Pattern and process in the biogeography of subterranean amphipods

The comparative data from studies of two ‘superfamily’ groups with large numbers of subterranean taxa, the exclusively freshwater Crangonyctoidea and the predominately marine Hadzioidea, support the hypothesis that distributional patterns and evolutionary processes of stygobiont amphipods are closely linked and that the former can be a useful indicator of the latter. Three major biogeographic patterns are indicated by the distribution of subterranean species in these groups, each apparently reflecting a particular mode of origin: (1) freshwater stygobionts (limnostygobionts) derived from epigean freshwater ancestors through colonizations probably influenced by adaptive shifts, or assisted by stream capture and spring failure; (2) freshwater stygobionts derived from marine/brackish water ancestors by stranding during regression of marine embayments; and (3) marine/brackish water stygobionts (thalassostygobionts) derived from epigean marine/brackish water ancestors through adaptive shifts possibly in concert with fluctuating sea levels.     

Hypothesis testing in biogeography

Often, biogeography is applied only as a narrative addition to phylogenetic studies and lacks scientific rigour. However, if research questions are framed as hypotheses, biogeographical scenarios become testable. In this review, we explain some problems with narrative biogeography and show how the use of explicit hypotheses is changing understanding of how organisms came to be distributed as they are. Developing synergies between biogeography, ecology, molecular dating and palaeontology are providing novel data and hypothesis-testing opportunities. New approaches are challenging the classic 'Gondwana' paradigm and a more complicated history of the Southern Hemisphere is emerging, involving not only general drivers such as continental drift and niche conservatism, but also drowning and re-emergence of landmasses, biotic turnover and long-distance colonization.     

Urban biogeography

Summary Species richness and abundance of Diptera and Coleoptera were assessed in nine city parks in Cincinnati, Ohio, USA. Species richness for each park was related to the area of the park in a manner predicted by island biogeography theory. The z values for the Diptera and Coleoptera were 0.235 and 0.222 respectively. These values are somewhat higher than expected for continental islands and suggest that the Diptera and Coleoptera in these parks are as isolated as many species which occur on true oceanic islands.A stepwise multiple regression was conducted, regressing species richness against several aspects of habitat diversity in the parks. It was found that area alone was the best predictor of species richness. This result, coupled with data on population sizes, suggests that increased area acts primarily to reduce extinction rates rather than to provide new habitats for specialized species.     

Biotic element analysis in biogeography

Biotic element analysis is an alternative to the areas-of-endemism approach for recognizing the presence or absence of vicariance events in a given region. If an ancestral biota was fragmented by vicariance events, biotic elements or clusters of distribution areas should emerge. We propose a statistical test for clustering of distribution areas based on a Monte Carlo simulation with a null model that considers the spatial autocorrelation in the data. The hypothesis tested is that the observed degree of clustering of ranges can be explained by the range size distribution, the varying number of taxa per cell, and the spatial autocorrelation of the occurrences of a taxon alone. A method for the delimitation of biotic elements which uses model-based Gaussian clustering is introduced. We demonstrate our methods and show the importance of grid size by means of a case study, an analysis of the distribution patterns of southern African species of the weevil genus Scobius. The example highlights the difficulties in delimiting areas of endemism if dispersal has occurred and illustrates the advantages of the biotic element approach.     

Calanoid copepod biogeography in New Zealand

The distribution of four calanoid copepod species of Boeckella in New Zealand are mapped and described. An explanation of their distribution patterns based on panbiogeographic methods is compared to an explanation based on dispersalist concepts. The panbiogeographic explanation is simpler, and is consistent with explanation of distribution patterns among other genera of plants, invertebrates, amphibians and birds. This revised version was published online in July 2006 with corrections to the Cover Date.     

