High nuclear genetic diversity, high levels of outcrossing and low differentiation among remnant populations of Quercus petraea at the margin of its range in Ireland

Background and Aims Quercus petraea colonized Ireland after the last glaciation from refugia on mainland Europe. Deforestation. however. beginning in Neolithic times, has resulted in small, scattered forest fragments, now covering less than 12 000 ha. Methods Plastid (three fragments) and microsatellite variation (13 loci) were characterized in seven Irish populations sampled along a north-south gradient. Using Bayesian approaches and Wright's F-statistics, the effects of colonization and fragmentation on the genetic structure and mating patterns of extant oak populations were investigated. Key-Results All Populations possessed cytotypes common to the Iberian Peninsula. Despite the distance from the refugial core and the extensive deforestation in Ireland, nuclear genetic variation was high and comparable to mainland Europe. Low population differentiation was observed within Ireland and populations showed no evidence for isolation by distance. As expected of a marker with an effective Population size of one-quarter relative to the nuclear genome, plastid variation indicated higher differentiation. Individual inbreeding coefficients indicated high levels of outcrossing. Conclusions Consistent with a large effective Population size in the historical migrant gene pool and/or with high gene flow among populations, high within-population diversity and low population differentiation was observred within Ireland. It is proposed that native Q. petraea populations in Ireland share a common phylogeographic history and that the present genetic structure does not reflect founder effects. (C) 2004 Annals of Botany Company.

Year-round presence of dugongs in Pumicestone Passage, south-east Queensland, examined in relation to water temperature and seagrass distribution

Pumicestone Passage is a narrow waterway that lies to the north of and adjacent to Moreton Bay, and between mainland Queensland and Bribie Island, Australia. Anecdotal reports have suggested that the Passage is home to dugongs year-round despite winter water temperatures that are known to cause dugongs to migrate elsewhere. To examine the pattern of distribution and abundance of dugongs within the passage on a year-round basis, eight years of sightings data collected by a charter boat operator were examined. Dedicated aerial surveys of the passage were also conducted at two-monthly intervals over two years, and more intensively over a single winter. Dugong sightings were examined in relation to water temperatures and seagrass prevalence. The number of dugongs sighted in the area on any one survey varied from 0 to 13. Dugongs were seen in all months of the year and in each of the eight winters, indicating that Pumicestone Passage is used year-round despite winter water temperatures dropping to below 18 degrees C from June to August inclusive and below 16 degrees C in June. All dugong sightings occurred in the southern part of the passage, south of Tripcony Bight. Dugongs were associated with shallows that support Halophila and Halodule species of seagrass, food species that are favoured elsewhere in their range. The northern part of the passage also supports seagrasses that are eaten by dugongs and has water temperature ranges that are not appreciably different to those of the southern passage. However, the narrow channels and very shallow nature of the northern passage provides little to no deep-water refugia for dugongs and the seagrass beds are less extensive. This study suggests that southern Pumicestone Passage requires protection concomitant with it being a year-round refuge of the vulnerable dugong.

Understanding the phylogeographic patterns of European hedgehogs, Erinaceus concolor and E-europaeus using the MHC

The genome of the European hedgehog, Erinaceus concolor and E. europaeus, shows a strong signal of cycles of restriction to glacial refugia and postglacial expansion. Patterns of expansion, however, differ for mitochondrial DNA (mtDNA) and preliminary analysis of nuclear markers. In this study, we determine phylogeographic patterns in the hedgehog using two loci of the major histocompatibility complex (MHC), isolated for the first time in hedgehogs. These genes show long persistence times and high polymorphism in many species because of the actions of balancing selection. Among 84 individuals screened for variation, only two DQA alleles were identified in each species, but 10 DQB alleles were found in E. concolor and six in E. europaeus. A strong effect of demography on patterns of DQB variability is observed, with only weak evidence of balancing selection. While data from mtDNA clearly subdivide both species into monophyletic subgroups, the MHC data delineate only E. concolor into distinct subgroups, supporting the preliminary findings of other nuclear markers. Together with differences in variability, this suggests that the refugia history and/or expansion patterns of E. concolor and E. europaeus differ.

