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• jaehee kim, filippo disanto, and naama kopelman report a study of the properties of the neighbor-joining algorithm when applied to data from admixed populations. The study shows that tree properties conjectured by kopelman et al. [ 99] do not necessarily hold for every distance matrix, but they do hold much more frequently than in a null model without an admixed taxon.

• filippodisanto examines thenumber of nonequivalent ancestral configurations for matching gene treesand species trees. Nonequivalent ancestral configurations atfirst appear to be less numerous than ancestral configurations withoutapplying the equivalence relation — studied previously by filippo[ 152]. Here, filipposhows that asymptotic growth for nonequivalent configurations is alsoexponential.This pair of studies extends the lab’s workon theory of admixture and combinatorics of evolutionarytrees.


• 10-31-2018 — congratulations to ilana arbisser on defending her thesis anoxic brain injury recovery statistics "mathematical investigations into fundamental population genetics statistics and models." ilana’s thesis examines the joint distribution of the height and length of coalescent trees, the relationship of the population-genetic statistic F ST to the triangle inequality, and the state space of a discrete-state coalescent model with recombination and migration. Dr. Arbisser’s wise words about making hard decisions, such as square root transformation vs. Cailliez constant in multidimensional scaling: "it’s important to consider what choices we’re making and the consequences of those choices." congrats ilana!

• 10-18-2018 — the lab examines the potential for determining that relatives genotyped with nonoverlapping marker sets are anoxia cerebral consecuencias in fact relatives. This analysis demonstrates that people typed with microsatellites used in forensic genetics can be connected to close relatives typed with single-nucleotide polymorphisms used in biomedical, genealogical, personal-genomic, and population-genetic studies. Lead author is jaehee kim with former lab members doc edge and bridget algee-hewitt also contributing. [ CNN] [ nature] [ new scientist] [ science] [ scientific american] [ stanford report] [ wired]

• 8-30-2018 — rohan mehta has defended his phd thesis "mathematical modeling of genetic and cultural traits." rohan’s thesis studies a variety of mathematical modeling problems in diverse areas of population genetics and evolutionary biology. He examines combinatorial and probabilistic aspects of genealogical lineages along the branches of species trees, mathematical properties of F ST statistics in relation to homozygosities and haploypes, and a gene-culture coevolutionary model of health-related behaviors. Congrats rohan!

• A commentary on anthony edwards’s 2003 essay of multivariate classification of individuals into populations on the basis of genetic markers appears in a new book edited by rasmus winther about edwards’s career and contributions. Among other topics, the commentary discusses the influence of edwards’s model on a phenotypic model from the lab [ 129].

• 7-18-2018 — ilana arbisser reports a mathematical investigation of the relationship between two of the most frequently used features of gene genealogies, the height and length of coalescent trees. The study also includes simulations describing the effect of population growth and population subdivision on the relationship between tree height and tree length. PhD graduate ethan jewett contributed to the project.

• 5-30-2018 — we congratulate jonathan kang onthe defense of his phd thesis "analysis and application of linkagedisequilibrium in population and statistical genetics." in histhesis, jonathan focuses on three questions concerning linkagedisequilibrium (LD) and genomic sharing: the identification of optimalsubsamples to prioritize for sequencing in order to enhance LD-basedimputation, the relationship of runs of homozygosity to consanguinityin jewish populations, and mathematical properties of measures ofld. Congrats to jon!

• 9-14-2017 — the lab reports a study of consanguinity and runs of homozygosity in jewish populations. PhD student jonathan kang compares runs of homozygosity in contemporary jewish nanoxia deep silence 5 review populations to estimates of consanguinity measured in the 1950s from interviews with mothers in maternity wards. The study finds that the demographic consanguinity rates predict the fraction of the genome that resides in long runs of homozygosity. PhD graduates amy goldberg and doc edge contributed to the study.

