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Papers by Paul Barber

DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges o... more DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the curated, regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compare...

Marine Protected Areas (MPAs) are widely considered to be one of the best strategies available fo... more Marine Protected Areas (MPAs) are widely considered to be one of the best strategies available for protecting species diversity and ecosystem processes in marine environments, particularly in developing, tropical nations. While data on connectivity and genetic structure of marine populations are critical to designing appropriately sized and spaced networks of MPAs, such data are rarely available. Here we present an assessment of genetic structure in reef-building corals from Papua and West Papua, Indonesia, among the most biologically diverse and least disturbed coral reef regions in the world, and the focus of the multi-institutional Bird's Head Seascape initiative to design and implement a functional network of MPAs. Microsatellite variation was assessed within and among populations of Pocillopora damicornis (Linnaeus , 1758) and Seriatopora hystrix (Dana 1846) (family: Pocilloporidae) from three regions, each currently under a different conservation regime: Teluk Cenderawasih...

1. Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community ... more 1. Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable, and non-invasive. Longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference databases, flexibility across high-throughput sequencing platforms, fast multilocus metabarcode processing, and accurate taxonomic assignment. As bioinformatics tools continue to improve, addressing each of these demands within a single bioinformatics toolkit is becoming a reality.2. We present the modular metabarcode sequence toolkit Anacapa (https://github.com/limey-bean/Anacapa/), which addresses the above needs, allowing users to build comprehensive reference databases and assign taxonomy to raw multilocus metabarcode sequence data A novel aspect of Anacapa is our database building module, Creating Reference libraries Using eXisting tools (CRUX), which generates comprehensive reference databases for specific user-defin...

Journal of morphology, Jan 25, 2016

As fish move and interact with their aquatic environment by swimming, small morphological variati... more As fish move and interact with their aquatic environment by swimming, small morphological variations of the locomotor system can have profound implications on fitness. Damselfishes (Pomacentridae) have inhabited coral reef ecosystems for more than 50 million years. As such, habitat preferences and behavior could significantly constrain the morphology and evolvability of the locomotor system. To test this hypothesis, we used phylogenetic comparative methods on morphometric, ecological and behavioral data. While body elongation represented the primary source of variation in the locomotor system of damselfishes, results also showed a diverse suite of morphological combinations between extreme morphologies. Results show clear associations between behavior, habitat preferences, and morphology, suggesting ecological constraints on shape diversification of the locomotor system. In addition, results indicate that the three modules of the locomotor system are weakly correlated, resulting in ...

Bulletin of Marine Science, 2014

Molecular Ecology, 2011

Natural hybrid zones provide opportunities to study a range of evolutionary phenomena from specia... more Natural hybrid zones provide opportunities to study a range of evolutionary phenomena from speciation to the genetic basis of fitness-related traits. We show that widespread hybridization has occurred between two neo-tropical stream fishes with partial reproductive isolation. Phylogenetic analyses of mitochondrial sequence data showed that the swordtail fish Xiphophorus birchmanni is monophyletic and that X. malinche is part of an independent monophyletic clade with other species. Using informative single nucleotide ...

Ecology and Evolution, 2013

While studies of ecological speciation in the ocean are still in their infancy, there are several... more While studies of ecological speciation in the ocean are still in their infancy, there are several reasons to believe that this process may occur in the sea. First, absolute dispersal barriers are exceedingly rare. As a result, speciation must proceed with varying levels of gene flow and this process is aided by divergent selection. Secondly, strong interspecific interactions (e.g. host-parasite) believed to promote ecological speciation in terrestrial species, are ubiquitous in the marine realm. DNA sequence data from the parasitic snail Coralliophila violacea show that sympatric populations living on different coral hosts (e.g. Porites lobata vs P. cylindrica) within the Coral Triangle are diverging (2-3% COI mtDNA). A key piece of evidence in understanding speciation is being able to differentiate between neutral divergence that can come from divergence without gene flow (allopatry) and true sympatric divergence where speciation is promoted through divergent selection. However, th...

CBE life sciences education, 2015

The 6-yr degree-completion rate of undergraduate science, technology, engineering, and mathematic... more The 6-yr degree-completion rate of undergraduate science, technology, engineering, and mathematics (STEM) majors at U.S. colleges and universities is less than 40%. Persistence among women and underrepresented minorities (URMs), including African-American, Latino/a, Native American, and Pacific Islander students, is even more troubling, as these students leave STEM majors at significantly higher rates than their non-URM peers. This study utilizes a matched comparison group design to examine the academic achievement and persistence of students enrolled in the Program for Excellence in Education and Research in the Sciences (PEERS), an academic support program at the University of California, Los Angeles, for first- and second-year science majors from underrepresented backgrounds. Results indicate that PEERS students, on average, earned higher grades in most "gatekeeper" chemistry and math courses, had a higher cumulative grade point average, completed more science courses, ...

