Martin H. Villet

Comparing models for predicting species' potential distributions: a case study using correlative and mechanistic predictive modelling techniques

Abstract Models used to predict species’ potential distributions have been described as either correlative or mechanistic. We attempted to determine whether correlative models could perform as well as mechanistic models for predicting species potential distributions, using a case study. We compared potential distribution predictions made for a coastal dune plant ( Scaevola plumieri ) along the coast of South Africa, using a mechanistic model based on summer water balance (SWB), and two correlative models (a profile and a group discrimination technique). The profile technique was based on principal components analysis (PCA) and the group-discrimination technique was based on multiple logistic regression (LR). Kappa ( κ ) statistics were used to objectively assess model performance and model agreement. Model performance was calculated by measuring the levels of agreement (using κ ) between a set of testing localities (distribution records not used for model building) and each of the model predictions. Using published interpretive guidelines for the kappa statistic, model performance was “excellent” for the SWB model ( κ =0.852), perfect for the LR model ( κ =1.000), and “very good” for the PCA model ( κ =0.721). Model agreement was calculated by measuring the level of agreement between the mechanistic model and the two correlative models. There was “good” model agreement between the SWB and PCA models ( κ =0.679) and “very good” agreement between the SWB and LR models ( κ =0.786). The results suggest that correlative models can perform as well as or better than simple mechanistic models. The predictions generated from these three modelling designs are likely to generate different insights into the potential distribution and biology of the target organism and may be appropriate in different situations. The choice of model is likely to be influenced by the aims of the study, the biology of the target organism, the level of knowledge the target organism’s biology, and data quality.

Phylogenetics of Advanced Snakes (Caenophidia) Based on Four Mitochondrial Genes

Phylogenetic relationships among advanced snakes (Acrochordus + Colubroidea = Caenophidia) and the position of the genus Acrochordus relative to colubroid taxa are contentious. These concerns were investigated by phylogenetic analysis of fragments from four mitochondrial genes representing 62 caenophidian genera and 5 noncaenophidian taxa. Four methods of phylogeny reconstruction were applied: matrix representation with parsimony (MRP) supertree consensus, maximum parsimony, maximum likelihood, and Bayesian analysis. Because of incomplete sampling, extensive missing data were inherent in this study. Analyses of individual genes retrieved roughly the same clades, but branching order varied greatly between gene trees, and nodal support was poor. Trees generated from combined data sets using maximum parsimony, maximum likelihood, and Bayesian analysis had medium to low nodal support but were largely congruent with each other and with MRP supertrees. Conclusions about caenophidian relationships were based on these combined analyses. The Xenoderminae, Viperidae, Pareatinae, Psammophiinae, Pseudoxyrophiinae, Homalopsinae, Natricinae, Xenodontinae, and Colubrinae (redefined) emerged as monophyletic, whereas Lamprophiinae, Atractaspididae, and Elapidae were not in one or more topologies. A clade comprising Acrochordus and Xenoderminae branched closest to the root, and when Acrochordus was assessed in relation to a colubroid subsample and all five noncaenophidians, it remained associated with the Colubroidea. Thus, Acrochordus + Xenoderminae appears to be the sister group to the Colubroidea, and Xenoderminae should be excluded from Colubroidea. Within Colubroidea, Viperidae was the most basal clade. Other relationships appearing in all final topologies were (1) a clade comprising Psammophiinae, Lamprophiinae, Atractaspididae, Pseudoxyrophiinae, and Elapidae, within which the latter four taxa formed a subclade, and (2) a clade comprising Colubrinae, Natricinae, and Xenodontinae, within which the latter two taxa formed a subclade. Pareatinae and Homalopsinae were the most unstable clades.

