Zachary Fuller

Zachary Fuller
Columbia University | CU · Department of Biological Sciences

About

35
Publications
3,600
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
491
Citations

Publications

Publications (35)
Preprint
Full-text available
When adaptive phenotypic variation maps within an inverted segment of a chromosome, researchers often despair because it is thought that the suppression of crossing over will prevent the discovery of selective target genes through fine scale genetic mapping. If an inversion polymorphism is old enough, then the accumulation of gene conversion tracts...
Preprint
Full-text available
Causal loss-of-function (LOF) variants for Mendelian and severe complex diseases are enriched in "mutation intolerant" genes. We show how such observations can be interpreted in light of a model of mutation-selection balance, and use the model to relate the pathogenic consequences of LOF mutations at present-day to their evolutionary fitness effect...
Article
Full-text available
At the Rowley Shoals in Western Australia, the prominent reef flat becomes exposed on low tide and the stagnant water in the shallow atoll lagoons heats up, creating a natural laboratory for characterizing the mechanisms of coral resilience to climate change. To explore these mechanisms in the reef coral Acropora tenuis, we collected samples from l...
Article
Full-text available
New emerging infectious diseases are identified every year, a subset of which become global pandemics like COVID-19. In the case of COVID-19, many governments have responded to the ongoing pandemic by imposing social policies that restrict contacts outside of the home, resulting in a large fraction of the workforce either working from home or not w...
Article
Full-text available
Broadcast‐spawning coral species have wide geographic ranges spanning strong environmental gradients, but it is unclear how much spatially varying selection these gradients actually impose. Strong divergent selection might present a considerable barrier for demographic exchange between disparate reef habitats. We investigated whether the cross‐shel...
Preprint
Full-text available
Broadcast-spawning coral species have wide geographic ranges, spanning strong environmental gradients, but it is unclear how much spatially varying selection these gradients actually impose. Strong divergent selection might present a considerable barrier for demographic exchange between disparate reef habitats. We investigated whether the cross-she...
Article
Sex-Ratio ( SR ) chromosomes are selfish X -chromosomes that distort Mendelian segregation and are commonly associated with inversions. These chromosomal rearrangements suppress recombination with Standard ( ST ) X -chromosomes and are hypothesized to maintain multiple alleles important for drive in a single large haplotype. Here, we conduct a mult...
Article
Full-text available
Conservation help from genomics Corals worldwide are under threat from rising sea temperatures and pollution. One response to heat stress is coral bleaching—the loss of photosynthetic endosymbionts that provide energy for the coral. Fuller et al. present a high-resolution genome of the coral Acropora millepora (see the Perspective by Bay and Guerre...
Preprint
Many governments have responded to the ongoing COVID-19 pandemic by imposing social policies that restrict interactions outside of the home, resulting in a large fraction of the workforce either working from home or not working. However, to maintain essential services, a substantial number of workers are not subject to these limitations, and mainta...
Preprint
Full-text available
Although reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly her-itable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We...
Article
In numerous applications, from working with animal models to mapping the genetic basis of human disease susceptibility, knowing whether a single disrupting mutation in a gene is likely to be deleterious is useful. With this goal in mind, a number of measures have been developed to identify genes in which protein-truncating variants (PTVs), or other...
Preprint
Segregation distorters violate Mendelian Inheritance by over-representing themselves in the progeny of carrier individuals and are commonly associated with chromosomal inversions. When distorting alleles are found on sex chromosomes, the progeny of carrier individuals will exhibit skewed sex ratios, as exemplified by the array of Sex-Ratio ( SR ) d...
Article
Full-text available
The gene arrangements of Drosophila have played a prominent role in the history of evolutionary biology from the original quantification of genetic diversity to current studies of the mechanisms for the origin and establishment of new inversion mutations within populations and their subsequent fixation between species supporting reproductive barrie...
Preprint
Full-text available
In numerous applications, from working with animal models to mapping the genetic basis of human disease susceptibility, it is useful to know whether a single disrupting mutation in a gene is likely to be deleterious. With this goal in mind, a number of measures have been developed to identify genes in which protein-truncating variants (PTVs), or ot...
Article
Full-text available
Understanding the role of chromosomal inversions in speciation is a fundamental problem in evolutionary genetics. Here, we perform a comprehensive reconstruction of the evolutionary histories of the chromosomal inversions in Drosophila persimilis and D. pseudoobscura. We provide a solution to the puzzling origins of the selfish Sex-Ratio arrangemen...
