The effects of habitat fragmentation on the demography and population genetic structure of Uromys Caudimaculatus

Habitat fragmentation can have an impact on a wide variety of biological processes including abundance, life history strategies, mating system, inbreeding and genetic diversity levels of individual species. Although fragmented populations have received much attention, ecological and genetic responses of species to fragmentation have still not been fully resolved. The current study investigated the ecological factors that may influence the demographic and genetic structure of the giant white-tailed rat (Uromys caudimaculatus) within fragmented tropical rainforests. It is the first study to examine relationships between food resources, vegetation attributes and Uromys demography in a quantitative manner. Giant white-tailed rat densities were strongly correlated with specific suites of food resources rather than forest structure or other factors linked to fragmentation (i.e. fragment size). Several demographic parameters including the density of resident adults and juvenile recruitment showed similar patterns. Although data were limited, high quality food resources appear to initiate breeding in female Uromys. Where data were sufficient, influx of juveniles was significantly related to the density of high quality food resources that had fallen in the previous three months. Thus, availability of high quality food resources appear to be more important than either vegetation structure or fragment size in influencing giant white-tailed rat demography. These results support the suggestion that a species’ response to fragmentation can be related to their specific habitat requirements and can vary in response to local ecological conditions. In contrast to demographic data, genetic data revealed a significant negative effect of habitat fragmentation on genetic diversity and effective population size in U. caudimaculatus. All three fragments showed lower levels of allelic richness, number of private alleles and expected heterozygosity compared with the unfragmented continuous rainforest site. Populations at all sites were significantly differentiated, suggesting restricted among population gene flow. The combined effects of reduced genetic diversity, lower effective population size and restricted gene flow suggest that long-term viability of small fragmented populations may be at risk, unless effective management is employed in the future. A diverse range of genetic reproductive behaviours and sex-biased dispersal patterns were evident within U. caudimaculatus populations. Genetic paternity analyses revealed that the major mating system in U. caudimaculatus appeared to be polygyny at sites P1, P3 and C1. Evidence of genetic monogamy, however, was also found in the three fragmented sites, and was the dominant mating system in the remaining low density, small fragment (P2). High variability in reproductive skew and reproductive success was also found but was less pronounced when only resident Uromys were considered. Male body condition predicted which males sired offspring, however, neither body condition nor heterozygosity levels were accurate predictors of the number of offspring assigned to individual males or females. Genetic spatial autocorrelation analyses provided evidence for increased philopatry among females at site P1, but increased philopatry among males at site P3. This suggests that male-biased dispersal occurs at site P1 and female-biased dispersal at site P3, implying that in addition to mating systems, Uromys may also be able to adjust their dispersal behaviour to suit local ecological conditions. This study highlights the importance of examining the mechanisms that underlie population-level responses to habitat fragmentation using a combined ecological and genetic approach. The ecological data suggested that habitat quality (i.e. high quality food resources) rather than habitat quantity (i.e. fragment size) was relatively more important in influencing giant white-tailed rat demographics, at least for the populations studied here . Conversely, genetic data showed strong evidence that Uromys populations were affected adversely by habitat fragmentation and that management of isolated populations may be required for long-term viability of populations within isolated rainforest fragments.

Communities of gastrointestinal helminths of fish in historically connected habitats: habitat fragmentation effect in a carnivorous catfish Pelteobagrus fulvidraco from seven lakes in flood plain of the Yangtze River, China

