scholarly journals The impacts of drift and selection on genomic evolution in insects

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3241 ◽  
Author(s):  
K. Jun Tong ◽  
Sebastián Duchêne ◽  
Nathan Lo ◽  
Simon Y.W. Ho
Keyword(s):  
Gene Tree ◽  
Evolutionary Process ◽  
Branch Length ◽  
Rate Variation ◽  
Gene Trees ◽  
Genomic Evolution ◽  
Genomic Dataset ◽  
Phylogenetic Methods ◽  
Strong Negative Selection ◽  
Shed Light

Genomes evolve through a combination of mutation, drift, and selection, all of which act heterogeneously across genes and lineages. This leads to differences in branch-length patterns among gene trees. Genes that yield trees with the same branch-length patterns can be grouped together into clusters. Here, we propose a novel phylogenetic approach to explain the factors that influence the number and distribution of these gene-tree clusters. We apply our method to a genomic dataset from insects, an ancient and diverse group of organisms. We find some evidence that when drift is the dominant evolutionary process, each cluster tends to contain a large number of fast-evolving genes. In contrast, strong negative selection leads to many distinct clusters, each of which contains only a few slow-evolving genes. Our work, although preliminary in nature, illustrates the use of phylogenetic methods to shed light on the factors driving rate variation in genomic evolution.

scholarly journals The impacts of drift and selection on genomic evolution in holometabolous insects

2016 ◽  
Author(s):  
K. Jun Tong ◽  
Sebastián Duchêne ◽  
Nathan Lo ◽  
Simon Y. W. Ho
Keyword(s):  
Negative Selection ◽  
Evolutionary Rate ◽  
Evolutionary Process ◽  
Rate Variation ◽  
Diverse Group ◽  
Relative Importance ◽  
Genomic Evolution ◽  
Rate Heterogeneity ◽  
Genomic Dataset ◽  
Strong Negative Selection

AbstractGenomes evolve through a medley of mutation, drift, and selection, all of which act heterogeneously across genes and lineages. The pacemaker models of genomic evolution describe the resulting patterns of evolutionary rate variation: genes that are governed by the same pacemaker exhibit the same pattern of rate heterogeneity across lineages. However, the relative importance of drift and selection in determining the structure of these pacemakers is unknown. Here, we propose a novel phylogenetic approach to explain the formation of pacemakers. We apply this method to a genomic dataset from holometabolous insects, an ancient and diverse group of organisms. We show that when drift is the dominant evolutionary process, each pacemaker tends to govern a large number of fast-evolving genes. In contrast, strong negative selection leads to many distinct pacemakers, each of which governs a few slow-evolving genes. Our results provide new insights into the interplay between drift and selection in driving genomic evolution.

scholarly journals SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees

2015 ◽  
Author(s):  
Diego Mallo ◽  
Leonardo de Oliveira Martins ◽  
David Posada
Keyword(s):  
Incomplete Lineage Sorting ◽  
A Priori ◽  
Gene Tree ◽  
Gene Families ◽  
Rate Variation ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Sequence Alignments ◽  
Large Trees

We present here a fast and flexible software–SimPhy–for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to the species tree/gene tree discordance—and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, pre-compiled executables, a detailed manual and example cases.

scholarly journals Integrated Likelihood for Phylogenomics under a No-Common-Mechanism Model

2018 ◽  
Author(s):  
Hunter Tidwell ◽  
Luay Nakhleh
Keyword(s):  
Sequence Data ◽  
Gene Tree ◽  
Branch Length ◽  
Biological Data ◽  
Common Mechanism ◽  
Sequence Evolution ◽  
Gene Trees ◽  
Species Trees ◽  
Integrated Likelihood ◽  
Species Phylogeny

The availability of genome-wide sequence data from a large number of species as well as data from multiple individuals within a species has ushered in the era of phylogenomics. In this era, species phylogeny inference is based on models of sequence evolution on gene trees as well as models of gene tree evolution within the branches of species phylogenies. Parsimony, likelihood, Bayesian, and distance methods have been introduced for species phylogeny inference based on such models. All methods, except for the parsimony ones, assume a common mechanism across all loci as captured by a single value of each branch length of the species phylogeny. In this paper, we propose a ``no common mechanism" (NCM) model, where every gene tree evolves according to its own parameters of the species phylogeny. An analogous model was proposed and explored, both mathematically and experimentally, for sites, or characters, in a sequence alignment in the context of the classical phylogeny problem. For example, a famous equivalence between the maximum parsimony and maximum likelihood phylogeny estimates was established under certain NCM models by Tuffley and Steel. Here we derive an analytically integrated likelihood of both species trees and networks given the gene trees of multiple loci under an NCM model. We demonstrate the performance of inference under this integrated likelihood on both simulated and biological data. The model presented here will afford opportunities for exploring connections among various methods for estimating species phylogenies from multiple, independent loci.

