A simple method to estimate the probable distribution of species

Species distribution models (SDMs) are broadly used to predict species distributions from available presence data. However, SDMs results have been criticized for several reasons mainly related to two basic characteristics of most SDMs: 1) general lack of reliable species absence information, 2) the frequent use of an arbitrary geographical extent (GE) or accessible area of the species. These impediments have motivated us to generate a procedure called niche of occurrence (NOO). NOO provides the probable distribution of species (realized niche) relying solely on partial information about presence of species. It operates within a natural geographical extent delimited by available observations and avoids using misleading thresholds to obtain binary presence–absence estimations when the species prevalence is unknown. In this study the main characteristics of NOO are presented, comparing its performance with other recognized and more complex SDMs by using virtual species to avoid the omnipresent error sources of real data sets.     

Ecological principles of species distribution models: the habitat matching rule

Most species distribution models (SDMs) assume that habitats are closed, stable and without competition. In that environmental context, it is ecologically correct to assume that members of a species will be distributed in direct relation to the suitability of the habitat, that is, according to the so‐called habitat matching rule. This paper examines whether it is possible to maintain the assumption of the habitat matching rule in the following circumstances: (1) when habitats are connected and organisms can move between them, (2) when there are disturbances and seasonal cycles that generate instability, and (3) when there is inter‐specific and intra‐specific competition. Here I argue that it is possible as long as the following aspects are taken into account. In open habitats at equilibrium, in which habitat selection and competition operate, the habitat matching rule can be applied in some conditions, while competition tends to homogenize the species distribution in other environmental contexts. In the latter case, two methods can be used to incorporate these effects into SDMs: new parameters can be incorporated into the response functions, or the occurrence of proportions of categories of individuals (adult/young, male/female, or dominant/subordinate species in guilds) can be used instead of the occurrence of organisms. The habitat matching rule is not fulfilled in non‐equilibrium environments. The solution to this problem lies in the design of SDMs with two strategies that depend on scale. Locally, the disequilibrium can be encapsulated using average environmental conditions, with sufficiently large cells (in the case of metapopulations) and/or long enough sampling periods (in the case of seasonal cycles). At coarse scales, the use of presence‐only models can in some cases avoid the destabilizing effect of catastrophic historical processes. The matching law is a strong assumption of SDMs because it is based on population ecology theory and the principle of evolution by natural selection.     

Habitat heterogeneity drives bird species richness,nestedness and habitat selection by individual species in fluvial wetlands of the Paraná River,Argentina

We assessed the relationship between habitat heterogeneity and bird species richness and composition within wetlands of the floodplain of the Middle Paraná River, Argentina. Given the high habitat heterogeneity in these wetland systems, we sought to determine whether (i) there was a positive relationship between bird species richness and habitat heterogeneity; (ii) whether bird species richness was associated with certain types of individual habitat types; (iii) whether there was a pattern of species nestedness and turnover between sites as a function of habitat heterogeneity and composition, respectively; and (iv) whether individual species exhibited associations with habitat heterogeneity. Point counts were used to survey birds at 60 sites. We estimated the area of eight habitat types found within a 200‐m radius from the centre of each site and calculated number and Pielou's evenness of habitat types. These indices, together with area proportion of each habitat type, were used as explanatory factors of bird species richness in linear regression models. Habitat heterogeneity per se rather than area of individual habitat types was a more important predictor of species richness in these fluvial wetlands. Sites with more habitat types supported more bird species. Results showed that individual bird species were associated with different habitat types and, therefore, sites that contained more habitat types contained more species. Number of habitat types accounted for species nestedness between sites whereas composition of habitat types accounted for species turnover between sites. Results suggest that selection of heterogeneous sites by individual species could help explain the positive heterogeneity–species richness relationship. Our findings highlight the importance of habitat heterogeneity per se resulting from flood disturbances in maintaining bird richness in fluvial systems.     

