Signatures of mito-nuclear discordance in Schistosoma turkestanicum indicate a complex evolutionary history of emergence in Europe

Parasitology ◽  
2017 ◽  
Vol 144 (13) ◽  
pp. 1752-1762 ◽  
Author(s):  
SCOTT P. LAWTON ◽  
LAUREN I. BOWEN ◽  
AIDAN M. EMERY ◽  
GÁBOR MAJOROS
Keyword(s):  
Evolutionary History ◽  
Molecular Diversity ◽  
Population Expansion ◽  
Its Sequences ◽  
Cox1 Gene ◽  
Internal Transcribed Spacer Region ◽  
Recent Population Expansion ◽  
Haplotype Frequencies ◽  
History Of ◽  
Low Levels

SUMMARYHigh levels of molecular diversity were identified in mitochondrial cytochrome c oxidase (cox1) gene sequences of Schistosoma turkestanicum from Hungary. These cox1 sequences were all specific to Hungary which contrasted with the low levels of diversity seen in the nuclear internal transcribed spacer region (ITS) sequences, the majority of which were shared between China and Iran isolates. Measures of within and between host molecular variation within S. turkestanicum showed there to be substantial differences in molecular diversity, with cox1 being significantly more diverse than the ITS. Measures of haplotype frequencies revealed that each host contained its own subpopulation of genetically unique parasites with significant levels of differentiation. Pairwise mismatch analysis of cox1 sequences indicated S. turkestanicum populations to have a bimodal pairwise difference distribution and to be stable unlike the ITS sequences, which appeared to have undergone a recent population expansion event. Positive selection was also detected in the cox1 sequences, and biochemical modelling of the resulting protein illustrated significant mutational events causing an alteration to the isoelectric point of the cox1 protein, potentially altering metabolism. The evolutionary signature from the cox1 indicates local adaptation and long establishment of S. turkestanicum in Hungary with continual introgression of nuclear genes from Asian isolates. These processes have led to the occurrence of mito-nuclear discordance in a schistosome population

Population Genetics ofCaenorhabditis elegans: The Paradox of Low Polymorphism in a Widespread Species

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 147-157 ◽  
Author(s):  
Arjun Sivasundar ◽  
Jody Hey
Keyword(s):  
Genetic Variation ◽  
Microsatellite Loci ◽  
Population Expansion ◽  
Widespread Species ◽  
C Elegans ◽  
Model Research ◽  
The World ◽  
Natural Isolates ◽  
History Of ◽  
Low Levels

AbstractCaenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.

scholarly journals Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 737
Author(s):  
Issiaka Bagayoko ◽  
Marcos Giovanni Celli ◽  
Gustavo Romay ◽  
Nils Poulicard ◽  
Agnès Pinel-Galzi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Sierra Leone ◽  
Evolutionary History ◽  
Molecular Diversity ◽  
Genomic Data ◽  
Gene Recombination ◽  
Necrosis Virus ◽  
History Of ◽  
Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

scholarly journals Genetic and ecological differentiation between the butterfly sisterspecies Colias alfacariensis and Colias hyale

2002 ◽  
Vol 71 (4) ◽  
pp. 131-139 ◽  
Author(s):  
Daniel F.R. Cleary ◽  
Henri Descimon ◽  
Steph B.J. Menken
Keyword(s):  
Evolutionary History ◽  
Ice Sheets ◽  
Geographic Area ◽  
Sister Species ◽  
Distributional Pattern ◽  
The West ◽  
History Of ◽  
Large Geographic Area ◽  
The Alps ◽  
Low Levels

Clear habitat separation between the sister species Colias alfacariensis and C. hyale is shown when occurring sympatrically. Colias hyale is found more often in moist cultivated pastures while Colias alfacariensis is more abundant in dry uncultivated habitat. Out of a total of 16 loci, no diagnostic loci were found between C. alfacariensis and C. hyale, and both species shared most major polymorphisms. Exceptions were the marked differences in allele frequencies at the HK locus and only C. hyale, but not C. alfacariensis was further invariable at the GOT2 locus, which is usually highly polymorphic in the Pieridae. Colias hyale has a significantly lower level of heterozygosity than its sister species C. alfacariensis. In Colias alfacariensis heterozygosity is highest in the Alps and lowest in the low-lying region of Northern France, Both species show high levels of gene flow over a large geographic area. Within C. alfacariensis, but not in C. hyale, the FST value of the PGI locus is significantly different from zero effectively separating the species into populations with high levels of the ’ b’ allele to the west and North, and low levels of the allele in the Alps and Italy. This could point to selection within the PGI locus in line with the well established pattern of selection at the PGI locus in other species of Colias. Glaciations have been an important force in shaping the evolutionary history of European biota, leading to extinction, but also allowing new species to evolve into the newly available land as the ice sheets retreated. The genetic and distributional pattern found between both Colias species suggests that habitat shifts and subsequent adaptation during glaciations could have played an important role in their speciation.

