize the role of this integrative approach for the identification and delimitation of evolutionary lineages.

scholarly journals RIP mutated ITS genes in populations of Ophiocordyceps sinensis and their implications for molecular systematics

IMA Fungus ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yi Li ◽  
Lan Jiang ◽  
Ke Wang ◽  
Hai-Jun Wu ◽  
Rui-Heng Yang ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Its Region ◽  
Wide Distribution ◽  
Specific Primers ◽  
Ophiocordyceps Sinensis ◽  
Single Genome ◽  
History Of ◽  
Geographic Populations ◽  
Internal Transcribed Spacer Sequences

Abstract Different hypotheses have been proposed to interpret the observed unusual ITS (internal transcribed spacer) sequences in Ophiocordyceps sinensis. The coexistence of diverged ITS paralogs in a single genome was previously shown by amplifying the ITS region from mono-ascospore isolates using specific primers designed for different ITS paralog groups. Among those paralogs, are AT-biased ITS sequences which were hypothesized to result from repeat-induced point mutation (RIP). This is a process that detects and mutates repetitive DNA and frequently leads to epigenetic silencing, and these mutations have been interpreted as pseudogenes. Here we investigate the occurrence and frequency of ITS pseudogenes in populations of O. sinensis using large-scale sampling, and discusses the implications of ITS pseudogenes for fungal phylogenetic and evolutionary studies. Our results demonstrate a wide distribution of ITS pseudogenes amongst different geographic populations, and indicate how ITS pseudogenes can contribute to the reconstruction of the evolutionary history of the species.

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