Jonathan B Puritz

Jonathan B Puritz
University of Rhode Island | URI · Department of Biological Sciences

PhD University of Hawaii

About

42
Publications
11,749
Reads
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1,850
Citations
Additional affiliations
January 2014 - February 2016
Texas A&M University - Corpus Christi
Position
  • PostDoc Position
August 2012 - January 2014
Texas A&M University
Position
  • PostDoc Position
January 2012 - August 2012
University of Hawaiʻi at Mānoa
Position
  • PostDoc Position

Publications

Publications (42)
Article
Full-text available
The ecological impact of large coastal human populations on marine ecosystems remains relatively unknown. Here, we examine the population structure of Patiria miniata, the bat star, and correlate genetic distances with a model based on flow rates and proximity to P. miniata populations for the four major stormwater runoff and wastewater effluent so...
Article
Full-text available
Exome capture is an effective tool for surveying the genome for loci under selection. However, traditional methods require annotated genomic resources. Here, we present a method for creating cDNA probes from expressed mRNA, which are then used to enrich and capture genomic DNA for exon regions. This approach, called “EecSeq”, eliminates the need fo...
Article
Full-text available
Standing genetic variation enables or restricts a population's capacity to respond to changing conditions, including the extreme disturbances expected to increase in frequency and intensity with continuing anthropogenic climate change. However, we know little about how populations might respond to extreme events with rapid genetic shifts, or how po...
Article
Full-text available
We are writing in response to the population and phylogenomics meeting review by Andrews & Luikart (2014) entitled “Recent novel approaches for population genomics data analysis.” Restriction-site associated DNA (RAD) sequencing has become a powerful and useful approach in molecular ecology, with several different published methods now available to...
Article
Full-text available
Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high level...
Article
Full-text available
Marine protected areas (MPAs) have the potential to conserve biodiversity and improve fishery sustainability, but their efficacy depends on sound design and implementation, which requires an understanding of connectivity among reserves and between reserves and fished areas. Most studies of connectivity involving reserves focus on fishes with charac...
Article
Red snapper, Lutjanus campechanus, supports one of the more important fisheries in marine waters of the United States. Consequently, it has been the focus of intensive fisheries research for more than 20 years. Here, we present a genomic analysis of population structure that uses a landscape genetics approach to characterize patterns of variation i...
Article
Dispersal drives diverse processes from population persistence to community dynamics. However, the amount of temporal variation in dispersal and its consequences for metapopulation dynamics is largely unknown for organisms with environmentally driven dispersal (e.g., many marine larvae, arthropods and plant seeds). Here, we used genetic parentage a...
Preprint
Dispersal drives diverse processes from population persistence to community dynamics. However, the amount of temporal variation in dispersal and its consequences for metapopulation dynamics is largely unknown for organisms with environmentally driven dispersal (e.g., many marine larvae, arthropods, and plant seeds). Here, we quantify variation in t...
Experiment Findings
Full-text available
Use EecSeq data from Crassostrea virginica (Eastern Oyster) to identify de novo exome assembly programs strengths and weakness in non model species. Prepare exome sequences, build six different exome assemblies from five programs, and assess using N 50 values, Annotations, and BUSCO.
Article
Full-text available
Sequencing reduced‐representation libraries of restriction‐site associated DNA (RADseq) to identify single nucleotide polymorphisms (SNPs) is quickly becoming a standard methodology for molecular ecologists. Because of the scale of RADseq data sets, putative loci cannot be assessed individually, making the process of filtering noise and correctly i...
Preprint
Full-text available
Exome capture is an effective tool for surveying the genome for loci under selection. However, traditional methods require annotated genomic resources. Here, we present a method for creating cDNA probes from expressed mRNA, which are then used to enrich and capture genomic DNA for exon regions. This approach, called “EecSeq”, eliminates the need fo...
Article
Full-text available
Life-history traits, especially the mode and duration of larval development, are expected to strongly influence the population connectivity and phylogeography of marine species. Comparative analysis of sympatric, closely related species with differing life histories provides the opportunity to specifically investigate these mechanisms of evolution...
Article
Full-text available
Next-generation sequencing of reduced-representation genomic libraries provides a powerful methodology for genotyping thousands of single nucleotide polymorphisms (SNPs) among individuals of non-model species. Utilizing genotype data in the absence of a reference genome, however, presents a number of challenges. One major challenge is the tradeoff...
Article
Full-text available
Conservation and management of exploited species depends on accurate knowledge of how genetic variation is partitioned across a shery, especially as it relates to recruitment. Using double-digest restriction-site associated DNA sequencing, we surveyed variation in 7,382 single nucleotide polymorphisms (SNPs) in red snapper (Lutjanus campechanus) yo...
Article
Full-text available
Seascape genetics, a term coined in 2006, is a fast growing area of population genetics that draws on ecology, oceanography and geography to address challenges in basic understanding of marine connectivity and applications to management. We provide an accessible overview of the latest developments in seascape genetics that merge exciting new ideas...
Article
Full-text available
Sex-biased dispersal is expected to homogenize nuclear genetic variation relative to variation in genetic material inherited through the philopatric sex. When site fidelity occurs across a heterogeneous environment, local selective regimes may alter this pattern. We assessed spatial patterns of variation in nuclear-encoded, single nucleotide polymo...
