Intraspecific Diversity and Phylogeography in Southern Appalachian Dasycerus carolinensis (Coleoptera: Staphylinidae: Dasycerinae)

2019 ◽  
Vol 3 (6) ◽  
Author(s):  
Michael S Caterino ◽  
Shelley S Langton-Myers
Keyword(s):  
Genetic Diversity ◽  
Anthropogenic Disturbance ◽  
Secondary Growth ◽  
Intraspecific Diversity ◽  
Nuclear Marker ◽  
Old Growth ◽  
Rove Beetle ◽  
Southern Appalachian ◽  
History Of ◽  
Cryptic Divergence

Abstract The southern Appalachian Mountains in eastern North America host exceptional diversity, a substantial proportion of which has been generated in place. Yet, beyond broad generalities, bio- and phylogeographical patterns, and the temporal scale of diversification in the region are poorly resolved. Using one mitochondrial and one nuclear marker, we analyze intraspecific diversity patterns in a flightless, litter-inhabiting rove beetle Dasycerus carolinensis Horn. Our goals were to reconstruct the phylogeographical history of this species, producing a dated intraspecific phylogeny, and to examine previous hypotheses of possible cryptic divergence across populations of the species. Samples derive from a mix of old-growth fragments and secondary growth forests, and we also ask whether old-growth remnants host a larger proportion of genetic diversity in the species. We recover a strong primary subdivision among major lineages across the French Broad River basin (dated to ~5.8 MYBP), and a secondary subdivision among western populations dating to ~4.5 MYBP. Most interpopulation uncorrected divergences exceed 5%, strongly suggesting cryptic differentiation. Old-growth populations do not show greater genetic diversity than secondary-growth populations, indicating that most populations have persisted through recent anthropogenic disturbance.

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.

Holocene stand-scale vegetation dynamics and fire history of an old-growth spruce forest in southern Finland

2015 ◽  
Vol 24 (6) ◽  
pp. 731-741 ◽  
Author(s):  
Jennifer L. Clear ◽  
Heikki Seppä ◽  
Niina Kuosmanen ◽  
Richard H. W. Bradshaw
Keyword(s):  
Vegetation Dynamics ◽  
Fire History ◽  
Spruce Forest ◽  
Old Growth ◽  
History Of

Genetic Diversity and Population Size in Four Rare Southern Appalachian Plant Species

1996 ◽  
Vol 10 (3) ◽  
pp. 796-805 ◽  
Author(s):  
Mary Jo W. Godt ◽  
Bart R. Johnson ◽  
J.L. Hamrick
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Plant Species ◽  
Southern Appalachian

Genetic diversity and breeding history of Winter Mushroom (Flammulina velutipes) in China uncovered by genomic SSR markers

Gene ◽  
2016 ◽  
Vol 591 (1) ◽  
pp. 227-235 ◽  
Author(s):  
Xiao Bin Liu ◽  
Bang Feng ◽  
Jing Li ◽  
Chen Yan ◽  
Zhu L. Yang
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Flammulina Velutipes ◽  
Genomic Ssr ◽  
History Of ◽  
Breeding History

Season of birth interacts with measures of inbreeding in multiplex schizophrenia pedigrees: evidence from genetic isolates in Daghestan

Open Medicine ◽  
2006 ◽  
Vol 1 (4) ◽  
pp. 392-398
Author(s):  
Kazima Bulayeva ◽  
John McGrath
Keyword(s):  
Genetic Diversity ◽  
Family History ◽  
Age Of Onset ◽  
Population Genetic Study ◽  
Season Of Birth ◽  
High Genetic Diversity ◽  
Low Genetic Diversity ◽  
High Prevalence ◽  
History Of ◽  
Genetic Isolates