scholarly journals Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Yun-Peng Zhao ◽  
Guangyi Fan ◽  
Ping-Ping Yin ◽  
Shuai Sun ◽  
Ning Li ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Charles Darwin ◽  
Eastern China ◽  
Population Expansion ◽  
Fossil Species ◽  
Living Fossil ◽  
Living Fossils ◽  
Bioclimatic Variables ◽  
The World ◽  
History Of

Abstract As Charles Darwin anticipated, living fossils provide excellent opportunities to study evolutionary questions related to extinction, competition, and adaptation. Ginkgo (Ginkgo biloba L.) is one of the oldest living plants and a fascinating example of how people have saved a species from extinction and assisted its resurgence. By resequencing 545 genomes of ginkgo trees sampled from 51 populations across the world, we identify three refugia in China and detect multiple cycles of population expansion and reduction along with glacial admixture between relict populations in the southwestern and southern refugia. We demonstrate multiple anthropogenic introductions of ginkgo from eastern China into different continents. Further analyses reveal bioclimatic variables that have affected the geographic distribution of ginkgo and the role of natural selection in ginkgo’s adaptation and resilience. These investigations provide insights into the evolutionary history of ginkgo trees and valuable genomic resources for further addressing various questions involving living fossil species.

scholarly journals Ape Origins of Human Malaria

2020 ◽  
Vol 74 (1) ◽  
pp. 39-63 ◽  
Author(s):  
Paul M. Sharp ◽  
Lindsey J. Plenderleith ◽  
Beatrice H. Hahn
Keyword(s):  
Evolutionary History ◽  
Plasmodium Species ◽  
Population Expansion ◽  
Plasmodium Malariae ◽  
Human Infection ◽  
Parasite Lineage ◽  
African Apes ◽  
History Of ◽  
Genetic Bottlenecks ◽  
Duffy Negative

African apes harbor at least twelve Plasmodium species, some of which have been a source of human infection. It is now well established that Plasmodium falciparum emerged following the transmission of a gorilla parasite, perhaps within the last 10,000 years, while Plasmodium vivax emerged earlier from a parasite lineage that infected humans and apes in Africa before the Duffy-negative mutation eliminated the parasite from humans there. Compared to their ape relatives, both human parasites have greatly reduced genetic diversity and an excess of nonsynonymous mutations, consistent with severe genetic bottlenecks followed by rapid population expansion. A putative new Plasmodium species widespread in chimpanzees, gorillas, and bonobos places the origin of Plasmodium malariae in Africa. Here, we review what is known about the origins and evolutionary history of all human-infective Plasmodium species, the time and circumstances of their emergence, and the diversity, host specificity, and zoonotic potential of their ape counterparts.

scholarly journals Phantom histories of misspecified pasts

2020 ◽  
Author(s):  
Alexander Platt ◽  
Daniel N. Harris
Keyword(s):  
Natural Population ◽  
Population Decline ◽  
Natural Populations ◽  
Population Expansion ◽  
Purifying Selection ◽  
Genome Sequences ◽  
Recent Population Expansion ◽  
A Genome ◽  
History Of

AbstractThe observation that even a tiny sample of genome sequences from a natural population contains a plethora of information about the history of the population has enticed researchers to use these data to fit complex demographic histories and make detailed inference about the changes a population has experienced through time. Unfortunately, the standard assumptions required to make these inferences are often violated by natural populations in such ways as to produce specious results. This paper examines two phenomena of particular concern: when a sample is drawn from a single sub-population of a larger meta-population these models infer a spurious recent population decline, and when a genome contains loci under weak or recessive purifying selection these models infer a spurious recent population expansion.

