Annual Review of Ecology, Evolution, and Systematics - Volume 30, 1999

The Human Genome Project (HGP) originally sought to sequence the human genome but excluded studies on genetic diversity. Now genetic diversity is a major focus, and evolutionary theory provides needed analytical tools. One type of diversity research focuses on complex traits. This is often done by screening genetic variation at candidate loci functionally related to a trait followed by gene/phenotype association tests. Linkage disequilibrium creates difficulties for association tests, but evolutionary analyses using haplotype trees can circumvent these problems and result in greater statistical power, better disease risk prediction, the elimination of some polymorphisms as causative, and physical localization of causative variation when combined with an analysis of recombination. The HGP also now proposes to map over 100,000 single nucleotide polymorphisms to test for gene/phenotype associations through linkage disequilibrium in isolated human populations affected by past founder or bottleneck events. This strategy requires prior knowledge of recent human evolutionary history and current population structure, but other evolutionary considerations dealing with disequilibrium and nonrandom mutation pose difficulties for this approach. Studies on population structure also focus upon traits of medical relevance, and an understanding of the evolutionary ultimate cause for the predisposition of some populations to certain diseases is a useful predictor for shaping public health policies. Studies on the genetic architecture of common traits reveal much epistasis and variation in norms of reaction, including drug response. Because of these interactions, context dependency and sampling bias exist in disease association studies that require population information for effective use. Overall, the population thinking of evolutionary biology is an important counterweight to naive genetic determinism in applying the results of the HGP to issues of human health and well-being.

Streams in mediterranean-climate regions (areas surrounding the Mediterranean Sea, parts of western North America, parts of west and south Australia, southwestern South Africa and parts of central Chile) are physically, chemically, and biologically shaped by sequential, predictable, seasonal events of flooding and drying over an annual cycle. Correspondingly, aquatic communities undergo a yearly cycle whereby abiotic (environmental) controls that dominate during floods are reduced when the discharge declines, which is also a time when biotic controls (e.g. predation, competition) can become important. As the dry season progresses, habitat conditions become harsher; environmental pressures may again become the more important regulators of stream populations and community structure. In contrast to the synchronous input of autumn litterfall in forested temperate streams, riparian input to mediterranean-type streams is more protracted, with fall and possibly spring peaks occurring in streams in the Northern Hemisphere and a summer peak existing in their Southern Hemisphere counterparts. We present 25 testable hypotheses that relate to the influence of the stream hydrograph on faunal richness, abundance, and diversity; species coexistence; seasonal changes in the relative importance of abiotic and biotic controls on the biotic structure; riparian inputs and the relative importance of heterotrophy compared to autotrophy; and the impact of human activities on these seasonally water-stressed streams. Population increases in mediterranean-climate regions (particularly in fertile regions) result in an intensification of the competition for water among different users; consequently, water abstraction, flow regulation, increased salinity, and pollution severely limit the ability of the streams to survive as sustainable, self-regulated systems.

Over the past ten years the scientific basis for reserve selection and design have rapidly developed. This period has also been characterized by a shift in emphasis toward large spatial and organizational scales of conservation efforts. I discuss the evidence in support of this shift toward larger scale conservation by contrasting the success of fine-filter (genes, populations, species) conservation and coarse-filter (communities, habitats, ecosystems, landscapes) conservation. Conservation at both organizational scales has been successful and merits continued support, although fine-filter conservation is more straightforward. Ecological theory suggests that conservation at large scales is preferred. Despite this preference, both fine- and coarse-filter conservation objectives have been met by small reserves. In many landscapes there are no opportunities for the conservation of native species diversity that encompass a large spatial scale. Thus, reserve selection at any organizational scale may include conservation at a variety of spatial scales. A variety of methods have been suggested that integrate across scales of conservation. Some, such as umbrella, flagship, and indicator species, remain very problematic. Reserve selection algorithms and gap analyses, in contrast, offer promising opportunities to increase the efficiency of conservation at all scales.

The evolution of reproductive isolation is perhaps the most significant stage in the process of species formation, and the study of reproductive barriers currently dominates investigations of speciation. The discovery that conspecific sperm and pollen precedence play an important role in the reproductive isolation of some closely related animals and plants is one of the real surprises to emerge from this field in recent years. This review begins with a brief history of the study of reproductive isolation with the aim of understanding why conspecific sperm and pollen precedence were generally overlooked in early work on reproductive barriers. It then examines: case studies, the prevalence of conspecific sperm and pollen precedence, the isolating potential of this class of reproductive barriers, the mechanisms that account for the operation of these barriers, and potential explanations for the rapid divergence of populations in traits related to fertilization. Conspecific sperm and pollen precedence appear to be quite effective in limiting gene exchange; these barriers are widespread although not universal in animals and plants, and they operate through a number of different mechanisms. Much more work remains to be done on a number of fronts to elucidate the processes responsible for the evolution of these reproductive barriers.

