Short-term genetic consequences of habitat loss and fragmentation for the neotropical palm Oenocarpus bataua

Habitat loss and fragmentation may impact animal-mediated dispersal of seed and pollen, and a key question is how the genetic attributes of plant populations respond to these changes. Theory predicts that genetic diversity may be less sensitive to such disruptions in the short term, whereas inbreeding and genetic structure may respond more strongly. However, results from studies to date vary in relation to species, context and the parameter being assessed, triggering calls for more empirical studies, especially from the tropics, where plant–animal dispersal mutualisms are both disproportionately common and at risk. We compared the genetic characteristics of adults and recruits in a long-lived palm Oenocarpus bataua in a recently fragmented landscape (<2 generations) in northwest Ecuador using a suite of 10 polymorphic microsatellite markers. We sampled individuals from six forest fragments and one nearby continuous forest. Our goal was to assess short-term consequences of fragmentation, with a focus on how well empirical data from this system follow theoretical expectations. Mostly congruent with predictions, we found stronger genetic differentiation and fine-scale spatial genetic structure among recruits in fragments compared with recruits in continuous forest, but we did not record differences in genetic diversity or inbreeding, nor did we record any differences between adults in fragments and adults in continuous forest. Our findings suggest that genetic characteristics of populations vary in their sensitivity to change in response to habitat loss and fragmentation, and that fine-scale spatial genetic structure may be a particularly useful indicator of genetic change in recently fragmented landscapes.     

The population genetic consequences of habitat fragmentation for plants

Habitat fragmentation reduces the size and increases the spatial isolation of plant populations. Initial predictions have been that such changes will be accompanied by an erosion of genetic variation and increased interpopulation genetic divergence due to increased random genetic drift, elevated inbreeding and reduced gene flow. Results of recent empirical studies suggest that while genetic variation may decrease with reduced remnant population size, not all fragmentation events lead to genetic losses and different types of genetic variation (e.g. allozyme and quantitative variation) may respond differently. In some circumstances, fragmentation actually appears to increase gene flow among remnant populations, breaking down local genetic structure.     

Low genetic differentiation between populations of an endemic prairie katydid despite habitat loss and fragmentation

Tallgrass prairie habitats within North America have suffered severe fragmentation and habitat loss as land has been converted for agricultural purposes. Habitat loss and fragmentation can affect gene flow and the genetic structure of insect populations. Neoconocephalus bivocatus is a prairie obligate katydid found only in isolated prairie patches. We compared genetic diversity and population differentiation using AFLP markers in N. bivocatus and N. robustus, a grassland generalist that is not isolated to prairie fragments and occupies a more contiguous range. Similar levels of genetic diversity were present within populations of both species. While population genetic structure was found in both species, there was no relationship between assigned genotypes and sampling localities. This genetic structure may instead be evidence of a past barrier to gene flow that has since been removed. Genetic differentiation within both species was low, with no evidence of a correlation with geographic distance, indicating neither species is dispersal limited at these distances. We see no significant reduction in genetic diversity or genetic differentiation within N. bivocatus when compared to N. robustus. We therefore conclude that while N. bivocatus utilizes a fragmented landscape, long-distance dispersal likely maintains gene flow between isolated prairie patches.     

