Genetic variation of loci potentially under selection confounds species–genetic diversity correlations in a fragmented habitat

Positive species–genetic diversity correlations (SGDCs) are often thought to result from the parallel influence of neutral processes on genetic and species diversity. Yet, confounding effects of non‐neutral mechanisms have not been explored. Here, we investigate the impact of non‐neutral genetic diversity on SGDCs in high Andean wetlands. We compare correlations between plant species diversity and genetic diversity (GD) calculated with and without loci potentially under selection (outlier loci). The study system includes 2188 specimens from five species (three common aquatic macroinvertebrate and two dominant plant species) that were genotyped for 396 amplified fragment length polymorphism loci. We also appraise the importance of neutral processes on SGDCs by investigating the influence of habitat fragmentation features. Significant positive SGDCs were detected for all five species (mean SGDC = 0.52 ± 0.05). While only a few outlier loci were detected in each species, they resulted in significant decreases in GD and in SGDCs. This supports the hypothesis that neutral processes drive species–genetic diversity relationships in high Andean wetlands. Unexpectedly, the effects on genetic diversity GD of the habitat fragmentation characteristics in this study increased with the presence of outlier loci in two species. Overall, our results reveal pitfalls in using habitat features to infer processes driving SGDCs and show that a few loci potentially under selection are enough to cause a significant downward bias in SGDC. Investigating confounding effects of outlier loci thus represents a useful approach to evidence the contribution of neutral processes on species–genetic diversity relationships.     

Species and genetic diversity are not congruent in fragmented dry grasslands

Biological diversity comprises both species diversity (SD) and genetic diversity (GD), and it has been postulated that both levels of diversity depend on similar mechanisms. Species‐genetic diversity correlations (SGDC) are therefore supposed to be generally positive. However, in contrast to theory, empirical data are contradictory. Furthermore, there is a pronounced lack of multispecies studies including also the ecological factors potentially driving species and genetic diversity. We analyzed the relationship between the species diversity of dry grasslands and the genetic diversity of several dry grassland plant species, therefore, in the context of habitat fragmentation and habitat conditions. Our study revealed a lack of correlation between species and genetic diversity. We demonstrated previously that SD mainly depends on habitat conditions (vegetation height and cover of litter), whereas GD is significantly affected by habitat fragmentation (distance to the nearest dry grassland in 1830 and connectivity in 2013). This seems to be the main reason why SD and GD are not congruent in fragmented grasslands. Our results support, hence, the observation that positive SGDCs can mainly be found in natural, island‐like study systems in equilibrium and at similar levels of heterogeneity. In fragmented dry grassland ecosystems, which differ in heterogeneity, this state of equilibrium may not have been reached mitigating the positive relationship between SD and GD. From our study, it can be concluded that in fragmented dry grasslands, the protection of SD does not necessarily ensure the conservation of GD.     

Genetic structure in remnant populations of an endangered cyprinodontid fish, <Emphasis Type="Italic">Orestias ascotanensis</Emphasis>, endemic to the Ascotán salt pan of the Altiplano

The impact of recent habitat fragmentation on population genetic diversity and structure has often been studied, mainly related to anthropogenic causes; however its long-term effect has been much less evaluated. In this study we analyzed the genetic variability of Orestias ascotanensis, a fish endemic to the Ascotán salt pan of Chile. This species, which formed a single and large population during the last wet period that ended 10,000 years ago, is currently represented by small populations inhabiting freshwater springs on the eastern border of the salt pan. Therefore, this species represents a unique model to evaluate the consequences of a drastic habitat fragmentation process that initiated thousands of years ago. Analysis of the control region of the mitochondrial DNA revealed high genetic diversity (haplotipic diversity ranged between 0.78 and 0.94) and marked differences among populations (Φ_ST = 0.46). Estimated effective population sizes greatly surpassed the real sizes, particularly among springs that remained connected. These results reflect the long-term consequences of habitat fragmentation on natural populations: structuring of the populations and loss of genetic diversity of the isolated fragments.     

