Joshua S. Reece

Evolutionary history of plant multisubunit RNA polymerases IV and V: subunit origins via genome-wide and segmental gene duplications, retrotransposition, and lineage-specific subfunctionalization.

Eukaryotes have three multisubunit DNA-dependent RNA polymerases that are essential for viability, abbreviated as Pol I, Pol II, and Pol III. Remarkably, Arabidopsis thaliana and other higher plants contain two additional nuclear multisubunit RNA polymerases, Pol IV and Pol V. These plant-specific polymerases are not essential for viability but have nonredundant roles in RNA-mediated gene-silencing pathways. Proteomic analyses have revealed that Arabidopsis Pol IV and Pol V have a 12-subunit composition like Pol II. In fact, half of the subunits of Pols II, IV, and V are encoded by the same genes. The remaining Pol IV- or Pol V-specific subunit genes arose through duplication and subfunctionalization of ancestral Pol II subunit genes. These include the genes encoding the largest subunits unique to Pol IV or Pol V, the genes encoding the second- and the fourth-largest subunits that are used by both Pol IV and Pol V, the gene encoding the fifth-largest subunit unique to Pol V and the genes encoding the seventh-largest subunits that are unique to Pol IV and Pol V. On the basis of phylogenetic reconstructions, the gene duplication events giving rise to the first-, second-, fourth-, fifth-, and seventh-largest subunits of Pol IV and/or Pol V occurred independently. Interestingly, a cDNA-mediated duplication of the Pol II seventh-largest subunit gene via retro-tranposition was an early event in Pol IV evolution, preceded only by the duplications of the largest and second-largest subunit genes. Secondary duplication of this cDNA-like gene to generate Pol IV- and Pol V-specific seventh-largest subunits has occurred in Arabidopsis but not all dicotyledonous plants or monocots, indicative of the dynamic evolution of RNA Pol IV and Pol V in plants.

Historical perspectives on population genetics and conservation of three marine turtle species

Considerable phylogeographic and population genetic research has been conducted on marine turtles. Less attention, however, has been paid to the historical patterns and processes that have led to present patterns of genetic structure, and particularly, how these populations have responded to major climatic changes in the past. To address these questions, we analyzed previously published mitochondrial haplotype data independently for three marine turtle species, the loggerhead (Caretta caretta), hawksbill (Eretmochelys imbricata), and green turtle (Chelonia mydas). Considering all three species, we conducted analyses on a total of 657 individuals from 36 nesting beaches in the Atlantic and Mediterranean. Our results suggest that much of the contemporary genetic structure has been significantly affected by complex patterns of historical population subdivision, long-distance dispersal, and restricted geneflow. These inferences also imply that the climatic and sea level fluctuations during the Pleistocene may have had contrasting effects on genetic structure (e.g., fragmenting versus homogenizing) and on population sizes. Estimates of historical and current effective population sizes further highlight differential demographic responses across species to historical climatic cycles. Collectively, our results provide evidence for the occurrence of historical refugia through climatic cycles and complex historical metapopulation dynamics, and identify common and unique patterns of metapopulation structure across species. These historical patterns provide a basis for predictive estimates of metapopulation responses to habitat loss, population extirpation, and global climatic change.

A Vulnerability Assessment of 300 Species in Florida: Threats from Sea Level Rise, Land Use, and Climate Change

Species face many threats, including accelerated climate change, sea level rise, and conversion and degradation of habitat from human land uses. Vulnerability assessments and prioritization protocols have been proposed to assess these threats, often in combination with information such as species rarity; ecological, evolutionary or economic value; and likelihood of success. Nevertheless, few vulnerability assessments or prioritization protocols simultaneously account for multiple threats or conservation values. We applied a novel vulnerability assessment tool, the Standardized Index of Vulnerability and Value, to assess the conservation priority of 300 species of plants and animals in Florida given projections of climate change, human land-use patterns, and sea level rise by the year 2100. We account for multiple sources of uncertainty and prioritize species under five different systems of value, ranging from a primary emphasis on vulnerability to threats to an emphasis on metrics of conservation value such as phylogenetic distinctiveness. Our results reveal remarkable consistency in the prioritization of species across different conservation value systems. Species of high priority include the Miami blue butterfly (Cyclargus thomasi bethunebakeri), Key tree cactus (Pilosocereus robinii), Florida duskywing butterfly (Ephyriades brunnea floridensis), and Key deer (Odocoileus virginianus clavium). We also identify sources of uncertainty and the types of life history information consistently missing across taxonomic groups. This study characterizes the vulnerabilities to major threats of a broad swath of Florida’s biodiversity and provides a system for prioritizing conservation efforts that is quantitative, flexible, and free from hidden value judgments.