How fire interacts with habitat loss and fragmentation

Biodiversity faces many threats and these can interact to produce outcomes that may not be predicted by considering their effects in isolation. Habitat loss and fragmentation (hereafter ‘fragmentation’) and altered fire regimes are important threats to biodiversity, but their interactions have not been systematically evaluated across the globe. In this comprehensive synthesis, including 162 papers which provided 274 cases, we offer a framework for understanding how fire interacts with fragmentation. Fire and fragmentation interact in three main ways: (i) fire influences fragmentation (59% of 274 cases), where fire either destroys and fragments habitat or creates and connects habitat; (ii) fragmentation influences fire (25% of cases) where, after habitat is reduced in area and fragmented, fire in the landscape is subsequently altered because people suppress or ignite fires, or there is increased edge flammability or increased obstruction to fire spread; and (iii) where the two do not influence each other, but fire interacts with fragmentation to affect responses like species richness, abundance and extinction risk (16% of cases). Where fire and fragmentation do influence each other, feedback loops are possible that can lead to ecosystem conversion (e.g. forest to grassland). This is a well-documented threat in the tropics but with potential also to be important elsewhere. Fire interacts with fragmentation through scale-specific mechanisms: fire creates edges and drives edge effects; fire alters patch quality; and fire alters landscape-scale connectivity. We found only 12 cases in which studies reported the four essential strata for testing a full interaction, which were fragmented and unfragmented landscapes that both span contrasting fire histories, such as recently burnt and long unburnt vegetation. Simulation and empirical studies show that fire and fragmentation can interact synergistically, multiplicatively, antagonistically or additively. These cases highlight a key reason why understanding interactions is so important: when fire and fragmentation act together they can cause local extinctions, even when their separate effects are neutral. Whether fire–fragmentation interactions benefit or disadvantage species is often determined by the species' preferred successional stage. Adding fire to landscapes generally benefits early-successional plant and animal species, whereas it is detrimental to late-successional species. However, when fire interacts with fragmentation, the direction of effect of fire on a species could be reversed from the effect expected by successional preferences. Adding fire to fragmented landscapes can be detrimental for species that would normally co-exist with fire, because species may no longer be able to disperse to their preferred successional stage. Further, animals may be attracted to particular successional stages leading to unexpected responses to fragmentation, such as higher abundance in more isolated unburnt patches. Growing human populations and increasing resource consumption suggest that fragmentation trends will worsen over coming years. Combined with increasing alteration of fire regimes due to climate change and human-caused ignitions, interactions of fire with fragmentation are likely to become more common. Our new framework paves the way for developing a better understanding of how fire interacts with fragmentation, and for conserving biodiversity in the face of these emerging challenges.     

Estimating plant migration rates under habitat loss and fragmentation

Changes in the global environment are modifying the geographical locations of habitats suitable for plant growth. The capacity of plants to migrate to sites of suitable environmental quality will strongly influence future distributions of plant diversity. However, it is not well understood how rates of plant migration are influenced by the habitat loss and habitat fragmentation that characterise contemporary landscapes. In this study we develop a model that can predict migration rates in both intact landscapes (potential migration rate) and in fragmented landscapes (realised migration rates). Migration rates in fragmented landscapes might be slower for many reasons. In this study we focus on two, non‐exclusive reasons. First, the processes that move seeds may break down in fragmented landscapes causing seeds to be dispersed shorter distances. Second, in fragmented landscapes some proportion of seeds will not be deposited in habitats suitable for recruitment. We describe the breakdown of dispersal processes as a competing risk between the factors influencing dispersal in intact landscapes and the factors that may disrupt dispersal processes in fragmented landscapes. We show how the parameters that influence dispersal in fragmented landscapes can be estimated, and how these estimates can be used to forecast migration rates using an integrodifference equation (IDE). The forecasts of the IDE described the effects of reduced dispersal distances adequately. However, the IDE produced biased estimates of the effects of a reduction in plant habitat on migration rates. Model analyses showed that, although we can expect realised migration rates to be lower than potential migration rates, we can also expect the sensitivity of migration rate to habitat loss to vary. In addition, simulations showed that the qualitative nature of the responses of migration rate to habitat loss were variable – some model species responded non‐linearly to habitat loss, others responded linearly. While our method provides guidelines for empirical data collection and model parameterisation, we recognise that obtaining these data will be challenging.     

Local native plant diversity responds to habitat loss and fragmentation over different time spans and spatial scales

Separating the threats that habitat loss and habitat fragmentation pose to biodiversity is challenging because these processes usually occur simultaneously. Additionally, their importance may be underestimated due to time-delayed extinction. In central Texas savannas, woody plant encroachment reduces the amount of habitat available to herbaceous species while fragmenting remaining habitat. We examined the relationships between present species richness and present and past habitat amount and fragmentation (measured as fractal dimension) using a series of aerial photographs taken over nearly 60 years. We show that woody plant encroachment, a common phenomenon in savannas worldwide, reduces the diversity of herbaceous vegetation through both habitat loss and fragmentation. Habitat loss has the strongest impact on species richness over short time spans and small spatial scales in these savannas. Habitat fragmentation, however, has the strongest impact over longer time spans and larger spatial scales and generates long-term extinction debts. We also demonstrate that examining habitat loss and habitat fragmentation across different time periods and at different spatial scales is essential for understanding their joint and individual effects on plant community composition.     