Spatial and temporal dynamics of habitat selection across canopy gradients generates patterns of species richness and composition in aquatic beetles

Abstract 1. Colonisation is a critical ecological process influencing both population and community level dynamics by connecting spatially discrete habitat patches. How communities respond to both natural and anthropogenic disturbances, furthermore, requires a basic understanding of how any environmental change modifies colonisation rates. For example, disturbance‐induced shifts in the quantity of forest cover surrounding aquatic habitats have been associated with the distribution and abundance of numerous aquatic taxa. However, the mechanisms generating these broad and repeatable field patterns are unclear. 2. Such patterns of diversity could result from differential spatial mortality post colonisation, or from colonisation alone if species select sites non‐randomly along canopy coverage gradients. We examined the colonisation/oviposition dynamics of aquatic beetles in experimental ponds placed under both open and closed forest canopies. 3. Canopy coverage imposed a substantial behavioural filter on the colonisation and reproduction of aquatic beetles representing multiple trophic levels, and resulted in significantly higher abundance, richness, and oviposition activity in open canopy ponds. These patterns strengthened overtime; although early in the experiment, the most abundant beetle had similar abundance in open and closed ponds. However, its abundance subsequently declined and then most other species heavily colonised open canopy ponds. 4. The primary response of many aquatic species to disturbances that generate canopy coverage gradients surrounding aquatic ecosystems is behavioural. The magnitude of the colonisation responses reported here rivals, if not exceeds, those produced by predators, suggesting that aquatic landscapes are behaviourally assessed and partitioned across multiple environmental gradients. The community level structure produced solely by selective colonisation, is predicted to strongly modify how patch area and isolation affect colonisation rates and the degree to which communities are linked by the flux of individuals and species.     

The bark and ambrosia beetles (Curculionidae, Scolytinae) of Cocos Island, Costa Rica and the role of mating systems in island zoogeography

Cocos Island is a small oceanic island midway between Costa Rica and the Galápagos Archipelago; about 2 Myr in age, it is the only tropical oceanic island in the eastern Pacific with tropical wet forest. We identified several hundred bark beetle specimens collected during recent expeditions by INBio, the National Biodiversity Institute of Costa Rica, and re-examined all specimens from earlier collections. We report 19 species in ten genera, seven or eight of which are endemic, making scolytines the largest group of beetles known from the island. We describe as new Pycnarthrum pseudoinsulare , Xyleborinus cocoensis , and Xyleborus sparsegranulosus , resurrect Xyleborus bispinatus as separate from X. ferrugineus , and report six other species as new to Cocos Island. Three-quarters of the scolytines reproduce by brother–sister mating, and we argue that inbreeders are superior island colonists because they are less affected than are outbreeders by problems of mate location and inbreeding depression. The fauna and flora of Cocos Island arrived by dispersal and human transport. We examine natural colonization patterns for the fauna, using the distributions of the relatives of island endemics: most colonization came from the Americas, but the closest relatives to some endemics are found on Caribbean or Galápagos islands. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 729–743.     

Coral in Alaska: distribution,abundance, and species associations

To help identify fishery management actions that minimize the adverse impacts of fishing activities on corals in Alaska, the distribution and abundance of corals were analyzed based on trawl survey data collected during 1975–1998. We also examined the species of commercially managed fish that are associated with coral. Soft corals, primarily Gersemia sp. (=Eunephthya sp.), were the most frequently encountered corals in the Bering Sea. In the Aleutian Islands gorgonian corals, primarily in the genera Callogorgia, Primnoa, Paragorgia, Thouarella, and Arthrogorgia were the most common corals. In the Gulf of Alaska, gorgonian corals, primarily in the genera Callogorgia and Primnoa, and cup corals, primarily `Scleractinia unidentified', occurred most frequently. The Aleutian Islands area appears to have the highest abundance and diversity of corals. Some fish groups are associated with particular types of coral. Rockfish (Sebastes spp. and Sebastolobus alascanus) and Atka mackerel (Pleurogrammus monopterygius) were the most common fish captured with gorgonian, cup, and hydrocorals, whereas flatfish and gadids were the most common fish captured with soft corals.     

