Beyond biogeographic patterns: processes shaping the microbial landscape

Recently, microbiologists have established the existence of biogeographic patterns among a wide range of microorganisms. The focus of the field is now shifting to identifying the mechanisms that shape these patterns. Here, we propose that four processes - selection, drift, dispersal and mutation - create and maintain microbial biogeographic patterns on inseparable ecological and evolutionary scales. We consider how the interplay of these processes affects one biogeographic pattern, the distance-decay relationship, and review evidence from the published literature for the processes driving this pattern in microorganisms. Given the limitations of inferring processes from biogeographic patterns, we suggest that studies should focus on directly testing the underlying processes.     

Stoichiometry of nutrient recycling by vertebrates in a tropical stream: linking species identity and ecosystem processes

Ecological stoichiometry offers a framework for predicting how animal species vary in recycling nutrients, thus providing a mechanism for how animal species identity mediates ecosystem processes. Here we show that variation in the rates and ratios at which 28 vertebrate species (fish, amphibians) recycled nitrogen (N) and phosphorus (P) in a tropical stream supports stoichiometry theory. Mass-specific P excretion rate varied 10-fold among taxa and was negatively related to animal body P content. In addition, the N : P ratio excreted was negatively related to body N : P. Body mass (negatively related to excretion rates) explained additional variance in these excretion parameters. Body P content and P excretion varied much more among taxonomic families than among species within families, suggesting that familial composition may strongly influence ecosystem-wide nutrient cycling. Interspecific variation in nutrient recycling, mediated by phylogenetic constraints on stoichiometry and allometry, illustrates a strong linkage between species identity and ecosystem function.     

Substitution patterns in congeneric arachnid species in the northern Alps

Complementary abundance gradients of substituting congeneric arachnids along the northern margin of the Alps are described, and the possible historical and contemporary factors that have produced these distributions are explored. The intensities of activity of epigeous arachnids were determined in pitfall traps along seven altitudinal transects approximately 35 km apart in the Bavarian Alps (Germany) and in the county of Salzburg (Austria). No supraregional gradient of physical factors exists within the region investigated. Six pairs of congeners show vicariances or alternating abundance gradients. For each species pair, the abundance gradient is represented in diagrams and compared with a graphic model of substitution types. Three patterns are evident: strict vicariances, abrupt replacement in a narrow belt, and gradual substitution over a wide zone of sympatric occurrence. The different extent of range overlap suggests distinctive classes and intensities of interspecific interactions. With regard to biogeographic histories, one prevailing pattern emerged: endemic species of the eastern Alps are replaced by Eurosiberian counterparts towards the west. It appears that geographical abundance variation reflects colonization history.     

流域景观格局变化的河流生物响应研究进展

流域景观格局变化会造成河流生物群落组成、结构和功能的改变,流域景观格局变化的河流生物响应研究受到重视。本文分析了流域景观格局变化对河流生物的影响途径,归纳了流域景观格局变化的河流生物响应研究中选取的指标、方法和研究尺度,总结了主要研究结论。最后,从研究指标和尺度选取、监测点布设等方面提出了展望。     

Tree diseases and landscape processes: the challenge of landscape pathology

Forest pathology inherently involves a landscape perspective, because tree pathogens propagate according to heterogeneous spatial patterns of flow and isolation. Landscape pathology is a field that is now emerging from the transdisciplinary cooperation of forest pathologists with landscape ecologists. Here, we review recent broad-scale assessments of tree disease risk, investigations of site and host preferences for several root rot pathogens, and regional historical analyses of pathogen outbreak in plantations. Crucial topics include fragmentation effects on pathogen spread and geophysical features that predispose forest patches to disease expression. Recent methodological developments facilitate the spatially explicit analysis of reciprocal coarse-scale relationships among hosts and pathogens. Landscape pathology studies fill a significant research gap in the context of our understanding of sustainable forest management, the introduction of exotic organisms and how climate change might affect the spread of disease.     

Random processes and geographic species richness patterns: why so few species in the north?

