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.

scholarly journals Phylogeography of post-Pleistocene population expansion in Dasyscyphella longistipitata (Leotiomycetes, Helotiales), an endemic fungal symbiont of Fagus crenata in Japan

MycoKeys ◽  
2020 ◽  
Vol 65 ◽  
pp. 1-24
Author(s):  
Jaime Gasca-Pineda ◽  
Patricia Velez ◽  
Tsuyoshi Hosoya
Keyword(s):  
Genetic Diversity ◽  
Environmental Changes ◽  
Continuous Distribution ◽  
Population Expansion ◽  
Fagus Crenata ◽  
High Genetic Diversity ◽  
Environmental Suitability ◽  
The Japanese Archipelago ◽  
The Last Glacial Maximum ◽  
The Last Glacial

During the Last Glacial Maximum (LGM), drastic environmental changes modified the topology of the Japanese Archipelago, impacting species distributions. An example is Fagus crenata, which has a present continuous distribution throughout Japan. However, by the end of the LGM it was restricted to southern refugia. Similarly, Dasyscyphella longistipitata (Leotiomycetes, Helotiales, Lachnaceae) occurs strictly on cupules of F. crenata, sharing currently an identical distribution. As the effects of the LGM remain poorly understood for saprobiotic microfungal species, herein we identified past structuring forces that shaped the current genetic diversity within D. longistipitata in relation to its host using a phylogeographic approach. We inferred present and past potential distributions through species distribution modeling, identifying environmental suitability areas in mid-southern Japan from which subsequent colonizations occurred. Our findings suggest that current high genetic diversity and lack of genetic structure within D. longistipitata are the result of recent multiple re-colonization events after the LGM.

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.

Genetic diversity of the swamp rat in South America: Population expansion after transgressive-regressive marine events in the Late Quaternary

2015 ◽  
Vol 80 (6) ◽  
pp. 510-517 ◽  
Author(s):  
Fernando M. Quintela ◽  
Gislene L. Gonçalves ◽  
Fabrício Bertuol ◽  
Enrique M. González ◽  
Thales R.O. Freitas
Keyword(s):  
Genetic Diversity ◽  
South America ◽  
Late Quaternary ◽  
Population Expansion

scholarly journals Comparative Genetic Analysis of Invasive Fall Armyworm Populations Provides Evidence for Population Expansion in India

2020 ◽  
Author(s):  
Nishtha Nayyar ◽  
Gracy Ramasamy ◽  
Ashika Thotambyl ◽  
Mohan Govindasamy ◽  
Mohan Muthugounder ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Fall Armyworm ◽  
Western Hemisphere ◽  
Coi Gene ◽  
Polymorphism Analysis ◽  
Distribution Analysis ◽  
Maize Production ◽  
The World

Abstract Fall Armyworm (FAW), Spodoptera frugiperda, is a polyphagous pest capable of feeding over 80 plant species and was indigenous to Western Hemisphere until recently. Within a span of four years, FAW has established itself throughout most of the regions in Africa and Asia incurring significant losses in maize production. Owing to its revamped distribution range, it would be prudent to analyse the ensuing genetic changes and study the emerging phylogeographic patterns across the world. In this regard, we would like to provide a current snapshot of genetic diversity of FAW in India after two years of the initial introduction and compare it with the worldwide diversity in order to trace the origins and evolutionary trajectories of FAW in India.We have investigated around 145 FAW samples from different regions in India for strain identity and polymorphism analysis on the basis of partial mitochondrial cytochrome oxidase I (COI) gene sequences. Apart from the ancestral rice and corn strain haplotype, our study demonstrates the presence of 19 more haplotypes unique to India at a haplotype diversity of 0.498. We were also able to record the occurrence of inter-strain hybrid haplotypes of rice and corn strain in India. Regional heterogeneity within Indian populations seems to be quite low representative of extensive migration of FAW within India. Distribution analysis of pairwise differences and rejection of neutrality tests suggest that the FAW population in India is undergoing expansion. However, the scenario is much different for rest of the invaded regions like Africa and other Asian countries where FAW still appear to evolve neutrally. Our data is consistent with the findings suggesting a recent and common origin for invasive FAW populations in Asia and Africa, with significant population structure observed in Indian populations.This study reports the highest genetic diversity for Indian FAW populations till date and identifies India as the emerging hotspot for expansion of COIA rice haplotypes across the world. The findings will be useful to track the subsequent evolution of FAW and would have important ramifications for FAW behaviour and composition throughout the world.

scholarly journals Population genetic structure of Marbled Rockfish, Sebastiscus marmoratus (Cuvier, 1829), in the northwestern Pacific Ocean

ZooKeys ◽  
2019 ◽  
Vol 830 ◽  
pp. 127-144 ◽  
Author(s):  
Lu Liu ◽  
Xiumei Zhang ◽  
Chunhou Li ◽  
Hui Zhang ◽  
Takashi Yanagimoto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic ◽  
Fishery Management ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Northwestern Pacific ◽  
Distribution Analysis ◽  
Recent Population Expansion