Data
Polytene squash of a D. persimilis ST/SR female heterozygote. The XR chromosome is contains a single inversion as observed by a characteristic inversion loop. The remainder of the genome is homosequential. (PDF)
Data
Species clustering within inversion polymorphisms on chromosome 3. The D. pseudoobscura 3rd chromosome arrangements Standard (ST) and Arrowhead (AR) lack the large breakpoint-specific phylogenetic discordance observed at the inversion break points of the inversion between D. pseudoobscura and D. persimilis SR on chromosome XR. While some windows de...
Data
PCR amplification of the proximal breakpoint. Genomic template from D. pseudoobscura and D. persimilis SR, but not D. persimilis ST, generated an approximately 1.5kb amplicon of the proximal breakpoint with primers specific for the ancestral orientation of the XR chromosome. (PDF)
Data
Isolation with initial migration model. The width of the bars are proportional to the population sizes and the heights of bars indicate time using the maximum likelihood approach of Costa and Wilkinson-Herbots (2017). The ancestral population for each set of data is indicated by a single colored bar that splits into two subpopulations at time t0. F...
Data
Supplementary methods for phylogenetic and divergence analyses in D. pseudoobscura. This text details the methods used to analyze phylogenetic discordance on the third chromosome of D. pseudoosbcura and D. persimilis. Further, this text contains the methods used to determine the relative age of the Arrowhead (3AR) and Pikes Peak (3PP) arrangements...
Data
Introgression of the D. pseudoobscura ST arrangement into a D. persimilis genetic background. Despite 15 generations of marker-assisted backcrossing, all hybrid males that carry the D. pseudoobscura XR material in an otherwise D. persimilis genetic background are sterile. These results indicate that the chromosome-level gene exchange must have happ...
Data
Divergence in sliding windows across chromosomes. Smoothing splines are shown for divergence measured as relative node depth (RND) in 10kb windows across chromosomes XR (A), XL (B), and 2 (C). The different colors for each line indicate the taxa pair RND is estimated for, with the key in the legend. Colored dots represent individual windows that ar...
Data
D. pseudoobscura and D. persimilis reference alignment statistics. Statistics are presented for the total number of reads mapped to the D. pseudoosbcura reference genome for each sample and the D. miranda outgroup. (PDF)
Data
Reference alignment statistics for each sample across scaffolds. Each scaffold in the D. pseudoobscura reference genome is listed, with corresponding coverage and mapping statistics for each sample and the D. miranda outgroup. (PDF)
Article
Full-text available
Bee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studies o...
Preprint
Full-text available
Bee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate the impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studi...
Preprint
Full-text available
The chromosomal inversions of D. persimilis and D. pseudoobscura have deeply influenced our understanding of the evolutionary forces that shape natural variation, speciation, and selfish chromosome dynamics. Here, we perform a comprehensive reconstruction of the evolutionary histories of the chromosomal inversions in these species. We provide a sol...
Article
The evolution of complex traits in heterogeneous environments may shape the order of genes within chromosomes. Drosophila pseudoobscura has a rich gene arrangement polymorphism that allows one to test evolutionary genetic hypotheses about how chromosomal inversions are established in populations. D. pseudoobscura has >30 gene arrangements on a sing...
Preprint
The evolution of complex traits in heterogeneous environments may shape the order of genes within chromosomes. Drosophila pseudoobscura has a rich gene arrangement polymorphism that allows one to test evolutionary genetic hypotheses about how chromosomal inversions are established in populations. D. pseudoobscura has >30 gene arrangements on a sing...
Article
Chromosomal rearrangements can shape the structure of genetic variation in the genome directly through alteration of genes at breakpoints or indirectly by holding combinations of genetic variants together due to reduced recombination. The third chromosome of Drosophila pseudoobscura is a model system to test hypotheses about how rearrangements are...
Article
Full-text available
With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population d...
Article
Full-text available
There has been a renewed interest in investigating the role of stabilizing selection acting on genome-wide traits such as codon usage bias. Codon bias, when synonymous codons are utilized at unequal frequencies, occurs in a wide variety of taxa. Standard evolutionary models explain the maintenance of codon bias through a balance of genetic drift, m...

Network

Cited By

Projects

Project (1)
Project
The laboratory uses genomic and transciptomic data to understand the evolutionary genomic mechanisms that lead to the establish and maintain inversion mutations in populations. Inversions are chromosomal mutations occur when a chromosome breaks at two sites on a chromosome and the central sequence rejoins in reverse order.