Phylogenetic approaches in coevolution and biogeography

I review phylogenetic approaches to problems in coevolution and biogeography, illustrating with case studies. In coevolution, genealogical trees are essential in differentiating between ancient and recent associations, in identifying cospeciation events, and in studying host-switching patterns. Cospeciating associations are of particular interest because they allow powerful tests of molecular clocks and accurate comparison of evolutionary rates across groups of organisms. In biogeography, phylogenies can help reconstruct the distribution history of individual groups and identify past geological events that have affected the evolution of entire communities. Parsimony analysis in coevolution and biogeography should be based on identification of different types of events, each of which is associated with a specific cost. Similar event-based methods are applicable to coevolutionary and biogeographic inference, as well as in the mapping of gene trees onto organism trees. The discussed examples span a variety of organisms and spatiotemporal scales: primate pin worms, HIV, pocket gophers and their lice, aphids and their bacterial symbionts, gall wasps and their host plants, the root of the tree of life, the historical biogeography of the Holarctic, and the geographical origin of our own species.     

Sympatry inference and network analysis in biogeography

A new approach for biogeography to find patterns of sympatry, based on network analysis, is proposed. Biogeographic analysis focuses basically on sympatry patterns of species. Sympatry is a network (= relational) datum, but it has never been analyzed before using relational tools such as Network Analysis. Our approach to biogeographic analysis consists of two parts: first the sympatry inference and second the network analysis method (NAM). The sympatry inference method was designed to propose sympatry hypothesis, constructing a basal sympatry network based on punctual data, independent of a priori distributional area determination. In this way, two or more species are considered sympatric when there is interpenetration and relative proximity among their records of occurrence. In nature, groups of species presenting within-group sympatry and between-group allopatry constitute natural units (units of co-occurrence). These allopatric units are usually connected by intermediary species. The network analysis method (NAM) that we propose here is based on the identification and removal of intermediary species to segregate units of co-occurrence, using the betweenness measure and the clustering coefficient. The species ranges of the units of co-occurrence obtained are transferred to a map, being considered as candidates to areas of endemism. The new approach was implemented on three different real complex data sets (one of them a classic example previously used in biogeography) resulting in (1) independence of predefined spatial units; (2) definition of co-occurrence patterns from the sympatry network structure, not from species range similarities; (3) higher stability in results despite scale changes; (4) identification of candidates to areas of endemism supported by strictly endemic species; (5) identification of intermediary species with particular biological attributes.     

Latitudinal and longitudinal barriers in global biogeography

Due to changes in climate and continental arrangement, plant and animal assemblages faced different dispersal barriers at different moments in Earth's history. It is generally accepted that groups which diversified during times of Gondwanan-Laurasian separation show different distribution patterns from those of more recent origin. Here I present principal component-derived maps for two globally distributed groups, with ca 1000 species each. Gymnosperm assemblages perfectly illustrate the existence of southern and northern components, corresponding to the Gondwanan and Laurasian temperate floras at the time when angiosperms started becoming dominant in the tropics, thus imposing a latitudinal barrier. Bat (chiropteran) assemblages indicate that the major biogeographical barrier in their Cenozoic dispersal was the longitudinal separation between the Old and New World.     

Moss biogeography in the Tasman Sea region

Abstract

Panbiogeographic track analysis is applied to the distribution of several groups of mosses which occur in the New Zealand region. The analysis highlights areas of biogeographic interest (nodes) in the New Zealand region as follows: 1. New Guinea, 2. New Caledonia, 3. New South Wales/Queensland border in Australia, 4. northern New Zealand, 5. Rapa Island, 6. subantarctic New Zealand.

New Zealand is connected to these nodes by the following standard tracks: 1. New Guinea—New South Wales/Queensland border—Tasmania—subantarctic New Zealand, 2. New Guinea—New Caledonia—New Zealand—subantarctic New Zealand, 3. a central Tasman Sea transversal track; New South Wales/Queensland border—New Caledonia. Rapa Island is connected to the Tasman region by northern New Zealand and New Caledonia.     

