scholarly journals Adaptive Metropolis-coupled MCMC for BEAST 2

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9473
Author(s):  
Nicola F. Müller ◽  
Remco R. Bouckaert
Keyword(s):  
Phylogenetic Analyses ◽  
Cold Chain ◽  
Acceptance Probability ◽  
Evolutionary Patterns ◽  
Bayesian Phylogenetics ◽  
State Spaces ◽  
New States ◽  
Complex Models ◽  
Speed Up ◽  
Mcmc Chain

With ever more complex models used to study evolutionary patterns, approaches that facilitate efficient inference under such models are needed. Metropolis-coupled Markov chain Monte Carlo (MCMC) has long been used to speed up phylogenetic analyses and to make use of multi-core CPUs. Metropolis-coupled MCMC essentially runs multiple MCMC chains in parallel. All chains are heated except for one cold chain that explores the posterior probability space like a regular MCMC chain. This heating allows chains to make bigger jumps in phylogenetic state space. The heated chains can then be used to propose new states for other chains, including the cold chain. One of the practical challenges using this approach, is to find optimal temperatures of the heated chains to efficiently explore state spaces. We here provide an adaptive Metropolis-coupled MCMC scheme to Bayesian phylogenetics, where the temperature difference between heated chains is automatically tuned to achieve a target acceptance probability of states being exchanged between individual chains. We first show the validity of this approach by comparing inferences of adaptive Metropolis-coupled MCMC to MCMC on several datasets. We then explore where Metropolis-coupled MCMC provides benefits over MCMC. We implemented this adaptive Metropolis-coupled MCMC approach as an open source package licenced under GPL 3.0 to the Bayesian phylogenetics software BEAST 2, available from https://github.com/nicfel/CoupledMCMC.

scholarly journals Adaptive parallel tempering for BEAST 2

2019 ◽  
Author(s):  
Nicola F. Müller ◽  
Remco R. Bouckaert
Keyword(s):  
Phylogenetic Analyses ◽  
Cold Chain ◽  
Parallel Tempering ◽  
Acceptance Probability ◽  
Evolutionary Patterns ◽  
Bayesian Phylogenetics ◽  
New States ◽  
Complex Models ◽  
Speed Up ◽  
Mcmc Chain

AbstractWith ever more complex models used to study evolutionary patterns, approaches that facilitate efficient inference under such models are needed. Parallel tempering has long been used to speed up phylogenetic analyses and to make use of multi-core CPUs. Parallel tempering essentially runs multiple MCMC chains in parallel. All chains are heated except for one cold chain that explores the posterior probability space like a regular MCMC chain. This heating allows chains to make bigger jumps in phylogenetic state space. The heated chains can then be used to propose new states for other chains, including the cold chain. One of the practical challenges using this approach, is to find optimal temperatures of the heated chains to efficiently explore state spaces. We here provide an adaptive parallel tempering scheme to Bayesian phylogenetics, where the temperature difference between heated chains is automatically tuned to achieve a target acceptance probability of states being exchanged between individual chains. We first show the validity of this approach by comparing inferences of adaptive parallel tempering to MCMC on several datasets. We then explore where parallel tempering provides benefits over MCMC. We implemented this adaptive parallel tempering approach as an open source package licensed under GPL 3.0 to the Bayesian phylogenetics software BEAST2, available from https://github.com/nicfel/CoupledMCMC.

scholarly journals An elusive new species of gymnophthalmid lizard (Cercosaurinae, Selvasaura) from the Andes of northern Peru

2021 ◽  
Vol 5 (2) ◽  
pp. 177-187
Author(s):  
Lourdes Y. Echevarría ◽  
Pablo J. Venegas ◽  
Luis A. García-Ayachi ◽  
Pedro M. Sales Nunes
Keyword(s):  
New Species ◽  
Natural History ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
The Other ◽  
Adult Males ◽  
The Andes ◽  
New States ◽  
Northern Peru ◽  
A New Species

We describe a new species of Selvasaura from the montane forests of the eastern slopes of the Andes in northern Peru, based on external and hemipenial morphological characters and previous phylogenetic analyses. The new species can be differentiated from the other two Selvasaura species in having keeled dorsal scales usually flanked by longitudinal striations, in adults and juveniles; adult males with a yellow vertebral stripe bordered by broad dark brown stripes on each side and a unilobed hemipenis surrounded by the branches of the sulcus spermaticus. The description of the new species contributes information about new states of diagnostic characters of Selvasaura and natural history.

