scholarly journals Patterns of Genetic Variation in the Eisenia nordenskioldi Complex (Oligochaeta: Lumbricidae) along an Elevation Gradient in Northern China

Diversity ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 35
Author(s):  
Yufeng Zhang ◽  
Yiming Zhang ◽  
Hui Wu ◽  
Congsheng Li ◽  
Nonillon M. Aspe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Elevation Gradient ◽  
Northern China ◽  
External Morphology ◽  
Distribution Analysis ◽  
Limited Sample ◽  
Southern Limit ◽  
Earthworm Species ◽  
Mismatch Distribution Analysis ◽  
Eisenia Nordenskioldi

Eisenia nordenskioldi is the dominant earthworm species in many tundra and boreal habitats. Nothing is known about the genetic diversity of this species along the elevation gradient in China. This study sampled 28 individuals in the E. nordenskioldi complex from Wuling Mountain, northern China, to examine their external morphology and genetic diversity. Mt. Wuling is the southern limit of the distribution of the E. nordenskioldi complex. The specimens from Mt. Wuling were classified into three groups along an elevation gradient. Mismatch distribution analysis suggested that the Pleistocene glaciations possibly did not significantly affect the distribution of earthworm species in this region. We also found that elevation affected the genetic diversity, but not the external morphology of E. nordenskioldi. Given the altitudinal genetic diversity within the E. nordenskioldi complex, the phylogeography of this species provides important information for the zoogeographic reconstruction of the mountains in northern China. With the relatively limited sample size, the result is not conclusive, and further studies need to be conducted in the future to verify the results.

scholarly journals Influence of Quaternary environmental changes on mole populations inferred from mitochondrial sequences and evolutionary rate estimation

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Azusa Nakamoto ◽  
Masashi Harada ◽  
Reiko Mitsuhashi ◽  
Kimiyuki Tsuchiya ◽  
Alexey P. Kryukov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Environmental Changes ◽  
Late Quaternary ◽  
Population Expansion ◽  
Rapid Expansion ◽  
Dependent Manner ◽  
Distribution Analysis ◽  
Land Bridge ◽  
Mismatch Distribution Analysis ◽  
Expansion Event

AbstractQuaternary environmental changes fundamentally influenced the genetic diversity of temperate-zone terrestrial animals, including those in the Japanese Archipelago. The genetic diversity of present-day populations is taxon- and region-specific, but its determinants are poorly understood. Here, we analyzed cytochrome b gene (Cytb) sequences (1140 bp) of mitochondrial DNA (mtDNA) to elucidate the factors determining the genetic variation in three species of large moles: Mogera imaizumii and Mogera wogura, which occur in central and southern mainland Japan (Honshu, Shikoku, and Kyushu), and Mogera robusta, which occurs on the nearby Asian continent. Network construction with the Cytb sequences revealed 10 star-shaped clusters with apparent geographic affinity. Mismatch distribution analysis showed that modes of pairwise nucleotide differences (τ values) were grouped into five classes in terms of the level, implying the occurrence of five stages for rapid expansion. It is conceivable that severe cold periods and subsequent warm periods during the late Quaternary were responsible for the population expansion events. The first and third oldest events included island-derived haplotypes, indicative of the involvement of land bridge formation between remote islands, hence suggesting an association of the ends of the penultimate (PGM, ca. 130,000 years ago) and last (LGM, ca. 15,000 years ago) glacial maxima, respectively. Since the third event was followed by the fourth, it is plausible that the termination of the Younger Dryas and subsequent abrupt warming ca. 11,500 years ago facilitated the fourth expansion event. The second event most likely corresponded to early marine isotope stage (MIS) 3 (ca. 53,000 years ago) when the glaciation and subsequent warming period were predicted to have influenced biodiversity. Utilization of the critical times of 130,000, 53,000, 15,000, and 11,500 years ago as calibration points yielded evolutionary rates of 0.03, 0.045, 0.10 and 0.10 substitutions/site/million years, respectively, showing a time-dependent manner whose pattern was similar to that seen in small rodents reported in our previous studies. The age of the fifth expansion event was calculated to be 5800 years ago with a rate of 0.10 substitutions/site/million years ago during the mid-Holocene, suggestive of the influence of humans or other unspecified reasons, such as the Jomon marine transgression.

Distribution of mating types and genetic diversity induced by sexual recombination in Setosphaeria turcica in northern China

2007 ◽  
Vol 1 (4) ◽  
pp. 368-376 ◽  
Author(s):  
Yongshan Fan ◽  
Jifang Ma ◽  
Xiumei Gui ◽  
Xinlong An ◽  
Shuqin Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Northern China ◽  
Mating Types ◽  
Setosphaeria Turcica ◽  
Sexual Recombination

scholarly journals Genetic Diversity of Wild Asian Lotus (Nelumbo nucifera) from Northern China

2021 ◽  
Author(s):  
Yanrong Fu ◽  
Fengluan Liu ◽  
Shuo Li ◽  
Daike Tian ◽  
Li Dong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Northern China ◽  
Nelumbo Nucifera

scholarly journals Low Genetic Diversity of the Endangered Franciscana (Pontoporia blainvillei) in Its Northernmost, Isolated Population (FMAIa, Espírito Santo, Brazil)

