@article{maurer_seminoff_reiskind_stapleton_2024, title={Diverse migratory strategies for a hawksbill sea turtle population}, volume={1}, ISSN={["1099-0755"]}, url={http://dx.doi.org/10.1002/aqc.4080}, DOI={10.1002/aqc.4080}, abstractNote={

Outside of short, infrequent visits to reproductive habitats, sea turtle lifespans are largely spent in foraging areas. Supporting imperilled populations in an era of biodiversity declines and environmental change requires improvements in the understanding of foraging distributions, plus the migratory corridors that connect foraging and reproductive habitats.
This study evaluates the migratory strategies and foraging geography of hawksbill sea turtles (Eretmochelys imbricata) in the Western Atlantic. The post‐nesting migrations of 22 females were tracked via satellite telemetry from Long Island, Antigua, during 2016–2019, and a state‐space model was utilized to estimate true turtle locations from Argos satellite fixes. Model output was used to characterize migratory routes and home ranges occupied during non‐migratory inter‐nesting and foraging periods.
Hawksbill migrations (N = 19) resulted in displacements to foraging areas ranging 7–2300 km. Foraging geography varied considerably—whereas eight turtles remained in the immediate vicinity of Antigua and Barbuda (<30 km), there were also longer‐distance migrations (>470 km) to locations such as The Bahamas and Nicaragua. Inter‐nesting core home ranges (50% utilization distributions) ranged from 7 to 72 km2, while foraging core areas ranged from 7 to 46 km2.
These results add to evidence suggesting that, broadly, post‐nesting hawksbills forage in neritic habitats throughout the Wider Caribbean, including several high‐use areas. Short displacements to foraging habitats relatively nearby to nesting beaches appear to be the most common migratory behaviour, but individuals in a single population may exhibit various migratory strategies, resulting in basin‐wide connectivity between nesting and foraging sites. Given that a single individual or nesting population may inhabit several management jurisdictions, an idealized scenario for regional hawksbill conservation would entail data sharing between managers at linked nesting areas, foraging habitats and migratory corridors such that policies to protect key habitats and mitigate human impacts are designed and evaluated based on best‐available science.
}, journal={AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS}, author={Maurer, Andrew S. and Seminoff, Jeffrey A. and Reiskind, Martha O. Burford and Stapleton, Seth P.}, year={2024}, month={Jan} }
 @article{dillon_thomas_mousseau_betz_kleiman_reiskind_breen_2023, title={Population dynamics and genome-wide selection scan for dogs in Chernobyl}, volume={10}, url={http://dx.doi.org/10.1186/s40575-023-00124-1}, DOI={10.1186/s40575-023-00124-1}, abstractNote={Abstract Background Natural and anthropogenic disasters can have long-lasting impacts on the genetics and structure of impacted populations. The 1986 Chernobyl Nuclear Power Plant disaster led to extensive contamination of the local environment and the wildlife therein. Several ecological, environmental, and genetic studies reported various effects of this disaster on animal, insect, and plant species; however, little work has been done to investigate the genetics of the free-breeding dogs that occupy the Chernobyl Exclusion Zone (CEZ). Results We define the population genetic structure of two groups of dogs that reside within the CEZ, one around the reactor site itself and another living within Chernobyl City. We found little evidence of gene flow and a significant degree of genetic differentiation between the two populations dogs, suggesting that these are two distinct populations despite occupying areas located just 16 km apart. With an F ST -based outlier analysis, we then performed a genome-wide scan for evidence of directional selection within the dog populations. We found 391 outlier loci associated with genomic regions influenced by directional selection, from which we identified 52 candidate genes. Conclusions Our genome scan highlighted outlier loci within or near genomic regions under directional selection, possibly in response to the multi-generational exposure faced. In defining the population structure and identifying candidate genes for these dog populations, we take steps towards understanding how these types of prolonged exposures have impacted these populations.}, number={1}, journal={Canine Medicine and Genetics}, publisher={Springer Science and Business Media LLC}, author={Dillon, Megan and Thomas, Rachael and Mousseau, Timothy and Betz, Jennifer Anne and Kleiman, Norman and Reiskind, Martha Burford and Breen, Matthew}, year={2023}, month={Mar} }