scholarly journals Phylogenomic assessment of the role of hybridization and introgression in trait evolution

2020 ◽  
Author(s):  
Yaxuan Wang ◽  
Zhen Cao ◽  
Huw A. Ogilvie ◽  
Luay Nakhleh
Keyword(s):  
Gene Tree ◽  
Evolutionary Process ◽  
Species Tree ◽  
Biological Data ◽  
Gene Trees ◽  
Data Set ◽  
Trait Evolution ◽  
Branching Patterns ◽  
Hybridization And Introgression

AbstractTrait evolution in a set of species—a central theme in evolutionary biology—has long been understood and analyzed with respect to a species tree. However, the field of phylogenomics, which has been propelled by advances in sequencing technologies, has ushered in the era of species/gene tree incongruence and, consequently, a more nuanced understanding of trait evolution. For a trait whose states are incongruent with the branching patterns in the species tree, the same state could have arisen independently in different species (homoplasy) or followed the branching patterns of gene trees, rather than the species tree (hemiplasy). Recent work by Guerrero and Hahn (PNAS 115:12787-12792, 2018) provided a significant step towards teasing apart the roles of homoplasy and hemiplasy in trait evolution by analyzing it with respect to the species tree and the gene trees within its branches.Another evolutionary process whose extent and significance are better revealed by phylogenomic studies is hybridization between different species. In this work, we present a phylogenomic method for assessing the role of hybridization and introgression in the evolution of bi-allelic traits, including polymorphic ones. We apply the method to simulated evolutionary scenarios to demonstrate the interplay between the parameters of the evolutionary history and the role of introgression in a trait’s evolution (which we call xenoplasy). Very importantly, we demonstrate, including on a biological data set, that inferring a species tree and using it for trait evolution analysis when hybridization had occurred could provide misleading hypotheses about trait evolution.

scholarly journals Linking Branch Lengths Across Loci Provides the Best Fit for Phylogenetic Inference

2018 ◽  
Author(s):  
David A. Duchêne ◽  
K. Jun Tong ◽  
Charles S. P. Foster ◽  
Sebastián Duchêne ◽  
Robert Lanfear ◽  
...  
Keyword(s):  
Gene Tree ◽  
Branch Length ◽  
Phylogenetic Inference ◽  
Data Sets ◽  
Length Variation ◽  
Gene Trees ◽  
Data Set ◽  
Branch Lengths ◽  
Future Work ◽  
Best Fit

AbstractEvolution leaves heterogeneous patterns of nucleotide variation across the genome, with different loci subject to varying degrees of mutation, selection, and drift. Appropriately modelling this heterogeneity is important for reliable phylogenetic inference. One modelling approach in statistical phylogenetics is to apply independent models of molecular evolution to different groups of sites, where the groups are usually defined by locus, codon position, or combinations of the two. The potential impacts of partitioning data for the assignment of substitution models are well appreciated. Meanwhile, the treatment of branch lengths has received far less attention. In this study, we examined the effects of linking and unlinking branch-length parameters across loci. By analysing a range of empirical data sets, we find that the best-fitting model for phylogenetic inference is consistently one in which branch lengths are proportionally linked: gene trees have the same pattern of branch-length variation, but with varying absolute tree lengths. This model provided a substantially better fit than those that either assumed identical branch lengths across gene trees or that allowed each gene tree to have its own distinct set of branch lengths. Using simulations, we show that the fit of the three different models of branch lengths varies with the length of the sequence alignment and with the number of taxa in the data set. Our findings suggest that a model with proportionally linked branch lengths across loci is likely to provide the best fit under the conditions that are most commonly seen in practice. In future work, improvements in fit might be afforded by models with levels of complexity intermediate to proportional and free branch lengths. The results of our study have implications for model selection, computational efficiency, and experimental design in phylogenomics.

scholarly journals Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1645-1656 ◽  
Author(s):  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Dna Sequences ◽  
Gene Tree ◽  
Species Tree ◽  
Bayes Estimation ◽  
Ancestral Population ◽  
Divergence Times ◽  
Gene Trees ◽  
Species Divergence ◽  
Multiple Loci ◽  
Population Sizes

