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The northern quahog (Mercenaria mercenaria) supports lucrative aquaculture industries in the USA. In the southeastern USA, aquacultured M. mercenaria faces increasing risks of summer die-offs from prolonged heat waves. We used a comparative transcriptomic approach to investigate the molecular responses of M. mercenaria and its southern congener, Mercenaria campechiensis, to controlled incremental heat stress over a 4-week period. Mercenaria were exposed to temperatures from 24 to 34 °C with 2.5 °C/week, after which, gill transcriptomes were de novo assembled and annotated. During the 4 weeks of chronic heat exposure, both species had the same survival rate (96%); M. mercenaria experienced body weight gain/loss depending on the originated hatcheries while M. campechiensis experienced an average net weight loss. The upregulated genes in both species included those in chaperone-mediated protein folding and regulation of cell death pathways, while the downregulated genes in both species involved in mRNA processing and splicing pathways. Compared to M. mercenaria, M. campechiensis appears to be more sensitive to prolonged heat stress as indicated by upregulating significantly more genes in coping with oxidative stress and in the protein degradation pathways, while downregulating some inhibitors of apoptosis. We discussed this finding within their ecological and evolutionary context. Our findings highlighted the potential vulnerability of the two quahogs, especially the southern quahog, to continued ocean warming.

Pocket gophers provide vital ecosystem services; however, species like the southeastern pocket gopher (Geomys pinetis), endemic to the southeastern United States, are declining. Long-term conservation of this species requires greater understanding of its habitat characteristics. Our objective here was to determine habitat features associated with southeastern pocket gopher occurrence at the local (100 ha) and home-range (0.09 ha) scales. We assessed occurrence and carried out vegetation surveys at 177 sites across the species’ range during the growing season (March–September) 2016–2017. At the local scale, we found a negative relationship between occurrence and groundcover height and a quadratic relationship with canopy closure. At the home-range scale, occurrence was positively related to grass groundcover and had a quadratic relationship with canopy closure. Restoration of southeastern pocket gopher habitat should focus on creating or maintaining areas with intermediate canopy (~45–55%) and an understory dominated by grasses and forbs.

We investigated the landscape epidemiology of a globally distributed mammal, the wild pig (Sus scrofa), in Florida (U.S.), where it is considered an invasive species and reservoir to pathogens that impact the health of people, domestic animals, and wildlife. Specifically, we tested the hypothesis that two commonly cited factors in disease transmission, connectivity among populations and abundant resources, would increase the likelihood of exposure to both pseudorabies virus (PrV) and Brucella spp. (bacterial agent of brucellosis) in wild pigs across the Kissimmee Valley of Florida. Using DNA from 348 wild pigs and sera from 320 individuals at 24 sites, we employed population genetic techniques to infer individual dispersal, and an Akaike information criterion framework to compare candidate logistic regression models that incorporated both dispersal and land cover composition. Our findings suggested that recent dispersal conferred higher odds of exposure to PrV, but not Brucella spp., among wild pigs throughout the Kissimmee Valley region. Odds of exposure also increased in association with agriculture and open canopy pine, prairie, and scrub habitats, likely because of highly localized resources within those land cover types. Because the effect of open canopy on PrV exposure reversed when agricultural cover was available, we suggest that small-scale resource distribution may be more important than overall resource abundance. Our results underscore the importance of studying and managing disease dynamics through multiple processes and spatial scales, particularly for non-native pathogens that threaten wildlife conservation, economy, and public health. Supplementary Information The online version of this article (10.1007/s10393-020-01508-6) contains supplementary material, which is available to authorized users.

Knowledge of genetic structure is essential for the long-term management and conservation of endangered species. We report the results from a genetic examination of the federally endangered Florida bonneted bat (Eumops floridanus) sampled from its range in southern Florida, USA. Bonneted bats are primarily found in four regions separated by approximately 100 to 250 kms, including three western natural areas (BW, PC, and CC) and one urban population on the east coast [Miami-Dade County (MD)]. We used 22 microsatellite loci and cytochrome b sequences to assess the extent of connectivity and levels of genetic diversity. Regional populations were highly differentiated (FST = 0.178) and model-based and multivariate analyses showed that MD was the most distinct among pairwise comparisons. Regional populations are small (i.e., Ne < 100) but demographically stable. Estimates of contemporary migration and historic gene flow suggest that regional populations do not frequently exchange migrants, but simulations suggest that the divergence among western regions is likely a result of recent genetic drift rather than long-term isolation. Significantly, mitochondrial DNA revealed that haplotypes from MD were similar or shared with those recognized as Eumops ferox from Cuba and Jamaica, and divergent (1.5%) from the remainder of bonneted bats in Florida. Our data support the management of each of the four populations as distinct population segments, and that BW, PC and CC combined are on an independent evolutionary trajectory from bats in MD. Critically, bonneted bats in Florida appear to harbor cryptic diversity that will require a reassessment of their taxonomy.

