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 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.

Geographic patterns of genetic diversity in North American trees: a continent-wide analysis

2021 ◽  
Author(s):  
Andrew V. Gougherty
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
North America ◽  
North American ◽  
Tree Species ◽  
Geographic Patterns ◽  
Study Characteristics ◽  
Dispersal Traits ◽  
The Last Glacial Maximum ◽  
The Last Glacial

In the northern hemisphere, many species have been reported to have greater genetic diversity in southern populations than northern populations - ostensibly due to migration northward following the last glacial maximum (LGM). The generality of this pattern, while well-established for some taxa, remains unclear for North American trees. To address this issue, I collected published population genetics data for 73 North American tree species, and tested whether genetic diversity was associated with latitude or longitude and whether geographic trends were associated with dispersal traits, range or study characteristics. I found there were no general geographic patterns in genetic diversity, and the strength of the geographic gradients were not associated with any species or study characteristics. Species in the northern and western regions of North America tended to have more species with genetic diversity that declined with latitude, but most species had no significant trend. This work shows that North American trees have complex, individualistic, patterns of genetic diversity that may negate explanation by any particular dispersal trait or range characteristic.

scholarly journals High unexpected genetic diversity of a narrow endemic terrestrial mollusc

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3069 ◽  
Author(s):  
Pedro M. Madeira ◽  
Rosa M. Chefaoui ◽  
Regina L. Cunha ◽  
Francisco Moreira ◽  
Susana Dias ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Data ◽  
Land Snails ◽  
Physical Conditions ◽  
Narrow Endemic ◽  
Terrestrial Mollusc ◽  
Central Portugal ◽  
Genetic Survey ◽  
The Last Glacial Maximum ◽  
The Last Glacial

The Iberian Peninsula has an extensive record of species displaying strong genetic structure as a result of their survival in isolated pockets throughout the Pleistocene ice ages. We used mitochondrial and nuclear sequence data to analyze phylogeographic patterns in endemic land snails from a valley of central Portugal (Vale da Couda), putatively assigned toCandidula coudensis, that show an exceptionally narrow distributional range. The genetic survey presented here shows the existence of five main mitochondrial lineages in Vale da Couda that do not cluster together suggesting independent evolutionary histories. Our results also indicate a departure from the expectation that species with restricted distributions have low genetic variability. The putative past and contemporary models of geographic distribution of Vale da Couda lineages are compatible with a scenario of species co-existence in more southern locations during the last glacial maximum (LGM) followed by a post-LGM northern dispersal tracking the species optimal thermal, humidity and soil physical conditions.

scholarly journals A new terrestrial palaeoenvironmental record from the Bering Land Bridge and context for human dispersal

2018 ◽  
Vol 5 (6) ◽  
pp. 180145 ◽  
Author(s):  
Matthew J. Wooller ◽  
Émilie Saulnier-Talbot ◽  
Ben A. Potter ◽  
Soumaya Belmecheri ◽  
Nancy Bigelow ◽  
...  
Keyword(s):  
Climate Models ◽  
Environmental Changes ◽  
Land Bridge ◽  
Human Dispersal ◽  
South Central ◽  
Bering Land Bridge ◽  
Last Glaciation ◽  
Close Proximity ◽  
The Last Glacial Maximum ◽  
The Last Glacial

Palaeoenvironmental records from the now-submerged Bering Land Bridge (BLB) covering the Last Glacial Maximum (LGM) to the present are needed to document changing environments and connections with the dispersal of humans into North America. Moreover, terrestrially based records of environmental changes are needed in close proximity to the re-establishment of circulation between Pacific and Atlantic Oceans following the end of the last glaciation to test palaeo-climate models for the high latitudes. We present the first terrestrial temperature and hydrologic reconstructions from the LGM to the present from the BLB's south-central margin. We find that the timing of the earliest unequivocal human dispersals into Alaska, based on archaeological evidence, corresponds with a shift to warmer/wetter conditions on the BLB between 14 700 and 13 500 years ago associated with the early Bølling/Allerød interstadial (BA). These environmental changes could have provided the impetus for eastward human dispersal at that time, from Western or central Beringia after a protracted human population standstill. Our data indicate substantial climate-induced environmental changes on the BLB since the LGM, which would potentially have had significant influences on megafaunal and human biogeography in the region.

Comparative genetic diversity of Cryptosporidium species causing human infections

Parasitology ◽  
2020 ◽  
Vol 147 (13) ◽  
pp. 1532-1537 ◽  
Author(s):  
Juan C. Garcia-R ◽  
Murray P. Cox ◽  
David T. S. Hayman
Keyword(s):  
Genetic Diversity ◽  
Population Expansion ◽  
Recent Population Expansion ◽  
Cryptosporidium Hominis ◽  
High Genetic Diversity ◽  
Genetic Changes ◽  
Low Genetic Diversity ◽  
Human Infections ◽  
Host Parasite ◽  
Founder Events

AbstractParasites sometimes expand their host range and cause new disease aetiologies. Genetic changes can then occur due to host-specific adaptive alterations, particularly when parasites cross between evolutionarily distant hosts. Characterizing genetic variation in Cryptosporidium from humans and other animals may have important implications for understanding disease dynamics and transmission. We analyse sequences from four loci (gp60, HSP-70, COWP and actin) representing multiple Cryptosporidium species reported in humans. We predicted low genetic diversity in species that present unusual human infections due to founder events and bottlenecks. High genetic diversity was observed in isolates from humans of Cryptosporidium meleagridis, Cryptosporidium cuniculus, Cryptosporidium hominis and Cryptosporidium parvum. A deviation of expected values of neutrality using Tajima's D was observed in C. cuniculus and C. meleagridis. The high genetic diversity in C. meleagridis and C. cuniculus did not match our expectations but deviations from neutrality indicate a recent decrease in genetic variability through a population bottleneck after an expansion event. Cryptosporidium hominis was also found with a significant Tajima's D positive value likely caused by recent population expansion of unusual genotypes in humans. These insights indicate that changes in genetic diversity can help us to understand host-parasite adaptation and evolution.