2020 ◽  
Vol 7 ◽  
Author(s):  
Vanessa K. M. de Oliveira ◽  
Drienne M. Faria ◽  
Haydée A. Cunha ◽  
Teresa E. C. dos Santos ◽  
Adriana C. Colosio ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Control Region ◽  
Microsatellite Loci ◽  
Distribution Analysis ◽  
Sample Number ◽  
Espírito Santo ◽  
Low Genetic Diversity ◽  
Southwestern Atlantic Ocean ◽  
Espirito Santo ◽  
Pontoporia Blainvillei

The franciscana, Pontoporia blainvillei, is the most endangered small cetacean in the Southwestern Atlantic Ocean, occurring from Itaúnas, Espírito Santo, Brazil to Chubut province, Argentina. This area is divided into four Franciscana Management Areas (FMA). The northern portion of this species distribution is not continuous and a previous genetic study using mitochondrial DNA (mtDNA) separated it into FMAIa (Espírito Santo state) and FMAIb (North of Rio de Janeiro state). In order to increase the information about this population we expanded the sample number and evaluated mitochondrial and nuclear DNA diversity. Samples of 68 franciscanas found stranded on beaches from 2005 to 2020 were analyzed. Analyses included 350 bp of the mtDNA control region (D-loop) and 12 microsatellite loci. We identified three control region haplotypes in FMAIa, two of them not previously observed in this population, one being a new haplotype. Haplotype and nucleotide diversities were 0.0408 and 0.00012 respectively, the lowest reported for all FMAs analyzed until now. The Neutrality tests were not significant and Mismatch Distribution analysis did not reject the hypothesis of population expansion. One of the microsatellite loci was monomorphic, and for the other loci, two to nine alleles were identified, with expected heterozygosities ranging from 0.306 to 0.801. No substructure was revealed and effective population size (Ne) was estimated in 117.9 individuals. Even with an increased sample size, the high mitochondrial genetic homogeneity suggested for the population in a previous study was confirmed. Among six loci previously analyzed in other franciscana populations, five showed the lowest observed heterozygosities for the Espírito Santo population. The novel microsatellite data also showed low genetic diversity and could not reject the hypothesis of a single, panmitic population along the coast of Espírito Santo. This species has been intensively impacted in the last years by incidental capture during fishing activities and habitat degradation, caused by pollution, coastal development and environmental disasters in FMAIa. Considering that this population is small, isolated, and with low levels of genetic diversity, we reinforce the necessity of different conservation actions, focusing mainly on the reduction of bycatch of this species in the region.

scholarly journals Environmental determinants of genetic diversity inCaragana microphylla(Fabaceae) in northern China

2016 ◽  
Vol 181 (2) ◽  
pp. 269-278 ◽  
Author(s):  
Wen-Da Huang ◽  
Xue-Yong Zhao ◽  
Xin Zhao ◽  
Yu-Lin Li ◽  
Cheng-Chen Pan
Keyword(s):  
Genetic Diversity ◽  
Northern China ◽  
Environmental Determinants

scholarly journals Investigation of genetic diversity and population structure of common wheat cultivars in northern China using DArT markers

BMC Genetics ◽  
2011 ◽  
Vol 12 (1) ◽  
pp. 42 ◽  
Author(s):  
LiYi Zhang ◽  
DongCheng Liu ◽  
XiaoLi Guo ◽  
WenLong Yang ◽  
JiaZhu Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Common Wheat ◽  
Northern China ◽  
Dart Markers ◽  
Wheat Cultivars

scholarly journals A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands

2022 ◽  
Vol 12 ◽  
Author(s):  
Carla López-Causapé ◽  
Pablo A. Fraile-Ribot ◽  
Santiago Jiménez-Serrano ◽  
Gabriel Cabot ◽  
Ester del Barrio-Tofiño ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Temporal Distribution ◽  
Balearic Islands ◽  
Distribution Analysis ◽  
Key Factors ◽  
Consensus Sequences ◽  
Genomic Epidemiology ◽  
Size Population ◽  
Lineage Distribution ◽  
Selection Of

