scholarly journals A69 Phylodynamics of language evolution

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
K Hoffmann ◽  
D Kühnert
Keyword(s):  
Phylogenetic Trees ◽  
Language Evolution ◽  
Death Process ◽  
Divergence Times ◽  
Evolutionary Analysis ◽  
Informative Priors ◽  
Bayes Formula ◽  
Shared Ancestry ◽  
Available Information ◽  
Binary Strings

Abstract We used Bayesian evolutionary analysis to study linguistic data and infer phylogenetic trees of language evolution. Languages were encoded as binary strings indicating the presence or absence of members of cognate classes, the equivalence of classes of words with similar meaning, and shared ancestry. These strings formed the alignment data used to compute the posterior likelihood of a tree with respect to Bayes’ formula. Informative priors are crucial for testing hypotheses regarding the age of common ancestry and divergence times and should include as much available information as possible. Here, we investigated the birth–death process as a method to construct tree priors specifically suitable for modeling the evolution of cognate data. To test these models, we will use a dataset of the languages from Vanuatu, an island nation featuring world’s highest language density.

Identification and molecular evolution of new dynein-like protein sequences in rat brain

1995 ◽  
Vol 108 (5) ◽  
pp. 1883-1893 ◽  
Author(s):  
Y. Tanaka ◽  
Z. Zhang ◽  
N. Hirokawa
Keyword(s):  
Rat Brain ◽  
Heavy Chain ◽  
Phylogenetic Trees ◽  
Cytoplasmic Dynein ◽  
Amino Acid Sequences ◽  
Adult Brain ◽  
Chain Gene ◽  
Evolutionary Analysis ◽  
Degenerate Primers ◽  
Dynein Heavy Chain

RT-PCR cloning was performed to find unknown members of the dynein superfamily expressed in rat brain. Six kinds of degenerate primers designed for the dynein catalytic domain consensuses were used for extensive PCR amplifications. We have sequenced 550 plasmid clones which turned out to include 13 kinds of new dynein-like sequences (DLP1-8, 9A/B, 10–12) and cytoplasmic dynein heavy chain. In these clones, alternative splicing was detected for a 105 nt-domain containing the CFDEFNRI consensus just downstream of the most N-terminal P-loop (DLP9A and 9B). By using these obtained sequences, initial hybridization studies were performed. Genomic Southern blotting showed each sequence corresponds to a single copy of the gene, while northern blotting of adult brain presented more than one band for some subtypes. We further accomplished molecular evolutionary analysis to recognize their phylogenetic origins for the axonemal and non-axonemal (cytoplasmic) functions. Different methods (UPGMA, NJ and MP) presented well coincident phylogenetic trees from 44 partial amino acid sequences of dynein heavy chain from various eukaryotes. The trunk for all the cytoplasmic dynein heavy chain homologues diverged directly from the root of the phylogenetic tree, suggesting that the first dynein gene duplication defined two distinct functions as respective subfamilies. Of particular interest, we found a duplication event of the cytoplasmic dynein heavy chain gene giving rise to another subtype, DLP4, located between the divergence of yeast and that of Dictyostelium. Such evolutionary topology builds up an inceptive hypothesis that there are at least two non-axonemal dynein heavy chains in mammals.

scholarly journals Simultaneous Bayesian inference of phylogeny and molecular coevolution

2019 ◽  
Vol 116 (11) ◽  
pp. 5027-5036 ◽  
Author(s):  
Xavier Meyer ◽  
Linda Dib ◽  
Daniele Silvestro ◽  
Nicolas Salamin
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Organic Molecules ◽  
Evolutionary Process ◽  
Protein Coding ◽  
Rrna Molecule ◽  
Shared Ancestry ◽  
History Of ◽  
Dependent Site ◽  
Synthetic Datasets

Patterns of molecular coevolution can reveal structural and functional constraints within or among organic molecules. These patterns are better understood when considering the underlying evolutionary process, which enables us to disentangle the signal of the dependent evolution of sites (coevolution) from the effects of shared ancestry of genes. Conversely, disregarding the dependent evolution of sites when studying the history of genes negatively impacts the accuracy of the inferred phylogenetic trees. Although molecular coevolution and phylogenetic history are interdependent, analyses of the two processes are conducted separately, a choice dictated by computational convenience, but at the expense of accuracy. We present a Bayesian method and associated software to infer how many and which sites of an alignment evolve according to an independent or a pairwise dependent evolutionary process, and to simultaneously estimate the phylogenetic relationships among sequences. We validate our method on synthetic datasets and challenge our predictions of coevolution on the 16S rRNA molecule by comparing them with its known molecular structure. Finally, we assess the accuracy of phylogenetic trees inferred under the assumption of independence among sites using synthetic datasets, the 16S rRNA molecule and 10 additional alignments of protein-coding genes of eukaryotes. Our results demonstrate that inferring phylogenetic trees while accounting for dependent site evolution significantly impacts the estimates of the phylogeny and the evolutionary process.