scholarly journals Mitochondrial DNA in Siberian conifers indicates multiple postglacial colonization centers

2019 ◽  
Vol 49 (8) ◽  
pp. 875-883 ◽  
Author(s):  
Vladimir L. Semerikov ◽  
Svetlana A. Semerikova ◽  
Yuliya A. Putintseva ◽  
Natalia V. Oreshkova ◽  
Konstantin V. Krutovsky
Keyword(s):  
Mitochondrial Dna ◽  
Siberian Larch ◽  
Population Expansion ◽  
Glacial Refugia ◽  
Phylogeographic Pattern ◽  
Southern Siberia ◽  
Siberian Fir ◽  
Clear Differentiation ◽  
The Last Glacial Maximum ◽  
The Last Glacial

The geographic variation of the mitochondrial DNA in Siberian fir (Abies sibirica Ledeb.) was studied using the newly developed markers and compared with the phylogeographic pattern of another previously studied Siberian conifer, Siberian larch (Larix sibirica Ledeb.). Similar to Siberian larch, the distribution of mtDNA haplotypes in Siberian fir revealed clear differentiation among distinct geographic regions of southern Siberia and the Urals, likely indicating postglacial recolonization from several sources. The northern part of the range of both species was genetically homogeneous, which is probably due to its recent colonization from one of the glacial refugia. This conclusion is in agreement with published pollen and macrofossil data in Siberian fir and with the reconstruction of environmental niches indicating a dramatic reduction of the range and a likely survival of fir in certain southern areas during the Last Glacial Maximum (LGM), 21 thousand years ago. Although the modeling of the Siberian larch ecological niche reconstructed a shift of the range to the south at that period, the paleontological data indicated the presence of this species in most areas of the current range during LGM, which corresponds to the results of a previous historical demographic study suggesting that the population expansion preceding the LGM.

Problems in the Stone Age of South-East Asia

1993 ◽  
Vol 59 ◽  
pp. 1-15 ◽  
Author(s):  
T. E. G. Reynolds
Keyword(s):  
East Asia ◽  
Late Pleistocene ◽  
Environmental Changes ◽  
Middle Pleistocene ◽  
South East Asia ◽  
Site Location ◽  
Land Area ◽  
Dominant Characteristic ◽  
The Last Glacial Maximum ◽  
The Last Glacial

Whilst research has shown many faults with the Movius scheme of a Middle Pleistocene group of Chopper/Chopping tool industries in South-East Asia, it remains a fact that pebble tool industries are still the dominant characteristic of the South-East Asian record. Exploration has now revealed hundreds of Late Pleistocene and Holocene sites in Mainland South-East Asia and these are archaeologically very different from cave sites in Europe. Further problems exist with the current nomenclature of later industries, such as the Hoabinhian and the Neolithic, for there is a large amount of overlap between such assemblages. Should such factors as economy, site location, etc. be used to assist clarification of such problems?This paper outlines some of these issues and reveals that the pebble tool tradition as it is widely known in South-East Asia is a relatively recent phenomenon dating back to the Last Glacial Maximum (LGM). A possible reason for the change from flake to pebble tool industrial types and in the visibility of sites is the environmental changes and rise in sea level which submerged over half the available land area in the region during the Late Pleistocene. An existing broad spectrum system of exploitation was likely to have been intensified as a result of this.

scholarly journals Exploring the phylogeography and population dynamics of the giant deer ( Megaloceros giganteus ) using Late Quaternary mitogenomes

2021 ◽  
Vol 288 (1950) ◽  
Author(s):  
Alba Rey-Iglesia ◽  
Adrian M. Lister ◽  
Paula F. Campos ◽  
Selina Brace ◽  
Valeria Mattiangeli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Last Glacial Maximum ◽  
Late Pleistocene ◽  
Late Quaternary ◽  
Glacial Maximum ◽  
Climatic Fluctuations ◽  
The Holocene ◽  
Last Glacial ◽  
The Last Glacial Maximum ◽  
The Last Glacial

Late Quaternary climatic fluctuations in the Northern Hemisphere had drastic effects on large mammal species, leading to the extinction of a substantial number of them. The giant deer ( Megaloceros giganteus ) was one of the species that became extinct in the Holocene, around 7660 calendar years before present. In the Late Pleistocene, the species ranged from western Europe to central Asia. However, during the Holocene, its range contracted to eastern Europe and western Siberia, where the last populations of the species occurred. Here, we generated 35 Late Pleistocene and Holocene giant deer mitogenomes to explore the genetics of the demise of this iconic species. Bayesian phylogenetic analyses of the mitogenomes suggested five main clades for the species: three pre-Last Glacial Maximum clades that did not appear in the post-Last Glacial Maximum genetic pool, and two clades that showed continuity into the Holocene. Our study also identified a decrease in genetic diversity starting in Marine Isotope Stage 3 and accelerating during the Last Glacial Maximum. This reduction in genetic diversity during the Last Glacial Maximum, coupled with a major contraction of fossil occurrences, suggests that climate was a major driver in the dynamics of the giant deer.

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