We investigated how herpetofauna respond to burning and burn season in longleaf pine (Pinus palustris Mill.) sandhills by contrasting preburn species richness, diversity, and evenness and captures of six reptile and six amphibian species to the first (Y+1) or second (Y+2) year after burn or between dormant-season burns (DSB) and growing-season burns (GSB). Responses to burning overall or burn season were inconsistent among species; several showed no response, whereas others responded positively or negatively. Most responses were evident only in Y+1. Reptile species richness, diversity, and evenness responses were not detected. Amphibian richness increased after burning overall; diversity and evenness decreased more in GSB than in DSB in Y+1. Southern toad (Anaxyrus terrestris (Bonnaterre, 1789)) captures increased and Florida crowned snake (Tantilla relicta Telford, 1966) captures decreased following burns overall in Y+1. Ground skink (Scincella lateralis (Say in James, 1823)) captures increased more in DSB than GSB in Y+1. Florida gopher frog (Lithobates capito (LeConte, 1855)) and southeastern five-lined skink (Plestiodon inexpectatus; Taylor, 1932) captures increased, and oak toad (Anaxyrus quercicus (Holbrook, 1840)) decreased more in GSB than DSB in Y+2. Responses were likely due to changes in aboveground activity affecting captures or (for amphibians especially) annual variability in captures unrelated to burns. Our results indicated that reptiles and amphibians of sandhills are resilient to short-term effects of burning overall and burn season.

Determining the scale of genetic variation informs studies of dispersal, connectivity, and population dynamics particularly in heterogeneous landscapes. Mastomys natalensis and Mus minutoides are generalist rodents that utilize multiple habitat types within the agro-ecological landscapes of southern African savannas. To study the comparative spatial genetic structure of these species we developed 9 new microsatellites for Mus and used 14 microsatellite loci previously developed for Mastomys, to genotype rodents sampled across an agro-ecological landscape (˜200 km2). Spatial genetic structure was measured using spatial autocorrelation and Moran’s Eigenvector Maps analysis. In both species, non-random genetic similarity was limited to only the smallest spatial scales (

Connectivity is central to ecology and evolution as it focuses on the movement of individuals or genes across landscapes. Genetic connectivity approaches aim to understand gene flow but often estimate it indirectly based on metrics of genetic differentiation, which can also be affected by other evolutionary forces such as genetic drift. Gene flow and genetic drift are driven by separate ecological mechanisms with potentially differing effects on genetic differentiation and interpretations of genetic connectivity. The ecological mechanisms contributing to gene flow and genetic drift are primarily effective dispersal, or movement followed by successful reproduction, and the number of breeders in a local population, Nb , respectively. Yet, rarely are these ecological mechanisms and genetic connectivity measured simultaneously across landscapes. We examine the roles of effective dispersal and Nb on genetic connectivity across the entire range of the endangered snail kite (Rostrhamus sociabilis plumbeus), between 2006-2015. We find that both Nb and effective dispersal are important predictors of genetic connectivity across this landscape, but that Nb has a 3 × stronger effect on genetic connectivity. Furthermore, Nb is positively correlated with heterozygosity and allelic richness within patches, suggesting a potentially important role of genetic drift, in addition to gene flow, on genetic connectivity. These results emphasize that conservation efforts should focus on not only between-patch processes of movement but also within-patch processes regarding habitat quality and local population size for increasing genetic connectivity.

Biofluorescence in mammal pelage is considered rare, but has been documented in multiple taxa in recent years. Herein, we provide the first observations of biofluorescence in fossorial mammals. We documented biofluorescence in live Geomys pinetis (southeastern pocket gopher) and in museum specimens of four additional geomyid species. Although unknown, the adaptive significance of biofluorescence in pocket gophers is likely similar to that documented in terrestrial and arboreal species previously, including communication or predator evasion.

Increased agricultural intensification and extensive woody plant encroachment are having widespread effects on the functioning of grass-dominated systems at multiple spatial scales. Yet there is little understanding of how the provisioning of biodiversity-based ecosystem services might be altered by these ongoing changes. One fundamental ecosystem service that is decreasing globally, especially in human-altered landscapes, is scavenging that regulates disease processes, alters species distributions, and influences nutrient cycling. Accordingly, our goal was to understand how facultative scavenging, particularly that of mesocarnivores, was affected by landscape heterogeneity and woody encroachment in tropical-grassy savannas within an agricultural landscape mosaic. We baited (using chicken carcasses) plots across a gradient of land cover heterogeneity in areas with an open and closed canopy and subsequently measured scavenging rates. We found that scavenging efficiency of mesocarnivores and other small vertebrates was dependent on environmental variation at multiple spatial scales within our savanna agroecosystem. Mesocarnivores removed more bait when the overstory canopy at the plot (i.e., exact location of bait station) was more closed; in contrast, mesocarnivore scavenging was less efficient when patches (50 × 50 m area around the bait station) within the site had a higher density of shrubs. At the landscape scale, increased land cover fragmentation resulted in decreased amounts of scavenging by mesocarnivores. This study demonstrates that a relatively transformed agroecosystem can support the provision of important ecosystem services and offer an important buffer against loss of ecosystem services. Our results suggest that targeted woody encroachment control, protection of large trees, and management or mitigation of extreme levels of fragmentation can help maintain ecosystem service provision and biodiversity.