Independent effects of habitat loss,habitat fragmentation and structural connectivity on forest‐dependent birds

Aim Habitat loss and fragmentation are amongst the greatest threats to biodiversity world‐wide. However, there is still little evidence on the relative influence of these two distinct processes on biodiversity, and no study, to date, has investigated the independent contribution of structural connectivity in addition to habitat loss and fragmentation. The aim of this study is to evaluate the independent effects of habitat loss (the decrease in total amount of habitat), habitat fragmentation per se (habitat subdivision) and structural connectivity (in the form of hedgerow networks) on the distribution of seven resident forest‐dependent birds in central Italy. Location Central Italy. Methods We strategically selected 30 landscapes (each of 16 km² in size) with decreasing total amount of forest cover and with contrasting configuration of patches and contrasting lengths of hedgerow networks. Presence/absence of birds in each landscape unit was studied through point counts. Results The amount of forest cover in the landscape had the strongest relative influence on birds’ occupancy, whilst habitat subdivision played a negligible role. Structural connectivity and the geographic position of the landscape unit played a relatively important role for four species. Main conclusions Our study shows the importance of disentangling the contribution of different landscape properties in determining distribution patterns. Our results are consistent with the fact that halting habitat loss and carrying out habitat restoration should be conservation priorities, since habitat loss is the main factor affecting the distribution of the target species; implementation of structural connectivity through hedgerows, instead, should be evaluated with caution since its contribution is secondary to the predominant role of habitat loss.     

Genetic drift on networks: ploidy and the time to fixation

Genetic drift in finite populations ultimately leads to the loss of genetic variation. This paper examines the rate of neutral gene loss for a range of population structures defined by a graph. We show that, where individuals reside at fixed points on an undirected graph with equal degree nodes, the mean time to loss differs from the panmictic value by a positive additive term that depends on the number of individuals (not genes) in the population. The effect of these spatial structures is to slow the time to fixation by an amount that depends on the way individuals are distributed, rather than changing the apparent number of genes available to be sampled. This relationship breaks down, however, for a broad class of spatial structures such as random, small-world and scale-free networks. For the latter structures there is a counter-intuitive acceleration of fixation proportional to the level of ploidy.     

Slow response of plant species richness to habitat loss and fragmentation

We examined the response of vascular plant species richness to long-term habitat loss and fragmentation of Estonian calcareous grasslands (alvars). The current number of habitat specialist species in 35 alvars was not explained by their current areas and connectivities but it was explained by their areas and connectivities 70 years ago ( R ² = 0.27). We estimated the magnitude of extinction debt in local communities by assuming an equilibrium species richness in 14 alvars that had lost only a small amount of area and by applying this model to the remaining alvars, in which the average area has declined from 3.64 km² in the 1930s to 0.21 km² at present. The extinction debt estimated for individual alvars was around 40% of their current species number. Our conclusions are applicable to temperate grasslands in general, which have lost much area because of agricultural intensification and cessation of traditional management.     

Genetic drift on networks: Ploidy and the time to fixation

Genetic drift in finite populations ultimately leads to the loss of genetic variation. This paper examines the rate of neutral gene loss for a range of population structures defined by a graph. We show that, where individuals reside at fixed points on an undirected graph with equal degree nodes, the mean time to loss differs from the panmictic value by a positive additive term that depends on the number of individuals (not genes) in the population. The effect of these spatial structures is to slow the time to fixation by an amount that depends on the way individuals are distributed, rather than changing the apparent number of genes available to be sampled. This relationship breaks down, however, for a broad class of spatial structures such as random, small-world and scale-free networks. For the latter structures there is a counter-intuitive acceleration of fixation proportional to the level of ploidy.     

