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bruce rannala toggle navigation about current blog people publications all publications selected with commentary repositories cv teaching touring bruce rannala professor department of evolution and ecology uc davis brannala ucdavis edu 530 754 7729 welcome to the home page of bruce rannala i develop statistical methods computer software and sometimes new theory i also teach a course on human genetic variation eve 131 each fall my research focuses on statistical genetics population genetics and phylogenetics however our methods are often applied to real world problems such as pandemics hiv covid19 cancer genetics conservation biology and disease gene mapping examples of current projects bayesian inference of hybrid and backcross individuals using genomic sequences new models aimed at early identification of sars cov2 variants of concern using phylogenetic information postdoc mike may news feb 7 2026 bpp suite web tools updated jan 30 2026 bayesass ba3 version 3 4 4 released dec 30 2025 mongrail2 version 2 1 released jul 31 2024 former phd student anna nagel is now a postdoc in michael landis s group at washington university jun 1 2024 former phd student sneha chakraborty is now a postdoc in kirk lohmueller s group at ucla selected publications systbiol bayesian inference under the multispecies coalescent with ancient dna sequences anna a nagel tomáš flouri ziheng yang and bruce rannala systematic biology jul 2024 abs bib html pdf ancient dna adna is increasingly being used to investigate questions such as the phylogenetic relationships and divergence times of extant and extinct species if adna samples are sufficiently old expected branch lengths in units of nucleotide substitutions are reduced relative to contemporary samples this can be accounted for by incorporating sample ages into phylogenetic analyses existing methods that use tip sample dates infer gene trees rather than species trees which can lead to incorrect or biased inferences of the species tree methods using a multispecies coalescent msc model overcome these issues we developed an msc model with tip dates and implemented it in the program bpp the method performed well for a range of biologically realistic scenarios estimating calibrated divergence times and mutation rates precisely simulations suggest that estimation precision can be best improved by prioritizing sampling of many loci and more ancient samples incorrectly treating ancient samples as contemporary in analyzing simulated data mimicking a common practice of empirical analyses led to large systematic biases in model parameters including divergence times two genomic datasets of mammoths and elephants were analyzed demonstrating the method s empirical utility article 10 1093 sysbio syae047 author nagel anna a and flouri tomáš and yang ziheng and rannala bruce title bayesian inference under the multispecies coalescent with ancient dna sequences journal systematic biology pages syae047 year 2024 month jul issn 1063 5157 doi 10 1093 sysbio syae047 url https doi org 10 1093 sysbio syae047 scienceadvances early detection of highly transmissible viral variants using phylogenomics michael r may and bruce rannala science advances jul 2024 abs bib html pdf as demonstrated by the sars cov 2 pandemic the emergence of novel viral strains with increased transmission rates poses a serious threat to global health statistical models of genome sequence evolution may provide a critical tool for early detection of these strains using a novel stochastic model that links transmission rates to the entire viral genome sequence we study the utility of phylogenetic methods that use a phylogenetic tree relating viral samples versus count based methods that use case counts of variants over time exclusively to detect increased transmission rates and identify candidate causative mutations we find that phylogenies in particular can detect novel transmission enhancing variants very soon after their origin and may facilitate the development of early detection systems for outbreak surveillance phylogenetic trees of viruses facilitate the early detection of highly transmissible variants of concern article doi 10 1126 sciadv adk7623 author may michael r and rannala bruce title early detection of highly transmissible viral variants using phylogenomics journal science advances volume 10 number 33 pages eadk7623 year 2024 doi 10 1126 sciadv adk7623 url https www science org doi abs 10 1126 sciadv adk7623 philtransb reading tree leaves inferring speciation and extinction processes using phylogenies bruce rannala and ziheng yang philosophical transactions of the royal society b biological sciences feb 2025 abs bib html pdf the birth death process bdp is widely used in evolutionary biology as a model for generating phylogenetic trees of species the generalized birth death process gbdp allows rate variation over time with speciation and extinction rates as arbitrary functions of time we review the probability theory underpinning the gbdp as a model of cladogenesis and recent findings concerning its identifiability the gbdp with arbitrary continuous rate functions has been shown to be non identifiable from lineage through time data meaning even with species phylogenies of infinite size the parameters cannot be estimated however a restricted class of birth death processes with piecewise constant rates has been shown to be identifiable we illustrate these findings through examples and discuss implications for biologists interested in inferring the past tempo and mode of evolution using reconstructed phylogenetic trees article rannala2025reading author rannala bruce and yang ziheng title reading tree leaves inferring speciation and extinction processes using phylogenies journal philosophical transactions of the royal society b biological sciences volume 380 number 1919 pages 20230309 year 2025 month feb doi 10 1098 rstb 2023 0309 evollinnsoc recombination and phylogenetic inference bruce rannala evolutionary journal of the linnean society feb 2025 abs bib html pdf phylogenetic tree inference when recombination is