Annual Review of Ecology, Evolution, and Systematics - Volume 36, 2005

Cooperation is common across nonhuman animal taxa, from the hunting of large game in lions to the harvesting of building materials in ants. Theorists have proposed a number of models to explain the evolution of cooperative behavior. These ultimate explanations, however, rarely consider the proximate constraints on the implementation of cooperative behavior. Here we review several types of cooperation and propose a suite of cognitive abilities required for each type to evolve. We propose that several types of cooperation, though theoretically possible and functionally adaptive, have not evolved in some animal species because of cognitive constraints. We argue, therefore, that future modeling efforts and experimental investigations into the adaptive function of cooperation in animals must be grounded in a realistic assessment of the psychological ingredients required for cooperation. Such an approach can account for the puzzling distribution of cooperative behaviors across taxa, especially the seemingly unique occurrence of cooperation observed in our own species.

Niche conservatism is the tendency of species to retain ancestral ecological characteristics. In the recent literature, a debate has emerged as to whether niches are conserved. We suggest that simply testing whether niches are conserved is not by itself particularly helpful or interesting and that a more useful focus is on the patterns that niche conservatism may (or may not) create. We focus specifically on how niche conservatism in climatic tolerances may limit geographic range expansion and how this one type of niche conservatism may be important in (a) allopatric speciation, (b) historical biogeography, (c) patterns of species richness, (d) community structure, (e) the spread of invasive, human-introduced species, (f) responses of species to global climate change, and (g) human history, from 13,000 years ago to the present. We describe how these effects of niche conservatism can be examined with new tools for ecological niche modeling.

The continuous flow of genomic data is creating unprecedented opportunities for the reconstruction of molecular phylogenies. Access to whole-genome data means that phylogenetic analysis can now be performed at different genomic levels, such as primary sequences and gene order, allowing for reciprocal corroboration of the results. We critically review the different kinds of phylogenomic methods currently available, paying particular attention to method reliability. Our emphasis is on methods for the analysis of primary sequences because these are the most advanced. We discuss the important issue of statistical inconsistency and show how failing to fully capture the process of sequence evolution in the underlying models leads to tree reconstruction artifacts. We suggest strategies for detecting and potentially overcoming these problems. These strategies involve the development of better models, the use of an improved taxon sampling, and the exclusion of phylogenetically misleading data.

Agriculture has evolved independently in three insect orders: once in ants, once in termites, and seven times in ambrosia beetles. Although these insect farmers are in some ways quite different from each other, in many more ways they are remarkably similar, suggesting convergent evolution. All propagate their cultivars as clonal monocultures within their nests and, in most cases, clonally across many farmer generations as well. Long-term clonal monoculture presents special problems for disease control, but insect farmers have evolved a combination of strategies to manage crop diseases: They (a) sequester their gardens from the environment; (b) monitor gardens intensively, controlling pathogens early in disease outbreaks; (c) occasionally access population-level reservoirs of genetically variable cultivars, even while propagating clonal monocultures across many farmer generations; and (d) manage, in addition to the primary cultivars, an array of “auxiliary” microbes providing disease suppression and other services. Rather than growing a single cultivar solely for nutrition, insect farmers appear to cultivate, and possibly “artificially select” for, integrated crop-microbe consortia. Indeed, crop domestication in the context of coevolving and codomesticated microbial consortia may explain the 50-million year old agricultural success of insect farmers.

The diversity and composition of herbivore assemblages was a favored theme for community ecology in the 1970s and culminated in 1984 with Insects on Plants by Strong, Lawton and Southwood. We scrutinize findings since then, considering analyses of country-wide insect-host catalogs, field studies of local herbivore communities, and comparative studies at different spatial scales. Studies in tropical forests have advanced significantly and offer new insights into stratification and host specialization of herbivores. Comparative and long-term data sets are still scarce, which limits assessment of general patterns in herbivore richness and assemblage structure. Methods of community phylogenetic analysis, complex networks, spatial and among-host diversity partitioning, and metacommunity models represent promising approaches for future work.

The reconstruction of evolutionary trees from mitochondrial DNA (mtDNA) data is a common tool with which to infer the relationships of living organisms. The wide use of mtDNA stems from the ease of getting new sequence data for a set of orthologus genes and from the availability of many existing mtDNA sequences for a wide array of species. In this review we argue that developing a fuller understanding of the biology of mitochondria is essential for the rigorous application of mtDNA to inferences about the evolutionary history of species or populations. Though much progress has been made in understanding the parameters that shape the evolution of mitochondria and mtDNA, many questions still remain, and a better understanding of the role this organelle plays in regulating organismal fitness is becoming increasingly critical for accurate phylogeny reconstruction. In population biology, the limited information content of one nonrecombining genetic marker can compromise evolutionary inference, and the effects of nuclear genetic variation—and environmental factors—in mtDNA fitness differences can compound these problems. In systematics, the limited gene set, biased amino acid composition, and problems of compensatory substitutions can cloud phylogenetic signal. Dissecting the functional bases of these biases offers both challenges and opportunities in comparative biology.

Oysters have been introduced worldwide to 73 countries, but the ecological consequences of the introductions are not fully understood. Economically, introduced oysters compose a majority of oyster harvests in many areas. Oysters are ecosystem engineers that influence many ecological processes, such as maintenance of biodiversity, population and food web dynamics, and nutrient cycling. Consequently, both their loss, through interaction of overharvest, habitat degradation, disease, poor water quality, and detrimental species interactions, and their gain, through introductions, can cause complex changes in coastal ecosystems. Introductions can greatly enhance oyster population abundance and production, as well as populations of associated native species. However, introduced oysters are also vectors for non-native species, including disease-causing organisms. Thus, substantial population, community, and habitat changes have accompanied new oysters. In contrast, ecosystem-level consequences of oyster introductions, such as impacts on flow patterns, sediment and nutrient dynamics, and native bioengineering species, are not well understood. Ecological risk assessments for future introductions must emphasize probabilities of establishment, spread, and impacts on vulnerable species, communities, and ecosystem properties. Many characteristics of oysters lead to predictions that they would be successful, high-impact members of recipient ecosystems. This conclusion leaves open the discussion of whether such impacts are desirable in terms of restoration of coastal ecosystems, especially where restoration of native oysters is possible.