High gene flow in epiphytic ferns despite habitat loss and fragmentation

Tropical montane forests suffer from increasing fragmentation and replacement by other types of land-use such as coffee plantations. These processes are known to affect gene flow and genetic structure of plant populations. Epiphytes are particularly vulnerable because they depend on their supporting trees for their entire life-cycle. We compared population genetic structure and genetic diversity derived from AFLP markers of two epiphytic fern species differing in their ability to colonize secondary habitats. One species, Pleopeltis crassinervata, is a successful colonizer of shade trees and isolated trees whereas the other species, Polypodium rhodopleuron, is restricted to forests with anthropogenic separation leading to significant isolation between populations. By far most genetic variation was distributed within rather than among populations in both species, and a genetic admixture analysis did not reveal any clustering. Gene flow exceeded by far the benchmark of one migrant per generation to prevent genetic divergence between populations in both species. Though populations are threatened by habitat loss, long-distance dispersal is likely to support gene flow even between distant populations, which efficiently delays genetic isolation. Consequently, populations may rather be threatened by ecological consequences of habitat loss and fragmentation.     

苜蓿草地生境丧失与破碎化对昆虫物种丧失与群落重建的影响

生境破碎化包括生境丧失与破碎化两个相对独立的过程,为探讨这两个过程各自对生物多样性的影响,本文利用苜蓿草地实验模型系统(EMS)构建了36个小区研究不同生境丧失与破碎化对昆虫群落及不同类群的影响,包括18个破碎化小区与18个连续小区,破碎化小区全部采用1 m×1 m(H=1)破碎,连续小区苜蓿连片(H=0),生境丧失采...     

Climate change and human colonization triggered habitat loss and fragmentation in Madagascar

The relative effect of past climate fluctuations and anthropogenic activities on current biome distribution is subject to increasing attention, notably in biodiversity hot spots. In Madagascar, where humans arrived in the last ~4 to 5,000 years, the exact causes of the demise of large vertebrates that cohabited with humans are yet unclear. The prevailing narrative holds that Madagascar was covered with forest before human arrival and that the expansion of grasslands was the result of human‐driven deforestation. However, recent studies have shown that vegetation and fauna structure substantially fluctuated during the Holocene. Here, we study the Holocene history of habitat fragmentation in the north of Madagascar using a population genetics approach. To do so, we infer the demographic history of two northern Madagascar neighbouring, congeneric and critically endangered forest dwelling lemur species—Propithecus tattersalli and Propithecus perrieri—using population genetic analyses. Our results highlight the necessity to consider population structure and changes in connectivity in demographic history inferences. We show that both species underwent demographic fluctuations which most likely occurred after the mid‐Holocene transition. While mid‐Holocene climate change probably triggered major demographic changes in the two lemur species range and connectivity, human settlements that expanded over the last four millennia in northern Madagascar likely played a role in the loss and fragmentation of the forest cover.     

Reversing habitat loss: deciduous habitat fragmentation matters to birds in a larch plantation matrix

Whereas matrix management has recently been suggested as a useful tool in biodiversity conservation, patterns and processes within matrices remain unknown. We examined the effects of the loss and fragmentation (configuration) of original deciduous habitats on birds in larch plantation matrix in the winter and during the breeding season in a montane region in Nagano Prefecture, central Japan. Birds were counted using a plot-count method from 32 (winter) and 46 (breeding) matrix (plantation) sites with a range of surrounding habitat loss and fragmentation at a 1600-m scale. Birds were assigned to species groups based on ecological traits, and three groups for which larch plantation would function as low-quality matrix were analyzed. Bird occurrences were explained primarily by habitat structure. Although the effects of landscape structure were less than those of habitat structure, three of five groups across the two seasons experienced significant landscape effects. All effects were of habitat fragmentation (scatteredness of deciduous habitats), i.e. two groups (flycatchers in the breeding season and tree nesters in both seasons) frequently occurred in matrix surrounded by highly scattered deciduous habitats. However, most of these effects were confounded by local habitat structure. That is, the variation in bird occurrences explained purely by fragmentation variables was <6%. Nonetheless, because these effects were marginally significant at p<0.10, there was some support for fragmentation effects after covariation with habitat structure was considered. Based on these results and associated theoretical studies, we hypothesized that habitat fragmentation leads to loss of individuals and is more important than habitat loss in landscapes with a structurally similar matrix. We also hypothesized that matrix within landscapes with highly scattered habitats should be managed with high priority.     

