scholarly journals Exploring and Reconstructing Ancestral Anatomies using Ontology-Informed Approaches

2019 ◽  
Vol 3 ◽  
Author(s):  
Sergei Tarasov ◽  
Istvan Miko ◽  
Matthew Yoder ◽  
Josef Uyeda
Keyword(s):  
Phylogenetic Trees ◽  
Character State ◽  
Ancestral Reconstruction ◽  
Anatomy Ontology ◽  
Insect Order ◽  
Ancestral Character State ◽  
Body Regions ◽  
Individual Traits ◽  
History Of ◽  
Complex Characters

Ancestral character state reconstruction has been long used to gain insight into the evolution of individual traits in organisms. However, organismal anatomies (= entire phenotypes) are not merely ensembles of individual traits, rather they are complex systems where traits interact with each other due to anatomical dependencies (when one trait depends on the presence of another trait) and developmental constraints. Comparative phylogenetics has been largely lacking a method for reconstructing the evolution of entire organismal anatomies or organismal body regions. Herein, we present a new approach named PARAMO (Phylogenetic Ancestral Reconstruction of Anatomy by Mapping Ontologies, Tarasov and Uyeda 2019) that takes into account anatomical dependencies and uses stochastic maps (i.e., phylogenetic trees with an instance of mapped evolutionary history of characters, Huelsenbeck et al. 2003) along with anatomy ontologies to reconstruct organismal anatomies. Our approach treats the entire phenotype or its component body regions as single complex characters and allows exploring and comparing phenotypic evolution at different levels of anatomical hierarchy. These complex characters are constructed by ontology-informed amalgamation of elementary characters (i.e., those coded in character matrix) using stochastic maps. In our approach, characters are linked with the terms from an anatomy ontology, which allows viewing them not just as an ensemble of character state tokens but as entities that have their own biological meaning provided by the ontology. This ontology-informed framework provides new opportunities for tracking phenotypic radiations and anatomical evolution of organisms, which we explore using a large dataset for the insect order Hymenoptera (sawflies, wasps, ants and bees).

Convergence to the tiniest detail: vocal sac structure in torrent-dwelling frogs

2019 ◽  
Author(s):  
Agustín J Elias-Costa ◽  
Julián Faivovich
Keyword(s):  
Background Noise ◽  
Evolutionary History ◽  
Visual Display ◽  
Character State ◽  
Visual Displays ◽  
State Reconstruction ◽  
Ancestral Character State ◽  
History Of ◽  
Ancestral Character State Reconstruction ◽  
Detection And Recognition

Abstract Cascades and fast-flowing streams impose severe restrictions on acoustic communication, with loud broadband background noise hampering signal detection and recognition. In this context, diverse behavioural features, such as ultrasound production and visual displays, have arisen in the evolutionary history of torrent-dwelling amphibians. The importance of the vocal sac in multimodal communication is being increasingly recognized, and recently a new vocal sac visual display has been discovered: unilateral inflation of paired vocal sacs. In the diurnal stream-breeding Hylodidae from the Atlantic forest, where it was first described, this behaviour is likely to be enabled by a unique anatomical configuration of the vocal sacs. To assess whether other taxa share this exceptional structure, we surveyed torrent-dwelling species with paired vocal sacs across the anuran tree of life and examined the vocal sac anatomy of exemplar species across 18 families. We found striking anatomical convergence among hylodids and species of the distantly related basal ranid genera Staurois, Huia, Meristogenys and Amolops. Ancestral character state reconstruction identified three new synapomorphies for Ranidae. Furthermore, we surveyed the vocal sac configuration of other anuran species that perform visual displays and report observations on what appears to be unilateral inflation of paired vocal sacs, in Staurois guttatus – an extremely rare behaviour in anurans.

scholarly journals The accessory neural arch: development, morphology, and systematic distribution

Zoomorphology ◽  
2021 ◽  
Author(s):  
Philipp Thieme ◽  
Timo Moritz
Keyword(s):  
State Estimation ◽  
Evolutionary History ◽  
Taxon Sampling ◽  
Character State ◽  
Neural Arch ◽  
Ancestral Character State ◽  
History Of ◽  
Similar Character ◽  
Morphology Development ◽  
State Estimations

