scholarly journals Allopatric divergence, local adaptation, and multiple Quaternary refugia in a long-lived tree (Quercus spinosa) from subtropical China

2017 ◽  
Author(s):  
Li Feng ◽  
Yan-Ping Zhang ◽  
Xiao-Dan Chen ◽  
Jia Yang ◽  
Tao Zhou ◽  
...  
Keyword(s):  
Ecological Niche Modeling ◽  
Eastern China ◽  
Divergence Time ◽  
Genetic Data ◽  
Climatic Changes ◽  
Eastern Himalaya ◽  
List Type ◽  
Subtropical China ◽  
Allopatric Divergence ◽  
Genetic Structure And Diversity

SummaryThe complex geography and climatic changes occurring in subtropical China during the Tertiary and Quaternary might have provided substantial opportunities for allopatric speciation. To gain further insight into these processes, we reconstruct the evolutionary history of Quercus spinosa, a common evergreen tree species mainly distributed in this area.Forty-six populations were genotyped using four chloroplast DNA regions and 12 nuclear microsatellite loci to assess genetic structure and diversity, which was supplemented by divergence time and diversification rate analyses, environmental factor analysis, and ecological niche modeling of the species distributions in the past and at present.The genetic data consistently identified two lineages: the western Eastern Himalaya-Hengduan Mountains lineage and the eastern Central-Eastern China lineage, mostly maintained by populations’ environmental adaptation. These lineages diverged through climate/orogeny-induced vicariance during the Neogene and remained separated thereafter. Genetic data strongly supported the multiple refugia (per se, interglacial refugia) or refugia within refugia hypotheses to explain Q. spinosa phylogeography in subtropical China.Q. spinosa population structure highlighted the importance of complex geography and climatic changes occurring in subtropical China during the Neogene in providing substantial opportunities for allopatric divergence.

Allopatric divergence and secondary contacts in Euphorbia spinosa L: Influence of climatic changes on the split of the species

2011 ◽  
Vol 11 (5) ◽  
pp. 357-372 ◽  
Author(s):  
G. Zecca ◽  
G. Casazza ◽  
L. Minuto ◽  
M. Labra ◽  
F. Grassi
Keyword(s):  
Climatic Changes ◽  
Allopatric Divergence

scholarly journals Dynamism and context dependency in the diversification of the megadiverse plant genus Solanum L. (Solanaceae)

2018 ◽  
Author(s):  
Susy Echeverrĩa-Londoño ◽  
Tiina Särkinen ◽  
Isabel S Fenton ◽  
Sandra Knapp ◽  
Andy Purvis
Keyword(s):  
Climatic Changes ◽  
Context Dependency ◽  
List Type ◽  
Geological Time ◽  
Long Distance ◽  
Climatic Trend ◽  
Constituent Species ◽  
Dispersal Events ◽  
Diverse Plant

SummaryExplosive radiations have been considered one of the most intriguing diversification patterns across the Tree of Life, but the subsequent change, movement and extinction of the constituent species makes radiations hard to discern or understand as geological time passes.We synthesised phylogenetic and distributional data for an ongoing radiation — the mega-diverse plant genus Solanum L. — to show how dispersal events and past climatic changes have interacted to shape diversification.We found that despite the vast diversity of Solanum lineages in the Neotropics, lineages in the Old World are diversifying more rapidly. This recent explosive diversification coincides with a long-distance dispersal event from the Neotropics, at the time when, and to places where, major climatic changes took place. Two different groups of Solanum have migrated and established in Australia, but only the arid-adapted lineages experienced significant increases in their diversification, which is consistent with adaptation to the continent’s long-term climatic trend and the diversification of other arid-adapted groups.Our findings provide a clear example of how successful colonisation of new areas and niches can – but do not always – drive explosive radiations.

scholarly journals Molecular phylogenetic and phylogeography of Soriculus nigrescens in southwest China

2021 ◽  
Author(s):  
Haijun Jiang ◽  
Changkun Fu ◽  
Keyi Tang ◽  
Fengjun Li ◽  
Fei Xie ◽  
...  
Keyword(s):  
Southwest China ◽  
Ecological Niche Modeling ◽  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Species Status ◽  
Putative Species ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Different Altitudes