Pentaschistis (Poaceae) diversity in the Cape mediterranean region: habitat heterogeneity and climate stability

Aim To evaluate the role of habitat heterogeneity on species richness and turnover in the mega species‐rich Cape Floristic Region (Cape), the mediterranean region of southern Africa. Location The Cape and Drakensberg regions of southern Africa. Methods Bioclimatic data were used to estimate habitat amount and habitat heterogeneity in the Cape and Drakensberg regions; these data were then used to explain the patterns of species diversity in the Pentaschistis clade (Poaceae) in these two regions. Habitat variables were used to create ‘bioclimatic units’ to characterize 1′× 1′ cells in southern Africa and to describe the niches of species. Using these bioclimatic units, the niche and range sizes of species in the two regions were compared. A phylogram was used to test for age and lineage effects. Results Pentaschistis species diversity and turnover are higher in the Cape than the Drakensberg. There is no significant difference in the habitat amount and heterogeneity between the two regions. Species occupy the same range of estimated niche sizes, yet there are significantly more range‐restricted Pentaschistis species in the Cape. Main conclusions The roles of age‐ and lineage‐related effects are rejected; biodiversity differences lie in the regions. Current macrohabitat does not explain the differences in biodiversity between the two regions. The larger number of range‐restricted species in the Cape cannot be explained by dispersal mechanism or the occupation of range‐restricted habitats. Species of Pentaschistis and other Cape clades share characteristics associated with species from historically climatically stable areas, and palaeoclimatic and palaeontological evidence indicates the Cape climate has been more stable than the Drakensberg climate throughout the Pleistocene. We conclude that the corresponding lack of extinction might have allowed an accumulation of species in the Cape. Similar climatic and biological evidence for the south‐west Australian Floristic and Mediterranean regions indicate that the same mechanism might explain the high species richness of these mediterranean regions.     

Effects of environment,habitat configuration and forest continuity on the distribution of forest plant species

In present day European landscapes many forest plant species are restricted to isolated remnants of a formerly more or less continuous forest cover. The two major objectives of this study were (1) to determine the relative importance of habitat quality (mainly in terms of soil parameters), habitat configuration (patch size and isolation) and habitat continuity for the distribution of herbaceous forest plant species in a highly fragmented landscape and (2) to examine if groups of species with different habitat requirements are affected differently. Deciduous forest patches in northwestern Germany were surveyed for the presence of a large set of forest species. For each patch, habitat quality, configuration and continuity were determined. Data were analysed by Redundancy Analysis with variation partitioning for effects on total species composition and multivariate logistic regression for effects on individual species, for two different data sets (base‐rich and base‐poor forest patches). Overall, we found strong effects of habitat quality (particularly of soil pH, water content and topographic heterogeneity in the base‐rich forest patches; and of calcium content and disturbance in the base‐poor patches), but only relatively weak effects of habitat configuration and habitat continuity. However, a number of species were positively affected by patch area and negatively affected by patch isolation. Furthermore, the relative importance of habitat configuration tended to be higher for species predominantly growing in closed forests compared to species occurring both in the forest and in the open landscape.     

Recruitment hotspots and bottlenecks mediate the distribution of corals on a Caribbean reef

Recruitment hotspots are locations where organisms are added to populations at high rates. On tropical reefs where coral abundance has declined, recruitment hotspots are important because they have the potential to promote population recovery. Around St. John, US Virgin Islands, coral recruitment at five sites revealed a hotspot that has persistent for 14 years. Recruitment created a hotspot in density of juvenile corals that was 600 m southeast of the recruitment hotspot. Neither hotspot led to increased coral cover, thus revealing the stringency of the demographic bottleneck impeding progression of recruits to adult sizes and preventing population growth. Recruitment hotspots in low-density coral populations are valuable targets for conservation and sources of corals for restoration.     