AbstractThe accessory neural arch is an oddly distributed character present in several non-acanthomorph teleostean taxa. Its homology was often implied but never satisfyingly tested. In this study, we attended this pending problem. We analyzed the morphology, development, and systematic distribution of the accessory neural arch in teleosts. Using a comprehensive taxon sampling of cleared and stained specimens, we evaluated if the accessory neural arch fulfils existing homology criteria. We then combined these data with recent genetic phylogenies and ancestral character state estimation to reconstruct the evolutionary history of the accessory neural arch. While its gross morphology and development fit homology criteria, results from ancestral character state estimations suggest multiple independent evolutions within teleosts. Although the accessory neural arch cannot be homologous between several teleostean taxa, the concept of parallelism may explain the presence of such a similar character in a variety of non-acanthomorph teleostean taxa.

scholarly journals PastView: a user-friendly interface to explore evolutionary scenarios

2019 ◽  
Author(s):  
François Chevenet ◽  
Guillaume Castel ◽  
Emmanuelle Jousselin ◽  
Olivier Gascuel
Keyword(s):  
Phylogenetic Trees ◽  
Character State ◽  
Combinatorial Explosion ◽  
New Methods ◽  
Research Fields ◽  
Ancestral Character State ◽  
Tree Topologies ◽  
State Inference ◽  
User Friendly ◽  
Ancestral Character States

AbstractBackgroundAncestral character states computed from the combination of phylogenetic trees with extrinsic traits are used to decipher evolutionary scenarios in various research fields such as phylogeography, epidemiology, and ecology. Despite the existence of powerful methods and software in ancestral character state inference, difficulties may arise when interpreting the outputs of such inferences. The growing complexity of data (trees, annotations), the diversity of optimization criteria for computing trees and ancestral character states, the combinatorial explosion of potential evolutionary scenarios if some ancestral characters states do not stand out clearly from others, requires the design of new methods that operate on tree topologies and extrinsic traits associations to ease the identification of evolutionary scenarios.ResultWe developed a tool, PastView, a user-friendly interface that includes numerical and graphical features to help users to import and/or compute ancestral character states and extract evolutionary scenario as a set of successive transitions of ancestral character states from the tree root to its leaves. PastView offers synthetic views such as transition maps and integrates comparative analysis methods to highlight agreements or discrepancies between methods of ancestral annotations inference.ConclusionThe main contribution of PastView is to assemble known numerical and graphical methods into a multi-maps graphical user interface dedicated to the computing, searching and viewing of evolutionary scenarios based on phylogenetic trees and ancestral character states. PastView is available publicly as a standalone software on www.pastview.org.

Challenges for Diadromous Fishes in a Dynamic Global Environment

2009 ◽  
Keyword(s):  
Life Cycle ◽  
Phylogenetic Trees ◽  
Sister Group ◽  
Life Cycles ◽  
Character State ◽  
Freshwater Species ◽  
Larval Stages ◽  
Ancestral Character State ◽  
Coastal Marine ◽  
Group Relationships

