scholarly journals Parasitism in Eukaryota - Reconstruction of Ancestral and Unavailable Extant States

2018 ◽  
Vol 2 ◽  
pp. e25739
Author(s):  
Lydia Buntrock ◽  
Bernhard Renard ◽  
Emanuel Heitlinger
Keyword(s):  
Phylogenetic Trees ◽  
Cross Validation ◽  
Biotic Interactions ◽  
Species Interaction ◽  
State Information ◽  
Large Sets ◽  
Computational Reconstruction ◽  
Important Trait ◽  
Topology Information ◽  
Available Information

Parasitism can be defined as an interaction between species in which one of the interaction partners, the parasite, lives in or on the other, the host. The parasite draws food from its host and harms it in the process. According to some estimates, over 40% of all eukaryotes are parasites. Nevertheless, it is difficult to obtain information about a particular taxon is a parasite computationally making it difficult to query large sets of taxa. Here we test to what extend it is possible to use the Open Tree of Life (OTL), a synthesis of phylogenetic trees on a backbone taxonomy (resulting in unresolved nodes), to expand available information via phylogenetic trait prediction. We use the Global Biotic Interactions (GloBI) database to categorise 25,992 and 34,879 species as parasites and free-living, respectively, and predict states for over ~2.3 million (97.34%) leaf nodes without state information. We estimate the accuracy of our maximum parsimony based predictions using cross-validation and simulation at roughly 60-80% overall, but strongly varying between clades. The cross-validation resulted in an accuracy of 98.17% which is explained by the fact that the data are not uniformly distributed. We describe this variation across taxa as associated with available state and topology information. We compare our results with several smaller scale studies, which used manual expert curation and conclude that computationally inferred state changes largely agree in number and placement with those. In clades in which available state information is biased (mostly towards parasites, e.g. in Nematodes) phylogenetic prediction is bound to provide results contradicting conventional wisdom. This represents, to our knowledge, the first comprehensive computational reconstruction of the emergence of parasitism in eukaryotes. We argue that such an approach is necessary to allow further incorporation of parasitism as an important trait in species interaction databases and in individual studies on eukaryotes, e.g. in the microbiome.

scholarly journals Improved Core Genes Prediction for Constructing Well-Supported Phylogenetic Trees in Large Sets of Plant Species

2015 ◽  
pp. 379-390 ◽  
Author(s):  
Bassam AlKindy ◽  
Huda Al-Nayyef ◽  
Christophe Guyeux ◽  
Jean-Franc̨ois Couchot ◽  
Michel Salomon ◽  
...  
Keyword(s):  
Plant Species ◽  
Phylogenetic Trees ◽  
Large Sets ◽  
Core Genes

scholarly journals The latitudinal gradient in rates of evolution for bird beaks, a species interaction trait

2020 ◽  
Author(s):  
Benjamin G Freeman ◽  
Dolph Schluter ◽  
Joseph A Tobias
Keyword(s):  
Meta Analysis ◽  
Biotic Interactions ◽  
Species Interaction ◽  
Temperate Zone ◽  
Ecological Opportunity ◽  
Evolutionary Diversification ◽  
Diversity Gradient ◽  
Rates Of Evolution ◽  
Speciation Rates ◽  
Beak Size

AbstractWhere is evolution fastest? The biotic interactions hypothesis proposes that greater species richness creates more ecological opportunity, driving faster evolution at low latitudes, whereas the “empty niches” hypothesis proposes that ecological opportunity is greater where diversity is low, spurring faster evolution at high latitudes. Here we tested these contrasting predictions by analyzing rates of bird beak evolution for a global dataset of 1141 sister pairs of birds. Beak size evolves at similar rates across latitudes, while beak shape evolves faster in the temperate zone, consistent with the empty niches hypothesis. We show in a meta-analysis that trait evolution and recent speciation rates are faster in the temperate zone, while rates of molecular evolution are slightly faster in the tropics. Our results suggest that drivers of evolutionary diversification are more potent at higher latitudes, thus calling into question multiple hypotheses invoking faster tropical evolution to explain the latitudinal diversity gradient.

scholarly journals Conditions under which distributions of edge length ratios on phylogenetic trees can be used to order evolutionary events

2021 ◽  
Author(s):  
Edward Susko ◽  
Mike Steel ◽  
Andrew J. Roger
Keyword(s):  
Molecular Clock ◽  
Phylogenetic Trees ◽  
Branch Length ◽  
Edge Length ◽  
Eukaryotic Cells ◽  
High Profile ◽  
Large Sets ◽  
Different Origins ◽  
Alternative Set ◽  
Strict Molecular Clock

