Bruce D. Patterson

The measure of order and disorder in the distribution of species in fragmented habitat

Species distribution patterns within naturally fragmented habitat have been found to often exhibit patterns of pronounced nestedness. Highly predictable extinction sequences are implied by these nested species distribution patterns, thus the patterns are important to both the philosophy and practice of conservation biology. A simple thermodynamic measure of the order and disorder apparent in the nested patterns is described. The metric offers (i) a measure of the uncertainty in species extinction order, (ii) a measure of relative populational stabilities, (iii) a means of identifying minimally sustainable population sizes, and (iv) an estimate of the historical coherence of the species assemblage. Four presumptions govern the development of the metric and its theory: (i) the fragmented habitat was once whole and originally populated by a single common source biota, (ii) the islands were initially uniform in their habitat heterogeneity and type mix, and have remained so throughout their post-fragmentation history, (iii) no significant clinal (latitudinal) gradation exists across the archipelago so as to promote species turnover across the archipelago, and (iv) all species of interest are equally isolated on all islands. The violation of these conditions promotes species distributions which are idiosyncratic to the general extinction order expected in fragmentation archipelagos. While some random variation in extinction order is to be expected, idiosyncratic distributional patterns differ from randomness and are readily segregatable from such noise. A method of identifying idiosyncratic species and sites is described.

A comparative analysis of nested subset patterns of species composition

Abstract We present a broad comparative assessment of nested subsets in species composition among ecological communities. We assembled presence-absence data from a broad range of taxa, geographic regions, and spatial scales; and subjected this collection of datasets to common analyses, including a variety of metrics for measuring nestedness and null hypotheses against which to evaluate them. Here we identify ecological patterns in the prevalence and strength of nested subset structure, and assess differences and biases among the available methodologies. In all, we compiled 279 presence-absence matrices, of which 163 do not overlap in their coverage of species and sites. The survey includes studies on vertebrates, arthropods, mollusks, plants, and other taxa; from north temperate, tropical, and south temperate latitudes. Our results were as follows. Statistically significant nestedness was common. Assemblages from landbridge archipelagos were strongly nested, and immigration experiments were least nested. This adds further empirical support to the hypothesis that extinction plays a major role in producing nested structure. Nestedness was positively correlated with the ratio of the areas of the largest and smallest sites, suggesting that the range in area of sites affects nestedness. Taxonomic differences in nestedness were weak. Higher taxonomic levels showed stronger nesting than their constituent lower taxa. We observed no effect of distance of isolation on nestedness; nor any effects of latitude. With regard to methodology, the metrics Nc and Ut yielded similar results, although Nc proved slightly more flexible in use, and deals differently with tied sites. Similarities also exist in the behavior of N0 (“N”) and Up, and between N1 and Ua. Standardized nestedness metrics were mostly insensitive to matrix size, and were useful in comparative analyses among presence-absence matrices. Most metrics were affected by the proportion of presences in the matrix. All analyses of nestedness, therefore, should test for bias due to matrix fill. We suggest that the factors controlling nested subset structure can be thought of as four filters that species pass to occur at a site: a sampling filter, a distance filter, a habitat filter, and an area filter – and three constraints on community homogeneity: evolutionary history, recent history, and spatial variation in the environment. The scale of examination can also have important effects on the degree of nestedness observed.

Diversification and biogeography of the Neotropical caviomorph lineage Octodontoidea (Rodentia: Hystricognathi)

The rodent superfamily Octodontoidea comprises 6 families, 38 genera, and 193 living species of spiny rats, tuco-tucos, degus, hutias, and their relatives. All are endemic to the Neotropical Region where they represent roughly three-quarters of extant caviomorphs. Although caviomorph monophyly is well established and phylogenetic hypotheses exist for several families, understanding of octodontoid relationships is clouded by sparse taxon sampling and single-gene analyses. We examined sequence variation in one mitochondrial (12S rRNA) and three nuclear genes (vWF, GHR, and RAG1) across all caviomorph families (including 47 octodontoid species), all phiomorph families, and the sole remaining hystricognath family, using the gundi (Ctenodactylus) and springhaas (Pedetes) as outgroups. Our analyses support the monophyly of Phiomorpha, Caviomorpha, and the caviomorph superfamilies Cavioidea (Dasyproctidae, Cuniculidae, and Caviidae, the latter including Hydrochoerus), Erethizontoidea, Chinchilloidea (including Dinomyidae), and Octodontoidea. Cavioids and erethizontoids are strongly supported as sisters, whereas chinchilloids appear to be sister to octodontoids. Among octodontoids, Abrocomidae is consistently recovered as the basal element, sister to a pair of strongly supported clades; one includes Octodontidae and Ctenomyidae as reciprocally monophyletic lineages, whereas the other includes taxa currently allocated to Echimyidae, Capromyidae and Myocastoridae. Capromys appears near the base of this clade, in keeping with current classification, but Myocastor is nested securely inside a clade of Echimyidae that also contains eumysopines, echimyines and dactylomyines. Another, more weakly supported clade of Echimyidae contains fossorial and scansorial taxa from the Chaco-Cerrado-Caatinga and the Atlantic Forest. Biogeographic analyses robustly recover the Patagonia-Southern Andes complex as ancestral for the Octodontoidea, with three component lineages emerging by the Oligocene-Miocene boundary (∼23Ma): (1) stem abrocomids in the Central and Southern Andes; (2) a lineage leading to octodontids plus ctenomyids in Patagonia, later dispersing into the Chaco-Cerrado-Caatinga; and (3) a lineage leading to echimyids, capromyids, and myocastorids that subsequently radiated in more mesic biomes, including Amazonia, Atlantic Forest, and the Antilles. This reconstruction refutes earlier ideas that the diverse, generalized, mainly lowland family Echimyidae, which appears early in the fossil record, gave rise to the Andean lineages of octodontoids-instead, the reverse derivation appears to be true. We recommend formal synonymy of Myocastoridae with Echimyidae but defer a similar treatment of Capromyidae until additional hutia taxa and sequences can be analyzed.

