Daren C. Card

Daren C. Card
Harvard University | Harvard · Department of Organismic and Evolutionary Biology

Doctor of Philosophy

About

82
Publications
32,752
Reads
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1,568
Citations
Introduction
I am an NSF Postdoctoral Fellow in Scott Edwards' lab at Harvard University. I use primarily genomic data to study various questions in evolutionary biology, normally using squamate reptiles as a model system.
Additional affiliations
September 2018 - present
Harvard University
Position
  • PostDoc Position
September 2012 - May 2018
University of Texas at Arlington
Position
  • Research Assistant
Description
  • Zoology Laboratory (Fall 2012, 2014, 2015, 2016, 2017; Spring 2013, 2014, 2015, 2016, 2017, 2018; Summer 2013, 2014, 2015, 2016) Human Anatomy Lecture & Laboratory (Fall 2013)
September 2012 - August 2018
University of Texas at Arlington
Position
  • Researcher
Education
August 2012 - August 2018
University of Texas at Arlington
Field of study
  • Quantitative Biology
August 2009 - May 2011
August 2006 - May 2008
Jamestown Community College
Field of study
  • Individual Studies

Publications

Publications (82)
Article
Full-text available
Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic a...
Article
Boa is a neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within...
Article
Full-text available
As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome covera...
Article
Genome scans are widely used to identify "outliers" in genomic data: loci with different patterns compared with the rest of the genome due to the action of selection or other non-adaptive forces of evolution. These genomic datasets are often high-dimensional, with complex correlation structures among variables, making it a challenge to identify out...
Article
Full-text available
Snake venom gene evolution has been studied intensively over the past several decades, yet most previous studies have lacked the context of complete snake genomes and the full context of gene expression across diverse snake tissues. We took a novel approach to studying snake venom evolution by leveraging the complete genome of the Burmese python, i...
Article
Full-text available
Sex chromosomes diverge after the establishment of recombination suppression, resulting in differential sex-linkage of genes involved in genetic sex determination and dimorphic traits. This process produces systems of male or female heterogamety wherein the Y and W chromosomes are only present in one sex and are often highly degenerated. Sex-limite...
Article
Full-text available
Background The increasing number of chromosome-level genome assemblies has advanced our knowledge and understanding of macroevolutionary processes. Here, we introduce the genome of the desert horned lizard, Phrynosoma platyrhinos, an iguanid lizard occupying extreme desert conditions of the American southwest. We conduct analysis of the chromosomal...
Article
Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on...
Article
Full-text available
Facultative parthenogenesis (FP) is widespread in the animal kingdom. In vertebrates it was first described in poultry nearly 70 years ago, and since then reports involving other taxa have increased considerably. In the last two decades, numerous reports of FP have emerged in elasmobranch fishes and squamate reptiles (lizards and snakes), including...
Article
Objectives: Metallo-β-lactamases (MBLs) are an emerging class of antimicrobial resistance enzymes that degrade β-lactam antibiotics, including last-resort carbapenems. Infections caused by carbapenemase-producing Enterobacteriaceae (CPE) are increasingly prevalent, but treatment options are limited. While several serine-dependent β-lactamase inhib...
Article
Full-text available
Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew spe...
Article
Full-text available
Convergent evolution is often documented in organisms inhabiting isolated environments with distinct ecological conditions and similar selective regimes. Several Central America islands harbor dwarf Boa populations that are characterized by distinct differences in growth, mass, and craniofacial morphology, which are linked to the shared arboreal an...
Article
The study of recently diverged lineages whose geographical ranges come into contact can provide insight into the early stages of speciation and the potential roles of reproductive isolation in generating and maintaining species. Such insight can also be important for understanding the strategies and challenges for delimiting species within recently...
Article
Full-text available
Background: The Veiled Chameleon (Chamaeleo calyptratus) is an emerging model system for studying functional morphology and evolutionary developmental biology (evo-devo). Chameleons possess body plans that are highly adapted to an arboreal life style, featuring laterally compressed bodies, split hands/feet for grasping, a projectile tongue, turret...
Article
Several snake species that feed infrequently in nature have evolved the ability to massively upregulate intestinal form and function with each meal. While fasting, these snakes downregulate intestinal form and function, and upon feeding restore intestinal structure and function through major increases in cell growth and proliferation, metabolism an...
Article
Full-text available
Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of geno...
Article