AbstractTwo recent high profile studies have attempted to use edge (branch) length ratios from large sets of phylogenetic trees to determine the relative ages of genes of different origins in the evolution of eukaryotic cells. This approach can be straightforwardly justified if substitution rates are constant over the tree for a given protein. However, such strict molecular clock assumptions are not expected to hold on the billion-year timescale. Here we propose an alternative set of conditions under which comparisons of edge length distributions from multiple sets of phylogenies of proteins with different origins can be validly used to discern the order of their origins. We also point out scenarios where these conditions are not expected to hold and caution is warranted.

scholarly journals The Ecology of Plant Interactions: A Giant with Feet of Clay

2021 ◽  
Author(s):  
Ciro Cabal ◽  
Ricardo Martínez-García ◽  
Fernando Valladares
Keyword(s):  
Biotic Interactions ◽  
Phenomenological Approach ◽  
Species Interaction ◽  
Spatial And Temporal Variability ◽  
Plant Interactions ◽  
Individual Level ◽  
Biophysical Processes ◽  
Individual Scale ◽  
The Individual ◽  
The Right

Ecologists use the net biotic interactions among plants as a major factor to predict other ecosystem features, such as species diversity, community structure, or plant atmospheric carbon uptake. By adopting this approach, ecologists have built a giant body of theory founded on observational evidence. However, growing evidence points out that this may not be the right approach. The literature addressing the biophysical mechanisms underlying the plant interactions is much scarcer. A rising number of scientists claim the need for a mechanistic understanding of plant interactions due to the limitations that a phenomenological approach raises both in empirical and theoretical studies. Scattered studies have recently taken such a mechanistic approach, but we still lack a general theoretical framework to study mechanistically plant interactions. In this review, we first recapitulate the elementary units of plant interactions, i.e., all the known biophysical processes affected by the presence of an influencing plant and the possible phenotypic responses of plants influenced by those processes. Second, we discuss how a net interaction between two plants emerges from the simultaneous effect of these elementary units. Third, we touch upon the spatial and temporal variability of the net interaction and discuss the links between this variability and the underlying biophysical processes. We conclude by discussing how to integrate these processes into a mechanistic framework for plant interactions that must necessarily focus on the individual scale and explicitly incorporate the spatial structure of the community and environmental factors: the plant interaction models (PIM). A PIM incorporates a pair or few plants interacting with their physical environment so that the biotic interaction is not imposed but emerges from the model. This type of model can provide concise, mechanistic hypotheses to be tested empirically. This review calls for a paradigm shift in the ecology of plant interactions, from the classic species interaction study towards a more mechanistic individual-level approach. It also presents a comprehensive foundation for studying the mechanisms underpinning the net interaction between two plants.

scholarly journals Fruit Development and Primary Metabolism in Apple

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1160
Author(s):  
Verónica Tijero ◽  
Francesco Girardi ◽  
Alessandro Botton
Keyword(s):  
Primary Metabolism ◽  
Key Factors ◽  
New Techniques ◽  
Fruit Thinning ◽  
Agronomic Practices ◽  
Organoleptic Characteristics ◽  
Technological Advances ◽  
Important Trait ◽  
Available Information ◽  
Apple Quality

Apples (Malus domestica Borkh.) represent one of the most produced fruits worldwide, along with citrus and bananas. As high quality is an important trait for the consumer, many studies have focused on the research of new techniques to ensure and preserve the optimal organoleptic characteristics of this fruit. However, despite the huge number of studies on recent technological advances dealing with fruit final quality, less research has focused on the physiological aspects of apple development, including a variety of processes triggered after fertilization, such as photosynthesis, assimilation of carbohydrates, cell division, and cell enlargement, which determine apple final quality. In the present review, we summarize some of the most important changes and mechanisms linked to the primary metabolism of apples, as well as the effect of agronomic practices, such as fruit thinning, as key factors to improve apple quality and meet consumer demands, with the aim of amassing available information and suggesting future directions of research.

scholarly journals Comparative Morphology, Phylogeny, Classification and Evolution of Interstitial Habits in Microcambevine Catfishes (Siluriformes: Trichomycteridae)

Taxonomy ◽  
2021 ◽  
Vol 1 (4) ◽  
pp. 313-344
Author(s):  
Wilson J. E. M. Costa ◽  
Axel M. Katz
Keyword(s):  
Morphological Traits ◽  
Phylogenetic Trees ◽  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Morphological Diversity ◽  
Comparative Morphology ◽  
Morphological Characters ◽  
Morphological Data ◽  
High Level ◽  
Available Information

