Combining data in phylogenetic analysis

doi:10.1016/0169-5347(96)10006-9

Trends in Ecology & Evolution

Volume 11, Issue 4, April 1996, Pages 152-158

https://doi.org/10.1016/0169-5347(96)10006-9 Get rights and content

Abstract

Systematists have access to multiple sources of character information in phylogenetic analysis. For example, it is not unusual to have nucleotide sequences from several different genes, or to have molecular and morphological data. How should diverse data be analyzed in phylogenetic analysis? Several methods have been proposed for the treatment of partitioned data: the total evidence, separate analysis, and conditional combination approaches. Here, we review some of the advantages and disadvantages of the different approaches, with special concentration on which methods help us to discern the evolutionary process and provide the most accurate estimates of phylogeny.

References (45)

C-C. Luo
Structure and expression of dog apolipoprotein A-1, E, and C-I mRNAs: Implications for the evolution and functional constraints of apolipoprotein structure
J. Lipid Res.
(1989)
A.G. Kluge et al.
Cladistics: what's in a word?
Cladistics
(1993)
S.M. Lanyon
Phylogenetic frameworks: towards a firmer foundation for the comparative approach
Biol. J Linn. Soc.
(1993)
T.H. Jukes et al.
Evolution of protein molecules
C. Médigue
Evidence for horizontal gene transfer in Escherichia coli spectation
J. Mot Biol.
(1991)
P.H. Harvey et al.
The Comparative Method in Evolutionary Biology
(1991)
K.H. Wolfe
Mutation rates differ among regions of the mammalian genome
Nature
(1988)
C-B. Stewart et al.
Sequence convergence and functional adaptation of stomach lysozymes from foregut fermenters
A.G. Kluge
A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes)
Syst. Zool.
(1989)
D.M. Hillis
Molecular versus morphological approaches to systematics
Annu. Rev. Ecol. Syst
(1987)

M.M. Miyamoto et al.

Testing species phylogenies and phylogenetic methods with congruence

Syst Biol.

(1995)

A. de Queiroz

For consensus (sometimes)

Syst Biol.

(1993)

D. Penny et al.

Estimating the reliability of evolutionary trees

Mol Biol. Evol.

(1986)

D.L. Swofford

When are phylogeny estimates from molecular and morphological data incongruent?

J.J. Bull

Partitioning and combining data in phylogenetic analysis

Syst Biol.

(1993)

A.G. Rodrigo

A randomization test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree

N. Z. J. Bot

(1993)

P.T. Chippindale et al.

Weighting, partitioning, and combining characters in phylogenetic analysis

Syst Biol.

(1994)

D.J. Eernisse et al.

Taxonomic congruence versus total evidence, and the phylogeny of amntotes inferred from fossils, molecules and morphology

Mol Biol. Evol.

(1993)

T.R. Jones

When theories and methodologies clash: a phylogenetic reanalysis of the North American ambystomatid salamanders (Caudata: Ambystomatidae)

Syst Biol.

(1993)

M. Barrett

Against consensus

Syst. Biol.

(1991)

M.M. Miyamoto

A congruence test of reliability using linked mitochondrial DNA sequences

Syst Biol.

(1994)

M.F. Michevich et al.

The implications of congruence in Menidia

Syst Zool.

(1981)

Cited by (712)