Genetic population structure and call variation in a passerine bird, the satin bowerbird, Ptilonorhynchus violaceus

Geographic variation in vocalizations is widespread in passerine birds, but its origins and maintenance remain unclear. One hypothesis to explain this variation is that it is associated with geographic isolation among populations and therefore should follow a vicariant pattern similar to that typically found in neutral genetic markers. Alternatively, if environmental selection strongly influences vocalizations, then genetic divergence and vocal divergence may be disassociated. This study compared genetic divergence derived from 11 microsatellite markers with a metric of phenotypic divergence derived from male bower advertisement calls. Data were obtained from 16 populations throughout the entire distribution of the satin bowerbird, an Australian wet-forest-restricted passerine. There was no relationship between call divergence and genetic divergence, similar to most other studies on birds with learned vocalizations. Genetic divergence followed a vicariant model of evolution, with the differentiation of isolated populations and isolation-by-distance among continuous populations. Previous work on Ptilonorhynchus violaceus has shown that advertisement call structure is strongly influenced by the acoustic environment of different habitats. Divergence in vocalizations among genetically related populations in different habitats indicates that satin bowerbirds match their vocalizations to the environment in which they live, despite the homogenizing influence of gene flow. In combination with convergence of vocalizations among genetically divergent populations occurring in the same habitat, this shows the overriding importance that habitat-related selection can have on the establishment and maintenance of variation in vocalizations.

Population dynamics and gene flow of Helicoverpa armigera (Lepidoptera : Noctuidae) on cotton and grain crops in the Murrumbidgee Valley, Australia

The population dynamics of Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae) in the Murrumbidgee Valley, Australia, has been characterized using five highly variable microsatellite loci. In the 2001-2002 growing season, there were very high levels of migration into the Murrumbidgee Valley with no detectable genetic structuring, consistent with previous analyses on a national scale. By contrast, there was significant genetic structuring over the 2002-2003 growing season, with three distinct genetic types detected. The first type corresponded to the first two generations and was derived from local individuals emerging from diapause and their progeny. The second genetic type corresponded to generation 3 and resulted from substantial immigration into the region. There was another genetic shift in generation 4, which accounts for the third genetic type of the season. This genetic shift occurred despite low levels of immigration. During the third generation of the 2002-2003 growing season, different population dynamics was characterized for H. armigera on maize, Zea mays L., and cotton Gossipium hirsutum L. Populations on cotton tended to cycle independently with very little immigration from outside the region or from maize within the region. Maize acted as a major sink for immigrants from cotton and from outside the region. If resistance were to develop on cotton under these circumstances, susceptible individuals from maize or from other regions would not dilute this resistance. In addition, resistance is likely to be transferred to maize and be perpetuated until diapause, from where it may reemerge next season. If low levels of immigration were to occur on transgenic cotton, this may undermine the effectiveness of refugia, especially noncotton refugia.

Spatial and temporal variation in algal-assemblage structure in isolated dryland river waterholes, Cooper Creek and Warrego River, Australia

The scale at which algal biodiversity is partitioned across the landscape, and the biophysical processes and biotic interactions which shape these communities in dryland river refugia was studied on two occasions from 30 sites in two Australian dryland rivers. Despite the waterholes studied having characteristically high levels of abiogenic turbidity, a total of 186 planktonic microalgae, 253 benthic diatom and 62 macroalgal species were recorded. The phytoplankton communities were dominated by flagellated cryptophytes, euglenophytes and chlorophytes, the diatom communities by cosmopolitan taxa known to tolerate wide environmental conditions, and the macroalgal communities by filamentous cyanobacteria. All algal communities showed significant differences between catchments and sampling times, with a suite of between 5 and 12 taxa responsible for similar to 50% of the observed change. In general, algal assemblage patterns were poorly correlated with the measured environmental variables. Phytoplankton and diatom assemblage patterns were weakly correlated with several waterhole geomorphic measures, whereas macroalgal assemblage patterns showed some association with variability in ionic concentration.

