Proposal to recognise the tribes Adinobotryeae and Glycyrrhizeae (Leguminosae subfamily Papilionoideae) based on chloroplast phylogenomic evidence

Within the legume family, the taxonomic status of subtribe Glycyrrhizinae of tribe Galegeae and of the genus Adinobotrys has been re-assessed. Based on genome skimming data, we conducted phylogenomic analyses of the inverted repeat-lacking clade within subfamily Papilionoideae. The results support the sister relationship between Glycyrrhizeae and Adinobotrys. Glycyrrhizeae is resurrected based on Glycyrrhiza and Glycyrrhizopsis, and a new tribe, Adinobotryeae, is proposed to accommodate Adinobotrys.

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Assessing the status of critically endangered Kondana soft-furred rat (Millardia kondana) using integrative taxonomy: combining evidence from morphological, molecular and environmental niche modeling

Mammalia ◽

10.1515/mammalia-2019-0056 ◽

2020 ◽

Vol 84 (4) ◽

pp. 392-406

Author(s):

Sameer B. Bajaru ◽

Aparna Lajmi ◽

Ranjit Manakadan ◽

Amol R. Kulavmode ◽

Uma Ramakrishnan

Keyword(s):

Taxonomic Status ◽

Niche Modeling ◽

Critically Endangered ◽

Morphological Data ◽

Integrative Approach ◽

Environmental Niche ◽

Sister Relationship ◽

Environmental Niche Modeling ◽

Precipitation Seasonality ◽

Significant Difference

AbstractKondana soft-furred rat is a critically endangered (CR) species, known from a single locality – Sinhgad in the northern Western Ghats, India. However, the taxonomic status of this species is uncertain due to its close resemblance to the widely distributed soft-furred field rat Millardia meltada, which has serious implications on the conservation status of Millardia kondana. In this study, we assessed the current taxonomic status of M. kondana through an integrative approach combining morphological, molecular and environmental niche modeling analyses. We collected morphological data from the specimens around Sinhgad as well as preserved specimens in the museum. Both morphological and two-dimensional (2D) morphometrical analyses showed a significant difference between M. kondana and M. meltada. Molecular phylogeny based on cytochrome b gene revealed a sister relationship between M. kondana and M. meltada, and both species form distinct well-supported monophyletic clades. Niche modeling also predicted niche segregation between the two species: M. kondana preferred areas with a high elevation and precipitation seasonality while M. meltada favored regions with a low elevation and precipitation. We confirmed that M. kondana is taxonomically distinct from M. meltada, and based on our estimates of its occurrence and occupancy, M. kondana continues to be treated as CR until further detailed investigations.

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Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae)

Plants ◽

10.3390/plants9091143 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1143 ◽

Cited By ~ 1

Author(s):

Hang Ran ◽

Yanyan Liu ◽

Cui Wu ◽

Yanan Cao

Keyword(s):