Recent habitat fragmentation caused by major roads leads to reduction of gene flow and loss of genetic variability in ground beetles

Although habitat fragmentation is suspected to jeopardize the long-term survival of many species, few data are available on its impact on the genetic variability of invertebrates. We assess the genetic population structure of the flightless ground beetle Carabus violaceus L., 1758 in a Swiss forest, which is divided into several fragments by a highway and two main roads. Eight samples were collected from different forest fragments and analysed at six microsatellite loci. The largest genetic differentiation was observed between samples separated by roads and in particular by the highway. The number of roads between sites explained 44% of the variance in pairwise F(ST) estimates, whereas the age of the road and the geographical distance between locations were not significant factors. Furthermore, a comparison of allelic richness showed that the genetic variability in a small forest fragment isolated by the highway was significantly lower than in the rest of the study area. These findings strongly support the hypothesis that large roads are absolute barriers to gene flow in C. violaceus, which may lead to a loss of genetic variability in fragmented populations.     

The distinct effects of habitat fragmentation on population size

We sought to understand how the separation of habitats into spatially isolated fragments influences the abundance of organisms. Using a simple, deterministic model of population growth, we compared analytically exact solutions predicting abundance of consumers in two isolated patches with abundance of consumers in a single large patch where the carrying capacity of the large patch is the sum of the carrying capacities of the isolated ones. For the deterministic model, the effect of fragmentation was to slow the rate of population growth in the fragmented habitat relative to the intact one. We also analyzed a stochastic version of the model to examine the effect of fragmentation on population abundance when resources vary randomly in time. For the stochastic model, the effect of fragmentation was to reduce population abundance. We proved in closed-form, that for a non-equilibrium population exhibiting logistic population growth, fragmentation will reduce population size even when the total carrying capacity is not affected by fragmentation. We provide a theoretical basis for the prediction that habitat fragmentation amplifies the effect of habitat loss on the abundance of mobile organisms.     

Accounting for the causal basis of collinearity when measuring the effects of habitat loss versus habitat fragmentation

Collinearity among metrics of habitat loss and habitat fragmentation is typically treated as a nuisance in landscape ecology, and it is the norm to use statistical approaches that remove collinear information prior to estimating model parameters. However, collinearity may arise from causal relationships among landscape metrics and may therefore signal the occurrence of indirect effects (where one model predictor influences the response variable by driving changes in another influential predictor). Here we suggest that, far from being merely a statistical nuisance, collinearity may be crucial for accurately quantifying the effects of habitat loss versus habitat fragmentation. We use simulation modelling to create datasets of collinear landscape metrics in which collinearity arose from causal relationships, then test the ability of two statistical approaches to estimate the effects of these metrics on a simulated response variable: 1) multiple regression, which statistically removes collinearity, and was identified in a recent study as the best approach for estimating the effects of collinear landscape metrics (although this study did not account for any indirect effects implied by collinearity among metrics); and 2) path analysis, which accounts for the causal basis of collinearity. In agreement with this previous study, we found that multiple regression gave unbiased estimates of direct effects (effects not mediated by other model predictors). However, it gave biased estimates of total (direct + indirect) effects when indirect effects occurred. In contrast, path analysis reliably identified the causal basis of collinearity and gave unbiased estimates of direct, indirect, and total effects. We suggest that effective research on the impacts of habitat loss versus fragmentation will often require tools that can empirically test whether collinear landscape metrics are causally related, and if so, account for the indirect effects that these causal relationships imply. Path analysis, but not multiple regression, provides such a tool.