Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus)

Habitat loss and fragmentation due to urbanization are the most pervasive threats to biodiversity in southern California. Loss of habitat and fragmentation can lower migration rates and genetic connectivity among remaining populations of native species, reducing genetic variability and increasing extinction risk. However, it may be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric fragmentation due to previous natural geological and climatic changes. To address these challenges, we examined the phylogenetic and population genetic structure of a flightless insect endemic to cismontane southern California, Stenopelmatus'mahogani' (Orthoptera: Stenopelmatidae). Analyses of mitochondrial DNA sequence data suggest that diversification across southern California began during the Pleistocene, with most haplotypes currently restricted to a single population. Patterns of genetic divergence correlate with contemporary urbanization, even after correcting for (geographical information system) GIS-based reconstructions of fragmentation during the Pleistocene. Theoretical simulations confirm that contemporary patterns of genetic structure could be produced by recent urban fragmentation using biologically reasonable assumptions about model parameters. Diversity within populations was positively correlated with current fragment size, but not prehistoric fragment size, suggesting that the effects of increased drift following anthropogenic fragmentation are already being seen. Loss of genetic connectivity and diversity can hinder a population's ability to adapt to ecological perturbations commonly associated with urbanization, such as habitat degradation, climatic changes and introduced species. Consequently, our results underscore the importance of preserving and restoring landscape connectivity for long-term persistence of low vagility native species.     

Effects of habitat fragmentation and disturbance on howler monkeys: a review

We examined the literature on the effects of habitat fragmentation and disturbance on howler monkeys (genus Alouatta) to (1) identify different threats that may affect howlers in fragmented landscapes; (2) review specific predictions developed in fragmentation theory and (3) identify the empirical evidence supporting these predictions. Although howlers are known for their ability to persist in both conserved and disturbed conditions, we found evidence that they are negatively affected by high levels of habitat loss, fragmentation and degradation. Patch size appears to be the main factor constraining populations in fragmented habitats, probably because patch size is positively related to food availability, and negatively related to anthropogenic pressures, physiological stress and parasite loads. Patch isolation is not a strong predictor of either patch occupancy or population size in howlers, a result that may be related to the ability of howlers to move among forest patches. Thus, we propose that it is probable that habitat loss has larger consistent negative effects on howler populations than habitat fragmentation per se. In general, food availability decreases with patch size, not only due to habitat loss, but also because the density of big trees, plant species richness and howlers' home range size are lower in smaller patches, where howlers' population densities are commonly higher. However, it is unclear which vegetation attributes have the biggest influence on howler populations. Similarly, our knowledge is still limited concerning the effects of postfragmentation threats (e.g. hunting and logging) on howlers living in forest patches, and how several endogenous threats (e.g. genetic diversity, physiological stress, and parasitism) affect the distribution, population structure and persistence of howlers. More long‐term studies with comparable methods are necessary to quantify some of the patterns discussed in this review, and determine through meta‐analyses whether there are significant inter‐specific differences in species' responses to habitat loss and fragmentation. Am. J. Primatol. 72:1–16, 2010. © 2009 Wiley‐Liss, Inc.     

Fragmentation,grazing and the species–area relationship

Habitat loss is one of the greatest threats to species persistence. Gauging the scale of this problem requires quantitative methods that can predict the number of extinctions resulting from habitat loss. For the past three decades, the species–area relationship, an empirical relationship between the number of species present in an area and the size of that area, has been this tool. However, it fails to incorporate threats to species aside from habitat loss and the heterogeneous distribution of these threats across habitats. Recent studies have improved species–area predictions by incorporating not only direct effects of area on richness, but also indirect effects of area (through area‐mediated predator abundance), on prey species richness. We extend this work to test the hypotheses that the indirect effects of the multiple threats of grazing and trampling in addition to fragmentation will amplify the effect of area on species richness and that this effect will be greatest in zones closest to the fragment edge. Further, we test for species and population level effects of fragmentation and grazing, including the non‐random pattern of species loss and the decline in population sizes. We test our hypotheses with a field study of land snail richness in fragments with and without the additional threats of grazing and trampling. Our study supports the hypotheses that fragments with multiple threats in addition to habitat loss harbour fewer species than fragments without these threats, and that this effect is non‐uniform across fragments, populations and species.     

