Research papers
2003 · Bioinformatics · 29,493 citations
Abstract Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters. Availability: http://morphbank.ebc.uu.se/mrbayes Contact: fredrik.ronquist@ebc.uu.se * To whom correspondence should be addressed.
2012 · Systematic Biology · 28,381 citations
Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
2001 · Palaeontologia Electronica · 18,005 citations
A comprehensive, but simple-to-use software package for executing a range of standard numerical analysis and operations used in quantitative paleontology has been developed. The program, called PAST (PAleontological STatistics), runs on standard Windows computers and is available free of charge. PAST integrates spreadsheet-type data entry with univariate and multivariate statistics, curve fitting, timeseries analysis, data plotting, and simple phylogenetic analysis. Many of the functions are specific to paleontology and ecology, and these functions are not found in standard, more extensive, statistical packages. PAST also includes fourteen case studies (data files and exercises) illustrating use of the program for paleontological problems, making it a complete educational package for courses in quantitative methods.
2011 · Methods in Ecology and Evolution · 9,933 citations
Summary 1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks. 3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples. 4. Finally, I conclude by briefly describing an active web‐log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.
1991 · 4,386 citations
Abstract From Darwin onward, it has been second nature for evolutionary biologists to think comparatively because comparisons establish the generality of evolutionary phenomena. Do large genomes slow down development? What lifestyles select for large brains? Are extinction rates related to body size? These are all questions for the comparative method, and this book is about how such questions can be answered. The first chapter elaborates on suitable questions for the comparative approach and shows how it complements other approaches to problem-solving in evolution. The second chapter identifies the biological causes of similarity among closely related species for almost any observed character. The third chapter discusses methods for reconstructing phylogenetic trees and ancestral character states. The fourth chapter sets out to develop statistical tests that will determine whether different characters that exist in discrete states show evidence for correlated evolution. Chapter 5 turns to comparative analyses of continuously varying characters. Chapter 6 looks at allometry to exemplify the themes and methods discussed earlier, while the last chapter looks to future development of the comparative approach in both molecular and organismic biology.
2001 · Science · 2,780 citations
As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.
1988 · Journal of Mammalogy · 208 citations
Cryptomys damarensis occurs in semiarid regions of southwestern and central Africa. It lives in colonies in which reproduction is restricted to one or two of the largest-sized males and the largest female in the colony. Some division of labor, into frequent and infrequent workers, occurs within the remaining colony members. Reproduction and details of colony size and the number of breeding animals in a colony are described for two complete and five incomplete wild-captured colonies; one of the complete colonies and mole-rats from the incomplete colonies were maintained in captivity for more than 2 years. The breeding female initiated precopulatory behavior, mating occurred for about 2 weeks, the gestation length was 78–92 days, mean litter size was 2.8 (n = 10), and a maximum of four pups was born. The pups were precocial, wandered out of the nest within 24 h after birth, began to eat solids when 6 days old, and were fully weaned when 3 weeks old. When 6 weeks old, pups began to spar with each other and with some colony members, but levels of aggression were never high and the pups were incorporated into the colony. In the colony, subordinate and frequent-worker mole-rats weighed less than dominant animals and infrequent workers; mass, therefore, was not necessarily indicative of the age of the animal. During the 2-year study period, three mole-rats that were frequent workers on capture changed their castes to infrequent workers, two of them showed a concomitant increase in body mass. The colony structure and reproduction of C. damarensis are compared with those of the eusocial Heterocephalus glaber.
2021 · Biological reviews/Biological reviews of the Cambridge Philosophical Society · 131 citations
The naked mole-rat (Heterocephalus glaber) has fascinated zoologists for at least half a century. It has also generated considerable biomedical interest not only because of its extraordinary longevity, but also because of unusual protective features (e.g. its tolerance of variable oxygen availability), which may be pertinent to several human disease states, including ischemia/reperfusion injury and neurodegeneration. A recent article entitled 'Surprisingly long survival of premature conclusions about naked mole-rat biology' described 28 'myths' which, those authors claimed, are a 'perpetuation of beautiful, but falsified, hypotheses' and impede our understanding of this enigmatic mammal. Here, we re-examine each of these 'myths' based on evidence published in the scientific literature. Following Braude et al., we argue that these 'myths' fall into four main categories: (i) 'myths' that would be better described as oversimplifications, some of which persist solely in the popular press; (ii) 'myths' that are based on incomplete understanding, where more evidence is clearly needed; (iii) 'myths' where the accumulation of evidence over the years has led to a revision in interpretation, but where there is no significant disagreement among scientists currently working in the field; (iv) 'myths' where there is a genuine difference in opinion among active researchers, based on alternative interpretations of the available evidence. The term 'myth' is particularly inappropriate when applied to competing, evidence-based hypotheses, which form part of the normal evolution of scientific knowledge. Here, we provide a comprehensive critical review of naked mole-rat biology and attempt to clarify some of these misconceptions.
2012 · Transactions of the Royal Society of South Africa · 110 citations
Forerunners of Mammals: Radiation, Histology, Biology, edited by Anusuya Chinsamy-Turan. 2012. Bloomington, Indiana, Indiana University Press. Price: US$60. Pp. 330. ISBN 978 0 253 35697 0. The Gre...
1976 · The Journal of Foraminiferal Research · 25 citations
Other| April 01, 1976 Biology of Trochammina cf. T. quadriloba Hoeglund (1947), an agglutinating foraminifer M. Babajide Salami M. Babajide Salami Univ. Ife, Dep. Geol., Ile-Ife, Nigeria Search for other works by this author on: GSW Google Scholar Journal of Foraminiferal Research (1976) 6 (2): 142–153. https://doi.org/10.2113/gsjfr.6.2.142 Article history first online: 03 Mar 2017 Cite View This Citation Add to Citation Manager Share Icon Share Twitter LinkedIn Tools Icon Tools Get Permissions Search Site Citation M. Babajide Salami; Biology of Trochammina cf. T. quadriloba Hoeglund (1947), an agglutinating foraminifer. Journal of Foraminiferal Research 1976;; 6 (2): 142–153. doi: https://doi.org/10.2113/gsjfr.6.2.142 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu nav search search input Search input auto suggest search filter All ContentBy SocietyJournal of Foraminiferal Research Search Advanced Search This content is PDF only. Please click on the PDF icon to access. First Page Preview Close Modal You do not currently have access to this article.