Pattern recognition analysis of in vivo enzyme-substrate fluorescence velocities in microorganism detection and identification

A spectrometric technique is presented that combines most of the important criteria necessary for efficient detection and identification of microorganisms. These criteria include simplicity of experimental design, various degrees of sensitivity and selectivity, convenience, and total reaction times of less than 15 min. The study takes advantage of the inherent extracellular enzymes present in living as opposed to dead, non-enzyme-producing organisms. Sequentially these are harnessed in in vivo reactions with a substrate containing a select organic functional group that is known to be cleaved or hydrolyzed by a certain enzyme. The substrate is tailored so that one of the products can be induced to fluoresce, and by using a conventional spectrofluorimeter the rate at which the fluorescence appears can be recorded. By subjecting the same bacterial sample to a number of different enzyme substrates, a pattern of fluorescence response rates emerges from a 7 by 7 microorganism-substrate matrix. Detection limits ranged from 3.6 X 10(2) to 3.5 X 10(8) cells per ml for the Bacillus globigii-indoxyl acetate and Escherichia coli-diacetylfluorescein pairs, respectively. The specificity and versatility of the method for bacterial determination is demonstrated in probing different bacterial enzymes through their spectrally active metabolic products.     

The historical biogeography of Mammalia

Palaeobiogeographic reconstructions are underpinned by phylogenies, divergence times and ancestral area reconstructions, which together yield ancestral area chronograms that provide a basis for proposing and testing hypotheses of dispersal and vicariance. Methods for area coding include multi-state coding with a single character, binary coding with multiple characters and string coding. Ancestral reconstruction methods are divided into parsimony versus Bayesian/likelihood approaches. We compared nine methods for reconstructing ancestral areas for placental mammals. Ambiguous reconstructions were a problem for all methods. Important differences resulted from coding areas based on the geographical ranges of extant species versus the geographical provenance of the oldest fossil for each lineage. Africa and South America were reconstructed as the ancestral areas for Afrotheria and Xenarthra, respectively. Most methods reconstructed Eurasia as the ancestral area for Boreoeutheria, Euarchontoglires and Laurasiatheria. The coincidence of molecular dates for the separation of Afrotheria and Xenarthra at approximately 100 Ma with the plate tectonic sundering of Africa and South America hints at the importance of vicariance in the early history of Placentalia. Dispersal has also been important including the origins of Madagascar's endemic mammal fauna. Further studies will benefit from increased taxon sampling and the application of new ancestral area reconstruction methods.     

Biome-level biogeography of streambed microbiota

A field study was conducted to determine the microbial community structures of streambed sediments across diverse geographic and climatic areas. Sediment samples were collected from three adjacent headwater forest streams within three biomes, eastern deciduous (Pennsylvania), southeastern coniferous (New Jersey), and tropical evergreen (Guanacaste, Costa Rica), to assess whether there is biome control of stream microbial community structure. Bacterial abundance, microbial biomass, and bacterial and microbial community structures were determined using classical, biochemical, and molecular methods. Microbial biomass, determined using phospholipid phosphate, was significantly greater in the southeastern coniferous biome, likely due to the smaller grain size, higher organic content, and lower levels of physical disturbance of these sediments. Microbial community structure was determined using phospholipid fatty acid (PLFA) profiles and bacterial community structure from terminal restriction fragment length polymorphism and edited (microeukaryotic PLFAs removed) PLFA profiles. Principal component analysis (PCA) was used to investigate patterns in total microbial community structure. The first principal component separated streams based on the importance of phototrophic microeukaryotes within the community, while the second separated southeastern coniferous streams from all others based on increased abundance of fungal PLFAs. PCA also indicated that within- and among-stream variations were small for tropical evergreen streams and large for southeastern coniferous streams. A similar analysis of bacterial community structure indicated that streams within biomes had similar community structures, while each biome possessed a unique streambed community, indicating strong within-biome control of stream bacterial community structure.     

Conservation biogeography of anurans in Brazilian Cerrado

The increasing rates of declines in anuran populations worldwide are creating demands for urgent strategies to maximize conservation efforts. This may be critical in regions for which few detailed data on diversity, abundance and distribution are available, such as in the Cerrado of Central Brazil. In this paper, we used a macroecological approach based on the extent of occurrence of 131 species of Anura (Amphibia) in the Cerrado region to design a regional network of potential areas that preserves all anuran species. The final network, obtained using a simulation annealing algorithm based on complementarity, has a total of 17 cells, widely distributed throughout the biome. Minimum costs solutions were obtained in respect to total human population size, soybean production and bovine density, because these are the factors associated with human occupation that historically are more likely to cause broad scale habitat losses. The macro-scale approach used here can provide overall guidelines for conservation and define the focus for more local and effective conservation efforts.