Landscape genetics of a recent population extirpation in a burnet moth species

The intensification of agricultural land use over wide parts of Europe has led to the decline of semi-natural habitats, such as extensively used meadows, with those that remain often being small and isolated. These rapid changes in land use during recent decades have strongly affected populations inhabiting these ecosystems. Increasing habitat deterioration and declining permeability of the surrounding landscape matrix disrupt the gene flow within metapopulations. The burnet moth species Zygaena loti has suffered strongly from recent habitat fragmentation, as reflected by its declining abundance. We have studied its population genetic structure and found a high level of genetic diversity in some of the populations analysed, while others display low genetic diversity and a lack of heterozygosity. Zygaena loti was formerly highly abundant in meadows and along the skirts of forests. However, the species is currently restricted to isolated habitat remnants, which is reflected by the high genetic divergence among populations (F _ST: 0.136). Species distribution modelling as well as the spatial examination of panmictic clusters within the study area strongly support a scattered population structure for this species. We suggest that populations with a high level of genetic diversity still represent the former genetic structure of interconnected populations, while populations with low numbers of alleles, high F _IS values, and a lack of heterozygosity display the negative effects of reduced interconnectivity. A continuous exchange of individuals is necessary to maintain high genetic variability. Based on these results, we draw the general conclusion that more common taxa with originally large population networks and high genetic diversity suffer stronger from sudden habitat fragmentation than highly specialised species with lower genetic diversity which have persisted in isolated patches for long periods of time.     

Crumbling diversity: comparison of historical archived and contemporary natural populations indicate reduced genetic diversity and increasing genetic differentiation in the golden-cheeked warbler

Genetic viability of threatened and endangered species is of increasing concern with habitat loss and fragmentation. Valuable assessments of the genetic status of endangered species are difficult in most cases, where only single sample estimates are available. Using historical and contemporary samples, we assessed the impact of both historical and recent demographic changes on population genetics of the endangered golden-cheeked warbler, (Dendroica chrysoparia). Our study documents a steep decline in genetic diversity in an endangered species over a 100-year period, along with concurrent increase in genetic differentiation, and low contemporary effective sizes for all the populations we evaluated. While adding to the growing body of literature that describes the genetic impacts of habitat fragmentation, our study may also serve as an informative guide to future management of endangered species. Our study underlines the importance of long term population genetic monitoring in understanding the full extent of genetic changes in endangered species.     

Landscape scale genetic effects of habitat fragmentation on a high gene flow species: Speyeria idalia (Nymphalidae)

Detection of the genetic effects of recent habitat fragmentation in natural populations can be a difficult task, especially for high gene flow species. Previous analyses of mitochondrial DNA data from across the current range of Speyeria idalia indicated that the species exhibited high levels of gene flow among populations, with the exception of an isolated population in the eastern portion of its range. However, some populations are found on isolated habitat patches, which were recently separated from one another by large expanses of uninhabitable terrain, in the form of row crop agriculture. The goal of this study was to compare levels of genetic differentiation and diversity among populations found in relatively continuous habitat to populations in both recently and historically isolated habitat. Four microsatellite loci were used to genotype over 300 individuals from five populations in continuous habitat, five populations in recently fragmented habitat, and one historically isolated population. Results from the historically isolated population were concordant with previous analyses and suggest significant differentiation. Also, microsatellite data were consistent with the genetic effects of habitat fragmentation for the recently isolated populations, in the form of increased differentiation and decreased genetic diversity when compared to nonfragmented populations. These results suggest that given the appropriate control populations, microsatellite markers can be used to detect the effects of recent habitat fragmentation in natural populations, even at a large geographical scale in high gene flow species.     

Genetic consequences of habitat fragmentation in plant populations: susceptible signals in plant traits and methodological approaches

