Research Vision

Background and Motivation

Human beings have impacted every ecosystem on the planet, with the most rapid and extensive change happening in the last 50 years.  Anthropogenic changes, such as global climate change and global ocean change, have led to an unprecedented loss of biodiversity, nearly 1000X higher than expected.  I believe that there is a critical need for biologists to investigate the natural processes that maintain biodiversity AND to understand human impacts upon these processes. Marine species also present a unique challenge for ecologists: the biphasic life cycle- benthic, sedentary adults and dispersing larvae that can traverse pelagic waters from minutes to several months.  For many species, population connectivity via larval dispersal is the only means of maintaining genetic diversity among populations; additionally, larvae are more sensitive than adults to stressors, making them a conduit for environmental selection to alter genetic diversity.  During my career, I have built a genomics-based research program investigating how natural and anthropogenic processes impact the evolution of marine populations through the lens of larval dispersal.

Research Accomplishments and Current Directions

Developing Genomic and Bioinformatic Tools

Over the last few years, next-generation sequencing technology has transcended population genetics to population genomics.  Sequencer outputs have expanded from kilobases to gigabases while becoming over 30,000 times less expensive per base pair of DNA sequenced.  This allows population levels studies to use thousands of genetic markers across the entire genome, and to survey both neutral and adaptive loci.  I have focused the early part of my career on adopting next-generation sequencing technology and embracing an ever-adapting genomic toolkit to take advantage of this unprecedented amount of genetic data.  I have published multiple laboratory methods taking advantage of various next-generation sequencing (NGS) technologies (Puritz et al. 2012, Puritz et al. 2013; Toonen et al. 2013).  In addition, I have created custom analysis pipelines for NGS technologies, including the most accurate software pipeline (dDocent; for analyzing all types of Restriction Association DNA (RAD) data sets (Puritz et al. 2014; Puritz et al. In Prep), and have co-authored one of the most widely cited overviews of RAD methodologies and analysis to date (Puritz et al. 2014).  Currently, I am working collaboratively with David Portnoy at Texas A&M University Corpus Christi to sequence the red snapper (Lutjanus campechanus) genome using a hybrid approach of Illumina and Pacific Biosciences (third-generation) sequencing, and I’m working with Kathleen Lotterhos of Northeastern University on a new molecular approach to create exome capture probes directly from expressed RNA.

Population Connectivity


Natural- Life history traits, such as location of fertilization and mode of larval development, have long been thought to influence the evolutionary process of marine organisms, from fine- scale genetic structure to the tempo and mode of speciation. In my dissertation, I used comparative population genetic studies of sister species that differ in life history traits (pelagic vs. direct development) and of two sympatric species that differ in life history strategy (pelagic larvae vs. benthic egg masses and larvae).  Using traditional and custom developed NGS methods, I discovered the fastest known marine faunal speciation event (Puritz et al. 2012), and showed that the associated transition from planktonic development has severe consequences for genetic diversity, heterozygosity, population connectivity, and the response of species to the last glacial maxima (Puritz et al. In Prep).  During my postdoctoral work at Texas A&M, I used RADseq to discover that young-of-the-year red snapper separated by less than 2 km come from distinct groups of reproductive individuals within what is thought to be a panmictic fishery. 


Anthropogenic- Coastal pollution is most likely to enter the marine environment by one of two pathways: sewage effluent (wastewater) from wastewater treatment facilities, or via runoff (stormwater) from rivers and municipal drainage systems. For example, in the Southern California Bight (SCB), there are over 60 point sources that discharge approximately 4.7 billion liters into the ocean per dry day, with the potential increase of another 40 billion liters during a storm. Stormwater and wastewater actively transport a variety of chemicals and substances into the ocean. I conducted the first comprehensive study on the effects of urban runoff and wastewater effluent on genetic structure. Surveying 16 populations of a non-harvested species of sea star, Patiria miniata, I used a multivariate seascape model that led to two critical inferences: 1) stormwater and wastewater are effective barriers to larval dispersal and significantly reduce gene flow between populations, and 2) wastewater sources effectively lower genetic diversity (Puritz et al 2011). In short, I found provocative evidence for an entirely novel process that is likely pervasive throughout much of the world’s coastal oceans, and that has been largely unexplored in terms of its effects on larval transport, population connectivity, and

evolutionary dynamics. 

Environmental Selection

Natural- Selection can have a profound influence on genetic diversity, driving divergence at certain times while promoting diversity at others.  Understanding selection, natural and anthropogenic, is critical for predicting how species will respond to global ocean change.  In a collaborative project with David Portnoy of Texas A&M Corpus Christi, we were able to combine traditional population genetic tools and RADseq to tease apart the effects of sex-biased dispersal and environmental selection in bonnethead sharks, showing that philopatry can facilitate sorting of locally adaptive variation, with the dispersing sex facilitating movement of potentially adaptive variation among locations and environments (Portnoy et al. 2015).

Anthropogenic- Building upon previous work on coastal pollution, I focused on four populations (two closest to pollution sources, and two farthest away from pollution sources) from my original P. miniata study.   Using RADseq, I examined over 8,000 SNPs for evidence of selection using a combination of outlier and Cochran-Mantel-Haenszel tests, and identified 32 loci showing a putative response to coastal pollution.  These loci correspond to genes in transposons (linked to rapid environmental adaptation), metabolism, development, and immune response (Puritz et al. In Prep). 

Short-term Vision

Seascape Genomics of Coastal Pollution


A recent coauthored review of seascape genetics (Selkoe et al. 2016) showed that variety of different forces impact the connectivity and evolution of marine populations, and that rigor in statistical design and analysis is critical for generating hypothesis driven insights instead of documenting casual correlations.  Last year, I received funding for a seascapes genomics project involving the response of Fiddler crabs (Uca rapax) to sewage effluent around the Corpus Christi area.  This project involves a multiscale spatial design focused around three different effluent sources, but will also incorporate other seascape variables such as temperature, salinity, and flow rates.  Additionally, the design incorporates both a paired site and gradient design to inform genomic analysis, aiding in the identification of portions of the genome that may be under selection via exposure to sewage effluent.

The Synergistic Effects of Global Ocean Change and Localized Anthropogenic Stressors


The environmental impacts of an ever-growing human population cross multiple spatial and temporal boundaries, and localized impacts such as pollution and hypoxia need to be put into the context of global ocean change.  Additionally, marine organisms experience all of these stressors simultaneously, increasing the need for research on synergistic effects.  Currently, I’m using a factorial design to test phenotypic and genotypic changes of oyster larvae after exposure to ocean acidification conditions, sewage effluent, and the combination of the two.  Future work will build upon these results, incorporating more levels of environmental stressors. 

Long-term Vision


Integrating Across Life History Stages, Life History Strategies, and Communities


As an environmentally sensitive conduit of gene flow, larvae are the likely vehicle for evolution to environmental conditions, likely dictating the genomic composition of adult populations.  Future research projects will integrate information across life history stages, examining environmental impacts on adaptation and gene flow.  Larval exposure studies can be used to identify candidate loci under selection, and then adult populations can be surveyed across environmental gradients at both neutral loci and candidate loci.  This type of integrative study will help to unravel the complex interaction of selection and migration on genetic diversity.  Building upon this foundation, I will expand my research vision to comparative projects looking at sympatric species with differing life history strategies, looking for shared and discordant evolutionary responses to anthropogenic stressors.  The culmination of my research vision will be to expand to the community level with the hopes of unraveling ecosystem response to environmental stress.

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©2017 by Jonathan B. Puritz.