Distribution and Abundance of Small Mammals along an Elevational Transect in Temperate Rainforests of Chile

Assemblages of small mammals in temperate Andean rainforests of southern South America are diverse but poorly known. Herein, we describe an elevational transect through temperate rainforests in Valle de La Picada, Chile, during February and March, 1984. The transect consisted of standardized removal trapping (165 traps set in lines at ca. 7-m intervals and operated for 6 consecutive days) at each of seven elevations: 425 m, 505 m, 620 m, 715 m, 820 m, 920 m, and 1,135 m. A total of 514 small mammals representing two species of marsupials and seven species of sigmodontine rodents was collected. Trap success averaged 7.4% across traps, days, and elevations. Number of captures by individual traps during the sample period was indistinguishable from a Poisson distribution, both throughout the transect and at individual levels, suggesting independence of captures among traps. Captures were biased significantly by trap type, with museum specials securing significantly more Dromiciops australis and all forms of Akodon than Sherman live traps; the same biases were suggested by captures of Irenomys tarsalis and Auliscomys micropus . As expected, total number of individuals taken at each elevation declined throughout the sampling period while the cumulative number of species rose. Number of species, number of individuals, and species diversity varied inversely with elevation. Number of species and species diversity taken each day reached a maximum after 2–4 days of sampling. Captures of Rhyncholestes raphanurus, Akodon sanborni , putative hybrids of A. sanborni and Akodon longipilis , and I. tarsalis were correlated inversely with elevation. Conversely, D. australis, A. longipilis , and A. micropus were taken more commonly at higher elevations, whereas captures of Oryzomys longicaudatus, Akodon olivaceus , and Geoxus valdivianus appeared unrelated to elevation. Systematic sampling procedures are viewed as essential for describing fundamental patterns of abundance and distribution that can be compared with other studies.

Roosting habits of bats affect their parasitism by bat flies (Diptera: Streblidae)

The Smithsonian Venezuela Project (SVP) conducted extensive surveys of mammals and ectoparasites in the 1960s. The 25 238 individuals and 130 species of bat collected by SVP hosted 36 663 streblid bat flies, representing 116 species of these ectoparasitic dipterans. Roosts of bat species differ in durability and protection, and bat flies separate from the host to pupate in the roost. We predicted higher levels of parasitism and more parasitic associates for bats roosting in more permanent structures (e.g. caves, tunnels) that would facilitate their association with hosts. We also predicted wing development of flies should correlate inversely with roost duration, restricting flightless forms to bats in permanent roosts. Ranking roosting structures by durability and protection, we sought correlations among bat species in prevalence, mean intensity and number of associated fly species. All three measures of parasitism were positively and significantly related to roosting habits: bats roosting in more permanent, enclosed structures were more likely to be infested, to carry heavier parasite loads, and to harbour more species of ectoparasitic flies. However, roosting habits were not correlated with the average wing development of bat flies. Although other factors affect parasitism rates in bats, the study provides a compelling example of both ecological and evolutionary responses of parasites to features of the hosts environment.

Bat flies: Obligate ectoparasites of bats

Bat flies are highly specialized for a nearly permanent ectoparasitic relationship with their hosts, the Chiroptera. Although known life-histories are rather similar across all taxa, bat flies exhibit a variety of morphological adaptations, most suiting them for the two physical substrates offered to them by their bat hosts, the fur and the flight membranes. These morphological adaptations and the ecological diversity of their hosts make bat flies an excellent group in which to study the parasitic relationship, including morphological accommodations, cospeciation, and coevolution.

