scholarly journals Subtle East–West Phylogeographic Break of Asteropyrum (Ranunculaceae) in Subtropical China and Adjacent Areas

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 627
Author(s):  
Shanmei Cheng ◽  
Weidong Zeng ◽  
Dengmei Fan ◽  
Hua Liang ◽  
Yi Yang ◽  
...  
Keyword(s):  
Plant Species ◽  
Dna Sequences ◽  
Population Differentiation ◽  
Climate Changes ◽  
Environmental Heterogeneity ◽  
Divergence Time ◽  
Genetic Admixture ◽  
Subtropical China ◽  
Phylogeographic Break ◽  
East West

East–west phylogeographic break is common among plant species in subtropical China. However, the estimation time of east–west phylogeographic break has always relied on inferences of calibrated phylogenies, and the contribution of environmental heterogeneity to population differentiation has largely been ignored. In this study, we estimated the divergence time of Asteropyrum populations through coalescent-based approaches based on DNA sequences of ten nuclear loci and evaluated the contribution of environmental heterogeneity to population differentiation. The results showed that there were two chloroplast clades and nuclear groups within Asteropyrum, displaying a subtle pattern of east–west differentiation. The divergence time of the two nuclear groups was dated to ~1.2 Ma, which is associated with climate changes during the Mid-Pleistocene transition. A genetic admixture event between the two genetic groups happened at ~0.46 Ma, resulting in several admixed populations. Isolation by environmental distance (IBE) explained the majority (46.32%) of population differentiation, but that isolation by geographic distance (IBD) only contributed 4.66%. The results of this study suggest that climate changes during the Pleistocene may be a major cause for the east–west phylogeographic break in subtropical China. However, the complex terrain and high environmental heterogeneity in the west of subtropical China (and adjacent regions such as the Hengduan Mountains and the Himalayan Moutains) caused by strong geological uplift may have profoundly shaped the population structure of plant species in subtropical China.

scholarly journals New insight into the phylogeographic pattern ofLiriodendron chinense(Magnoliaceae) revealed by chloroplast DNA: east–west lineage split and genetic mixture within western subtropical China

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6355 ◽  
Author(s):  
Aihong Yang ◽  
Yongda Zhong ◽  
Shujuan Liu ◽  
Lipan Liu ◽  
Tengyun Liu ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Genetic Resources ◽  
Coniferous Forest ◽  
Genetic Admixture ◽  
Phylogeographic Structure ◽  
Distribution Area ◽  
Eastern Region ◽  
Similar Species ◽  
Subtropical China ◽  
East West

BackgroundSubtropical China is a global center of biodiversity and one of the most important refugia worldwide. Mountains play an important role in conserving the genetic resources of species.Liriodendron chinenseis a Tertiary relict tree largely endemic to subtropical China. In this study, we aimed to achieve a better understanding of the phylogeographical pattern ofL. chinenseand to explore the role of mountains in the conservation ofL. chinensegenetic resources.MethodsThree chloroplast regions (psbJ-petA,rpl32-ndhF, andtrnK5’-matK) were sequenced in 40 populations ofL. chinensefor phylogeographical analyses. Relationships among chloroplast DNA (cpDNA) haplotypes were determined using median-joining networks, and genetic structure was examined by spatial analysis of molecular variance (SAMOVA). The ancestral area of the species was reconstructed using the Bayesian binary Markov Chain Monte Carlo (BBM) method according to its geographic distribution and a maximum parsimony (MP) tree based on Bayesian methods.ResultsObvious phylogeographic structure was found inL. chinense. SAMOVA revealed seven groups matching the major landscape features of theL. chinensedistribution area. The haplotype network showed three clades distributed in the eastern, southwestern, and northwestern regions. Separate northern and southern refugia were found in the Wu Mountains and Yungui Plateau, with genetic admixture in the Dalou Mountains and Wuling Mountains. BBM revealed a more ancient origin ofL. chinensein the eastern region, with a west–east split most likely having occurred during the Mindel glacial stage.DiscussionThe clear geographical distributions of haplotypes suggested multiple mountainous refugia ofL. chinense. The east–west lineage split was most likely a process of gradual genetic isolation and allopatric lineage divergence when the Nanling corridor was frequently occupied by evergreen or coniferous forest during Late Quaternary oscillations. Hotspots of haplotype diversity in the Dalou Mountains and Wuling Mountains likely benefited from gene flow from the Wu Mountains and Yungui Plateau. Collectively, these results indicate that mountain regions should be the main units for conserving and collecting genetic resources ofL. chinenseand other similar species in subtropical China.

