Habitat specialization predicts genetic response to fragmentation in tropical birds

Habitat fragmentation is one of the most severe threats to biodiversity as it may lead to changes in population genetic structure, with ultimate modifications of species evolutionary potential and local extinctions. Nonetheless, fragmentation does not equally affect all species and identifying which ecological traits are related to species sensitivity to habitat fragmentation could help prioritization of conservation efforts. Despite the theoretical link between species ecology and extinction proneness, comparative studies explicitly testing the hypothesis that particular ecological traits underlies species‐specific population structure are rare. Here, we used a comparative approach on eight bird species, co‐occurring across the same fragmented landscape. For each species, we quantified relative levels of forest specialization and genetic differentiation among populations. To test the link between forest specialization and susceptibility to forest fragmentation, we assessed species responses to fragmentation by comparing levels of genetic differentiation between continuous and fragmented forest landscapes. Our results revealed a significant and substantial population structure at a very small spatial scale for mobile organisms such as birds. More importantly, we found that specialist species are more affected by forest fragmentation than generalist ones. Finally, our results suggest that even a simple habitat specialization index can be a satisfying predictor of genetic and demographic consequences of habitat fragmentation, providing a reliable practical and quantitative tool for conservation biology.     

Genetic and ecological consequences of recent habitat fragmentation in a narrow endemic plant species within an urban context

Understanding the timescales that shape spatial genetic structure is pivotal to ascertain the impact of habitat fragmentation on the genetic diversity and reproductive viability of long-lived plant populations. Combining genetic and ecological information with current and past fragmentation conditions allows the identification of the main drivers important in shaping population structure and declines in reproduction, which is crucial for informing conservation strategies. Using historic aerial photographs, we defined the past fragmentation conditions for the shrub Conospermum undulatum, a species now completely embedded in an urban area. We explored the impact of current and past conditions on its genetic layout and assessed the effects of genetic and environmental factors on its reproduction. The historically high structural connectivity was evident in the genetics of the species. Despite the current intense fragmentation, we found similar levels of genetic diversity across populations and a weak spatial genetic structure. Historical connectivity was negatively associated with genetic differentiation among populations and positively related to within-population genetic diversity. Variation partitioning of reproductive performance explained?~?66% of the variance, showing significant influences for genetic (9%), environmental (15%), and combined (42%) fractions. Our study highlights the importance of considering the historical habitat dynamics when investigating fragmentation consequences in long-lived plants. A detailed characterization of fragmentation from 1953 has shown how low levels of genetic fixation are due to extensive gene flow through the non-fragmented landscape. Moreover, knowledge of the relationships between genetic and environmental variation and reproduction can help to implement effective conservation strategies, particularly in highly dynamic landscapes.

     

Land‐use history and fragmentation of traditionally managed grasslands in Scandinavia

Abstract. Plants associated with traditional agricultural landscapes in northern Europe and Scandinavia are subjected to drastic habitat fragmentation. In this paper we discuss species response to fragmentation, against a background of vegetation and land‐use history. Recent evidence suggests that grassland‐forest mosaics have been prevalent long before the onset of human agriculture. We suggest that the creation of infield meadows and outland grazing (during the Iron Age) increased the amount and spatial predictability of grasslands, resulting in plant communities with exceptionally high species densities. Thus, distribution of plant species in the present‐day landscape reflects historical land‐use. This holds also when traditional management has ceased, due to a slow response by many species to abandonment and fragmentation. The distribution patterns are thus not in equilibrium with the present habitat distribution. Fragmentation influences remaining semi‐natural grasslands such that species density is likely to decline as a result of local extinctions and invasion by habitat generalists. However, species that for a long time have been subjected to changing mosaic landscapes may be more resistant to fragmentation than is usually believed. Conservation should focus not only on ‘hot‐spots’ with high species richness, but also consider species dynamics in a landscape context.     

Time-Lag in Responses of Birds to Atlantic Forest Fragmentation: Restoration Opportunity and Urgency