The study of recently diverged lineages whose geographical ranges come into contact can provide insight into the early stages of speciation and the potential roles of reproductive isolation in generating and maintaining species. Such insight can also be important for understanding the strategies and challenges for delimiting species within recently...
Article
Here we use a chromosome-level genome assembly of a prairie rattlesnake (Crotalus viridis), together with Hi-C, RNA-seq, and whole-genome resequencing data, to study key features of genome biology and evolution in reptiles. We identify the rattlesnake Z Chromosome, including the recombining pseudoautosomal region, and find evidence for partial dosa...
Preprint
Full-text available
Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part due to the advent of genomic...
Article
Full-text available
Invasive species provide powerful in situ experimental systems for studying evolution in response to selective pressures in novel habitats. While research has shown that phenotypic evolution can occur rapidly in nature, few examples exist of genome‐wide adaptation on short ‘ecological’ timescales. Burmese pythons (Python molurus bivittatus) have be...
Article
Full-text available
Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, beha...
Article
Full-text available
Broad paradigms of vertebrate genomic repeat element evolution have been largely shaped by analyses of mammalian and avian genomes. Here, based on analyses of genomes sequenced from over 60 squamate reptiles (lizards and snakes), we show that patterns of genomic repeat landscape evolution in squamates challenge such paradigms. Despite low variance...
Article
The Mojave rattlesnake (Crotalus scutulatus) inhabits deserts and arid grasslands of the western United States and Mexico. Despite considerable interest in its highly toxic venom and the recognition of two subspecies, no molecular studies have characterized range-wide genetic diversity and population structure or tested species limits within C. scu...
Article
The visual systems of snakes are heavily modified relative to other squamates, a condition often thought to reflect their fossorial origins. Further modifications are seen in caenophidian snakes, where evolutionary transitions between rod and cone photoreceptors, termed photoreceptor transmutations, have occurred in many lineages. Little previous w...
Article
Full-text available
The assumption of strictly neutral evolution is fundamental to the multispecies coalescent model and permits the derivation of gene tree distributions and coalescent times conditioned on a given species tree. In this study, we conduct computer simulations to explore the effects of violating this assumption in the form of species-specific positive s...
Article
Full-text available
How does climate variation limit the range of species and what does it take for species to colonize new regions? In this issue of Molecular Ecology, Campbell‐Staton et al. (2018) address these broad questions by investigating cold tolerance adaptation in the green anole lizard (Anolis carolinensis) across a latitudinal transect. By integrating phys...
Article
Full-text available
We describe ThetaMater, an open source R package comprising a suite of functions for efficient and scalable Bayesian estimation of the population size parameter θ from genomic data. Availability: ThetaMater is available at Github (https://github.com/radamsRHA/ThetaMater). Contact: todd.castoe@uta.edu. Supplementary information: Supplementary...
Article
For over 50 years, biologists have accepted that all extant snakes share the same ZW sex chromosomes derived from a common ancestor [1–3], with different species exhibiting sex chromosomes at varying stages of differentiation. Accordingly, snakes have been a well-studied model for sex chromosome evolution in animals [1, 4]. A review of the literatu...
Article
Full-text available
Research has shown that a change in environmental conditions can alter the expression of traits during development (i.e., 'within-generation phenotypic plasticity') as well as induce heritable phenotypic responses that persist for multiple generations (i.e., 'transgenerational plasticity'). It has long been assumed that shifts in gene expression ar...
Article
The growing wealth of genomic data is yielding new insights into the genetic basis of adaptation, but it also presents the challenge of extracting the relevant signal from multi-dimensional datasets. Different statistical approaches vary in their power to detect selection depending on the demographic history, type of selection, genetic architecture...
Article
Full-text available
Background Previous studies examining post-feeding organ regeneration in the Burmese python (Python molurus bivittatus) have identified thousands of genes that are significantly differentially regulated during this process. However, substantial gaps remain in our understanding of coherent mechanisms and specific growth pathways that underlie these...
Article
Full-text available
Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake (Crotalus atrox) to determine whethe...
Article
Full-text available
Despite continued advances in sequencing technologies, there is a need for methods that can efficiently sequence large numbers of genes from diverse species. One approach to accomplish this is targeted capture (hybrid enrichment). While these methods are well established for genome resequencing projects, cross-species capture strategies are still b...
