Investigating the distribution of prairie dogs in an urban landscape

Habitat fragmentation is a prevalent threat to biological diversity, and urbanization is a primary agent of fragmentation and a leading cause of species endangerment. Landscape biogeographic and local habitat characteristics can be important determinants of the distribution of species in habitat patches in urban landscapes. However, the specifics of which characteristics are most critical to maintaining biological diversity are not fully known for prairie ecosystems, especially in fragmented urban habitat. This study focuses on black-tailed prairie dogs along an urban gradient in Denver, CO. Prairie dogs have declined precipitously throughout the region and are an essential part of the prairie ecosystem, making them excellent study subjects. We identified a series of habitat fragments along a gradient of urbanization in the fully urbanized areas and south suburbs of Denver, CO, both containing and not containing prairie dogs. Local characteristics, including fragment slope and vegetative cover, and landscape characteristics, including fragment size, age and connectivity, were measured on each fragment. We used likelihood-based methods to explore which variables most accurately predicted prairie dog occurrence within our study area. Multiple factors influenced the distribution of prairie dogs in urban settings, with colony connectivity the strongest predictor of occupancy. Large and recently isolated fragments near other prairie dog colonies, flat areas and those with high graminoid cover were most likely to support prairie dog populations. Our study provides the first attempt to model prairie dog occurrence in highly fragmented urban habitat and has important implications for the management and conservation of prairie dogs.     

Fine-scale spatial genetic structure and gene flow in a small, fragmented population of Sinojackia rehderiana (Styracaceae), an endangered tree species endemic to China

Populations of Sinojackia rehderiana are highly threatened and have small and scattered distribution due to habitat fragmentation and human activities. Understanding changes in genetic diversity, the fine-scale spatial genetic structure (SGS) at different life stages and gene flow of S. rehderiana is critical for developing successful conservation strategies for fragmented populations of this endangered species. In this study, 208 adults, 114 juveniles and 136 seedlings in a 50 × 100-m transect within an old-growth forest were mapped and genotyped using eight microsatellite makers to investigate the genetic diversity and SGS of this species. No significant differences in genetic diversity among different life-history stages were found. However, a significant heterozygote deficiency in adults and seedlings may result from substantial biparental inbreeding. Significant fine-scale spatial structure was found in different life-history stages within 19 m, suggesting that seed dispersal mainly occurred near a mother tree. Both historical and contemporary estimates of gene flow (13.06 and 16.77 m) indicated short-distance gene dispersal in isolated populations of S. rehderiana. The consistent spatial structure revealed in different life stages is most likely the result of limited gene flow. Our results have important implications for conservation of extant populations of S. rehderiana. Measures for promoting pollen flow should be taken for in situ conservation. The presence of a SGS in fragmented populations implies that seeds for ex situ conservation should be collected from trees at least 19-m apart to reduce genetic similarity between neighbouring individuals.     

Genetic management of the red squirrel,Sciurus vulgaris: a practical approach to regional conservation

The progressive decline in red squirrel (Sciurus vulgaris) numbers in Wales has led to conservation and reintroduction projects being established on the island of Anglesey. The recovery of the island’s remnant wild population was initially successful, however concern remained over potential loss of genetic diversity resulting from an observed demographic bottleneck. We used mitochondrial DNA (mtDNA) control region sequences and six microsatellite loci to assess current levels of genetic variation in the population. Samples were monomorphic for control region sequences and a historic specimen from the same area carrying a different haplotype demonstrated a loss of mtDNA diversity during the last 20 years. Inclusion of other Welsh haplotypes indicated phylogeographic structure in the region, in contrast to previous UK studies. Genotyping results showed allelic diversity and heterozygosity to be less than 50% of that recorded in other UK populations, with strong evidence for a recent genetic bottleneck. A parallel reintroduction programme on Anglesey included genetic analysis of individuals during the selection of captive breeding pairs. We present analysis of sequence and microsatellite data, and subsequent management decisions taken to maximise diversity in the founder and F1 generations. Population and Habitat Viability Analysis applied to both populations modelled future levels of heterozygosity and allelic diversity. Supplementation of the remnant and reintroduced populations with translocated squirrels was simulated as a potential management tool; results support use of this strategy to reduce loss of diversity and increase survival. The limitations of applying conservation genetic theory within small-scale management projects are discussed.     