Animals living underground deal with multiple physiological challenges, such as hypoxia and hypercarbia, but may have reduced thermoregulation demands because of the more stable underground microclimate. Southeastern pocket gophers (Geomys pinetis Rafinesque) occur in the fire-adapted, open-pine forests of the southeastern Atlantic Coastal Plain where prescribed fire is commonly used to manage understory vegetation. They are almost exclusively fossorial, and their tunnels provide ecological services, including shelter, for a suite of commensal vertebrates and invertebrates. To quantify potential thermoregulation benefits of southeastern pocket gopher tunnels, we compared temperatures in active tunnels (n = 31) to aboveground temperatures during winter (December 2018–February 2019), and to aboveground temperatures during prescribed fire events (n = 16) occurring in spring (March–May 2019). During winter, tunnels provided a more stable thermal environment (average range = 6.5 ± 0.8 C; mean ± se) relative to aboveground (average range = 24.8 ± 1.8 C) temperatures. Similarly, mean tunnel temperature range (2.05 ± 0.5 C) was significantly narrower than aboveground temperature range associated with fire events (497.0 ± 101.4 C). Clearly, tunnels provide a stable thermal environment for pocket gophers and commensals that use their tunnel systems.

The goal of this study was to evaluate the efficacy of phenotypic traits and two genetic assays to distinguish between Mercenaria mercenaria, an important aquaculture species, and Mercenaria campechiensis, a conspecific species that is partially sympatric, but that has not been successfully farmed. The objectives were to evaluate (1) four established diagnostic phenotypic traits (lunule shape, thickness of concentric shell ridges, prominence of anterior side of the concentric ridges, and presence of purple nacre inside of the shells) to distinguish between species, (2) size polymorphism of PCR fragments from four genes [16S rRNA, 18S rRNA, Internal Transcribed Spacer genes (ITS1 and ITS2)], and (3) PCR-restriction fragment length polymorphism (RFLP) on three of these genes (16S, ITS1, and ITS2). Phenotypic traits correctly distinguished two geographically distant conspecific populations (two locations in Maine for M. mercenaria and in Bradenton, FL, for M. campechiensis); however, among all other locations, both species had overlapping phenotypic trait values. Although PCR fragments were obtained for all genes tested, size polymorphism was not identified between the two species. Restriction enzyme digestion of PCR fragments resulted in diagnostic fragments distinguishing the two species for 16S, ITS1, and ITS2. Although phenotypic scores failed to delineate between the two species in most locations, PCR-RFLP results failed to identify hybrids in wild or hatchery samples. Further investigation is needed to apply the PCR-RFLP assays on known hybrid offspring from crosses of M. mercenaria and M. campechiensis. Results have elucidated the difficulties in confidently detecting hybridization in quahogs; however, determining effective methods for species identification and hybrid detection will be important to address issues such as the prevalence and distribution of hybridization in aquaculture and in wild populations, and to determin the presence of M. campechiensis which are currently difficult to find.

The genus Procambarus represents a diverse genus of freshwater crayfish that includes epigean species, stygobitic species, and at least one parthenogenic species. Despite its evolutionary, ecological, and economic importance, most genomic and transcriptomic resources for this genus are limited to a couple of model species. We sequenced the transcriptome of a non-model species, P. erythrops, a geographically restricted stygobitic species from Florida. RNA isolated from gill, muscle and eye tissue was pooled to create a de novo transcriptome assembly using Single Molecule Real-Time sequencing (PacBio), resulting in 19,442 full-length isoforms. The assembly has been deposited in the NCBI (BioProject PRJNA657230). These data will make an important contribution to the comparative study of transcriptome evolution in crayfish and crustaceans.

The widespread introduction of Largemouth Bass (Micropterus salmoides) and Florida Bass (M. floridanus) to establish sport fisheries represents a significant conservation concern given their role as apex predators and their ability to alter community diversity and species abundance. In regions like southern Africa, which has both high levels of aquatic endemism and imperilment, limiting the spread of invasive predators is a primary goal of current alien species legislation. Here, we applied two panels of species-diagnostic SNPs for a total of 60 markers to map the distribution of Largemouth Bass, Florida Bass, and their hybrids in 13 southern African water bodies. Using Bayesian clustering algorithms we documented the introgression of Florida Bass alleles across a broad geographic range, from the Cape Floristic region of South Africa to Mozambique. Several populations previously considered pure Largemouth Bass based on mitochondrial DNA sequences were found to consist exclusively of hybrids. Samples collected from Lake Chicamba, which was initially established with pure Largemouth Bass, are now almost exclusively comprised of Florida Bass alleles (89.3 % Florida Bass). The estimated hybrid class of sampled fish (e.g., F1 hybrid, pure Largemouth Bass, pure Florida Bass) showed that with few exceptions, populations were dominated by a single hybrid class. The present work provides enhanced resolution of the distribution and dynamics of Florida Bass, Largemouth Bass, and their hybrids in southern Africa.