Conservation of genetic diversity, one of the three main forms of biodiversity, is a fundamental concern in conservation biology as it provides the raw material for evolutionary change and thus the potential to adapt to changing environments. By means of meta‐analyses, we tested the generality of the hypotheses that habitat fragmentation affects genetic diversity of plant populations and that certain life history and ecological traits of plants can determine differential susceptibility to genetic erosion in fragmented habitats. Additionally, we assessed whether certain methodological approaches used by authors influence the ability to detect fragmentation effects on plant genetic diversity. We found overall large and negative effects of fragmentation on genetic diversity and outcrossing rates but no effects on inbreeding coefficients. Significant increases in inbreeding coefficient in fragmented habitats were only observed in studies analyzing progenies. The mating system and the rarity status of plants explained the highest proportion of variation in the effect sizes among species. The age of the fragment was also decisive in explaining variability among effect sizes: the larger the number of generations elapsed in fragmentation conditions, the larger the negative magnitude of effect sizes on heterozygosity. Our results also suggest that fragmentation is shifting mating patterns towards increased selfing. We conclude that current conservation efforts in fragmented habitats should be focused on common or recently rare species and mainly outcrossing species and outline important issues that need to be addressed in future research on this area.     

通过遗传多样性探讨极小种群野生植物的致濒机理及保护策略: 以裸子植物为例

遗传多样性是生物多样性的重要组成部分, 然而由于资源的过度开发利用和生境的破碎化影响了物种的遗传多样性, 甚至威胁到物种的生存适应性和生物多样性。极小种群野生植物是亟待保护的国家重点保护濒危植物,遗传多样性研究对揭示极小种群致濒机理及保护策略具有重要意义。生境破碎化会造成物种遗传多样性降低、种群间分化增加、基因流减少等, 使种群濒危。但在某些物种中, 繁殖特征、进化历史等生物和生态因素的不同也可能造成近期生境破碎化后遗传效应的延迟。裸子植物进化历史悠久, 包含许多孑遗物种, 由于生活史周期长, 遭受生境破碎化后可能短期内显示不出遗传效应的改变, 但长期很难恢复。本文以裸子植物为例综述了濒危植物的遗传多样性研究的案例, 探讨了濒危裸子植物应对环境恶化的维持机制、致濒因素和保护方案, 旨在说明通过遗传多样性研究充分认识极小种群致濒机理对高效保护极小种群野生植物的重要性。     

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.     

Microsatellite variation and structure of 28 populations of the common wetland plant, Lychnis flos-cuculi L., in a fragmented landscape

Habitat fragmentation is known to cause genetic differentiation between small populations of rare species and decrease genetic variation within such populations. However, common species with recently fragmented populations have rarely been studied in this context. We investigated genetic variation and its relationship to population size and geographical isolation of populations of the common plant species, Lychnis flos-cuculi L., in fragmented fen grasslands. We analysed 467 plants from 28 L. flos-cuculi populations of different sizes (60 000-54 000 flowering individuals) in northeastern Switzerland using seven polymorphic microsatellite loci. Genetic differentiation between populations is small (F(ST) = 0.022; amova; P < 0.001), suggesting that gene flow among populations is still high or that habitat fragmentation is too recent to result in pronounced differentiation. Observed heterozygosity (H(O) = 0.44) significantly deviates from Hardy-Weinberg equilibrium, and within-population inbreeding coefficient F(IS) is high (0.30-0.59), indicating a mixed mating breeding system with substantial inbreeding in L. flos-cuculi. Gene diversity is the only measure of genetic variation which decreased with decreasing population size (R = 0.42; P < 0.05). While our results do not indicate pronounced effects of habitat fragmentation on genetic variation in the still common L. flos-cuculi, the lower gene diversity of smaller populations suggests that the species is not entirely unaffected.     

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.     

Genetic diversity in butterflies: Interactive effects of habitat fragmentation and climate-driven range expansion

Some species are expanding their ranges polewards during current climate warming. However, anthropogenic fragmentation of suitable habitat is affecting expansion rates and here we investigate interactions between range expansion, habitat fragmentation and genetic diversity. We examined three closely related Satyrinae butterflies, which differ in their habitat associations, from six sites along a transect in England from distribution core to expanding range margin. There was a significant decline in allozyme variation towards an expanding range margin in Pararge aegeria, which has the most restricted habitat availability, but not in Pyronia tithonus whose habitat is more widely available, or in a non-expanding 'control species' (Maniola jurtina). Moreover, data from another transect in Scotland indicated that declines in genetic diversity in P. aegeria were evident only on the transect in England, which had greater habitat fragmentation. Our results indicate that fragmentation of breeding habitats leads to more severe founder events during colonization, resulting in reduced diversity in marginal populations in more specialist species. The continued widespread loss of suitable habitats in the future may increase the likelihood of loss of genetic diversity in expanding species, which may affect whether or not species can adapt to future environmental change.     