 @article{reed_reiskind_reiskind_2022, title={Life-history stage and the population genetics of the tiger mosquito Aedes albopictus at a fine spatial scale}, volume={10}, ISSN={["1365-2915"]}, url={http://dx.doi.org/10.1111/mve.12618}, DOI={10.1111/mve.12618}, abstractNote={As a widespread vector of disease with an expanding range, the mosquito Aedes albopictus Skuse (Diptera: Culicidae) is a high priority for research and management. A. albopictus has a complex life history with aquatic egg, larval and pupal stages, and a terrestrial adult stage. This requires targeted management strategies for each life stage, coordinated across time and space. Population genetics can aid in A. albopictus control by evaluating patterns of genetic diversity and dispersal. However, how life stage impacts population genetic characteristics is unknown. We examined whether patterns of A. albopictus genetic diversity and differentiation changed with life stage at a spatial scale relevant to management efforts. We first conducted a literature review of field‐caught A. albopictus population genetic papers and identified 101 peer‐reviewed publications, none of which compared results between life stages. Our study uniquely examines population genomic patterns of egg and adult A. albopictus at five sites in Wake County, North Carolina, USA, using 8425 single nucleotide polymorphisms. We found that the level of genetic diversity and connectivity between sites varied between adults and eggs. This warrants further study and is critical for research aimed at informing local management.}, journal={MEDICAL AND VETERINARY ENTOMOLOGY}, publisher={Wiley}, author={Reed, Emily M. X. and Reiskind, Michael H. and Reiskind, Martha O. Burford}, year={2022}, month={Oct} }
 @article{wallace_reed_aguilar_reiskind_2022, title={Resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus Sebastosomus}, volume={173}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2022.107515}, abstractNote={Rapid speciation is an important aspect of adaptive radiations, but can obfuscate phylogenetic relationships among taxa. For recent radiations, there are challenges to reconstructing the relationships among the species due to often shorter branch lengths. Resolution of these relationships is further confounded when studies only use a few genetic markers. Double digest restriction-site associated DNA sequencing (ddRADseq) is a method of next generation sequencing that identifies many single nucleotide polymorphisms (SNPs) throughout the genome. This increases statistical power to resolve close phylogenetic relationships like those found within an adaptive radiation. We used this approach to understand the evolutionary history of the rockfishes of the genus Sebastes, which experienced an adaptive radiation between 3 and 5 mya. Here, we reconstructed the phylogenetic relationships among six species of rockfish within the subgenus Sebastosomus using over 11,600 SNPs. This reconstruction includes the two recently diverged species, Sebastes mystinus and S. diaconus, that were first described genetically in 2008 using mtDNA control region sequence data and six microsatellite loci. We confirmed the relationship of these cryptic species as sister-taxa and found evidence that S. melanops and S. flavidus were also sister-taxa. The latter contradicts prior studies but is supported by our reconstruction using nuclear DNA and measures of genetic differentiation tests and a discriminant analysis of principal components. The relationships between the species of Sebastosomus are further supported by morphological, biological, and ecological justifications.}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Wallace, E. N. and Reed, E. M. X. and Aguilar, A. and Reiskind, M. O. Burford}, year={2022}, month={Aug} }
 @misc{resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus sebastosomus_2022, DOI={10.5061/dryad.6t1g1jx1n}, journal={Dryad}, year={2022}, month={Apr} }
 @article{gabor_kivlin_hua_bickford_reiskind_wright_2022, title={Understanding Organismal Capacity to Respond to Anthropogenic Change: Barriers and Solutions}, volume={61}, ISSN={["1557-7023"]}, url={http://dx.doi.org/10.1093/icb/icab162}, DOI={10.1093/icb/icab162}, abstractNote={Global environmental changes induced by human activities are forcing organisms to respond at an unprecedented pace. At present we have only a limited understanding of why some species possess the capacity to respond to these changes while others do not. We introduce the concept of multidimensional phenospace as an organizing construct to understanding organismal evolutionary responses to environmental change. We then describe five barriers that currently challenge our ability to understand these responses: 1) Understanding the parameters of environmental change and their fitness effects, 2) Mapping and integrating phenotypic and genotypic variation, 3) Understanding whether changes in phenospace are heritable, 4) Predicting consistency of genotype to phenotype patterns across space and time, and 5) Determining which traits should be prioritized to understand organismal response to environmental change. For each we suggest one or more solutions that would help us surmount the barrier and improve our ability to predict, and eventually manipulate, organismal capacity to respond to anthropogenic change. Additionally, we provide examples of target species that could be useful to examine interactions between phenotypic plasticity and adaptive evolution in changing phenospace.}, number={6}, journal={INTEGRATIVE AND COMPARATIVE BIOLOGY}, publisher={Oxford University Press (OUP)}, author={Gabor, Caitlin R. and Kivlin, Stephanie N. and Hua, Jessica and Bickford, Nate and Reiskind, Martha O. Burford and Wright, Timothy F.}, year={2022}, month={Feb}, pages={2132–2144} }