Mixed stock analysis of juvenile loggerheads (Caretta caretta) in Indian River Lagoon, Florida: implications for conservation planning

Key words: Bayesian mixed-stock analysis, Indian River Lagoon, juvenile recruitment, loggerhead, marineturtlesIntroductionConservation of marine animals often is limited bythe ability of researchers to identify biologicaltrends and potential threats to organisms thatmake long distance migrations. For example, sal-mon production in California may be affected bylogging hundreds of miles inland (Caffereta andSpittler 1998) and marine turtle bycatch duringMediterranean shrimping operations decreasesbreeding populations on nesting beaches in Flor-ida and Mexico (Laurent et al. 1998). Attempts tosolve this problem by censusing rookeries, whilelogistically feasible, fail to incorporate predictivemodels and primarily record the results of trendsdisplayed by juveniles from distinct foraging areas(termed here as juvenile aggregations) in the priordecade. In the case of Florida marine turtles, theprimary measure of population change is thenumber of nests deposited on a beach, whichignores the effects of juvenile mortality caused bydisease (Work 2001), commercial fisheries (Crow-der 1995), and pollution on the future breedingpopulation. Understanding the factors dictatingjuvenile recruitment permits a more forwardlooking, predictive approach that incorporates theeffects of pollution, disease, natural disasters, andcommercial fisheries by-catch on juvenile popula-tions to predict future trends. Our detailed mixed-stock analysis of a large juvenile aggregation withseveral contributing rookeries reveals a novelapproach to understanding these factors and de-scribes patterns that are broadly applicable toregional and possibly global loggerhead rookeries.Loggerheads nest on sandy beaches throughouttemperate latitudes. The species was federally lis-ted as threatened in the North Atlantic in 1978 andis a CITES Appendix I listed species. The MarineTurtle Specialist Group and the IUCN Red Listconsider the loggerhead to be endangeredthroughout much of its range (Marine TurtleSpecialist Group 1996). Atlantic loggerheads leavetheir nesting beaches and enter oceanic currentsystems such as the Gulf Stream which laterbecomes part of the North Atlantic Gyre. Aftercircumnavigating the Atlantic for 3–10 years theyrecruit to a juvenile foraging area for the next 10–12 years (Carr 1986; Musick and Limpus 1997).Some of the juvenile (foraging) loggerheads in theNorth Atlantic recruit to juvenile foraging areas inthe Azores and Madeira (Bolten et al. 1998), butmany individuals enter foraging areas in IndianRiver Lagoon (IRL) on the east coast of centralFlorida.Aggregations of juvenile marine turtles mayinclude individuals from nesting beaches aroundthe globe, but until very recently, biologists hadnot devised a method for modeling contributionsof local rookeries to juvenile aggregations (Norr-gard and Graves 1995; Lahanas et al. 1998; Bass

Prioritizing Species by Conservation Value and Vulnerability: A New Index Applied to Species Threatened by Sea-Level Rise and Other Risks in Florida

