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Introduction
Additional affiliations
August 2011 - present
February 2008 - July 2011
August 1996 - January 2004
Publications
Publications (71)
The idea of introducing genetic modifications into wild populations of insects to stop them from spreading diseases is more than 40 years old. Synthetic disease refractory genes have been successfully generated for mosquito vectors of dengue fever and human malaria. Equally important is the development of population transformation systems to drive...
A SNP in the gene encoding lactase (LCT) (C/T-13910) is associated with the ability to digest milk as adults (lactase persistence) in Europeans, but the genetic basis of lactase persistence in Africans was previously unknown. We conducted a genotype-phenotype association study in 470 Tanzanians, Kenyans and Sudanese and identified three SNPs (G/C-1...
The animal gut microbiome can have a strong influence on the health, fitness, and behavior of its hosts. The composition of the gut microbial community can be influenced by factors such as diet, environment, and evolutionary history (phylosymbiosis). However, the relative influence of these factors is unknown in most bird species. Furthermore, phyl...
Background
The gut microbiome of animals is an important component that has strong influence on the health, fitness, and behavior of its host. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the mi...
Culex quinquefasciatus mosquitoes are a globally widespread vector of several human and animal pathogens. Their biology and behavior allow them to thrive in proximity to urban areas, rendering them a constant public health threat. Their mixed bird/mammal feeding behavior further offers a vehicle for zoonotic pathogens transmission to people and, se...
Population genetics is an inherently quantitative discipline. Because the focus of population genetics studies is usually on abstract concepts like the frequencies of genetic variants over time, it can at first glance be difficult to conceptualize and appropriately visualize. As more and more quantitative models and methods have become established...
An introduction to randomness and the neutral theory of molecular evolution and how it contributes to levels of genetic diversity in populations. The estimation of random shifts in allele frequencies over time is discussed using the binomial probability distribution. This chapter visualizes how different initial allele frequencies relate to their p...
Population genetics is an inherently quantitative discipline. Because the focus of population genetics studies is usually on abstract concepts like the frequencies of genetic variants over time, it can at first glance be difficult to conceptualize and appropriately visualize. As more and more quantitative models and methods have become established...
Here non-random shifts in allele frequencies over time are introduced, as well as how to incorporate varying levels of selection into a model of a single population through time. This chapter highlights the difference between weak and strong selection, the dynamics of single allele versus genotype-level selection, and how selection strength and pop...
This concluding chapter highlights many of the concepts that are important to understanding modern-day population genetics research and explains that while they may not have been covered in this book, they are built on the foundations laid out in the preceding chapters. A series of small sections are provided which briefly introduce important conce...
Population genetics is an inherently quantitative discipline. Because the focus of population genetics studies is usually on abstract concepts like the frequencies of genetic variants over time, it can at first glance be difficult to conceptualize and appropriately visualize. As more and more quantitative models and methods have become established...
Population genetics is an inherently quantitative discipline. Because the focus of population genetics studies is usually on abstract concepts like the frequencies of genetic variants over time, it can at first glance be difficult to conceptualize and appropriately visualize. As more and more quantitative models and methods have become established...
Population genetics is an inherently quantitative discipline. Because the focus of population genetics studies is usually on abstract concepts like the frequencies of genetic variants over time, it can at first glance be difficult to conceptualize and appropriately visualize. As more and more quantitative models and methods have become established...
Population genetics is an inherently quantitative discipline. Because the focus of population genetics studies is usually on abstract concepts like the frequencies of genetic variants over time, it can at first glance be difficult to conceptualize and appropriately visualize. As more and more quantitative models and methods have become established...
Ribosomal proteins (RPs) are critical to all cellular operations through their key roles in ribosome biogenesis and translation, as well as their extra-ribosomal functions. Although highly tissue- and time-specific in expression, little is known about the macro-level roles of RPs in shaping transcriptomes. A wealth of RP mutants exist, including th...
Culex mosquitoes are a globally widespread vector of several human and animal pathogens. Their biology and behavior allow them to thrive in proximity to urban areas, rendering them a constant public health threat. Their mixed bird/mammal feeding behavior further offers a vehicle for zoonotic pathogens transmission to people, and separately, poses a...
The pan-tropical sea urchin Tripneustes gratilla is an ecologically and economically important shallow water algal grazer. The aquaculture of T. gratilla has spurred growing interest in the population biology of the species, and by extension the generation of more molecular resources. To this purpose, de novo transcriptomes of T. gratilla were gene...
Despite the advent of several novel, synthetic gene drive mechanisms and their potential to one-day control a number of devastating diseases, among other applications, practical use of these systems remains contentious and risky. In particular, there is little in the way of empirical evidence of the long-term robustness of these synthetic systems a...
The pan-tropical sea urchin Tripneustes gratilla is an ecologically and economically important shallow water algal grazer. The aquaculture of T. gratilla has spurred growing interest in the population biology of the species, and by extension the generation of more molecular resources. To this purpose, de novo transcriptomes of T. gratilla were gene...