Phylogeny, biogeography and classification of the snake superfamily Elapoidea: a rapid radiation in the Late Eocene

The snake superfamily Elapoidea presents one of the most intransigent problems in systematics of the Caenophidia. Its monophyly is undisputed and several cohesive constituent lineages have been identified (including the diverse and clinically important family Elapidae), but its basal phylogenetic structure is obscure. We investigate phylogenetic relationships and spatial and temporal history of the Elapoidea using 94 caenophidian species and approximately 2300–4300 bases of DNA sequence from one nuclear and four mitochondrial genes. Phylogenetic reconstruction was conducted in a parametric framework using complex models of sequence evolution. We employed Bayesian relaxed clocks and Penalized Likelihood with rate smoothing to date the phylogeny, in conjunction with seven fossil calibration constraints. Elapoid biogeography was investigated using maximum likelihood and maximum parsimony methods. Resolution was poor for early relationships in the Elapoidea and in Elapidae and our results imply rapid basal diversification in both clades, in the late Eocene of Africa (Elapoidea) and the mid‐Oligocene of the Oriental region (Elapidae). We identify the major elapoid and elapid lineages, present a phylogenetic classification system for the superfamily (excluding Elapidae), and combine our phylogenetic, temporal and biogeographic results to provide an account of elapoid evolution in light of current palaeontological data and palaeogeographic models.

Molecular identification of some forensically important blowflies of southern Africa and Australia

Abstract.  One major aspect of research in forensic entomology is the investigation of molecular techniques for the accurate identification of insects. Studies to date have addressed the corpse fauna of many geographical regions, but generally neglected the southern African calliphorid species. In this study, forensically significant calliphorids from South Africa, Swaziland, Botswana and Zimbabwe and Australia were sequenced over an 1167 base pair region of the COI gene. Phylogenetic analysis was performed to examine the ability of the region to resolve species identities and taxonomic relationships between species. Analyses by neighbour‐joining, maximum parsimony and maximum likelihood methods all showed the potential of this region to provide the necessary species‐level identifications for application to post‐mortem interval (PMI) estimation; however, higher level taxonomic relationships did vary according to method of analysis. Intraspecific variation was also considered in relation to determining suitable maximum levels of variation to be expected during analysis. Individuals of some species in the study represented populations from both South Africa and the east coast of Australia, yet maximum intraspecific variation over this gene region was calculated at 0.8%, with minimum interspecific variation at 3%, indicating distinct ranges of variation to be expected at intra‐ and interspecific levels. This region therefore appears to provide southern African forensic entomologists with a new technique for providing accurate identification for application to estimation of PMI.

A global study of forensically significant calliphorids: implications for identification.

A proliferation of molecular studies of the forensically significant Calliphoridae in the last decade has seen molecule-based identification of immature and damaged specimens become a routine complement to traditional morphological identification as a preliminary to the accurate estimation of post-mortem intervals (PMI), which depends on the use of species-specific developmental data. Published molecular studies have tended to focus on generating data for geographically localised communities of species of importance, which has limited the consideration of intraspecific variation in species of global distribution. This study used phylogenetic analysis to assess the species status of 27 forensically important calliphorid species based on 1167 base pairs of the COI gene of 119 specimens from 22 countries, and confirmed the utility of the COI gene in identifying most species. The species Lucilia cuprina, Chrysomya megacephala, Ch. saffranea, Ch. albifrontalis and Calliphora stygia were unable to be monophyletically resolved based on these data. Identification of phylogenetically young species will require a faster-evolving molecular marker, but most species could be unambiguously characterised by sampling relatively few conspecific individuals if they were from distant localities. Intraspecific geographical variation was observed within Ch. rufifacies and L. cuprina, and is discussed with reference to unrecognised species.

Contemporary Precision, Bias and Accuracy of Minimum Post-Mortem Intervals Estimated Using Development of Carrion-Feeding Insects

Medicocriminal forensic entomology focuses primarily on providing evidence of the amount of time that a corpse or carcass has been exposed to colonization by insects, which helps to estimate the post mortem interval (PMI). Specifically, the estimate is of a minimum post mortem interval (PMImin), because death may occur a variable amount of time before colonization (Fig. 7.1); the maximum post mortem interval (PMImax) is estimated using the time that the person was last seen alive. Forensic entomology derives the bulk of its evidence from two sources: the ecological succession of carrion insect communities and the development of immature insects (Byrd and Castner 2001; Catts and Haskel 1990; Smith 1986). This chapter is concerned with assessing the confidence that can be placed in the accuracy of estimates derived from insect development. (Schoenly et al. 1996) dealt with this theme in succession-based estimates of PMImin.