• 9-8-2017 — filippo disanto reports a study of the number of ancestral configurations possessed by matching gene trees and species trees. Ancestral configurations represent a combinatorial structure useful in producing probability formulas for gene trees given species trees, and they are hence connected to coalescent histories. Filippo’s work is the latest in his series of combinatorial enumerations of structures that arise in the study of gene trees and species trees [ 123] [ 135] [ 142].

• 8-21-2017 — A new study from the lab anxiety attack symptoms shows that in the admixed population of cape verde, genetic admixture is correlated with a measure of linguistic admixture evaluated by tabulating words of portuguese and african origin in individuals’ speech in the cape verde kriolu lnaguage. The analyses suggest a mechanism of cotransmission of genetic and linguistic admixture during the descent of a creole-speaking admixed population. We congratulate lab alumni paul verdu*, ethan jewett*, and trevor pemberton on the study.

• 8-5-2017 — olga kamneva reports a phylogenetic study of 20 worldwide species of strawberries ( fragaria) on the basis of next-generation sequencing data assembled via a bioinformatics pipeline designed specifically for polyploids of mixed ploidy. The study suggests new hypotheses for the diploid progenitors of polyploid species of fragaria.

• 7-6-2017 — nicolas alcala has obtained mathematical bounds on population-genetic statistic F ST in the case of a biallelic marker whose mean frequency across a set of populations is fixed. His bounds provide an explanation of a frequently observed dependence of F ST on the number of populations under consideration. Nicolas’s paper expands on two earlier studies from the lab concerning bounds on F ST [ 102] [ 121].

• 5-30-2017 — recent phd graduate docedge reports in anew study that on the basis ofcorrelations between genotypes at neighboring markers, profilescontaining nonoverlapping sets of genetic markers can beconnected to the same individual. This "record-matching" is demonstratedusing genomic and forensic genetic markers, and it has implications forforensic genetics and genomicprivacy. Postdoc bridgetalgee-hewitt and formerpostdoc trevorpemberton contributed to the project.[ stanfordreport news story]

• 5-8-2017 — congratulations to amygoldberg on the defense of her thesis "mathematical andstatistical approaches to elucidate recent human evolutionaryhistory." amy’s thesis considers mechanistic mathematical models ofadmixture, including the effect of sex-biased admixture on autosomes andon the X chromosome, and the inference from ancient autosomes and xchromosomes of sex-biased migration during prehistoric admixture events ineurope. She also examines the human population size history of southamerica on the basis of the density and location of archaeologicalsites. Congratulations amy!

• 4-24-2017 — we congratulate amy goldberg on receiving the 2017 sherwood washburn prize from the american association of physical anthropologists! This prize recognizes the best student presentation at the AAPA annual meeting. Amy spoke about her work on the contrast between neolithic and bronze age migrations in europe in their levels of male and female migration. [ read the paper]

• 3-15-2017 — amy goldberg reports that two ancient migration events in europe involved different proportions of male and female migrants, the earlier neolithic migration from anatolia having similar numbers of males and cerebral anoxia definition females and the later pontic-caspian migration having a greater proportion of males. The result, relying on comparisons of ancient DNA patterns from the X chromosome and the autosomes, builds on amy’s earlier work on sex bias in genetic admixture models [ 122] [ 133].[ science news story]

• 2-27-2017 — postdoc alum olga kamneva diffuse hypoxic brain injury radiology reports in plos computational biology a study of the relationship between genome composition of microbes and the co-occurrence of microbes in the environment. She finds that comparisons of microbial genomes can contribute to predictions about whether microbes are associated ecologically. Congrats olga!

• nicolas alcala — postdoc with matthieu foll, international agency for research on cancer, world health organization, lyon.• filippo disanto — junior faculty, department of mathematics, university of pisa (sponsored by the rita levi montalcini researcher program).• doc edge — postdoc with graham coop, department of evolution and ecology, university of california, davis.• olga kamneva — bioinformatics scientist, affymetrix, inc.

• 11-14-2016 — postdoc lawrence uricchio has reported an upper bound on the size of gene tree sets required before all splits of a species tree appear in a gene tree set with a specified probability. His upper bound depends on a single parameter — the shortest internal branch in the species tree. The computation extends the lab’s work on methods for species tree inference from gene trees.