Amphibians are declining worldwide due to habitat destruction, disease, and environmental stressors. Extremely variable breeding populations and a paucity of long-term monitoring data limits rigorous testing of amphibian population trends, or bias associated with sampling regimes. We used 24 years of continuous trapping data to compare annual probability of presence, and population trends and statistical power for six species among seven wetlands using five sampling scenarios (SS) based on the interval and span of years analyzed. Richness within a year and wetland ranged 29–89% of total species captured there (all years), and 27–82% of total species captured during the study (all years, pooled wetlands). SS had little effect on probability of presence for most common species but did for less common species. Population trends were inconsistently significant or nonsignificant among wetlands within SSs, and among SSs within the same wetlands. The direction (+/−) of trends among wetlands and scenarios for a species generally agreed, but not always. Low statistical power for virtually all population trend estimates, including the All-years SS indicated results were inconclusive. Juvenile recruitment was correlated with adult populations in some subsequent years for four of the six species. We illustrate how probability of presence and population trend estimates can differ among similar wetlands within a landscape, and according to the span, or subset of years sampled. Our results indicate that amphibian monitoring at wetlands cannot conclusively gauge population trends for breeding populations that fluctuate widely among wetlands and from year to year.

The Florida bass ( Micropterus floridanus ) is a species endemic to peninsular Florida that is held in high esteem by bass anglers for its tendency to attain a larger maximum size and aggressiveness relative to that of its sister taxon, the Northern largemouth bass, Micropterus salmoides . Hatchery rearing and stocking of Florida bass outside of their native range are commonplace, particularly in the southern United States. In many cases, however, there has been minimal assessment of the persistence and success of these fish. Genetic markers are an important tool for tagging and tracing the contributions of particular lines and crosses of fish. Single nucleotide polymorophism (SNP) markers, in particular, can provide rapid and affordable genotyping of large numbers of fish. In the present study, we generated 58,450 genome-wide SNPs and population-level genotypes for Florida bass using a cost-effective genotyping-by-sequencing method. A total of 58 SNPs were shown to assign parents to offspring with 100% accuracy, irrespective of sex and with the presence of full-sib relationships. Depending on the population, sex information, and genetic relationships between parents, we also demonstrated that smaller SNP subsets may be sufficient for parentage assignment. The accuracy and assignment power of the SNP panels were found to compare favorably to those of 10 microsatellites genotyped on the same parents and progeny. This study demonstrated the utility of simple and low-cost GBS techniques for SNP discovery and the relatively small number of variable SNPs needed for accurate parentage assignment in Florida bass. The SNP resources created in this study should facilitate parentage-based research and breeding, genetic tagging, and conservation of Florida bass.

Wild pigs (Sus scrofa) are the most widely distributed invasive wild ungulate in the United States, yet the factors that influence wild pig dispersal and colonization at the regional level are poorly understood. Our objective was to use a population genetic approach to describe patterns of dispersal and colonization among populations to gain a greater understanding of the invasion process contributing to the expansion of this species. We used 52 microsatellite loci to produce individual genotypes for 482 swine sampled at 39 locations between 2014 and 2016. Our data revealed the existence of genetically distinct subpopulations (F ST = 0.1170, p

Integrative taxonomy seeks to approach the complex topic of species diagnosis using independent, complementary lines of evidence. Despite their ubiquity throughout North and Central America, taxono...

The landscape heterogeneity hypothesis states that increased heterogeneity in agricultural landscapes will promote biodiversity. However, this hypothesis does not detail which components of landscape heterogeneity (compositional or configurational) most affect biodiversity and how these compare to the effects of surrounding agricultural land-use. Our objectives were to: (1) assess the influence of the components of structural landscape heterogeneity on taxonomic diversity; and (2) compare the effects of landscape heterogeneity to those of different types of agricultural land-use in the same landscape across different taxonomic groups. We identified a priori independent gradients of compositional and configurational landscape heterogeneity within an agricultural mosaic of north-eastern Swaziland. We tested how bird, dung beetle, ant and meso-carnivore richness and diversity responded to compositional and configurational heterogeneity and agricultural land-use across five different spatial scales. Compositional heterogeneity best explained species richness in each taxonomic group. Bird and ant richness were both positively correlated with compositional heterogeneity, whilst dung beetle richness was negatively correlated. Commercial agriculture positively influenced bird species richness and ant diversity, but had a negative influence on dung beetle richness. There was no effect of either component of heterogeneity on the combined taxonomic diversity or richness at any spatial scale. Our results suggest that increasing landscape compositional heterogeneity and limiting the negative effects of intensive commercial agriculture will foster diversity across a greater number of taxonomic groups in agricultural mosaics. This will require the implementation of different strategies across landscapes to balance the contrasting influences of compositional heterogeneity and land-use. Strategies that couple large patches of core habitat across broader scales with landscape structural heterogeneity at finer scales could best benefit biodiversity.

