scholarly journals Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models

2018 ◽  
Author(s):  
Tanja Stadler ◽  
Mike Steel
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Death Rate ◽  
Evolutionary Trees ◽  
Rate Parameter ◽  
Death Rates ◽  
Fundamental Symmetries ◽  
Inference Methods ◽  
Curious Feature ◽  
Birth Death

AbstractStochastic birth–death models provide the foundation for studying and simulating evolutionary trees in phylodynamics. A curious feature of such models is that they exhibit fundamental symmetries when the birth and death rates are interchanged. In this paper, we explain and formally derive these transformational symmetries. We also show that these transformational symmetries (encoded in algebraic identities) are preserved even when taxa at the present are sampled with some probability. However, these extended symmetries require the death rate parameter to sometimes take a negative value. In the last part of this paper, we describe the relevance of these transformations and their application to computational phylodynamics, particularly to maximum likelihood and Bayesian inference methods, as well as to model selection. Phylodynamics, phylogenetics, speciation-extinction models, birth-death models, algebraic symmetries, maximum likelihood, Bayesian inference

scholarly journals Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models

2019 ◽  
Vol 68 (5) ◽  
pp. 852-858 ◽  
Author(s):  
Tanja Stadler ◽  
Mike Steel
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Model Selection ◽  
Death Rate ◽  
Evolutionary Trees ◽  
Rate Parameter ◽  
Death Rates ◽  
Fundamental Symmetries ◽  
Inference Methods ◽  
Curious Feature

Abstract Stochastic birth–death models provide the foundation for studying and simulating evolutionary trees in phylodynamics. A curious feature of such models is that they exhibit fundamental symmetries when the birth and death rates are interchanged. In this article, we first provide intuitive reasons for these known transformational symmetries. We then show that these transformational symmetries (encoded in algebraic identities) are preserved even when individuals at the present are sampled with some probability. However, these extended symmetries require the death rate parameter to sometimes take a negative value. In the last part of this article, we describe the relevance of these transformations and their application to computational phylodynamics, particularly to maximum likelihood and Bayesian inference methods, as well as to model selection.

Xylodon bambusinus and X. xinpingensis spp. nov. (Hymenochaetales) from southern China

Phytotaxa ◽  
2021 ◽  
Vol 511 (3) ◽  
Author(s):  
XIANG MA ◽  
CHANG-LIN ZHAO
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Growth Habit ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Two New Species ◽  
Thin Walled ◽  
Inference Methods

Two new species, Xylodon bambusinus and X. xinpingensis, are proposed based on morphological and molecular evidences. Both species share the annual growth habit, resupinate basidiomata and monomitic hyphal system with clamped, colorless generative hyphae, smooth, thin-walled basidiospores, but X. bambusinus is characterized by the smooth to tuberculate hymenial surface, presence of capitate and fusiform cystidia, broad ellipsoid basidiospores, while X. xinpingensis by the reticulate hymenophore with cream hymenial surface, and subglobose basidiospores (4.5–6 × 3.5–5 µm). Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analyses based on molecular data of ITS and ITS+nLSU sequences showed that X. bambusinus was sister to X. subclavatus, while X. xinpingensis grouped with X. astrocystidiatus and X. paradoxus. The nLSU dataset revealed that X. bambusinus grouped with X. asperus and X. brevisetus with lower supports, and that X. xinpingensis grouped with X. astrocystidiatus and X. paradoxus and then with X. rimosissimus without supports. Both morphological and molecular evidences confirmed the placement of two new species in Xylodon. Description and figures from the new species and a key to the known species of Xylodon from China are presented.

Gloeodontia yunnanensis sp. nov. (Russulales, Basidiomycota) from China, evidenced by morphological characters and phylogenetic analyses

Phytotaxa ◽  
2020 ◽  
Vol 432 (2) ◽  
pp. 111-118
Author(s):  
LU CHEN ◽  
ZHENG-JUN SHI ◽  
CHUN-HUA WU ◽  
CHANG-LIN ZHAO
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Morphological Characters ◽  
Fungal Species ◽  
Monophyletic Lineage ◽  
Thin Walled ◽  
Inference Methods

A new wood-inhabiting fungal species, Gloeodontia yunnanensis, is proposed based on a combination of morphological features and DNA data. The species is characterized by an annual, resupinate basidiomata with smooth hymenial surface, a monomitic hyphal system with thin-walled, clamped generative hyphae and obclavate cystidia and subglobose to globose, hyaline, thick-walled, asperulate, strongly amyloid, acyanophilous basidiospores measuring 3.3–4.3 × 2.5–3.5 µm. Sequences of ITS and 28S gene regions of the studied samples were generated and phylogenetic analyses were performed with Maximum Likelihood, Maximum Parsimony and Bayesian Inference methods. The analyses based on ITS+28S sequences showed that G. yunnanensis nested in the Gloeodontia clade and formed a monophyletic lineage with strong support (100% BS, 100% BP, 1.00 BPP).

