scholarly journals Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

2019 ◽  
Author(s):  
Yunheng Ji ◽  
Lifang Yang ◽  
Mark W. Chase ◽  
Changkun Liu ◽  
Zhenyan Yang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Northern China ◽  
Molecular Dating ◽  
Nuclear Ribosomal Dna ◽  
Tibet Plateau ◽  
Climatic Fluctuations ◽  
Difficult Genus ◽  
Ancestral Area Reconstruction ◽  
Phylogenetic Framework ◽  
Inference Methods

Abstract Background: Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus. Results: All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary. Conclusions: Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris . Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris . Our findings challenge the theoretical prediction that large genome sizes may limit speciation.

scholarly journals Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

2019 ◽  
Author(s):  
Yunheng Ji ◽  
Lifang Yang ◽  
Mark W. Chase ◽  
Changkun Liu ◽  
Zhenyan Yang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Northern China ◽  
Molecular Dating ◽  
Nuclear Ribosomal Dna ◽  
Tibet Plateau ◽  
Climatic Fluctuations ◽  
Difficult Genus ◽  
Ancestral Area Reconstruction ◽  
Phylogenetic Framework ◽  
Inference Methods

Abstract Background: Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus.Results: All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary.Conclusions: Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.

scholarly journals Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

2019 ◽  
Author(s):  
Yunheng Ji ◽  
Lifang Yang ◽  
Mark W. Chase ◽  
Changkun Liu ◽  
Zhenyan Yang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Northern China ◽  
Molecular Dating ◽  
Nuclear Ribosomal Dna ◽  
Tibet Plateau ◽  
Climatic Fluctuations ◽  
Difficult Genus ◽  
Ancestral Area Reconstruction ◽  
Phylogenetic Framework ◽  
Inference Methods

Abstract Background: Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus. Results: All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary. Conclusions: Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris . Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris . Our findings challenge the theoretical prediction that large genome sizes may limit speciation.

scholarly journals Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yunheng Ji ◽  
Lifang Yang ◽  
Mark W. Chase ◽  
Changkun Liu ◽  
Zhenyan Yang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Northern China ◽  
Molecular Dating ◽  
Nuclear Ribosomal Dna ◽  
Tibet Plateau ◽  
Climatic Fluctuations ◽  
Difficult Genus ◽  
Ancestral Area Reconstruction ◽  
Phylogenetic Framework ◽  
Inference Methods

Abstract Background Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus. Results All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary. Conclusions Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.

scholarly journals Phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

2019 ◽  
Author(s):  
Yunheng Ji ◽  
Lifang Yang ◽  
Mark W. Chase ◽  
Changkun Liu ◽  
Zhenyan Yang ◽  
...  
Keyword(s):  
Late Miocene ◽  
Phylogenetic Relationships ◽  
Northern China ◽  
Molecular Dating ◽  
Nuclear Ribosomal Dna ◽  
Tibet Plateau ◽  
Climatic Fluctuations ◽  
Difficult Genus ◽  
Ancestral Area Reconstruction ◽  
Inference Methods

Abstract Background Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus. Results All 29 species currently recognized in Paris were sampled. Complete plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the late Miocene. Conclusions Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.

scholarly journals Complete chloroplast genome of Hordeum brevisubulatum: Genome organization, synonymous codon usage, phylogenetic relationships, and comparative structure analysis

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261196
Author(s):  
Guangxin Cui ◽  
Chunmei Wang ◽  
Xiaoxing Wei ◽  
Hongbo Wang ◽  
Xiaoli Wang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Genome Engineering ◽  
De Novo ◽  
Synonymous Codon ◽  
Northern China ◽  
Synonymous Codon Usage ◽  
The Other ◽  
Coding Regions ◽  
Cp Genome ◽  
Hordeum Brevisubulatum

