Multi-gene phylogenetic analysis reveals the multiple origin and evolution of mangrove physiological traits through exaptation

2016 ◽  
Vol 183 ◽  
pp. 41-51 ◽  
Author(s):  
Sunil Kumar Sahu ◽  
Reena Singh ◽  
Kandasamy Kathiresan
Keyword(s):  
Phylogenetic Analysis ◽  
Physiological Traits ◽  
Origin And Evolution ◽  
Multiple Origin

scholarly journals A Comparative Genomic and Phylogenetic Analysis of the Origin and Evolution of the CCN Gene Family

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Kuan Hu ◽  
Yiming Tao ◽  
Juanni Li ◽  
Zhuang Liu ◽  
Xinyan Zhu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Evolutionary Relationship ◽  
Evolutionary Process ◽  
Structural Features ◽  
Comparative Genomic ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Origin And Evolution ◽  
Functional Sites

CCN gene family members have recently been identified as multifunctional regulators involved in diverse biological functions, especially in vascular and skeletal development. In the present study, a comparative genomic and phylogenetic analysis was performed to show the similarities and differences in structure and function of CCNs from different organisms and to reveal their potential evolutionary relationship. First, CCN homologs of metazoans from different species were identified. Then we made multiple sequence alignments, MEME analysis, and functional sites prediction, which show the highly conserved structural features among CCN metazoans. The phylogenetic tree was further established, and thus CCNs were found undergoing extensive lineage-specific duplication events and lineage-specific expansion during the evolutionary process. Besides, comparative analysis about the genomic organization and chromosomal CCN gene surrounding indicated a clear orthologous relationship among these species counterparts. At last, based on these research results above, a potential evolutionary scenario was generated to overview the origin and evolution of the CCN gene family.

Origin and evolution of a new exon of 14-3-3ξ in bees and phylogenetic analysis

Genome ◽  
2013 ◽  
Vol 56 (4) ◽  
pp. 233-237
Author(s):  
Leilei Zhan ◽  
Chao Jiang
Keyword(s):  
Phylogenetic Analysis ◽  
Parasitic Wasp ◽  
Nasonia Vitripennis ◽  
Origin And Evolution ◽  
Hymenopteran Species ◽  
Alternatively Spliced ◽  
Corbiculate Bees ◽  
Exclusive Exon ◽  
Alternatively Spliced Exons ◽  
Selection Of

Mutually exclusive splicing, one type of alternative splicing, involves selection of alternatively spliced exons arranged in tandem and creates protein products with substitution of one segment of the amino acid sequence for another. Previous studies revealed that exon 5 of 14-3-3ξ from Apis mellifera (western honeybee) had three mutually exclusive exons, while orthologous exon of Nasonia vitripennis (parasitic wasp) had only two, suggesting that cases of exon gain or loss might have happened during the evolution of hymenopteran species. In the current study, we annotated and analyzed the 14-3-3ξ genes from 20 hymenopteran species successfully, and the results of phylogenetic analysis revealed the presence of a new mutually exclusive exon in corbiculate bees. In addition, we found that duplication via staggered homologous recombination was responsible for the origin of the new exon.

The tibia and tarsus in Herrerasauridae (Dinosauria, incertae sedis) and the origin and evolution of the dinosaurian tarsus

1989 ◽  
Vol 63 (5) ◽  
pp. 677-690 ◽  
Author(s):  
Fernando E. Novas
Keyword(s):  
Phylogenetic Analysis ◽  
Articular Surface ◽  
Morphological Characters ◽  
Close Relative ◽  
Origin And Evolution ◽  
Incertae Sedis ◽  
Evolutionary Changes ◽  
Distal Articular Surface

The tarsus and distal end of the tibia are described in Herrerasauridae, a family that includes the oldest known dinosaurs. This tarsal configuration is compared to those of more advanced dinosaurs and to other archosaurs. Through phylogenetic analysis of the morphological characters, a picture emerges of the evolutionary changes in the ankles of early dinosaurs.The tibia of the herrerasaurids has a quadrangular distal articular surface, with a shallow ventrolateral notch. This morphology is strikingly similar to that of the lagosuchid thecodontsPseudolagosuchusandLagosuchusand represents the most primitive tibial condition known for Dinosauria.Aside from the derived states possessed by Theropoda, Sauropodomorpha, and Ornithischia, respectively, it was impossible to recognize synapomorphies in tibiotarsal anatomy shared by these groups exclusive of Herrerasauridae. The transverse broadening of the distal end of the tibia seems to have been attained independently by ornithischians, theropods, and sauropodomorphs.The tarsus of herrerasaurids is characterized by an astragalus with a small but conspicuous lateroventral depression, by a pyramidal calcaneum with a ventromedial projection that articulates into the cavity of the astragalus just mentioned, and by a posterolaterally directed calcaneal tuber. These characters are also seen inLagosuchus(a close relative of dinosaurs), in the prosauropodRiojasaurusand, insofar as the astragalus is concerned, in the primitive dinosaurWalkeria, which suggests that dinosaurs of different lineages shared the same tarsal condition.By definition, this type of articulation between the astragalus and calcaneum follows the “crocodile-reversed” tarsal condition, suggesting that the tarsus in lagosuchids and dinosaurs could be derived from the “crocodile-reversed” pattern present in Ornithosuchidae andEuparkeria. In contrast, the mesotarsal ankle of lagosuchids and dinosaurs lacks the synapomorphies of the “crocodile-normal” ankle present in Crocodylia, Rauisuchidae, Aetosauria, and other archosaurs.It is concluded that Herrerasauridae retained the primitive tibiotarsal condition for Dinosauria, from which those of the Ornithischia, Sauropodomorpha, and Theropoda were derived. Furthermore, tibiotarsal anatomy supports monophyly of Dinosauria.

