Evolutionary history of woodpeckers and allies (Aves: Picidae): Placing key taxa on the phylogenetic tree

2006 ◽  
Vol 40 (2) ◽  
pp. 389-399 ◽  
Author(s):  
Brett W. Benz ◽  
Mark B. Robbins ◽  
A. Townsend Peterson
Keyword(s):  
Phylogenetic Tree ◽  
Evolutionary History ◽  
History Of

INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

2006 ◽  
Vol 04 (01) ◽  
pp. 59-74 ◽  
Author(s):  
YING-JUN HE ◽  
TRINH N. D. HUYNH ◽  
JESPER JANSSON ◽  
WING-KIN SUNG
Keyword(s):  
Approximation Algorithms ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Network ◽  
Evolutionary Relationships ◽  
Large Set ◽  
Tree Network ◽  
History Of ◽  
Overlapping Sets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

scholarly journals Proteomic similarity of the Littorinid snails in the evolutionary context

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8546 ◽  
Author(s):  
Arina L. Maltseva ◽  
Marina A. Varfolomeeva ◽  
Arseniy A. Lobov ◽  
Polina Tikanova ◽  
Marina Panova ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Evolutionary History ◽  
Geographic Location ◽  
Body Part ◽  
Specific Protein ◽  
Protein Markers ◽  
Cophenetic Correlation ◽  
Additional Information ◽  
History Of ◽  
Using Data

Background The introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions. Methods Here we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering—using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson–Foulds distance, the Fowlkes–Mallows index and cophenetic correlation. Results Overall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two Littoraria species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related Littorina fabalis and L. obtusata, possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups (“saxatilis” and “obtusata” groups in the Littorina genus) and for genera (Littoraria and Echinolittorina species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five Littorina species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of species.

scholarly journals Eversion and withdrawal of an intromittent organ before sexual maturation prepares male beetles for copulation

2017 ◽  
Vol 4 (8) ◽  
pp. 161029 ◽  
Author(s):  
Yoko Matsumura ◽  
Takuya Kubo
Keyword(s):  
Phylogenetic Tree ◽  
Sexual Maturation ◽  
Related Species ◽  
Evolutionary History ◽  
Active State ◽  
Surface Structures ◽  
Closely Related Species ◽  
Spermathecal Duct ◽  
History Of ◽  
Coiled State

Some species of criocerine beetles have a hyper-elongated part of the intromittent organ called a flagellum. In resting position, the flagellum is stored in a specialized internal sac in the intromittent organ. This specialized state of the flagellum and internal sac is indispensable during copulation for flagellar insertion into the female spermathecal duct for sperm transfer. However, the morphogenesis of the flagellum does not generate the active state of the flagellum; rather, the flagellum is generated in an inactive and completely coiled state. After eclosion, males of Lema coronata evert and withdraw the internal sac multiple times before sexual maturation, without mounting a female. This behaviour serves to uncoil the flagellum and guide it into the active state with the aid of surface structures on the internal sac. A closely related species, Lema dilecta , also has a long flagellum and undergoes the same behaviour to place the flagellum in the active position. However, some other species of criocerine beetles with much shorter flagella can attain the active state without exhibiting this behaviour. Based on a previously proposed phylogenetic tree, we discuss the evolutionary history of the hyper-elongation of the flagellum and associated behaviour.

Evolution of physiological dormancy multiple times in Melastomataceae from Neotropical montane vegetation

2011 ◽  
Vol 22 (1) ◽  
pp. 37-44 ◽  
Author(s):  
Fernando A.O. Silveira ◽  
Rafaella C. Ribeiro ◽  
Denise M.T. Oliveira ◽  
G. Wilson Fernandes ◽  
José P. Lemos-Filho
Keyword(s):  
Phylogenetic Tree ◽  
Seed Dormancy ◽  
Rainy Season ◽  
Evolutionary History ◽  
Selective Pressure ◽  
Strong Selective Pressure ◽  
Montane Vegetation ◽  
Physiological Dormancy ◽  
History Of ◽  
Seed Coats

AbstractWe investigated seed dormancy among species of Melastomataceae from Neotropical montane vegetation of Brazil. Four out of 50 studied species had dormant seeds:Miconia corallina(Miconieae), Tibouchina cardinalis(Melastomeae), Comolia sertularia(Melastomeae) andChaetostoma armatum(Microlicieae). For these four species, germinability of seeds collected in different years was always < 10% and the percentages of embryoless seeds and non-viable embryos were both insufficient to explain low or null germinability. This is the first unequivocal report of seed dormancy in tropical Melastomataceae. The production of seeds with permeable seed coats and fully developed, differentiated embryos indicates the occurrence of physiological dormancy. The reconstructed phylogenetic tree of the 50 species suggests that physiological dormancy evolved multiple times during the evolutionary history of Melastomataceae in this vegetation. Physiological dormancy evolved in species and populations associated with xeric microhabitats, where seeds are dispersed in unfavourable conditions for establishment. Therefore, drought-induced mortality may have been a strong selective pressure favouring the evolution of physiological dormancy in Melastomataceae. We argue that dormancy may have been independently selected in other lineages of Cerrado plants colonizing xeric microhabitats and dispersing seeds at the end of the rainy season. The contributions of our data to the understanding of seed dormancy in tropical montane vegetation are discussed.

