scholarly journals Community phylogenetics require phylogenies reconstructed from plastid genomes

2021 ◽  
Author(s):  
Lu Jin ◽  
Jia-Jia Liu ◽  
Tian-Wen Xiao ◽  
Qiao-Ming Li ◽  
Luxiang Lin ◽  
...  
Keyword(s):  
Functional Traits ◽  
Phylogenetic Trees ◽  
Phylogenetic Signal ◽  
Maximum Height ◽  
Type I ◽  
Community Phylogenetics ◽  
Phylogenetic Structure ◽  
Plastid Genomes ◽  
A Genome ◽  
Genome Tree

Phylogenetic trees have been extensively used in community ecology. However, how the phylogenetic reconstruction affects ecological inferences is poorly understood. In this study, we reconstructed three different types of phylogenetic trees (a synthetic-tree generated using VPhylomaker, a barcode-tree generated using rbcL+matK+trnH-psbA and a genome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the genome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith’s PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the genome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and genome-tree detected phylogenetic signal in maximum height, but only the genome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the outperformance of genome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of Type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.

scholarly journals Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maria Alejandra Serna-Sánchez ◽  
Oscar A. Pérez-Escobar ◽  
Diego Bogarín ◽  
María Fernanda Torres-Jimenez ◽  
Astrid Catalina Alvarez-Yela ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Times ◽  
Molecular Clocks ◽  
Phylogenetic Placement ◽  
Plastid Genomes ◽  
Phylogenetic Reconstructions ◽  
A Genome ◽  
Tree Models ◽  
Phylogenomic Analyses ◽  
First Time

AbstractRecent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

scholarly journals Jaw biomechanics and the evolution of biting performance in theropod dinosaurs

2010 ◽  
Vol 277 (1698) ◽  
pp. 3327-3333 ◽  
Author(s):  
Manabu Sakamoto
Keyword(s):  
Function Space ◽  
Phylogenetic Signal ◽  
Space Distribution ◽  
Phylogenetic Structure ◽  
Unique Region ◽  
Theropod Dinosaurs ◽  
Polynomial Coefficients ◽  
Evolutionary Changes ◽  
Ancestral Function ◽  
Space Occupation

Despite the great diversity in theropod craniomandibular morphology, the presence and distribution of biting function types across Theropoda has rarely been assessed. A novel method of biomechanical profiling using mechanical advantage computed for each biting position along the entirety of the tooth row was applied to 41 extinct theropod taxa. Multivariate ordination on the polynomial coefficients of the profiles reveals the distribution of theropod biting performance in function space. In particular, coelophysoids are found to occupy a unique region of function space, while tetanurans have a wide but continuous function space distribution. Further, the underlying phylogenetic structure and evolution of biting performance were investigated using phylogenetic comparative methods. There is a strong phylogenetic signal in theropod biomechanical profiles, indicating that evolution of biting performance does not depart from Brownian motion evolution. Reconstructions of ancestral function space occupation conform to this pattern, but phylogenetically unexpected major shifts in function space occupation can be observed at the origins of some clades. However, uncertainties surround ancestor estimates in some of these internal nodes, so inferences on the nature of these evolutionary changes must be viewed with caution.

Using functional traits and phylogenetic trees to examine the assembly of tropical tree communities

2012 ◽  
Vol 100 (3) ◽  
pp. 690-701 ◽  
Author(s):  
Christopher Baraloto ◽  
Olivier J. Hardy ◽  
C. E. Timothy Paine ◽  
Kyle G. Dexter ◽  
Corinne Cruaud ◽  
...  
Keyword(s):  
Functional Traits ◽  
Phylogenetic Trees ◽  
Tropical Tree ◽  
Tree Communities

scholarly journals Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1460
Author(s):  
Irene Hoxie ◽  
John J. Dennehy
Keyword(s):  
Immune Responses ◽  
Codon Usage ◽  
Host Species ◽  
Phylogenetic Trees ◽  
Translational Efficiency ◽  
Rotavirus A ◽  
A Genome ◽  
Usage Patterns ◽  
Dsrna Genome ◽  
Codon Deoptimization

Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.

scholarly journals Mapping oligogenes for atopy and asthma by meta-analysis

2000 ◽  
Vol 23 (1) ◽  
pp. 1-10 ◽  
Author(s):  
A. Collins ◽  
S. Ennis ◽  
W. Tapper ◽  
N.E. Morton
Keyword(s):  
Alternative Hypothesis ◽  
Rank Order ◽  
Meta Analysis ◽  
Genetic Effect ◽  
Allelic Association ◽  
Type I ◽  
A Genome ◽  
Significance Levels ◽  
Complex Inheritance ◽  
Candidate Regions

