scholarly journals The Evolution and Population Diversity of Bison in Pleistocene and Holocene Eurasia: Sex Matters

Diversity ◽  
2018 ◽  
Vol 10 (3) ◽  
pp. 65 ◽  
Author(s):  
Thierry Grange ◽  
Jean-Philip Brugal ◽  
Laurence Flori ◽  
Mathieu Gautier ◽  
Antigone Uzunidis ◽  
...  
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Nuclear Genome ◽  
Population Diversity ◽  
Ecological Niches ◽  
Unified Framework ◽  
Putative Gene ◽  
Behavioral Studies ◽  
History Of ◽  
Genome Analyses

Knowledge about the origin and evolutionary history of the bison has been improved recently owing to several genomic and paleogenomic studies published in the last two years, which elucidated large parts of the evolution of bison populations during the Upper Pleistocene and Holocene in Eurasia. The produced data, however, were interpreted in contradicting manners. Here, we have gathered, reanalyzed and compared previously published or unpublished morphometric and genetic data that have not yet been integrated and that we synthesize in a unified framework. In particular, we re-estimate dates of divergence of mitogenome lineages based on an extended dataset comprising 81 complete ancient bison mitogenomes and we revisit putative gene flow between the Bos and Bison genera based on comparative analyses of ancient and modern bison genomes, thereby questioning published conclusions. Morphometric analyses taking into account sexual dimorphism invalidate a previous claim that Bison schoetensacki was present in France during the Late Pleistocene. Both morphometric and genome analyses reveal that Eurasian bison belonging to different Bison priscus and Bison bonasus lineages maintained parallel evolutionary paths with gene flow during a long period of incomplete speciation that ceased only upon the migration of B. priscus to the American continent establishing the American bison lineage. Our nuclear genome analysis of the evolutionary history of B. bonasus allows us to reject the previous hypothesis that it is a hybrid of B. priscus and Bos primigenius. Based on present-day behavioral studies of European and American bison, we propose that apparently conflicting lines of evidence can be reconciled by positing that female bison drove the specialization of bison populations to different ecological niches while male bison drove regular homogenizing genetic exchanges between populations.

Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant Genus Polemonium (Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nuclear Signal

2020 ◽  
Vol 70 (1) ◽  
pp. 162-180
Author(s):  
Jeffrey P Rose ◽  
Cassio A P Toledo ◽  
Emily Moriarty Lemmon ◽  
Alan R Lemmon ◽  
Kenneth J Sytsma
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Plastid Genome ◽  
Incomplete Lineage Sorting ◽  
Nuclear Genome ◽  
Reticulate Evolution ◽  
Phylogenetic Networks ◽  
Flowering Plant ◽  
Lineage Sorting ◽  
History Of

Abstract Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting (ILS) as a cause of intra- or intergenomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both ILS and introgression as a cause for nuclear and cytoplasmic-nuclear discordance using phylogenomic data from the recently radiated flowering plant genus Polemonium (Polemoniaceae), an ecologically diverse genus in Western North America with known and suspected gene flow between species. We find evidence for widespread discordance among nuclear loci that can be explained by both ILS and reticulate evolution in the evolutionary history of Polemonium. Furthermore, the histories of organellar genomes show strong discordance with the inferred species tree from the nuclear genome. Discordance between the nuclear and plastid genome is not completely explained by ILS, and only one case of discordance is explained by detected introgression events. Our results suggest that multiple processes have been involved in the evolutionary history of Polemonium and that the plastid genome does not accurately reflect species relationships. We discuss several potential causes for this cytoplasmic-nuclear discordance, which emerging evidence suggests is more widespread across the Tree of Life than previously thought. [Cyto-nuclear discordance, genomic discordance, phylogenetic networks, plastid capture, Polemoniaceae, Polemonium, reticulations.]

scholarly journals copia-, gypsy- and LINE-Like Retrotransposon Fragments in the Mitochondrial Genome of Arabidopsis thaliana

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 579-585 ◽  
Author(s):  
Volker Knoop ◽  
Michael Unseld ◽  
Joachim Marienfeld ◽  
Petra Brandt ◽  
Sabine Sünkel ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Mitochondrial Genome ◽  
Evolutionary History ◽  
Nuclear Genome ◽  
Plant Mitochondrial Genome ◽  
Gypsy Group ◽  
History Of

Abstract Several retrotransposon fragments are integrated in the mitochondrial genome of Arabidopsis thaliana. These insertions are derived from all three classes of nuclear retrotransposons, the Tyl/copia, Ty3/gypsy- and non-LTR/LINE-families. Members of the Ty3/gypsy group of elements have not yet been identified in the nuclear genome of Arabidopsis. The varying degrees of similarity with nuclear elements and the dispersed locations of the sequences in the mitochondrial genome suggest numerous independent transfer-insertion events in the evolutionary history of this plant mitochondrial genome. Overall, we estimate remnants of retrotransposons to cover ≥5% of the mitochondrial genome in Arabidopsis.