Genetic diversity and conservation of Ipomoea microdactyla (Convolvulaceae): an endemic vine from the Bahamas,Cuba, and southeastern Florida

Ipomoea microdactyla Griseb. (Convolvulaceae) is restricted to the Bahamian archipelago, Cuba, and southeastern Florida. The species is listed as a state endangered species in Florida, where it is mostly restricted to the hyperfragmented pine rockland of Miami‐Dade County. Using seven DNA microsatellite loci, we assessed levels of genetic diversity for 12 populations of this species from Andros Island in the Bahamas (six sites), Cuba (one site), and Florida (five sites). We found significantly greater mean numbers of alleles, and higher mean values for both observed and expected heterozygosity in populations from the continuous forest on Andros than those from the habitat fragments in Florida. It is unknown if these patterns of genetic diversity in the Florida populations are the result of habitat fragmentation or founder effects. The population from Cuba exhibited relatively high levels of genetic variation, suggesting that this island is a major center of diversity and dispersal for this species. It appears that hybrid introgression for I. carolina alleles within I. microdactyla individuals occurred at a single site on Andros Island. Overall, the mean inbreeding coefficient value was 0.089, suggesting low levels of inbreeding. The highest inbreeding coefficient values were mostly recorded in Florida. Two groups were revealed, one containing the populations from Florida, and the second one encompassing those from the Bahamas and Cuba. Our results highlight the negative genetic consequences of habitat fragmentation and support initiatives recently established to establish corridors to connect the remnants of the pine forest of the Miami‐Dade County.     

Freshwater icefishes (Salangidae) in the Yangtze River basin of China: Spatial distribution patterns and environmental determinants

Synopsis We surveyed 86 lakes affiliated to the Yangtze River to assess the status of natural freshwater icefishes, and to study their spatial distribution patterns and environmental relationships. Results showed that the spatial patterns of icefish diversity and the occupancy of each species related closely to the historical process of habitat fragmentation. Statistical analyses indicated that the spatial structure of the icefish assemblage significantly related to the area- and isolation-related environmental variables. These results illustrated the significant impacts of hydrological engineering (dykes and floodgates) on the historical dynamics of the icefish populations, and shed light on the essentiality and feasibility of conserving and wise using freshwater icefishes by managing suitable habitats and re-connecting the river-lake network in the Yangtze River basin.     

Genetic differentiation and relationships of populations in the Cycas balansae complex (Cycadaceae) and its conservation implications

BACKGROUND AND AIMS: The Cycas balansae complex is arguably a controversial group with regard to species delineation. Some taxonomists recognize a single polymorphic species while others distinguish five narrowly defined ones. The unresolved taxonomy has the potential to bring about significant problems for species conservation. Thus, an investigation to examine the genetic diversity and differentiation in the C. balansae complex was performed to determine the relationship of populations and to test whether the morphologically defined segregations represent genetically distinct units. METHODS: Inter-simple sequence repeat (ISSR) markers were employed to assess the genetic diversity in the C. balansae complex with a sample of 158 individuals from all extant populations in China. KEY RESULTS: ISSR markers revealed low genetic diversity in all populations studied (H(E) and H(O) averaged 0.0639 and 0.0798 at the population level, respectively). Phenetic analysis showed that the C. balansae complex grouped into five clusters closely corresponding to the narrowly defined C. balansae, C. parvula, C. shiwandashanica, C. tanqingii and C. simplicipinna. CONCLUSIONS: ISSR data suggest that the C. balansae complex has evolved into five genetically distinct units. These might be derived from a relatively widespread common ancestor through multiple vicariant events including geographical isolation resulting from the collision of the Indian plate with the Eurasian plate and from Pleistocene glaciations. In conservation, attention should be paid to each genetic unit.     