Background: Habitat fragmentation may result in the reduction of diversity of parasite communities by affecting population size and dispersal pattern of species. In the flood plain of the Yangtze River in China, many lakes, which were once connected with the river, have become isolated since the 1950s from the river by the construction of dams and sluices, with many larger lakes subdivided into smaller ones by road embankments. These artificial barriers have inevitably obstructed the migration of fish between the river and lakes and also among lakes. In this study, the gastrointestinal helminth communities were investigated in a carnivorous fish, the yellowhead catfish Pelteobagrus fulvidraco, from two connected and five isolated lakes in the flood plain in order to detect the effect of lake fragmentation on the parasite communities. Results: A total of 11 species of helminths were recorded in the stomach and intestine of P. fulvidraco from seven lakes, including two lakes connected with the Yangtze River, i.e. Poyang and Dongting lakes, and five isolated lakes, i.e. Honghu, Liangzi, Tangxun, Niushan and Baoan lakes. Mean helminth individuals and diversity of helminth communities in Honghu and Dongting lakes was lower than in the other five lakes. The nematode Procamallanus fulvidraconis was the dominant species of communities in all the seven lakes. No significant difference in the Shannon-Wiener index was detected between connected lakes (0.48) and isolated lakes (0.50). The similarity of helminth communities between Niushan and Baoan lakes was the highest (0.6708), and the lowest was between Tangxun and Dongting lakes (0.1807). The similarity was low between Dongting and the other lakes, and the similarity decreased with the geographic distance among these lakes. The helminth community in one connected lake, Poyang Lake was clustered with isolated lakes, but the community in Dongting Lake was separated in the tree. Conclusion: The similarity in the helminth communities of this fish in the flood-plain lakes may be attributed to the historical connection of these habitats and to the completion of the life-cycles of this fish as well as the helminth species within the investigated habitats. The diversity and the digenean majority in the helminth communities can be related to the diet of this fish, and to the lacustrine and macrophytic characters of the habitats. The lake isolation from the river had little detectable effect on the helminth communities of the catfish in flood-plain lakes of the Yangtze River. The low similarities in helminth communities between the Dongting Lake and others may just be a reflection of its unique water environment and anthropogenic alterations or fragmentation in this lake.

Genetic variation of fish parasite populations in historically connected habitats: undetected habitat fragmentation effect on populations of the nematode Procamallanus fulvidraconis in the catfish Pelteobagrus fulvidraco

Habitat fragmentation may have some significant effects on population genetic structure because geographic distance and physical barriers may impede gene flow between populations. In this study, we investigated whether recent habitat fragmentation affected genetic structure and diversity of populations of the nematode Procamallanus fulvidraconis in the yellowhead catfish, Pelteobagrus fin't4draco. The nematode was collected from 12 localities in 7 floodplain lakes of the Yangtze River. Using I I intersirnple sequence repeat markers, analysis of molecular variance showed that genetic diversity occurred mainly within populations (70.26%). Expected heterozygosity (He) of P. fulvidraconis was barely different between connected (0.2105) and unconnected lakes (0.2083). Population subdivision (Fst) between connected lakes (0.2177) was higher than in unconnected lakes (0. 1676). However, the connected and unconnected lakes did not Cluster into 2 clades. A Mantel test revealed significant positive correlation between genetic and geographic distances (R = 0.5335, P < 0.01). These results suggest that habitat fragmentation did not cause genetic differentiation among populations or a reduction of diversity in isolated populations of P. fulvidraconis. At least 2 factors may increase the dispersal range of the nematode, i.e., flash flooding in summer and other species of fish that may serve as the definitive hosts. Moreover, lake fragmentation is probably a recent process; population size of the nematode in these lakes is large enough to maintain Population structure.

Modeling the Effects of Habitat Fragmentation on the Movements of the Mongolian Gazelle in the Eastern Mongolian Steppe

The Mongolian gazelle, Procapra gutturosa, resides in the immense and dynamic ecosystem of the Eastern Mongolian Steppe. The Mongolian Steppe ecosystem dynamics, including vegetation availability, change rapidly and dramatically due to unpredictable precipitation patterns. The Mongolian gazelle has adapted to this unpredictable vegetation availability by making long range nomadic movements. However, predicting these movements is challenging and requires a complex model. An accurate model of gazelle movements is needed, as rampant habitat fragmentation due to human development projects - which inhibit gazelles from obtaining essential resources - increasingly threaten this nomadic species. We created a novel model using an Individual-based Neural Network Genetic Algorithm (ING) to predict how habitat fragmentation affects animal movement, using the Mongolian Steppe as a model ecosystem. We used Global Positioning System (GPS) collar data from real gazelles to “train” our model to emulate characteristic patterns of Mongolian gazelle movement behavior. These patterns are: preferred vegetation resources (NDVI), displacement over certain time lags, and proximity to human areas. With this trained model, we then explored how potential scenarios of habitat fragmentation may affect gazelle movement. This model can be used to predict how fragmentation of the Mongolian Steppe may affect the Mongolian gazelle. In addition, this model is novel in that it can be applied to other ecological scenarios, since we designed it in modules that are easily interchanged.