The Microcambevinae are a catfish subfamily endemic to the Brazilian Atlantic Forest, comprising rare species with interstitial habits. Microcambevines have been classified in two genera, Listrura and Microcambeva, but the relationships among included intrageneric lineages are still poorly understood. The objectives of this study are to conduct a phylogenetic analysis integrating morphological characters and a multigene dataset, and to propose a classification better reflecting morphological diversity and phylogenetic relationships. Phylogenetic analyses combining 57 morphological characters and a 2563 bp molecular dataset generated similar phylogenetic trees with high support values for most clades, including the two genera and some intrageneric groups. Six morphologically distinctive infrageneric lineages, three in Listrura and three in Microcambeva, are classified as subgenera, as well as two new species are described. The morphological diversity here recorded integrated to available information about habitat indicate high level of divergent specialisation among lineages. The analyses indicate a series of convergent morphological traits between Listrura and other teleosts sharing a fossorial lifestyle, as well as specialised traits independently occurring within Listrura lineages. Similarly, a great diversity of morphological traits occurs convergently in Microcambeva lineages and other teleosts sharing psammophilic habits. This study shows that combining molecular and morphological data yields well-supported phylogenies, making possible to unambiguously diagnose clades and to establish evolutionary hypothesis on morphological evolution.

scholarly journals A geography aware reconciliation method to investigate diversification patterns in host/parasite interactions

2017 ◽  
Author(s):  
V. Berry ◽  
F. Chevenet ◽  
J-P. Doyon ◽  
E. Jousselin
Keyword(s):  
Phylogenetic Trees ◽  
Biotic Interactions ◽  
Geographic Information ◽  
Fig Wasp ◽  
Host Shifts ◽  
Host Phylogeny ◽  
Host Parasite ◽  
Reconciliation Method ◽  
Generation Sequencing ◽  
Ancestral Character States

ABSTRACTCospeciation studies aim at investigating whether hosts and symbionts speciate simultaneously or whether the associations diversify through host shifts. This problem is often tackled through reconciliation analyses that map the symbiont phylogeny onto the host phylogeny by mixing different types of diversification events. These reconciliations can be difficult to interpret and not always biologically realistic. Researchers have underlined that the biogeographic histories of both hosts and symbionts influence the probability of cospeciation and host switches, but up to now no reconciliation software integrates geographic data. We present a new functionality in the Mowgli software that bridges this gap. The user can provide geographic information on both the host and symbiont extant and ancestral taxa. Constraints in the reconciliation algorithm have been implemented to generate biologically realistic codiversification scenarios. We apply our method to the fig/fig wasp association and infer diversification scenarios that differ from reconciliations ignoring geographic information. In addition, we updated the reconciliation viewer SylvX in order to visualize ancestral character states on the phylogenetic trees and highlight zones that are geographically inconsistent in reconciliations computed without geographic constraints. We suggest that the comparison of reconciliations obtained with and without constraints can help solving ambiguities in the biogeographic histories of the partners. With the development of robust methods in historical biogeography and the advent of next-generation sequencing that leads to better-resolved trees, a geography aware reconciliation method represents a substantial advance that is likely to be useful to researchers studying the evolution of biotic interactions and biogeography.

scholarly journals Global biotic interactions: An open infrastructure to share and analyze species-interaction datasets

2014 ◽  
Vol 24 ◽  
pp. 148-159 ◽  
Author(s):  
Jorrit H. Poelen ◽  
James D. Simons ◽  
Chris J. Mungall
Keyword(s):  
Biotic Interactions ◽  
Species Interaction

scholarly journals A Nano(publication) Approach Towards Big Data in Biodiversity

2021 ◽  
Vol 5 ◽  
Author(s):  
Mariya Dimitrova ◽  
Teodor Georgiev ◽  
Lyubomir Penev
Keyword(s):  
De Novo ◽  
Biotic Interactions ◽  
Species Interaction ◽  
Automatic Extraction ◽  
Data Generation ◽  
Data Interoperability ◽  
Publication Process ◽  
Related Data ◽  
Biodiversity Knowledge ◽  
Efficient Data