Genomic Structure ◽

Phylogenetic Analyses ◽

Sister Relationship ◽

Plastome Evolution ◽

Chloroplast Genomes ◽

Flora Of China ◽

Phylogenetic Resolution ◽

Sister Relationships ◽

Phylogenomic Analyses ◽

Cp Genome

Phylogenetic analyses of complete chloroplast genome sequences have yielded significant improvements in our understanding of relationships in the woody flowering genus Viburnum (Adoxaceae, Dipsacales); however, these relationships were evaluated focusing only on Viburnum species within Central and South America and Southeast Asia. By contrast, despite being a hotspot of Viburnum diversity, phylogenetic relationships of Viburnum species in China are less well known. Here, we characterized the complete chloroplast (cp) genomes of 21 Viburnum species endemic to China, as well as three Sambucus species. These 24 plastomes were highly conserved in genomic structure, gene order and content, also when compared with other Adoxaceae. The identified repeat sequences, simple sequence repeats (SSRs) and highly variable plastid regions will provide potentially valuable genetic resources for further population genetics and phylogeographic studies on Viburnum and Sambucus. Consistent with previous combined phylogenetic analyses of 113 Viburnum species, our phylogenomic analyses based on the complete cp genome sequence dataset confirmed the sister relationship between Viburnum and the Sambucus-Adoxa-Tetradoxa-Sinadoxa group, the monophyly of four recognized sections in Flora of China (i.e., Viburnum sect. Tinus, Viburnum sect. Solenotinus, Viburnum sect. Viburnum and Viburnum sect. Pseudotinus) and the nonmonophyly of Viburnum sect. Odontotinus and Viburnum sect. Megalotinus. Additionally, our study confirmed the sister relationships between the clade Valvatotinus and Viburnum sect. Pseudotinus, as well as between Viburnum sect. Opulus and the Odontotinus-Megalotinus group. Overall, our results clearly document the power of the complete cp genomes in improving phylogenetic resolution, and will contribute to a better understanding of plastome evolution in Chinese Adoxaceae.

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Plastome Phylogenomics and Historical Biogeography of Aquatic Plant Genus Hydrocharis (Hydrocharitaceae)

10.21203/rs.3.rs-1022437/v1 ◽

2021 ◽

Author(s):

Zhi-Zhong Li ◽

Samuli Lehtonen ◽

Andrew W. Gichira ◽

Karina Martins ◽

Efremov Andrey ◽

...

Keyword(s):

Aquatic Plant ◽

Genome Structure ◽

Central Africa ◽

Taxonomic Status ◽

Land Bridge ◽

African Species ◽

Repeat Sequences ◽

Bering Land Bridge ◽

History Of ◽

Phylogenomic Analyses

Abstract Background Hydrocharis L. and Limnobium Rich. are small aquatic genera, including three and two species, respectively. The taxonomic status, phylogenetic relationships and biogeographical history of these genera have remained unclear, owing to the lack of Central African endemic H. chevalieri from all previous studies. We sequenced and assembled plastomes of all three Hydrocharis species and Limnobium laevigatum to explore the phylogenetic and biogeographical history of these aquatic plants. Results All four newly generated plastomes were conserved in genome structure, gene content, and gene order. However, they differed in size, the number of repeat sequences, and inverted repeat borders. Our phylogenomic analyses recovered non-monophyletic Hydrocharis. African species H. chevalieri was fully supported as sister to the rest of the species, and L. laevigatum was nested in Hydrocharis as a sister to H. dubia. Hydrocharis-Limnobium initially diverged from the remaining genera at ca. 53.3 Ma, then began to diversify at ca. 30.9 Ma. The biogeographic analysis suggested that Hydrocharis probably originated in Europe and Central Africa. Conclusion Based on the phylogenetic results, morphological similarity and small size of the genera, the most reasonable taxonomic solution to the non-monophyly of Hydrocharis is to treat Limnobium as its synonym. The African endemic H. chevalieri is fully supported as a sister to the remaining species. Hydrocharis mainly diversified in the Miocene, during which rapid climate change may have contributed to the speciation and extinctions. The American species of former Limnobium probably dispersed to America through the Bering Land Bridge during the Miocene.

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The two-domain tree of life is linked to a new root for the Archaea

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1420858112 ◽

2015 ◽

Vol 112 (21) ◽

pp. 6670-6675 ◽

Cited By ~ 152

Author(s):

Kasie Raymann ◽

Céline Brochier-Armanet ◽

Simonetta Gribaldo

Keyword(s):