Effect of habitat fragmentation on the macroinvertebrate infaunal communities associated with the seagrass Zostera marina

1. The effect of habitat fragmentation was investigated in two adjacent, yet separate, intertidal Zostera marina beds in the Salcombe Estuary, Devon, UK. The seagrass bed on the west bank comprised a continuous meadow of ca. 2.3 ha, whilst the bed on the east bank of the estuary was fragmented into patches of 6–9 m2.2. Three 10 cm diameter core samples for infaunal macroinvertebrates were taken from three stations within each bed. No significant difference was found in univariate community parameters between beds, or in measured seagrass parameters. However, multivariate analysis revealed a significant difference in community composition, due mainly to small changes in species abundance rather than differences in the species present.3. The species contributing most to the dissimilarity between the two communities were polychaetes generally associated with unvegetated habitats (e.g. Magelona mirabilis) and found to be more common in the fragmented bed.4. A significant difference in median grain size and sorting coefficient was recorded between the two beds, and median grain size was found to be the variable best explaining multivariate community patterns.5. The results of the study provide evidence for the effects of habitat fragmentation on the communities associated with seagrass beds, habitats which are of high conservation importance. As the infaunal community is perhaps intuitively the component least likely to be affected by fragmentation at the scale observed, the significant difference in community composition recorded has consequences for more sensitive and high-profile parts of the biota (e.g. fish), and thus for the conservation of seagrass habitats and their associated communities.

Effect of habitat fragmentation on levels and patterns of genetic diversity in natural populations of the peat moss Polytrichum commune

Peat bogs represent unique ecosystems that are under particular threat from fragmentation due to peat harvesting, with only 38% of the original peatland in Europe remaining intact and unaffected by peat cutting, drainage and silviculture. In this study, we have used microsatellite markers to determine levels and patterns of genetic diversity in both cut and uncut natural populations of the peat moss Polytrichum commune. Overall diversity levels suggest that there is more genetic variation present than had previously been assumed for bryophytes. Despite this, diversity values from completely cut bogs were found to be lower than those from uncut peatlands (average 0.729 versus 0.880). In addition, the genetic diversity was more highly structured in the cut populations, further suggesting that genetic drift is already affecting genetic diversity in peat bogs subjected to fragmentation.

Gastrointestinal symbionts of chimpanzees in Cantanhez National Park, Guinea-Bissau with respect to habitat fragmentation

One of the major factors threatening chimpanzees (Pan troglodytes verus) in Guinea-Bissau is habitat fragmentation. Such fragmentation may cause changes in symbiont dynamics resulting in increased susceptibility to infection, changes in host specificity and virulence. We monitored gastrointestinal symbiotic fauna of three chimpanzee subpopulations living within Cantanhez National Park (CNP) in Guinea Bissau in the areas with different levels of anthropogenic fragmentation. Using standard coproscopical methods (merthiolate-iodine formalin concentration and Sheather's flotation) we examined 102 fecal samples and identified at least 13 different symbiotic genera (Troglodytella abrassarti, Troglocorys cava, Blastocystis spp., Entamoeba spp., Iodamoeba butschlii, Giardia intestinalis, Chilomastix mesnili, Bertiella sp., Probstmayria gombensis, unidentified strongylids, Strongyloides stercoralis, Strongyloides fuelleborni, and Trichuris sp.). The symbiotic fauna of the CNP chimpanzees is comparable to that reported for other wild chimpanzee populations, although CNP chimpanzees have a higher prevalence of Trichuris sp. Symbiont richness was higher in chimpanzee subpopulations living in fragmented forests compared to the community inhabiting continuous forest area. We reported significantly higher prevalence of G. intestinalis in chimpanzees from fragmented areas, which could be attributed to increased contact with humans and livestock.

Interacting effects of climate change and habitat fragmentation on drought-sensitive butterflies

Climate change is expected to increase the frequency of some climatic extremes. These may have drastic impacts on biodiversity, particularly if meteorological thresholds are crossed, leading to population collapses. Should this occur repeatedly, populations may be unable to recover, resulting in local extinctions. Comprehensive time series data on butterflies in Great Britain provide a rare opportunity to quantify population responses to both past severe drought and the interaction with habitat area and fragmentation. Here, we combine this knowledge with future projections from multiple climate models, for different Representative Concentration Pathways (RCPs), and for simultaneous modelled responses to different landscape characteristics. Under RCP8.5, which is associated with ‘business as usual’ emissions, widespread drought-sensitive butterfly population extinctions could occur as early as 2050. However, by managing landscapes and particularly reducing habitat fragmentation, the probability of persistence until mid-century improves from around zero to between 6 and 42% (95% confidence interval). Achieving persistence with a greater than 50% chance and right through to 2100 is possible only under both low climate change (RCP2.6) and semi-natural habitat restoration. Our data show that, for these drought-sensitive butterflies, persistence is achieved more effectively by restoring semi-natural landscapes to reduce fragmentation, rather than simply focusing on increasing habitat area, but this will only be successful in combination with substantial emission reductions.

