scholarly journals The interaction of phylogeny and community structure: linking clades’ ecological structures and trait evolution

2018 ◽  
Author(s):  
William D. Pearse ◽  
Pierre Legendre ◽  
Pedro Peres-Neto ◽  
T. Jonathan Davies
Keyword(s):  
Evolutionary History ◽  
Species Traits ◽  
Phylogenetic Structure ◽  
Trait Evolution ◽  
Independent Evidence ◽  
Phylogenetic Studies ◽  
Species Trait ◽  
Ecological Patterns ◽  
Evolutionary Trajectories ◽  
Species Evolution

1AbstractAimCommunity phylogenetic studies use information about species’ evolutionary relationships to understand the processes of community ecological assembly. A central premise of the field is that species’ evolution maps onto ecological patterns, and phylogeny reveals something more than species’ traits alone. We argue, therefore, that there is a need to better understand and model the interaction of phylogeny with species’ traits and community composition.InnovationWe outline a new method that identifies clades with unusual ecological structures, based around partitioning the variation of species’ site occupancies (β-diversity). Eco-phylogenetic theory would predict that these clades should also demonstrate distinct evolutionary trajectories. We suggest that modelling the evolution of independent trait data in these clades represents a strong test of whether there is an association between species’ ecological structure and evolutionary history.Main conclusionsUsing an empirical dataset of mammals from around the world, we identify two clades of rodents that tend not to co-occur (are phylogenetically overdispersed), and then find independent evidence of slower rates of body mass evolution in these clades. We suggest that our approach, which assumes nothing about the mode of species’ trait evolution but rather seeks to explain it using ecological information, presents a new way to examine eco-phylogenetic structure.

scholarly journals Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution

Diversity ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 70 ◽  
Author(s):  
Juan C. Garcia-R ◽  
Emily Moriarty Lemmon ◽  
Alan R. Lemmon ◽  
Nigel French
Keyword(s):  
Evolutionary History ◽  
State Of The Art ◽  
Molecular Techniques ◽  
Evolutionary Significance ◽  
Phylogenetic Structure ◽  
Bayesian Approaches ◽  
Phylogenetic Studies ◽  
Anchored Phylogenomics ◽  
History Of ◽  
Phylogenomic Analyses

The integration of state-of-the-art molecular techniques and analyses, together with a broad taxonomic sampling, can provide new insights into bird interrelationships and divergence. Despite their evolutionary significance, the relationships among several rail lineages remain unresolved as does the general timescale of rail evolution. Here, we disentangle the deep phylogenetic structure of rails using anchored phylogenomics. We analysed a set of 393 loci from 63 species, representing approximately 40% of the extant familial diversity. Our phylogenomic analyses reconstruct the phylogeny of rails and robustly infer several previously contentious relationships. Concatenated maximum likelihood and coalescent species-tree approaches recover identical topologies with strong node support. The results are concordant with previous phylogenetic studies using small DNA datasets, but they also supply an additional resolution. Our dating analysis provides contrasting divergence times using fossils and Bayesian and non-Bayesian approaches. Our study refines the evolutionary history of rails, offering a foundation for future evolutionary studies of birds.

Akamboja gen. nov., a new genus of railroad-worm beetle endemic to the Atlantic Rainforest, with five new species (Coleoptera: Phengodidae, Mastinocerinae)

Zootaxa ◽  
2017 ◽  
Vol 4306 (4) ◽  
pp. 501 ◽  
Author(s):  
ANDRÉ SILVA ROZA ◽  
HINGRID YARA SOUZA QUINTINO ◽  
JOSÉ RICARDO MIRAS MERMUDES ◽  
LUIZ FELIPE LIMA DA SILVEIRA
Keyword(s):  
New Species ◽  
Evolutionary History ◽  
New Genus ◽  
Landscape Heterogeneity ◽  
Atlantic Rainforest ◽  
Disjunct Distribution ◽  
Key To Species ◽  
Diagnostic Features ◽  
Mountain Ranges ◽  
Phylogenetic Studies

The Atlantic Rainforest is a hotspot of biodiversity, housing several endemic species. Environmental stasis through broad time scales, vast latitudinal extension and landscape heterogeneity are thought to contribute in explaining the greater species richness of this biome. Unfortunately, it is threatened mainly due to anthropic-driven habitat loss. Ectotherms of low-mobility, such as tropical, small soft-bodied railroad-worms, may be especially threatened by anthropogenic climate changes. Many of such species have narrow climatic niches and therefore might become extinct before we know them. Here we describe a new genus endemic of the Atlantic Rainforest mountain ranges, and five spatially disjunct new species. Akamboja gen. nov. is unique by its ten-segmented antenna, IV to VIII with two short symmetrical branches, branches of antennomere IX fused in a singular flabellum, slightly depressed medially; elytron short, surpassing the second to fourth abdominal segment (depending on species); first tarsomere of anterior leg with a ventral comb; claws with six long and asymmetrical teeth; aedeagus with patch of bristles at paramere apex. We provide a key to species as well as illustrations for the diagnostic features. We highlight that Akamboja cleidae sp. nov., as defined here, has a disjunct distribution and its populations are surrounded by an unsuitable environmental matrix, thus are probably reproductively isolated. Future phylogenetic studies should address the evolutionary history and delimitation of this taxon. We also provide a key to genera of Mastinocerinae with ten antennomeres, including Akamboja gen. nov. 