Phylogenetic relationships among Elymus and related diploid genera (Triticeae: Poaceae) based on nuclear rDNA ITS sequences

Biologia ◽  
2015 ◽  
Vol 70 (2) ◽  
Author(s):  
Gang Gao ◽  
Jia-bin Deng ◽  
Xue-mei Gou ◽  
Qian Wang ◽  
Chun-bang Ding ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Its Sequences ◽  
Neighbor Joining ◽  
Rdna Its ◽  
Genome Donor ◽  
Rdna Its Sequences ◽  
History Of ◽  
Elymus Species

AbstractTo investigate the phylogenetic relationships among Elymus and related diploid genera, the genome donor of Elymus, and the evolutionary history of polyploid Elymus species, nuclear ribosomal internal transcribed spacer (ITS) sequences were analyzed for 10 Elymus species, together with 17 diploid taxa from 5 monogenomic genera. The phylogenetic analyses (Neighbor-Joining) supported two major clades (St and H). Sequence diversity and genealogical analysis suggested that (1) Elymus species were unambiguously closely related to Pseudoroegeria; (2) Pse. stipifolia might be serve as the St genome donor of polyploid Elymus species; (3) the Y genome might be originated from ancestral lineage of Pseudoroegneria (St); (4) the ITS sequences of Elymus were evolutionarily distinct and may clarify parental lineages and phylogenetic relationships in Elymus.

Evolutionary History of the Ostracoda and the Origin of Nonmarine Faunas

2003 ◽  
Vol 9 ◽  
pp. 11-36 ◽  
Author(s):  
Lisa E. Park ◽  
R. Douglas Ricketts
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Adductor Muscle ◽  
Morphological Characters ◽  
Character State ◽  
Parsimony Analysis ◽  
Hard Part ◽  
History Of ◽  
Low Levels ◽  
Pore Canals

The Ostracoda are one of the most diverse arthropod groups alive today; they also have a tremendous fossil record. Because of their widespread environmental distributions, small size and carbonate shell, they have become extremely useful biostratigraphic and paleoenvironmental proxy indicators, particularly in nonmarine environments. Despite this utility, little is known about the phylogenetic history of this important group. We reconstructed a phylogenetic history of the major orders and suborders of Ostracoda in order to test the legitimacy of current classification schemes, determine if it is possible for ostracodes to have a Precambrian origin, and test the fidelity of some of the major morphological characters that have documented trends of either increased complexity, such as the hinge and marginal pore canals, or reduction in segments, such as the adductor muscle scar.In our phylogenetic analysis to test taxonomic fidelity, we coded seven morphological hard part characters for nine taxa from the orders Archaeocopida, Leperditicopida, Palaeocopida, Podocopida, and Myodocopida. A parsimony analysis was performed using PAUP (v. 4.0) yielding 4 trees of 17 steps with low levels of homoplasy and a strong phylogenetic signal. A majority rule consensus tree indicates there is not complete agreement between the standard classification scheme and the phylogeny produced by the characters used to establish the classification. In our complete analysis of Ostracoda, we coded 28 morphological characters that included 14 hard part and 14 soft part characters for twelve taxa that include the Archaeocopida, Leperditicopida, Podocopida, and Myodocopida. A parsimony analysis was completed using PAUP (v. 4.0) yielding 1 tree of 125 steps with low levels of homoplasy and a strong phylogenetic signal. An unrooted analysis of this character set has the Cambrian Archaeopodocopida and the Ordovician-Devonian Leperditicopida in an unresolved polytomy with much younger groups such as the Myodocopina, suggesting a much deeper split in the lineage and a possible Precambrian origin for the Ostracoda. Testing the various character state acquisitions over the tree indicates that the hinge does not show an increase in complexity within a phylogenetic context, while the adductor muscle scars do show a significant trend of decrease in complexity across the tree topology. The marginal pore canals, which are functionally tied to osmoregulation as well as carapace secretion, are extremely homoplastic, indicating that this character, which is related to nonmarine invasions and tolerances, was acquired many times throughout the evolutionary history of Ostracoda.By creating an evolutionary framework for the Ostracoda such as is presented here, we can further assess character state acquisition, and how it functionally and evolutionarily relates to ostracode paleoenvironmental tolerances. The framework will not only allow us to understand the overall evolution ofthis group but will also allow us to compare the history of the ostracode clade with other groups that also have a history ofmarine and nonmarine transitions.

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