scholarly journals Phylogeographical Structure of Liquidambar formosana Hance Revealed by Chloroplast Phylogeography and Species Distribution Models

Forests ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 858 ◽  
Author(s):  
Sun ◽  
Lin ◽  
Huang ◽  
Ye ◽  
Lai ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Species Distribution ◽  
Species Distribution Models ◽  
Central China ◽  
Recent Common Ancestor ◽  
Interglacial Period ◽  
Last Interglacial ◽  
Distribution Models ◽  
Last Interglacial Period

To understand the origin and evolutionary history, and the geographical and historical causes for the formation of the current distribution pattern of Lquidambar formosana Hance, we investigated the phylogeography by using chloroplasts DNA (cpDNA) non-coding sequences and species distribution models (SDM). Four cpDNA intergenic spacer regions were amplified and sequenced for 251 individuals from 25 populations covering most of its geographical range in China. A total of 20 haplotypes were recovered. The species had a high level of chloroplast genetic variation (Ht = 0.909 ± 0.0192) and a significant phylogeographical structure (genetic differentiation takes into account distances among haplotypes (Nst) = 0.730 > population differentiation that does not consider distances among haplotypes (Gst) = 0.645; p < 0.05), whereas the genetic variation within populations (Hs = 0.323 ± 0.0553) was low. The variation of haplotype mainly occurred among populations (genetic differentiation coefficient (Fst) = 0.73012). The low genetic diversity within populations may be attributed to the restricted gene flow (Nm = 0.18). The time of the most recent common ancestor for clade V mostly distributed in Southwestern China, Central China, Qinling and Dabieshan mountains was 10.30 Ma (95% Highest posterior density (HPD): 9.74–15.28) dating back to the middle Miocene, which revealed the genetic structure of L. formosana was of ancient origin. These results indicated that dramatic changes since the Miocene may have driven the ancestors of L. formosana to retreat from the high latitudes of the Northern Hemisphere to subtropical China in which the establishment and initial intensification of the Asian monsoon provided conditions for their ecological requirements. This scenario was confirmed by the fossil record. SDM results indicated there were no contraction–expansion dynamics, and there was a stable range since the last interglacial period (LIG, 130 kya). Compared with the population expansion detected by Fu’s Fs value and the mismatch distribution, we speculated the expansion time may happen before the interglacial period. Evidence supporting L. formosana was the ancient origin and table range since the last interglacial period.

Deposits and Soils of the Past 130,000 Years at the Desert–Loess Transition in Northern China

1998 ◽  
Vol 50 (2) ◽  
pp. 148-156 ◽  
Author(s):  
Jimin Sun ◽  
Zhongli Ding
Keyword(s):  
Northern China ◽  
Loess Soil ◽  
Transitional Zone ◽  
Central China ◽  
Interglacial Period ◽  
Glacial Cycle ◽  
Last Interglacial ◽  
Last Glacial Period ◽  
North Central ◽  
Last Interglacial Period

The desert–loess transitional zone in north-central China has long been thought sensitive to Quaternary climatic change. However, reconstruction of Quaternary climates in this area has been hindered by incompleteness of geological sections. Here we report the analytical results of two recently found sand–loess–soil sections. Both sections have thick eolian deposits from the last interglacial–glacial cycle and can be correlated with one another. Field observations, thermoluminescence dating, and other laboratory analyses show that the last interglacial period produced three paleosols and two intercalated loess layers. Loess from the last glacial period is interbedded with three sand horizons that represent desert extension. The expansion and contraction of desert in northern China may have been forced by the east Asia monsoon.

Phylogeographical spatial diffusion analysis reveals the journey of Geoffroy’s cat through the Quaternary glaciations of South America

2020 ◽  
Vol 129 (3) ◽  
pp. 603-617
Author(s):  
María Jimena Gómez Fernández ◽  
Alberto Fameli ◽  
Julio Rojo Gómez ◽  
Javier A Pereira ◽  
Patricia Mirol
Keyword(s):  
Interglacial Period ◽  
Spatial Diffusion ◽  
Molecular Evidence ◽  
Last Interglacial ◽  
Distribution Models ◽  
Diffusion Analysis ◽  
Last Interglacial Period ◽  
Broad Array ◽  
Present Distribution ◽  
Time Plot

Abstract Leopardus geoffroyi is a small feline with a widespread distribution in a broad array of habitats. Here we investigate its evolutionary history to characterize the phylogeographical patterns that led to its present distribution using mitochondrial DNA from 72 individuals collected throughout its entire range. All haplotypes conformed to a monophyletic group, including two clades with a central/marginal disposition that is incongruent to the proposed subspecies. Spatial diffusion analysis showed the origin of the species within the oldest and more diverse central clade. A Bayesian Skyline Plot combined with a dispersal through time plot revealed two population increases at 190 000–170 000 and 45 000–35 000 years ago, the latter period accompanied by an increase in the dispersal rate. Species distribution models showed similar patterns between the present and Last Interglacial Period, and a reduction of high-probability areas during the Last Glacial Maximum (LGM). Molecular evidence confirms L. geoffroyi as a monotypic species whose origin is located in Central Argentina. The last glaciation had little effect on the pattern of distribution of the species: the population and range expansion that started before the LGM, although probably being halted, continued after the glaciation and resulted in the presence of this felid in the far south of Patagonia.

scholarly journals A Robust Prediction Model for Species Distribution Using Bagging Ensembles with Deep Neural Networks

2021 ◽  
Vol 13 (8) ◽  
pp. 1495
Author(s):  
Jehyeok Rew ◽  
Yongjang Cho ◽  
Eenjun Hwang
Keyword(s):  
Neural Networks ◽  
Species Distribution ◽  
Best Practice ◽  
Deep Neural Networks ◽  
Species Distribution Models ◽  
Species Distribution Model ◽  
Environmental Data ◽  
Distribution Model ◽  
Distribution Models ◽  
Robust Prediction

Species distribution models have been used for various purposes, such as conserving species, discovering potential habitats, and obtaining evolutionary insights by predicting species occurrence. Many statistical and machine-learning-based approaches have been proposed to construct effective species distribution models, but with limited success due to spatial biases in presences and imbalanced presence-absences. We propose a novel species distribution model to address these problems based on bootstrap aggregating (bagging) ensembles of deep neural networks (DNNs). We first generate bootstraps considering presence-absence data on spatial balance to alleviate the bias problem. Then we construct DNNs using environmental data from presence and absence locations, and finally combine these into an ensemble model using three voting methods to improve prediction accuracy. Extensive experiments verified the proposed model’s effectiveness for species in South Korea using crowdsourced observations that have spatial biases. The proposed model achieved more accurate and robust prediction results than the current best practice models.

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