In response to the suggestion that the latitudinal gradient in species richness is the result of stochastic processes of species distributions, we created a computer simulation program that enabled us to study random species distributions over irregularly shaped areas. Our model could not explain latitudinal variation in species richness of New World mammals and created species richness patterns that differed dramatically from previous stochastic models. The interplay of speciation and species migration in our simulation generated the highest species richness in the middle of a landmass, not in the middle of its latitudinal stretch as was found in previous one-dimensional models. The discrepancy between the results of this study and previous empirical studies suggests that the effect of randomness in species-richness distribution is on a continental scale restricted by other, dominant determinants that limit the effect of chance.     

The herpetofauna of Timor-Leste: a first report

Fieldwork conducted throughout Timor-Leste in September 2004 and July 2009 resulted in a collection or recording of 263 herpetological specimens (100 amphibians, 163 reptiles), comprising at least seven species of frogs and toads, 20 species of lizards, seven species of snakes, two species of turtles, and one species of crocodile. Among the amphibians, the most frequently encountered species were toads (Duttaphrynus melanostictus), rice paddy frogs (genus Fejervarya), and rhacophorid treefrogs (Polypedates cf. leucomystax). All three variants of rice paddy frogs encountered represent undescribed species similar to Fejervarya verruculosa from neighboring Wetar Island. Records of Fejervarya cancrivora and Fejervarya limnocharis for Timor Island are apparently errors based on misidentification. We obtained voucher specimens for a total of 147 lizards and voucher photographs only for four specimens of Varanus timorensis. Aside from geckos frequently associated with human habitations (e.g., Gehyra mutilata, Gekko gecko, Hemidactylus frenatus, Hemidactylus platyurus), we discovered an as yet undescribed species of bent-toed gecko, genus Cyrtodactylus, in the Same valley. Our specimens of Hemidactylus platyurus are the first record of this species from Timor-Leste. Commonly encountered skinks included four-fingered skinks (genus Carlia), wedge skinks (genus Sphenomorphus), and night skinks (genus Eremiascincus). Notable among the 15 snakes collected was the frequency of pitvipers (Cryptelytrops insularis), which amounted to over 25% of all snakes. Our specimen of the wolfsnake Lycodon subcinctus is the first record of this species for Timor-Leste. Based on these findings, it appears that the biodiversity of amphibians and reptiles in this remote corner of Wallacea is much greater than previously thought, particularly with respect to scincid lizards. The detail we provide in the species accounts is designed to allow the use of this report as a preliminary field guide to the amphibians and reptiles of Timor-Leste. However, survey work is ongoing.     

Distributional patterns of herpetofauna in monsoon rainforests of the Northern Territory,Australia

Abstract The herpetofauna of 50 monsoon rainforest patches in the Top End of the Northern Territory was surveyed during the dry season of 1990. This fauna contains few obligate monsoon rainforest species, many species which favour this habitat as part of a broad habitat range and a large number of species (indeed most of the regional species pool) that occasionally occur within monsoon rainforests. The taxonomic composition of species favouring monsoon rainforests is a non-random selection from the regional pool, with relatively few species in the families Agamidae and Scincidae occurring commonly in monsoon rainforests. Environmental variation among the rainforest patches sampled was portrayed by ordination, with the first axis corresponding to an environmental gradient from coastal sites to inland rocky rainforests and the second a gradient from relatively dry thickets to tall dense rainforests close to water. The distributions of herpetofauna species were depicted on this ordination space. Most frog species occurred in relatively wet rainforests and most gecko species were relatively restricted to drier rainforests. A substantial component of the herpetofauna was associated with rainforests on rocky substrate. In contrast to this relatively good association with these defined gradients, there was little apparent influence of patch size or level of disturbance on the distribution of individual species of herpetofauna. Sampling month was related to the abundance of many species, with many frog species and some snake and skink species declining (but some skink and one frog species increasing) in abundance in rainforest patches during the late dry season. This seasonal change in abundance is not due to movements from rainforest patches to adjacent vegetation types (or vice versa) but rather to total landscape (cross-habitat) changes in abundance (or detectability). The species composition of patches tended to be idiosyncratic, with substantial variability in composition, even between nearby patches of like environment. Hence it is not possible to nominate a representative rainforest herpetofauna, and indeed a classification of all quadrats (including those from rainforests, rainforest edges and adjacent habitats) based on herpetofauna species composition grouped many non-rainforest quadrats with those from rainforests. There was no rainforest edge herpetofauna assemblage. The herpetofauna from rainforests of the Northern Territory was similar to but somewhat richer than that recorded from the even more attenuated monsoon rainforest area of the Kimberley of northwestern Australia, but shared relatively few species with a sampling from monsoon rainforests from western Cape York. Frog species were more likely to be recorded across these three regions than were snake species. The number of herpetofaunal species per patch was low compared to tropical forests in northeastern Australia, Asia and central America. The long dry season of the Top End may contribute to this impoverishment. However, the small total area of monsoon rainforests in this region, the current scattered network of patches and historical fluctuations in extent and distribution of this habitat are probably at least as important.     