Population structure of the large Japanese field mouse, Apodemus speciosus (Rodentia: Muridae), in suburban landscape, based on mitochondrial D-loop sequences

Genetic structure of the large Japanese field mouse populations in suburban landscape of West Tokyo, Japan was determined using mitochondrial DNA control region sequence. Samples were collected from six habitats linked by forests and green tract along the Tama River, and from two forests segregated by urban areas from those continuous habitats. Thirty-five haplotypes were detected in 221 animals. Four to eight haplotypes were found within each local population belonging to the continuous landscape. Some haplotypes were shared by two or three adjacent local populations. On the other hand, two isolated habitats were occupied by one or two indigenous haplotypes. Significant genetic differentiation between all pairs of local populations, except for one pair in the continuous habitats, was found by analysis of molecular variance (amova). The geographical distance between habitats did not explain the large variance of pairwise F(ST)-values among local populations. F(ST)-values between local populations segregated by urban areas were higher than those between local populations in the continuous habitat, regardless of geographical distance. The results of this study demonstrated quantitatively that urban areas inhibit the migration of Apodemus speciosus, whereas a linear green tract along a river functions as a corridor. Moreover, it preserves the metapopulation structure of A. speciosus as well as the corridors in suburban landscape.     

The narrow endemic Scrophularia valdesii Ortega-Olivencia & Devesa (Scrophulariaceae) in the Iberian Peninsula: an evaluation of its conservation status

The aim of this study is to determine the conservation status of Scrophularia valdesii Ortega-Olivencia & Devesa, a threatened narrow endemism of the Duero Basin (central-western Spain and north-eastern Portugal, Lusitan Duriensean biogeographical sector), by using the IUCN (2001) IUCN Red List Categories and Criteria: version 3.1. IUCN Species Survival Commision. IUCN, Gland, Switzerland and Cambridge, UK. The species is listed as threatened in several Spanish compilatory works on threatened flora, such as `The Spanish Red List of Vascular Flora' and the `Atlas and Red Book of Threatened Vascular Flora of Spain', although it does not figure as such in any Portuguese document. Here we report detailed studies of its distribution, and assess its current conservation status with respect to this, the sizes of its populations, and the threats it faces. Our estimation of the size of the Iberian populations was based on our own census data from those sites at which we found the species. All censuses were performed by direct counting of all potentially reproductive individuals. Fourteen populations were found, and the total members thought to exist are 161, with a highly fragmented distribution on the Spanish–Portuguese border along the valley of the River Duero. Exhaustive bibliographical and field surveys were carried out and herbarium specimens housed in several herbaria were revised in order to determine the Extent of Occurrence and the Area of Occupancy. Based on our data, the species is classifiable as Critically Endangered and Endangered in Portugal and Spain, respectively. The risk of local population extinction is high due to its typically small local population sizes and suitable conservation strategies should be developed in order to preserve the species.     

Modelling the influence of change in fire regime on the local distribution of a Mediterranean pyrophytic plant species (Cistus salviifolius) at its northern range limit

Aims To assess the potential distribution of an obligate seeder and active pyrophyte, Cistus salviifolius, a vulnerable species in the Swiss Red List; to derive scenarios by changing the fire return interval; and to discuss the results from a conservation perspective. A more general aim is to assess the impact of fire as a natural factor influencing the vegetation of the southern slopes of the Alps. Location Alps, southern Switzerland. Methods Presence–absence data to fit the model were obtained from the most recent field mapping of C. salviifolius. The quantitative environmental predictors used in this study include topographic, climatic and disturbance (fire) predictors. Models were fitted by logistic regression and evaluated by jackknife and bootstrap approaches. Changes in fire regime were simulated by increasing the time‐return interval of fire (simulating longer periods without fire). Two scenarios were considered: no fire in the past 15 years; or in the past 35 years. Results Rock cover, slope, topographic position, potential evapotranspiration and time elapsed since the last fire were selected in the final model. The Nagelkerke R² of the model for C. salviifolius was 0.57 and the Jackknife area under the curve evaluation was 0.89. The bootstrap evaluation revealed model robustness. By increasing the return interval of fire by either up to 15 years, or 35 years, the modelled C. salviifolius population declined by 30–40%, respectively. Main conclusions Although fire plays a significant role, topography and rock cover appear to be the most important predictors, suggesting that the distribution of C. salviifolius in the southern Swiss Alps is closely related to the availability of supposedly competition‐free sites, such as emerging bedrock, ridge locations or steep slopes. Fire is more likely to play a secondary role in allowing C. salviifolius to extend its occurrence temporarily, by increasing germination rates and reducing the competition from surrounding vegetation. To maintain a viable dormant seed bank for C. salviifolius, conservation managers should consider carrying out vegetation clearing and managing wild fire propagation to reduce competition and ensure sufficient recruitment for this species.     