Genetic structure and genetic diversity are key population characteristics that can inform conservation decisions, such as delineating management units or assessing potential risks for inbreeding depression. Evidence of genetic structuring or low genetic diversity in the critically endangered snail kite (Rostrhamus sociabilis plumbeus) would have implications for monitoring and planning decisions. Recent work on understanding connectivity across the snail kite range indicated that there is less dispersal between northern and southern parts of the current range, and that dispersal is shaped by individual habitat preference. We examine whether there is neutral genetic structure and the amount of genetic variation in the population by non-lethally sampling 235 nestlings from unique nests across the entire breeding range between 2013 and 2014. Data on 15 microsatellite revealed low diversity (e.g., N a = 2.54, H e = 0.37) and range-wide panmixia based on AMOVA, Bayesian clustering, spatial autocorrelation, isolation by distance, and spatially explicit ordination analyses. Our results emphasize that long-term recovery goals and management strategies should be based on viewing snail kites as a single genetic population, despite evidence for non-random dispersal between wetlands over ecological time scales. These results also highlight the need to understand potential effects of low genetic diversity on population dynamics and viability of snail kites. More broadly, these results add to the growing evidence for potential discrepancies between dispersal and genetic patterns, emphasizing that care should be taken if using one to interpret the other, particularly for widely-ranging species.

Black basses Micropterus spp. are the focus of extensive management efforts throughout North America, where they support a multibillion-dollar recreational sport fishery. Harvest rates in many bass fisheries have declined in recent decades, yet a growing number of studies have proposed that catch-and-release angling practices, such as bed-fishing in which anglers intentionally target bass while the fish are defending their nests, can decrease individual reproductive success. In response, management agencies have restricted fishing during the spawning period in some regions. We evaluated the impacts of catch-and-release bed-fishing on Florida Bass M. salmoides floridanus nest success, reproductive success, production of fall recruits, and the number of parents that contributed to reproduction. Eighteen replicate populations simulating natural Florida lakes were established, and ponds were assigned either a bed-fishing (n = 10) or a control treatment (n = 8). Snorkel surveys were conducted throughou...

Support was provided by All Out Africa Inc., and the University of Florida. Thanks to UF and UNISWA students on the UF in Swaziland study abroad course.

Summary The decision to disperse or remain philopatric between breeding seasons has important implications for both ecology and evolution, including the potential for carry-over effects, where an individual's previous history affects its current performance. Carry-over effects are increasingly documented although underlying mechanisms remain unclear. Here we test for potential carry-over effects and their mechanisms by uniting hypotheses for the causes and consequences of habitat selection and dispersal across space and time. We linked hypotheses regarding different types of factors and information (environmental conditions, personal and public information) predicted to impact reproductive success and dispersal for an endangered, wetland-dependent bird, the snail kite (Rostrhamus sociabilis plumbeus). To do so, we coupled structural equation modelling with 20 years of mark–recapture and nesting data across the breeding range of this species to isolate potential direct and indirect effects of these factors. We found that water depth at nest sites explained subsequent emigration rates via an indirect path through the use of personal, not public, information. Importantly, we found that these dispersers tended to initiate nests later the following breeding season. This pattern explained a phenological mismatch of nesting with hydrological conditions, whereby immigrants tended to nest later, late nesters tended to experience lower water depths, higher nest failure occurred at lower water depths and higher nest failure explained subsequent breeding dispersal. These results identified a novel potential mechanism for carry-over effects: a phenological mismatch with environmental conditions (water depth) that occurred potentially due to time costs of dispersal. Our results also highlighted a substantial benefit of philopatry – earlier initiation of reproduction – which allows philopatric individuals to better coincide with environmental conditions that are beneficial for successful reproduction. These results have implications for our mechanistic understanding and prediction of carryover effects, and emphasize that local conservation strategies, such as water management, can explain future demography at distant sites connected through dispersal.