scholarly journals A rapid loss of stripes: the evolutionary history of the extinct quagga

2005 ◽  
Vol 1 (3) ◽  
pp. 291-295 ◽  
Author(s):  
Jennifer A Leonard ◽  
Nadin Rohland ◽  
Scott Glaberman ◽  
Robert C Fleischer ◽  
Adalgisa Caccone ◽  
...  
Keyword(s):  
South African ◽  
Dna Sequences ◽  
Evolutionary History ◽  
Climate Changes ◽  
Rapid Loss ◽  
Mt Dna ◽  
Pleistocene Climate ◽  
Equus Burchelli ◽  
History Of ◽  
Plains Zebra

Twenty years ago, the field of ancient DNA was launched with the publication of two short mitochondrial (mt) DNA sequences from a single quagga ( Equus quagga ) museum skin, an extinct South African equid ( Higuchi et al . 1984 Nature 312 , 282–284). This was the first extinct species from which genetic information was retrieved. The DNA sequences of the quagga showed that it was more closely related to zebras than to horses. However, quagga evolutionary history is far from clear. We have isolated DNA from eight quaggas and a plains zebra (subspecies or phenotype Equus burchelli burchelli ). We show that the quagga displayed little genetic diversity and very recently diverged from the plains zebra, probably during the penultimate glacial maximum. This emphasizes the importance of Pleistocene climate changes for phylogeographic patterns in African as well as Holarctic fauna.

scholarly journals Identification of a Natural Hybrid between Castanopsis sclerophylla and Castanopsis tibetana (Fagaceae) Based on Chloroplast and Nuclear DNA Sequences

Forests ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 873
Author(s):  
Xiaorong Zeng ◽  
Risheng Chen ◽  
Yunxin Bian ◽  
Xinsheng Qin ◽  
Zhuoxin Zhang ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Genetic Admixture ◽  
Natural Hybrid ◽  
Hybrid Species ◽  
Chloroplast Haplotype ◽  
Flora Of China ◽  
Nuclear Microsatellite ◽  
Chloroplast Dna Sequences ◽  
Genetic Pools

Castanopsis × kuchugouzhui Huang et Y. T. Chang was recorded in Flora Reipublicae Popularis Sinicae (FRPS) as a hybrid species on Yuelushan mountain, but it is treated as a hybrid between Castanopsis sclerophylla (Lindl.) Schott. and Castanopsis tibetana Hance in Flora of China. After a thorough investigation on Yuelushan mountain, we found a population of C. sclerophylla and one individual of C. × kuchugouzhui, but no living individual of C. tibetana. We collected C. × kuchugouzhui, and we sampled 42 individuals of C. sclerophylla from Yuelushan and Xiushui and 43 individuals of C. tibetana from Liangyeshan and Xiushui. We used chloroplast DNA sequences and 29 nuclear microsatellite markers to investigate if C. × kuchugouzhui is a natural hybrid between C. sclerophylla and C. tibetana. The chloroplast haplotype analysis showed that C. × kuchugouzhui shared haplotype H2 with C. sclerophylla on Yuelushan. The STRUCTURE analysis identified two distinct genetic pools that corresponded well to C. sclerophylla and C. tibetana, revealing the genetic admixture of C. × kuchugouzhui. Furthermore, the NewHybrids analysis suggested that C. × kuchugouzhui is an F2 hybrid between C. sclerophylla and C. tibetana. Our results confirm that C. × kuchugouzhui recorded in FRPS is a rare hybrid between C. sclerophylla and C. tibetana.

A new species of Deltamys Thomas, 1917 (Rodentia: Cricetidae) endemic to the southern Brazilian Araucaria Forest and notes on the expanded phylogeographic scenario of D. kempi 

Zootaxa ◽  
2017 ◽  
Vol 4294 (1) ◽  
pp. 71 ◽  
Author(s):  
FERNANDO MARQUES QUINTELA ◽  
FABRÍCIO BERTUOL ◽  
ENRIQUE MANUEL GONZÁLEZ ◽  
PEDRO CORDEIRO-ESTRELA ◽  
THALES RENATO OCHOTORENA DE FREITAS ◽  
...  
Keyword(s):  
New Species ◽  
South America ◽  
Dna Sequences ◽  
Posterior Margin ◽  
Southeastern Brazil ◽  
Patos Lagoon ◽  
Araucaria Forest ◽  
Phylogeographic Break ◽  
Skull Measurements ◽  
A New Species

