Ross H. Crozier

Integrative Taxonomy: A Multisource Approach to Exploring Biodiversity

Good alpha taxonomy is central to biology. On the basis of a survey of arthropod studies that used multiple disciplines for species delimitation, we evaluated the performance of single disciplines. All included disciplines had a considerable failure rate. Rigor in species delimitation can thus be increased when several disciplines chosen for complementarity are used. We present a flexible procedure and stopping rule for integrative taxonomy that uses the information from different disciplines separately. Disagreement among disciplines over the number and demarcation of species is resolved by elucidating and invoking evolutionary explanations for disagreement. With the identification of further promising study organisms and of new questions for in-depth analysis, evolutionary biology should profit from integrative taxonomy. An important rationale is clarity in researcher bias in the decision-making process. The success of integrative taxonomy will further increase through methodological progress, taxonomic training of evolutionary biologists, and balanced resource allocation.

Sex determination and population biology in the hymenoptera.

The Hymenoptera (ants, bees, wasps and sawflies) display a great variety of social systems and sex ratios and have played a key role in the development and testing of many evolutionary models. Traditionally, considerable emphasis was placed on the fact that hymenopterans have haploid males and diploid females but it is now clear that many species also regularly produce sterile, diploid males. Recent studies explore the diverse ways in which production of these diploid males influences selection on mating systems, sex ratios and social behaviour.

The cytochrome b region in the mitochondrial DNA of the ant Tetraponera rufoniger: Sequence divergence in hymenoptera may be associated with nucleotide content

Polymerase chain reaction (PCR) followed by sequencing of single-stranded DNA yielded sequence information from the cytochrome b (cyt b) region in mitochondrial DNA from the ant Tetraponera rufoniger. Compared with the cyt b genes from Apis mellifera, Drosophila melanogaster, and D. yakuba, the overall A + T content (A + T%) of that of T. rufoniger is lower (69.9% vs 80.7%, 74.2%, and 73.9%, respectively) than those of the other three. The codon usage in the cyt b gene of T. rufoniger is biased although not as much as in A. mellifera, D. melanogaster, and D. yakuba; T. rufoniger has eight unused codons whereas D. melanogaster, D. yakuba, and A. mellifera have 21, 20, and 23, respectively. The inferred cyt b polypeptide chain (PPC) of T. rufoniger has diverged at least as much from a common ancestor with D. yakuba as has that of A. mellifera (∼3.5 vs ∼2.9). Despite the lower A + T%, the relative frequencies of amino acids in the cyt b PPC of T. rufoniger are significantly (P < 0.05) associated with the content of adenine and thymine (A + T%) and size of codon families. The mitochondrially located cytochrome oxidase subunit 11 genes (CO-II) of endopterygote insects have significantly higher average A + T% (∼75%) than those of exopterygous (∼69%o) and paleopterous (∼69%) insects. The increase in A + T% of endopterygote insects occurred in Upper Carboniferous and coincided with a significant acceleration of PPC divergence. However, acceleration of PPC divergence is not significantly correlated with the increase of the A + T% (P > 0.1). The high A + T%, the biased codon usage, and the increased PPC divergence of Hymenoptera can in that respect most easily be explained by directional mutation pressure which began in the Upper Carboniferous and still occurs in most members of the order. Given the roughly identical A + T% of the cyt b and CO-II genes from the other insects whose DNA sequences are known (A. mellifera, D. melanogaster, and D. yakuba), it seems most likely that the A + T% of T. rufoniger declined secondarily within the last 100 Myr as a result of a reduced directional mutation pressure.

Genetic diversity and the agony of choice

Abstract Vane-Wright et al. (Biol. Conserv., 55, 1991) correctly stress the importance of using the evolutionary distinctiveness of taxa when assigning them priorities for preservation — ‘the agony of choice’. In the absence of other information, the crucial quantity is the preservation of genetic diversity. The method of Vane-Wright et al. uses exclusively the topology of the inferred phylogeny of the group. This cladistic method will err on occasion because it does not take into account the accumulation of genetic divergence along branches of the evolutionary tree, and because it relies on the tree being rooted. When available, the use of reliable genetic data following tree construction is preferable. The species with the highest priority for conservation is then that with the highest overall probability of having unique character states. If there is a linear relationship between distance and the probability of character state change, the relative probability of uniqueness of a taxon may be estimated by the product of its genetic distances to other taxa along the branches of the dendrogram. Habitats or reserve systems can be ranked according either to the priorities assigned to their constituent species, or their preservation of biodiversity estimated by using a simple product rule applied to the lengths of the branches conserved.