Phylogeographic lineages and species comparisons in conservation analyses: a case study of california herpetofauna

Many phylogeographic studies have revealed strongly diverged lineages within species that are masked by a lack of congruent morphological differentiation. To assess the extent to which the genetic component of diversity affects conservation assessments, we compared spatial patterns of endemism and conservation value for 22 species of Californian amphibians and reptiles with the 75 phylogeographic lineages that they contain. We used bioclimatic distribution modeling with environmental layers to generate 5-km spatial-resolution maps of predicted distribution for each species and lineage. We found concentrations of lineage breaks across the Central Valley, San Francisco Bay, the Sierra Nevada, and the Tehachapi and Trinity ranges. Subdivision of the ranges of species into phylogeographic units revealed novel areas of endemism. Several areas of very high conservation value for lineages were not evident in the species-level analysis. These observations illustrate the importance of considering multiple levels of biodiversity in conservation assessments.     

Vegetation patterns related to environmental factors in a Negev Desert watershed

Three strip transects, each ca 100 contiguous 0.5×1 m² quadrats, were sampled during the spring bloom of March 1981 across four surface structural units of a Negev Desert research watershed at Sede Boqer, Israel. Presence of all vascular plants was recorded. Data were subjected to detrended correspondence analysis (DCA ordination), and resulting spatial patterns of species distribution and abundance were compared. Large-scale gradients of vegetation were related to differences in soil moisture availability among the four structural units. Where micro-scale vegetation patterns were important, these correlated with rock and crevice microtopography. Species richness was influenced by high numbers of therophytes on the dry upper slope of the watershed and their reduced importance on the lower three units. Relationships between vegetational patterns and known ecosystem properties of the watershed are discussed.     

Elephant response to spatial heterogeneity in a savanna landscape of northern Tanzania

Landscape heterogeneity, namely the variation of a landscape property across space and time, can influence the distribution of a species and its abundance. Quantifying landscape heterogeneity is important for the management of semi‐natural areas through predicting species response to landscape changes, such as habitat fragmentation. In this paper, we tested whether the change in spatial heterogeneity of the vegetation cover due to farming expansion affected the distribution of the African elephant in the Tarangire‐Manyara ecosystem, northern Tanzania. Spatial heterogeneity (based on the normalized difference vegetation index) was characterized at multiple spatial scales using the wavelet transform and the intensity‐dominant scale method. Elephant distribution was estimated from time‐series aerial surveys using a kernel density function. The intensity, which relates to the contrast in vegetation cover, quantified the maximum variation in NDVI across multiple spatial scales, whereas the dominant scale, which represents the scale at which this maximum variation occurs, identified the dominant inter‐patches distance, i.e. the size of dominant landscape features. We related the dominant scale of spatial heterogeneity to the probability of elephant occurrence in order to identify: 1) the scale that maximizes elephant occurrence, and 2) its change between 1988 and 2001. Neither the dominant scale and intensity of spatial heterogeneity, nor the probability of the elephant occurrence changed significantly between 1988 and 2001. The spatial scale maximizing elephant occurrence remained constant at 7000 to 8000 m during each wet season. Compared to the findings of a recent, similar study in Zimbabwe, our results suggest that the change in the dominant scale was relatively small in Tarangire‐Manyara ecosystem and well within the critical threshold for elephant persistence. The method is a useful tool for monitoring ecosystems and their properties.     