Background Hordeum brevisubulatum, known as fine perennial forage, is used for soil salinity improvement in northern China. Chloroplast (cp) genome is an ideal model for assessing its genome evolution and the phylogenetic relationships. We de novo sequenced and analyzed the cp genome of H. brevisubulatum, providing a fundamental reference for further studies in genetics and molecular breeding. Results The cp genome of H. brevisubulatum was 137,155 bp in length with a typical quadripartite structure. A total of 130 functional genes were annotated and the gene of accD was lost in the process of evolution. Among all the annotated genes, 16 different genes harbored introns and the genes of ycf3 and rps12 contained two introns. Parity rule 2 (PR2) plot analysis showed that majority of genes had a bias toward T over A in the coding strand in all five Hordeum species, and a slight G over C in the other four Hordeum species except for H. bogdanil. Additionally, 52 dispersed repeat sequences and 182 simple sequence repeats were identified. Moreover, some unique SSRs of each species could be used as molecular markers for further study. Compared to the other four Hordeum species, H. brevisubulatum was most closely related to H. bogdanii and its cp genome was relatively conserved. Moreover, inverted repeat regions (IRa and IRb) were less divergent than other parts and coding regions were relatively conserved compared to non-coding regions. Main divergence was presented at the SSC/IR border. Conclusions This research comprehensively describes the architecture of the H. brevisubulatum cp genome and improves our understanding of its cp biology and genetic diversity, which will facilitate biological discoveries and cp genome engineering.

Molecular data provide new insights into the phylogeny of Cladonotinae (Orthoptera: Tetrigoidea) from China with the description of a new genus and species

Zootaxa ◽  
2020 ◽  
Vol 4809 (3) ◽  
pp. 547-559
Author(s):  
RONG-JIAO ZHANG ◽  
CONG-LIN ZHAO ◽  
FEI-PENG WU ◽  
WEI-AN DENG
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Molecular Data ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Close Relationship ◽  
Phylogenetic Framework ◽  
Mitochondrial Cytochrome Oxidase

Considerable effort has been devoted to elucidating the phylogenetic relationships of tetrigides. However, there is still no commonly accepted phylogenetic hypothesis. Therefore, the phylogenetic relationships among some subfamilies remain unclear; e.g., Cladonotinae is a controversial group, in which the phylogenetic relationships between genera and the boundaries of some of the included genera are unclear, causing some of the taxa to be difficult to identify. Therefore, an in-depth phylogenetic analysis of Cladonotinae is urgently needed. In this study, a robust phylogenetic framework for the tetrigides was reconstructed based on the combined mitochondrial cytochrome oxidase subunit I (COI), 16S ribosomal RNA (16S rRNA), and nuclear 18S ribosomal RNA (18S rRNA) gene sequences of 25 species belonging to 16 genera of Tetrigoidea from China, which included 13 species from 8 genera of Cladonotinae. Phylogenetic inferences were performed using the combined dataset and Bayesian inference (BI) and Maximum Parsimony (MP) methods, and the phylogenetic tree of Cladonotinae was reconstructed. All inferences based on the results of the present study supported the Cladonotinae subfamily as a polyphyletic group; within the Cladonotinae subfamily, Tetradinodula, and Tuberfemurus were closely related to Tetriginae, while Austrohancockia and Gibbotettix showed a close relationship to the Scelimenidae subfamily. Additionally, a new genus and new species of the Cladonotinae subfamily are described and illustrated: Hainantettix Deng, gen. nov. and Hainantettix strictivertex Deng, sp. nov. 

scholarly journals Contrasting Performance of the Remotely-Derived GPP Products over Different Climate Zones across China

2019 ◽  
Vol 11 (16) ◽  
pp. 1855 ◽  
Author(s):  
Yanan Chen ◽  
Hongfan Gu ◽  
Munan Wang ◽  
Qing Gu ◽  
Zhi Ding ◽  
...  
Keyword(s):  
Large Scale ◽  
Climatic Factors ◽  
Southern China ◽  
Gross Primary Production ◽  
Terrestrial Ecosystems ◽  
Northern China ◽  
Tibet Plateau ◽  
Semiarid Region ◽  
Interannual Variations ◽  
Climate Zones