Factors determining mammal species richness on habitat islands and isolates: habitat diversity, disturbance, species interactions and guild assembly rules

• 1 For over three decades the equilibrium theory of island biogeography has galvanized studies in ecological biogeography. Studies of oceanic islands and of natural habitat islands share some similarities to continental studies, particularly in developed regions where habitat fragmentation results from many land uses. Increasingly, remnant habitat is in the form of isolates created by the clearing and destruction of natural areas. Future evolution of a theory to predict patterns of species abundance may well come from the application of island biogeography to habitat fragments or isolates.
• 2 In this paper we consider four factors other than area and isolation that influence the number and type of mammal species coexisting in one place: habitat diversity, habitat disturbance, species interactions and guild assembly rules. In all examples our data derive from mainland habitat, fragmented to differing degrees, with different levels of isolation.
• 3 Habitat diversity is seen to be a good predictor of species richness. Increased levels of disturbance produce a relatively greater decrease in species richness on smaller than on larger isolates. Species interactions in the recolonization of highly disturbed sites, such as regenerating mined sites, is analogous to island colonization. Species replacement sequences in secondary successions indicate not just how many, but which species are included. Lastly, the complement of species established on islands, or in insular habitats, may be governed by guild assembly rules. These contributions may assist in taking a renewed theory into the new millennium.

     

Phylogeny of Hypselodoris (Nudibranchia: Chromodorididae) with a review of the monophyletic clade of Indo-Pacific species, including descriptions of twelve new species

This work provides an account of the systematics and phylogeny of Hypselodoris . Aspects of the morphology of 42 species are described and the systematic status of an additional 11 species is discussed. Twelve new species are described: Hypselodoris alboterminata, H. bertschi, H. bollandi, H. fucata, H. iacula, H. insulana, H. krakatoa, H. paulinae, H. reidi, H. rudmani, H. violabranchia and H. zephyra. A phylogenetic analysis supports the monophyly of Hypselodoris and Risbecia . Two distinct clades of Hypselodoris are present. One contains species from the Atlantic and eastern Pacific while the other contains species limited to the Indo-Pacific tropics and adjacent temperate regions. Species from the Atlantic and eastern Pacific are bluish in body colour and have a plesiomorphically large receptaculum seminis while Indo-Pacific taxa are variably coloured and all have a minute receptaculum seminis. The distribution and size of mantle glands provides a wealth of morphological characters. With few exceptions, mantle glands vary in closely related species and are important for distinguishing members of smaller clades. Mantle gland distribution is therefore useful in identifying preserved material that is difficult to identify to species in the absence of the pigment of living specimens. Similar colour patterns found in sympatric species of Hypselodoris appear to be a result of both common descent and convergence between less closely related lineages. Biogeographic distributions of sister taxa provide several examples of vicariance. Examination of these cases shows that no single vicariant pattern is present, but vicariance appears to occur at the margins of the Indo-Pacific rather than centrally. Some vicariance occurs even within archipelagos such as the Hawaiian Islands. These cases largely refute the generality of the hypothesis of Springer (1982), that Pacific Plate and Australasian Plate endemic sister taxa should predominate.     

Species delimitation of common reef corals in the genus Pocillopora using nucleotide sequence phylogenies, population genetics and symbiosis ecology