scholarly journals A global database for metacommunity ecology, integrating species, traits, environment and space

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Alienor Jeliazkov ◽  
Darko Mijatovic ◽  
Stéphane Chantepie ◽  
Nigel Andrew ◽  
Raphaël Arlettaz ◽  
...  
Keyword(s):  
Environmental Variables ◽  
Environmental Changes ◽  
Spatial Scales ◽  
Species Traits ◽  
Global Database ◽  
Metacommunity Ecology ◽  
Species Trait ◽  
Spatial Coordinates ◽  
Taxonomic Groups ◽  
Case Basis

AbstractThe use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology.

scholarly journals tRNA functional signatures classify plastids as late-branching cyanobacteria

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Travis J Lawrence ◽  
Katherine CH Amrine ◽  
Wesley D Swingley ◽  
David H Ardell
Keyword(s):  
Machine Learning ◽  
Trna Gene ◽  
Learning Algorithm ◽  
Oxygenic Photosynthesis ◽  
Evolutionary Models ◽  
Independent Evidence ◽  
Phylogenetic Studies ◽  
Plastid Genomes ◽  
Unbalanced Sampling

Abstract Background Eukaryotes acquired the trait of oxygenic photosynthesis through endosymbiosis of the cyanobacterial progenitor of plastid organelles. Despite recent advances in the phylogenomics of Cyanobacteria, the phylogenetic root of plastids remains controversial. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies are contradictory on whether plastids branch early or late within Cyanobacteria. One underlying cause may be poor fit of evolutionary models to complex phylogenomic data. Results Using Posterior Predictive Analysis, we show that recently applied evolutionary models poorly fit three phylogenomic datasets curated from cyanobacteria and plastid genomes because of heterogeneities in both substitution processes across sites and of compositions across lineages. To circumvent these sources of bias, we developed CYANO-MLP, a machine learning algorithm that consistently and accurately phylogenetically classifies (“phyloclassifies”) cyanobacterial genomes to their clade of origin based on bioinformatically predicted function-informative features in tRNA gene complements. Classification of cyanobacterial genomes with CYANO-MLP is accurate and robust to deletion of clades, unbalanced sampling, and compositional heterogeneity in input tRNA data. CYANO-MLP consistently classifies plastid genomes into a late-branching cyanobacterial sub-clade containing single-cell, starch-producing, nitrogen-fixing ecotypes, consistent with metabolic and gene transfer data. Conclusions Phylogenomic data of cyanobacteria and plastids exhibit both site-process heterogeneities and compositional heterogeneities across lineages. These aspects of the data require careful modeling to avoid bias in phylogenomic estimation. Furthermore, we show that amino acid recoding strategies may be insufficient to mitigate bias from compositional heterogeneities. However, the combination of our novel tRNA-specific strategy with machine learning in CYANO-MLP appears robust to these sources of bias with high accuracy in phyloclassification of cyanobacterial genomes. CYANO-MLP consistently classifies plastids as late-branching Cyanobacteria, consistent with independent evidence from signature-based approaches and some previous phylogenetic studies.

ESTIMATION OF TIME OF DIVERGENCE FROM PHYLOGENETIC STUDIES

1977 ◽  
Vol 19 (2) ◽  
pp. 217-223 ◽  
Author(s):  
Ranajit Chakraborty
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
Amino Acid Sequences ◽  
Evolutionary Significance ◽  
Simultaneous Estimation ◽  
Homologous Proteins ◽  
Phylogenetic Structure ◽  
Phylogenetic Studies ◽  
Base Sequences ◽  
Time Of Divergence

Recent studies with comparative data on base sequences of homologous DNAs or amino acid sequences of homologous proteins indicate that simultaneous estimation of phylogenetic structure and time of divergence is often cumbersome and time consuming. On the other hand, when the topology of an evolutionary tree is known, it is shown in this paper that the least squares theory may be applied to obtain simple estimates of the relative time lengths for each segment of the tree under the assumption of uniform random substitutions in each segment. The method is illustrated with amino acid sequence data on various globin molecules and cytochrome c. The evolutionary significance of some of the estimates is also discussed.

scholarly journals Evolution of Courtship Songs in Xenopus: Vocal Pattern Generation and Sound Production

2015 ◽  
Vol 145 (3-4) ◽  
pp. 302-314 ◽  
Author(s):  
Elizabeth C. Leininger ◽  
Darcy B. Kelley
Keyword(s):  
Sex Differences ◽  
Evolutionary History ◽  
Molecular Mechanisms ◽  
Sound Production ◽  
Pattern Generation ◽  
Model Species ◽  
Extant Species ◽  
Evolutionary Trajectories ◽  
Strong Candidate ◽  
Species Specific

