A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data

Lewis, Paul O.

doi:10.1080/106351501753462876

Cited by 2,584 publications

(2,018 citation statements)

References 36 publications

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“…Our solution of down-weighting non-independent data sets does not optimally account for any redundancy, but does represent a conservative solution insofar as it assumes complete redundancy among all studies within a data partition. Finally, inclusion of the literature data within a supermatrix context also presents analytical problems in that molecular sequence data are arguably best analyzed within a likelihood framework whereas maximum parsimony is better suited for non-molecular data (despite the existence of models of evolution for such data; for example, [85,86]). Thus, at least one of the two partitions will be analyzed suboptimally through the use of a common optimization criterion needed under a supermatrix framework.…”

Section: Resultsmentioning

confidence: 99%

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

2012

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BackgroundAlthough it has proven to be an important foundation for investigations of carnivoran ecology, biology and evolution, the complete species-level supertree for Carnivora of Bininda-Emonds et al. is showing its age. Additional, largely molecular sequence data are now available for many species and the advancement of computer technology means that many of the limitations of the original analysis can now be avoided. We therefore sought to provide an updated estimate of the phylogenetic relationships within all extant Carnivora, again using supertree analysis to be able to analyze as much of the global phylogenetic database for the group as possible.ResultsIn total, 188 source trees were combined, representing 114 trees from the literature together with 74 newly constructed gene trees derived from nearly 45,000 bp of sequence data from GenBank. The greater availability of sequence data means that the new supertree is almost completely resolved and also better reflects current phylogenetic opinion (for example, supporting a monophyletic Mephitidae, Eupleridae and Prionodontidae; placing Nandinia binotata as sister to the remaining Feliformia). Following an initial rapid radiation, diversification rate analyses indicate a downturn in the net speciation rate within the past three million years as well as a possible increase some 18.0 million years ago; numerous diversification rate shifts within the order were also identified.ConclusionsTogether, the two carnivore supertrees remain the only complete phylogenetic estimates for all extant species and the new supertree, like the old one, will form a key tool in helping us to further understand the biology of this charismatic group of carnivores.

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Section: Resultsmentioning

confidence: 99%

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

2012

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“…In molecular phylogenetics, it is now common to consider multiple models of molecular evolution before selecting a single best model to be used in maximum likelihood or Bayesian phylogenetic reconstruction [8,26,27]. Recent advances in model-based morphological phylogenetics [28,29] suggest that model selection can also be used to address a variety of new questions relating to the , ecologists and evolutionary biologists have only recently expanded and incorporated this tool. Wildlife biologists and molecular systematists have been at the forefront of bringing model selection to ecology and evolution, yet the approach has been applied almost independently in these two fields.…”

Section: Evolutionmentioning

confidence: 99%

Model selection in ecology and evolution

Johnson¹,

Omland²

2004

Trends in Ecology & Evolution

3,216

2,660

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Recently, researchers in several areas of ecology and evolution have begun to change the way in which they analyze data and make biological inferences. Rather than the traditional null hypothesis testing approach, they have adopted an approach called model selection, in which several competing hypotheses are simultaneously confronted with data. Model selection can be used to identify a single best model, thus lending support to one particular hypothesis, or it can be used to make inferences based on weighted support from a complete set of competing models. Model selection is widely accepted and well developed in certain fields, most notably in molecular systematics and markrecapture analysis. However, it is now gaining support in several other areas, from molecular evolution to landscape ecology. Here, we outline the steps of model selection and highlight several ways that it is now being implemented. By adopting this approach, researchers in ecology and evolution will find a valuable alternative to traditional null hypothesis testing, especially when more than one hypothesis is plausible.Science is a process for learning about nature in which competing ideas about how the world works are evaluated against observations [1]. These ideas are usually expressed first as verbal hypotheses, and then as mathematical equations, or models. Models depict biological processes in simplified and general ways that provide insight into factors that are responsible for observed patterns. Hence, the degree to which observed data support a model also reflects the relative support for the associated hypothesis.Two basic approaches have been used to draw biological inferences. The dominant paradigm is to generate a null hypothesis (typically one with little biological meaning [2]) and ask whether the hypothesis can be rejected in light of observed data. Rejection occurs when a test statistic generated from observed data falls beyond an arbitrary probability threshold (usually P , 0.05), which is interpreted as tacit support for a biologically more meaningful alternative hypothesis. Hence, the actual hypothesis of interest (the alternative hypothesis) is accepted only in the sense that the null hypothesis is rejected. By contrast, model selection offers a way to draw inferences from a set of multiple competing hypotheses. Model selection is grounded in likelihood theory, a robust framework that supports most modern statistical approaches. Moreover, this approach is rapidly gaining support across several fields in ecology and evolution as a preferred alternative to null hypothesis testing [1,3,4]. Advocates of model selection argue that it has three primary advantages. First, practitioners are not restricted to evaluating a single model where significance is measured against some arbitrary probability threshold. Instead, competing models are compared to one another by evaluating the relative support in the observed data for each model. Second, models can be ranked and weighted, thereby providing a quantitative measure of relative sup...

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“…ML reconstructions were performed using the Markov k-state 1-parameter model (Mk1; Lewis, 2001), which gives equal probability for changes between any two character states. Similarly, parsimony analysis used Fitch (unordered or non-additive) optimisation, which gives equal cost to all character-state changes.…”

Section: Ancestral-state Reconstructionmentioning

confidence: 99%

The phylogenetic position and diversity of the enigmatic mongrel frog Nothophryne Poynton, 1963 (Amphibia, Anura)

Bittencourt-Silva

Conradie

Siu-Ting

et al. 2016

Molecular Phylogenetics and Evolution

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Highlights• Using a two-tiered phylogenetic approach proves to be an efficient way to add new taxa into phylogenies.• Nothophryne is a member of Pyxicephalidae and is the sister group of Tomopterna.• First phylogeny to include representatives of all pyxicephalid genera.• Cryptic diversity of Nothophryne species revealed. 2 Graphical abstract AbstractThe phylogenetic relationships of the African mongrel frog genus Nothophryne are poorly understood. We provide the first molecular assessment of the phylogenetic position of, and diversity within, this monotypic genus from across its range -the Afromontane regions of Malawi and Mozambique. Our analysis using a two-tiered phylogenetic approach allowed us to place the genus in Pyxicephalidae. Within the family, Nothophryne grouped with Tomopterna, a hypothesis judged significantly better than alternative hypotheses proposed based on morphology. Our analyses of populations across the range of Nothophryne suggest the presence of several cryptic species, at least one species per mountain. Formal recognition of these species is pending but there is a major conservation concern for these narrowly distributed populations in an area impacted by major habitat change. The phylogenetic tree of pyxicephalids is used to examine evolution of life history, ancestral habitat, and biogeography of this group.

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A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data

Cited by 2,584 publications

References 36 publications

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

Model selection in ecology and evolution

The phylogenetic position and diversity of the enigmatic mongrel frog Nothophryne Poynton, 1963 (Amphibia, Anura)

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