The phylogenetic reconstruction of the Neotropical cycad genus Ceratozamia (Zamiaceae) reveals disparate patterns of niche evolution
2024, Molecular Phylogenetics and Evolution
The cycad genus Ceratozamia comprises 40 species from Mexico, Guatemala, Belize, and Honduras, where cycads occur throughout climatically varied montane habitats. Ceratozamia has the potential to reveal the history and processes of species diversification across diverse Neotropical habitats in this region. However, the species relationships within Ceratozamia and the ecological trends during its evolution remain unclear. Here, we aimed to clarify the phylogenetic relationships, the timing of clade and species divergences, and the niche evolution throughout the phylogenetic history of Ceratozamia. Genome-wide DNA sequences were obtained with MIG-seq, and multiple data-filtering steps were used to optimize the dataset used to construct an ultrametric species tree. Divergence times among branches and ancestral niches were estimated. The niche variation among species was evaluated, summarized into two principal components, and their ancestral states were reconstructed to test whether niche shifts among branches can be explained by random processes, under a Brownian Motion model. Ceratozamia comprises three main clades, and most species relationships within the clades were resolved. Ceratozamia has diversified since the Oligocene, with major branching events occurring during the Miocene. This timing is consistent with fossil evidence, the timing estimated for other Neotropical plant groups, and the major geological events that shaped the topographic and climatic variation in Mexico. Patterns of niche evolution in the genus do not accord with the Brownian Motion model. Rather, non-random evolution with shifts towards more seasonal environments at high latitudes, or shifts towards humid or dry environments at low latitudes explain the diversification of Ceratozamia. We present a comprehensive phylogenetic reconstruction for Ceratozamia and identify for the first time the environmental factors involved in clade and species diversification within the genus. This study alleviates the controversies regarding the species relationships in the genus and provides the first evidence that latitude-associated environmental factors may influence processes of niche evolution in cycads.
A dated molecular phylogeny and biogeographical analysis reveals the evolutionary history of the trans-pacifically disjunct tropical tree genus Ormosia (Fabaceae)
2022, Molecular Phylogenetics and Evolution
The papilionoid legume genus Ormosia (Fabaceae) comprises about 150 species of trees and exhibits a striking disjunct geographical distribution between the New World- and Asian and Australasian wet tropics and subtropics. Modern classifications of Ormosia are not grounded on a well-substantiated phylogenetic hypothesis and have been limited to just portions of the geographical range of the genus. The lack of an evolutionarily-based foundation for systematic studies has hindered taxonomic work on the genus and prevented the testing of biogeographical hypotheses related to the origin of the Old World/New World disjunction and the individual dispersal histories within both areas. Here, we present the most comprehensively sampled molecular phylogeny of Ormosia to date, based on analysis of both nuclear (ITS) and plastid (matK and trnL–F) DNA sequences from 82 species of the genus. Phylogenetically-based divergence times and ancestral range estimations are employed to test hypotheses related to the biogeographical history of the genus. We find strong support for the monophyly of Ormosia and the grouping of all sampled Asian species of the genus into two comparably sized clades, one of which is sister to another large clade containing all sampled New World species. Within the New World clade, additional resolution supports the grouping of most species into three mutually exclusive subordinate clades. The remaining New World species form a fourth well-supported clade in the analyses of plastid sequences, but that result is contradicted by the analysis of ITS. With few exceptions the supported clades have not been previously recognized as taxonomic groups. The biogeographical analysis suggests that Ormosia originated in continental Asia and dispersed to the New World in the Oligocene or early Miocene via long-distance trans-oceanic dispersal. We reject the hypothesis that the inter-hemispheric disjunction in Ormosia resulted from fragmentation of a more continuous “Boreotropical” distribution since the dispersal post-dates Eocene climatic maxima. Both of the Old World clades appear to have originated in mainland Asia and subsequently dispersed into the Malay Archipelago and beyond, at least two lineages dispersing across Wallace’s Line as far as the Solomon Islands and northeastern Australia. In the New World, the major clades all originated in Amazonia. Dispersal from Amazonia into peripheral areas in Central America, the Caribbean, and Extra-Amazonian Brazil occurred multiple times over varying time scales, the earliest beginning in the late Miocene. In a few cases, these dispersals were followed by local diversification, but not by reverse migration back to Amazonia. Within each of the two main areas of distribution, multiple modest bouts of oceanic dispersal were required to achieve the modern distributions.
ITS 2 and RNA secondary structure-based analysis reveals a clear picture on phylogeny of South Indian Salacia spp.
2021, Computational Biology and Chemistry
The genus Salacia (Celastraceae) consists of many important medicinal plants used mainly against type II diabetes. Segregation and delimitation of species is difficult based on morphological features alone. DNA barcoding is the most effective and emerging method of molecular identification. It was reported that ITS2 has better discriminating power in the genus Salacia in comparison to other barcode loci. This paper describe the analysis of sequence and structural information of ITS2 to discriminate the species of Salacia. A total of 8 species of Salacia in South India and the available sequences in NCBI database were taken for the present study. NJ method based phylogenetic trees were constructed using MEGAX with primary sequence as well as using sequence and secondary structural information. Primary structure based phylogeny did not give much information whereas the dendrogram based on sequence and structural information was more informative to decipher the phylogeny of South Asian species of Salacia. The present study revealed some interesting facts regarding the genus. Secondary structure of the ITS2 sequence of S. chinensis reported from Kerala differs consistently from that of S. chinensis reported from other parts of India and of South Asia. Probably the S. chinensis in Kerala, India has diverged a lot from the original S. chinensis. ITS2 sequence of S. reticulata reported from Sri Lanka was identical to S. chinensis reported by other groups from Thailand and Udupi, India. The molecular level identity of ITS2 sequence of S. chinensis with S. reticulata suggest merger of the two species. ITS2 sequence of S. beddomei is only reported from Kerala, India showed it to be identical to S. macrosperma. This observation points to a mistaken identity of S. beddomei which could be elusive from Kerala. Phylogenetic trees constructed based on sequence and structural features of ITS2 suggest that the ancestor species of S.chinensis diversified in two evolutionary lines. One line leads to the present day S. chinensis and the other line further diversified and lead to the rest of the present day Salacia species.
Bioassay guided fractionation of bioactive metabolite from Corynascus verrucosus inhabiting Croton bonplandianus Baill
2020, Process Biochemistry
Mycoendophytes have been a promising source of bioactive metabolites for new developments in pharmaceuticals and industrial relevance. During the screening of mycoendophytes diversity from C. bonplandianus, bioactive C. verrucosus CBF 22 was isolated from the leaf. The bioactive isolate was subjected to fermentation and the ethyl acetate fraction was evaluated for antimicrobial activity by disc diffusion and microbroth dilution methods, followed by cytotoxicity using MTT assay. The results revealed significant activity against Gram negative bacteria, Gram positive bacteria, and human pathogenic dermatophytic fungi, C. albicans. The TLC Bioautography-Guided approach employed for the detection of antimicrobial metabolite from bioactive fraction was depicted by a zone of inhibition. Antimicrobial screening of mycoendophytes C. bonplandianus could envision a unique potential niche for bioactive compounds of pharmaceutical importance. These findings suggest C. verrucosus as a potent candidate for producing natural bioactives, to combat multidrug-resistant pathogens. This work is the first report on the incidence of C. verrucosus as mycoendophyte and its bioactive potential of inhabiting C. bonplandianus Baill.
Metabolic networks classification and knowledge discovery by information granulation
2020, Computational Biology and Chemistry
Graphs are powerful structures able to capture topological and semantic information from data, hence suitable for modelling a plethora of real-world (complex) systems. For this reason, graph-based pattern recognition gained a lot of attention in recent years. In this paper, a general-purpose classification system in the graphs domain is presented. When most of the information of the available patterns can be encoded in edge labels, an information granulation-based approach is highly discriminant and allows for the identification of semantically meaningful edges. The proposed classification system has been tested on the entire set of organisms (5299) for which metabolic networks are known, allowing for both a perfect mirroring of the underlying taxonomy and the identification of most discriminant metabolic reactions and pathways. The widespread diffusion of graph (network) structures in biology makes the proposed pattern recognition approach potentially very useful in many different fields of application. More specifically, the possibility to have a reliable metric to compare different metabolic systems is instrumental in emerging fields like microbiome analysis and, more in general, for proposing metabolic networks as a universal phenotype spanning the entire tree of life and in direct contact with environmental cues.
Plant pangenomes for crop improvement, biodiversity and evolution
2024, Nature Reviews Genetics