scholarly journals Spatiotemporal Distribution and Evolution of the A/H1N1 2009 Pandemic Influenza Virus in Pigs in France from 2009 to 2017: Identification of a Potential Swine-Specific Lineage

2018 ◽  
Vol 92 (24) ◽  
Author(s):  
Amélie Chastagner ◽  
Séverine Hervé ◽  
Emilie Bonin ◽  
Stéphane Quéguiner ◽  
Edouard Hirchaud ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Influenza A ◽  
Phylogenetic Analyses ◽  
Swine Influenza ◽  
H1n1 Influenza ◽  
Antigenic Drift ◽  
Influenza A Viruses ◽  
Evolutionary Patterns ◽  
Increased Risk ◽  
Na Sequences

ABSTRACT The H1N1 influenza virus responsible for the most recent pandemic in 2009 (H1N1pdm) has spread to swine populations worldwide while it replaced the previous seasonal H1N1 virus in humans. In France, surveillance of swine influenza A viruses in pig herds with respiratory outbreaks led to the detection of 44 H1N1pdm strains between 2009 and 2017, regardless of the season, and findings were not correlated with pig density. From these isolates, 17 whole-genome sequences were obtained, as were 6 additional hemagglutinin (HA)/neuraminidase (NA) sequences, in order to perform spatial and temporal analyses of genetic diversity and to compare evolutionary patterns of H1N1pdm in pigs to patterns for human strains. Following mutation accumulation and fixation over time, phylogenetic analyses revealed for the first time the divergence of a swine-specific genogroup within the H1N1pdm lineage. The divergence is thought to have occurred around 2011, although this was demonstrated only through strains isolated in 2015 to 2016 in the southern half of France. To date, these H1N1pdm swine strains have not been related to any increased virulence in swine herds and have not exhibited any antigenic drift compared to seasonal human strains. However, further monitoring is encouraged, as diverging evolutionary patterns in these two species, i.e., swine and humans, may lead to the emergence of viruses with a potentially higher risk to both animal and human health.IMPORTANCE Pigs are a “mixing vessel” for influenza A viruses (IAVs) because of their ability to be infected by avian and human IAVs and their propensity to facilitate viral genomic reassortment events. Also, as IAVs may evolve differently in swine and humans, pigs can become a reservoir for old human strains against which the human population has become immunologically naive. Thus, viruses from the novel swine-specific H1N1pdm genogroup may continue to diverge from seasonal H1N1pdm strains and/or from other H1N1pdm viruses infecting pigs and lead to the emergence of viruses that would not be covered by human vaccines and/or swine vaccines based on antigens closely related to the original H1N1pdm virus. This discovery confirms the importance of encouraging swine IAV monitoring because H1N1pdm swine viruses could carry an increased risk to both human and swine health in the future as a whole H1N1pdm virus or gene provider in subsequent reassortant viruses.

scholarly journals Evolutionary history of the porpoises (Phocoenidae) across the speciation continuum: a mitogenome phylogeographic perspective

2019 ◽  
Author(s):  
Yacine Ben Chehida ◽  
Julie Thumloup ◽  
Cassie Schumacher ◽  
Timothy Harkins ◽  
Alex Aguilar ◽  
...  
Keyword(s):  
Marine Mammals ◽  
Evolutionary History ◽  
Environmental Changes ◽  
Phylogenetic Analyses ◽  
Food Resources ◽  
Recent Common Ancestor ◽  
Cetacean Species ◽  
Evolutionary Patterns ◽  
Speciation Continuum ◽  
Southern Species

AbstractHistorical changes affecting food resources are a major driver of cetacean evolution. Small cetaceans like porpoises (Phocoenidae) are among the most metabolically challenged marine mammals and are particularly sensitive to changes in their food resources. The seven species of this family inhabit mostly temperate waters and constitute a textbook example of antitropical distribution. Yet, their evolutionary history remains poorly known despite major conservation issues threatening the survival of some porpoises (e.g., vaquita and Yangzte finless porpoises). Here, we reconstructed their evolutionary history across the speciation continuum, from intraspecific subdivisions to species divergence. Phylogenetic analyses of 63 mitochondrial genomes suggest that, like other toothed whales, porpoises radiated during the Pliocene in response to deep environmental changes. However, all intra-specific phylogeographic patterns were shaped during the Quaternary Glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent adaptations to coastal versus oceanic environments. This result suggests that the mechanism(s) driving species diversification in the relatively well-known species from the northern hemisphere may apply also to the poorly-known southern species. In contrast to previous studies, we showed that the spectacled and Burmeister’s porpoises share a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size throughout at least the last 5,000 years, leaving one single relict mitochondrial lineage. Finally, we observed unreported subspecies level divergence within Dall’s, spectacled and Pacific harbor porpoises, suggesting a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanism driving the adaptation and speciation processes involved in the diversification of cetacean species. This knowledge can illuminate their demographic trends and provide an evolutionary framework for their conservation.

