Adam H Freedman

Adam H Freedman
Harvard University | Harvard · Faculty of Arts and Sciences Informatics Group

Ph.D

About

73
Publications
18,408
Reads
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1,805
Citations
Introduction
Currently, my research has two tracks. The first of these focuses on bioinformatics methods, specifically for gene expression analysis with RNA-seq, and genome annotation. The second track involves a number of empirical evolutionary genomics projects, including a) speciation in African rainforest lizards, b) developmental transcriptomics of butterflies and frogs, and c) population genetics of wild canids.
Additional affiliations
June 2015 - present
Harvard University
Position
  • Data Scientist
Description
  • Genome and transcriptome hacking and tackling sundry thorny data analysis methods issues related to such things
May 2012 - May 2015
Harvard University
Position
  • Comparative Transcriptomics: Evaluating Convergence and Constraint in Dewlap Pigmentation Across the Anolis Phylogeny
Description
  • Integration of RNA-seq for de novo transcriptome assembly and DE analyses, along with HPLC, and spectral data to understand the genetic basis of dewlap coloration at inter and intra-specific levels in Anolis lizards.
October 2009 - April 2012
University of California, Los Angeles
Position
  • comparative genomics of wolves and dogs
Description
  • NSF Postdoctoral Fellowship -supported comparative genomics of wolves and dogs using NGS data generated on SOLiD and Illumina platforms, to investigation demographic history and natural selection.
Education
January 2004 - June 2005
University of Massachusetts Amherst
Field of study
  • Environmental Science
August 2002 - June 2009
June 1997 - May 2000
University of Florida
Field of study
  • Wildlife Ecology & Conservation