Stony corals in the genus Pocillopora are among the most common and widely distributed of Indo-Pacific corals and, as such, are often the subject of physiological and ecological research. In the far Tropical Eastern Pacific (TEP), they are major constituents of shallow coral communities, exhibiting considerable variability in colony shape and branch morphology and marked differences in response to thermal stress. Numerous intermediates occur between morphospecies that may relate to extensive hybridization. The diversity of the Pocillopora genus in the TEP was analysed genetically using nuclear ribosomal (ITS2) and mitochondrial (ORF) sequences, and population genetic markers (seven microsatellite loci). The resident dinoflagellate endosymbiont (Symbiodinium sp.) in each sample was also characterized using sequences of the internal transcribed spacer 2 (ITS2) rDNA and the noncoding region of the chloroplast psbA minicircle. From these analyses, three symbiotically distinct, reproductively isolated, nonhybridizing, evolutionarily divergent animal lineages were identified. Designated types 1, 2 and 3, these groupings were incongruent with traditional morphospecies classification. Type 1 was abundant and widespread throughout the TEP; type 2 was restricted to the Clipperton Atoll; and type 3 was found only in Panama and the Galapagos Islands. Each type harboured a different Symbiodinium'species lineage' in Clade C, and only type 1 associated with the 'stress-tolerant'Symbiodinium glynni (D1). The accurate delineation of species and implementation of a proper taxonomy may profoundly improve our assessment of Pocillopora's reproductive biology, biogeographic distributions, and resilience to climate warming, information that must be considered when planning for the conservation of reef corals.     

Connections between ecology,biogeography, and paleobiology: Relationship between local abundance and geographic distribution in fossil and recent molluscs

Summary We used data on Contemporary and Pleistocene molluscs at one site in the Gulf of California to evaluate and extend earlier ideas about the relationship between local abundance and geographic distribution. For each species whose shells occurred in one Recent and two Pleistocene deposits, we measured its abundance in the sample and relative latitudinal position within its contemporary geographic range. Species near the edges of their ranges showed uniformly low abundances, whereas those near the centres exhibited a wide range of abundances. Species near the edges of their ranges also appear to have exhibited greater changes in abundance, including more colonization and extinction events, between the Pleistocene interglacial sample and the Recent one. The constraint of location in the geographic range on maximal local and regional abundance appears to offer an example of a connection between patterns and processes on local, regional, and geographical scales. Characteristics of community structure, such as relative abundance of individual species and frequency of local co-existence of multiple species, may be influenced by the location of the sample site with respect to the geographic ranges of the constituent species. These results demonstrate emergent, statistical features of population ecology and community organization that are manifest over geographic space and evolutionary time.     

Factors affecting the distribution of vascular plants, springtails, butterflies and birds on small tropical islands

Aim

The primary objective of our study was to examine the factors affecting the distribution of vascular plants, springtails, butterflies and birds on small tropical islands to understand how different groups of organisms with distinct biological traits respond to biogeographical variables, such as island area.

Location

The Republic of Singapore (103°50′E, 1°20′N) located at the southern tip of Peninsular Malaysia.

Methods

Seventeen islands were surveyed for vascular plants, springtails, butterflies and birds. Correlation analysis, simple linear and multiple regression analyses and the nestedness index were used to test the hypotheses that (1) area is the best predictor of species/genus richness at both the community and specific/generic levels; (2) there is no correlation between population density and island area; and (3) species/genera are distributed as nested subsets.

Results

Area was the most significant factor in determining the island distribution of springtails, butterflies and birds at both the community and specific/generic levels, although there were disparate responses to the biogeographical variables between the three taxonomic groups, as well as between common species within each group. Individual species displayed disparate responses to biogeographical variables, suggesting that patterns of distribution at the community level may not be a good indicator of the population dynamics of individual species/genera. Plant species richness did not show any correlation with any of the tested variables. Population densities of springtails, butterflies and birds were positively correlated with area, contradicting the assumption of the equilibrium theory of island biogeography that population density of island species is independent of area. Population densities of plants showed no correlation with any of the tested biogeographical variables. Vascular plant, springtail, butterfly and bird communities on the islands showed significant patterns of nestedness, indicating there may be species/genus‐specific responses to biogeographical variables.

Main conclusions

We conclude that although area was the most important factor affecting the island distribution of springtails, butterflies and birds, conservation planning must take into consideration how target taxonomic groups respond to biogeographical variables, instead of relying on general principles (e.g. those derived from the equilibrium theory). On a local scale, in order to preserve the island biodiversity of Singapore, the highest priority should be given to preserving the larger islands (e.g. Pulau Ubin) which not only have higher numbers of species, but also species that are absent on smaller islands.