<em>Abstract</em>.-We develop the view, based on life cycle differences and recently published sister group relationships, that the freshwater life cycle was the ancestral character state leading to anadromy among salmoniforms, whereas the marine life cycle was the ancestral character state leading to anadromy among osmeriforms. In contrast to most salmonid fishes, the reproductive migrations of smelts are generally characterized by brief excursions to spawn in freshwater, and larvae may spend no more than 24 h in freshwater before being transported to coastal marine or estuarine environments. We reconstructed the phylogeny of the suborder Osmeroidei to establish the phylogenetic relationships among anadromous, marine, and freshwater species of this taxon. We mapped these life cycles onto phylogenetic trees of osmeriforms and salmoniforms and applied character-reconstruction methodology based on simple parsimony and likelihood methodologies. A freshwater origin of salmonids was supported by our analyses, whereas either marine or anadromous life cycles characterized the evolution of osmeroids. The possibility that the evolution of anadromy in salmonids and osmeroids followed separate paths requires a reconsideration of some generalizations concerning anadromy. We hypothesize that anadromy in osmeroids may be first and foremost an adaptation to place embryos and the early larval stages in reproductive safe sites to maximize their survival. The evolution of exclusive freshwater species of osmeriforms has occurred via anadromy through the various processes associated with landlocking. Freshwater amphidromy in osmeroids is most likely a consequence of anadromy rather than a precursor and may be contingent upon the availability of food resources in freshwater. Finally, marine osmeroids have been derived from anadromous ancestors and are "safe-site" specialists, exploiting principally the upper intertidal zone for reproduction. We also suggest that such contrasting evolutionary pathways to anadromy may provide insight into the evolution of partial migration, observed uniquely in salmonids, and the nature and extent of population genetic structure found in the two groups of fishes.

Evolution of trichome morphology in Mimosa (Leguminosae-Mimosoideae)

Phytotaxa ◽  
2013 ◽  
Vol 119 (1) ◽  
pp. 1 ◽  
Author(s):  
JULIANA SANTOS-SILVA ◽  
ANA MARIA GOULART DE AZEVEDO TOZZI ◽  
MARCELO FRAGOMENI SIMON ◽  
NAZARETH GUEDES URQUIZA ◽  
MATÍAS MORALES
Keyword(s):  
Glandular Trichomes ◽  
Character State ◽  
Optimization Analysis ◽  
Ancestral Character State ◽  
History Of ◽  
Ancestral Character State Reconstruction ◽  
Species Groups ◽  
Trichome Types ◽  
Trichome Morphology ◽  
Insight Into

With more than 500 species, Mimosa L. is one of the largest genera of the Leguminosae. It exhibits considerable trichome diversity among species. Trichome types have been used as diagnostic characters, but some are not well known and have been poorly described in taxonomic works, causing some difficulties for species identification and description. The morphology of trichomes of 35 species was studied using scanning electron microscopy and light microscopy to define the types of trichomes precisely. An ancestral character state reconstruction using a densely-sampled phylogeny of the genus was performed in order to investigate the evolution of trichome types in Mimosa. Two basic types of trichomes can be distinguished: glandular and non-glandular. The glandular trichomes can be sessile or stalked. The non-glandular trichomes can be unbranched or branched. Unbranched trichomes are unicellular and conical or cylindrical, whereas branched trichomes are multicellular and verruciform, medusiform, plumose, barbellate, stellate, stellate-lepidote, or lepidote. Character optimization analysis suggests that glandular and branched trichomes are derived and evolved independently in different lineages within Mimosa. The ancestral condition in Mimosa was probably non-glandular and unbranched trichomes, which was retained from piptadenioid ancestors. Our study provides a first insight into the evolutionary history of trichome morphology in the genus. Despite high levels of homoplasy, trichome morphology offers a set of characters that can be used for differentiating species and species groups in combination with other characters. 

scholarly journals Evolution of Philodendron (Araceae) species along Neotropical biomes

2016 ◽  
Author(s):  
Leticia Loss-Oliveira ◽  
Cassia CMS Sakuragui ◽  
Maria de Lourdes Soares ◽  
Carlos G Schrago
Keyword(s):  
Morphological Diversity ◽  
Neotropical Region ◽  
Last Common Ancestor ◽  
Amazon Forest ◽  
Ancestral Reconstruction ◽  
Biogeographic History ◽  
Early Diversification ◽  
Sister Clade ◽  
History Of ◽  
Wide Geographic Distribution