The effect of habitat on the range expansion of a native and an introduced bird species

Aim Range expansion across a heterogeneous landscape may depend on the habitat selected and used by the expanding species. If habitat selection influences range expansion then localities colonized by a species should contain a greater proportion of favoured habitat (and less non‐habitat) than other nearby localities not colonized. White‐winged doves (Zenaida asiatica) and Eurasian collared doves (Streptopelia decaocto) are two bird species that provide an excellent opportunity to test this hypothesis, because the geographic ranges of both species have been expanding in North America for more than two decades. Location Continental USA. Methods We used distribution data from the North American Breeding Bird Survey to test whether the landscapes occupied by each species contained a greater proportion of favoured habitat (urban land, grassland/pasture, shrub land and cropland) and a lower proportion of non‐habitat (forest land) than landscapes where doves were not found. We tested each species separately in each of three broad expansion areas, namely East, Central and West. We also compared rates of spatial spread between expansion areas and between the two species. Results As predicted, both species tended to occupy landscapes with greater proportions of urban land, shrub land and cropland but with less forest land compared with landscapes without doves, in all three expansion areas. Contrary to prediction, occupied landscapes tended to have slightly less grassland/pasture than unoccupied landscapes. Rates of spread differed between the two species and among expansion areas. Main conclusions Range expansion and the extent to which a species fills or saturates its range are influenced by the habitat ecology of the expanding species. Species colonize localities based on the availability of suitable habitat. However, the role of habitat in a species’ range expansion does depend somewhat on the greater geographical setting. Over large regional and geographical scales, range expansion (rate of spread and saturation) may proceed unevenly, suggesting that range expansion is a very dynamic and context‐specific process.     

Role of a geodatabase to assess the distribution of plants of conservation interest in a large protected area: A case study for a major national park in Italy

We use a geodatabase to investigate the distribution patterns of an important subset of floristic reports recorded for the Parco Nazionale delle Foreste Casentinesi, Monte Falterona, Campigna in the northern Apennines, Italy. This database was analysed using spatial statistical techniques and a digital elevation model. Significant relationships between species presence, sampling effort and species richness were then analysed in relation to topographical variables and to an existing vegetation map. Report-based rarefaction techniques were used to compare areas having different numbers of species recorded. Overall, the analysis shows that some areas of the park are richer in species of conservation interest than others, and that these have been more intensely investigated. Meanwhile, for other areas, botanical knowledge is scarce or even absent. This has led to clustering and redundancy of floristic data in some areas. The study confirms that the existence of a complete and up-to-date geodatabase creates a valuable resource which enables information gaps to be bridged. Such gaps often exist in biological databases for rare and narrowly distributed species. The wider application of these analyses should also give useful indications of how the incidences of these species of conservation interest are associated with particular environmental variables.     