Deltamys is a monotypic sigmodontine rodent from the Pampas of South America. In addition to the formally recognized D. kempi that inhabits lowlands, an undescribed form Deltamys sp. 2n=40 was recently found in the highlands of southeastern Brazil. In the present study, we perform a phylogeographic reassessment of Deltamys and describe a third form of the genus, endemic to the Brazilian Araucaria Forest. We describe this new species based on an integrative analysis, using complete cytochrome b DNA sequences, karyology and morphology. Bayesian tree recovered two allopatric clades (lowlands vs. highlands) and three lineages: (i) the lowland D. kempi, (ii) the highland Deltamys sp. 2n=40, and (iii) Deltamys araucaria sp. n. Deltamys araucaria sp. n. is karyotypically (2n=34) and morphologically distinguishable from D. kempi (2n=37-38), showing a tawnier dorsum/flank pelage, presence of a protostyle, M1 alveolus positioned anteriorly to the posterior margin of the zygomatic plate, and several other distinguishing characteristics. A phylogeographic assessment of D. kempi recovered two haplogroups with significant differences in skull measurements. This phylogeographic break seems to have been shaped by the Patos Lagoon estuarine channel. The diversification in Deltamys might have been triggered by dispersal of older lineages over different altitudinal ranges in the Paraná geological basin. 

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.

scholarly journals Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary

2021 ◽  
Author(s):  
Andrew M Ritchie ◽  
Xia Hua ◽  
Lindell Bromham
Keyword(s):  
Dna Sequences ◽  
Empirical Studies ◽  
Divergence Time ◽  
Molecular Dating ◽  
Rate Variation ◽  
Substitution Rates ◽  
Molecular Change ◽  
Dna Evidence ◽  
Dating Methods ◽  
Speciation Rates

Background An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used models of molecular rate variation, such as the uncorrelated and autocorrelated lognormal clocks, rely on idealised models of rate variation and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as evidence indicates, they may have a significant influence on molecular dates. Results We simulate phylogenies and molecular sequences under three different realistic rate variation models - one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test two commonly used "relaxed clock" molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior, to up to 93% when punctuated simulations are reconstructed under an autocorrelated prior. Conclusions We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships.

scholarly journals Phytolith records of flourishing early Holocene Pooideae linked to an 8.2 ka cold event in subtropical China

Elem Sci Anth ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Xinxin Zuo ◽  
Houyuan Lu ◽  
Zhen Li ◽  
Bing Song ◽  
Deke Xu ◽  
...  
Keyword(s):  
Climate Change ◽  
Climate Changes ◽  
Asian Monsoon ◽  
Early Holocene ◽  
Subtropical China ◽  
Cold Event ◽  
Ecological Zones ◽  
Lower Yangtze Region ◽  
Dry Conditions ◽  
Lower Yangtze

The grass subfamily Pooideae originated in a temperate niche during the late Cretaceous; it is the largest Poaceae subfamily, consisting of almost 4,000 species, which are distributed worldwide. Pooideae responses to climate changes at different time scales, and different ecological zones are thus important in understanding Poaceae evolutionary processes and their relationship with climate change. In the study described in this article, we reconstructed Pooideae variability during the early Holocene, as inferred by a phytolith sequence from the Lower Yangtze in subtropical China. The phytolith assemblage was marked by three increases in Pooideae phytoliths, dated to ca 8.4–8.0, 7.8–7.6, and 7.4–7.2 ka BP (before present, 1950 AD), with each representing pronounced increases in Pooideae extent and distribution. All these increases were within age ranges that agreed well with the timing of weak Asian Monsoon events, at 8.2, 7.7, and 7.3 ka BP. The first Pooideae flourishing period in subtropical China was the most significant, lasting for approximately four centuries and being characterized by a double peak, which equated with an event at 8.2 ka. This suggested that cold and/or dry conditions—which occurred over a period of several hundred years and were linked to weakening of the Asian monsoon—probably caused Pooideae to flourish in the Lower Yangtze region. Comparison of two diagnostic trapezoid phytolith types—namely wavy and wavy narrow—which showed different changes between ca 8.4 and 8.0 ka BP, suggested that they responded differently to the climate change represented by the 8.2 ka event. Our phytolith records have provided not only new data clarifying the detailed Pooideae response to the 8.2 ka event but also a reliable index for past cold climates in subtropical China.

scholarly journals Phylogenetic relationships of the cuscuses (Diprotodontia : Phalangeridae) of island Southeast Asia and Melanesia based on the mitochondrial ND2 gene