Early Life ◽

Evolutionary Biology ◽

Separate Analysis ◽

Tree Reconstruction ◽

High Quality ◽

Sister Relationship ◽

Distinct Root ◽

The Third ◽

Phylogenomic Analyses ◽

Relationship Of

One of the most fundamental questions in evolutionary biology is the origin of the lineage leading to eukaryotes. Recent phylogenomic analyses have indicated an emergence of eukaryotes from within the radiation of modern Archaea and specifically from a group comprising Thaumarchaeota/“Aigarchaeota” (candidate phylum)/Crenarchaeota/Korarchaeota (TACK). Despite their major implications, these studies were all based on the reconstruction of universal trees and left the exact placement of eukaryotes with respect to the TACK lineage unclear. Here we have applied an original two-step approach that involves the separate analysis of markers shared between Archaea and eukaryotes and between Archaea and Bacteria. This strategy allowed us to use a larger number of markers and greater taxonomic coverage, obtain high-quality alignments, and alleviate tree reconstruction artifacts potentially introduced when analyzing the three domains simultaneously. Our results robustly indicate a sister relationship of eukaryotes with the TACK superphylum that is strongly associated with a distinct root of the Archaea that lies within the Euryarchaeota, challenging the traditional topology of the archaeal tree. Therefore, if we are to embrace an archaeal origin for eukaryotes, our view of the evolution of the third domain of life will have to be profoundly reconsidered, as will many areas of investigation aimed at inferring ancestral characteristics of early life and Earth.

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Taxonomic status of the three color variants in sea cucumber (Apostichopus japonicus): evidence from mitochondrial phylogenomic analyses

Mitochondrial DNA Part A ◽

10.3109/19401736.2015.1022765 ◽

2015 ◽

Vol 27 (4) ◽

pp. 2330-2333 ◽

Cited By ~ 1

Author(s):

Wei Zhang ◽

Zhengfei Cao ◽

Yuchun Li ◽

Hong Zhao ◽

Jianjun Huang ◽

...

Keyword(s):

Sea Cucumber ◽

Apostichopus Japonicus ◽

Taxonomic Status ◽

Phylogenomic Analyses ◽

Color Variants

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Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families

Biology Letters ◽

10.1098/rsbl.2017.0393 ◽

2017 ◽

Vol 13 (9) ◽

pp. 20170393 ◽

Cited By ~ 38

Author(s):

Jeffrey W. Streicher ◽

John J. Wiens

Keyword(s):

Strong Support ◽

Sister Group ◽

Species Tree ◽

Sister Relationship ◽

Weak Support ◽

Terrestrial Vertebrates ◽

Squamate Reptiles ◽

Tree Methods ◽

Nuclear Loci ◽

Phylogenomic Analyses

Squamate reptiles (lizards and snakes) are the most diverse group of terrestrial vertebrates, with more than 10 000 species. Despite considerable effort to resolve relationships among major squamates clades, some branches have remained difficult. Among the most vexing has been the placement of snakes among lizard families, with most studies yielding only weak support for the position of snakes. Furthermore, the placement of iguanian lizards has remained controversial. Here we used targeted sequence capture to obtain data from 4178 nuclear loci from ultraconserved elements from 32 squamate taxa (and five outgroups) including representatives of all major squamate groups. Using both concatenated and species-tree methods, we recover strong support for a sister relationship between iguanian and anguimorph lizards, with snakes strongly supported as the sister group of these two clades. These analyses strongly resolve the difficult placement of snakes within squamates and show overwhelming support for the contentious position of iguanians. More generally, we provide a strongly supported hypothesis of higher-level relationships in the most species-rich tetrapod clade using coalescent-based species-tree methods and approximately 100 times more loci than previous estimates.