The Largemouth Bass (Micropterus salmoides) is a global invader with demonstrated ecological impacts on native fish communities. Introductions of fishes in freshwater ecosystems are often characterized as complex processes, yet an understanding of the nature of the introduction can inform management and conservation actions. Early in the twentieth century, two introductions of Largemouth Bass were made into South Africa for the establishment of a recreational fishery, and subsequent translocations have expanded their distribution to include much of southern Africa. In this study we quantified neutral genetic variation, modeled potential introduction scenarios, and identified potential source regions from within the native range. We documented limited levels of genetic diversity in nuclear microsatellite genotypes across populations (mean allelic richness = 1.80 and mean observed heterozygosity = 0.16) and observed low levels of genetic differentiation among four of the five focal populations (mean pairwise fixation index = 0.09), with a fifth population displaying greater levels of genetic divergence (mean pairwise fixation index = 0.27). A total of three cytochrome b haplotypes were recovered from South Africa samples and the single most common haplotype (93% of individuals) was identical to a haplotype from a population of Largemouth Bass in Maryland, USA. Using limited available stocking data along with outputs from Principal Component Analysis and approximate Bayesian evaluation of competing introduction scenarios we confirm the presence of multiple introductions. Despite evidence for multiple introductions, Largemouth Bass in South African water bodies harbor extremely low neutral genetic diversity, suggesting that even a very limited number of propagules can experience a high likelihood of success in invading nonnative waters.

Conversion of native habitats into agricultural monocultures is a major cause of biodiversity loss favouring a small number of generalist species. Rodents can cause significant declines in crop yield, hence understanding the factors affecting their population dynamics is of importance to the agricultural sector. Sugarcane plantations in African savannas harbour a low diversity of small mammals, with a single genus (Mastomys spp.) often dominating the community. Our study investigated the factors that shape the composition of the small mammal community and the life-history traits of the dominant species in a savanna-sugarcane landscape mosaic. We surveyed small mammals at eight sites, six in sugarcane and two in neighbouring savannas at five-week intervals over the course of a year. Sugarcane and native savanna sites were categorised into vegetation height classes. We captured a total of 845 individual small mammals belonging to eight species across all sites. Species diversity was higher in the savanna than in sugarcane fields. Although the composition of the community overlapped in the two habitats, it was most similar between tall sugarcane and savanna, than between sites that had recently planted (emerging or short) sugarcane and either tall sugarcane or savanna. Furthermore, population densities of the dominant species (Mastomys natalensis) were significantly higher in sugarcane than in native savanna. Additionally, the interactions between habitat and season influenced survival and body condition of M. natalensis; apparent survival decreased in savanna and body condition improved in sugarcane during the wet season. Furthermore, the survival of M. natalensis was also significantly reduced in sugarcane fields that had been burnt prior to harvesting. However, there was no significant difference in the extent of breeding between the two habitats. This study provides novel insight into the mechanisms that allow for the persistence of high densities of rodent pest species. Keywords: Small mammals, Crop pests, Agriculture, Sugarcane, Population dynamics, Community structure

Numerous vertebrate species including Pituophis spp. (pine snakes) and birds of prey have been shown to consume Geomys pinetis (Southeastern Pocket Gopher), but its full spectrum of predators remains undocumented. As a part of a larger project involving radiotracking Southeastern Pocket Gophers in southwestern Georgia, a female Pocket Gopher was consumed by a Crotalus horridus (Timber Rattlesnake) while making an aboveground movement. Timber Rattlesnakes are a previously undocumented predator for Southeastern Pocket Gophers. Our observation further demonstrates predation risks associated with aboveground movement.

Occupancy modeling may be the most effective tool for studying the occurrence of secretive fossorial squamates. Our objective was to use occupancy models to test whether Florida Crowned Snakes (Tantilla relicta) are a suitable model species for other, more-secretive fossorial squamates. Tantilla relicta are easier to study than other fossorial squamates and likely respond to habitat management (e.g., fire frequency) similarly to these harder-to-study species of concern. We sampled T. relicta using 24 groups of drift fences in longleaf pine-wiregrass sandh ills, Ocala National Forest, Florida, USA to assess how habitat characteristics and weather influenced their occupancy, detection, colonization, and extinction rates. We predicted that temperature, rainfall, substrate composition, and prescribed burn history would influence T. relicta occupancy, detection, and movement in variable directions. The best-supported multiseason occupancy model included 1) initial occupancy influenced by time since last burn, 2) extinction and colonization as random processes, and 3) detection influenced by percent leaf litter and rainfall. Tantilla relicta were most likely to occupy recently burned sites and were most easily detected during dry periods and at sites with low leaf litter cover. Our results are consistent with research suggesting that short-return prescribed fires benefit many reptile species in central Florida's xeric longleaf pine-wiregrass forests. Further, our results provide modest evidence that T. relicta are suitable model organisms for studying fossorial squamate assemblages. Public domain – authored by a U.S. government employee