scholarly journals A transcriptome-based phylogenetic study of hard ticks (Ixodidae)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
N. Pierre Charrier ◽  
Axelle Hermouet ◽  
Caroline Hervet ◽  
Albert Agoulon ◽  
Stephen C. Barker ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Nuclear Genome ◽  
Single Copy ◽  
Phylogenetic Study ◽  
Data Sets ◽  
Hard Tick ◽  
Rna Seq ◽  
Hard Ticks ◽  
History Of ◽  
Mitochondrial Sequences

Abstract Hard ticks are widely distributed across temperate regions, show strong variation in host associations, and are potential vectors of a diversity of medically important zoonoses, such as Lyme disease. To address unresolved issues with respect to the evolutionary relationships among certain species or genera, we produced novel RNA-Seq data sets for nine different Ixodes species. We combined this new data with 18 data sets obtained from public databases, both for Ixodes and non-Ixodes hard tick species, using soft ticks as an outgroup. We assembled transcriptomes (for 27 species in total), predicted coding sequences and identified single copy orthologues (SCO). Using Maximum-likelihood and Bayesian frameworks, we reconstructed a hard tick phylogeny for the nuclear genome. We also obtained a mitochondrial DNA-based phylogeny using published genome sequences and mitochondrial sequences derived from the new transcriptomes. Our results confirm previous studies showing that the Ixodes genus is monophyletic and clarify the relationships among Ixodes sub-genera. This work provides a baseline for studying the evolutionary history of ticks: we indeed found an unexpected acceleration of substitutions for mitochondrial sequences of Prostriata, and for nuclear and mitochondrial genes of two species of Rhipicephalus, which we relate with patterns of genome architecture and changes of life-cycle, respectively.

scholarly journals The evolutionary history of bears is characterized by gene flow across species

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Vikas Kumar ◽  
Fritjof Lammers ◽  
Tobias Bidon ◽  
Markus Pfenninger ◽  
Lydia Kolter ◽  
...  
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
History Of

scholarly journals The evolutionary history of bears is shaped by gene flow across species

2016 ◽  
Author(s):  
Vikas Kumar ◽  
Fritjof Lammers ◽  
Tobias Bidon ◽  
Markus Pfenninger ◽  
Lydia Kolter ◽  
...  
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Black Bear ◽  
Specific Gene ◽  
Brown Bears ◽  
Ancestral Gene ◽  
Asiatic Black Bear ◽  
American Black Bear ◽  
A Genome ◽  
Genome Analyses

AbstractBears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to the closely related polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using three different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains numerous uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to massive amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. The increasing evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow.

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 Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

2020 ◽  
Vol 287 (1938) ◽  
pp. 20201960
Author(s):  
Matheus E. Bianconi ◽  
Luke T. Dunning ◽  
Emma V. Curran ◽  
Oriane Hidalgo ◽  
Robyn F. Powell ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Nuclear Genome ◽  
Its Region ◽  
Grass Species ◽  
Region Of Origin ◽  
Ploidy Levels ◽  
Lower Elevation ◽  
Limited Dispersal ◽  
Genome Analyses

C 4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C 4 and non-C 4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata . We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C 4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C 4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C 4 physiology away from its region of origin.

scholarly journals The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals

2021 ◽  
Author(s):  
Stéphane Peyrégne ◽  
Janet Kelso ◽  
Benjamin Marco Peter ◽  
Svante Pääbo
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Modern Human ◽  
Modern Humans ◽  
Ancestral Gene ◽  
Cytoskeletal Structure ◽  
Spindle Apparatus ◽  
History Of ◽  
Segregation Of Chromosomes

Proteins associated with the spindle apparatus, a cytoskeletal structure that ensures the proper segregation of chromosomes during cell division, experienced an unusual number of amino acid substitutions in modern humans after the split from the ancestors of Neandertals and Denisovans. Here, we analyze the history of these substitutions and show that some of the genes in which they occur may have been targets of positive selection. We also find that the two changes in the kinetochore scaffold 1 (KNL1) protein, previously believed to be specific to modern humans, were present in some Neandertals. We show that the KNL1 gene of these Neandertals shared a common ancestor with present-day Africans about 200,000 years ago due to gene flow from the ancestors (or relatives) of modern humans into Neandertals. Subsequently, some non-Africans inherited this modern human-like gene variant from Neandertals, but none inherited the ancestral gene variants. These results add to the growing evidence of early contacts between modern humans and archaic groups in Eurasia and illustrate the intricate relationships among these groups.

Sign in / Sign up

Export Citation Format

Share Document