The extant species of African clawed frogs (Xenopus and Silurana) provide an opportunity to link the evolution of vocal characters to changes in the responsible cellular and molecular mechanisms. In this review, we integrate several robust lines of research: evolutionary trajectories of Xenopus vocalizations, cellular and circuit-level mechanisms of vocalization in selected Xenopus model species, and Xenopus evolutionary history and speciation mechanisms. Integrating recent findings allows us to generate and test specific hypotheses about the evolution of Xenopus vocal circuits. We propose that reduced vocal sex differences in some Xenopus species result from species-specific losses of sexually differentiated neural and neuromuscular features. Modification of sex-hormone-regulated developmental mechanisms is a strong candidate mechanism for reduced vocal sex differences.

scholarly journals The roles of standing genetic variation and evolutionary history in determining the evolvability of anti-predator strategies

2014 ◽  
Author(s):  
Jordan Fish ◽  
Daniel R O'Donnell ◽  
Abhijna Parigi ◽  
Ian Dworkin ◽  
Aaron P Wagner
Keyword(s):  
Genetic Variation ◽  
Evolutionary History ◽  
Relative Importance ◽  
Digital Evolution ◽  
Relative Ease ◽  
Evolutionary Response ◽  
Two Factors ◽  
The Face ◽  
Evolutionary Trajectories ◽  
Different Levels

Standing genetic variation and the historical environment in which that variation arises (evolutionary history) are both potentially significant determinants of a population’s capacity for evolutionary response to a changing environment. We evaluated the relative importance of these two factors in influencing the evolutionary trajectories in the face of sudden environmental change. We used the open-ended digital evolution software Avida to examine how historic exposure to predation pressures, different levels of genetic variation, and combinations of the two, impact anti-predator strategies and competitive abilities evolved in the face of threats from new, invasive, predator populations. We show that while standing genetic variation plays some role in determining evolutionary responses, evolutionary history has the greater influence on a population’s capacity to evolve effective anti-predator traits. This adaptability likely reflects the relative ease of repurposing existing, relevant genes and traits, and the broader potential value of the generation and maintenance of adaptively flexible traits in evolving populations.

scholarly journals A modeling platform for the simultaneous emergence of ecological patterns

2017 ◽  
Author(s):  
Kenneth J Locey ◽  
Jay T. Lennon
Keyword(s):  
Species Traits ◽  
Basic Principles ◽  
Ecological Selection ◽  
Resource Limited ◽  
Trade Offs ◽  
Individual Based Models ◽  
Holistic Understanding ◽  
Simulation Based ◽  
Ecological Patterns ◽  
Starting Conditions

Patterns underpin ecological theories and paradigms. While over a dozen ecological patterns are considered to be classic or even law-like, most are divided among non-overlapping theories and subfields. As a result, ecology lacks a holistic understanding for how primary patterns can emerge in unison. We developed a simulation-based platform for this purpose. The Emergence platform encodes energetic costs, ecological selection, stochasticity, and multiplicative interactions. These phenomena capture the basis of life history trade-offs, resource-limited growth, the importance of stochasticity and determinism, and the nonlinear nature of ecological dynamics. Emergence builds individual-based models from random starting conditions and allows ecological selection to operate on random variation in species traits. Emergence generates established patterns of commonness and rarity, scaling patterns from metabolic theory and biodiversity theory, growth and abundance patterns of population ecology. Our platform reveals that iconic ecological patterns that span paradigms, theories, and sub-disciplines can simultaneously emerge from random starting conditions when basic principles are observed.

scholarly journals Ecological Insights from the Evolutionary History of Microbial Innovations

2017 ◽  
Author(s):  
Mario E. Muscarella ◽  
James P. O’Dwyer
Keyword(s):  
Evolutionary History ◽  
Selective Advantage ◽  
Ecological Function ◽  
Transition Rates ◽  
Independent Evidence ◽  
Resource Degradation ◽  
A Genome ◽  
Evolutionary Relatedness ◽  
History Of ◽  
Open Question

Bacteria and Archaea represent the base of the evolutionary tree of life and contain the vast majority of phylogenetic and functional diversity. Because these organisms and their traits directly impact ecosystems and human health, a focus on functional traits has become increasingly common in microbial ecology. These trait-based approaches have the potential to link microbial communities and their ecological function. But an open question is how, why, and in what order microorganisms acquired the traits we observe in the present day. To address this, we reconstructed the evolutionary history of microbial traits using genomic data to understand the evolution, selective advantage, and similarity of traits in extant organisms and provide insights into the composition of genomes and communities. We used the geological timeline and physiological expectations to provide independent evidence in support of this evolutionary history. Using this reconstructed evolutionary history, we explored hypotheses related to the composition of genomes. We showed that gene transition rates can be used to make predictions about the size and type of genes in a genome: generalist genomes comprise many evolutionarily labile genes while specialist genomes comprise more highly conserved functional genes. These findings suggest that generalist organisms do not build up and hoard an array of functions, but rather tend to experiment with functions related to environmental sensing, transport, and complex resource degradation. Our results provide a framework for understanding the evolutionary history of extant microorganisms, the origin and maintenanceof traits, and linking evolutionary relatedness and ecological function.

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