Phlebia nigrodontea sp. nov. in Meruliaceae (Polyporales) with a black hymenial surface

Phytotaxa ◽  
2020 ◽  
Vol 458 (3) ◽  
pp. 195-206
Author(s):  
RUO-XIA HUANG ◽  
KAI-YUE LUO ◽  
CHANG-LIN ZHAO
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Molecular Data ◽  
Molecular Evidence ◽  
Monophyletic Lineage ◽  
Phlebioid Clade ◽  
Thin Walled ◽  
Inference Methods

A new wood-inhabiting fungus, Phlebia nigrodontea, is proposed based on a combination of morphological features and molecular evidence. The species is characterized by a grandinioid hymenophore with vinaceous brown to black colour, a monomitic hyphal system with clamped generative hyphae and ellipsoid, colourless, thin-walled, smooth basidiospores (3.9–4.9 × 2.3–3.1 µm). Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses carried out using maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analyses based on the molecular data of ITS+nLSU sequences showed that P. nigrodontea nested within the phlebioid clade. A further investigation of more representative taxa from Phlebia, based on ITS+nLSU sequences, demonstrated that the species P. nigrodontea formed a monophyletic lineage with strong support (100% BS, 100% BT, 1.00 BPP) and closely grouped with P. chrysocreas.

scholarly journals The Phylogenetic Relationship Revealed Three New Wood-Inhabiting Fungal Species From Genus Trechispora

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei Zhao ◽  
Chang-Lin Zhao
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Maximum Parsimony ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Fungal Species ◽  
Molecular Evidence ◽  
Wood Degradation ◽  
Inference Methods

Wood-inhabiting fungi play a significant role in wood degradation and the cycle of matter in the ecological system. In the present study, three new wood-inhabiting fungal species, Trechispora bambusicola, Trechispora fimbriata, and Trechispora fissurata spp. nov., are nested in Trechispora, which are proposed based on a combination of morphological features and molecular evidence. Sequences of internal transcribed spacer (ITS) and large subunit (nLSU) regions of the studied samples were generated, and the phylogenetic analyses were performed with maximum likelihood, maximum parsimony, and Bayesian inference methods. The phylogenetic analyses inferred from ITS showed that T. bambusicola was sister to Trechispora stevensonii, T. fimbriata grouped with Trechispora nivea, and T. fissurata grouped with Trechispora echinospora. The phylogenetic tree based on ITS + nLSU sequences demonstrated that T. bambusicola formed a single lineage and then grouped with Trechispora rigida and T. stevensonii. T. fimbriata was sister to T. nivea. T. fissurata grouped with Trechispora thelephora.

scholarly journals A Multitype Birth–Death Model for Bayesian Inference of Lineage-Specific Birth and Death Rates

2020 ◽  
Vol 69 (5) ◽  
pp. 973-986 ◽  
Author(s):  
Joëlle Barido-Sottani ◽  
Timothy G Vaughan ◽  
Tanja Stadler
Keyword(s):  
Bayesian Inference ◽  
Simulated Data ◽  
Pathogen Transmission ◽  
Type Model ◽  
Model Parameters ◽  
Data Sets ◽  
Death Rates ◽  
Joint Inference ◽  
Extinction Rates ◽  
Birth Death

Abstract Heterogeneous populations can lead to important differences in birth and death rates across a phylogeny. Taking this heterogeneity into account is necessary to obtain accurate estimates of the underlying population dynamics. We present a new multitype birth–death model (MTBD) that can estimate lineage-specific birth and death rates. This corresponds to estimating lineage-dependent speciation and extinction rates for species phylogenies, and lineage-dependent transmission and recovery rates for pathogen transmission trees. In contrast with previous models, we do not presume to know the trait driving the rate differences, nor do we prohibit the same rates from appearing in different parts of the phylogeny. Using simulated data sets, we show that the MTBD model can reliably infer the presence of multiple evolutionary regimes, their positions in the tree, and the birth and death rates associated with each. We also present a reanalysis of two empirical data sets and compare the results obtained by MTBD and by the existing software BAMM. We compare two implementations of the model, one exact and one approximate (assuming that no rate changes occur in the extinct parts of the tree), and show that the approximation only slightly affects results. The MTBD model is implemented as a package in the Bayesian inference software BEAST 2 and allows joint inference of the phylogeny and the model parameters.[Birth–death; lineage specific rates, multi-type model.]

scholarly journals Families of birth-death processes with similar time-dependent behaviour

2000 ◽  
Vol 37 (03) ◽  
pp. 835-849 ◽  
Author(s):  
R. B. Lenin ◽  
P. R. Parthasarathy ◽  
W. R. W. Scheinhardt ◽  
E. A. van Doorn
Keyword(s):  
Death Rate ◽  
General Setting ◽  
Time Dependent ◽  
Death Process ◽  
Similar Time ◽  
Death Rates ◽  
Transition Functions ◽  
Time Dependent Behaviour ◽  
Dependent Behaviour ◽  
Birth Death