There are few opportunities to evaluate the relative importance of landscape structure and dynamics upon biodiversity, especially in highly fragmented tropical landscapes. Conservation strategies and species risk evaluations often rely exclusively on current aspects of landscape structure, although such limited assumptions are known to be misleading when time-lag responses occur. By relating bird functional-group richness to forest patch size and isolation in ten-year intervals (1956, 1965, 1978, 1984, 1993 and 2003), we revealed that birds with different sensitivity to fragmentation display contrasting responses to landscape dynamics in the Brazilian Atlantic Forest. For non-sensitive groups, there was no time-lag in response: the recent degree of isolation best explains their variation in richness, which likely relates to these species’ flexibility to adapt to changes in landscape structure. However, for sensitive bird groups, the 1978 patch area was the best explanatory variable, providing evidence for a 25-year time-lag in response to habitat reduction. Time-lag was more likely in landscapes that encompass large patches, which can support temporarily the presence of some sensitive species, even when habitat cover is relatively low. These landscapes potentially support the most threatened populations and should be priorities for restoration efforts to avoid further species loss. Although time-lags provide an opportunity to counteract the negative consequences of fragmentation, it also reinforces the urgency of restoration actions. Fragmented landscapes will be depleted of biodiversity if landscape structure is only maintained, and not improved. The urgency of restoration action may be even higher in landscapes where habitat loss and fragmentation history is older and where no large fragment remained to act temporarily as a refuge.     

Impact of urban fragmentation on the genetic structure of the eastern red-backed salamander

Urban development is a major cause of habitat loss and fragmentation. Few studies, however, have dealt with fragmentation in an urban landscape. In this paper, we examine the genetic structure of isolated populations of the eastern red-backed salamander (Plethodon cinereus) in a metropolitan area. We sampled four populations located on a mountain in the heart of Montréal (Québec, Canada), which presents a mosaic of forested patches isolated by roads, graveyards and buildings. We assessed the genetic structure of these populations using microsatellite loci and compared it to the genetic structure of four populations located in a continuous habitat in southern Québec. Our results indicate that allelic richness and heterozygosity are lower in the urban populations. Exact differentiation tests and pairwise F _ST also show that the populations found in the fragmented habitat are genetically differentiated, whereas populations located in the continuous habitat are genetically homogeneous. These results raise conservation concerns for these populations as well as for rare or threatened species inhabiting urban landscapes.     

Species-genetic diversity correlations in habitat fragmentation can be biased by small sample sizes

Predicted parallel impacts of habitat fragmentation on genes and species lie at the core of conservation biology, yet tests of this rule are rare. In a recent article in Ecology Letters, Struebig et al. (2011) report that declining genetic diversity accompanies declining species diversity in tropical forest fragments. However, this study estimates diversity in many populations through extrapolation from very small sample sizes. Using the data of this recent work, we show that results estimated from the smallest sample sizes drive the species-genetic diversity correlation (SGDC), owing to a false-positive association between habitat fragmentation and loss of genetic diversity. Small sample sizes are a persistent problem in habitat fragmentation studies, the results of which often do not fit simple theoretical models. It is essential, therefore, that data assessing the proposed SGDC are sufficient in order that conclusions be robust.     

Mating patterns and pollinator mobility are critical traits in forest fragmentation genetics

Most woody plants are animal-pollinated, but the global problem of habitat fragmentation is changing the pollination dynamics. Consequently, the genetic diversity and fitness of the progeny of animal-pollinated woody plants sired in fragmented landscapes tend to decline due to shifts in plant-mating patterns (for example, reduced outcrossing rate, pollen diversity). However, the magnitude of this mating-pattern shift should theoretically be a function of pollinator mobility. We first test this hypothesis by exploring the mating patterns of three ecologically divergent eucalypts sampled across a habitat fragmentation gradient in southern Australia. We demonstrate increased selfing and decreased pollen diversity with increased fragmentation for two small-insect-pollinated eucalypts, but no such relationship for the mobile-bird-pollinated eucalypt. In a meta-analysis, we then show that fragmentation generally does increase selfing rates and decrease pollen diversity, and that more mobile pollinators tended to dampen these mating-pattern shifts. Together, our findings support the premise that variation in pollinator form contributes to the diversity of mating-pattern responses to habitat fragmentation.     

Integrating population genetics and conservation biology in the era of genomics

As one of the final activities of the ESF-CONGEN Networking programme, a conference entitled ‘Integrating Population Genetics and Conservation Biology’ was held at Trondheim, Norway, from 23 to 26 May 2009. Conference speakers and poster presenters gave a display of the state-of-the-art developments in the field of conservation genetics. Over the five-year running period of the successful ESF-CONGEN Networking programme, much progress has been made in theoretical approaches, basic research on inbreeding depression and other genetic processes associated with habitat fragmentation and conservation issues, and with applying principles of conservation genetics in the conservation of many species. Future perspectives were also discussed in the conference, and it was concluded that conservation genetics is evolving into conservation genomics, while at the same time basic and applied research on threatened species and populations from a population genetic point of view continues to be emphasized.     