Trophic relationships of small mammals in a Chilean temperate rainforest

Food habits were determined from analysis of stomach contents of nine species of small mammals that inhabit primary-growth temperate rainforest in southern Chile. Species included rodents ( Akodon olivaceus, A. longipilis, A. sanborni , putative A. longipilis × sanborni hybrids, Oryzomys longicaudatus, Geoxus valdivianus, Irenomys tarsalis , and Auliscomys mi-cropus ) and marsupials ( Rhyncholestes raphanurus and Dromiciops australis ). Diets throughout the year were determined for the first three species, but primarily during summer (December-March) for the remaining species. Species of Akodon generally were omnivorous, with the stomach contents of A. olivaceus containing smaller proportions of vegetation and fungi than those of other species in most periods. A. olivaceus also had seasonally greater, but approximately equal overall proportions of arthropods, seeds, and fruits in the diet. O. longicaudatus, I. tarsalis , and A. micropus were broadly granivorous-frugivorous with plant material, but not fungi, comprising significant proportions of the diet. Invertebrates, primarily arthropods and annelids, dominated diets of G. valdivianus and R. raphanurus , but significant amounts of nonepidermal plant material and fungi also were present. D. australis fed on arthropods, but also ate some seeds and vegetation. Overall, diets of these small mammals were relatively omnivorous; because this contrasts with patterns of trophic specialization for many of the same species elsewhere, resource availability rather than evolutionary specialization may contribute more in determining patterns of use of local food resources.

Global distribution and genetic diversity of Bartonella in bat flies (Hippoboscoidea, Streblidae, Nycteribiidae)

Recently, a growing number Bartonella spp. have been identified as causative agents for a broadening spectrum of zoonotic diseases, emphasizing their medical importance. Many mammalian reservoirs and vectors however are still unknown, hindering our understanding of pathogen ecology and obscuring epidemiological connections. New Bartonella genotypes were detected in a global sampling of 19 species of blood-feeding bat flies (Diptera, Hippoboscoidea, Nycteribiidae, Streblidae) from 20 host bat species, suggesting an important role of bat flies in harboring bartonellae. Evolutionary relationships were explored in the context of currently known Bartonella species and genotypes. Phylogenetic and gene network analyses point to an early evolutionary association and subsequent radiation of bartonellae with bat flies and their hosts. The recovery of unique clades, uniting Bartonella genotypes from bat flies and bats, supports previous ideas of these flies potentially being vectors for Bartonella. Presence of bartonellae in some female bat flies and their pupae suggests vertical transmission across developmental stages. The specific function of bartonellae in bats and bat flies remains a subject of debate, but in addition to pathogenic interactions, parasitic, mutualistic, or reservoir functions need to be considered.

Phylogenetics and biogeography of the broad-nosed bats, genus Platyrrhinus (Chiroptera: Phyllostomidae).

The Neotropical broad-nosed bats, genus Platyrrhinus, represent a well-defined monophyletic group of 14 recognized species. A recent study of morphological characters confirmed Platyrrhinus monophyly and species diagnosis, but offered little support to their intra-specific relationships. We conducted phylogenetic analyses of the genus, using dense taxonomic sampling in combination with four gene sequences representing both mitochondrial and nuclear DNA transmission systems. Our aim was to elucidate the phylogenetic structure among species, using the resulting 3341 bp of DNA. Maximum parsimony, maximum likelihood, and Bayesian inference analyses produced similar topologies that confirm the monophyly of the genus Platyrrhinus and strongly support many previously unrecognized groups. Paraphyly of Platyrrhinus helleri and the unclear position of P. brachycephalus in the clades were also apparent in the data. Our biogeographical analysis suggests a Brazilian Shield origin for Platyrrhinus, followed by subsequent radiations of lineages in the Amazon Basin and Andes. Secondary dispersal from Amazonian and Andean centers is responsible for the Platyrrhinus inhabiting the Guianan Shield and the Pacific lowlands and Central America, respectively.

Quantitative Habitat Associations of Small Mammals along an Elevational Transect in Temperate Rainforests of Chile

Distribution and abundance of small mammals in temperate Andean rainforests are correlated with elevation. To interpret such patterns, we examined elevational variation in habitats and habitat use by small mammals. Elevation accounts for significant variation in 22 of 24 habitat metrics, reflecting the diminishing stature and more open canopies of higher-elevation rainforests. Principal-components analysis of habitat shows significant multivariate effects of elevation. Mammal species differ significantly in use of about half of the habitat variables, in ways generally consistent with morphology, behavior, and diet. Abundant species appear to occupy typical habitats along the transect, whereas rarer species are associated with more distinctive habitat types. Species overlap substantially in their use of habitats, but analyses of trap captures indicate that species are segregated at finer spatial scales. Spatial segregation at this scale may contribute to the coexistence of abundant species and congeners. Elevational variation in habitat and specific habitat associations provide a plausible explanation for correlations of mammalian distribution and abundance with elevation.