AbstractWhile the season-of-birth effect is one of the most consistent epidemiological features of schizophrenia, there is a lack of consistency with respect to the interaction between season of birth and family history of schizophrenia. Apart from family history, measures related to consanguinity can be used as proxy markers of genomic heterogeneity. Thus, these measures may provide an alternate, indirect index of genetic susceptibility. We had the opportunity to explore the interaction between season of birth and measure of consanguinity in well-described genetic isolates in Daghestan, some of which are known for their relatively high prevalence of schizophrenia. Our previous population-genetic study showed Daghestan has an extremely high genetic diversity between the ethnic populations and a low genetic diversity within them. The isolates selected for this study include some with more than 200 and some with less than 100 generations of demographical history since their founding. Based on pedigrees of multiply-affected families, we found that among individuals with schizophrenia, the measure of consanguinity was significantly higher in the parents of those born in winter/spring compared to those born in summer/autumn. Furthermore, compared to summer/autumn born, winter/spring born individuals with schizophrenia had an earlier age-of-onset, and more prominent auditory hallucinations. Our results suggest that the offspring of consanguineous marriages, and thus those with reduced allelic heterogeneity, may be more susceptible to the environmental factor(s) underpinning the season-of-the effect in schizophrenia.

scholarly journals Genetic variation in native and farmed populations of Tambaqui (Colossoma macropomum) in the Brazilian Amazon: regional discrepancies in farming systems

2013 ◽  
Vol 85 (4) ◽  
pp. 1439-1447 ◽  
Author(s):  
Jonas Aguiar ◽  
Horacio Schneider ◽  
Fatima Gomes ◽  
Jeferson Carneiro ◽  
Simoni Santos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Dna Sequences ◽  
Amazon Basin ◽  
Farming Systems ◽  
Wild Populations ◽  
The West ◽  
Colossoma Macropomum ◽  
Breeding Stock ◽  
History Of

The tambaqui, Colossoma macropomum, is the most popular fish species used for aquaculture in Brazil but there is no study comparing genetic variation among native and farmed populations of this species. In the present study, we analyzed DNA sequences of the mitochondrial DNA to evaluate the genetic diversity among two wild populations, a fry-producing breeding stock, and a sample of fish farm stocks, all from the region of Santarém, in the west of the Brazilian state of Pará. Similar levels of genetic diversity were found in all the samples and surprisingly the breeding stock showed expressive representation of the genetic diversity registered on wild populations. These results contrast considerably with those of the previous study of farmed stocks in the states of Amapá, Pará, Piauí, and Rondônia, which recorded only two haplotypes, indicating a long history of endogamy in the breeding stocks used to produce fry. The results of the two studies show two distinct scenarios of tambaqui farming in the Amazon basin, which must be better evaluated in order to guarantee the successful expansion of this activity in the region, and the rest of Brazil, given that the tambaqui and its hybrids are now farmed throughout the country.

Canopy disturbances over the five-century lifetime of an old-growth Douglas-fir stand in the Pacific Northwest

2002 ◽  
Vol 32 (6) ◽  
pp. 1057-1070 ◽  
Author(s):  
Linda E Winter ◽  
Linda B Brubaker ◽  
Jerry F Franklin ◽  
Eric A Miller ◽  
Donald Q DeWitt
Keyword(s):  
Pacific Northwest ◽  
Variable Density ◽  
Tsuga Heterophylla ◽  
Douglas Fir ◽  
Western Hemlock ◽  
Old Growth ◽  
The Pacific ◽  
History Of ◽  
Horizontal Heterogeneity ◽  
Restoration Strategies

The history of canopy disturbances over the lifetime of an old-growth Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) stand in the western Cascade Range of southern Washington was reconstructed using tree-ring records of cross-dated samples from a 3.3-ha mapped plot. The reconstruction detected pulses in which many western hemlock (Tsuga heterophylla (Raf.) Sarg.) synchronously experienced abrupt and sustained increases in ringwidth, i.e., "growth-increases", and focused on medium-sized or larger ([Formula: see text]0.8 ha) events. The results show that the stand experienced at least three canopy disturbances that each thinned, but did not clear, the canopy over areas [Formula: see text]0.8 ha, occurring approximately in the late 1500s, the 1760s, and the 1930s. None of these promoted regeneration of the shade-intolerant Douglas-fir, all of which established 1500–1521. The disturbances may have promoted regeneration of western hemlock, but their strongest effect on tree dynamics was to elicit western hemlock growth-increases. Canopy disturbances are known to create patchiness, or horizontal heterogeneity, an important characteristic of old-growth forests. This reconstructed history provides one model for restoration strategies to create horizontal heterogeneity in young Douglas-fir stands, for example, by suggesting sizes of areas to thin in variable-density thinnings.