Meta-analysis is presented for published studies on linkage or allelic association that have in common only reported significance levels. Reporting is biassed, and nonsignificance is seldom quantified. Therefore meta-analysis cannot identify oligogenes within a candidate region nor establish their significance, but it defines candidate regions well. Applied to a database on atopy and asthma, candidate regions are identified on chromosomes 6, 5, 16, 11, 12, 13, 14, 7, 20, and 10, in rank order from strongest to weakest evidence. On the other hand, there is little support for chromosomes 9, 8, 18, 1, and 15 in the same rank order. The evidence from 156 publications is reviewed for each region. With reasonable type I and II errors several thousand affected sib pairs would be required to detect a locus accounting for 1/10 of the genetic effect on asthma. Identification of regions by a genome scan for linkage and allelic association requires international collaborative studies to reach the necessary sample size, using lod-based methods that specify a weakly parametric alternative hypothesis and can be combined over studies that differ in ascertainment, phenotypes, and markers. This has become the central problem in complex inheritance.

scholarly journals Local and regional controls of phylogenetic structure at the high-latitude range limits of corals

2017 ◽  
Vol 284 (1861) ◽  
pp. 20170915 ◽  
Author(s):  
Brigitte Sommer ◽  
Eugenia M. Sampayo ◽  
Maria Beger ◽  
Peter L. Harrison ◽  
Russ C. Babcock ◽  
...  
Keyword(s):  
Climate Change ◽  
High Latitude ◽  
Species Interactions ◽  
Phylogenetic Signal ◽  
Range Limits ◽  
High Turnover ◽  
Phylogenetic Structure ◽  
Phylogenetic Clustering ◽  
Latitude Range ◽  
Eastern Australia

Understanding how range-edge populations will respond to climate change is an urgent research priority. Here, we used a phylogenetic community ecology approach to examine how ecological and evolutionary processes shape biodiversity patterns of scleractinian corals at their high-latitude range limits in eastern Australia. We estimated phylogenetic signal in seven ecologically important functional traits and conducted tests of phylogenetic structure at local and regional scales using the net relatedness (NRI) and nearest taxon indices (NTI) for the presence/absence and abundance data. Regional tests showed light phylogenetic clustering, indicating that coral species found in this subtropical-to-temperate transition zone are more closely related to each other than are species on the nearby, more northerly Great Barrier Reef. Local tests revealed variable patterns of phylogenetic clustering and overdispersion and higher than expected phylogenetic turnover among sites. In combination, these results are broadly consistent with the hierarchical filtering model, whereby species pass through a regional climatic filter based on their tolerances for marginal conditions and subsequently segregate into local assemblages according to the relative strength of habitat filtering and species interactions. Conservatism of tested traits suggests that corals will likely track their niches with climate change. Nevertheless, high turnover of lineages among sites indicates that range shifts will probably vary among species and highlights the vulnerability and conservation significance of high-latitude reefs.

scholarly journals Comprehensive Genome-Wide Analysis of The Catalase Enzyme Toolbox In Potato (Solanum Tuberosum L.)

2021 ◽  
Author(s):  
Rania Jbir Koubaa ◽  
Mariem Ayadi ◽  
Mohamed Najib Saidi ◽  
Safa Charfeddine ◽  
Radhia Gargouri Bouzid ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Profiling ◽  
Phylogenetic Trees ◽  
Solanum Tuberosum L ◽  
Potato Cultivar ◽  
Promoter Sequence ◽  
3D Protein Structure ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Abstract As antioxidant enzymes, catalase (CAT) protects organisms from oxidative stress via the production of reactive oxygen species (ROS). These enzymes play important roles in diverse biological processes. However, little is known about the CAT genes in potato plants despite its important economical rank of this crop in the world. Yet, abiotic and biotic stresses severely hinder growth and development of the plants which affects the production and quality of the crop. To define the possible roles of CAT genes under various stresses, a genome-wide analysis of CAT gene family has been performed in potato plant.In this study, the StCAT gene’s structure, secondary and 3D protein structure, physicochemical properties, synteny analysis, phylogenetic tree and also expression profiling under various developmental and environmental cues were predicted using bioinformatics tools. The expression analysis by RT-PCR was performed using commercial potato cultivar. Three genes encoding StCAT that code for three proteins each of size 492 aa, interrupted by seven introns have been identified in potatoes. StCAT proteins were found to be localized in the peroxisome which is judged as the main H2O2 cell production site during different processes. Many regulating cis-elements related to stress responses and plant hormones signaling were found in the promoter sequence of each gene. The analysis of motifs and phylogenetic trees showed that StCAT are closer to their homologous in S. lycopersicum and share a 41% – 95% identity with other plants’ CATs. Expression profiling revealed that StCAT1 is the constitutively expressive member; while StCAT2 and StCAT3 are the stress-responsive members.

scholarly journals Discordant evolution of organellar genomes in peas (Pisum L.)