scholarly journals The Bayesian reconstruction and the evolutionary history of Salivirus type 1 and type 2: the worldwide spreading

2021 ◽  
Vol 15 (02) ◽  
pp. 280-288
Author(s):  
Silvia Angeletti ◽  
Domenico Benvenuto ◽  
Marta Fogolari ◽  
Cecilia De Flora ◽  
Giancarlo Ceccarelli ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Evolutionary History ◽  
Homology Modelling ◽  
Model Fitting ◽  
Evolutionary Model ◽  
History Of ◽  
Probable Origin ◽  
Pressure Analysis

Introduction: Salivirus (SalV) represents an emerging problem in public health especially during the recent years. In this study, the Bayesian evolutionary history and the spread of the virus through the different countries have been reported. Methodology: a database of 81 sequences of SalV structural VP1 fragment were downloaded from GenBank, aligned and manually edited by Bioedit Software. ModelTest v. 3.7 software was used to estimate the simplest evolutionary model fitting the sequence dataset. A Maximum-Likelihood tree has been generated using MEGA-X to test the “clockliness” signal using TempEst 1.5.1. The Bayesian phylogenetic tree was built by BEAST. Homology modelling was performed by SWISS-Model and protein variability evaluated by ConSurf server. Results: the phylogenetic tree showed a clade of SalV A2 and three main clades of SalV A1, revealing several infections in humans in South Korea, India, Tunisia, China, Nigeria, Ethiopia and USA. The Bayesian maximum clade credibility tree and the time of the most common recent ancestor dated back the root of the tree to the year 1788 with the probable origin in USA. Selective pressure analysis revealed two positive selection sites, His at 100th and Leu at 116th positions that at the homology modelling resulted important to guarantee protein stability and variability. This could contribute to the development of new mutations modifying the clinical features of this evolving virus. Conclusions: Bayesian phylogenetic and phylodynamic represented a useful tool to follow the transmission dynamic of SalV and to prevent new epidemics worldwide.

scholarly journals Comparison of Phylogenetic Tree Topologies for Nitrogen Associated Genes Partially Reconstruct the Evolutionary History of Saccharomyces cerevisiae

2019 ◽  
Vol 8 (1) ◽  
pp. 32
Author(s):  
Manuel Villalobos-Cid ◽  
Francisco Salinas ◽  
Eduardo I. Kessi-Pérez ◽  
Matteo De Chiara ◽  
Gianni Liti ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Total Evidence ◽  
Sequence Information ◽  
Phylogenetic Cluster ◽  
History Of ◽  
Tree Topologies ◽  
Yeast Genomes

Massive sequencing projects executed in Saccharomyces cerevisiae have revealed in detail its population structure. The recent “1002 yeast genomes project” has become the most complete catalogue of yeast genetic diversity and a powerful resource to analyse the evolutionary history of genes affecting specific phenotypes. In this work, we selected 22 nitrogen associated genes and analysed the sequence information from the 1011 strains of the “1002 yeast genomes project”. We constructed a total evidence (TE) phylogenetic tree using concatenated information, which showed a 27% topology similarity with the reference (REF) tree of the “1002 yeast genomes project”. We also generated individual phylogenetic trees for each gene and compared their topologies, identifying genes with similar topologies (suggesting a shared evolutionary history). Furthermore, we pruned the constructed phylogenetic trees to compare the REF tree topology versus the TE tree and the individual genes trees, considering each phylogenetic cluster/subcluster within the population, observing genes with cluster/subcluster topologies of high similarity to the REF tree. Finally, we used the pruned versions of the phylogenetic trees to compare four strains considered as representatives of S. cerevisiae clean lineages, observing for 15 genes that its cluster topologies match 100% the REF tree, supporting that these strains represent main lineages of yeast population. Altogether, our results showed the potential of tree topologies comparison for exploring the evolutionary history of a specific group of genes.

Elaborating the role of reflection and individual differences in the study of folk-economic beliefs

2018 ◽  
Vol 41 ◽  
Author(s):  
Kevin Arceneaux
Keyword(s):  
Decision Making ◽  
Individual Differences ◽  
Cognitive Processes ◽  
Evolutionary History ◽  
Behavioral Responses ◽  
History Of ◽  
Economic Beliefs

AbstractIntuitions guide decision-making, and looking to the evolutionary history of humans illuminates why some behavioral responses are more intuitive than others. Yet a place remains for cognitive processes to second-guess intuitive responses – that is, to be reflective – and individual differences abound in automatic, intuitive processing as well.

Sequencing Analysis and Phylogenetic Tree of HPV Isolated from Breast Cancer Patients at Thi-Qar Province/Iraq

2020 ◽  
pp. 37-40
Keyword(s):  
Nucleotide Sequence ◽  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Nucleotide Sequencing ◽  
Sequencing Analysis ◽  
Breast Cancer Patients ◽  
The North ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
History Of

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.

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