Papyrus swamp drainage and the conservation status of their avifauna

Papyrus Cyperus papyrus swamps sustain the livelihoods of millions of people, but threats to this habitat have never been quantified formally. Birds are useful indicators of threats that cannot be measured directly. Using satellite imagery classification and habitat associated modelling, we quantify drainage and present International Union for Conservation of Nature (IUCN) Red List assessments for the eight taxa most closely associated with this habitat. We show that, between 1984–1987 and 1999–2001 the areal extent of papyrus declined by 6.7 % from 1,643 to 1,532 km². Papyrus-specialist avifauna has undergone much greater declines, due in part to fragmentation effects and in part to geographical overlap between areas of highest population densities and areas that have experienced greatest habitat loss. Our assessment does not alter the IUCN Red List status of any full species, but it improves current knowledge of the drivers of their extinction risk. Papyrus gonolek Laniarius mufumbiri should remain at least near threatened, but on the basis of population decline rather than a purported small and decreasing range size, and papyrus yellow warbler Chloropeta gracilirostris should remain vulnerable, but again due to declines rather than on the basis of previous under-estimates of population size. Other species should remain listed as least concern. However, taxonomically, likely specifically, distinct populations of papyrus yellow warbler in Zambia and Kenya are highly threatened and should be listed as endangered and critically endangered respectively. We propose several conservation priorities and discuss means of achieving these in a manner consistent with maintaining the livelihoods of people.     

Assessing multi-taxa sensitivity to the human footprint,habitat fragmentation and loss by exploring alternative scenarios of dispersal ability and population size: a simulation approach

Quantifying the effects of landscape change on population connectivity is compounded by uncertainties about population size and distribution and a limited understanding of dispersal ability for most species. In addition, the effects of anthropogenic landscape change and sensitivity to regional climatic conditions interact to strongly affect habitat fragmentation and loss. To further develop conservation theory and to understand the interplay between all of these factors, we simulated habitat fragmentation and loss across the Western United States for several hypothetical species associated with four biome types, and a range of habitat requirements and dispersal abilities. We found dispersal ability and population size of the focal species to be equally sensitive to habitat extent, while dispersal ability is more sensitive to habitat fragmentation. There were also strong critical threshold effects where habitat connectivity decreased disproportionately to decreases in life-history traits making these species near these thresholds more sensitive to changes in habitat loss and fragmentation. Overall, grassland and forest associated species are also most at risk from habitat loss and fragmentation driven by human related land-use. These two largest biome types were most sensitive at large contiguous patch sizes which is often considered most important for metapopulation viability and biodiversity conservation. Hypothetical simulation studies such as this can be of great value to scientists in further conceptualizing and developing conservation theory, and evaluating spatially-explicit scenarios of habitat connectivity. Our results are available for download in a web-based interactive mapping prototype useful for accessing the results of this study.     

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.     

Small-Scale Fragmentation Effects on Local Genetic Diversity in Two Phyllostomid Bats with Different Dispersal Abilities in Panama

Habitat fragmentation is one of the greatest threats to biodiversity. Despite their importance for conservation, the genetic consequences of small-scale habitat fragmentation for bat populations are largely unknown. In this study, we linked genetic with ecological and demographic data to assess the effects of habitat fragmentation on two species of phyllostomid bats ( Uroderma bilobatum and Carollia perspicillata ) that differ in their dispersal abilities and demographic response to fragmentation. We hypothesized that population differentiation and the effect of habitat fragmentation on levels of genetic diversity will be a function of the species' mobility. We sequenced mtDNA from 232 bats caught on 11 islands in Gatún Lake, Panamá, isolated from the mainland for ca 90 yr, and in adjacent, continuous forest on the mainland. Populations of both species showed significant genetic differentiation ( F _ST). Consistent with our prediction, population subdivision was lower in the highly mobile U. bilobatum ( F _ST= 0.01) compared to the less vagile C. perspicillata ( F _ST= 0.06), and only the latter species showed a pattern indicative of isolation by distance and, in addition, an effect of fragmentation. Genetic erosion as a result of fragmentation was also only detectable in the less mobile species, C. perspicillata , where haplotype diversity was lower in island compared to mainland populations. Our results suggest that some Neotropical bat species are prone to loss of genetic variation in response to anthropogenic small-scale habitat fragmentation. In this context, our findings point toward mobility as a good predictor of a species' vulnerability to fragmentation and altered population genetic structure.     

Complexity in conservation: lessons from the global decline of amphibian populations

As part of an overall "biodiversity crisis" many amphibian populations are in decline throughout the world. Numerous causes have been invoked to explain these declines. These include habitat destruction, climate change, increasing levels of ultraviolet radiation, environmental contamination, disease, and the introduction of non-native species. In this paper, we argue that amphibian population declines are caused by different abiotic and biotic factors acting together in a context-dependent fashion. Moreover, different species and different populations of the same species may react in different ways to the same environmental insult. Thus, the causes of amphibian population declines will vary spatially and temporally. Although some generalizations (e.g. those concerning environmental stress and disease outbreaks) can be made about amphibian population declines, we suggest that these generalizations take into account the context-dependent dynamics of ecological systems.     