Forest fragmentation genetics in a formerly widespread island endemic tree: Vateriopsis seychellarum (Dipterocarpaceae)

Habitat fragmentation and changed land use have seriously reduced population size in many tropical forest tree species. Formerly widespread species with limited gene flow may be particularly vulnerable to the negative genetic effects of forest fragmentation and small population size. Vateriopsis seychellarum (Dipterocarpaceae) is a formerly widespread canopy tree of the Seychelles, but is now reduced to 132 adult individuals distributed in eleven sites. Using ten microsatellite loci, a genetic inventory of all adult trees and a sample of 317 progeny, we demonstrate that despite its restricted range, overall genetic diversity was relatively high (H(E) : 0.56). The juvenile cohort, however, had significantly lower allelic richness (adults R(S) : 3.91; juveniles R(S) : 2.83) and observed heterozygosity than adult trees (adults H(O) : 0.62; juveniles H(O) : 0.48). Rare alleles were fewer and kinship between individuals was stronger in juveniles. Significant fine-scale spatial genetic structure was observed in remnant adults, and parentage analysis indicated that more than 90% of sampled progeny disperse <25 m and pollen dispersed <50 m. The molecular data confirmed that two populations were derived entirely from self-fertilized offspring from a single surviving mother tree. These populations produce viable offspring. Despite this extreme genetic bottleneck, self-compatibility may provide V. seychellarum with some resistance to the genetic consequences of habitat fragmentation, at least in the short term. We discuss our findings in the context of other rare and threatened dipterocarp species which are vulnerable to miss-management of genetic resources and population fragmentation.     

Genetic footprints of habitat fragmentation in the extant populations of Sinojackia (Styracaceae): implications for conservation

Sinojackia, a member of the family Styracaceae, is an endangered genus endemic to China. The number of populations and population size of Sinojackia have decreased sharply because of habitat fragmentation and destruction. We studied the genetic diversity of extant populations in two different cohorts (adult and seedling) using eight microsatellite markers to investigate the genetic footprints of habitat fragmentation in four recognized Sinojackia spp. and to develop appropriate conservation measures. Data on intrapopulational genetic diversity suggest that Sinojackia populations have maintained relatively high levels of genetic diversity and low levels of genetic differentiation despite severe fragmentation. The high genetic diversity may be explained by the outcrossing mating system and high longevity of Sinojackia spp. The amount of genetic variation is not associated with population size, which was also supported by bottleneck analysis. In the species studied, there was no significant difference in the genetic diversity between the two cohorts analysed. However, inbreeding increased from adult trees to seedling populations, suggesting that the higher proportion of biparental inbreeding in the recent generations of seedlings is the result of restricted current genetic flow caused by habitat fragmentation. Average seed set per population was not significantly correlated with either population size or genetic diversity. Conservation management should aim to monitor inbreeding and outbreeding depression carefully to ensure the in situ and ex situ conservation of Sinojackia spp. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ?? , ??–??.     

The Habitat Amount Hypothesis implies negative effects of habitat fragmentation on species richness

The habitat amount hypothesis (HAH) predicts that species richness in a habitat site increases with the amount of habitat in the ‘local landscape’ defined by an appropriate distance around the site, with no distinct effects of the size of the habitat patch in which the site is located. It has been stated that a consequence of the HAH, if supported, would be that it is unnecessary to consider habitat configuration to predict or manage biodiversity patterns, and that conservation strategies should focus on habitat amount regardless of fragmentation. Here, I assume that the HAH holds and apply the HAH predictions to all habitat sites over entire landscapes that have the same amount of habitat but differ in habitat configuration. By doing so, I show that the HAH actually implies clearly negative effects of habitat fragmentation, and of other spatial configuration changes, on species richness in all or many of the habitat sites in the landscape, and that these habitat configuration effects are distinct from those of habitat amount in the landscape. I further show that, contrary to current interpretations, the HAH is compatible with a steeper slope of the species–area relationship for fragmented than for continuous habitat, and with higher species richness for a single large patch than for several small patches with the same total area (SLOSS). This suggests the need to revise the ways in which the HAH has been interpreted and can be actually tested. The misinterpretation of the HAH has arisen from confounding and overlooking the differences in the spatial scales involved: the individual habitat site at which the HAH gives predictions, the local landscape around an individual site and the landscapes or regions (with multiple habitat sites and different local landscapes) that need to be analysed and managed. The HAH has been erroneously viewed as negating or diminishing the relevance of fragmentation effects, while it actually supports the importance of habitat configuration for biodiversity. I conclude that, even in the cases where the HAH holds, habitat fragmentation and configuration are important for understanding and managing species distributions in the landscape.     