scholarly journals Strengths and potential pitfalls of hay-transfer for ecological restoration revealed by RAD-seq analysis in floodplain Arabis species

2018 ◽  
Author(s):  
Hannes Dittberner ◽  
Christian Becker ◽  
Wen-Biao Jiao ◽  
Korbinian Schneeberger ◽  
Norbert Hölzel ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ecological Restoration ◽  
Habitat Restoration ◽  
De Novo ◽  
Flood Plain ◽  
Intraspecific Diversity ◽  
Close Relative ◽  
Its Sequencing ◽  
Adaptive Potential ◽  
Local Material

AbstractAchieving high intraspecific genetic diversity is a critical goal in ecological restoration as it increases the adaptive potential and long-term resilience of populations. Thus, we investigated genetic diversity within and between pristine sites in a fossil floodplain and compared it to sites restored by hay-transfer between 1997 and 2014. RAD-seq genotyping revealed that the stenoecious flood-plain species Arabis nemorensis is co-occurring with individuals that, based on ploidy, ITS-sequencing and morphology, probably belong to the close relative Arabis sagittata, which has a documented preference for dry calcareous grasslands but has not been reported in floodplain meadows. We show that hay-transfer maintains genetic diversity for both species. Additionally, in A. sagittata, transfer from multiple genetically isolated pristine sites resulted in restored sites with increased diversity and admixed local genotypes. In A. nemorensis, transfer did not create novel admixture dynamics because genetic diversity between pristine sites was less differentiated. Thus, the effects of hay-transfer on genetic diversity also depend on the genetic makeup of the donor communities of each species, especially when local material is mixed. Our results demonstrate the efficiency of hay-transfer for habitat restoration and emphasize the importance of pre-restoration characterization of micro-geographic patterns of intraspecific diversity of the community to guarantee that restoration practices reach their goal, i.e. maximize the adaptive potential of the entire restored plant community. Overlooking these patterns may alter the balance between species in the community. Additionally, our comparison of summary statistics obtained from de novo and reference-based RAD-seq pipelines shows that the genomic impact of restoration can be reliably monitored in species lacking prior genomic knowledge.

scholarly journals SARS-Like Coronaviruses in Horseshoe Bats (Rhinolophus spp.) in Russia, 2020

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 113
Author(s):  
Sergey Alkhovsky ◽  
Sergey Lenshin ◽  
Alexey Romashin ◽  
Tatyana Vishnevskaya ◽  
Oleg Vyshemirsky ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
Structural Proteins ◽  
Rt Pcr ◽  
Phylogenetic Lineage ◽  
History Of ◽  
Horseshoe Bats ◽  
Regions Of Russia ◽  
Nonstructural Genes

We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the greater (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern regions of Russia. The viruses, named Khosta-1 and Khosta-2, together with related viruses from Bulgaria and Kenya, form a separate phylogenetic lineage. We found evidence of recombination events in the evolutionary history of Khosta-1, which involved the acquisition of the structural proteins S, E, and M, as well as the nonstructural genes ORF3, ORF6, ORF7a, and ORF7b, from a virus that is related to the Kenyan isolate BtKY72. The examination of bats by RT-PCR revealed that 62.5% of the greater horseshoe bats in one of the caves were positive for Khosta-1 virus, while its overall prevalence was 14%. The prevalence of Khosta-2 was 1.75%. Our results show that SARS-like coronaviruses circulate in horseshoe bats in the region, and we provide new data on their genetic diversity.

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