2020 ◽  
Author(s):  
Vera S. Bogdanova ◽  
Natalia V. Shatskaya ◽  
Anatoliy V. Mglinets ◽  
Oleg E. Kosterin ◽  
Gennadiy V. Vasiliev
Keyword(s):  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Plant Evolution ◽  
Hybrid Origin ◽  
Mitochondrial Genomes ◽  
North East ◽  
Plastid Genomes ◽  
First Time ◽  
Evolutionary Fate

AbstractPlastids and mitochondria have their own small genomes which do not undergo meiotic recombination and may have evolutionary fate different from each other and nuclear genome, thus highlighting interesting phenomena in plant evolution. We for the first time sequenced mitochondrial genomes of pea (Pisum L.), in 38 accessions mostly representing diverse wild germplasm from all over pea geographical range. Six structural types of pea mitochondrial genome were revealed. From the same accessions, plastid genomes were sequenced. Bayesian phylogenetic trees based on the plastid and mitochondrial genomes were compared. The topologies of these trees were highly discordant implying not less than six events of hybridisation of diverged wild peas in the past, with plastids and mitochondria differently inherited by the descendants. Such discordant inheritance of organelles is supposed to have been driven by plastid-nuclear incompatibility, known to be widespread in pea wide crosses and apparently shaping the organellar phylogenies. The topology of a phylogenetic tree based on the nucleotide sequence of a nuclear gene His5 coding for a histone H1 subtype corresponds to the current taxonomy and resembles that based on the plastid genome. Wild peas (Pisum sativum subsp. elatius s.l.) inhabiting Southern Europe were shown to be of hybrid origin resulting from crosses of peas similar to those presently inhabiting south-east and north-east Mediterranean in broad sense.

scholarly journals Characterization of the early response of Arabidopsis thaliana to Dickeya dadantii infection using expression profiling

2018 ◽  
Author(s):  
Frédérique Van Gijsegem ◽  
Frédérique Bitton ◽  
Anne-Laure Laborie ◽  
Yvan Kraepiel ◽  
Jacques Pédron
Keyword(s):  
Arabidopsis Thaliana ◽  
Early Stage ◽  
Plant Defence ◽  
Plant Responses ◽  
Type I ◽  
In Planta ◽  
Secretion Systems ◽  
Dickeya Dadantii ◽  
A Genome

AbstractTo draw a global view of plant responses to interactions with the phytopathogenic enterobacterale Dickeya dadantii, a causal agent of soft rot diseases on many plant species, we analysed the early Arabidopsis responses to D. dadantii infection. We performed a genome-wide analysis of the Arabidopsis thaliana transcriptome during D. dadantii infection and conducted a genetic study of identified responses.A limited set of genes related to plant defence or interactions with the environment were induced at an early stage of infection, with an over-representation of genes involved in both the metabolism of indole glucosinolates (IGs) and the jasmonate (JA) defence pathway. Bacterial type I and type II secretion systems are required to trigger the induction of IG and JA-related genes while the type III secretion system appears to partially inhibit these defence pathways. Using Arabidopsis mutants impaired in JA biosynthesis or perception, we showed that induction of some IG metabolism genes was COI1-dependent but, surprisingly, JA-independent. Moreover, characterisation of D. dadantii disease progression in Arabidopsis mutants impaired in JA or IG pathways showed that JA triggers an efficient plant defence response that does not involve IGs.The induction of the IG pathway by bacterial pathogens has been reported several times in vitro. This study shows for the first time, that this induction does indeed occur in planta, but also that this line of defence is ineffective against D. dadantii infection, in contrast to its role to counteract herbivorous or fungal pathogen attacks.

Phylogenomics of orchids and their mycorrhizal fungi : trees, diversity, and the pursuit of symbiosis

2019 ◽  
Author(s):  
◽  
Sarah Unruh
Keyword(s):  
Mycorrhizal Fungi ◽  
Phylogenetic Trees ◽  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Mycorrhizal Symbiosis ◽  
Sequencing Data ◽  
Phylogenetic Structure ◽  
University Of Missouri ◽  
Fungal Symbiosis

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Phylogenetic trees show us how organisms are related and provide frameworks for studying and testing evolutionary hypotheses. To better understand the evolution of orchids and their mycorrhizal fungi, I used high-throughput sequencing data and bioinformatic analyses, to build phylogenetic hypotheses. In Chapter 2, I used transcriptome sequences to both build a phylogeny of the slipper orchid genera and to confirm the placement of a polyploidy event at the base of the orchid family. Polyploidy is hypothesized to be a strong driver of evolution and a source of unique traits so confirming this event leads us closer to explaining extant orchid diversity. The list of orthologous genes generated from this study will provide a less expensive and more powerful method for researchers examining the evolutionary relationships in Orchidaceae. In Chapter 3, I generated genomic sequence data for 32 fungal isolates that were collected from orchids across North America. I inferred the first multi-locus nuclear phylogenetic tree for these fungal clades. The phylogenetic structure of these fungi will improve the taxonomy of these clades by providing evidence for new species and for revising problematic species designations. A robust taxonomy is necessary for studying the role of fungi in the orchid mycorrhizal symbiosis. In chapter 4 I summarize my work and outline the future directions of my lab at Illinois College including addressing the remaining aims of my Community Sequencing Proposal with the Joint Genome Institute by analyzing the 15 fungal reference genomes I generated during my PhD. Together these chapters are the start of a life-long research project into the evolution and function of the orchid/fungal symbiosis.

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