 @article{reiskind_moody_bolnick_hanifin_farrior_2021, title={Nothing in Evolution Makes Sense Except in the Light of Biology}, volume={71}, ISSN={["1525-3244"]}, DOI={10.1093/biosci/biaa170}, abstractNote={Abstract A key question in biology is the predictability of the evolutionary process. If we can correctly predict the outcome of evolution, we may be better equipped to anticipate and manage species’ adaptation to climate change, habitat loss, invasive species, or emerging infectious diseases, as well as improve our basic understanding of the history of life on Earth. In the present article, we ask the questions when, why, and if the outcome of future evolution is predictable. We first define predictable and then discuss two conflicting views: that evolution is inherently unpredictable and that evolution is predictable given the ability to collect the right data. We identify factors that generate unpredictability, the data that might be required to make predictions at some level of precision or at a specific timescale, and the intellectual and translational value of understanding when prediction is or is not possible.}, number={4}, journal={BIOSCIENCE}, author={Reiskind, Martha O. Burford and Moody, Michael L. and Bolnick, Daniel I and Hanifin, Charles T. and Farrior, Caroline E.}, year={2021}, month={Apr}, pages={370–382} }
 @article{maurer_seminoff_layman_stapleton_godfrey_reiskind_2021, title={Population Viability of Sea Turtles in the Context of Global Warming}, volume={71}, ISSN={["1525-3244"]}, DOI={10.1093/biosci/biab028}, abstractNote={
 Sea turtles present a model for the potential impacts of climate change on imperiled species, with projected warming generating concern about their persistence. Various sea turtle life-history traits are affected by temperature; most strikingly, warmer egg incubation temperatures cause female-biased sex ratios and higher embryo mortality. Predictions of sea turtle resilience to climate change are often focused on how resulting male limitation or reduced offspring production may affect populations. In the present article, by reviewing research on sea turtles, we provide an overview of how temperature impacts on incubating eggs may cascade through life history to ultimately affect population viability. We explore how sex-specific patterns in survival and breeding periodicity determine the differences among offspring, adult, and operational sex ratios. We then discuss the implications of skewed sex ratios for male-limited reproduction, consider the negative correlation between sex ratio skew and genetic diversity, and examine consequences for adaptive potential. Our synthesis underscores the importance of considering the effects of climate throughout the life history of any species. Lethal effects (e.g., embryo mortality) are relatively direct impacts, but sublethal effects at immature life-history stages may not alter population growth rates until cohorts reach reproductive maturity. This leaves a lag during which some species transition through several stages subject to distinct biological circumstances and climate impacts. These perspectives will help managers conceptualize the drivers of emergent population dynamics and identify existing knowledge gaps under different scenarios of predicted environmental change.}, number={8}, journal={BIOSCIENCE}, author={Maurer, Andrew S. and Seminoff, Jeffrey A. and Layman, Craig A. and Stapleton, Seth P. and Godfrey, Matthew H. and Reiskind, Martha O. Burford}, year={2021}, month={Aug}, pages={790–804} }
 @article{population viability of sea turtles in the context of global warming_2021, DOI={doi:10.1093/biosci/biab028}, abstractNote={Abstract Sea turtles present a model for the potential impacts of climate change on imperiled species, with projected warming generating concern about their persistence. Various sea turtle life-history traits are affected by temperature; most strikingly, warmer egg incubation temperatures cause female-biased sex ratios and higher embryo mortality. Predictions of sea turtle resilience to climate change are often focused on how resulting male limitation or reduced offspring production may affect populations. In the present article, by reviewing research on sea turtles, we provide an overview of how temperature impacts on incubating eggs may cascade through life history to ultimately affect population viability. We explore how sex-specific patterns in survival and breeding periodicity determine the differences among offspring, adult, and operational sex ratios. We then discuss the implications of skewed sex ratios for male-limited reproduction, consider the negative correlation between sex ratio skew and genetic diversity, and examine consequences for adaptive potential. Our synthesis underscores the importance of considering the effects of climate throughout the life history of any species. Lethal effects (e.g., embryo mortality) are relatively direct impacts, but sublethal effects at immature life-history stages may not alter population growth rates until cohorts reach reproductive maturity. This leaves a lag during which some species transition through several stages subject to distinct biological circumstances and climate impacts. These perspectives will help managers conceptualize the drivers of emergent population dynamics and identify existing knowledge gaps under different scenarios of predicted environmental change.