Spatial and temporal patterns of genetic diversity in an endangered Hawaiian honeycreeper,the Hawaii Akepa (<Emphasis Type="Italic">Loxops coccineus coccineus</Emphasis>)

As a result of disease, habitat destruction, and other anthropogenic factors, the Hawaii Akepa (Loxops coccineus coccineus) currently occupies <10% of its original range and exists in five disjunct populations, raising concerns about what effect such reduction and fragmentation has had on the connectivity and diversity of Akepa populations. In this study, we used both historical and contemporary samples to assess genetic diversity and structure in this endangered Hawaiian honeycreeper. We generated sequence data from two mtDNA regions (ND2, control region) and two nuclear introns for contemporary samples representing three of the five current populations. We also generated control region sequence data for museum specimens collected over 100 years ago from throughout the historical range of the bird. Results indicate that despite recent declines and fragmentation, genetic diversity has not been lost. We detected a modest level of genetic differentiation, which followed a combined pattern of isolation-by-barriers and isolation-by-distance, across the historical range of Akepa. The similarly low level of differentiation observed between the contemporary populations indicates that not much divergence, if any, has occurred post-fragmentation. Rather, the present structure seen likely reflects the historical pattern of distribution. Ironically, this declining species exhibits the genetic signal of an expanding population, demonstrating that earlier demographic events are outweighing the effects of recent changes in population size, and genetic estimates of N_e, though crude, suggest Hawaii Akepa were at least an order of magnitude more abundant prior to the decline.     

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.     

Genetic variation in <Emphasis Type="Italic">Delonix s.l.</Emphasis> (Leguminosae) in Madagascar revealed by AFLPs: fragmentation,conservation status and taxonomy

The distribution of genetic diversity has potential to inform conservation efforts but is rarely incorporated when conservation status is assigned to a species. These data can be beneficial to the conservation assessment process by providing information on subpopulations, gene flow and effective population sizes, thus achieving more successful assessments. In order to obtain a better understanding of the patterns of genetic variation and their relationship to conservation in the fragmented flora of Madagascar, this study assessed genetic diversity among and within Delonix s.l. (Leguminosae) using AFLP markers. The genetic diversity of eight species of Delonix s.l. (covering 79 sample sites and 254 individuals) showed a range of values (25–61% for polymorphic loci, and 0.076–0.192 Shannon’s Index). Results from an analysis of molecular variance (AMOVA) suggest that a majority of the genetic variance is attributed to variation within species (87%), which is also supported by a principle coordinate analysis of genetic distances between sites. The results were used to compare the genetic difference between species of different threat status and show that even closely related species with the same IUCN threat status differ in their genetic structure, probably arising from differences in life history traits, pollen and seed dispersal, and fragmentation. Species that are recently affected by habitat destruction and fragmentation are likely to be at high potential risk of genetic erosion contributing to their ongoing decline. Thus, genetic variation should be taken into consideration in conservation assessments, whenever possible, to provide accurate and targeted conservation recommendations in order to achieve more successful conservation outcomes.     

Overcoming the issue of small sample sizes in fragmentation genetics

Nazareno & Jump (2012) highlight potential issues with using small sample sizes in population genetic studies. By reanalysing allelic richness data from our recent publication on habitat fragmentation (Struebig et al. 2011), they assert that the observed relationship has been driven by three sites with the lowest number of individuals sampled. While sample size issues have been raised before in the genetic literature, Nazareno & Jump’s (2012) comment serves as a useful reminder to us all. Nevertheless, we disagree that our findings were significantly biased by sampling limitations. Here, we demonstrate by jackknifing that, contrary to the claims of Nazareno & Jump (2012), our correlations of allelic richness and fragment area are not driven solely by sites with low sample sizes. We maintain that small sample sizes can be accounted for in fragmentation studies and that sampling limitations should not detract from undertaking conservation genetic research.     