Animal performance and stress: responses and tolerance limits at different levels of biological organisation

Recent advances in molecular biology and the use of DNA microarrays for gene expression profiling are providing new insights into the animal stress response, particularly the effects of stress on gene regulation. However, interpretation of the complex transcriptional changes that occur during stress still poses many challenges because the relationship between changes at the transcriptional level and other levels of biological organisation is not well understood. To confront these challenges, a conceptual model linking physiological and transcriptional responses to stress would be helpful. Here, we provide the basis for one such model by synthesising data from organismal, endocrine, cellular, molecular, and genomic studies. We show using available examples from ectothermic vertebrates that reduced oxygen levels and oxidative stress are common to many stress conditions and that the responses to different types of stress, such as environmental, handling and confinement stress, often converge at the challenge of dealing with oxygen imbalance and oxidative stress. As a result, a common set of stress responses exists that is largely independent of the type of stressor applied. These common responses include the repair of DNA and protein damage, cell cycle arrest or apoptosis, changes in cellular metabolism that reflect the transition from a state of cellular growth to one of cellular repair, the release of stress hormones, changes in mitochondrial densities and properties, changes in oxygen transport capacities and changes in cardio‐respiratory function. Changes at the transcriptional level recapitulate these common responses, with many stress‐responsive genes functioning in cell cycle control, regulation of transcription, protein turnover, metabolism, and cellular repair. These common transcriptional responses to stress appear coordinated by only a limited number of stress‐inducible and redox‐sensitive transcription factors and signal transduction pathways, such as the immediate early genes c‐fos and c‐jun, the transcription factors NFκB and HIF‐1α, and the JNK and p38 kinase signalling pathways. As an example of environmental stress responses, we present temperature response curves at organismal, cellular and molecular levels. Acclimation and physiological adjustments that can shift the threshold temperatures for the onset of these responses are discussed and include, for example, adjustments of the oxygen delivery system, the heat shock response, cellular repair system, and transcriptome. Ultimately, however, an organism’s ability to cope with environmental change is largely determined by its ability to maintain aerobic scope and to prevent loss in performance. These systemic constraints can determine an organism’s long‐term survival well before cellular and molecular functions are disturbed. The conceptual model we propose here discusses some of the crosslinks between responses at different levels of biological organisation and the central role of oxygen balance and oxidative stress in eliciting these responses with the aim to help the interpretation of environmental genomic data in the context of organismal function and performance.

The Evolution of Worker Caste Diversity in Social Insects

Morphological diversification of workers is predicted to improve the division of labor within social insect colonies, yet many species have monomorphic workers. Individual‐level selection on the reproductive capacities of workers may counter colony‐level selection for diversification, and life‐history differences between species (timing of caste determination, colony size, genetic variation available) may mediate the strength of this selection. We tested this through phylogenetically independent contrast analyses on a new data set for 35 ant species. Evidence was found that early divergence of queen‐worker developmental pathways may facilitate the evolution of worker diversity because queen‐worker dimorphism was strongly positively associated with diversity. By contrast, risks for colonies that invest in specialized workers and colony size effects on costs of worker reproduction seem unlikely to strongly affect the evolution of worker diversity because there was no significant association between colony size and diversity when controlling statistically for queen‐worker dimorphism. Finally, worker diversity was greater in species with multiple lineages per colony, and it was negatively associated with relatedness in monogynous species. This could be due to high intracolonial genetic variance favoring the expression and evolution of great worker diversity or to diversity evolving more easily when there is selection for repression of worker reproduction (worker policing).

Phylogenetic evidence for a single, ancestral origin of a ‘true’ worker caste in termites

Phylogenetic analysis based on sequence variation in mitochondrial large‐subunit rRNA and cytochrome oxidase II genes was used to investigate the evolutionary relationships among termite families. Maximum likelihood and parsimony analyses of a combined nucleotide data set yield a single well‐supported topology, which is: (((((Termitidae, Rhinotermitidae), Serritermitidae), Kalotermitidae), (Hodotermitidae, Termopsidae)), Mastotermitidae). Although some aspects of this topology are consistent with previous schemes, overall it differs from any published. Optimization of ‘true’ workers onto the tree suggests that this caste originated once, early in the history of the lineage and has been lost secondarily twice. This scenario differs from the more widely accepted notion that workers are derived and of polyphyletic origin and that extant pseudergates, or ‘false’ workers, are their developmentally unspecialized ancestor caste. Worker gains and losses covary directly in number and direction with shifts in ‘ecological life type’. A test for correlated evolution which takes phylogenetic structure into account indicates that this pattern is of biological significance and suggests that the variable occurrence of a worker caste in termites has ecological determinants, apparently linked to differences in feeding and nesting habits.