}, journal={BioScience}, year={2021} }
 @article{maurer_stapleton_layman_reiskind_2021, title={The Atlantic Sargassum invasion impedes beach access for nesting sea turtles}, volume={2}, url={http://dx.doi.org/10.1016/j.ecochg.2021.100034}, DOI={10.1016/j.ecochg.2021.100034}, abstractNote={One characteristic of global change is an increase in the frequency and magnitude of algae blooms. Although a large body of work has documented severe ecological impacts, such as mortality due to toxins or hypoxia, less research has described sublethal effects that may still affect population dynamics. Here, we focus on blooming Sargassum macroalgae in the North Atlantic and describe effects on nesting sea turtles. Since 2011, large masses of the algae have been inundating Atlantic nesting habitats. We documented the accumulation of Sargassum at Long Island, Antigua, and quantified effects on a rookery of hawksbill sea turtles (Eretmochelys imbricata). Using monitoring data from 2010 to 2019, we analyzed population- and individual-level patterns in nesting. Our results suggest that sea turtles respond to Sargassum at nesting beaches by shifting space use away from heavily impacted areas. We also tested for an effect on nesting success, but found no change in the years and areas most impacted by Sargassum. The algae may not increase the energetic costs of nesting after a turtle has emerged onto the beach, but we speculate that costs are imposed in algae-filled waters as turtles initially seek to emerge. As the Sargassum “invasion” continues, sea turtles at impacted sites will need to exhibit plasticity when choosing nesting sites, and nest densities may increase in areas with less Sargassum present. Individuals may also be required to expend more energy per nesting season. More broadly, this work demonstrates that algae blooms can have sublethal effects on fauna that affect population dynamics.}, journal={Climate Change Ecology}, publisher={Elsevier BV}, author={Maurer, Andrew S. and Stapleton, Seth P. and Layman, Craig A. and Reiskind, Martha O. Burford}, year={2021}, month={Dec}, pages={100034} }
 @article{gridlock and beltways: the genetic context of urban invasions_2020, url={http://dx.doi.org/10.1007/s00442-020-04614-y}, DOI={10.1007/s00442-020-04614-y}, journal={Oecologia}, year={2020}, month={Mar} }
 @article{identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads_2020, url={http://dx.doi.org/10.1002/ece3.6602}, DOI={10.1002/ece3.6602}, abstractNote={Abstract Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (Spea multiplicata). Spea tadpoles normally develop into an “omnivore” morph that is favored in long‐lasting, low‐density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can alternatively develop (via plasticity) into a “carnivore” morph that is favored in ephemeral, high‐density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with each morph (carnivores vs. omnivores) and loci associated with adaptive phenotypic plasticity (adaptive vs. maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 14 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might mediate adaptive plasticity.}, journal={Ecology and Evolution}, year={2020}, month={Jul} }
 @article{maintaining historic disturbance regimes increases species' resilience to catastrophic hurricanes_2019, url={http://dx.doi.org/10.1111/gcb.14932}, DOI={10.1111/gcb.14932}, abstractNote={As habitat loss and fragmentation, urbanization, and global climate change accelerate, conservation of rare ecosystems increasingly relies on human intervention. However, any conservation strategy is vulnerable to unpredictable, catastrophic events. Whether active management increases or decreases a system's resilience to these events remains unknown. Following Hurricane Irma's landfall in our habitat restoration study sites, we found that rare ecosystems with active, human‐imposed management suffered less damage in a hurricane's path than unmanaged systems. At the center of Irma's landfall, we found Croton linearis' (a locally rare plant that is the sole host for two endangered butterfly species) survival and population growth rates in the year of the hurricane were higher in previously managed plots than in un‐managed controls. In the periphery of Irma's circulation, the effect of prior management was stronger than that of the hurricane. Maintaining the historical disturbance regime thus increased the resilience of the population to major hurricane disturbance. As climate change increases the probability and intensity of severe hurricanes, human management of disturbance‐adapted landscapes will become increasingly important for maintaining populations of threatened species in a storm's path. Doing nothing will accelerate extinction.}, journal={Global Change Biology}, year={2019}, month={Dec} }