present is examined two primary methodologies are compared concatenation approaches treat all loci as sharing one gene tree while species tree methods assume each locus has its own gene tree with no intralocus recombination three strategies for managing recombination effects are evaluated assessing statistical robustness when recombination goes unaccounted for identifying and eliminating recombinant regions and employing methods that accommodate varying gene trees across sequences recombination is likely to be more detrimental for concatenation methods having little impact on topology or divergence time estimates for species tree inference methods recombination detection may prove unnecessary for species tree analysis and removing recombinant loci could introduce bias in parameter calculations article rannala2025recombination author rannala bruce title recombination and phylogenetic inference journal evolutionary journal of the linnean society volume 4 number 1 pages kzaf016 year 2025 doi 10 1093 evolinnean kzaf016 systbiol inferring branch specific rates of lineage diversification under the birth death shift process sebastian höhna william a freyman zachary nolen john p huelsenbeck michael r may and 2 more authors systematic biology jan 2026 abs bib html pdf the birth death shift bds process is a stochastic diversification model in which diversification rates may vary across both extant and extinct and unsampled lineages we present a general approach for inferring branch specific rates of lineage diversification using bayesian statistics from phylogenies containing only living species we validate our approach through computer simulations and test it on primate data finding that estimates of branch specific diversification rates are robust to the assumed prior distribution on the number of diversification rate shifts the implementation of the lineage specific birth death shift model in revbayes provides biologists with a statistically principled tool for studying lineage diversification patterns article hohna2026inferring author h o hna sebastian and freyman william a and nolen zachary and huelsenbeck john p and may michael r and rannala bruce and moore brian r title inferring branch specific rates of lineage diversification under the birth death shift process journal systematic biology year 2026 month jan doi 10 1093 sysbio syag003 mbe on the robustness of bayesian inference of gene flow to intragenic recombination and natural selection yuttapong thawornwattana bruce rannala and ziheng yang molecular biology and evolution jan 2026 abs bib html pdf the multispecies coalescent model provides a framework for detecting gene flow using genomic data between species this study uses simulation to examine false positive rates in a bayesian test of gene flow considering factors including recombination natural selection species divergence timing and whether gene flow involves sister or nonsister lineages the test has very low false positives in most scenarios however gene flow detection between sister lineages may be prone to high false positives in cases of very recent species divergence and very high recombination rate the test demonstrates robustness to various selection types at low recombination rates though prolonged balancing selection can produce false gene flow signals between sister lineages recent species divergence alone with no recombination does not cause false positives gene flow detection between nonsister lineages remains robust across all recombination and divergence levels article thawornwattana2026robustness author thawornwattana yuttapong and rannala bruce and yang ziheng title on the robustness of bayesian inference of gene flow to intragenic recombination and natural selection journal molecular biology and evolution volume 43 number 1 pages msaf327 year 2026 month jan doi 10 1093 molbev msaf327 genetics mutation ages and population origins inferred from genomes in structured populations anna a nagel and bruce rannala genetics jan 2026 abs bib html a method is developed to jointly estimate the time and population of origin of a mutation as well as the ancestral and derived states in a structured population using population genomic data the method is evaluated using simulations and applied to genome data from the 1000 genomes project analyzing seven single nucleotide polymorphisms across six skin pigmentation genes in populations from great britain china and kenya results demonstrate that mutation age and population of origin can be quite uncertain even with long sequences or many samples but this uncertainty is accurately captured using credible intervals and sets article nagel2026mutation author nagel anna a and rannala bruce title mutation ages and population origins inferred from genomes in structured populations journal genetics volume 232 number 1 pages iyaf204 year 2026 month jan doi 10 1093 genetics iyaf204 arees inferring admixture in genomes bruce rannala annual review of ecology evolution and systematics jan 2025 abs bib html pdf hybridization of individuals from genetically differentiated populations causes their genomes to become a mosaic of population ancestries widespread availability of genetic markers during the late twentieth century stimulated the development of statistical methods for inferring both recent hybrids and population admixture proportions in individuals newer methods focus on population ancestries of chromosomal segments in individuals local ancestry inference or chromosome painting this review covers established statistical methods for inferring recent hybrids specifically f1 f2 and first generation backcrosses individual population admixture proportions and population ancestry of chromosome segments in individuals focusing on the biological assumptions underlying different methods article rannala2025admixture author rannala bruce title inferring admixture in genomes journal annual review of ecology evolution and systematics volume 56 pages 193 215 year 2025 doi 10 1146 annurev ecolsys 102723 064507 copyright 2026 bruce rannala powered by jekyll written using emacs and debian linux last updated june 04 2026