For species with geographically restricted distributions, the impacts of habitat loss and fragmentation on long-term persistence may be particularly pronounced. We examined the genetic structure of Panama City crayfish (PCC), Procambarus econfinae, whose historical distribution is limited to an area approximately 145 km2, largely within the limits of Panama City and eastern Bay County, FL. Currently, PCC occupy approximately 28% of its historical range, with suitable habitat composed of fragmented patches in the highly urbanized western portion of the range and managed plantations in the more contiguous eastern portion of the range. We used 1640 anonymous single-nucleotide polymorphisms to evaluate the effects of anthropogenic habitat modification on the genetic diversity and population structure of 161 PCC sampled from across its known distribution. First, we examined urban habitat patches in the west compared with less-developed habitat patches in the east. Second, we used approximate Bayesian computation to model inferences on the demographic history of eastern and western populations. We found anthropogenic habitat modifications explain the genetic structure of PCC range-wide. Clustering analyses revealed significant genetic structure between and within eastern and western regions. Estimates of divergence between east and west were consistent with urban growth in the mid-20th century. PCC have low genetic diversity and high levels of inbreeding and relatedness, indicating populations are small and isolated. Our results suggest that PCC have been strongly affected by habitat loss and fragmentation and management strategies, including legal protection, translocations, or reintroductions, may be necessary to ensure long-term persistence.

In poorly dispersing species gene flow can be facilitated when suitable habitat is widespread, allowing for increased dispersal between neighbouring locations. The Poweshiek skipperling [Oarisma poweshiek (Parker)], a federally endangered butterfly, has undergone a rapid, recent demographic decline following the loss of tallgrass prairie and fen habitats range wide. The loss of habitat, now restricted geographic range, and poor dispersal ability have left O. poweshiek at increased risk of extinction. We studied the population genetics of six remaining populations of O. poweshiek in order to test the hypothesis that gene flow was historically high despite limited long-distance dispersal capability. Utilising nine microsatellite loci developed by PacBio sequencing, we tested for patterns of isolation by distance, low population genetic structure and alternative gene flow models. Populations from southern Manitoba, Canada to the Lower Peninsula of Michigan, USA are only weakly genetically differentiated despite having low diversity. We found no support for isolation by distance, and Bayesian estimates of historical gene flow support our hypothesis that high levels of gene flow previously connected populations from Michigan to Wisconsin. Prairie grasslands have been reduced tremendously over the past century, but the low mobility of O. poweshiek suggests that rapid loss of populations over the past decade cannot be simply explained by fragmentation of habitat. As a species at high risk of extinction, understanding historical processes of gene flow will allow for informed management decisions with respect to head-starting individuals for population reintroductions and for conserving networks of habitat that will allow for high levels of gene flow.

Landscape connectivity is increasingly emphasized due to its relevance for interpreting effects of environmental change. Yet substantial uncertainty remains regarding the quantification of connectivity and the extent to which connectivity influences biodiversity. We review and synthesize 370 articles published since 2005 on the quantification and effects of landscape connectivity on biodiversity. We find a notable change in the quantification of connectivity from structural to functional approaches, a rise in network approaches, and a decline in approaches based on metapopulation theory. Most studies (54 %) did not test for the effects of connectivity, but of those that did, 91 % found effects on biodiversity, with over five times as many positive as negative effects reported. These effects were largely consistent across levels of biological organization, despite diverse perspectives on movement and connectivity across these domains. Nevertheless, we argue that several outstanding issues need to be addressed to advance our understanding of the effects of connectivity and its importance for conservation. These issues include the need for greater emphasis on estimating connectivity effects, explicitly incorporating the problem of scale, capturing impacts of movement processes relevant to different levels of organization, proper accounting of uncertainty, and isolating connectivity effects relative to other issues influencing biodiversity.

Movement is important for ecological and evolutionary theory as well as connectivity conservation, which is increasingly critical for species responding to environmental change. Key ecological and evolutionary outcomes of movement, such as population growth and gene flow, require effective dispersal: movement that is followed by successful reproduction. However, the relative roles of movement and postmovement reproduction for effective dispersal and connectivity remain unclear. Here we isolate the contributions of movement and immigrant reproduction to effective dispersal and connectivity across the entire breeding range of an endangered raptor, the snail kite (Rostrhamus sociabilis plumbeus). To do so, we unite mark-resight data on movement and reproduction across 9 years and 27 breeding patches with an integrated model that decomposes effective dispersal into its hierarchical levels of movement, postmovement breeding attempt, and postmovement reproductive success. We found that immigrant reproduction limits effective dispersal more than movement for this endangered species, demonstrating that even highly mobile species may have limited effective connectivity due to reduced immigrant reproduction. We found different environmental limitations for the reproductive component of effective dispersal compared with movement, indicating that different conservation strategies may be needed when promoting effective dispersal rather than movement alone. We also demonstrate that considering immigrant reproduction, rather than movement alone, alters which patches are the most essential for connectivity, thereby changing conservation priorities. These results challenge the assumption that understanding movement alone is sufficient to infer connectivity and highlight that connectivity conservation may require not only fostering movement but also successful reproduction of immigrants.

