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.

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 Parasite specialization from a phylogenetic perspective: a new index of host specificity

Parasitology ◽  
2003 ◽  
Vol 126 (5) ◽  
pp. 473-480 ◽  
Author(s):  
R. POULIN ◽  
D. MOUILLOT
Keyword(s):  
Host Specificity ◽  
Host Species ◽  
Taxonomic Distinctness ◽  
Phylogenetic Distance ◽  
Helminth Parasites ◽  
Phylogenetic Structure ◽  
Additional Information ◽  
History Of ◽  
Using Data ◽  
Index Value

The host specificity of a parasite is not merely a function of how many host species it can exploit, but also of how closely related these host species are to each other. Here, a new index of host specificity is proposed, one that takes into account the average taxonomic or phylogenetic distance between pairs of host species used by a parasite. The index is derived from measures of taxonomic distinctness used in biodiversity studies. It is easy to compute and interpret, ranging from a minimum value of 1 when all host species are members of the same genus, to a maximum of 5, when all host species belong to different classes. The variance of this measure can also be computed, and provides additional information on the taxonomic or phylogenetic structure of the host assemblage. Using data on helminth parasites of Canadian freshwater fishes, we show that the new index, unlike the mere number of known host species, is independent of study effort i.e. the number of published records of a parasite. Although the index and the number of known hosts are not entirely independent statistically, each captures a different aspect of host specificity. For instance, although acanthocephalans infect significantly more host species than trematodes, cestodes or nematodes, there is no difference in the average index value among these 4 helminth taxa, suggesting that the average taxonomic distances between the host species of a parasite do not vary among these higher taxa. We recommend the use of our new index in future comparative studies of host specificity, in particular when the focus is on the evolutionary history of parasites and of their past colonizations of host lineages.

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.

scholarly journals Accurate Prediction of Protein Functional Class from Sequence in theMycobacterium tuberculosisandEscherichia coliGenomes Using Data Mining

Yeast ◽  
2000 ◽  
Vol 1 (4) ◽  
pp. 283-293 ◽  
Author(s):  
Ross D. King ◽  
Andreas Karwath ◽  
Amanda Clare ◽  
Luc Dehaspe
Keyword(s):  
Data Mining ◽  
Evolutionary History ◽  
Inductive Logic ◽  
Rule Learning ◽  
Functional Class ◽  
E Coli ◽  
Data Mining Approach ◽  
History Of ◽  
Using Data ◽  
Insight Into

The analysis of genomics data needs to become as automated as its generation. Here we present a novel data-mining approach to predicting protein functional class from sequence. This method is based on a combination of inductive logic programming clustering and rule learning. We demonstrate the effectiveness of this approach on theM. tuberculosisandE. coligenomes, and identify biologically interpretable rules which predict protein functional class from information only available from the sequence. These rules predict 65% of the ORFs with no assigned function inM. tuberculosisand 24% of those inE. coli, with an estimated accuracy of 60–80% (depending on the level of functional assignment). The rules are founded on a combination of detection of remote homology, convergent evolution and horizontal gene transfer. We identify rules that predict protein functional class even in the absence of detectable sequence or structural homology. These rules give insight into the evolutionary history ofM. tuberculosisandE. coli.

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 Accurate Prediction of Protein Functional Class from Sequence in the Mycobacterium tuberculosis and Escherichia coli Genomes Using Data Mining

Yeast ◽  
2000 ◽  
Vol 1 (4) ◽  
pp. 283-293
Author(s):  
Ross D. King ◽  
Andreas Karwath ◽  
Amanda Clare ◽  
Luc Dehaspe
Keyword(s):  
Data Mining ◽  
Evolutionary History ◽  
Inductive Logic ◽  
Rule Learning ◽  
Functional Class ◽  
E Coli ◽  
Data Mining Approach ◽  
History Of ◽  
Using Data ◽  
Insight Into

The analysis of genomics data needs to become as automated as its generation. Here we present a novel data-mining approach to predicting protein functional class from sequence. This method is based on a combination of inductive logic programming clustering and rule learning. We demonstrate the effectiveness of this approach on the M. tuberculosis and E. coli genomes, and identify biologically interpretable rules which predict protein functional class from information only available from the sequence. These rules predict 65% of the ORFs with no assigned function in M. tuberculosis and 24% of those in E. coli, with an estimated accuracy of 60–80% (depending on the level of functional assignment). The rules are founded on a combination of detection of remote homology, convergent evolution and horizontal gene transfer. We identify rules that predict protein functional class even in the absence of detectable sequence or structural homology. These rules give insight into the evolutionary history of M. tuberculosis and E. coli.

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.

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

scholarly journals Evolution of Protein-Mediated Biomineralization in Scleractinian Corals

2021 ◽  
Vol 12 ◽  
Author(s):  
Tal Zaquin ◽  
Assaf Malik ◽  
Jeana L. Drake ◽  
Hollie M. Putnam ◽  
Tali Mass
Keyword(s):  
Protein Function ◽  
Evolutionary History ◽  
Evolutionary Process ◽  
Organic Matrix ◽  
Distinct Species ◽  
Specific Protein ◽  
Proteomic Profiling ◽  
Stony Corals ◽  
Core Set ◽  
History Of

While recent strides have been made in understanding the biological process by which stony corals calcify, much remains to be revealed, including the ubiquity across taxa of specific biomolecules involved. Several proteins associated with this process have been identified through proteomic profiling of the skeletal organic matrix (SOM) extracted from three scleractinian species. However, the evolutionary history of this putative “biomineralization toolkit,” including the appearance of these proteins’ throughout metazoan evolution, remains to be resolved. Here we used a phylogenetic approach to examine the evolution of the known scleractinians’ SOM proteins across the Metazoa. Our analysis reveals an evolutionary process dominated by the co-option of genes that originated before the cnidarian diversification. Each one of the three species appears to express a unique set of the more ancient genes, representing the independent co-option of SOM proteins, as well as a substantial proportion of proteins that evolved independently. In addition, in some instances, the different species expressed multiple orthologous proteins sharing the same evolutionary history. Furthermore, the non-random clustering of multiple SOM proteins within scleractinian-specific branches suggests the conservation of protein function between distinct species for what we posit is part of the scleractinian “core biomineralization toolkit.” This “core set” contains proteins that are likely fundamental to the scleractinian biomineralization mechanism. From this analysis, we infer that the scleractinians’ ability to calcify was achieved primarily through multiple lineage-specific protein expansions, which resulted in a new functional role that was not present in the parent gene.

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