scholarly journals Evolution of Australasian Plantago (Plantaginaceae)

2021 ◽  
Author(s):  
◽  
Mei Lin Tay
Keyword(s):  
New Zealand ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Molecular Dating ◽  
Evolutionary Patterns ◽  
Its Phylogeny ◽  
Suitable Habitats

<p>Phylogenetic analyses using molecular data were used to investigate biogeographic and evolutionary patterns of Australasian Plantago. The Internal Transcribed Spacers (ITS) from nuclear DNA, ndhF-rpl32 from chloroplast DNA and cox1 from mitochondrial DNA were selected from a primer assay of 24 primer pairs for further phylogenetic analyses. Phylogenetic reconstruction and molecular dating of a dataset concatenated from these regions comprising 20 Australasian Plantago species rejected a hypothesis of Gondwanan vicariance for the Australasian group. The phylogeny revealed three independent dispersal events from Australia to New Zealand that match expected direction because of West Wind Drift and ocean currents. Following this study, a dataset with 150 new ITS sequences from Australasian Plantago, combined with 89 Plantago sequences from previous studies, revealed that the New Zealand species appear to have a recent origin from Australia, not long after the formation of suitable habitats formed by the uplift of the Southern Alps (about 5 mya), followed by radiation. The ITS phylogeny also suggests that a single migration event of alpine species to lowland habitats has occurred and that recurrent polyploidy appears to be an important speciation mechanism in the genus. Species boundaries between New Zealand Plantago were unclear using both morphological and molecular data, which was a result of low genetic divergences and plastic morphology. The taxonomy of several New Zealand Plantago species need revision based on the ITS phylogeny.</p>

scholarly journals The Opiliones Tree of Life: shedding light on harvestmen relationships through transcriptomics

2016 ◽  
Author(s):  
Rosa Fernándeza ◽  
Prashant Sharma ◽  
Ana L.M. Tourinho ◽  
Gonzalo Giribet
Keyword(s):  
Phylogenetic Analyses ◽  
Tree Of Life ◽  
Molecular Techniques ◽  
Evolutionary Patterns ◽  
Factors Affecting ◽  
Biogeographic Patterns ◽  
The Family ◽  
The Times ◽  
Phylogenomic Study ◽  
Data Matrices

AbstractOpiliones are iconic arachnids with a Paleozoic origin and a diversity that reflects ancient biogeographical patterns dating back at least to the times of Pangea. Due to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to systematics. More recently, two studies utilized transcriptomics-based phylogenomics to explore their basal relationships and diversification, but sampling was limiting for understanding deep evolutionary patterns, as they lacked good taxon representation at the family level. Here we analyze a set of the 14 existing transcriptomes with 40 additional ones generated for this study, representing ca. 80% of the extant familial diversity in Opiliones. Our phylogenetic analyses, including a set of data matrices with different gene occupancy and evolutionary rates, and using a multitude of methods correcting for a diversity of factors affecting phylogenomic data matrices, provide a robust and stable Opiliones tree of life, where most families are precisely placed. Our dating analyses also using alternative calibration points, methods, and analytical parameters provide well-resolved old divergences, consistent with ancient regionalization in Pangea in some groups, and Pangean vicariance in others. The integration of state-of-the-art molecular techniques and analyses, together with the broadest taxonomic sampling to date presented in a phylogenomic study of harvestmen, provide new insights into harvestmen interrelationships, as well as a general overview of the general biogeographic patterns of this ancient arthropod group.

scholarly journals Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yacine Ben Chehida ◽  
Julie Thumloup ◽  
Cassie Schumacher ◽  
Timothy Harkins ◽  
Alex Aguilar ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Environmental Changes ◽  
Phylogenetic Analyses ◽  
Recent Common Ancestor ◽  
Evolutionary Patterns ◽  
Low Genetic Diversity ◽  
Speciation Continuum ◽  
New Perspective ◽  
Historical Variation ◽  
Southern Species