Publications

Publications (73)
Article
Full-text available
Background: Typical experimental design advice for expression analyses using RNA-seq generally assumes that single-end reads provide robust gene-level expression estimates in a cost-effective manner, and that the additional benefits obtained from paired-end sequencing are not worth the additional cost. However, in many cases (e.g., with Illumina N...
Article
De novo transcriptome assembly is a powerful tool, widely used over the last decade for making evolutionary inferences. However, it relies on two implicit assumptions: that the assembled transcriptome is an unbiased representation of the underlying expressed transcriptome, and that expression estimates from the assembly are good, if noisy approxima...
Preprint
Full-text available
De novo transcriptome assembly is a powerful tool, widely used over the last decade for making evolutionary inferences. However, it relies on two implicit assumptions: that the assembled transcriptome is an unbiased representation of the underlying expressed transcriptome, and that expression estimates from the assembly are good, if noisy approxima...
Preprint
Full-text available
Background: Typical experimental design advice for expression analyses using RNA-seq generally assumes that single-end reads provide robust gene-level expression estimates in a cost-effective manner, and that the additional benefits obtained from paired-end sequencing are not worth the additional cost. However, in many cases (e.g., with Illumina Ne...
Article
Full-text available
Climate change related risks and impacts on ectotherms will be mediated by habitats and their influence on local thermal environments. While many studies have documented morphological and genetic aspects of niche divergence across habitats, few have examined thermal performance across such gradients and directly linked this variation to contemporar...
Article
Full-text available
Background Whole genome re-sequencing data from dogs and wolves are now commonly used to study how natural and artificial selection have shaped the patterns of genetic diversity. Single nucleotide polymorphisms, microsatellites and variants in mitochondrial DNA have been interrogated for links to specific phenotypes or signals of domestication. How...
Article
The domestic dog represents one of the most dramatic long-term evolutionary experiments undertaken by humans. From a large wolf-like progenitor, unparalleled diversity in phenotype and behaviour has developed in dogs, providing a model for understanding the developmental and genomic mechanisms of diversification. We discuss pattern and process in d...
Article
The dog is our oldest domesticate and has experienced a wide variety of demographic histories, including a bottleneck associated with domestication and individual bottlenecks associated with the formation of modern breeds. Admixture with gray wolves, and among dog breeds and populations, has also occurred throughout its history. Likewise, the inten...
Article
Full-text available
Controlling for background demographic effects is important for accurately identifying loci that have recently undergone positive selection. To date, the effects of demography have not yet been explicitly considered when identifying loci under selection during dog domestication. To investigate positive selection on the dog lineage early in the dome...
Data
Genome-wide distribution of Δπ, FST, Δ Tajima’s D in 100kb sliding windows. (PDF)
Data
FDR of individual statistics vs. the joint percentile statistic for 100kb windows, used to identify outlier windows in the empirical outlier (non-FDR) approach, for (A) Δπ, (B) FST, and (C) Δ Tajima’s D. (PNG)
Data
Outlier regions identified with the FDR-based method, ranked according to CMS1-FDR. (XLS)
Data
Bi-plots of empirical percentile vs. FDR for individual summary statistics across 100 kb windows, demonstrating that the majority of windows in the top 1% have FDR > 0.01. (A) Entire range of empirical percentile and (B) Focus on the top 20% of the empirical distribution. Horizontal and vertical dotted lines indicate the 99th percentile and 1% FDR,...
Data
Venn diagram displaying overlap of candidate gene sets obtained with FDR-based and empirical outlier (EO) methods for detecting positive selection on the dog lineage. Genes unique to empirical methods relative to FDR methods are those falling within windows with a high false discovery rate (and thus are likely to be enriched with false positives) (...
Data
Distribution of sites fixed between dogs and wolves in neutral and outlier regions according to functional class, filtered according to the requirement that the dog-specific allele be at a frequency of 0.75 or greater among a panel of 12 additional breed dogs. Numbers above bars indicate counts of fixed sites. (PDF)
Data
Description of additional candidate genes. (PDF)
Data
Comparison of distributions computed from neutral coalescent simulations based up the posterior mean parameter estimates from the inferred demographic history, [19] and 1000 samples from the joint posterior distribution for (A) Δπ, (B) FST, and (C) Δ Tajima’s D. (PDF)
Data
Distribution of overlaps between outlier regions detected between methods for FDR and empirical outlier methods. (PDF)
Data
Distribution of CMS1-FDR and the joint percentile statistic for the top and 3rd ranked regions, demonstrating that CMS1-FDR localizes the peak of the outlier region signal more precisely than the joint percentile. (PDF)
Data
All 68 outlier regions identified using the FDR-based methodology using Δπ, FST, Δ Tajima’s D that were validated with the 12-breed dog diversity panel. Columns within “This study” are based on the sequencing data generated here, while those under CanMap are computed from a ~48k SNP data set for a large set of wolves and ancient/basal dog breeds. H...
Article
Full-text available
The tropical forests of the Congo Basin and Gulf of Guinea harbor some of the greatest terrestrial and aquatic biological diversity in the world. However, our knowledge of the rich biological diversity of this region and the evolutionary processes that have shaped it remains limited, as is our understanding of the capacity for species to adapt or o...
