scholarly journals Impact of Late Pleistocene-Holocene climatic fluctuations on the phylogeographic structure and historical demographics of Zamia prasina (Cycadales: Zamiaceae)

2019 ◽  
Vol 97 (4) ◽  
pp. 588-608 ◽  
Author(s):  
Grecia Montalvo-Fernández ◽  
Lorenzo Felipe Sánchez-Teyer ◽  
Germán Carnevali ◽  
Andrew P. Vovides ◽  
Ricardo Gaytán-Legaria ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Late Pleistocene ◽  
Population Expansion ◽  
Historical Demography ◽  
Phylogeographic Structure ◽  
Glacial Refugium ◽  
Tropical Species ◽  
High Genetic Diversity ◽  
Climatic Fluctuations ◽  
Glacial Periods

Background: Glacial periods during the Pleistocene have been hypothesized to have greatly influenced geographical patterns of genetic structure and demography of many tropical species. The Glacial Refugium Hypothesis proposes that, during cold, dry glacial periods, populations of moisture-affinities tropical species were restricted to sheltered, humid areas and that, during warmer and more humid interglacial periods, these populations expanded. Some mountain regions in the tropics acted as refugia during the cold, dry periods of the Pleistocene for several temperate forest taxa, which recolonized the humid areas farther north during the interglacial periods.Questions: (1) Did Late Pleistocene-Holocene climate changes affect the historical demophraphy of Zamia prasina? (2) Does the historical distribution of Zamia prasina agree with the Glacial Refugium Hypothesis?Study species: Zamia prasina W.Bull. (Zamiaceae), the only cycad native to the Yucatan Peninsula Biotic Province (YPBP). Methods: Five individuals were collected in 23 populations and characterized using two DNA regions: plastid atpF-atpH, and nuclear ITS2. Genetic diversity, phylogeographic structure, historical demography, and potential distributions were assessed. Results: Our results showed moderately high genetic diversity and low, but significant, phylogeographic structure. Two genetic groups were identified, one in the eastern part of the Peninsula, the other in the western. The changes in historical demography suggest that Z. prasina experienced a population expansion following the warm conditions of the Holocene.Conclusions: The population dynamics of Zamia prasina are in accordance with the Glacial Refugium Hypothesis.

scholarly journals Genetic diversification in the East Himalayas as revealed by comparative phylogeography of the black-throated bushtit and Elliot’s laughing thrush

2015 ◽  
Vol 61 (5) ◽  
pp. 935-942 ◽  
Author(s):  
Qing Quan ◽  
Yanhua Qu ◽  
Fumin Lei
Keyword(s):  
Genetic Diversity ◽  
Ecological Niche Modeling ◽  
Glacial Cycles ◽  
Comparative Phylogeography ◽  
High Genetic Diversity ◽  
Climatic Fluctuations ◽  
Genetic Lineages ◽  
The North ◽  
Suitable Habitats ◽  
Glacial Periods

Abstract The Southwest Mountainous region of the eastern Himalayas is a hotspot with extraordinarily high biodiversity and endemism, but the processes that have driven this unique diversity are largely unknown. We evaluated processes that have contributed to the current observed high genetic diversity in this region by integrating comparative phylogeography with ecological niche modeling in a study of two representative birds of the Southwest Mountains: the black-throated bushtit Aegithalos concinnus and the Elliot’s laughing thrush Garrulax elliotii. Mitochondrial DNA analyses revealed multiple divergent genetic lineages, which are roughly congruent with the north, south and east eco-subregion division of the Southwest Mountains. This strong geographical structure in these two species suggests that lineage diversification has proceeded in situ between the eco-subregions of the Southwest Mountains. During Pleistocene glaciations, the two species responded differently to climatic fluctuations. A. con-cinnus maintained rather stable habitats, mostly evergreen forests, during glacial cycles and thus kept a stable population size and further accumulated genetic diversity. In contrast, G. elliotii, which is mostly active in shrublands, has shifted its suitable habitats with glacial cycles. This species dispersed to low elevation areas during glacial periods, which provided multiple opportunities for gene admixture. The admixture causes the mixing of previously isolated genetic lineages and thus obscures the pattern of genetic variation.

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.

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 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.