We consider birth-death processes taking values in but allow the death rate in state 0 to be positive, so that escape from is possible. Two such processes with transition functions are said to be similar if, for all there are constants c ij such that for all t ≥ 0. We determine conditions on the birth and death rates of a birth-death process for the process to be a member of a family of similar processes, and we identify the members of such a family. These issues are also resolved in the more general setting in which the two processes are called similar if there are constants c ij and ν such that for all t ≥ 0.

scholarly journals Morphological and phylogenetic evidence for recognition of two new species of Hyphoderma (Basidiomycota) from southern China, with a key to all Chinese Hyphoderma

MycoKeys ◽  
2021 ◽  
Vol 83 ◽  
pp. 145-160
Author(s):  
Qian-Xin Guan ◽  
Yi-Fei Li ◽  
Chang-Lin Zhao
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Forest Ecosystems ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Molecular Evidence ◽  
Corticioid Fungi ◽  
Two New Species ◽  
Inference Methods

Wood-inhabiting fungi play crucial roles as decomposers in forest ecosystems and, in this study, two new wood-inhabiting corticioid fungi, Hyphoderma puerense and H. tenuissimumspp. nov., are proposed, based on a combination of morphological features and molecular evidence. Hyphoderma puerense is characterised by effused basidiomata with smooth to floccose hymenial surface, a monomitic hyphal system with clamped generative hyphae and ellipsoid basidiospores. Hyphoderma tenuissimum is characterised by resupinate basidiomata with tuberculate to minutely-grandinioid hymenial surface, septate cystidia and cylindrical to allantoid basidiospores. Sequences of ITS and nLSU rRNA markers of the studied samples were generated and phylogenetic analyses were performed with Maximum Likelihood, maximum parsimony and Bayesian Inference methods. These analyses showed that the two new species clustered into Hyphoderma, in which H. puerense grouped with H. moniliforme and H. tenuissimum formed a singleton lineage. In addition, an identification key to Chinese Hyphoderma is provided.

scholarly journals Families of birth-death processes with similar time-dependent behaviour

2000 ◽  
Vol 37 (3) ◽  
pp. 835-849 ◽  
Author(s):  
R. B. Lenin ◽  
P. R. Parthasarathy ◽  
W. R. W. Scheinhardt ◽  
E. A. van Doorn
Keyword(s):  
Death Rate ◽  
General Setting ◽  
Time Dependent ◽  
Death Process ◽  
Similar Time ◽  
Death Rates ◽  
Transition Functions ◽  
Time Dependent Behaviour ◽  
Dependent Behaviour ◽  
Birth Death

We consider birth-death processes taking values in but allow the death rate in state 0 to be positive, so that escape from is possible. Two such processes with transition functions are said to be similar if, for all there are constants cij such that for all t ≥ 0. We determine conditions on the birth and death rates of a birth-death process for the process to be a member of a family of similar processes, and we identify the members of such a family. These issues are also resolved in the more general setting in which the two processes are called similar if there are constants cij and ν such that for all t ≥ 0.

scholarly journals A Multi-State Birth-Death model for Bayesian inference of lineage-specific birth and death rates

2018 ◽  
Author(s):  
Joëlle Barido-Sottani ◽  
Timothy G. Vaughan ◽  
Tanja Stadler
Keyword(s):  
Bayesian Inference ◽  
Phylogenetic Trees ◽  
Environmental Changes ◽  
Morphological Changes ◽  
Model Parameters ◽  
Death Rates ◽  
Joint Inference ◽  
Wide Range ◽  
Prior Hypothesis ◽  
Birth Death

AbstractHeterogeneous populations can lead to important differences in birth and death rates across a phylogeny Taking this heterogeneity into account is thus critical to obtain accurate estimates of the underlying population dynamics. We present a new multi-state birth-death model (MSBD) that can estimate lineage-specific birth and death rates. For species phylogenies, this corresponds to estimating lineage-dependent speciation and extinction rates. Contrary to existing models, we do not require a prior hypothesis on a trait driving the rate differences and we allow the same rates to be present in different parts of the phylogeny. Using simulated datasets, we show that the MSBD model can reliably infer the presence of multiple evolutionary regimes, their positions in the tree, and the birth and death rates associated with each. We also present a re-analysis of two empirical datasets and compare the results obtained by MSBD and by the existing software BAMM. The MSBD model is implemented as a package in the Bayesian inference software BEAST2, which allows joint inference of the phylogeny and the model parameters.Significance statementPhylogenetic trees can inform about the underlying speciation and extinction processes within a species clade. Many different factors, for instance environmental changes or morphological changes, can lead to differences in macroevolutionary dynamics within a clade. We present here a new multi-state birth-death (MSBD) model that can detect these differences and estimate both the position of changes in the tree and the associated macroevolutionary parameters. The MSBD model does not require a prior hypothesis on which trait is driving the changes in dynamics and is thus applicable to a wide range of datasets. It is implemented as an extension to the existing framework BEAST2.

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