Article
The evolution of sexual dimorphismis predicted to occur through reductions in between-sex genetic correlations (rmf) for shared traits, but the physiological and genetic mechanisms that facilitate these reductions remain largely speculative. Here, we use a paternal half-sibling breeding design in captive brown anole lizards (Anolis sagrei) to show...
Article
Full-text available
Background In areas where schistosomiasis control programs have been implemented, morbidity and prevalence have been greatly reduced. However, to sustain these reductions and move towards interruption of transmission, new tools for disease surveillance are needed. Genomic methods have the potential to help trace the sources of new infections, and a...
Data
Recovery of loci in worm DNA sequences. The fraction of expected genomic fragments recovered in a single replicate from unamplified adult worm DNA is shown for each fragment size at different coverage depths. Individual samples are depicted as follows (a) index 1, barcode 1; (b) index 1, barcode 2; (c) index 1, barcode 3; (d) index 1, barcode 4; (e...
Data
Number of fragments sequenced between 300 and 600 bp recovered in each miracidium sample. Index barcode combinations correspond to individual miracidia as follows: index 1, barcode 1, miracidia 5; index 1, barcode 2, miracidia 6; index 1, barcode 3, miracidia 1; index 1, barcode 4, miracidia 2; index 2, barcode 1, miracidia 3; index 2, barcode 2, m...
Data
PCR primers for potentially amplifiable microsatellite loci. Primer sequences, annealing temperatures, and related information for potentially amplifiable microsatellite loci from paired-end sequencing of S. japonicum ddRADseq loci. (XLSX)
Data
Predicted fragment size distribution from double restriction enzyme digestion. The predicted distribution of double-digested fragment (those with one cut site from each enzyme) sizes is shown, as determined by in silico digestion of the reference S. japonicum genome [27]. (TIF)
Data
Number of loci recovered among eight miracidia samples. The number of genomic fragments recovered from each of the amplified miracidia is shown for expected fragment sizes up to 600bp at different coverage depths. Individual samples are depicted as follows (a) index 1, barcode 1, miracidia 5; (b) index 1, barcode 2, miracidia 6; (c) index 1, barcod...
Data
ddRADseq adaptor and primer sequences. Sequences of olionucleotides used as adaptors and PCR primers. (PDF)
Data
Number of fragments under 600 bp sequenced in each miracidium sample. Index barcode combinations correspond to individual miracidia as follows: index 1, barcode 1, miracidia 5; index 1, barcode 2, miracidia 6; index 1, barcode 3, miracidia 1; index 1, barcode 4, miracidia 2; index 2, barcode 1, miracidia 3; index 2, barcode 2, miracidia 7; index 2,...
Data
Genotype sharing among eight miracidia samples. Pairwise comparison of similarity between 8 miracidia samples at 67,525 bi-allelic variants. The mean similarity is depicted as the top number in each cell, with the mean ± 2 standard deviations shown as the bottom row in each cell. Shading within cells corresponds to the degree of similarity for the...
Data
Recovery of loci in miracidia DNA sequences from eight samples. The fraction of expected genomic fragments recovered from each of the amplified miracidia is shown for each fragment size up to 600bp at different coverage depths. Individual samples are depicted as follows (a) index 1, barcode 1, miracidia 5; (b) index 1, barcode 2, miracidia 6; (c) i...
Preprint
Full-text available
Despite continued advances in sequencing technologies, there is a need for methods that can efficiently sequence large numbers of genes from diverse species. One approach to accomplish this is targeted capture (hybrid enrichment). While these methods are well established for genome resequencing projects, cross-species capture strategies are still b...
Article
Full-text available
Availability: GppFst is available at Github (https://github.com/radamsRHA/GppFst). Contact: todd.castoe@uta.eduSupplementary information: Supplementary files are available at github.com/radamsRHA/GppFst.
Preprint
Full-text available
Genome scans are widely used to identify “outliers” in genomic data: loci with different patterns compared with the rest of the genome due to the action of selection or other non-adaptive forces of evolution. These genomic datasets are often high-dimensional, with complex correlation structures among variables, making it a challenge to identify out...
Article
Strong spatial sorting of genetic variation in contiguous populations is often explained by local adaptation or secondary contact following allopatric divergence. A third explanation, spatial sorting by stochastic effects of range expansion, has been considered less often though theoretical models suggest it should be widespread, if ephemeral. In a...
Article
Full-text available
The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray...
Chapter
Full-text available
Squamates exhibit some of the most extreme and fascinating biological adaptations among vertebrates, including the production of a wide diversity of venom toxins. The rapid accumulation of genomic information from squamate reptiles is generating important new context and insights into the biology, the regulation and diversity of venom toxins, and t...