The Himalayan Shrew belongs to the genus Soriculus, which is a monotypic genus. We investigated the phylogeographic patterns, speciation, divergence time, and demographic history of Soriculus nigrescens in southwestern China. A total of 128 samples from 29 regions were analyzed for both mitochondrial and nuclear genes. Phylogenetic analyses of the concatenated mtDNA and nuDNA data revealed three highly divergent lineages within the S. nigrescens. One group represented subspecies S. n. minors, another group represented subspecies S. n. nigrescens, which is made up of two Clades A and B. The species delimitation analyses, based on two methods, supported the species status of the two Clades of S. n. nigrescens. In addtion, it was found that individuals at different altitudes in Motuo were divided into two Clades. Bayesian skyline plotting analyses and ecological niche modeling also supported demographic and range expansions during the LGM for S. n. nigrescens. We propose that S. n. nigrescens appears to be composed of two putative species, and S. n. minor should be elevated to species status. Our study also suggested that climate change since the Miocene periods and the uplift of the QTP may have resulted in the diversification and speciation of S. nigrescens.

scholarly journals Natural selection and repeated patterns of molecular evolution following allopatric divergence

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Yibo Dong ◽  
Shichao Chen ◽  
Shifeng Cheng ◽  
Wenbin Zhou ◽  
Qing Ma ◽  
...  
Keyword(s):  
Positive Selection ◽  
Divergence Time ◽  
Purifying Selection ◽  
Single Copy ◽  
Orthologous Genes ◽  
Allopatric Species ◽  
Genome Wide ◽  
Allopatric Divergence ◽  
Selective Forces ◽  
Repeated Pattern

Although geographic isolation is a leading driver of speciation, the tempo and pattern of divergence at the genomic level remain unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) in 20 allopatric species/variety pairs from diverse angiosperm clades, with 16 pairs reflecting the classic eastern Asia-eastern North America floristic disjunction. In each pair, >90% of POGs are under purifying selection, and <10% are under positive selection. A set of POGs are under strong positive selection, 14 of which are shared by 10–15 pairs, and one shared by all pairs; 15 POGs are annotated to biological processes responding to various stimuli. The relative abundance of POGs under different selective forces exhibits a repeated pattern among pairs despite an ~10 million-year difference in divergence time. Species divergence times are positively correlated with abundance of POGs under moderate purifying selection, but negatively correlated with abundance of POGs under strong purifying selection.

scholarly journals Is Phylogeographic Congruence Predicted by Historical Habitat Stability, or Ecological Co-associations?

2021 ◽  
Vol 5 (5) ◽  
Author(s):  
Ryan C Garrick ◽  
Chaz Hyseni ◽  
Ísis C Arantes ◽  
Louis G Zachos ◽  
Peter C Zee ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Species Interactions ◽  
Ecological Niche Modeling ◽  
Nuclear Dna ◽  
Abiotic Factors ◽  
Genetic Data ◽  
Phylogeographic Structure ◽  
Biotic Factors ◽  
Effective Population ◽  
Species Responses

Abstract Comparative phylogeographic studies can distinguish between idiosyncratic and community-wide responses to past environmental change. However, to date, the impacts of species interactions have been largely overlooked. Here we used non-genetic data to characterize two competing scenarios about expected levels of congruence among five deadwood-associated (saproxylic) invertebrate species (i.e., a wood-feeding cockroach, termite, and beetle; a predatory centipede, and a detritivorous millipede) from the southern Appalachian Mountains—a globally recognized center of endemism. Under one scenario, abiotic factors primarily drove species’ responses, with predicted congruence based on the spatial overlap of climatically stable habitat areas estimated for each species via ecological niche modeling. The second scenario considered biotic factors to be most influential, with proxies for species interactions used to predict congruence. Analyses of mitochondrial and nuclear DNA sequences focused on four axes of comparison: the number and geographic distribution of distinct spatial-genetic clusters, phylogeographic structure, changes in effective population size, and historical gene flow dynamics. Overall, we found stronger support for the ecological co-associations scenario, suggesting an important influence of biotic factors in constraining or facilitating species’ responses to Pleistocene climatic cycles. However, there was an imperfect fit between predictions and outcomes of genetic data analyses. Thus, while thought-provoking, conclusions remain tentative until additional data on species interactions becomes available. Ultimately, the approaches presented here advance comparative phylogeography by expanding the scope of inferences beyond solely considering abiotic drivers, which we believe is too simplistic. This work also provides conservation-relevant insights into the evolutionary history of a functionally important ecological community.

