Diversification and historical demography of <i>Haloxylon ammodendron</i> in relation to Pleistocene climatic oscillations in northwestern China

Chen, Yuting; Ma, S.; Zhang, Dan; Wei, Bo; Huang, Gang; Zhang, Yunling; Ge, Benwei

doi:10.7717/peerj.14476

Cited by 3 publications

(3 citation statements)

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“…The Quaternary glacial period played an important role in the geographic structure and genetic diversity of species distribution [1,17,105]. Although arid Northwest China was not directly covered by glaciers [106], geological events and past climate changes have influenced the distribution pattern of plants and animals significantly [11,[13][14][15]79,107].…”

Section: Historical Population Demographymentioning

confidence: 99%

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Phylogeography and Ecological Niche Modeling of the Alashan Pit Viper (Gloydius cognatus; Reptilia, Viperidae) in Northwest China and Adjacent Areas

Xu,

Dujsebayeva,

Chen

et al. 2023

Animals

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The joint impacts of historical geological events and Quaternary climatic oscillations in Northwest China on species evolution have been examined extensively in plant under a phylogeographic perspective. However, animal phylogeographic analyses in this region are still limited. The Alashan pit viper, Gloydius cognatus, occurs primarily in arid Northwest China and adjacent areas. Based on variation at two mtDNA genes (ND4 and Cytb) in 27 individuals representing 24 populations, the spatial genetic structure and demographic history of G. cognatus were examined across its geographic range. Phylogenetic analyses revealed two well-supported allopatric clades (each with two distinct subclades/lineages), distributed across the southern (Qaidam Basin, Lanzhou Basin, and Zoige Basin [S1]; Loess Plateau [S2]) and northern (Ily Basin [N1]; Junggar Basin and Mongolian Plateau [N2]) regions. AMOVA analysis demonstrated that over 76% of the observed genetic variation was related to these lineage splits, indicating substantial genetic differentiation among the four lineages. A strong pattern of isolation-by-distance across the sampling populations suggested that geographic distance principally shaped the genetic structure. The four lineages diverged by 0.9–2.2% for the concatenated data, which were estimated to have coalesced ~1.17 million years ago (Mya), suggesting that the expansions of the Badain Jaran, Tengger, and Mu Us deserts during the Xixiabangma glaciation likely interrupted gene flow and triggered the observed divergence in the southern and northern regions. Subsequently, the early Pleistocene integration of the Yellow River and associated deserts expansion promoted the differentiation of S1 and S2 lineages (~0.9 Mya). Both mitochondrial evidence and ecological niche modeling (ENM) reject the signature of demographic and range contractions during the LGM for G. cognatus. In addition, ENM predicts that the suitable habitat of G. cognatus will contract in the future. As such, the conservation and management of ESUs should be a priority. Our findings provide the first insights on the lineage diversification and population dynamics of the Alashan pit viper in relation to geological history and Pleistocene climatic oscillations in arid Northwest China.

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Section: Historical Population Demographymentioning

confidence: 99%

“…Meanwhile, in recent years, phylogeographic studies in arid Northwest China have increased and mainly focus on the impact of the Quaternary climate fluctuations on species' phylogeographic patterns, e.g., [11][12][13][14]. Notably, phylogeographic studies of plants in this region have sprung up like mushrooms after rain [11].…”

Section: Introductionmentioning

confidence: 99%

Phylogeography and Ecological Niche Modeling of the Alashan Pit Viper (Gloydius cognatus; Reptilia, Viperidae) in Northwest China and Adjacent Areas

Xu,

Dujsebayeva,

Chen

et al. 2023

Animals

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“…For a thorough understanding of the resilience of H. ammodendron to drought stress, Gao et al [ 7 ] conducted a complete transcriptome analysis under osmotic conditions, paired with evaluations of physiological factors such as proline, betaine, soluble sugar levels, and peroxidase activity. Using cpDNA genes ( trnS-trnG and trnV ) and ITS (Internal transcribed spacer) (ITS1-ITS4) sequences, Chen at al [ 8 ]. assessed 420 individuals from 36 populations of Haloxylon for their genetic diversity and historical demography.…”

Section: Introductionmentioning

confidence: 99%

Insights into the multi-chromosomal mitochondrial genome structure of the xero-halophytic plant Haloxylon Ammodendron (C.A.Mey.) Bunge ex Fenzl