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 Genetic characteristics of yellow seabream Acanthopagrus latus (Houttuyn, 1782) (Teleostei: Sparidae) after stock enhancement in southeastern China coastal waters

2021 ◽  
Author(s):  
Puqing Song ◽  
Cheng Liu ◽  
Zizi Cai ◽  
Shigang Liu ◽  
Jiali Xiang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Coastal Waters ◽  
Population Expansion ◽  
Future Research ◽  
Beibu Gulf ◽  
High Genetic Diversity ◽  
Phylogenetic Structure ◽  
Genetic Characteristics ◽  
Nucleotide Mismatch ◽  
Baseline Information

Yellowfin seabream is an important economic fish that is widely distributed in the East and South China seas. Many attempts to enhance stocks of yellowfin seabream have occurred in China, but a lack of genetic information for this species after stock release represents an obstacle to its management and conservation. To provide scientific guidance for sustainable germplasm resource development, we sequence the mitochondrial DNA (mtDNA) control region (CR) of 123 yellowfin seabream from 6 sample populations (Xiamen, Dongshan I, Dongshan II, Yangjiang, Fangchenggang, and Beibu Gulf). Populations of both wild and cultured yellowfin seabream have high genetic diversity, which we relate to their breeding habits and growth rate. A neighbor-joining tree of CR haplotypes reveals no specific phylogenetic structure corresponding to location of fish capture. Both neutral test and nucleotide mismatch distribution analyses suggest that yellowfin seabream have experienced population expansion events. Pleistocene glacial periods and recent stock releases have played important roles in the formation of present-day phylogeographical patterns. Our study provides baseline information which will assist future research on genetic structure, genetic diversity, and historical demography of yellowfin seabream after stock release in southeast China coastal waters. The use of exotic seeds should be avoided in stock breeding and release, and relevant follow-up surveys and genetic monitoring should be undertaken to clarify the genetic impact of exotic seed use on wild populations.

scholarly journals Influence of Pleistocene climatic oscillations on the phylogeography and demographic history of endemic vulnerable trees (section Magnolia) of the Tropical Montane Cloud Forest in Mexico

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12181
Author(s):  
Yessica Rico ◽  
M. Ángel León-Tapia ◽  
Marisol Zurita-Solís ◽  
Flor Rodríguez-Gómez ◽  
Suria Gisela Vásquez-Morales
Keyword(s):  
Cloud Forest ◽  
Historical Demography ◽  
Range Shifts ◽  
Phylogeographic Structure ◽  
Tropical Montane Cloud Forest ◽  
Last Interglacial ◽  
Climatic Fluctuations ◽  
Climatic Oscillations ◽  
Network Analyses ◽  
Montane Cloud Forest

The Tropical Montane Cloud Forest (TMCF) is a highly dynamic ecosystem that has undergone frequent spatial changes in response to the interglacial-glacial cycles of the Pleistocene. These climatic fluctuations between cold and warm cycles have led to species range shifts and contractions-expansions, resulting in complex patterns of genetic structure and lineage divergence in forest tree species. In this study, we sequenced four regions of the chloroplast DNA (trnT-trnL, trnK5-matk, rpl32-trnL, trnS-trnG) for 20 populations and 96 individuals to evaluate the phylogeography, historical demography, and paleodistributions of vulnerable endemic TMCF trees in Mexico: Magnolia pedrazae (north-region), M. schiedeana (central-region), and M. schiedeana population Oaxaca (south-region). Our data recovered 49 haplotypes that showed a significant phylogeographic structure in three regions: north, central, and south. Bayesian Phylogeographic and Ecological Clustering (BPEC) analysis also supported the divergence in three lineages and highlighted the role of environmental factors (temperature and precipitation) in genetic differentiation. Our historical demography analyses revealed demographic expansions predating the Last Interglacial (LIG, ~125,000 years ago), while Approximate Bayesian Computation (ABC) simulations equally supported two contrasting demographic scenarios. The BPEC and haplotype network analyses suggested that ancestral haplotypes were geographically found in central Veracruz. Our paleodistributions modeling showed evidence of range shifts and expansions-contractions from the LIG to the present, which suggested the complex evolutionary dynamics associated to the climatic oscillations of the Pleistocene. Habitat management of remnant forest fragments where large and genetically diverse populations occur in the three TMCF regions analyzed would be key for the conservation of these magnolia populations.

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