View all citing articles on Scopus

View full text

Trends in Ecology & Evolution

ReviewCombining data in phylogenetic analysis

Abstract

J. Lipid Res.

Cladistics

Biol. J Linn. Soc.

J. Mot Biol.

The Comparative Method in Evolutionary Biology

Mutation rates differ among regions of the mammalian genome

Nature

Sequence convergence and functional adaptation of stomach lysozymes from foregut fermenters

A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes)

Syst. Zool.

Molecular versus morphological approaches to systematics

Annu. Rev. Ecol. Syst

Testing species phylogenies and phylogenetic methods with congruence

Syst Biol.

For consensus (sometimes)

Syst Biol.

Estimating the reliability of evolutionary trees

Mol Biol. Evol.

When are phylogeny estimates from molecular and morphological data incongruent?

Partitioning and combining data in phylogenetic analysis

Syst Biol.

A randomization test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree

N. Z. J. Bot

Weighting, partitioning, and combining characters in phylogenetic analysis

Syst Biol.

Taxonomic congruence versus total evidence, and the phylogeny of amntotes inferred from fossils, molecules and morphology

Mol Biol. Evol.

When theories and methodologies clash: a phylogenetic reanalysis of the North American ambystomatid salamanders (Caudata: Ambystomatidae)

Syst Biol.

Against consensus

Syst. Biol.

A congruence test of reliability using linked mitochondrial DNA sequences

Syst Biol.

The implications of congruence in Menidia

Syst Zool.

Review
Combining data in phylogenetic analysis