Florida bass, Micropterus floridanus, is the most popular freshwater sport fish in the state of Florida. Florida bass guard their nests for up to 2 weeks, and many anglers target the prized sport fish during this period using a procedure called bed fishing. This 7-page fact sheet written by John S. Hargrove and James D. Austin and published by the UF/IFAS School of Forest Resources and Conservation, Program in Fisheries and Aquatic Sciences, outlines the reproductive biology of Florida bass, the known consequences of bed fishing, and practices to minimize its impacts. http://edis.ifas.ufl.edu/fa204

The northern hard clam Mercenaria mercenaria is one of the most commercially important bivalve species produced via aquaculture in the eastern United States. Breeding practices associated with large-scale hatchery production of hard clamseedmayresultinunintended,potentiallynegativeconsequencesincludinginbreedingandreducedlevelsofgeneticdiversity. Seven microsatellite markers were used to compare levels of genetic diversity in six hatchery stocks and four wild stocks from the state of Florida. Wild stocks of M. mercenaria had slightly higher levels of allelic richness and similar observed heterozygosity (wild ¼Ar ¼3.61,Ho ¼0.448;hatchery ¼Ar ¼3.46,Ho ¼0.452);however,thesedifferenceswerenotstatisticallysignificant(Ar:P ¼ 0.145; Ho: P ¼ 0.931). Differentiation was highest between hatchery stocks (GST ¼ 0.03, SD ¼ 0.007; P < 0.001) but minimal among hatchery-by-wild comparisons. In contrast, wild stocks were not differentiated (GST ¼ -0.002, SD ¼ 0.004; P � 0.58) and Bayesian comparisons of competing gene flow models (panmixia, stepping stone, and full-migration) suggested that wild stocks were effectively panmictic at this scale. Together, these results indicate that some genetic drift has occurred within hatchery populations, possibly as a result of broodstock selection and spawning practices. The genetic divergence between wild and hatchery stocks observed in this study are not as pronounced as seen in other aquaculture bivalve species. Given the large scale of hard clam production in Florida we argue that hatchery practices should incorporate long-term genetic goals (i.e., avoidance of inbreeding) to maintain the integrity of hatchery stocks. A secondary objective of this study was to amplify a congeneric species, Mercenaria campechiensis, using the same suite of microsatellite markers to assess their utility for detecting interspecific hybridization. Amplification success was poor and failed for four of the seven loci. The identification of microsatellite loci for different species of Mercenaria should be identified de novo in the future.

Hydroregimes of ephemeral wetlands affect reproductive success of many amphibian species and are sensitive to altered weather patterns associated with climate change. We used 17 years of weekly temperature, precipitation, and water-depth measurements for eight small, ephemeral, groundwater-driven sinkhole wetlands in Florida sandhills to develop a hydroregime predictive model. To illustrate its utility for climate-change planning, we forecasted weekly wetland water-depths and hydroperiods (2012–2060) using our model and downscaled climate data from the CSIRO Mk3.5 Global Circulation Model under an A1B emissions scenario. We then examined how forecasted water depths and hydroperiods might alter reproductive success, and thereby populations, of five anuran species. Precipitation and water-depth from the prior week were significant predictors of water depth. Our model forecasted shallower depths and shortened hydroperiods for most wetlands when used with the CSIRO Mk3.5 A1B scenario. The forecasted hydroregimes would likely provide adequate reproductive opportunity for only one of the five species we examined. We demonstrate the utility of our model in examining how different climate-change scenarios might affect hydroregimes and, indirectly, biological diversity. Climate change uncertainty highlights the importance of retaining multiple, hydrologically diverse wetlands on landscapes to maximize the potential for successful reproduction by species having differing hydroregime requirements.

Grasscutter (Thryonomys swinderianus) is a large rodent distributed across sub-Saharan Africa that is highly valued as a source of protein. There has been little effort to evaluate the genetic structure of grasscutters despite long-term harvesting pressure and over 40 years of grasscutter domestication in West Africa. Our objectives were to quantify the genetic structure of wild grasscutters, and to compare genetic variation from wild samples to those from various farmed samples within south-western Nigeria. We genotyped 145 wild and 88 domesticated individuals at 11 microsatellite loci and present results quantifying regional genetic structuring and the relative patterns of diversity among wild and domesticated grasscutter populations. Our data reflect high differentiation between wild and domesticated grasscutters, and significantly greater allelic richness and gene diversity in the former. Despite this, domesticated populations appear to have similar levels of observed heterozygosity and comparable levels of differentiation among domesticated samples relative to wild samples. This may be the result of high turnover within captive colonies, or frequent infusion of new animals. More detailed molecular and quantitative genetic studies are recommended on this species to be able to understand their natural variation, degree of connectivity and to improve strategies for domestication. Keywords: domestication, farming, gene flow, genetic drift, genetic structure, microsatellites, Thryonomys swinderianus