Cryptic differences in dispersal lead to differential sensitivity to habitat fragmentation in two bumblebee species

Habitat loss has led to fragmentation of populations of many invertebrates, but social hymenopterans may be particularly sensitive to habitat fragmentation due to their low effective population sizes. The impacts of fragmentation depend strongly on dispersal abilities, but these are difficult to quantify. Here, we quantify and compare dispersal abilities of two bumblebee species, Bombus muscorum and Bombus jonellus , in a model island system. We use microsatellites to investigate population genetic structuring, dispersal and spatial patterns in genetic diversity. Populations of both species showed significant structuring, and isolation by distance, but this was markedly greater in B. muscorum (θ = 0.13) than in B. jonellus (θ = 0.034). This difference could reflect a higher effective population size in B. jonellus compared to B. muscorum , but this is not consistent with the observed abundance of the two species. We argue that it is more likely that B. jonellus has a higher propensity to disperse than B. muscorum . This will influence their relative susceptibility to habitat fragmentation and may in part explain differential declines of mainland populations of these and other bumblebee species.     

The influence of landscape structure on occurrence, abundance and genetic diversity of the common frog, Rana temporaria

Human‐caused habitat destruction and modification constitute one of the largest threats to population persistence and biodiversity, and are also suspected to be the major cause behind the global decline of amphibian populations. We assessed the potential role of agriculture‐related habitat fragmentation on population size and genetic variability in the common frog (Rana temporaria) by recording the occurrence, population density and genetic diversity in three geographically disparate regions in Sweden – each containing landscapes of high and low agricultural activity – and related these to landscape variables extracted from digital maps. We found a highly significant region‐by‐landscape interaction in occurrence, population density and genetic diversity revealing a reversed response to agriculture from south to north: while the effects of agriculture on R. temporaria populations were negative in the south, there were no effects in the central region, whereas positive effects were observed in the north. Spatial autocorrelation analyses of genetic data revealed that populations in high agricultural activity areas were more isolated than populations in low activity areas both in the southern and central regions of Sweden. Landscape diversity showed a strong positive correlation with both density and occurrence of frogs in Sweden as a whole, as well as in the southern region. Also, negative effects of roads and positive effects of ditches on genetic diversity were found in the south. Overall, these results suggest clear but regionally opposite effects of habitat structure on the population size and genetic diversity of amphibian populations. This means that the management strategy aiming to maximize the size and genetic diversity of local common frog populations, and perhaps also those of other amphibian populations, should account for regional differences in existing land‐use patterns.     

生境破碎化对动物种群存活的影响

生境破碎是生物多样性下降的主要原因之一。通常以岛屿生物地理学、异质种群生物学和景观生态学的理论来解释不同空间尺度中生境破碎化的生态学效应。生境破碎化引起面积效应、隔离效应和边缘效应。这些效应通过影响动物种群的绝灭阈值、分布和多度、种间关系以及生态系统过程,最终影响动物种群的存活。野外研究表明,破碎化对动物的影响,因物种、生境类型和地理区域不同而有所变化,因此,预测物种在破碎生境中的存活比较困难。研究热点集中于：确定生境面积损失和生境斑块的空间格局对破碎景观中物种绝灭的相对影响,破碎景观中物种的适宜生境比例和绝灭阈值,异质种群动态以及生态系统的生态过程。随着3S技术的发展,生境破碎化模型趋于复杂,而发展有效的模型和验证模型将成为一项富有挑战性的任务。     

Demographic and genetic factors shaping contemporary metapopulation effective size and its empirical estimation in salmonid fish

The preservation of biodiversity requires an understanding of the maintenance of its components, including genetic diversity. Effective population size determines the amount of genetic variance maintained in populations, but its estimation can be complex, especially when populations are interconnected in a metapopulation. Theory predicts that the effective size of a metapopulation (meta-N(e)) can be decreased or increased by population subdivision, but little empirical work has evaluated these predictions. Here, we use neutral genetic markers and simulations to estimate the effective size of a putative metapopulation in Atlantic salmon (Salmo salar). For a weakly structured set of rivers, we find that meta-N(e) is similar to the sum of local deme sizes, whereas higher genetic differentiation among demes dramatically reduces meta-N(e) estimates. Interdemic demographic processes, such as asymmetrical gene flow, may explain this pattern. However, simulations also suggest that unrecognized population subdivision can also introduce downward bias into empirical estimation, emphasizing the importance of identifying the proper scale of distinct demographic and genetic processes. Under natural patterns of connectivity, evolutionary potential may generally be maintained at higher levels than the local population, with implications for conservation given ongoing species declines and habitat fragmentation.     