scholarly journals Using genetics to differentiate patients with similar symptoms: application to inflammatory arthritis in the rheumatology outpatient clinic

2019 ◽  
Author(s):  
Rachel Knevel ◽  
Saskia le Cessie ◽  
Chikashi C. Terao ◽  
Kamil Slowikowski ◽  
Jing Cui ◽  
...  
Keyword(s):  
Lupus Erythematosus ◽  
Medical Records ◽  
Genetic Information ◽  
Inflammatory Arthritis ◽  
Genetic Data ◽  
List Type ◽  
Diagnostic Efficiency ◽  
Diagnostic Challenge ◽  
Discriminative Ability ◽  
Icd Codes

ABSTRACTSlow developing complex diseases are a clinical diagnostic challenge. Since genetic information is increasingly available prior to a patient’s first visit to a clinic, it might improve diagnostic accuracy. We aimed to devise a method to convert genetic information into simple probabilities discriminating between multiple diagnoses in patients presenting with inflammatory arthritis.We developed G-Prob, which calculates for each patient the genetic probability for each of multiple possible diseases. We tested this for inflammatory arthritis-causing diseases (rheumatoid arthritis, systemic lupus erythematosus, spondyloarthropathy, psoriatic arthritis and gout). After validating in simulated data, we tested G-Prob in biobank cohorts in which genetic data were linked to electronic medical records: -1,200 patients identified by ICD-codes within the eMERGE database (n= 52,623);-245 patients identified through ICD codes and review of medical records within the Partners Biobank (n=12,604);-243 patients selected prospectively with final diagnoses by medical record review within the Partners Biobank (n=12,604). The calibration of G-Prob with the disease status was high (with regression coefficients ranging from 0.90-1.08 (ideal would be 1.00) in all cohorts. G-Prob’s discriminative ability was high in all cohorts with pooled Area Under the Curve (AUC)=0.69 [95%CI 0.67-0.71], 0.81 [95%CI 0.76-0.84] and 0.84 [95%CI 0.81-0.86]. For all patients, at least one disease could be ruled out, and in 45% of patients a most likely diagnosis could be identified with an overall 64% positive predictive value. In 35% of instances the clinician’s initial diagnosis was incorrect. Initial clinical diagnosis explained 39% of the variance in final disease prediction which improved to 51% (P<0.0001) by adding G-Prob genetic data.In conclusion, by converting genotypes into an interpretable probability value for five different inflammatory arthritides, we can better discriminate and diagnose rheumatic diseases. Genotypes available prior to a clinical visit could be considered part of patients’ medical history and potentially used to improve precision and diagnostic efficiency in clinical practice.

scholarly journals Spatial Genetic Structure and Demographic History of the Dominant Forest Oak Quercus fabri Hance in Subtropical China

2021 ◽  
Vol 11 ◽  
Author(s):  
Xiao-Dan Chen ◽  
Jia Yang ◽  
Yu-Fan Guo ◽  
Yue-Mei Zhao ◽  
Tao Zhou ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Demographic History ◽  
Eastern China ◽  
Natural Populations ◽  
Population Group ◽  
Genetic Admixture ◽  
Subtropical China ◽  
History Of ◽  
Genetic Clusters