 @article{patterns of genetic divergence among populations of aedes aegypti l. (diptera: culicidae) in the southeastern usa_2019, url={http://dx.doi.org/10.1186/s13071-019-3769-0}, DOI={10.1186/s13071-019-3769-0}, abstractNote={Abstract Background The yellow fever mosquito, Aedes aegypti is a public health concern in the USA, especially in the wake of emergent diseases such as Zika and chikungunya. Aedes aegypti populations dwindled after the invasion of Aedes albopictus in the 1980s and many populations were extirpated. However, in some areas Ae. aegypti persisted in small populations and there are reports of recent resurgences of Ae. aegypti in Florida, Louisiana, Nevada and California. We assessed the population genetic structure of Ae. aegypti in Florida and Georgia, which has concomitant consequences related to mosquito dispersal, pesticide resistance and vectorial capacity. Methods We collected Ae. aegypti across Florida and in Georgia using ovitraps. We hatched the eggs and reared them to adults, and after sacrifice we extracted their DNA. We then probed each individual for variation in 6 microsatellite markers, which we used to address population genetic characteristics. Results We collected Ae. aegypti and genotyped seven Florida populations and one Georgia population using microsatellite markers. We found evidence of isolation by distance model of gene flow supported by driving distance among cities within Florida and two theoretic genetic clusters. Conclusions Significant genetic structure between some populations with substantial gene flow between geographically distant cities suggests regional genetic structuring of Ae. aegypti in Florida. This study provides information on the genetic exchange between populations of Ae. aegypti in the southeastern USA and suggests potential routes of spread of this species.}, journal={Parasites & Vectors}, year={2019}, month={Dec} }
 @article{reiskind_reed_elias_giacomini_mcnear_nieuwsma_parker_roberts_rossi_stephenson_et al._2019, title={The genomics of invasion: characterization of red lionfish (Pterois volitans) populations from the native and introduced ranges}, volume={21}, ISSN={["1573-1464"]}, url={http://dx.doi.org/10.1007/s10530-019-01992-0}, DOI={10.1007/s10530-019-01992-0}, number={7}, journal={BIOLOGICAL INVASIONS}, author={Reiskind, M. O. Burford and Reed, E. M. X. and Elias, A. and Giacomini, J. J. and McNear, A. F. and Nieuwsma, J. and Parker, G. A. and Roberts, R. B. and Rossi, R. E. and Stephenson, C. N. and et al.}, year={2019}, month={Jul}, pages={2471–2483} }
 @article{reiskind_reed_elias_giacomini_mcnear_nieuwsma_parker_roberts_rossi_stephenson_et al._2019, title={The genomics of invasion: characterization of red lionfish (Pterois volitans) populations from the native and introduced ranges (vol 21, pg 2471, 2019)}, volume={21}, ISSN={["1573-1464"]}, DOI={10.1007/s10530-019-01999-7}, abstractNote={In the original publication of this article, Figs. 2 and 3 were published incorrectly.}, number={7}, journal={BIOLOGICAL INVASIONS}, author={Reiskind, M. O. Burford and Reed, E. M. X. and Elias, A. and Giacomini, J. J. and McNear, A. F. and Nieuwsma, J. and Parker, G. A. and Roberts, R. B. and Rossi, R. E. and Stephenson, C. N. and et al.}, year={2019}, month={Jul}, pages={2485–2487} }
 @article{burford reiskind_labadie_bargielowski_lounibos_reiskind_2018, title={Rapid evolution and the genomic consequences of selection against interspecific mating}, volume={27}, ISSN={0962-1083}, url={http://dx.doi.org/10.1111/mec.14821}, DOI={10.1111/mec.14821}, abstractNote={While few species introduced into a new environment become invasive, those that do provide critical information on ecological mechanisms that determine invasions success and the evolutionary responses that follow invasion. Aedes albopictus (the Asian tiger mosquito) was introduced into the naturalized range of Aedes aegypti (the yellow fever mosquito) in the United States in the mid‐1980s, resulting in the displacement of A. aegypti in much of the south‐eastern United States. The rapid displacement was likely due to the superior competitive ability of A. albopictus as larvae and asymmetric mating interference competition, in which male A. albopictus mate with and sterilize A. aegypti females, a process called “satyrization.” The goal of this study was to examine the genomic responses of a resident species to an invasive species in which the mechanism of character displacement is understood. We used double‐digest restriction enzyme DNA sequencing (ddRADseq) to analyse outlier loci between selected and control lines of