2020 ◽  
Vol 42 (3) ◽  
pp. 266 ◽  
Author(s):  
Shimona Kealy ◽  
Stephen C. Donnellan ◽  
Kieren J. Mitchell ◽  
Michael Herrera ◽  
Ken Aplin ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Divergence Time ◽  
Taxonomic Status ◽  
Wide Distribution ◽  
Species Level ◽  
Source Population ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Multiple Species ◽  
Nd2 Gene

The species-level systematics of the marsupial family Phalangeridae, particularly Phalanger, are poorly understood, due partly to the family’s wide distribution across Australia, New Guinea, eastern Indonesia, and surrounding islands. In order to refine the species-level systematics of Phalangeridae, and improve our understanding of their evolution, we generated 36 mitochondrial ND2 DNA sequences from multiple species and sample localities. We combined our new data with available sequences and produced the most comprehensive molecular phylogeny for Phalangeridae to date. Our analyses (1) strongly support the monophyly of the three phalangerid subfamilies (Trichosurinae, Ailuropinae, Phalangerinae); (2) reveal the need to re-examine all specimens currently identified as ‘Phalanger orientalis’; and (3) suggest the elevation of the Solomon Island P. orientalis subspecies to species level (P. breviceps Thomas, 1888). In addition, samples of P. orientalis from Timor formed a clade, consistent with an introduction by humans from a single source population. However, further research on east Indonesian P. orientalis populations will be required to test this hypothesis, resolve inconsistencies in divergence time estimates, and locate the source population and taxonomic status of the Timor P. orientalis.

scholarly journals Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4896 ◽  
Author(s):  
Hongying Ma ◽  
Yajiang Wu ◽  
Hai Xiang ◽  
Yunzhou Yang ◽  
Min Wang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
East Asia ◽  
Dna Sequences ◽  
De Novo ◽  
Divergence Time ◽  
Upper Paleolithic ◽  
Phylogenetic Study ◽  
Mitochondrial Genomes ◽  
Domestic Horses ◽  
Matrilineal Inheritance

Objectives There are large populations of indigenous horse (Equus caballus) in China and some other parts of East Asia. However, their matrilineal genetic diversity and origin remained poorly understood. Using a combination of mitochondrial DNA (mtDNA) and hypervariable region (HVR-1) sequences, we aim to investigate the origin of matrilineal inheritance in these domestic horses. Methods To investigate patterns of matrilineal inheritance in domestic horses, we conducted a phylogenetic study using 31 de novo mtDNA genomes together with 317 others from the GenBank. In terms of the updated phylogeny, a total of 5,180 horse mitochondrial HVR-1 sequences were analyzed. Results Eightteen haplogroups (Aw-Rw) were uncovered from the analysis of the whole mitochondrial genomes. Most of which have a divergence time before the earliest domestication of wild horses (about 5,800 years ago) and during the Upper Paleolithic (35–10 KYA). The distribution of some haplogroups shows geographic patterns. The Lw haplogroup contained a significantly higher proportion of European horses than the horses from other regions, while haplogroups Jw, Rw, and some maternal lineages of Cw, have a higher frequency in the horses from East Asia. The 5,180 sequences of horse mitochondrial HVR-1 form nine major haplogroups (A-I). We revealed a corresponding relationship between the haplotypes of HVR-1 and those of whole mitochondrial DNA sequences. The data of the HVR-1 sequences also suggests that Jw, Rw, and some haplotypes of Cw may have originated in East Asia while Lw probably formed in Europe. Conclusions Our study supports the hypothesis of the multiple origins of the maternal lineage of domestic horses and some maternal lineages of domestic horses may have originated from East Asia.

scholarly journals Characterization of rbcL and trnL Plastid DNA Sequences of Vuralia turcica (Fabaceae; Papilionoideae)

2019 ◽  
Vol 7 (6) ◽  
pp. 908
Author(s):  
Dilek Tekdal
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Tree ◽  
Plant Species ◽  
Dna Sequences ◽  
Its Region ◽  
Plastid Dna ◽  
Accession Number ◽  
Molecular Information

Vuralia turcica is endemic to Turkey and currently endangered. Little molecular information is available for this plant. Previous characterization and classification of V. turcica have been based on the DNA sequences of the ITS region. Molecular markers are essential for studying of genotyping and biogeography, but any of each marker is not enough to characterize a plant species in its use alone. In this study, the chloroplast rbcL and trnL regions were amplified in V. turcica using the primers that have been published in the previous studies. Successfully amplified DNA fragments were extracted and commercially sequenced. The partial rbcL and trnL sequences were submitted to the NCBI database (accession number KX164510, KX164511, respectively). Amplified both DNA of two regions of rbcL and trnL were used to construct a phylogenetic tree.

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