Habitat fragmentation effects on fitness of plant populations – a review

Habitat fragmentation threatens the survival of many species and local populations. Habitat fragmentation has two major consequences: populations become more isolated and are reduced in size. Small compared with large populations have increased extinction risks because of different types stochasticity (e.g. genetic drift) and inbreeding, which can negatively affect the fitness of individuals or populations. Habitat fragmentation may also change the abiotic conditions of the surrounding landscape, which influences biotic interactions. This review gives an introduction to the theory of the effects of habitat fragmentation on mean fitness of plant populations. It intends to help bridge the gap between conservation biologists and conservation practitioners. The paper shortly introduces basic concepts of population biology, demography and genetics and cites relevant and new literature. Special attention is given to more common plant species, which have attracted far less conservation attention than rare species.     

Temporal bird community dynamics are strongly affected by landscape fragmentation in a Central American tropical forest region

Habitat loss and fragmentation are considered the main causes of species extinctions, particularly in tropical ecosystems. The objective of this work was to evaluate the temporal dynamics of tropical bird communities in landscapes with different levels of fragmentation in eastern Guatemala. We evaluated five bird community dynamic parameters for forest specialists and generalists: (1) species extinction, (2) species turnover, (3) number of colonizing species, (4) relative species richness, and (5) a homogeneity index. For each of 24 landscapes, community dynamic parameters were estimated from bird point count data, for the 1998–1999 and 2008–2009 periods, accounting for species’ detection probability. Forest specialists had higher extinction rates and a smaller number of colonizing species in landscapes with higher fragmentation, thus having lower species richness in both time periods. Alternatively, forest generalists elicited a completely different pattern, showing a curvilinear association to forest fragmentation for most parameters. Thus, greater community dynamism for forest generalists was shown in landscapes with intermediate levels of fragmentation. Our study supports general theory regarding the expected negative effects of habitat loss and fragmentation on the temporal dynamics of biotic communities, particularly for forest specialists, providing strong evidence from understudied tropical bird communities.     

Genetic signature of population fragmentation varies with mobility in seven bird species of a fragmented Kenyan cloud forest

Habitat fragmentation can restrict geneflow, reduce neighbourhood effective population size, and increase genetic drift and inbreeding in small, isolated habitat remnants. The extent to which habitat fragmentation leads to population fragmentation, however, differs among landscapes and taxa. Commonly, researchers use information on the current status of a species to predict population effects of habitat fragmentation. Such methods, however, do not convey information on species-specific responses to fragmentation. Here, we compare levels of past population differentiation, estimated from microsatellite genotypes, with contemporary dispersal rates, estimated from multi-strata capture-recapture models, to infer changes in mobility over time in seven sympatric, forest-dependent bird species of a Kenyan cloud forest archipelago. Overall, populations of sedentary species were more strongly differentiated and clustered compared to those of vagile ones, while geographical patterning suggested an important role of landscape structure in shaping genetic variation. However, five of seven species with broadly similar levels of genetic differentiation nevertheless differed substantially in their current dispersal rates. We conclude that post-fragmentation levels of vagility, without reference to past population connectivity, may not be the best predictor of how forest fragmentation affects the life history of forest-dependent species. As effective conservation strategies often hinge on accurate prediction of shifts in ecological and genetic relationships among populations, conservation practices based solely upon current population abundances or movements may, in the long term, prove to be inadequate.     

Distribution of specialist and generalist species along spatial gradients of habitat disturbance and fragmentation

In this paper, we tested whether the spatial distribution of a given species in more or less fragmented and disturbed landscapes depends on the species habitat specialization. We studied 891 spatial replicates from the French Breeding Bird Survey (FBBS) monitored at least two years during 2001–2005, and two independent landscape databases measuring respectively landscape fragmentation and recent landscape disturbance on each FBBS replicate. We used a continuous habitat specialization index for the 105 most common bird species monitored by the FBBS. We further modelled the spatial variation in abundance of each species according to fragmentation and disturbance across FBBS replicates, accounting for habitat differences and spatial trends. We then tested whether more or less specialized species responded to landscape fragmentation and disturbance. We found that the more specialist a species, the more negative its spatial response to landscape fragmentation and disturbance. Although there was a very high variation around these tendencies indicating that there are many other drivers of species distribution, our results suggest that measuring specialization may be helpful in predicting which species are likely to thrive in human degraded landscapes. We also emphasize the need to consider both positive and negative species responses when assessing consequences of habitat change in communities.     