Demographic analysis of a declining pika Ochotona collaris population: linking survival to broad-scale climate patterns via spring snowmelt patterns

1. Demographic analysis is essential in order to determine which factors, such as survival, fertility and other life-history characteristics, have the greatest influence on a population's rate of growth (lambda). 2. We used life-table response experiments (LTREs) to assess the relative importance of survival and fertility rates for an alpine lagomorph, the collared pika Ochotona collaris, using 12 years (1995-2006) of census data. The LTRE analysis was repeated for each of three subpopulations within the main study site that were defined by aspect (east, west and south). 3. Across the entire study site, the survival and fertility of adults contributed 35.6 and 43.5%, respectively, to the variance observed in the projected population growth rate, V(lambda), whereas juvenile survival contributed 20.9%. Adult survival and fertility contributed approximately equal amounts for each subpopulation when considered separately, although their rank order varied spatially. 4. Adult survival across the entire site was positively correlated to the Pacific Decadal Oscillation (PDO) with a time lag of 1 year, and was uncorrelated to adult density. The PDO was negatively correlated to the timing of spring snowmelt at our site, implicating the importance of earlier spring conditions and plant phenology on the subsequent winter survival of adults and therefore, population growth. 5. When subpopulations were analysed separately, survivals and fertilities were variously correlated to lagged PDO and adult densities, but the patterns varied spatially. Therefore, the mechanisms underlying V(lambda) can vary substantially over relatively short distances.     

Unravelling landscape variables with multiple approaches to overcome scarce species knowledge: a landscape genetic study of the slow worm

Landscape genetics was developed to detect landscape elements shaping genetic population structure, including the effects of fragmentation. Multifarious environmental variables can influence gene flow in different ways and expert knowledge is frequently used to construct friction maps. However, the extent of the migration and the movement of single individuals are frequently unknown, especially for non-model species, and friction maps only based on expert knowledge can be misleading. In this study, we used three different methods: isolation by distance (IBD), least-cost modelling and a strip-based approach to disentangle the human implication in the fragmentation process in the slow worm (Anguis fragilis), as well as the specific landscape elements shaping the genetic structure in a highly anthropized 16 km² area in Switzerland. Friction maps were constructed using expert opinion, but also based on the combination of all possible weightings for all landscape elements. The IBD indicated a significant effect of geographic distance on genetic differentiation. Further approaches demonstrated that highways and railways were the most important elements impeding the gene flow in this area. Surprisingly, we also found that agricultural areas and dense forests seemed to be used as dispersal corridors. These results confirmed that the slow worm has relatively unspecific habitat requirements. Finally, we showed that our models based on expert knowledge performed poorly compared to cautious analysis of each variable. This study demonstrated that landscape genetic analyses should take expert knowledge with caution and exhaustive analyses of each landscape element without a priori knowledge and different methods can be recommended.     

Mammal indicator species for protected areas and managed forests in a landscape conservation area of northern India

There is a realization that managed forests and other natural areas in the landscape matrix can and must make significant contributions to biodiversity conservation. Often, however, there are no consistent baseline vegetation or wildlife data for assessing the status of biodiversity elements across protected and managed areas for conservation planning, nor is there a rapid and efficient means to acquire those data. We used a unified vegetation classification and simple animal sampling design to describe the patterns of abundance of selected mammals as indicator, or characteristic, species in different vegetation types and protected areas vs. managed forest units in the Terai Conservation Area (TCA) in northern Uttar Pradesh state, India. We quantified the relative abundance of 15 mammals of conservation concern from dung counts in vegetation sampling plots within 122 sample patches in 13 vegetation types and 4 management units. Assemblages of species differed both among vegetation types and among management units. Species assemblages in the two protected areas differed strongly from those in two managed forests. Grasslands in protected areas were the most species diverse among vegetation types and had several indicator species. Protected forests were dominated by chital (Axis axis) and nilgai (Boselaphus tragocamelus) in a second species group. A third species group in open grasslands and savannas in managed forests was characterized by cattle (Bos taurus) and Indian hare (Lepus nigricollis). Protected areas clearly are the core conservation area of the TCA for their relatively high habitat value and species diversity, and their protected status minimizes human disturbance. Impacts of human use are high in managed forests, indicating their compromised value for biodiversity conservation. Our simple assessment methodology gives managers a simple way to assess the status of important mammals across landscape conservation units.     

Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data

The goal of landscape genetics is to detect and explain landscape effects on genetic diversity and structure. Despite the increasing popularity of landscape genetic approaches, the statistical methods for linking genetic and landscape data remain largely untested. This lack of method evaluation makes it difficult to compare studies utilizing different statistics, and compromises the future development and application of the field. To investigate the suitability and comparability of various statistical approaches used in landscape genetics, we simulated data sets corresponding to five landscape-genetic scenarios. We then analyzed these data with eleven methods, and compared the methods based on their statistical power, type-1 error rates, and their overall ability to lead researchers to accurate conclusions about landscape-genetic relationships. Results suggest that some of the most commonly applied techniques (e.g. Mantel and partial Mantel tests) have high type-1 error rates, and that multivariate, non-linear methods are better suited for landscape genetic data analysis. Furthermore, different methods generally show only moderate levels of agreement. Thus, analyzing a data set with only one method could yield method-dependent results, potentially leading to erroneous conclusions. Based on these findings, we give recommendations for choosing optimal combinations of statistical methods, and identify future research needs for landscape genetic data analyses.     

Spatial patterns of demography and genetic processes across the species' range: Null hypotheses for landscape conservation genetics

Compared with populations near the core of aspecies' range, edge populations tend to becharacterized by low density and high temporalvariation. Based on empirical studiesquantifying this pattern, we show thateffective population size (N_e)could be 2 to 30 times greater near the coreof the species' range than near the edge ofthe range. Hence, the rate of genetic driftmay be 2 to 30 times greater near the edge ofthe range. Despite these strong spatialpatterns in N_e, empirical findingsindicate that peripheral populations sometimeshave less but sometimes have more geneticdiversity than core populations. Our analysisindicates that this variation can be explainedby uncertainty in spatial patterns ofmigration rates. Nevertheless, our analysis:(1) provides a framework or null hypothesis forempirically assessing how spatial patterns ofmigration or selection influence large-scalespatial patterns of genetic diversity, (2)highlights the potential importance ofcontemporary processes, such as spatialpatterns in N_e (cf. historicalphenomena, such as range expansion) in thedevelopment and maintenance of large-scalespatial patterns in genetic diversity, and (3) provides new context for understanding the conservation value and vulnerability of peripheralpopulations. The conservation ofecological/evolutionary processes requiresunderstanding large scale spatial patterns ofdemographic and genetic processes such as thatdescribed here.     

A new species of Malmiana (Oligochaeta: Hirudinida: Piscicolidae) from tidepool fishes in northern California

Malmiana buthi n. sp. is described from the body and fins of the fluffy sculpin, Oligocottus snyderi, the tidepool sculpin, Oligocottus maculosus, and the woolly sculpin, Clinocottus analis, collected from tidepools at Horseshoe Cove on the Bodega Marine Reserve in Sonoma County, California. Prevalence of the leech was 32.6% on live-caught O. snyderi; mean intensity on O. snyderi was 3.3 leeches per fish, with a range from 1 to 7. The leech is not known to exceed 8 mm total length. The body is smooth, lacking papillae, tubercles, or pulsatile vesicles. Two pairs of crescentiform eyes are present on the oral sucker, and 1 pair of punctiform eyes occurs on the second annulus of the trachelosome. The caudal sucker has 14 small punctiform ocelli spaced evenly around the margin. The last 9 segments of the urosome have pairs of large punctiform ocelli both dorsally and ventrally. Body and caudal sucker pigmentation is uniformly reddish brown dorsally and ventrally with segental, lateral, unpigmented areas on both the urosome and trachelosome; pigmentation on the oral sucker is in the form of a cross. There are 5 pairs of testisacs; accessory gland cells on the atrial cornua and vector tissue are absent.