Patterns and processes underlying evolutionary significant units in the Platypleura stridula L. species complex (Hemiptera: Cicadidae) in the Cape Floristic Region, South Africa

Cicadas have been shown to be useful organisms for examining the effects of distribution, plant association and geographical barriers on gene flow between populations. The cicadas of the Platypleura stridula species complex are restricted to the biologically diverse Cape Floristic Region (CFR) of South Africa. They are thus an excellent study group for elucidating the mechanisms by which hemipteran diversity is generated and maintained in the CFR. Phylogeographical analysis of this species complex using mitochondrial DNA Cytochrome Oxidase I (COI) and ribosomal 16S sequence data, coupled with preliminary morphological and acoustic data, resolves six clades, each of which has specific host‐plant associations and distinct geographical ranges. The phylogeographical structure implies simultaneous or near‐simultaneous radiation events, coupled with shifts in host‐plant associations. When calibrated using published COI and 16S substitution rates typical for related insects, these lineages date back to the late Pliocene – early Pleistocene, coincident with vegetation change, altered drainage patterns and accelerated erosion in response to neotectonic crustal uplift and cyclic Pleistocene climate change, and glaciation‐associated changes in climate and sea level.

Factors affecting accuracy and precision of thermal summation models of insect development used to estimate post-mortem intervals

This paper investigates the effects that different summary statistics (minimum, median, mean, or maximum), temporal sampling resolutions (duration between sampling events), and sample sizes (number of individuals sampled per sampling event) had on the accuracy and precision of the regression coefficients of a typical thermal summation model used to calculate minimum post-mortem interval (PMI). No significant differences were found in the values of the developmental constants calculated from different summary statistics of the duration of development. Sample size was found to affect the precision of measurement of the duration of development but had little overall influence on thermal summation constant (K) and developmental threshold (D0) calculations (and therefore, subsequent PMI estimates), but temporal sampling resolution had a direct influence on the accuracy of K and D0 calculations. These data suggest that when numbers of experimental maggots are limited, it is more important to sample more frequently using smaller sample sizes than to sample less frequently with large sample sizes. Furthermore, we suggest that the median is the most representative summary measure of the duration of development and should be used preferentially.

INFLUENCE OF GRAZING BY LARGE MAMMALS ON THE SPIDER COMMUNITY OF A KENYAN SAVANNA BIOME

Abstract Pitfall trap and sweep net samples were taken over a period of fifteen months (2002– 2003) in the Kenya Long-term Exclosure Experiment (KLEE), in which the presence of domestic and wild herbivores have been independently manipulated since 1995. ANOVA and ANCOVA showed that the exclosure treatments significantly affected plant cover, with the presence of cattle significantly reducing the relative vegetation cover and spider diversity. Herbivory by indigenous mega- and meso–herbivores did not have a significant influence on the diversity of the spider fauna, but abundance of three dominant species (Cyclosa insulana Costa (Araneidae), Argiope trifasciata Forskål (Araneidae) and Runcinia flavida Simon (Thomisidae)) decreased in cattle-grazed plots. In contrast, Aelurillus sp. became more prevalent where cattle have been grazing. Multivariate analyses revealed that the spider community responded to grazing pressure by aggregating into three groups that reflected control, cattle grazing and non-cattle grazing clusters. It was probable that the direct effects on vegetation mediated an indirect influence of herbivores on spider diversity. The relative vegetation cover was a positive predictor of spider diversity. Spider communities were found to be an indicator of the activity of mammals and could be used as indicators of land use changes and for bio-monitoring.

Development of Thanatophilus micans (Fabricius 1794) (Coleoptera: Silphidae) at constant temperatures

Thanatophilus micans is capable of finding corpses at least as quickly as most fly species and, as the most widespread species of the Silphidae in Africa, offers a useful model for estimating post-mortem interval. Larvae were reared at ten constant temperatures from 15°C to 35°C and their length measured at 4, 8, or 12-h intervals depending on their instar. Length generally increased with increased rearing temperature, but decreased at extremely high temperatures. Note was made of the age at which individuals progressed past developmental milestones. Development took longer at lower temperatures. These results are presented as a combined isomegalen and isomorphen diagram. Developmental constants were generated for each milestone using major axis regression. Developmental threshold values did not differ significantly between milestones. Development took longer than in blow flies, but was faster than in Dermestidae. The three models presented here, therefore, cover an important time frame in estimating minimum PMI once fly larvae have matured to the point of leaving a corpse, and, therefore, provide a tool that was not previously available to forensic entomologists.