Oak trees (Quercus L.) are important models for estimating abiotic impacts on the population structure and demography of long life span tree species. In this study, we generated genetic data for 17 nuclear microsatellite loci in 29 natural populations of Quercus fabri to estimate the population genetic structure. We also integrated approximate Bayesian computation (ABC) and ecological niche analysis to infer the population differentiation processes and demographic history of this oak species. The genetic analyses indicated two genetic clusters across the 29 populations collected, where most approximately corresponded to the intraspecific differentiation among populations from western and eastern China, whereas admixed populations were mainly found in central mountains of China. The best model obtained from hierarchical ABC simulations suggested that the initial intraspecific divergence of Q. fabri potentially occurred during the late Pliocene (ca. 3.99 Ma) to form the two genetic clusters, and the admixed population group might have been generated by genetic admixture of the two differentiated groups at ca. 53.76 ka. Ecological analyses demonstrated clear differentiation among the Q. fabri population structures, and association estimations also indicated significant correlations between geography and climate with the genetic variation in this oak species. Our results suggest abiotic influences, including past climatic changes and ecological factors, might have affected the genetic differentiation and demographic history of Q. fabri in subtropical China.

Seasonal and regional temperature differences in subtropical China during the past 200 years

2020 ◽  
Author(s):  
Qiufang Cai ◽  
Yu Liu
Keyword(s):  
Tree Ring ◽  
Eastern China ◽  
Temperature Series ◽  
Seasonal Temperature ◽  
Subtropical China ◽  
The Past ◽  
Winter Half ◽  
Decadal Scale ◽  
Reconstructed Temperature ◽  
Summer Time

&lt;p&gt;Tree ring plays an important role in deciphering the paleoclimatic signals over the past 100-10000 years. However, tree-ring studies from tropical to subtropical regions are rarer than that from extratropical regions, which greatly limit our understanding of some critical climate change issues. Based on tree-ring-width chronologies in different area of Subtropical China (SC), seasonal temperature history of different seasons over the past 200 years were reconstructed. In addition to the warm and cold fluctuations in the reconstructed temperature series, main conclusions are drawn in the following two aspects: 1) Winter-half year temperature had good agreement with summer-time temperature variation in SC at decadal scale, while the winter-half year warming in recent decades was more evident than summer-time. 2) Comparison of the tree-ring based temperature series indicated that the start time of the recent warming in eastern China was regional different. It delayed gradually from north to south, starting at least around 1940 AD in the north part, around 1970 AD in the central part and around 1980s in the south part.&lt;/p&gt;

Colonization routes, microevolutionary genetic structure and conservation concerns in a remote widespread insular endemic grass: the case of the Azorean tussock grass Deschampsia foliosa

2019 ◽  
Vol 191 (3) ◽  
pp. 365-380 ◽  
Author(s):  
Mónica Moura ◽  
Pilar Catálan ◽  
António Brehm ◽  
Miguel Menezes De Sequeira
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Genetic Data ◽  
Phylogenetic Networks ◽  
Island Populations ◽  
Western Group ◽  
Principal Coordinates ◽  
Clear Differentiation ◽  
Insular Endemic ◽  
Genetic Structure And Diversity

Abstract Population genetic structure and diversity and phylogeographical dispersal routes were assessed for the Azorean endemic grass Deschampsia foliosa using AFLP markers. This species occurs on seven islands in the archipelago and a sampling of populations from the three main geographical groups of islands was used, covering its known distribution. Principal coordinates analyses (PCoAs), Bayesian analyses and phylogenetic networks revealed different degrees of admixture for the central group (C) populations and a clear differentiation for the western group (W) and São Miguel island (in the eastern group, E) populations. The best K values corresponded to nine and 11 genetic groups, which were also confirmed by analysis of molecular variance. A low but significant correlation between genetic data and geography was observed, with most relevant barriers to gene flow generally placed between sub-archipelagos. We suggest a west-to-east isolation by distance dispersal model across an island age continuum with Flores–Corvo (W) and Pico (C) at the extremes of the dispersal path. An alternative scenario, also supported by the genetic data, implies an initial colonization of São Jorge (C), dispersal within C and following bidirectional dispersal to the W and E. The phylogeographical framework detected might be related to island age and to highly destructive volcanic events, and it supports the occurrence of cryptic diversity within D. foliosa. Genetic diversity estimators were highest for Pico island populations (C), lowest for São Miguel (E) and Flores (W) populations, and more divergent for the Corvo population (W). Conservation measures should be taken to preserve the genetic structure found across sub-archipelagos and islands.

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