气候变化背景下秦岭地区羚牛生境脆弱性评估及适应性保护对策

脆弱性是指物种受气候变化影响的程度,开展脆弱性评估工作有助于人类认识气候变化对野生动物的影响,为制定野生动物适应气候变化的保护对策提供科学依据。采用最大熵模型评估气候变化背景下秦岭地区羚牛(Budorcas taxicolor bedfordi)生境脆弱性。结果表明：(1)当前秦岭地区羚牛适宜生境总面积为6473 km²,到2050s年,预测秦岭地区羚牛适宜生境总面积为4217 km²,减少34.85%,羚牛适宜生境将向更高海拔地区转移,转移约210 m;(2)已建保护区覆盖49.82%当前羚牛适宜生境,尚有3248 km²的适宜生境处于保护区之外;到2050s年,保护区覆盖了43.87%适宜生境,尚有2367 km²的适宜生境未被保护;(3)到2050s年,当前分布在太白县、佛坪县、洋县和宁陕县等地区的3490 km²羚牛适宜生境将会成为生境脆弱区域,丧失53.92%;(4)分布在秦岭核心区域的2983 km²当前和2050s年保持不变适宜生境,将成为羚...     

Forest fragmentation, the decline of an endangered primate, and changes in host-parasite interactions relative to an unfragmented forest

Forest fragmentation may alter host-parasite interactions in ways that contribute to host population declines. We tested this prediction by examining parasite infections and the abundance of infective helminths in 20 forest fragments and in unfragmented forest in Kibale National Park, Uganda. Over 4 years, the endangered red colobus (Procolobus rufomitratus) declined by 20% in fragments, whereas the black-and-white colobus (Colobus guereza) in fragments and populations of both colobines in unfragmented forest remained relatively stable. Seven nematodes (Strongyloides fulleborni, Strongyloides stercoralis, Oesophagostomum sp., an unidentified strongyle, Trichuris sp., Ascaris sp., and Colobenterobius sp.), one cestode (Bertiella sp.), and three protozoans (Entamoeba coli, Entamoeba histolytica/dispar, and Giardia sp.) were detected. Infection prevalence and the magnitude of multiple infections were greater for red colobus in fragmented than in unfragmented forest, but these parameters did not differ between forests for black-and-white colobus. Infective-stage colobus parasites occurred at higher densities in fragmented compared with unfragmented forest, demonstrating greater infection risk for fragmented populations. There was little evidence that the nature of the infection was related to the size of the fragment, the density of the host, or the nature of the infection in the other colobine, despite the fact that many of the parasites are considered generalists. This study suggests that forest fragmentation can alter host-parasite dynamics and demonstrates that such changes can correspond with changes in host population size in forest fragments.     

Genetic structure and AFLP variation of remnant populations in the rare plant Pedicularis palustris (Scrophulariaceae) and its relation to population size and reproductive components

We investigated plant reproduction in relation to genetic structure, population size, and habitat quality in 13 populations of the rare biennial plant Pedicularis palustris with 3-28500 flowering individuals. We used AFLP (amplified fragment length polymorphism) profiles to analyze genetic similarities among 129 individuals (3-15 per population). In a cluster analysis of genetic similarities most individuals (67%) were arranged in population-specific clusters. Analysis of molecular variance indicated significant genetic differentiation among populations and among and within subpopulations (P < 0.001). Gene flow (N(e) m) was low (0.298). On average, plants produced 55 capsules, 17 seeds per fruit, and 42 seedlings in the following growing season. The number of seeds per capsule was independent of population size and of genetic variability. In contrast, the number of capsules per plant (P < 0.05) and the number of seedlings per plant (P < 0.05) were positively correlated with population size. The relation between population size and the number of seeds per plant was not significant (P = 0.075). The number of capsules and of seeds and seedlings per plant (P < 0.01) were positively correlated with genetic variability. Genetic variability was independent of actual population size, suggesting that historical population processes have to be taken into account, too. Stepwise multiple regressions revealed additional significant relationships of habitat parameters (soil pH, C:N ratio), vegetation composition, and standing crop on reproductive components. We conclude that populations of P. palustris are genetically isolated and that reproductive success most likely is influenced by population size, genetic variability, and habitat quality. Management strategies such as moderate grazing, mowing, and artificial gene flow should endeavor to increase population size as well as genetic variation.     