scholarly journals Biosystematic study of the genus Lallemantia (Lamiaceae): species delimitation and relationship

2020 ◽  
Vol 63 (2) ◽  
pp. 157-168
Author(s):  
Fahimeh Koohdar ◽  
Masoud Sheidai
Keyword(s):  
Phylogenetic Trees ◽  
Molecular Study ◽  
Morphological Characters ◽  
Issr Markers ◽  
Evolutionary Analysis ◽  
Species Relationship ◽  
Beast Analysis ◽  
Cpdna Markers ◽  
Components Analysis ◽  
Relationship Of

Lallemantia (Lamiaceae) is a small genus with 5 species. In general, little biosystematics and molecular study has been performed on the genus Lallemantia. Moreover, the studies used only some of the species; none of them has considered all 5 species as a whole in one specific approach. Therefore, the species inter-relationship or nexus in the genus is not thoroughly probed. The present study investigated the molecular phylogeny and species relationship of all five species in the genus Lallemantia, using ribosomal protein L16 and the multilocus ISSR markers. It also compared their morphometric, anatomical and seed results. The species were efficaciously delimited by the morphological, anatomical and seed characters, as well as by ISSR and cpDNA markers. The PCA (Principal components analysis) plot of the species based upon the morphological characters, the MDS (Multidimensional Scaling) plot of the species based on the nutlet and anatomical characters, the NJ (neighbor joining) tree plot of ISSR dataand the ML tree of cpDNA revealed closer affinity between L. iberica and L. canescens and L. peltata was placed at some distance from these species. The phylogenetic trees displayed monophyly of the genus Lallemantia. The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) analysis unveiled that the studied Lallemantia species started to diverge about 25 million years ago.

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 Notes on the birth–death prior with fossil calibrations for Bayesian estimation of species divergence times

2016 ◽  
Vol 371 (1699) ◽  
pp. 20150128 ◽  
Author(s):  
Mario dos Reis
Keyword(s):  
Conditional Density ◽  
Death Process ◽  
Divergence Times ◽  
Large Set ◽  
Sources Of Information ◽  
Fossil Calibration ◽  
The Times ◽  
The Moment ◽  
Different Sources ◽  
Birth Death

Constructing a multi-dimensional prior on the times of divergence (the node ages) of species in a phylogeny is not a trivial task, in particular, if the prior density is the result of combining different sources of information such as a speciation process with fossil calibration densities. Yang & Rannala (2006 Mol. Biol. Evol . 23, 212–226. ( doi:10.1093/molbev/msj024 )) laid out the general approach to combine the birth–death process with arbitrary fossil-based densities to construct a prior on divergence times. They achieved this by calculating the density of node ages without calibrations conditioned on the ages of the calibrated nodes. Here, I show that the conditional density obtained by Yang & Rannala is misspecified. The misspecified density can sometimes be quite strange-looking and can lead to unintentionally informative priors on node ages without fossil calibrations. I derive the correct density and provide a few illustrative examples. Calculation of the density involves a sum over a large set of labelled histories, and so obtaining the density in a computer program seems hard at the moment. A general algorithm that may provide a way forward is given. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

scholarly journals Genetic Diversity and Evolution of Bradyrhizobium Populations Nodulating Erythrophleum fordii, an Evergreen Tree Indigenous to the Southern Subtropical Region of China

2014 ◽  
Vol 80 (19) ◽  
pp. 6184-6194 ◽  
Author(s):  
Yao Yao ◽  
Rui Wang ◽  
Jun Kun Lu ◽  
Xin Hua Sui ◽  
En Tao Wang ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Root Nodules ◽  
Rflp Analysis ◽  
Divergent Evolution ◽  
Evolutionary Analysis ◽  
Subtropical Region ◽  
Content Type ◽  
Evergreen Tree ◽  
Intergenic Sequences ◽  
Erythrophleum Fordii

ABSTRACTThe nodulation ofErythrophleum fordiihas been recorded recently, but its microsymbionts have never been studied. To investigate the diversity and biogeography of rhizobia associated with this leguminous evergreen tree, root nodules were collected from the southern subtropical region of China. A total of 166 bacterial isolates were obtained from the nodules and characterized. In a PCR-based restriction fragment length polymorphism (RFLP) analysis of ribosomal intergenic sequences, the isolates were classified into 22 types within the genusBradyrhizobium. Sequence analysis of 16S rRNA, ribosomal intergenic spacer (IGS), and the housekeeping genesrecAandglnIIclassified the isolates into four groups: theBradyrhizobium elkaniiandBradyrhizobium pachyrhizigroups, comprising the dominant symbionts,Bradyrhizobium yuanmingense, and an unclassified group comprising the minor symbionts. ThenodCandnifHphylogenetic trees defined five or six lineages among the isolates, which was largely consistent with the definition of genomic species. The phylogenetic results and evolutionary analysis demonstrated that mutation and vertical transmission of genes were the principal processes for the divergent evolution ofBradyrhizobiumspecies associated withE. fordii, while lateral transfer and recombination of housekeeping and symbiotic genes were rare. The distribution of the dominant rhizobial populations was affected by soil pH and effective phosphorus. This is the first report to characterizeE. fordiirhizobia.