Effects of forest fragmentation on small mammals in an Atlantic Forest landscape

Recent studies on the effects of tropical forest fragmentation indicate that fragmented landscapes are complex and heterogeneous systems influenced by factors other than the size or degree of isolation of forest remnants: of particular importance are the quality of the matrix and the edge-induced habitat changes. In order to investigate the influence of these factors, small mammals were surveyed in 36 sites in the landscape of Una, a region that encompasses some of the last and largest Atlantic Forest remnants in northeastern Brazil. Six sites were distributed on each of six landscape components – the interiors and edges of small remnants, the interiors and edges of large remnants, and the most common forested habitats found in the matrix. The survey comprised 46,656 trap-nights and yielded 1725 individuals of 20 species of rodents and marsupials. Results revealed: an increase in beta-diversity caused by fragmentation; the contrasting effects of the altered forested habitats of the matrix, which harbor both forest and disturbance-adapted species; a greater importance of edge effect than of patch size to the observed changes in small mammal community in remnants; an association among terrestrial forest species and among arboreal forest species in terms of the distribution and abundance in the Una mosaic; and a distinctive vulnerability of these two groups of species to fragmentation. Results emphasize the biological importance and conservation value of both fragmented landscapes and small remnants in the Atlantic Forest, as well as the importance of management techniques to control and attenuate edge effects.     

Conservation biology: predicting birds' responses to forest fragmentation

Understanding species' ecological responses to habitat fragmentation is critical for biodiversity conservation, especially in tropical forests. A detailed recent study has shown that changes in the abundances of bird species following fragmentation may be dramatic and unpredictable.     

Differential threshold effects of habitat fragmentation on gene flow in two widespread species of bush crickets

Effects of habitat fragmentation on genetic diversity vary among species. This may be attributed to the interacting effects of species traits and landscape structure. While widely distributed and abundant species are often considered less susceptible to fragmentation, this may be different if they are small sized and show limited dispersal. Under intensive land use, habitat fragmentation may reach thresholds at which gene flow among populations of small-sized and dispersal-limited species becomes disrupted. Here, we studied the genetic diversity of two abundant and widespread bush crickets along a gradient of habitat fragmentation in an agricultural landscape. We applied traditional (G(ST), θ) and recently developed (G'ST', D) estimators of genetic differentiation on microsatellite data from each of twelve populations of the grassland species Metrioptera roeselii and the forest-edge species Pholidoptera griseoaptera to identify thresholds of habitat fragmentation below which genetic population structure is affected. Whereas the grassland species exhibited a uniform genetic structuring (G(ST) = 0.020-0.033; D = 0.085-0.149) along the whole fragmentation gradient, the forest-edge species' genetic differentiation increased significantly from D < 0.063 (G(ST) < 0.018) to D = 0.166 (G(ST) = 0.074), once the amount of suitable habitat dropped below a threshold of 20% and its proximity decreased substantially at the landscape scale. The influence of fragmentation on genetic differentiation was qualitatively unaffected by the choice of estimators of genetic differentiation but quantitatively underestimated by the traditional estimators. These results indicate that even for widespread species in modern agricultural landscapes fragmentation thresholds exist at which gene flow among suitable habitat patches becomes restricted.     

Response of a small felid of conservation concern to habitat fragmentation

Habitat loss and fragmentation are major drivers of biodiversity loss. A key question, particularly relevant to carnivore conservation, is to which extent species are able to survive in human-modified landscapes. Currently, conservationists are concerned about the impact habitat fragmentation may have on the long-term persistence of the forest-dwelling guiña (Leopardus guigna), given the increasingly modified landscapes in which they live. Here we evaluate the effect habitat cover, fragmentation and anthropogenic pressure have on the occupancy probability for guiñas in privately-owned forest fragments. We collected camera-trap data from 100 temperate rainforest sites in Chile and used single-season occupancy modeling to evaluate the influence of 13 parameters of landscape structure/anthropogenic pressure and four parameters of detection probability on the ocurrence of guiñas. The camera-trap survey data comprised 4168 camera-trap days and 112 independent records of guiñas. Surprisingly, fragmented (defined as having a high perimeter-to-area ratio) and moderately sized habitat patches best predicted site occupancy. Occupancy also increased where habitat patches were closer to continuous forest and nearer to buildings. Our results imply that guiñas can benefit from a high degree of edge type habitats in fragmented landscapes, capable of adapting to habitat fragmentation in the proximity to large continuous forest patches. This suggests that guiñas have a broader niche than previously believed. Additionally, the guiña is tolerant of human infrastructure. Further research is required to identify potential ecological traps, long-term source-sink dynamics, and the habitat loss/fragmentation threshold beyond which guiña populations are no longer viable.