Abstract The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be ∼20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.

scholarly journals Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere

2020 ◽  
Author(s):  
Fernando Lopes ◽  
Larissa R Oliveira ◽  
Amanda Kessler ◽  
Yago Beux ◽  
Enrique Crespo ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Molecular Data ◽  
Species Tree ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Data Types ◽  
High Coverage ◽  
Sea Lions ◽  
The Family

Abstract The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 to 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be non-monophyletic, with California (Z. californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Z. wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family.

scholarly journals Application of Biomimetics to Architectural and Urban Design: A Review across Scales

2020 ◽  
Vol 12 (23) ◽  
pp. 9813 ◽  
Author(s):  
Yuta Uchiyama ◽  
Eduardo Blanco ◽  
Ryo Kohsaka
Keyword(s):  
Urban Design ◽  
Architectural Design ◽  
Evolutionary Process ◽  
Future Research ◽  
Conceptual Level ◽  
Sustainable Society ◽  
Types Of Knowledge ◽  
The Social ◽  
Different Types ◽  
Shed Light

Application of biomimetics has expanded progressively to other fields in recent years, including urban and architectural design, scaling up from materials to a larger scale. Besides its contribution to design and functionality through a long evolutionary process, the philosophy of biomimetics contributes to a sustainable society at the conceptual level. The aim of this review is to shed light on trends in the application of biomimetics to architectural and urban design, in order to identify potential issues and successes resulting from implementation. In the application of biomimetics to architectural design, parts of individual “organisms”, including their form and surface structure, are frequently mimicked, whereas in urban design, on a larger scale, biomimetics is applied to mimic whole ecosystems. The overall trends of the reviewed research indicate future research necessity in the field of on biomimetic application in architectural and urban design, including Biophilia and Material. As for the scale of the applications, the urban-scale research is limited and it is a promising research which can facilitate the social implementation of biomimetics. As for facilitating methods of applications, it is instrumental to utilize different types of knowledge, such as traditional knowledge, and providing scientific clarification of functions and systems based on reviews. Thus, interdisciplinary research is required additionally to reach such goals.

scholarly journals How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example

2022 ◽  
Vol 12 ◽  
Author(s):  
Martha Kandziora ◽  
Petr Sklenář ◽  
Filip Kolář ◽  
Roswitha Schmickl
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Species Tree ◽  
Secondary Contact ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Phylogenetic Discordance ◽  
Gene Tree Discordance ◽  
High Degree

A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading to gene tree discordance, i.e., not all gene trees represent the species tree. Phylogenetic discordance is common in phylogenomic datasets, and apart from ILS, additional sources include hybridization, whole-genome duplication, and methodological artifacts. Despite a high degree of gene tree discordance, species trees are often well supported and the sources of discordance are not further addressed in phylogenomic studies, which can eventually lead to incorrect phylogenetic hypotheses, especially in rapidly radiating groups. We chose the high-Andean Asteraceae genus Loricaria to shed light on the potential sources of phylogenetic discordance and generated a phylogenetic hypothesis. By accounting for paralogy during gene tree inference, we generated a species tree based on hundreds of nuclear loci, using Hyb-Seq, and a plastome phylogeny obtained from off-target reads during target enrichment. We observed a high degree of gene tree discordance, which we found implausible at first sight, because the genus did not show evidence of hybridization in previous studies. We used various phylogenomic analyses (trees and networks) as well as the D-statistics to test for ILS and hybridization, which we developed into a workflow on how to tackle phylogenetic discordance in recent radiations. We found strong evidence for ILS and hybridization within the genus Loricaria. Low genetic differentiation was evident between species located in different Andean cordilleras, which could be indicative of substantial introgression between populations, promoted during Pleistocene glaciations, when alpine habitats shifted creating opportunities for secondary contact and hybridization.

scholarly journals Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation

Diversity ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 164 ◽  
Author(s):  
Peter Houde ◽  
Edward L. Braun ◽  
Lawrence Zhou
Keyword(s):  
Evolutionary Biology ◽  
Gene Tree ◽  
Difficult Problem ◽  
Gene Trees ◽  
Effective Population ◽  
Deep Time ◽  
Ecological Release ◽  
Population Sizes ◽  
Demographic Inference ◽  
Gene Tree Discordance

Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction.

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