Crustacean Issues, 2011

ABSTRACT The Coral Triangle is the global epicenter of marine biodiversity as well as one of the ... more ABSTRACT The Coral Triangle is the global epicenter of marine biodiversity as well as one of the worlds most imperiled ecosystems. Conserving the biodiversity of the Coral Triangle along with the processes that generate biodiversity in this region requires understanding the mechanisms by which this bio- diversity hotspot has evolved. Although there are several theories to explain the origins of the Coral Triangle biodiversity hotspot, the Center of Origin theory has been criticized for lacking credible mechanisms for speciation within the center of the Coral Triangle. In this paper, we examine the phylogeography and evolutionary history of coral reef associated stomatopods. Results indicate significant regional population genetic structure in all 14 species of reef-associated stomatopods examined. Several species exhibit patterns of Indian-Pacific differentiation, suggesting vicariance during Pleistocene low sea level stands may promote lineage diversification. However, all species show a pronounced pattern of differentiation between populations east and west of the Maluku Sea. Although the precise location of this phylogeographic boundary varies among species, the most likely explanation for this pattern is that the Halmahera Eddy limits water flow, and thus larval transport and gene flow, across the Maluku Sea, promoting lineage diversification in this region and supporting the notion of a center of origin. In contrast, Bayesian Analysis of regional patterns of dif- ferentiation suggested that the most basal populations of Haptosquilla pulchella and H. glyptocercus were found in reefs in the peripheral parts of their Pacific Ocean ranges, potentially suggesting sup- port for the Center of Accumulation model. However, topology constraint tests indicated that the best trees were not significantly better than alternate topologies, limiting the inferences that can be drawn from this data. Although many processes are likely contributing to the Coral Triangle biodi- versity hotspot, data from stomatopods clearly shows evidence for filters to dispersal and gene flow within the center, a result consistent with a Center of Origin. The identification of these barriers in stomatopods and many other unrelated marine fish and invertebrates is helping define regional limits of connectivity within the Coral Triangle, supporting regional conservation planning in this imperiled ecosystem.

Journal of Marine Biology, 2011

Extreme concentration of marine biodiversity and exploitation of marine resources in the Coral Tr... more Extreme concentration of marine biodiversity and exploitation of marine resources in the Coral Triangle pose challenges to biogeographers and resource managers. Comparative phylogeography provides a powerful tool to test biogeographic hypotheses evoked to explain species richness in the Coral Triangle. It can also be used to delineate management units for marine resources. After about a decade of phylogeographical studies, patterns for the Coral Triangle are emerging. Broad connectivity in some species support the notion that larvae have maintained gene flow among distant populations for long periods. Other phylogeographic patterns suggest vicariant events resulting from Pleistocene sea level fluctuations, which have, at least occasionally, resulted in speciation. Divergence dates ranging back to the Miocene suggest that changing land configurations may have precipitated an explosion of species diversification. A synthesis of the marine phylogeographic studies reveals repeated patte...

Proceedings of the Royal Society B: Biological Sciences, 2006

There is a push to fully document the biodiversity of the world within 25 years. However, the mag... more There is a push to fully document the biodiversity of the world within 25 years. However, the magnitude of this challenge, particularly in marine environments, is not well known. In this study, we apply DNA barcoding to explore the biodiversity of gonodactylid stomatopods (mantis shrimp) in both the Coral Triangle and the Red Sea. Comparison of sequences from 189 unknown stomatopod larvae to 327 known adults representing 67 taxa in the superfamily Gonodactyloidea revealed 22 distinct larval operational taxonomic units (OTUs). In the Western Pacific, 10 larval OTUs were members of the Gonodactylidae and Protosquillidae where success of positive identification was expected to be 96.5%. However, only five OTUs could be identified to species and at least three OTUs represent new species unknown in their adult form. In the Red Sea where the identification rate was expected to be 75% in the Gonodactylidae, none of four larval OTUs could be identified to species; at least two represent new...

Proceedings of the Royal Society B: Biological Sciences, 2002

Molecular Ecology, 2012

Increasing dispersal duration should result in increasing dispersal distance, facilitating higher... more Increasing dispersal duration should result in increasing dispersal distance, facilitating higher gene flow among populations. As such, it has long been predicted that genetic structure (e.g. F(ST) ) among populations of marine species should be strongly correlated with pelagic larval duration (PLD). However, previous studies have repeatedly shown a surprisingly poor correspondence. This result has been frequently interpreted as evidence for larval behaviours or physical oceanographic processes that result in larvae failing to reach their dispersal potential, or error inherent in estimating PLD and F(ST) . This study employed a computer modelling approach to explore the impacts of various uncertainties on the correlation between measures of genetic differentiation such as F(ST) and PLD. Results indicate that variation resulting from PLD estimation error had minor impacts on the correlation between genetic structure and PLD. However, variation in effective population size between species, errors in F(ST) estimation and non-equilibrium F(ST) values all had major impacts, resulting in dramatically weaker correlations between PLD and F(ST) . These results suggest that poor correlations between PLD and F(ST) may result from variation and uncertainty in the terms associated with the calculation of F(ST) values. As such, PLD may be a much stronger determinant of realized larval dispersal than suggested by the weak-to-moderate correlations between PLD and F(ST) reported in empirical studies.

Journal of Wildlife Management, 2007

Page 1. Techniques and Technology Note A Remotely Operated Motorized Burrow Probe to Investigate ... more Page 1. Techniques and Technology Note A Remotely Operated Motorized Burrow Probe to Investigate Carnivore Neonates PAULA A. WHITE,1 Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University ...

Journal of Biogeography, 2009