One of the major challenges in biodiversity informatics is the generation of machine-readable data that is interoperable between different biodiversity-related data infrastructures. Producers of such data have to comply with existing standards and to be resourceful enough to enable efficient data generation, management and availability. Conversely, nanopublications offer a decentralised approach (Kuhn et al. 2016) towards achieving data interoperability in a robust and standarized way. A nanopublication is a named RDF graph, which serves to communicate a single fact and its original source (provenance) through the use of identifiers and linked data (Groth et al. 2010). It is composed of three constituent graphs (assertion, provenance, and publication info), which are linked to one another in the nanopublication header (Kuhn et al. 2016). For instance, a nanopublication has been published to assert a species interaction in which a hairy woodpecker (Picoides villosus) ate a beetle (genus Ips), along with the license and related bibliographic citation*1. In biodiversity, nanopublications can be used to exchange information between infrastructures in a standardised way (Fig. 1) and to enable curation and correction of knowledge. They can be implemented within different workflows to formalise biodiversity knowledge in self-enclosed graphs. We have developed several nanopublication models*2 for different biodiversity use cases: species occurrences, new species descriptions, biotic interactions, and links between taxonomy, sequences and institutions. Nanopublications can be generated by various means: semi-automatic extraction from the published literature with a consequent human curation and publication; generation during the publication process by the authors via dedicated formalisation tool and published together with the article; de novo generation of a nanopublication through decentralised networks such as Nanobench (Kuhn et al. 2021). semi-automatic extraction from the published literature with a consequent human curation and publication; generation during the publication process by the authors via dedicated formalisation tool and published together with the article; de novo generation of a nanopublication through decentralised networks such as Nanobench (Kuhn et al. 2021). One of the possible uses of nanopublications in biodiversity is communicating new information in a standardised way so that it can be accessed and interpreted by multiple infrastructures that have a common agreement on how information is expressed through the use of particular ontologies, vocabularies and sets of identifiers. In addition, we envision nanopublications to be useful for curation or peer-review of published knowledge by enabling any researcher to publish a nanopublication containing a comment of an assertion made in a previously published nanopublication. With this talk, we aim to showcase several nanopublication formats for biodiversity and to discuss the possible applications of nanopublications in the biodiversity domain.

scholarly journals Making Parasite-Host Associations Visible using Global Biotic Interactions

2020 ◽  
Vol 4 ◽  
Author(s):  
Katja Seltmann ◽  
Jorrit Poelen ◽  
Kathryn Sullivan ◽  
Jennifer Zaspel
Keyword(s):  
Grey Literature ◽  
Specific Interaction ◽  
Biotic Interactions ◽  
Species Interaction ◽  
Emergent Properties ◽  
Scientific Publications ◽  
Data Archives ◽  
Collection Data ◽  
Association Data ◽  
Occurrence Records

A wealth of information about how parasites interact with their hosts already exists in collections, scientific publications, specialized databases, and grey literature. The US National Science Foundation-funded Terrestrial Parasite Tracker Thematic Collection Network (TPT) project began in 2019 to help build a comprehensive picture of arthropod ectoparasites including the evolution of these parasite-host biotic associations, distributions, and the ecological interactions of disease vectors. TPT is a network of biodiversity collections whose data can assist scientists, educators, land managers, and policymakers to better understand the complex relationship between hosts and parasites including emergent properties that may explain the causes and frequency of human and wildlife pathogens. TPT member collections make their association information easier to access via Global Biotic Interactions (GloBI, Poelen et al. 2014), which is periodically archived through Zenodo to track progress in the TPT project. TPT leverages GloBI's ability to index biotic associations from specimen occurrence records that come from existing management systems (e.g., Arctos, Symbiota, EMu, Excel, MS Access) to avoid having to completely rework existing, or build new, cyber-infrastructures before collections can share data. TPT-affiliated collection managers use collection-specific translation tables to connect their verbatim (or original) terms used to describe associations (e.g., "ex", "found on", "host") to their interpreted, machine-readable terms in the OBO Relations Ontology (RO). These interpreted terms enable searches across previously siloed association record sets, while the original verbatim values remain accessible to help retain provenance and allow for interpretation improvements. TPT is an ambitious project, with the goal to database label data from over 1.2 million specimens of arthropod parasites of vertebrates coming from 22 collections across North America. In the first year of the project, the TPT collections created over 73,700 new records and 41,984 images. In addition, 17 TPT data providers and three other collaborators shared datasets that are now indexed by GloBI, visible on the TPT GloBI project page. These datasets came from collection specimen occurrence records and literature sources. Two TPT data archives that capture and preserve the changes in the data coming from TPT to GloBI were published through Zenodo (Poelen et al. 2020a, Poelen et al. 2020b). The archives document the changes in how data are shared by collections including the biotic association data format and quantity of data captured. The Poelen et al. 2020b report included all TPT collections and biotic interactions from Arctos collections in VertNet and the Symbiota Collection of Arthropods Network (SCAN). The total number of interactions included in this report was 376,671 records (500,000 interactions is the overall goal for TPT). In addition, close coordination with TPT collection data managers including many one-on-one conversations, a workshop, and a webinar (Sullivan et al. 2020) was conducted to help guide the data capture of biotic associations. GloBI is an effective tool to help integrate biotic association data coming from occurrence records into an openly accessible, global, linked view of existing species interaction records. The results gleaned from the TPT workshop and Zenodo data archives demonstrate that minimizing changes to existing workflows allow for custom interpretation of collection-specific interaction terms. In addition, including collection data managers in the development of the interaction term vocabularies is an important part of the process that may improve data sharing and the overall downstream data quality.

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