• 10-14-2016 — recent phd graduate doc edge has devised a general mathematical model to understand how genotypic differences between populations contribute to phenotypic differences between populations. He uses the model to analyze the relationship of genetics to "health disparities," concluding that health disparities that all trend in the same direction are incompatible with neutral genetic explanations. The work extends a simpler model of doc’s [ 129], allowing for diploidy, genetic drift, and general distributions of allele frequencies.

• 10-7-2016 — postdoc filippo disanto continues the lab’s work on coalescent histories with a study of the number of coalescent histories for anxiety meaning in tamil matching gene trees in caterpillar-like families of species trees. Filippo’s work solves an open problem from earlier work in the lab [ 111], showing that the number of coalescent histories is asymptotic to a constant multiple of the catalan numbers. He uses clever iterative enumerations and techniques of analytic combinatorics to obtain the result. See also [ 41], [ 68], and [ 135] for related work.

• 7-27-2016 — we are pleased to announce that thesoftware MONOPHYLER is now available. MONOPHYLER computes probabilitiesthat sets of lineages are monophyletic, both for general species trees andfor trees of small size. MONOPHYLERis reported by phd student rohan mehta. The software encodesformulas from rohan’srecent proceedings of the nationalacademy of sciences paper.

• 7-22-2016 — we congratulate phdstudent doc edge on his thesisdefense, "pick up the pieces: combining information from multiplegenetic loci." doc’s thesis examines several problems in themathematical modeling of the genotype-to-phenotype relationship instructured populations, mathematical properties ofthe F st measure of genetic differentiation, andpopulation-genetic aspects of forensic DNA testing and genetic associationstudies. Doc has been recognized with thesamuel karlin prize in mathematical biology, awarded by the department ofbiology. Congratulations doc!

• 7-19-2016 — phd student rohan mehta reports a computation of the probability that a set of gene lineages on an arbitrary species tree. The work generalizes earlier studies from the lab that considered trees of only two or three species. Rohan illustrates the new formula with an application in maize. The study is a contribution to the comparative phylogeography volume of the "in the light of evolution" special issue series of proceedings of the national academy of sciences USA.

• 6-27-2016 — we congratulate biology MS student briandonovan on the completion of his phd in science education "anexperimental exploration of how text-based instruction in school biologyaffects belief in genetic essentialism of race in adolescentpopulations." brian defended his phd in the graduate school ofeducation on may 26. He is continuing his studies as a postdoctoral fellowat the biological sciences curriculum study in colorado springs.

• 5-12-2016 — lab alumnus mike degiorgio reports on the consistency properties of species tree inference methods in a model with ancestral population structure. By introducing a model anxiety attack symptoms headache that includes population subdivision in ancestral species, his paper introduces a new direction for studying consistency in species tree inference. The work is related to several recent papers from the lab on consistency of species tree methods social anxiety disorder testimonials([ 85],[ 88],[ 89],[ 97],[ 109])

• 4-5-2016 — we congratulate phd student amy goldberg on the publication of her nature article entitled "post-invasion demography of prehistoric humans in south america." in this work, amy and her colleagues use the locations and dates of south american archaeological sites to estimate the time trajectory of the human population size history of the continent. Read the news story here.

• 4-4-2016 — lab members bridget algee-hewitt, doc edge, and jaehee kim report that forensic genetic markers selected for their use in individual identification possess a surprising level of information about genetic ancestry. Moreover, their study finds that a general correlation holds for genetic markers between their information about individual identity and ancestry information. The result makes use of theory from the lab on the connection between measures of genetic diversity and genetic differentiation ([ 102], [ 121]).

When phd student amy goldberg develops a model for sex-biased admixture on the X-chromosome, a curious mathematical sequence leads to an unexpected connection deep in the genetics archive. Read about the oscillatory functions and coupled recursions encountered in this scholarly adventure — with a surprise appearance of the fibonacci numbers.