Background:
Synthetic systems that use positive feedback have been developed to control human disease vectors and crop pests. The tTAV system, which has been deployed in several insect species, relies on a positive feedback circuit that can be inhibited via dietary tetracycline. Although insects carrying tTAV fail to survive until adulthood in the...
The letter by Garner et al. [1] continued an important discussion regarding the role genomics might play in conservation biology. In general, we do not see a dichotomy between our point of view [2] and that put forth by Garner et al. [1]. At the heart of the issue is how to define an actual impact of genomics on applied conservation and find suitab...
The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice, and we discuss how scaling-up to genome-wide inference can benefit traditional conservation genetic approaches and provide qualitatively novel insights. Yet, the generation of genomic data and subseque...
The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and in...
Transgenic constructs intended to be stably established at high frequencies in wild popu- lations have been demonstrated to drive from low frequencies in experimental insect populations. Link- ing such population transformation constructs to genes which render them unable to transmit pathogens could eventually be used to stop the spread of vector...
Background:
Transgenic constructs intended to be stably established at high frequencies in wild populations have been demonstrated to "drive" from low frequencies in experimental insect populations. Linking such population transformation constructs to genes which render them unable to transmit pathogens could eventually be used to stop the spread...
Heterozygote disadvantage in reproductive success is called underdominance. In a single locus system with two or more alleles, this leads to bistable evolutionary dynamics. Reciprocal balanced chromosomal translocations occur naturally and can lead to underdominance. The coexistence of two alleles that are in underdominance with each other is unsta...
In a way, the DNA sequences contained within each of our cells can be thought of as the text in microscopic book. This text is amazingly long, approximately one million pages if 6,000 letters fit on both sides of a page. This DNA contains the codes used to build RNA and proteins, which in turn assemble all the tissues in our bodies and direct the c...
Experimental releases of genetically modified (GM) insects are reportedly being evaluated in various countries, including Brazil, the Cayman Islands (United Kingdom), France, Guatemala, India, Malaysia, Mexico, Panama, Philippines, Singapore, Thailand, the United States of America, and Vietnam. GM mosquitoes ( Aedes aegypti ) have already been rele...
US regulatory experience 1996–2010.
(DOC)
Table of cited literature in 2008-EIS.
(DOC)
Figure 1 data.
(XLS)
Documents obtained through Freedom of Information Act request.
(PDF)
US Environmental Assessment 2001-EA.
(PDF)
Extended glossary to assist non-specialist readers.
(DOC)
Author Summary
Underdominance is a component of natural evolution: homozygotes – of either wildtypes or mutants – are advantageous. This can play a role in speciation and as a method to establish artificial genetic constructs in wild populations. The polymorphic state of wildtype and mutant alleles is unstable. However, in subdivided populations li...
Homoploid hybridization after secondary contact between related species can lead to mixtures of genotypes which have the potential for rapid adaptation to new environmental conditions. Here, we focus on a case where anthropogenic changes within the past 200 years have allowed the hybridization between two fish species (Cottus rhenanus and Cottus pe...
Motivation:
Sequencing capacity is currently growing more rapidly than CPU speed, leading to an analysis bottleneck in many genome projects. Alignment-free sequence analysis methods tend to be more efficient than their alignment-based counterparts. They may, therefore, be important in the long run for keeping sequence analysis abreast with sequenc...
Underdominance refers to natural selection against individuals with a heterozygous genotype. Here, we analyze a single-locus underdominant system of two large local populations that exchange individuals at a certain migration rate. The system can be characterized by fixed points in the joint allele frequency space. We address the conditions under w...
Africa is the source of all modern humans, but characterization of genetic variation and of relationships among populations
across the continent has been enigmatic. We studied 121 African populations, four African American populations, and 60 non-African
populations for patterns of variation at 1327 nuclear microsatellite and insertion/deletion mar...
The question of whether or not humans are still evolving often captures the popular imagination and regularly leads to conflicting claims. Here, some of the evolutionary forces predicted to act upon current and future human populations are reviewed. It is postulated that the increasing movement and panmixia of humans, coupled with an unprecedented...
[This corrects the article on p. e19 in vol. 4, PMID: 18208337.].
Will a group of people reach a collective target through individual contributions when everyone suffers individually if the target is missed? This “collective-risk social dilemma” exists in various social scenarios, the globally most challenging one being the prevention of dangerous climate change. Reaching the collective target requires individual...
Human genetic diversity in the Pacific has not been adequately sampled, particularly in Melanesia. As a result, population relationships there have been open to debate. A genome scan of autosomal markers (687 microsatellites and 203 insertions/deletions) on 952 individuals from 41 Pacific populations now provides the basis for understanding the rem...
Sample Descriptions
Language assignments, sample sizes, expected heterozygosity (He), estimated θ (θ), and mean alleles per locus.