Sebastiscusmarmoratus is an ovoviviparous fish widely distributed in the northwestern Pacific. To examine the gene flow and test larval dispersal strategy of S.marmoratus in Chinese and Japanese coastal waters, 421 specimens were collected from 22 localities across its natural distribution. A 458 base-pair fragment of the mitochondrial DNA (mtDNA) control region was sequenced to examine genetic diversity and population structure. One-hundred-six variable sites defined 166 haplotypes. The populations of S.marmoratus showed high haplotype diversity with a range from 0.8587 to 0.9996, indicating a high level of intrapopulation genetic diversity. Low non-significant genetic differentiation was estimated among populations except those of Hyogo, Behai, and Niiigata, which showed significant genetic differences from the other populations. The demographic history examined by neutrality tests, mismatch distribution analysis, and Bayesian skyline analysis suggested a sudden population expansion dating to the late Pleistocene. Recent population expansion in the last glacial period, wide dispersal of larvae by coastal currents, and the homogeneity of the environment may have important influences on the population genetic pattern. Knowledge of genetic diversity and genetic structure will be crucial to establish appropriate fishery management of S.marmoratus.

scholarly journals Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wen-Wen Li ◽  
Li-Qiang Liu ◽  
Qiu-Ping Zhang ◽  
Wei-Quan Zhou ◽  
Guo-Quan Fan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Chloroplast Dna ◽  
Population Expansion ◽  
Prunus Armeniaca ◽  
River Valley ◽  
Nuclear Ribosomal Dna ◽  
Glacial Refugium ◽  
Ili River Valley ◽  
Wild Apricot

AbstractTo clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: HT = 0.499; ITS: HT = 0.876) and a low level of genetic differentiation (cpDNA: FST = 0.1628; ITS: FST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (NST) was significantly higher than the number of substitution types (GST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

scholarly journals Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
H. De Kort ◽  
J. G. Prunier ◽  
S. Ducatez ◽  
O. Honnay ◽  
M. Baguette ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Life History ◽  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Peripheral Populations ◽  
Plant Dispersal ◽  
Weak Support ◽  
Animal Populations ◽  
Plant Groups ◽  
Conservation Genetic

AbstractUnderstanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales.

Late Pleistocene and Holocene Paleoenvironments of Chalco Lake, Central Mexico

1993 ◽  
Vol 40 (3) ◽  
pp. 332-342 ◽  
Author(s):  
Maria Socorro Lozano-Garcı́a ◽  
Beatriz Ortega-Guerrero ◽  
Margarita Caballero-Miranda ◽  
Jaime Urrutia-Fucugauchi
Keyword(s):  
Volcanic Activity ◽  
Lake Level ◽  
Environmental Changes ◽  
Late Quaternary ◽  
Cold Climate ◽  
Central Mexico ◽  
Pollen Record ◽  
Loss On Ignition ◽  
Southeastern Part ◽  
Saline Marsh

AbstractIn order to establish paleoenvironmental conditions during the late Quaternary, four cores from the Basin of Mexico (central Mexico) were drilled in Chalco Lake, located in the southeastern part of the basin. The upper 8 m of two parallel cores were studied, using paleomagnetic, loss-on-ignition, pollen, and diatom analyses. Based on 11 14C ages, the analyzed record spans the last 19,000 14C yr B.P. Volcanic activity has affected microfossil abundances, both directly and indirectly, resulting in absence or reduction of pollen and diatom assemblages. Important volcanic activity took place between 19,000 and 15,000 yr B.P. when the lake was a shallow alkaline marsh and an increase of grassland pollen suggests a dry, cold climate. During this interval, abrupt environmental changes with increasing moisture occurred. From 15,000 until 12,500 yr B.P. the lake level increased and the pollen indicates wetter conditions. The highest lake level is registered from 12,500 to ca. 9000 yr B.P. The end of the Pleistocene is characterized by an increase in humidity. From 9000 until ca. 3000 yr B.P. Chalco Lake was a saline marsh and the pollen record indicates warmer conditions. After 3000 yr B.P. the lake level increased and human disturbance dominates the lacustrine record.

scholarly journals Late Quaternary paleoenvironment of the Ross Sea continental shelf, Antarctica

1998 ◽  
Vol 27 ◽  
pp. 275-280 ◽  
Author(s):  
Akira Nishimura ◽  
Toru Nakasone ◽  
Chikara Hiramatsu ◽  
Manabu Tanahashi
Keyword(s):  
Organic Carbon ◽  
Marine Environment ◽  
Environmental Changes ◽  
Ross Sea ◽  
Late Quaternary ◽  
Sedimentary Environment ◽  
Sediment Cores ◽  
Ice Sheet ◽  
Ice Shelf ◽  
Accelerator Mass Spectrometer

Based on sedimenlological and micropaleontological work on three sediment cores collected at about 167° Ε in the western Ross Sea, Antarctica, and accelerator mass spectrometer l4C ages of organic carbon, we have reconstructed environmental changes in the area during the late Quaternary. Since 38 ka BP at latest, this area was a marine environment with low productivity. A grounded ice sheet advanced and loaded the sediments before about 30-25 ka BP. After 25 ka BP, the southernmost site (76°46'S) was covered by floating ice (shelf ice), preventing deposition of coarse terrigenous materials and maintaining a supply of diatom tests and organic carbon until 20 ka BP. The northernmost site (74°33'S) was in a marine environment with a moderate productivity influenced by shelf ice/ice sheet after about 20 ka BP. Since about 10 ka BP, a sedimentary environment similar to the present-day one has prevailed over this area.

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