Philodendron is the second most diverse genus of the Araceae, a tropical monocot family with significant morphological diversity along its wide geographic distribution in the Neotropics. Although evolutionary studies of Philodendron were conducted in recent years, the phylogenetic relationship among its species remains unclear. Additionally, analyses conducted to date suggested the inclusion of all American representatives of a closely related genus, Homalomena, within the Philodendron clade. A thorough evaluation of the phylogeny and timescale of these lineages is thus necessary to elucidate the tempo and mode of evolution of this large Neotropical genus and to unveil the biogeographic history of Philodendron evolution along the Amazonian and Atlantic Rain Forests, as well as open dry forests of South America. To this end, we have estimated the molecular phylogeny for 68 Philodendron species, which consists of the largest sampling assembled to date aiming the study of the evolutionary affinities. We have also performed ancestral reconstruction of species distribution along biomes. Finally, we contrasted these results with the inferred timescale of Philodendron and Homalomena lineage diversification. Our estimates indicate that American Homalomena is the sister clade to Philodendron. The early diversification of Philodendron took place in the Amazon Forest from Early to Middle Miocene, followed by colonization of the Atlantic Forest and the savanna-like landscapes, respectively. Based on the age of the last common ancestor of Philodendron, the species of this genus diversified by rapid radiations, leading to its wide extant distribution in the Neotropical region.

scholarly journals The Evolutionary History of the Chymase Locus -a Locus Encoding Several of the Major Hematopoietic Serine Proteases

2021 ◽  
Vol 22 (20) ◽  
pp. 10975
Author(s):  
Srinivas Akula ◽  
Zhirong Fu ◽  
Sara Wernersson ◽  
Lars Hellman
Keyword(s):  
Mast Cell ◽  
T Cell ◽  
Serine Proteases ◽  
Phylogenetic Trees ◽  
Granzyme B ◽  
Large Family ◽  
Cathepsin G ◽  
Immune Functions ◽  
New Class ◽  
History Of

Several hematopoietic cells of the immune system store large amounts of proteases in cytoplasmic granules. The absolute majority of these proteases belong to the large family of chymotrypsin-related serine proteases. The chymase locus is one of four loci encoding these granule-associated serine proteases in mammals. The chymase locus encodes only four genes in primates, (1) the gene for a mast-cell-specific chymotryptic enzyme, the chymase; (2) a T-cell-expressed asp-ase, granzyme B; (3) a neutrophil-expressed chymotryptic enzyme, cathepsin G; and (4) a T-cell-expressed chymotryptic enzyme named granzyme H. Interestingly, this locus has experienced a number of quite dramatic expansions during mammalian evolution. This is illustrated by the very large number of functional protease genes found in the chymase locus of mice (15 genes) and rats (18 genes). A separate expansion has also occurred in ruminants, where we find a new class of protease genes, the duodenases, which are expressed in the intestinal region. In contrast, the opossum has only two functional genes in this locus, the mast cell (MC) chymase and granzyme B. This low number of genes may be the result of an inversion, which may have hindered unequal crossing over, a mechanism which may have been a major factor in the expansion within the rodent lineage. The chymase locus can be traced back to early tetrapods as genes that cluster with the mammalian genes in phylogenetic trees can be found in frogs, alligators and turtles, but appear to have been lost in birds. We here present the collected data concerning the evolution of this rapidly evolving locus, and how these changes in gene numbers and specificities may have affected the immune functions in the various tetrapod species.

scholarly journals treeWidget: a BioJS component to visualise phylogenetic trees

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 49 ◽  
Author(s):  
Fabian Schreiber
Keyword(s):  
Phylogenetic Trees ◽  
Protein Domains ◽  
Gene Families ◽  
Sequence Information ◽  
Gene Duplications ◽  
Link Type ◽  
History Of ◽  
Conservation Patterns ◽  
Evolution Of Gene Families ◽  
The Web

Summary: Phylogenetic trees are widely used to represent the evolution of gene families. As the history of gene families can be complex (including lots of gene duplications), its visualisation can become a difficult task. A good/accurate visualisation of phylogenetic trees - especially on the web - allows easier understanding and interpretation of trees to help to reveal the mechanisms that shape the evolution of a specific set of gene/species. Here, I present treeWidget, a modular BioJS component to visualise phylogenetic trees on the web. Through its modularity, treeWidget can be easily customized to allow the display of sequence information, e.g. protein domains and alignment conservation patterns.Availability: http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7707

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.

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