(34 KB XLS)
“Supervised” STRUCTURE Analysis, with the Mãori, Samoans, and Micronesians,and Eight Specified Representative Populations (Europeans [French], East Asians, Taiwan Aborigines, New Guinea, New Britain [Ata and Baining], New Ireland [Kuot], and Bougainville [Aita])
The Mãori, Samoan, and Micronesian individual profiles are compared with eight specifie...
The Divisions of Austronesian Languages
The relationships are shown for, among others, the Taiwanese languages, Malayo-Polynesian, Proto Oceanic, Micronesian, Polynesian, and the Oceanic languages of Island Melanesia and New Guinea. After Blust [10,71,72] and Pawley (personal communication). Some relevant island specifications: Southeast Solomonic...
Neighbor-Joining Trees for the Combined CEPH-HDGP and Pacific Datasets, Using Various Pairwise Distance Statistics
(A) Cavalli-Sforza and Edwards' Chord Distance [33].
(B) Goldstein's (δμ)2 [31].
(C) Nei's chord distance [30].
(D) Proportion of shared alleles (PSA) [73].
(9.3 MB TIF)
Matrix of Pairwise FST “Coancestry” Distances (or Reynolds' D) for the Combined HGDP-CEPH and Pacific Datasets
(92 KB XLS)
Reproducibility of STRUCTURE Runs on the Asia–Pacific Dataset
(15 KB XLS)
Cluster Assignment Probabilities (K = 10) of Pacific Populations, plus HGDP-CEPH East Asian and French Samples
(30 KB XLS)
Asia–Pacific Pairwise FST Coancestry Distance Matrix
(45 KB XLS)
AMOVA Results for Melanesian Islands on 687 Microsatellites
(16 KB XLS)
Reproducibility of STRUCTURE Runs on the Combined Datasets
(15 KB XLS)
Austronesian Coancestry Proportions across 15 Most Consistent Runs (Similarity Coefficients > 0.90)
(39 KB XLS)
Changes to Allele Sizes
(29 KB XLS)
Little is known about the history of click-speaking populations in Africa. Prior genetic studies revealed that the click-speaking Hadza of eastern Africa are as distantly related to click speakers of southern Africa as are most other African populations. The Sandawe, who currently live within 150 km of the Hadza, are the only other population in ea...
An example is provided where, with antagonistic selection and epistatic interaction of alleles at two loci, an autosomal allele can rise in frequency, persist in the population, and even continue to fixation, despite having an apparently lower average fitness than the alternative allele, in a process similar to Parrondo's paradox.
Studies of human mitochondrial (mt) DNA genomes demonstrate that the root of the human phylogenetic tree occurs in Africa. Although 2 mtDNA lineages with an African origin (haplogroups M and N) were the progenitors of all non-African haplogroups, macrohaplogroup L (including haplogroups L0-L6) is limited to sub-Saharan Africa. Several L haplogroup...
The continent of Africa is thought to be the site of origin of all modern humans and is the more recent origin of millions of African Americans. Although Africa has the highest levels of human genetic diversity both within and between populations, it is under-represented in studies of human genetics. Recent advances have been made in understanding...
Several recent analyses provide growing evidence of the influence of positive selection acting in the ancestors of modern humans. Additionally, the best way to explain current fluctuations in neutral variation across the genome is by including negative selection against a high rate of deleterious mutants. We suggest that explaining these predicted...
Real-time PCR analysis is a sensitive template DNA quantitation strategy that has recently gained considerable attention in the forensic community. However, the utility of real-time PCR methods extends beyond quantitation and allows for simultaneous evaluation of template DNA extraction quality. This study presents a computational method that allow...
Simulations of positive directional selection, under parameter values appropriate for approximating human genetic diversity and rates of recombination, reveal that the effects of strong selective sweeps on patterns of linkage disequilibrium (LD) mimic the pattern expected with recombinant hotspots.
The roles of positive directional selection (selective sweeps) and negative selection (background selection) in shaping the genome-wide distribution of genetic variation in humans remain largely unknown. Here, we optimize the parameter values of a model of the removal of deleterious mutations (background selection) to observed levels of human polym...
There is mounting evidence consistent with a general role of positive selection acting on the Drosophila melanogaster X-chromosome. However, this positive selection need not necessarily arise from forces that are adaptive to the organism. Nonadaptive meiotic drive may exist on the X-chromosome and contribute to forces of selection. Females from a r...
Recovery of ancient DNA has become an increasingly important tool in elucidating the origins of past populations and their relationships. Unfortunately, many human skeletal remains do not contain original DNA amplifiable by polymerase chain reaction (PCR). Amino-acid racemization has proven to be a useful predictor of ancient DNA results. We analyz...
Average levels of nucleotide diversity are ten-fold lower in humans than in the fruitfly, Drosophila melanogaster. Despite this difference, apparently as a result of a lower population size, patterns of genomic diversity are strikingly similar in being correlated with local rates of recombination, and influenced by similar interactions between posi...