Fragmentation of Atlantic Forest has not affected gene flow of a widespread seed‐dispersing bat

Habitat loss and resultant fragmentation are major threats to biodiversity, particularly in tropical and subtropical ecosystems. It is increasingly urgent to understand fragmentation effects, which are often complex and vary across taxa, time and space. We determined whether recent fragmentation of Atlantic forest is causing population subdivision in a widespread and important Neotropical seed disperser: Artibeus lituratus (Chiroptera: Phyllostomidae). Genetic structure within highly fragmented forest in Paraguay was compared to that in mostly contiguous forest in neighbouring Misiones, Argentina. Further, observed genetic structure across the fragmented landscape was compared with expected levels of structure for similar time spans in realistic simulated landscapes under different degrees of reduction in gene flow. If fragmentation significantly reduced successful dispersal, greater population differentiation and stronger isolation by distance would be expected in the fragmented than in the continuous landscape, and genetic structure in the fragmented landscape should be similar to structure for simulated landscapes where dispersal had been substantially reduced. Instead, little genetic differentiation was observed, and no significant correlation was found between genetic and geographic distance in fragmented or continuous landscapes. Furthermore, comparison of empirical and simulated landscapes indicated empirical results were consistent with regular long‐distance dispersal and high migration rates. Our results suggest maintenance of high gene flow for this relatively mobile and generalist species, which could be preventing or significantly delaying reduction in population connectivity in fragmented habitat. Our conclusions apply to A. lituratus in Interior Atlantic Forest, and do not contradict broad evidence that habitat fragmentation is contributing to extinction of populations and species, and poses a threat to biodiversity worldwide.     

Conservation genetics of carnivores in Italy

Pleistocene climatic changes shaped the patterns of biodiversity in Europe and around the Mediterranean. Describing the phylogeographic structure of animal populations and inferring past population dynamics is essential to develop a framework for conservation biology in Europe. Direct persecution, habitat loss, population fragmentation and hybridization with domesticated conspecifics, are the main threats to the survival of large mammalian species. In this paper I will summarize the available information on phylogeography and population genetics of brown bear, wolf, wildcat and otters in Italy and in Europe.     

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.     

Little evidence that condition,stress indicators,sex ratio,or homozygosity are related to landscape or habitat attributes in declining woodland birds

Habitat loss, fragmentation and degradation are drivers of major declines in biodiversity and species extinctions. The actual causes of species population declines following habitat change are more difficult to discern and there is typically high covariation among the measures used to infer the causes of decline. The causes of decline may act directly on individual fitness and survival, or through disruption of population processes. We examined the relationships among configuration, extent and status of native vegetation and three commonly used indicators of individual body condition and chronic stress (haemoglobin level, haematocrit, residual body mass condition index) in 13 species of woodland‐dependent birds in south‐eastern Australia. We also examined two measures of changes to population processes (sex ratio and individual homozygosity) in ten species and alleic richness in five species. We found little support for relationships between site or landscape characteristics and individual or population response variables, notwithstanding that our simulations showed we had sufficient power to detect relatively small effects. We discuss possible causes of the absence of detectable habitat effects in this system and the implications for the usefulness of individual body condition and easily measured haematological indices as indicators of the response of avian populations to habitat change.     

Effects of a fire on a breeding population of Loggerhead Shrikes in sagebrush steppe habitat

ABSTRACT.   We studied the breeding biology of Loggerhead Shrikes ( Lanius ludovicianus ) in northeastern Oregon from 1995 to 1997 and 2000 to 2001. A wildfire in 1998 burned approximately half the big sagebrush ( Artemisia tridentata ) at this site, permitting comparison of population parameters before and after this event. Shrike density after the fire was half that before the fire, a reduction likely due to loss of suitable nesting habitat. Mayfield estimates of nest survivorship were 39% (range: 30–46%) in the years before and 19% (range: 12–26%) after the fire, among the lowest ever recorded for this species. In 2000, young fledged from only 21% of the territories. Due to persistent renesting, young fledged from 67% of the territories in 2001, a percentage similar to that before the fire. After the fire, shrikes nested more frequently in substrates other than big sagebrush, especially juniper trees ( Juniperus occidentalis ). Clutch size, fledglings per successful nest, and fledgling survival were similar in both periods of the study. Poor nesting success across all years suggests that productivity may play a role in regional declines of shrike populations, and that the loss and fragmentation of nesting habitat due to fire may further reduce productivity. Given the threats facing remaining sagebrush habitat, as well as Loggerhead Shrike population declines, we recommend aggressive fire control measures and further protection for remaining tall sagebrush communities.     