Article
Full-text available
A total of 2,206 base pairs of coding sequences of mitochondrial DNA from nine of 10 lutjanine (Lutjanidae) species endemic to the eastern Pacific Ocean were used in a phylogenetic analysis to infer species relationships among lutjanines on either side of the Isthmus of Panama. Monotypic Hoplopagrus (guentherii) appears to be at the base of all lut...
Article
Full-text available
Spawning patterns and reproductive variance of Spotted Seatrout Cynoscion nebulosus dams and sires at two restoration enhancement facilities in Texas were assessed across a spawning year by using parentage analysis based on 12 variable microsatellite loci. In total, 72.6% of all dams and sires contributed to at least one spawning event, although in...
Preprint
Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for organisms with large effective population sizes and high levels of genet...
Preprint
Full-text available
Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for organisms with large effective population sizes and high levels of genet...
Article
Full-text available
Here, we introduce ezRAD, a novel strategy for restriction site-associated DNA (RAD) that requires little technical expertise or investment in laboratory equipment, and demonstrate its utility for ten non-model organisms across a wide taxonomic range. ezRAD differs from other RAD methods primarily through its use of standard Illumina TruSeq library...
Conference Paper
Red snapper (Lutjanus campechanus) historically has supported extremely important commercial and recreational fisheries in U.S. waters, but has been overfished for at least the last 25 years. Successful rebuilding efforts and future management of these fisheries depend on accurate knowledge of genetic structure and connectivity among subpopulations...
Article
Full-text available
We document an extreme example of reproductive trait evolution that affects population genetic structure in sister species of Parvulastra cushion stars from Australia. Self-fertilization by hermaphroditic adults and brood protection of benthic larvae causes strong inbreeding and range-wide genetic poverty. Most samples were fixed for a single allel...
Article
Full-text available
Next-generation sequencing technology can now provide population biologists and phylogeographers with information at the genomic scale; however, many pertinent questions in population genetics and phylogeography can be answered effectively with modest levels of genomic information. For the past two decades, most population-level studies have lacked...
Article
Full-text available
The susceptibility of the Y chromosome to sexual selection may make this chromosome an important player in the formation of reproductive isolating barriers, and ultimately speciation. Here, we investigate the role of the Y chromosome in phenotypic divergence and reproductive isolation of spinner dolphin (Stenella longirostris) ecotypes. This specie...
Article
The present study investigated the fine-scale population genetic structure of sympatric asterinid sea stars with contrasting modes of larval development (benthic versus pelagic). Parvulastra exigua lacks a dispersive life phase yet is one of the worlds most widely distributed and abundant sea stars, whereas Meridiastra calcar, a sea star with a dis...
Article
Full-text available
Life history plays a critical role in governing microevolutionary processes such as gene flow and adaptation, as well as macroevolutionary processes such speciation. Here, we use multilocus phylogeographic analyses to examine a speciation event involving spectacular life-history differences between sister species of sea stars. Cryptasterina hystera...
Article
Full-text available
The field of phylogeography has long since realized the need and utility of incorporating nuclear DNA (nDNA) sequences into analyses. However, the use of nDNA sequence data, at the population level, has been hindered by technical laboratory difficulty, sequencing costs, and problematic analytical methods dealing with genotypic sequence data, especi...
Data
Allelic networks for GPI in Meridiastra calcar. Network on top was obtained via 454 sequencing and the bottom from direct Sanger Sequencing. Samples from New South Wales are colored in blue, Tasmania in red, and Southern Australia in green. Numbers on network branches represent the number of mutational steps (including INDEL) between alleles. (DOCX...
Data
Complete List of Primers. (DOCX)
Article
Full-text available
Disruptive selection caused by ecological differences among habitats is inferred to be an important cause of phenotypic evolution and reproductive isolation, but is often hard to distinguish from other drivers of speciation. Here, we use multilocus phylogeographic analyses to examine a speciation event involving spectacular life history differences...
Article
Full-text available
Determining the geographic scale at which to apply ecosystem-based management (EBM) has proven to be an obstacle for many marine conservation programs. Generalizations based on geographic proximity, taxonomy, or life history characteristics provide little predictive power in determining overall patterns of connectivity, and therefore offer little i...
Article
Patiria miniata, a broadcast-spawning sea star species with high dispersal potential, has a geographic range in the intertidal zone of the northeast Pacific Ocean from Alaska to California that is characterized by a large range gap in Washington and Oregon. We analyzed spatial genetic variation across the P. miniata range using multilocus sequence...
Article
Full-text available
Species distributions may be dramatically affected by climatic variability, such as occurred during Pleistocene glaciation. Populations of coastal organisms could have been affected directly by ice movement or through sea level change. Response could involve shifts in distribution southwards or persistence through the full range or in limited high-...
Article
Full-text available
Methoprene is a pesticide that acts as a juvenile hormone agonist. Although developed initially against insects, it has since been shown to have toxic effects on larval and adult crustaceans. Methoprene was one of several pesticides applied to the Western Long Island Sound (WLIS) watershed area during the summer of 1999; the other pesticides were m...

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Project (1)
Project
This is largely a filler so ResearchGate stops bugging me about this.