Urban ecosystems – tapping the human resource

In order to take an interest in environmental issues, people need an idea of what ‘the environment’ is, and to have access to something worth caring about. In the UK, around 90% of us already live in towns or cities, and by 2030, around 60% of the world’s population will live in urban areas. But without a vocal set of ‘owners’, public land such as parks and allotments can easily be lost. The majority of the UK's ‘natural’ areas have historically been created, managed or modified by humans. and we should appreciate urban habitats just as much as pristine reserves for the ecosystem services they provide. In particular, scruffy and overlooked brownfield sites can be amazing refugia for insect and plant species which can no longer persist in a countryside dominated by industrialised agriculture.

The interactive effects of predators, resources, and disturbance on freshwater snail populations from the Everglades

The origins of population dynamics depend on interplay between abiotic and biotic factors; the relative importance of each changing across space and time. Predation is a central feature of ecological communities that removes individuals (consumption) and alters prey traits (non-consumptive). Resource quality mitigates non-consumptive predator effects by stimulating growth and reproduction. Disturbance resets predator-prey interactions by removing both. I integrate experiments, time-series analysis, and performance trials to examine the relative importance of these on the population dynamics of a snail species by studying a variety of their traits. A review of ninety-three published articles revealed that snail abundance was much less in the Everglades and similar ecosystems compared to all other freshwater ecosystems considered. Separating consumptive from non-consumptive (cues) predator effects at different phosphorous levels with an experiment determined that phosphorous stimulated, but predator cues inhibited snail growth (34% vs. 23%), activity (38% vs. 53%), and reproductive effort (99% vs. 90%) compared to controls. Cues induced taller shells and smaller openings and moved to refugia where they reduced periphyton by 8%. Consumptive predator effects were minor in comparison. In a reciprocal transplant cage experiment along a predator cue and phosphorous gradient created by a canal, snails grew 10% faster and produced 37% more eggs far from the canal (fewer cues) when fed phosphorous-enriched periphyton from near the canal. Time-series analysis at four sites and predator performance trials reveal that phosphorous-enriched regions support larger snail populations, seasonal drying removes snails at all sites, crayfish negatively affect populations in enriched regions, and molluscivorous fish consume snails in the wet season. Combining these studies reveals interplay between resources, predators, and seasonality that limit snail populations in the Everglades and lead to their low abundance compared to other freshwater ecosystems. Resource quality is emerging as the critical factor because improving resources profoundly improved growth and reproduction; seasonal drying and predation become important at times and places. This work contributes to the general understanding in ecology of the relative importance of different factors that structure populations and provides evidence that bolsters monitoring efforts to assess the Comprehensive Everglades Restoration Plan that show phosphorous enrichment is a major driver of ecosystem change.

Fish population dynamics in a seasonally varying wetland

Small fishes in seasonally flooded environments such as the Everglades are capable of spreading into newly flooded areas and building up substantial biomass. Passive drift cannot account for the rapidity of observed population expansions. To test the ‘reaction–diffusion’ mechanism for spread of the fish, we estimated their diffusion coefficient and applied a reaction–diffusion model. This mechanism was also too weak to account for the spatial dynamics. Two other hypotheses were tested through modeling. The first—the ‘refuge mechanism’—hypothesizes that small remnant populations of small fishes survive the dry season in small permanent bodies of water (refugia), sites where the water level is otherwise below the surface. The second mechanism, which we call the ‘dynamic ideal free distribution mechanism’ is that consumption by the fish creates a prey density gradient and that fish taxis along this gradient can lead to rapid population expansion in space. We examined the two alternatives and concluded that although refugia may play an important role in recolonization by the fish population during reflooding, only the second, taxis in the direction of the flooding front, seems capable of matching empirical observations. This study has important implications for management of wetlands, as fish biomass is an essential support of higher trophic levels.