Current threats faced by amphibian populations in the southern cone of South America

In this work, we update and increase knowledge on the severity and extent of threats affecting 57 populations of 46 amphibian species from Chile and Argentina in southern South America. We analyzed the intrinsic conservation problems that directly impact these populations. We shared a questionnaire among specialists on threats affecting target amphibian populations with information on i) range, ii) historical occurrence and abundance, iii) population trends, iv) local extinctions, v) threats, and vi) ongoing and necessary conservation/research. We assessed association patterns between reported threats and population trends using multiple correspondence analysis. Since 2010, 25 of 57 populations have declined, while 16 experienced local extinctions. These populations were affected by 81% of the threat categories analyzed, with those related to agricultural activities and/or habitat modifications being the most frequently reported. Invasive species, emerging diseases, and activities related to grazing, ranching, or farming were the threats most associated with population declines. Low connectivity was the most frequent intrinsic conservation problem affecting 68% of the target populations, followed by low population numbers, affecting 60%. Ongoing monitoring activity was conducted in 32 (56%) populations and was the most frequent research activity. Threat mitigation was reported in 27 (47%) populations and was the most frequent ongoing management activity. We found that habitat management is ongoing in 5 (9%) populations. At least 44% of the amphibian populations surveyed in Chile and Argentina are declining. More information related to the effect of management actions to restore habitats, recover populations, and eliminate threats such as invasive species is urgently needed to reverse the conservation crisis facing amphibians in this Neotropical region.     

Fragmentation and Genetic Diversity in Romnalda (Dasypogonaceae), a Rare Rain forest Herbaceous Genus from New Guinea and Australia

Rain forests are expected to be amongst the ecosystem types most affected by fragmentation due to their high species diversity, high endemism, complexity of interactions, and contrast with surrounding altered matrix. Due to their shorter life cycles and dependence on canopy cover, rain forest understory herbs are expected to indicate the effects of recent fragmentation more rapidly than canopy trees. This study investigated all four known species of the genus Romnalda , all of which are rare rain forest herbaceous species, to investigate the possible effects of habitat fragmentation and isolation on genetic diversity and gene flow. Allozymes were used as genetic markers and regional remnant vegetation maps were used to compare landscape fragmentation. We found that R. strobilacea populations in a highly fragmented landscape were genetically depauperate compared with those of its congeneric species that are found within continuous rain forest habitats and that allelic diversity decreased with decreasing population size but not geographic distance in R. strobilacea . Given the similarity among the species, our results indicate that all Romnalda species are potentially susceptible to loss of genetic diversity due to habitat fragmentation within relatively short timeframes. The results indicate that populations are not highly genetically differentiated and there is little evidence of genetic provenance where the species have restricted geographic ranges. Thus, species recovery programs would be better to focus on maintaining population size and genetic diversity rather than population differentiation.     

Forest fragmentation and plant reproductive success: a case study in four perennial herbs

We assessed the effects of habitat fragmentation on reproductive success in natural populations of four forest herbs with differing life-history traits and whose distribution patterns appeared to be negatively affected by decreased habitat size and/or increased isolation: Carex sylvatica, Galium odoratum, Sanicula europaea and Veronica montana. Our aims were to test (1) whether habitat size and isolation are positively correlated with population size and isolation, respectively, (2) whether plant reproductive success, a major component of plant fitness, is reduced in small and/or isolated populations when also accounting for differences in habitat quality (edaphic conditions, light intensity) and the effects of plant size, and (3) whether species with different life histories are affected differently. There were significant positive relationships between habitat and population size and between habitat and population isolation in some, but not all of the species. We mostly found no negative effects of small population size or isolation on reproduction. However, reproductive success was reduced in small populations of Sanicula, and this effect was independent of differences in plant size and environmental conditions. The reduced fecundity in small populations may be a consequence of the Allee-effect, a possible mechanism being pollen limitation. Furthermore, the proportion of flowering ramets was reduced in small and isolated populations of Galium, which may have been caused by changes in population structure. Lastly, we found some evidence for largely outcrossing, non-clonal species to be more sensitive to reductions in population size, at least in terms of their reproductive success.