Yang,

Liu,

Guo

et al. 2024

BMC Genomics

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Background Haloxylon ammodendron holds significance as an ecological plant, showcasing remarkable adaptability to desert conditions, halophytic environments, and sand fixation. With its potential for carbon sequestration, it emerges as a promising candidate for environmental sustainability. Furthermore, it serves as a valuable C4 plant model, offering insights into the genetic foundations of extreme drought tolerance. Despite the availability of plastid and nuclear genomes, the absence of a mitochondrial genome (mitogenome or mtDNA) hinders a comprehensive understanding of its its mtDNA structure, organization, and phylogenetic implications. Results In the present study, the mitochondrial genome of H. ammodendron was assembled and annotated, resulting in a multi-chromosomal configuration with two circular chromosomes. The mtDNA measured 210,149 bp in length and contained 31 protein-coding genes, 18 tRNA and three rRNA. Our analysis identified a total of 66 simple sequence repeats along with 27 tandem repeats, 312 forward repeats, and 303 palindromic repeats were found. Notably, 17 sequence fragments displayed homology between the mtDNA and chloroplast genome (cpDNA), spanning 5233 bp, accounting for 2.49% of the total mitogenome size. Additionally, we predicted 337 RNA editing sites, all of the C-to-U conversion type. Phylogenetic inference confidently placed H. ammodendron in the Amaranthacea family and its close relative, Suaeda glacum. Conclusions H. ammodendron mtDNA showed a multi-chromosomal structure with two fully circularized molecules. This newly characterized mtDNA represents a valuable resource for gaining insights into the basis of mtDNA structure variation within Caryophyllales and the evolution of land plants, contributing to their identification, and classification.

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Insights into the multi-chromosomal mitochondrial genome structure of the Xero- halophytic plant Haloxylon ammodendron (C.A.Mey.) Bunge ex Fenzl

Yang,

Guo,

Zheng

et al. 2023

Preprint

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Background Haloxylon ammodendron is an important ecological plant due to its adaptation ability in desert conditions, halophytic environments, and the fixation of sand. It is a promising plant with the ecological value that could help carbon sequestration and a valuable C4 plant model for elucidating the genetic basis of extreme drought tolerance. Although plastid and nuclear genomes were made available, the lack of a mitochondrial genome hampered comprehensive insights into its mitogenome structure organization and phylogenetic implications. Results In the present study, the mitochondrial genome of H. ammodendron was assembled and annotated, resulting in a multi-chromosomal configuration with two circular chromosomes. The mitogenome was 210,149 bp in length and contained 31 protein-coding genes, 18 tRNA, and three rRNA. A total of 66 simple sequence repeats (SSRs) were identified. Besides, 27 tandem repeats, 312 forward repeats, and 303 palindromic repeats were found. A set of 17 sequence fragments were found homologous between the mitochondrial and chloroplast genomes, spanning 5,233 bp, accounting for 2.49% of the total mitogenome size. In total, 337 RNA editing sites were predicted, all C-to-U conversion types. Phylogenetic inference confidently placed H. ammodendron in the Amaranthacea family and its close relative, Suaeda glacum. Conclusions H. ammodendron mitogenome showed a multi-chromosome structure with two fully circularized molecules. The present mitogenome represents a valuable resource for understanding the basis of mitogenome structure variation within Caryophyllales and evolution in land plants, their identification, and classification.

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Diversification and historical demography of Haloxylon ammodendron in relation to Pleistocene climatic oscillations in northwestern China

Cited by 3 publications

References 65 publications

Phylogeography and Ecological Niche Modeling of the Alashan Pit Viper (Gloydius cognatus; Reptilia, Viperidae) in Northwest China and Adjacent Areas

Phylogeography and Ecological Niche Modeling of the Alashan Pit Viper (Gloydius cognatus; Reptilia, Viperidae) in Northwest China and Adjacent Areas

Insights into the multi-chromosomal mitochondrial genome structure of the xero-halophytic plant Haloxylon Ammodendron (C.A.Mey.) Bunge ex Fenzl

Insights into the multi-chromosomal mitochondrial genome structure of the Xero- halophytic plant Haloxylon ammodendron (C.A.Mey.) Bunge ex Fenzl

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