scholarly journals Titi monkeys combine alarm calls to create probabilistic meaning

2019 ◽  
Vol 5 (5) ◽  
pp. eaav3991 ◽  
Author(s):  
Mélissa Berthet ◽  
Geoffrey Mesbahi ◽  
Aude Pajot ◽  
Cristiane Cäsar ◽  
Christof Neumann ◽  
...  
Keyword(s):  
Animal Communication ◽  
Language Evolution ◽  
Alarm Call ◽  
Alarm Calls ◽  
Playback Experiments ◽  
Multimodel Inference ◽  
Titi Monkeys ◽  
Callicebus Nigrifrons ◽  
Available Information ◽  
Free Ranging

Previous work suggested that titi monkeys Callicebus nigrifrons combine two alarm calls, the A- and B-calls, to communicate about predator type and location. To explore how listeners process these sequences, we recorded alarm call sequences of six free-ranging groups exposed to terrestrial and aerial predator models, placed on the ground or in the canopy, and used multimodel inference to assess the information encoded in the sequences. We then carried out playback experiments to identify the features used by listeners to react to the available information. Results indicated that information about predator type and location were encoded by the proportion of B-call pairs relative to all call pairs of the sequence (i.e., proportion of BB-grams). The results suggest that the meaning of the sequence is not conveyed in a categorical but probabilistic manner. We discuss the implications of these findings for current theories of animal communication and language evolution.

Molecular evolution of serine protease and its inhibitor with special reference to domain evolution

1994 ◽  
Vol 344 (1310) ◽  
pp. 411-415 ◽  
Keyword(s):  
Special Reference ◽  
Serine Protease ◽  
Serine Proteases ◽  
Phylogenetic Trees ◽  
Evolutionary Process ◽  
Life Forms ◽  
Functional Domains ◽  
Functional Domain ◽  
Evolutionary Analysis ◽  
Domain Evolution

The evolution of serine protease and its inhibitor are discussed with special reference to domain evolution. It is now known that most proteins are composed of more than one functional domain. Because serine proteases such as urokinase and plasminogen are made of various functional domains, these proteins are typical examples of the so-called mosaic proteins. When Kringle domains in serine proteases and a Kunitz-type protease inhibitor domain in the amyloid B precursor protein in Alzheimer’s disease patients were examined by the molecular evolutionary analysis, the phylogenetic trees constructed showed that these functional domains had undergone dynamic changes in the evolutionary process. In particular, these domains are evolutionarily movable. Thus, it is concluded that various functional domains evolved independently of each other and that they have been shuffled to create the existent mosaic proteins. This conclusion leads us to the reasonable speculation that those functional domains must have been minigenes possibly at the time of primordial life or the origin of life. We call these minigenes ‘ancestral minigenes’. Every effort should be made to answer the question about the minimum set of ancestral minigenes that must have existed and must have been needed for maintaining life forms. The DNA sequence database is useful for making attempts to answer such difficult but significant questions.

scholarly journals Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth-death process

2018 ◽  
Author(s):  
Joëlle Barido-Sottani ◽  
Gabriel Aguirre-Fernández ◽  
Melanie Hopkins ◽  
Tanja Stadler ◽  
Rachel Warnock
Keyword(s):  
Divergence Time ◽  
Time Estimation ◽  
Death Process ◽  
Divergence Times ◽  
Point Estimate ◽  
Species Divergence ◽  
Divergence Time Estimation ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Birth Death

AbstractFossil information is essential for estimating species divergence times, and can be integrated into Bayesian phylogenetic inference using the fossilized birth-death (FBD) process. An important aspect of palaeontological data is the uncertainty surrounding specimen ages, which can be handled in different ways during inference. The most common approach is to fix fossil ages to a point estimate within the known age interval. Alternatively, age uncertainty can be incorporated by using priors, and fossil ages are then directly sampled as part of the inference. This study presents a comparison of alternative approaches for handling fossil age uncertainty in analysis using the FBD process. Based on simulations, we find that fixing fossil ages to the midpoint or a random point drawn from within the stratigraphic age range leads to biases in divergence time estimates, while sampling fossil ages leads to estimates that are similar to inferences that employ the correct ages of fossils. Second, we show a comparison using an empirical dataset of extant and fossil cetaceans, which confirms that different methods of handling fossil age uncertainty lead to large differences in estimated node ages. Stratigraphic age uncertainty should thus not be ignored in divergence time estimation and instead should be incorporated explicitly.

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