Article
Understanding the timing and geographic context of dog origins is a crucial component for understanding human history, as well as the evolutionary context in which the morphological and behavioral divergence of dogs from wolves occurred. A substantial challenge to understanding domestication is that dogs have experienced a complicated demographic h...
Article
Full-text available
To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences sup...
Article
Full-text available
The geographic and temporal origins of the domestic dog remain controversial, as genetic data suggest a domestication process in East Asia beginning 15,000 years ago, whereas the oldest doglike fossils are found in Europe and Siberia and date to >30,000 years ago. We analyzed the mitochondrial genomes of 18 prehistoric canids from Eurasia and the N...
Article
Full-text available
Masai (Giraffa tippelskirchi), Reticulated (G. reticulata) and Rothschild's (G. camelopardalis) giraffe lineages in East Africa are morphologically and genetically distinct, yet in Kenya their ranges abut. This raises the question of how divergence is maintained among populations of a large mammal capable of long-distance travel, and which readily...
Article
Full-text available
To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we analyzed novel high-quality genome sequences of three gray wolves, one from each of three putative centers of dog domestication, two ancient dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. We find dogs and wolves diverg...
Article
Full-text available
A five-day international workshop was recently convened at the Universite´ des Sciences et Techniques de Masuku in Gabon to enhance international collaboration among Central African, US and European scientists, conservation professionals and policy makers. The overall aims of the workshop were to: (1) discuss emerging priorities in biodiversity and...
Article
In the debate over modes of vertebrate diversification in tropical rainforests, two competing hypotheses of speciation predominate: those that emphasize the role of geographical isolation during glacial periods and those that stress the role of ecology and diversifying selection across ecotones or environmental gradients. To investigate the relativ...
Data
Additional detailed information concerning methods and results. (0.04 MB DOC)
Data
Full-text available
Weighted least-squares regressions of morphological traits on percent tree cover. (0.05 MB PDF)
Data
Coordinates, habitat classification, percent tree cover, and sample sizes for A. virens captured and measured by TBS in West and Central Africa. (0.06 MB PDF)
Data
Full-text available
Additional projections of morphological traits, based upon the associations between traits and tree cover. Associations are estimated with least-squares linear regression. For all traits, morphological diversity in West Africa has been lost due to flattening of the rainforest-savanna gradient. (3.16 MB PDF)
Data
Full-text available
Historical specimens of A. virens measured at the Natural History Museum at Tring, United Kingdom. (0.06 MB PDF)
Article
Full-text available
Ecological gradients have long been recognized as important regions for diversification and speciation. However, little attention has been paid to the evolutionary consequences or conservation implications of human activities that fundamentally change the environmental features of such gradients. Here we show that recent deforestation in West Afric...
Article
Studies of rainforest diversification that simultaneously consider the effects of genetic drift and natural selection are rare. We use Amplified Fragment Length Polymorphism genome scans of the African rainforest lizard Trachylepis affinis from Cameroon to examine the spatial patterns and environmental associations of both neutrally evolving loci a...
Article
Spatial analytical methods have been used by biologists for decades, but with new modelling approaches and data availability their application is accelerating. While early approaches were purely spatial in nature, it is now possible to explore the underlying causes of spatial heterogeneity of biological variation using a wealth of environmental dat...
Article
Full-text available
Landscape genetics is an emerging discipline that utilizes environmental and historical data to understand geographic patterns of genetic diversity. Niche modelling has added a new dimension to such efforts by allowing species-environmental associations to be projected into the past so that hypotheses about historical vicariance can be generated an...
Article
Full-text available
We used artificial nests modeled after those of Trachemys scripta, a wide-ranging freshwater turtle species, to evaluate the effects of deer feeders, habitat type and visual and olfactory cues on nest predation in northern Florida. Nests were placed at lake sites with and without deer feeders, and in three habitat types: road, edge and forest. Over...
Article
We used a species-distribution modeling approach, ground-based climate data sets, and newly available remote-sensing data on vegetation from the MODIS and Quick Scatterometer sensors to investigate the combined effects of human-caused habitat alterations and climate on potential invasions of rainforest by 3 savanna snake species in Cameroon, Centra...
Article
Full-text available
Spatial patterns of plant cover and species composition in arctic salt marsh and salt affected tundra near Prudhoe Bay, Alaska reflect gradients in elevation, soil conductivity, and soil concentrations of the ions prevalent in seawater. Soil conductivity and soil concentrations of Ca2+, Mg2+, Na+, K+, SO4 = and Cl– were significantly related to sit...
Article
We used matrix population models to evaluate the relative importance of different vital rates to population growth (λ) for female black bears on the Southeastern Coastal Plain (SCP) of the United States, and to determine whether reductions in subadult and adult survival due to ongoing habitat fragmentation and human disturbance will cause shifts in...

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