Disturbance and the rising tide: the challenge of biodiversity management on low-island ecosystems

Sea-level rise presents an imminent threat to freshwater-dependent ecosystems on small oceanic islands, which often harbor rare and endemic taxa. Conservation of these assemblages is complicated by feedbacks between sea level and recurring pulse disturbances (eg hurricanes, fire). Once sea level reaches a critical level, the transition from a landscape characterized by mesophytic upland forests and freshwater wetlands to one dominated by mangroves can occur suddenly, following a single storm-surge event. We document such a trajectory, unfolding today in the Florida Keys. With sea level projected to rise substantially during the next century, ex-situ actions may be needed to conserve individual species of special concern. However, within existing public conservation units, managers have a responsibility to conserve extant biodiversity. We propose a strategy that combines the identification and intensive management of the most defensible core sites within a broader reserve system, in which refugia for biota facing local extirpation may be sought.

Assessing the net effect of anthropogenic disturbance on aquatic communities in wetlands: community structure relative to distance from canals

Anthropogenic alterations of natural hydrology are common in wetlands and often increase water permanence, converting ephemeral habitats into permanent ones. Since aquatic organisms segregate strongly along hydroperiod gradients, added water permanence caused by canals can dramatically change the structure of aquatic communities. We examined the impact of canals on the abundance and structure of wetland communities in South Florida, USA. We sampled fishes and macroinvertebrates from marsh transects originating at canals in the central and southern Everglades. Density of all aquatic organisms sampled increased in the immediate proximity of canals, but was accompanied by few compositional changes based on analysis of relative abundance. Large fish (>8 cm), small fish (<8 >cm) and macroinvertebrates (>5 mm) increased in density within 5 m of canals. This pattern was most pronounced in the dry season, suggesting that canals may serve as dry-down refugia. Increases in aquatic animal density closely matched gradients of phosphorus enrichment that decreased with distance from canals. Thus, the most apparent impact of canals on adjacent marsh communities was as conduits for nutrients that stimulated local productivity; any impact of their role as sources of increased sources of predators was not apparent. The effect of predation close to canals was overcompensated by increased secondary productivity and/or immigration toward areas adjacent to canals in the dry season. Alternatively, the consumptive effect of predatory fishes using canals as dry-season refuges is very small or spread over the expanse of marshes with open access to canals.

Seasonal fish community variation in headwater mangrove creeks in the southwestern Everglades: an examination of their role as dry-down refuges

The connectivity between the fish community of estuarine mangroves and that of freshwater habitats upstream remains poorly understood. In the Florida Everglades, mangrove-lined creeks link freshwater marshes to estuarine habitats downstream and may act as dry-season refuges for freshwater fishes. We examined seasonal dynamics in the fish community of ecotonal creeks in the southwestern region of Everglades National Park, specifically Rookery Branch and the North and watson rivers. Twelve low-order creeks were sampled via electrofishing, gill nets, and minnow traps during the wet season, transition period, and dry season in 2004-2005. Catches were greater in Rookery Branch than in the North and watson rivers, particularly during the transition period. Community composition varied seasonally in Rookery Branch, and to a greater extent for the larger species, reflecting a pulse of freshwater taxa into creeks as marshes upstream dried periodically. The pulse was short-lived, a later sample showed substantial decreases in freshwater fish numbers. No evidence of a similar influx was seen in the North and watson rivers, which drain shorter hydroperiod marshes and exhibit higher salinities. These results suggest that head-water creeks can serve as important dry-season refugia. Increased freshwater flow resulting from Everglades restoration may enhance this connectivity.