鹅掌楸贵州烂木山居群的微卫星遗传多样性及空间遗传结构

濒危植物鹅掌楸(Liriodendron chinense)目前仅零散分布于我国亚热带及越南北部地区, 残存居群生境片断化较为严重。研究濒危植物片断化居群的遗传多样性及小尺度空间遗传结构(spatial genetic structure)有助于了解物种的生态进化过程以及制定相关的保育策略。本研究采用13对微卫星引物, 对鹅掌楸的1个片断化居群进行了遗传多样性及空间遗传结构的研究, 旨在揭示生境片断化条件下鹅掌楸的遗传多样性及基因流状况。研究结果表明: 鹅掌楸烂木山居群内不同生境斑块及不同年龄阶段植株的遗传多样性水平差异不显著(P>0.05), 居群内存在寨内和山林2个遗传分化明显的亚居群。烂木山居群个体在200 m以内呈现显著的空间遗传结构, 而2个亚居群内的个体仅在20 m的距离范围内存在微弱或不显著的空间遗传结构。鹅掌楸的空间遗传结构强度较低(Sp = 0.0090), 且寨内亚居群的空间遗传结构强度(Sp = 0.0067)要高于山林亚居群(Sp = 0.0053)。鹅掌楸以异交为主, 种子较轻且具翅, 借助风力传播, 在一定程度上降低了空间遗传结构的强度。此外, 居群内个体密度及生境特征也对鹅掌楸的空间遗传结构产生了一定影响。该居群出现显著的杂合子缺失, 近交系数(F_IS)为0.099 (P < 0.01), 表明生境片断化的遗传效应正逐渐显现。因此, 对鹅掌楸的就地保护应注意维护与强化生境的连续性, 促进基因交流。迁地保护时, 取样距离应不小于20 m, 以涵盖足够多的遗传变异。     

Response to De Silva et al. (2007): Endemic freshwater finfish of Asia: distribution and conservation status

De Silva et al . (2007) present an overview of the distribution and conservation status of the endemic freshwater fish of Asia. Within that review they use data from the IUCN Red List of Threatened Species™ (2006) to conduct an analysis of the conservation status of those endemic fish species. Their analysis is incorrect and provides a very misleading impression of the level of threat to Asian freshwater fish and to freshwater fish at the global scale. The errors stem from a misinterpretation of the data presented on the IUCN Red List. The sources of errors are discussed below and the opportunity is taken to clarify what the information on the IUCN Red List represents.     

Alpine glacial relict species losing out to climate change: The case of the fragmented mountain hare population (Lepus timidus) in the Alps

Alpine and Arctic species are considered to be particularly vulnerable to climate change, which is expected to cause habitat loss, fragmentation and—ultimately—extinction of cold‐adapted species. However, the impact of climate change on glacial relict populations is not well understood, and specific recommendations for adaptive conservation management are lacking. We focused on the mountain hare (Lepus timidus) as a model species and modelled species distribution in combination with patch and landscape‐based connectivity metrics. They were derived from graph‐theory models to quantify changes in species distribution and to estimate the current and future importance of habitat patches for overall population connectivity. Models were calibrated based on 1,046 locations of species presence distributed across three biogeographic regions in the Swiss Alps and extrapolated according to two IPCC scenarios of climate change (RCP 4.5 & 8.5), each represented by three downscaled global climate models. The models predicted an average habitat loss of 35% (22%–55%) by 2100, mainly due to an increase in temperature during the reproductive season. An increase in habitat fragmentation was reflected in a 43% decrease in patch size, a 17% increase in the number of habitat patches and a 34% increase in inter‐patch distance. However, the predicted changes in habitat availability and connectivity varied considerably between biogeographic regions: Whereas the greatest habitat losses with an increase in inter‐patch distance were predicted at the southern and northern edges of the species’ Alpine distribution, the greatest increase in patch number and decrease in patch size is expected in the central Swiss Alps. Finally, both the number of isolated habitat patches and the number of patches crucial for maintaining the habitat network increased under the different variants of climate change. Focusing conservation action on the central Swiss Alps may help mitigate the predicted effects of climate change on population connectivity.