Habitat fragmentation reduces genetic diversity and connectivity among toad populations in the Brazilian Atlantic Coastal Forest

Tropical rainforests are becoming increasingly fragmented and understanding the genetic consequences of fragmentation is crucial for conservation of their flora and fauna. We examined populations of the toad Rhinella ornata, a species endemic to Atlantic Coastal Forest in Brazil, and compared genetic diversity among small and medium forest fragments that were either isolated or connected to large forest areas by corridors. Genetic differentiation, as measured by F(ST), was not related to geographic distance among study sites and the size of the fragments did not significantly alter patterns of genetic connectivity. However, population genetic diversity was positively related to fragment size, thus haplotype diversity was lowest in the smallest fragments, likely due to decreases in population sizes. Spatial analyses of genetic discontinuities among groups of populations showed a higher proportion of barriers to gene flow among small and medium fragments than between populations in continuous forest. Our results underscore that even species with relatively high dispersal capacities may, over time, suffer the negative genetic effects of fragmentation, possibly leading to reduced fitness of population and cases of localized extinction. (C) 2008 Elsevier Ltd. All rights reserved.

Habitat fragmentation disrupts the demography of a widespread native mammal

Fragmentation theory predicts that population persistence should be positively correlated with the size of habitat fragments. The patterns of occurrence of many species are consistent with this prediction, but the demographic processes that determine how species respond to fragmentation are poorly understood. In addition, habitat quality may interact with fragment size as an influence on demographic performance. We investigated these predictions for the native bush rat Rattus fuscipes by testing the following hypotheses: 1) population performance (i.e. viability as determined by various demographic parameters) is positively correlated with fragment size; and 2) population performance is positively correlated with habitat quality. Populations of R. fuscipes were censused in two large (>49 ha) and eight small (<2.5 ha) forest fragments in an agricultural region of southeastern Australia. Fragments with high and low quality habitat were included in each size category. Fragment size influenced multiple aspects of population demography; populations in large fragments had higher densities, older age structures, received more potential immigrants, and were more likely to recruit adults than those in small fragments. Reproductive patterns were more predictable in large fragments. Habitat quality per se had less marked effects; adult females were heavier and subadults more prevalent in fragments with high quality habitat. However, high quality habitat enhanced population performance in small fragments more so than in large ones. Despite being widespread in the study area, R. fuscipes populations are profoundly impacted by habitat fragmentation, with population performance declining with fragment size. Studies based on patterns of species occurrence should be interpreted with caution as they may mask critical processes occurring at the population level. For a thorough understanding of the effects of habitat fragmentation, population-level studies are required.

Habitat fragmentation and landscape change

This chapter begins by summarizing the conceptual approaches used to understand conservation in fragmented landscapes. We then examine the biophysical aspects of landscape change, and how such change affects species and communities, posing two main questions: (i) what are the implications for the patterns of occurrence of species and communities?; and (ii) how does landscape change affect processes that influence the distribution and viability of species and communities. The chapter concludes by identifying the kinds of actions that will enhance the conservation of biota in fragmented landscapes.

Integrating edge effects into studies of habitat fragmentation: a test using meiofauna in seagrass

Habitat fragmentation is thought to be an important process structuring landscapes in marine and estuarine environments, but effects on fauna are poorly understood, in part because of a focus on patchiness rather than fragmentation. Furthermore, despite concomitant increases in perimeter:area ratios with fragmentation, we have little understanding of how fauna change from patch edges to interiors during fragmentation. Densities of meiofauna were measured at different distances across the edges of four artificial seagrass treatments [continuous, fragmented, procedural control (to control for disturbance by fragmenting then restoring experimental plots), and patchy] 1 day, 1 week and 1 month after fragmentation. Experimental plots were established 1 week prior to fragmentation/disturbance. Samples were numerically dominated by harpacticoid copepods, densities of which were greater at the edge than 0.5 m into patches for continuous, procedural control and patchy treatments; densities were similar between the edge and 0.5 m in fragmented patches. For taxa that demonstrated edge effects, densities exhibited log-linear declines to 0.5 m into a patch with no differences observed between 0.5 m and 1 m into continuous treatments. In patchy treatments densities were similar at the internal and external edges for many taxa. The strong positive edge effect (higher densities at edge than interior) for taxa such as harpacticoid copepods implies some benefit of patchy landscapes. But the lack of edge effects during patch fragmentation itself demonstrates the importance of the mechanisms by which habitats become patchy.