Precise quantification of terrestrial gross primary production (GPP) has been recognized as one of the most important components in understanding the carbon balance between the biosphere and the atmosphere. In recent years, although many large-scale GPP estimates from satellite data and ecosystem models have been generated, few attempts have been made to compare the different GPP products at national scales, particularly for various climate zones. In this study, two of the most widely-used GPP datasets were systematically compared over the eight climate zones across China’s terrestrial ecosystems from 2001 to 2015, which included the moderate resolution imaging spectroradiometer (MODIS) GPP and the breathing Earth system simulator (BESS) GPP products. Additionally, the coarse (0.05o) GPP estimates from the vegetation photosynthesis model (VPM) at the same time scale were used for auxiliary analysis with the two products. Both MODIS and BESS products exhibited a decreasing trend from the southeast region to the northwest inland. The largest GPP was found in the tropical humid region with 5.49 g C m−2 d−1 and 5.07 g C m−2 d−1 for MODIS and BESS, respectively, while the lowest GPP was distributed in the warm temperate arid region, midtemperate semiarid region and plateau zone. Meanwhile, the work confirmed that all these GPP products showed apparent seasonality with the peaks in the summertime. However, large differences were found in the interannual variations across the three GPP products over different climate regions. Generally, the BESS GPP agreed better than the MODIS GPP when compared to the seasonal and interannual variations of VPM GPP. Furthermore, the spatial correlation analysis between terrestrial GPP and the climatic factors, including temperature and precipitation, indicated that natural rainfall dominated the variability in GPP of Northern China, such as the midtemperate semiarid region, while temperature was a key controlling factor in the Southern China and the Tibet Plateau area.

Towards a new classification of tribe Stachydeae (Lamiaceae): naming clades using molecular evidence

2019 ◽  
Vol 190 (4) ◽  
pp. 345-358 ◽  
Author(s):  
Yasaman Salmaki ◽  
Günther Heubl ◽  
Maximilian Weigend
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Nuclear Ribosomal Dna ◽  
Molecular Evidence ◽  
New Classification ◽  
Formal Classification ◽  
Phylogenetic Nomenclature

AbstractStachydeae, comprising c. 470 species, are one of the most diverse and taxonomically puzzling groups in Lamioideae. In the present study, the phylogenetic relationships in the Eurystachys clade (a phylogenetic name for all genera attributed to Stachydeae except Melittis) were reconstructed utilizing nuclear ribosomal DNA sequences (nrETS, 5S-NTS) from 148 accessions in 12 genera. Our phylogenetic results recovered Stachys as paraphyletic with numerous traditionally recognized genera nested in it. A broadly defined Eurystachys clade, however, was monophyletic. Unlike previous studies, the present study was able to resolve the group into 12 well-supported clades, named here as (1) Eriostomum, (2) Stachys, (3) Prasium, (4) Setifolia, (5) Distantes, (6) Burgsdorfia, (7) Hesiodia, (8) Empedoclia, (9) Sideritis, (10) Marrubiastrum, (11) Swainsoniana and (12) Olisia. These 12 clades were formally named in a phylogenetic nomenclature for the Eurystachys clade. Several infrageneric units were retrieved as monophyletic, namely Sideritis sections Burgsdorfia, Empedoclia and Hesiodia, Sideritis subgenus Marrubiastrum and Stachys sections Eriostomum (including Stachys section Mucronata) and Setifolia. The findings of this study also provide the basis for a future formal classification, with two options: (1) splitting of the Eurystachys clade into 12 monophyletic genera, all of them based on pre-existing genus names and redefined to encompass additional taxa, but without clear morphological apomorphies; or (2) lumping of all segregates into a broadly defined Stachys, including widely recognized and well-defined segregates such as Prasium and Sideritis.

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