Objective: To analyze the SARS-CoV-2 genomic epidemiology in the Balearic Islands, a unique setting in which the course of the pandemic has been influenced by a complex interplay between insularity, severe social restrictions and tourism travels.Methods: Since the onset of the pandemic, more than 2,700 SARS-CoV-2 positive respiratory samples have been randomly selected and sequenced in the Balearic Islands. Genetic diversity of circulating variants was assessed by lineage assignment of consensus whole genome sequences with PANGOLIN and investigation of additional spike mutations.Results: Consensus sequences were assigned to 46 different PANGO lineages and 75% of genomes were classified within a VOC, VUI, or VUM variant according to the WHO definitions. Highest genetic diversity was documented in the island of Majorca (42 different lineages detected). Globally, lineages B.1.1.7 and B.1.617.2/AY.X were identified as the 2 major lineages circulating in the Balearic Islands during the pandemic, distantly followed by lineages B.1.177/B.1.177.X. However, in Ibiza/Formentera lineage distribution was slightly different and lineage B.1.221 was the third most prevalent. Temporal distribution analysis showed that B.1 and B.1.5 lineages dominated the first epidemic wave, lineage B.1.177 dominated the second and third, and lineage B.1.617.2 the fourth. Of note, lineage B.1.1.7 became the most prevalent circulating lineage during first half of 2021; however, it was not associated with an increased in COVID-19 cases likely due to severe social restrictions and limited travels. Additional spike mutations were rarely documented with the exception of mutation S:Q613H which has been detected in several genomes (n = 25) since July 2021.Conclusion: Virus evolution, mainly driven by the acquisition and selection of spike substitutions conferring biological advantages, social restrictions, and size population are apparently key factors for explaining the epidemic patterns registered in the Balearic Islands.

scholarly journals Distribution and genetic diversity of two earthworms, Helodrilus oculatus and Satchellius mammalis (Clitellata: Lumbricidae) in Scandinavia

2021 ◽  
Vol 41 ◽  
pp. 1-14
Author(s):  
Svante Martinsson ◽  
Mårten Klinth ◽  
Christer Erséus
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Type Species ◽  
The Other ◽  
Nuclear Genes ◽  
East Division ◽  
Earthworm Species ◽  
Haplotype Networks ◽  
The Family ◽  
Different Origin

We report on the Scandinavian distribution of two earthworm species, Helodrilus oculatus and Satchellius mammalis. Both appear relatively new to the Scandinavian Peninsula, as they were not included in the monographic revisions of the earthworm fauna of Sweden and Norway in the mid-1900s. We provide recent records of both species from Norway and Sweden, H. oculatus also from Denmark, and haplotype networks of four markers (COI, 16S, H3, and ITS2) are used to visualise the genetic diversity within each species. There is moderate genetic variation in COI for both taxa, and for H. oculatus, there is a West-East division between the specimens from Norway, Gothenburg (western Sweden) and Bavaria (Germany), and the ones from eastern Sweden and the Bornholm island (easternmost Denmark). This could potentially be explained by different origin and colonisation routes. In the other markers the variation is limited, and in the nuclear genes no pattern to support this split is seen. We also analyse the phylogenetic positions of H. oculatus and S. mammalis in the family Lumbricidae by combining our data (including also some12S, 18S and 28S sequences) with a published dataset. We conclude that neither Helodrilus nor Satchellius are monophyletic. Helodrilus oculatus (type species of Helodrilus), however, forms a clade with some of its current congeners.

scholarly journals Molecular Epidemiology Characteristics of Brucella Abortus Strains in China and Their Relationships With World Lineages

2020 ◽  
Author(s):  
Xu-Ming Wang ◽  
Zhongzhi Zhao ◽  
Miao Wang ◽  
Buyun Cui ◽  
Zhiguo Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Epidemiology ◽  
Brucella Abortus ◽  
Variable Number Tandem Repeat ◽  
Northern China ◽  
Variable Number ◽  
Snp Analysis ◽  
High Genetic Diversity ◽  
Geographic Origins ◽  
Epidemic Area

Abstract Background Brucella abortus is a facultative intracellular Gram-negative bacterium that causes chronic persistent infections in humans and livestock. In this study, conventional bio-typing, multiple-locus variable-number tandem repeat analysis (MLVA), and whole-genome sequencing-single-nucleotide polymorphism (WGS-SNP) were used to investigate the molecular epidemiology characteristics of Brucella abortus strains in China and their relationships to world lineages. Results A total of 100 strains were collected from 1953 to 2013, suggesting that B. abortus circulated in China in the past five decades. Moreover, most strains were mainly distributed in the Northwest areas, suggest that provinces in the Northwest were a dominant epidemic area of this disease. During this period, seven biovars were found, indicating that B. abortus had a high diversity of biovars and it is also a potential reason for the disease ongoing spread in the Northern provinces. Strains have high genetic diversity, and bruce07 is the most helpful locus for genotyping of this population. Moreover, 17 MLVA-11 genotypes were found; 13 of them are of known genotypes and four are unassigned genotypes, indicating that B. abortus in this study had several geographic origins. Still, strains from unassigned genotypes may originate from China. Many shared MLVA-16 genotypes were observed in strains from the same provinces in Northern China, which confirmed a B. abortus brucellosis outbreak within Northern regions. WGS-SNP analysis showed that eight Chinese strains formed a ladder-like phylogram (C. Ⅶ) with strains from nine countries, including Uganda, Iraq, Russia, Georgia, Spain, Italy, Egypt, Mongolia, and China; suggest that strains were introduced to these countries from a single source. Conclusions Chinese B. abortus strains had high biovars and genetic diversity as well as represent characteristics of multiple geographic origins, and B. abortus strains from several mainly epidemic areas were closely related to strains from Russia and Mongolia; frequent animal (cattle) trade and exchanges may promote this process. We will provide new and valuable information to strengthening surveillance and control of B. abortus brucellosis in China.

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