Polyandry in the genus Apis, particularly Apis andreniformis

Abstract Using four polymorphic microsatellite loci, we found that four Apis andreniformis queens collected in Thailand each mated at least 10–20 times, producing an average relatedness, gww, of workers of 0.30 ± 0.007, and an average effective number of matings of 9.1 ± 2.2. The degrees of polyandry and intra-colonial genetic relatedness in A. andreniformis are similar to those in A. mellifera, slightly more than in A. florea, and up to 6 times less than in A. dorsata. We argue that while presently favoured hypotheses for the evolution of polyandry in monogynous social insects may adequately explain the evolution of up to five or six matings, they are inadequate to explain the extreme polyandry (10–60 matings) observed in Apis. One alternative possibility is that colony fitness is a non-additive function of the fitness of individual subfamilies. Such behavioral over-dominance may mean that queen fitness is increased by high levels of polyandry, which increase the probability of desirable combinations of worker genotypes occurring in one colony. The special attributes of honey bees which may lead to behavioral over-dominance include colony aggregation (which may increase the incidence of disease), and frequent long-distance migration.

Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish

Coral reef fishes are expected to experience rising sea surface temperatures due to climate change. How well tropical reef fishes will respond to these increased temperatures and which genes are important in the response to elevated temperatures is not known. Microarray technology provides a powerful tool for gene discovery studies, but the development of microarrays for individual species can be expensive and time‐consuming. In this study, we tested the suitability of a Danio rerio oligonucleotide microarray for application in a species with few genomic resources, the coral reef fish Pomacentrus moluccensis. Results from a comparative genomic hybridization experiment and direct sequence comparisons indicate that for most genes there is considerable sequence similarity between the two species, suggesting that the D. rerio array is useful for genomic studies of P. moluccensis. We employed this heterologous microarray approach to characterize the early transcriptional response to heat stress in P. moluccensis. A total of 111 gene loci, many of which are involved in protein processing, transcription, and cell growth, showed significant changes in transcript abundance following exposure to elevated temperatures. Changes in transcript abundance were validated for a selection of candidate genes using quantitative real‐time polymerase chain reaction. This study demonstrates that heterologous microarrays can be successfully employed to study species for which specific microarrays have not yet been developed, and so have the potential to greatly enhance the utility of microarray technology to the field of environmental and functional genomics.

Analysis of directional mutation pressure and nucleotide content in mitochondrial cytochrome b genes

We present a new approach for analyzing directional mutation pressure and nucleotide content in protein-coding genes. Directional mutation pressure, the heterogeneity in the likelihood of different nucleotide substitutions, is used to explain the increasing or decreasing guanine-cytosine content (GC%) in DNA and is represented by µD, in agreement with Sueoka (1962, Proc Natl Acad Sci USA 48:582–592). The new method uses simulation to facilitate identification of significant A + T or G + C pressure as well as the comparison of directional mutation pressure among genes, even when they are translated by different genetic codes. We use the method to analyze the evolution of directional mutation pressure and nucleotide content of mitochondrial cytochrome b genes. Results from a survey of 110 taxa indicate that the cytochrome b genes of most taxa are subjected to significant directional mutation pressure and that the gene is subject to A + T pressure in most cases. Only in the anseriform bird Cairina moschata is the cytochrome b gene subject to significant G + C pressure. The GC% at nonsynonymous codon sites decreases proportionately with increasing A + T pressure, and with a slope less than one, indicating a presence of selective constraints. The cytochrome b genes of insects, nematodes, and eumycotes are subject to extreme A + T pressures (µD = 0.123, 0.224, and 0.130) and, in parallel, the GC% of the nonsynonymous codon sites has decreased from about 0.44 in organisms that are not subjected to A + T or G + C pressure to about 0.332, 0.323, and 0.367, respectively. The distribution of taxa according to the GC% at nonsynonymous codon sites and directional mutation pressure supports the notion that variation in these parameters is a phylogenetic component.