Abstract Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall’s) and southern species (spectacled and Burmeister’s). In contrast to previous studies, spectacled and Burmeister’s porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall’s, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation.

scholarly journals Toll-like receptor pathway evolution in deuterostomes

2017 ◽  
Vol 114 (27) ◽  
pp. 7055-7060 ◽  
Author(s):  
Michael G. Tassia ◽  
Nathan V. Whelan ◽  
Kenneth M. Halanych
Keyword(s):  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Negative Regulator ◽  
Cytokine Signaling ◽  
Evolutionary Patterns ◽  
Pathway Evolution ◽  
Pathogenic Microbes ◽  
Taxonomic Groups ◽  
Adaptive Immune Systems ◽  
Recognition Receptor

Animals have evolved an array of pattern-recognition receptor families essential for recognizing conserved molecular motifs characteristic of pathogenic microbes. One such family is the Toll-like receptors (TLRs). On pathogen binding, TLRs initiate specialized cytokine signaling catered to the class of invading pathogen. This signaling is pivotal for activating adaptive immunity in vertebrates, suggesting a close evolutionary relationship between innate and adaptive immune systems. Despite significant advances toward understanding TLR-facilitated immunity in vertebrates, knowledge of TLR pathway evolution in other deuterostomes is limited. By analyzing genomes and transcriptomes across 37 deuterostome taxa, we shed light on the evolution and diversity of TLR pathway signaling elements. Here, we show that the deuterostome ancestor possessed a molecular toolkit homologous to that which drives canonical MYD88-dependent TLR signaling in contemporary mammalian lineages. We also provide evidence that TLR3-facilitated antiviral signaling predates the origin of its TCAM1 dependence recognized in the vertebrates. SARM1, a negative regulator of TCAM1-dependent pathways in vertebrates, was also found to be present across all major deuterostome lineages despite the apparent absence of TCAM1 in invertebrate deuterostomes. Whether the presence of SARM1 is the result of its role in immunity regulation, neuron physiology, or a function of both is unclear. Additionally, Bayesian phylogenetic analyses corroborate several lineage-specific TLR gene expansions in urchins and cephalochordates. Importantly, our results underscore the need to sample across taxonomic groups to understand evolutionary patterns of the innate immunity foundation on which complex immunological novelties arose.

scholarly journals Evolutionary Patterns of Eastern Equine Encephalitis Virus in North versus South America Suggest Ecological Differences and Taxonomic Revision

2009 ◽  
Vol 84 (2) ◽  
pp. 1014-1025 ◽  
Author(s):  
Nicole C. Arrigo ◽  
A. Paige Adams ◽  
Scott C. Weaver
Keyword(s):  
South America ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
Open Reading Frames ◽  
Rate Variation ◽  
Nucleotide Substitution Rate ◽  
Evolutionary Patterns ◽  
Eastern Equine Encephalitis ◽  
Genetic Lineages

ABSTRACT The eastern equine encephalitis (EEE) complex consists of four distinct genetic lineages: one that circulates in North America (NA EEEV) and the Caribbean and three that circulate in Central and South America (SA EEEV). Differences in their geographic, pathogenic, and epidemiologic profiles prompted evaluation of their genetic diversity and evolutionary histories. The structural polyprotein open reading frames of all available SA EEEV and recent NA EEEV isolates were sequenced and used in evolutionary and phylogenetic analyses. The nucleotide substitution rate per year for SA EEEV (1.2 × 10−4) was lower and more consistent than that for NA EEEV (2.7 × 10−4), which exhibited considerable rate variation among constituent clades. Estimates of time since divergence varied widely depending upon the sequences used, with NA and SA EEEV diverging ca. 922 to 4,856 years ago and the two main SA EEEV lineages diverging ca. 577 to 2,927 years ago. The single, monophyletic NA EEEV lineage exhibited mainly temporally associated relationships and was highly conserved throughout its geographic range. In contrast, SA EEEV comprised three divergent lineages, two consisting of highly conserved geographic groupings that completely lacked temporal associations. A phylogenetic comparison of SA EEEV and Venezuelan equine encephalitis viruses (VEEV) demonstrated similar genetic and evolutionary patterns, consistent with the well-documented use of mammalian reservoir hosts by VEEV. Our results emphasize the evolutionary and genetic divergences between members of the NA and SA EEEV lineages, consistent with major differences in pathogenicity and ecology, and propose that NA and SA EEEV be reclassified as distinct species in the EEE complex.

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