Disturbance regime and limits on benefits of refuge use for fishes in a fluctuating hydroscape

Refuge habitats increase survival rate and recovery time of populations experiencing environmental disturbance, but limits on the ability of refuges to buffer communities are poorly understood. We hypothesized that importance of refuges in preventing population declines and alteration in community structure has a non-linear relationship with severity of disturbance. In the Florida Everglades, alligator ponds are used as refuge habitat by fishes during seasonal drying of marsh habitats. Using an 11-year record of hydrological conditions and fish abundance in 10 marshes and 34 alligator ponds from two regions of the Everglades, we sought to characterize patterns of refuge use and temporal dynamics of fish abundance and community structure across changing intensity, duration, and frequency of drought disturbance. Abundance in alligator ponds was positively related to refuge size, distance from alternative refugia (e.g. canals), and abundance in surrounding marsh prior to hydrologic disturbance. Variables negatively related to abundance in alligator ponds included water level in surrounding marsh and abundance of disturbance-tolerant species. Refuge community structure did not differ between regions because the same subset of species in both regions used alligator ponds during droughts. When time between disturbances was short, fish abundance declined in marshes, and in the region with the most spatially extensive pattern of disturbance, community structure was altered in both marshes and alligator ponds because of an increased proportion of species more resistant to disturbance. These changes in community structure were associated with increases in both duration and frequency of hydrologic disturbance. Use of refuge habitat had a modal relationship with severity of disturbance regime. Spatial patterns of response suggest that decline in refuge use was because of decreased effectiveness of refuge habitat in reducing mortality and providing sufficient time for recovery for fish communities experiencing reduced time between disturbance events.

Multi-Tissue Stable Isotope Analysis and Acoustic Telemetry Reveal Seasonal Variability in the Trophic Interactions of Juvenile Bull Sharks in a Coastal Estuary

Understanding how natural and anthropogenic drivers affect extant food webs is critical to predicting the impacts of climate change and habitat alterations on ecosystem dynamics. In the Florida Everglades, seasonal reductions in freshwater flow and precipitation lead to annual migrations of aquatic taxa from marsh habitats to deep-water refugia in estuaries. The timing and intensity of freshwater reductions, however, will be modified by ongoing ecosystem restoration and predicted climate change. Understanding the importance of seasonally pulsed resources to predators is critical to predicting the impacts of management and climate change on their populations. As with many large predators, however, it is difficult to determine to what extent predators like bull sharks (Carcharhinus leucas) in the coastal Everglades make use of prey pulses currently. We used passive acoustic telemetry to determine whether shark movements responded to the pulse of marsh prey. To investigate the possibility that sharks fed on marsh prey, we modelled the predicted dynamics of stable isotope values in bull shark blood and plasma under different assumptions of temporal variability in shark diets and physiological dynamics of tissue turnover and isotopic discrimination. Bull sharks increased their use of upstream channels during the late dry season, and although our previous work shows long-term specialization in the diets of sharks, stable isotope values suggested that some individuals adjusted their diets to take advantage of prey entering the system from the marsh, and as such this may be an important resource for the nursery. Restoration efforts are predicted to increase hydroperiods and marsh water levels, likely shifting the timing, duration and intensity of prey pulses, which could have negative consequences for the bull shark population and/or induce shifts in behaviour. Understanding the factors influencing the propensity to specialize or adopt more flexible trophic interactions will be an important step in fully understanding the ecological role of predators and how ecological roles may vary with environmental and anthropogenic changes.

Mapping and Assessing Fire Damage on Broadleaved Forest Communities in Big Cypress National Preserve

Within Big Cypress National Preserve (BICY), oak-dominated forests and woodlands as well as tropical and temperate hardwood hammocks are integral components of the landscape and are biodiversity hotpots for both flora and fauna. These broadleaved forest communities serve as refugia for many of the Preserve’s wildlife species during prolonged flooding and fires. However, both prolonged flooding and severe fires, which are important and necessary disturbance vectors within this landscape, can have deleterious effects on these forested communities. This is particularly true in the case of fires, which under extreme conditions associated with drought and elevated fuel loads, can burn through these forested communities consuming litter and understory vegetation and top killing most, if not all, of the trees present.