laboratory‐reared A. aegypti females from two populations (Tucson, AZ and Key West, Florida, USA), and individual females classified as either “resisted” or “mated with” A. albopictus males via mating trials of wild‐derived females from four populations in Florida. We found significant outlier loci in comparing selected and control lines and between mated and nonmated A. aegypti females in the laboratory and wild‐derived populations, respectively. We found overlap in specific outlier loci between different source populations that support consistent genomic signatures of selection within A. aegypti. Our results point to regions of the A. aegypti genome and potential candidate genes that may be involved in mating behaviour, and specifically in avoiding interspecific mating choices.}, number={18}, journal={Molecular Ecology}, publisher={Wiley}, author={Burford Reiskind, Martha O. and Labadie, Paul and Bargielowski, Irka and Lounibos, L. Philip and Reiskind, Michael H.}, year={2018}, month={Aug}, pages={3641–3654} }
 @article{reiskind_coyle_daniels_labadie_reiskind_roberts_roberts_schaff_vargo_2016, title={Application of a modified double digest RAD sequencing approach to non-model, ecologically important taxa}, volume={16}, journal={Mol Ecol Resources}, author={Reiskind, Burford and Coyle, K. and Daniels, H.V. and Labadie, P. and Reiskind, M.H. and Roberts, N.B. and Roberts, R.B. and Schaff, J.L. and Vargo, E.L.}, year={2016}, pages={1303–1314} }
 @article{burford reiskind_coyle_daniels_labadie_reiskind_roberts_roberts_schaff_vargo_2016, title={Development of a universal double-digest RAD sequencing approach for a group of nonmodel, ecologically and economically important insect and fish taxa}, volume={16}, ISSN={1755-098X}, url={http://dx.doi.org/10.1111/1755-0998.12527}, DOI={10.1111/1755-0998.12527}, abstractNote={The generation of genome‐scale data is critical for a wide range of questions in basic biology using model organisms, but also in questions of applied biology in nonmodel organisms (agriculture, natural resources, conservation and public health biology). Using a genome‐scale approach on a diverse group of nonmodel organisms and with the goal of lowering costs of the method, we modified a multiplexed, high‐throughput genomic scan technique utilizing two restriction enzymes. We analysed several pairs of restriction enzymes and completed double‐digestion RAD sequencing libraries for nine different species and five genera of insects and fish. We found one particular enzyme pair produced consistently higher number of sequence‐able fragments across all nine species. Building libraries off this enzyme pair, we found a range of usable SNPs between 4000 and 37 000 SNPS per species and we found a greater number of usable SNPs using reference genomes than de novo pipelines in STACKS. We also found fewer reads in the Read 2 fragments from the paired‐end Illumina Hiseq run. Overall, the results of this study provide empirical evidence of the utility of this method for producing consistent data for diverse nonmodel species and suggest specific considerations for sequencing analysis strategies.}, number={6}, journal={Molecular Ecology Resources}, publisher={Wiley}, author={Burford Reiskind, M. O. and Coyle, K. and Daniels, H. V. and Labadie, P. and Reiskind, M. H. and Roberts, N. B. and Roberts, R. B. and Schaff, J. and Vargo, E. L.}, year={2016}, month={May}, pages={1303–1314} }
 @article{burford_scarpa_cook_hare_2014, title={Local adaptation of a marine invertebrate with a high dispersal potential: evidence from a reciprocal transplant experiment of the eastern oyster Crassostrea virginica}, volume={505}, DOI={10.3354/meps10796}, abstractNote={We examined the role of local adaptation in structuring the stable genetic step-cline of the eastern oyster Crassostrea virginica along an environmental gradient in the lagoon system of eastern Florida, USA. Reciprocally transplanted progeny, produced by a 10 × 10 genetic cross of wild brood stock from northern and southern genetic lineages yielded significant evidence of local adaptation (interaction of genes and environment) in variables related to fitness, including survival, wet meat weight, and reproductive maturation. The strength of local adaptation was asymmetric, with greater effects on the northern compared to the southern genetic lineage. To a lesser extent, we found evidence of both the role of environment (in particular, adverse effects on both genetic crosses in the southern region), and the role of genetic differences between the 2 crosses independent of environment, with higher initial growth of the southern genetic lineage and higher condition of the northern lineage. These differences suggest that maintenance of the genetic step-cline involves natural selection. We discuss the potential role of temperature and phytoplankton community composition between the northern and southern regions. Our study is the first to determine the genetic basis for fitness-related phenotypes, and to relate this to local adaptation of the eastern oyster. Understanding the role of the environment in structuring the eastern oyster throughout its range is critical for effective management, and the results of this study also suggest that small environmental changes may have significant effects on conservation of the eastern oyster, particularly in the northern genetic lineage.}, journal={Marine Ecology Progress Series}, publisher={Inter-Research Science Center}, author={Burford, MO and Scarpa, J and Cook, BJ and Hare, MP}, year={2014}, month={May}, pages={161–175} }