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The Utility of Genome Skimming for Phylogenomic Analyses as Demonstrated for Glycerid Relationships (Annelida, Glyceridae)

Genome Biology and Evolution ◽

10.1093/gbe/evv224 ◽

2015 ◽

Vol 7 (12) ◽

pp. 3443-3462 ◽

Cited By ~ 26

Author(s):

Sandy Richter ◽

Francine Schwarz ◽

Lars Hering ◽

Markus Böggemann ◽

Christoph Bleidorn

Keyword(s):

Genome Skimming ◽

Phylogenomic Analyses

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Redescription of a forgotten nudibranch Miamira striata (Eliot, 1904) and review of the taxonomic status of the genus Orodoris (Nudibranchia: Chromodorididae: Miamirinae)

Zootaxa ◽

10.11646/zootaxa.4981.1.7 ◽

2021 ◽

Vol 4981 (1) ◽

pp. 151-165

Author(s):

YARA TIBIRIÇÁ ◽

TERRENCE M. GOSLINER ◽

LYNN J. BONOMO ◽

JUAN LUCAS CERVERA

Keyword(s):

Taxonomic Status ◽

Junior Synonym ◽

Phylogenetic Study ◽

Sister Relationship ◽

The Pacific ◽

The Status ◽

Taxonomic Changes ◽

The Indian Ocean ◽

The Pacific Ocean ◽

Small Genus

The genus Orodoris Bergh, 1875 is a small genus that together with Miamira Bergh, 1875, was considered as a junior synonym of Ceratosoma A. Adams & Reeve, 1850. This decision was based on a morphological phylogenetic study conducted in 1999 that recovered the monophyly of the Ceratosoma. However, in 2012, molecular evidences led to the resurrection of Miamira, while Orodoris was retained as a junior synonym of Miamira with no further details. Here we revise the status of the genus Orodoris in light of the rediscovery of M. striata (syn. Orodoris striata Eliot, 1904). Our phylogenetic analysis revealed a close sister relationship between Miamira striata and Miamira miamirana Bergh, 1875 which nested within the Miamira clade. Therefore, to retain the monophyly of Miamira, the genus Orodoris should be maintained as a junior synonym of the former. This study proposes a neotype for M. striata and underscores the importance of reviewing historical taxonomic changes and investigating ancient descriptions prior to describing new taxa. Our study also confirms that Miamira magnifica Eliot, 1910 from the Indian Ocean and Miamira flavicostata Baba, 1940 from the Pacific Ocean represent two distinct, sister species.

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Chloroplast Phylogenomic Analyses Reveal a Maternal Hybridization Event Leading to the Formation of Cultivated Peanuts

Frontiers in Plant Science ◽

10.3389/fpls.2021.804568 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xiangyu Tian ◽

Luye Shi ◽

Jia Guo ◽

Liuyang Fu ◽

Pei Du ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Evolutionary Relationship ◽

Taxonomic Status ◽

Human Beings ◽

Global Food Security ◽

Phylogenetic Studies ◽

Hybridization Event ◽

Cultivated Peanut ◽

Phylogenomic Analyses ◽

Wild Peanut

Peanuts (Arachis hypogaea L.) offer numerous healthy benefits, and the production of peanuts has a prominent role in global food security. As a result, it is in the interest of society to improve the productivity and quality of peanuts with transgenic means. However, the lack of a robust phylogeny of cultivated and wild peanut species has limited the utilization of genetic resources in peanut molecular breeding. In this study, a total of 33 complete peanut plastomes were sequenced, analyzed and used for phylogenetic analyses. Our results suggest that sect. Arachis can be subdivided into two lineages. All the cultivated species are contained in Lineage I with AABB and AA are the two predominant genome types present, while species in Lineage II possess diverse genome types, including BB, KK, GG, etc. Phylogenetic studies also indicate that all allotetraploid cultivated peanut species have been derived from a possible maternal hybridization event with one of the diploid Arachis duranensis accessions being a potential AA sub-genome ancestor. In addition, Arachis monticola, a tetraploid wild species, is placed in the same group with all the cultivated peanuts, and it may represent a transitional species, which has been through the recent hybridization event. This research could facilitate a better understanding of the taxonomic status of various Arachis species/accessions and the evolutionary relationship among them, and assists in the correct and efficient use of germplasm resources in breeding efforts to improve peanuts for the benefit of human beings.

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