scholarly journals Phylogenetic supertree reveals detailed evolution of SARS-CoV-2

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Tingting Li ◽  
Dongxia Liu ◽  
Yadi Yang ◽  
Jiali Guo ◽  
Yujie Feng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Virus Disease ◽  
Evolutionary Relationship ◽  
Critical Issue ◽  
Last Common Ancestor ◽  
Phylogenetic Tree Analysis ◽  
Origin And Evolution ◽  
Supertree Method ◽  
The Matrix

AbstractCorona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-2 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, yet limited progress was obtained, principally owing to the disability of these methods to reasonably integrate phylogenetic information from all genes of SARS-CoV-2. Supertree method based on multiple trees can produce the overall reasonable phylogenetic tree. However, the supertree method has been barely used for phylogenetic analysis of viruses. Here we applied the matrix representation with parsimony (MRP) pseudo-sequence supertree analysis to study the origin and evolution of SARS-CoV-2. Compared with other phylogenetic analysis methods, the supertree method showed more resolution power for phylogenetic analysis of coronaviruses. In particular, the MRP pseudo-sequence supertree analysis firmly disputes bat coronavirus RaTG13 be the last common ancestor of SARS-CoV-2, which was implied by other phylogenetic tree analysis based on viral genome sequences. Furthermore, the discovery of evolution and mutation in SARS-CoV-2 was achieved by MRP pseudo-sequence supertree analysis. Taken together, the MRP pseudo-sequence supertree provided more information on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.

scholarly journals A short guide to phylogeny reconstruction

2008 ◽  
Vol 53 (No. 10) ◽  
pp. 442-446 ◽  
Author(s):  
E. Michu
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Short Introduction ◽  
Closely Related Species ◽  
Origin And Evolution ◽  
Anatomical Characters

This review is a short introduction to phylogenetic analysis. Phylogenetic analysis allows comprehensive understanding of the origin and evolution of species. Generally, it is possible to construct the phylogenetic trees according to different features and characters (e.g. morphological and anatomical characters, RAPD patterns, FISH patterns, sequences of DNA/RNA and amino acid sequences). The DNA sequences are preferable for phylogenetic analyses of closely related species. On the other hand, the amino acid sequences are used for phylogenetic analyses of more distant relationships. The sequences can be analysed using many computer programs. The methods most often used for phylogenetic analyses are neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference.

scholarly journals An Ancestry Perspective of the Evolution of PBS1 Proteins in Plants

2021 ◽  
Vol 22 (13) ◽  
pp. 6819
Author(s):  
Edgar Yebrán Villegas-Vázquez ◽  
Beatriz Xoconostle-Cázares ◽  
Roberto Ruiz-Medrano
Keyword(s):  
Signal Transduction ◽  
Immune Response ◽  
Phylogenetic Analysis ◽  
Pseudomonas Syringae ◽  
3D Structure ◽  
Ancestral Reconstruction ◽  
Origin And Evolution ◽  
Pseudomonas Phaseolicola ◽  
Recognition Motifs ◽  
Cleavage Motif

The AVRPPHB SUSCEPTIBLE1 (PBS1) and RESISTANCE TO PSEUDOMONAS SYRINGAE 5 (RPS5) proteins are involved in signal transduction to evoke innate plant immune response. In Arabidopsis, PBS1 is cleaved by the AvrPphB (Pseudomonas phaseolicola Avirulence protein B) protease, activating RPS5 and turning in a hypersensitive response (HR). We searched for PBS1 orthologs to trace their origin and evolution. PBS1 orthologs were found in embryophytes and in other plant taxa but with lower similarity. PBS1 phylogenetic analysis indicates high divergence, suggesting that the decoy function described for Arabidopsis PBS1 might be associated with a small fraction of orthologs. Ancestral reconstruction analysis suggests an elevated diversity in the amino acid sequence within the described motifs. All the orthologs contain the conserved PBS1 kinase subdomains, whereas the cleavage motif is present in several embryophyte orthologs but absent in most other taxa. The putative resistance recognition motifs in PBS1 orthologs are highly diverse. PBS1 cleavage site motif is exposed in some 3D structure predictions, whereas it is not in others, suggesting different modes of regulation and functions in PBS1 orthologs. Our findings suggest that PBS1 originated in the lineage that gave rise to embryophytes, with the angiosperm sequences forming a separate clade from pteridophyte proteins.

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