 @article{burford_carr_bernardi_2011, title={Age-structured genetic analysis reveals temporal and geographic variation within and between two cryptic rockfish species}, volume={442}, DOI={10.3354/meps09329}, abstractNote={The spatial patterns of genetic structure among juveniles of long-lived species can reveal the extent of interannual and geographic variation in realized larval dispersal as well as the processes that determine ecologically relevant patterns of population connectivity. However, few studies examine this temporal and spatial variation over large portions of a species' geographic range or between cryptic species that overlap in their range. Despite the potential for long-dis- tance dispersal in blue rockfish Sebastes mystinus, a previous study of adults revealed two geo- graphically distinct, cryptic species. To determine year-to-year variation in the patterns of spatial connectivity and to elucidate the potential ecological mechanisms involved in shaping new year- classes and maintaining cryptic species, we sampled juveniles within California, USA, where both cryptic species coexist. Using microsatellite markers, we found geographic and temporal variation in the number of individuals from these distinct cryptic species within 2 new year-classes of juve- nile S. mystinus. We also found differences in the geographic patterns of genetic structure of the 2 cryptic species. Whereas one species exhibited little or no spatial genetic structure across the study region, the other exhibited a complex geographic pattern of genetic structure, with little or no genetic structure among regions, but small-scale structure within a region. The results of this study demonstrate that the spatial scales and patterns of realized dispersal of pelagic larvae vary geographically, interannually, and between closely related species with similar life-history strate- gies. Therefore, estimates of dispersal based on larval duration and patterns of adult structure need to be interpreted cautiously.}, journal={Marine Ecology Progress Series}, publisher={Inter-Research Science Center}, author={Burford, MO and Carr, MH and Bernardi, G}, year={2011}, pages={201–215} }
 @article{burford_bernardi_carr_2011, title={Analysis of individual year-classes of a marine fish reveals little evidence of first-generation hybrids between cryptic species in sympatric regions}, volume={158}, ISSN={0025-3162 1432-1793}, url={http://dx.doi.org/10.1007/s00227-011-1694-7}, DOI={10.1007/s00227-011-1694-7}, number={8}, journal={Marine Biology}, publisher={Springer Science and Business Media LLC}, author={Burford, Martha O. and Bernardi, Giacomo and Carr, Mark H.}, year={2011}, month={Apr}, pages={1815–1827} }
 @article{hare_nunney_schwartz_ruzzante_burford_waples_ruegg_palstra_2011, title={Understanding and Estimating Effective Population Size for Practical Application in Marine Species Management}, volume={25}, DOI={10.1111/j.1523-1739.2010.01637.x}, abstractNote={Abstract:  Effective population size (Ne) determines the strength of genetic drift in a population and has long been recognized as an important parameter for evaluating conservation status and threats to genetic health of populations. Specifically, an estimate of Ne is crucial to management because it integrates genetic effects with the life history of the species, allowing for predictions of a population's current and future viability. Nevertheless, compared with ecological and demographic parameters, Ne has had limited influence on species management, beyond its application in very small populations. Recent developments have substantially improved Ne estimation; however, some obstacles remain for the practical application of Ne estimates. For example, the need to define the spatial and temporal scale of measurement makes the concept complex and sometimes difficult to interpret. We reviewed approaches to estimation of Ne over both long‐term and contemporary time frames, clarifying their interpretations with respect to local populations and the global metapopulation. We describe multiple experimental factors affecting robustness of contemporary Ne estimates and suggest that different sampling designs can be combined to compare largely independent measures of Ne for improved confidence in the result. Large populations with moderate gene flow pose the greatest challenges to robust estimation of contemporary Ne and require careful consideration of sampling and analysis to minimize estimator bias. We emphasize the practical utility of estimating Ne by highlighting its relevance to the adaptive potential of a population and describing applications in management of marine populations, where the focus is not always on critically endangered populations. Two cases discussed include the mechanisms generating Ne estimates many orders of magnitude lower than census N in harvested marine fishes and the predicted reduction in Ne from hatchery‐based population supplementation.}, number={3}, journal={Conservation Biology}, publisher={Wiley}, author={HARE, MATTHEW P. and NUNNEY, LEONARD and SCHWARTZ, MICHAEL K. and RUZZANTE, DANIEL E. and BURFORD, MARTHA and WAPLES, ROBIN S. and RUEGG, KRISTEN and PALSTRA, FRISO}, year={2011}, month={Feb}, pages={438–449} }