ABSTRACT: Land-use change, climate change, and sea-level rise (SLR) pose substantial threats to biodiversity. Conservation resources are limited and must be directed toward the species and ecosystems that are most vulnerable, biologically distinct, likely to respond favorably to conservation interventions, and valuable ecologically, socially, or economically. Many prioritization and vulnerability assessment schemes exist, each emphasizing different types of vulnerabilities and values and often yielding disparate evaluations of the same species. We developed an integrative and flexible framework that incorporates existing assessments and is useful for illuminating the differences between systems such as the IUCN Red List, the US Endangered Species Act, and NatureServes Conservation Status Assessment and Climate Change Vulnerability Index. The Standardized Index of Vulnerability and Value Assessment (SIVVA) includes five advancements over existing tools: (1) the ability to import criteria and data from previous assessments, (2) explicit attention to SLR, (3) a flexible system of scoring, (4) metrics for both vulnerability and conservation value, and (5) quantitative and transparent accounting of multiple sources of uncertainty. We apply this system to 40 species in Florida previously identified as being vulnerable to SLR by the year 2100, describe the influence of different types of uncertainty on the resulting prioritizations, and explore the power of SIVVA to evaluate alternative prioritization schemes. This type of assessment is particularly relevant in low-lying coastal regions where vulnerability to SLR is predictable, severe, and likely to interact synergistically with other threats such as coastal development.

Threatened and endangered subspecies with vulnerable ecological traits also have high susceptibility to sea level rise and habitat fragmentation.

The presence of multiple interacting threats to biodiversity and the increasing rate of species extinction make it critical to prioritize management efforts on species and communities that maximize conservation success. We implemented a multi-step approach that coupled vulnerability assessments evaluating threats to Florida taxa such as climate change, sea-level rise, and habitat fragmentation with in-depth literature surveys of taxon-specific ecological traits. The vulnerability, adaptive capacity, and ecological traits of 12 threatened and endangered subspecies were compared to non-listed subspecies of the same parent species. Overall, the threatened and endangered subspecies showed high vulnerability and low adaptive capacity, in particular to sea level rise and habitat fragmentation. They also exhibited larger home ranges and greater dispersal limitation compared to non-endangered subspecies, which may inhibit their ability to track changing climate in fragmented landscapes. There was evidence for lower reproductive capacity in some of the threatened or endangered taxa, but not for most. Taxa located in the Florida Keys or in other low coastal areas were most vulnerable to sea level rise, and also showed low levels of adaptive capacity, indicating they may have a lower probability of conservation success. Our analysis of at-risk subspecies and closely related non-endangered subspecies demonstrates that ecological traits help to explain observed differences in vulnerability and adaptive capacity. This study points to the importance of assessing the relative contributions of multiple threats and evaluating conservation value at the species (or subspecies) level when resources are limited and several factors affect conservation success.

A multiscale natural community and species-level vulnerability assessment of the Gulf Coast, USA

Vulnerability assessments combine quantitative and qualitative evaluations of the exposure, sensitivity, and adaptive capacity of species or natural communities to current and future threats. When combined with the economic, ecological or evolutionary value of the species, vulnerability assessments quantify the relative risk to regional species and natural communities and can enable informed prioritization of conservation efforts. Vulnerability assessments are common practice in conservation biology, including the potential impacts of future climate scenarios. However, geographic variation in scenarios and vulnerabilities is rarely quantified. This gap is particularly limiting for informing ecosystem management given that conservation practices typically vary by sociopolitical boundaries rather than by ecological boundaries. To support prioritization of conservation actions across a range of spatial scales, we conducted the Gulf Coast Vulnerability Assessment (GCVA) for four natural communities and eleven focal species around the Gulf of Mexico based on current and future threats from climate change and land-use practices out to 2060. We used the Standardized Index of Vulnerability and Value (SIVVA) tool to assess both natural community and species vulnerabilities. We observed greater variation across ecologically delineated subregions within the Gulf Coast of the U.S. than across climate scenarios. This novel finding suggests that future vulnerability assessments incorporate regional variation and that conservation prioritization may vary across ecological subregions. Across subregions and climate scenarios the most prominent threats were legacy effects, primarily from habitat loss and degradation, that compromised the adaptive capacity of species and natural communities. The second most important threats were future threats from sea-level rise. Our results suggest that the substantial threats species and natural communities face from climate change and sea-level rise would be within their adaptive capacity were it not for historic habitat loss, fragmentation, and degradation.