Multi‐scale effects of impoundments on genetic structure of creek chub (Semotilus atromaculatus) in the Kansas River basin

1. Habitat fragmentation has been implicated as a primary cause for the ongoing erosion of global biodiversity, yet our understanding of the consequences in lotic systems is limited for many species and regions. Because of harsh environmental conditions that select for high colonisation rates, prairie stream fishes may be particularly vulnerable to the effects of fragmentation. Hence, there is urgent need for broader understanding of fragmentation in prairie streams such that meaningful conservation strategies can be developed. Further, examination at large spatial scales, including multiple impoundments and un‐impounded catchments, will help identify the spatial extent of species movement through the landscape. 2. Our study used data from 10 microsatellite loci to describe the genetic structure of creek chub (Semotilus atromaculatus) populations across four catchments (three impounded and one un‐impounded) in the Kansas River basin. We investigated whether genetic diversity was eroded in response to habitat fragmentation imposed by reservoirs and whether intervening lentic habitat increased resistance to dispersal among sites within a catchment. 3. Our analyses revealed that genetic diversity estimates were consistent with large populations regardless of the location of the sampled tributaries, and there was little evidence of recent population reductions. Nevertheless, we found a high degree of spatial genetic structure, suggesting that catchments comprise a set of isolated genetic units and that sample sites within catchments are subdivided into groups largely defined by intervening habitat type. Our data therefore suggest that lentic habitat is a barrier to dispersal among tributaries, thus reducing the opportunity for genetic rescue of populations in tributaries draining into reservoirs. Isolation by a reservoir, however, may not be immediately deleterious if the isolated tributary basin supports a large population.     

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.     

The influence of habitat fragmentation on genetic diversity of a rare bird species that commonly faces environmental fluctuations

Habitat loss and fragmentation is one of the main causes of biodiversity loss. Rare species are generally thought to be more sensitive to habitat fragmentation than common ones as small populations become even smaller. We did a population genetic study on a rare bird, the Worthen's sparrow Spizella wortheni which is endemic to semi‐arid and arid regions of northeast Mexico. Its population numbers suffer greatly from the transformation of grassland into farmland that leads to a patchy distribution with locally small population sizes. Our data show that its genetic diversity is nevertheless high, few to no differentiation between study localities was found, and gene flow was high. Although we can not exclude that is too early to see an impact on the genetic level, we think that these results might be explained by the species’ biology: like many other birds living in arid areas, the Worthen's sparrow has a nomadic life style; depending on local conditions individuals flexibly move between areas. This behavior could enhance their ability to find suitable habitat patches in a fragmented landscape. Our results imply that nomadic behavior, which is an adaptation to high temporal variability in environmental conditions, may make species more resilient to spatial variability caused by habitat fragmentation. This insight contributes to identifying common factors such as nomadism that predict a species’ sensitivity to habitat fragmentation.     

Population fragmentation leads to isolation by distance but not genetic impoverishment in the philopatric Lesser Kestrel: a comparison with the widespread and sympatric Eurasian Kestrel

Population fragmentation is a widespread phenomenon usually associated with human activity. As a result of habitat transformation, the philopatric and steppe-specialist Lesser Kestrel Falco naumanni underwent a severe population decline during the last century that increased population fragmentation throughout its breeding range. In contrast, the ubiquitous Eurasian Kestrel Falco tinnunculus did not suffer such adverse effects, its breeding range still remaining rather continuous. Using microsatellites, we tested the effects of population fragmentation on large-scale spatial patterns of genetic differentiation and diversity by comparing these two sympatric and phylogenetically related species. Our results suggest that habitat fragmentation has increased genetic differentiation between Lesser Kestrel populations, following an isolation-by-distance pattern, while the population of Eurasian Kestrels is panmictic. Contrary to expectations, we did not detect significant evidence of reduced genetic variation or increased inbreeding in Lesser Kestrels. Although this study reports genetic differentiation in a species that has potential for long-distance dispersal but philopatry-limited gene flow, large enough effective population sizes and migration may have been sufficient to mitigate genetic depauperation. A serious reduction of genetic diversity in Lesser Kestrels would, therefore, only be expected after severe population bottlenecks following extreme geographic isolation.