 @article{burford_2009, title={Demographic history, geographical distribution and reproductive isolation of distinct lineages of blue rockfish (Sebastes mystinus), a marine fish with a high dispersal potential}, volume={22}, DOI={10.1111/j.1420-9101.2009.01760.x}, abstractNote={Understanding the barriers to genetic exchange in taxonomic groups that have a high dispersal potential will provide critical information on speciation in general. Blue rockfish (Sebastes mystinus) are good taxa to examine speciation because they are nonmigratory inhabitants of shallow rocky reef habitats along the eastern North Pacific with a pelagic larval stage lasting 3–5 months. The goal of this study was to analyse the evolutionary history and distribution patterns of different lineages within S. mystinus described previously and use this information to understand the speciation process in this group of high dispersal fish. The molecular data derived from specimens sampled over approximately 1650 km of the S. mystinus range revealed a northerly and southerly distribution for the two lineages. Almost equal frequencies of both lineages occurred at centrally located sample locations, with evidence of reproductive isolation between the lineages. A demographic analysis showed that the two lineages diverged and experienced sudden expansion prior to the last glacial maximum, which affected the observed pattern of genetic structure. The spatial distribution, demographic history and degree of genetic distinctiveness found from the genetic analysis, despite the high potential for dispersal in S. mystinus, suggest both lineages diverged in allopatry.}, number={7}, journal={Journal of Evolutionary Biology}, publisher={Wiley}, author={BURFORD, M. O.}, year={2009}, month={Jul}, pages={1471–1486} }
 @article{vagelli_burford_bernardi_2008, title={Fine scale dispersal in Banggai Cardinalfish, Pterapogon kauderni, a coral reef species lacking a pelagic larval phase}, volume={1}, DOI={10.1016/j.margen.2009.01.001}, abstractNote={Dispersal in marine species results from complex interactions between biotic and abiotic factors. Importantly, the pelagic larval phase of most marine species adds a significant degree of complexity. Therefore, a growing body of work is focusing on those rare species that lack a pelagic larval phase (usually brooding species). For such species, large-scale gene flow has been shown to be very low, thus following the expectation of a relationship between realized dispersal and pelagic larval duration. Yet, little is known about the dispersal of those species at very small geographic scales. In this study, we focused on the Banggai Cardinalfish, Pterapogon kauderni, a mouthbrooding species that lacks a pelagic larval phase. Based on previously identified microsatellites, we scored 12 populations around the southern island of Bangkulu, in the Banggai Archipelago, Indonesia. While only 60 km in perimeter, we found that this island harbors very distinct populations of P. kauderni. Indeed, assignment tests self-assigned 10 out of those 12 populations. These results mirror the very high level of self-assignment at the level of the entire archipelago, where, out of 13 populations, 70% of the individuals were reassigned to their source population. Therefore, our data show consistency between small and large-scale dispersal. In addition, in light of the recent expansion in the harvesting of this species for the pet trade, our data have important conservation implications.}, number={3-4}, journal={Marine Genomics}, publisher={Elsevier BV}, author={Vagelli, Alejandro and Burford, Martha and Bernardi, Giacomo}, year={2008}, month={Sep}, pages={129–134} }
 @article{burford_bernardi_2008, title={Incipient speciation within a subgenus of rockfish (Sebastosomus) provides evidence of recent radiations within an ancient species flock}, volume={154}, DOI={10.1007/s00227-008-0963-6}, number={4}, journal={Marine Biology}, publisher={Springer Nature}, author={Burford, Martha O. and Bernardi, Giacomo}, year={2008}, month={Apr}, pages={701–717} }
 @article{burford_larson_2006, title={Genetic heterogeneity in a single year-class from a panmictic population of adult blue rockfish (Sebastes mystinus)}, volume={151}, DOI={10.1007/s00227-006-0475-1}, number={2}, journal={Marine Biology}, publisher={Springer Nature}, author={Burford, Martha O. and Larson, Ralph J.}, year={2006}, month={Oct}, pages={451–465} }