Declines and losses of amphibian populations are a global problem with complex local causes. These may include ultraviolet radiation, predation, habitat modification, environmental acidity and toxicants, diseases, changes in climate or weather patterns, and interactions among these factors. Understanding the extent of the problem and its nature requires an understanding of how local factors affect the dynamics of local populations. Hypotheses about population behavior must be tested against appropriate null hypotheses. We generated null hypotheses for the behavior of amphibian populations using a model, and we used them to test hypotheses about the behavior of 85 time series taken from the literature. Our results suggest that most amphibian populations should decrease more often than they increase, due to highly variable recruitment and less variable adult mortality. During the period covered by our data (1951–1997), more amphibian populations decreased than our model predicted. However, there was no indication that the proportion of populations decreasing changed over time. In addition, our review of the literature suggests that many if not most amphibians exist in metapopulations. Understanding the dynamics of amphibian populations will require an integration of studies on and within local populations and at the metapopulation level.

Until recently, studies of plant reproductive systems have been at the population level, using microevolutionary approaches. The development of cladistic approaches, combined with the emergence of molecular systematics, has resulted in an explosion of phylogenetic studies and an increase in interdisciplinary approaches combining ecological and systematic methodology. These new approaches offer the possibility of testing explicit hypotheses about the number of evolutionary transitions in reproductive characters and the evolutionary relationship of these characters to changes in the environment. Character mapping may be especially useful for detecting convergent evolution. In a number of cases, character mapping has provided new insights into the evolution of plant breeding systems and pollination biology, especially in suggesting the number of times evolutionary transitions have taken place, indicating where there have been reversals and suggesting when preadaptation has been important. The insights provided by character mapping are determined by a number of factors, including the degree of confidence in phylogenies underlying these studies and the identification of appropriate outgroups. Assumptions about character coding, character ordering, inclusion vs. exclusion of characters that are mapped on trees in the data matrix, and weighting of characters will have profound effects on interpretation of character evolution. Highly labile characters that evolve frequently and have the potential to undergo reversals may make it difficult to detect the pattern of character evolution. Characters that are very strongly correlated with each other or with ecological shifts may make prediction of cause and effect using phylogenetic approaches difficult because changes in characters and ecological shifts will occur, apparently simultaneously, on the same branches. Results from microevolutionary studies have been used in several cases to weight transitions, suggesting that results of phylogenetic studies may not provide fully independent assessments of character evolution. While not a simple cure to understanding problems that have been studied only in the realm of microevolutionary studies, phylogenetic approaches offer clear potential for providing new insights for evolutionary studies.

Mimicry and warning color are highly paradoxical adaptations. Color patterns in both Müllerian and Batesian mimicry are often determined by relatively few pattern-regulating loci with major effects. Many of these loci are “supergenes,” consisting of multiple, tightly linked epistatic elements. On the one hand, strong purifying selection on these genes must explain accurate resemblance (a reduction of morphological diversity between species), as well as monomorphic color patterns within species. On the other hand, mimicry has diversified at every taxonomic level; warning color has evolved from cryptic patterns, and there are mimetic polymorphisms within species, multiple color patterns in different geographic races of the same species, mimetic differences between sister species, and multiple mimicry rings within local communities. These contrasting patterns can be explained, in part, by the shape of a “number-dependent” selection function first modeled by Fritz Müller in 1879: Purifying selection against any warning-colored morph is very strong when that morph is rare, but becomes weak in a broad basin of intermediate frequencies, allowing opportunities for polymorphisms and genetic drift. This Müllerian explanation, however, makes unstated assumptions about predator learning and forgetting which have recently been challenged. Today's “receiver psychology” models predict that classical Müllerian mimicry could be much rarer than believed previously, and that “quasi-Batesian mimicry,” a new type of mimicry intermediate between Müllerian and Batesian, could be common. However, the new receiver psychology theory is untested, and indeed it seems to us unlikely; alternative assumptions could easily lead to a more traditional Müllerian/Batesian mimicry divide.

The squid-vibrio light-organ symbioses, which have been under investigation for just over 10 years, offer the opportunity to decipher aspects of the dynamics of stable associations between animals and bacteria. The two best-studied partners, the Hawaiian sepiolid squid Euprymna scolopes and the marine luminous bacterium Vibrio fischeri, engage in the most common type of animal-bacterial association, i.e., between extracellular, gram-negative bacteria and animal epithelia. Similar to most such symbioses, the squid-vibrio relationship begins anew each generation when thehost animal acquires the symbiont from the surrounding environment. To establish a specific association, mechanisms have evolved to ensure recognition between the host and symbiont and the exclusion of other potential partnerships. Once the association has been established, the bacteria induce significant morphological changes in the host that result in a transition of the light organ from a form associated with initiation of the symbiosis to one characteristic of the mature, functional relationship.

Recent overviews have suggested that the relationship between species richness and productivity (rate of conversion of resources to biomass per unit area per unit time) is unimodal (hump-shaped). Most agree that productivity affects species richness at large scales, but unanimity is less regarding underlying mechanisms. Recent studies have examined the possibility that variation in species richness within communities may influence productivity, leading to an exploration of the relative effect of alterations in species number per se as contrasted to the addition of productive species. Reviews of the literature concerning deserts, boreal forests, tropical forests, lakes, and wetlands lead to the conclusion that extant data are insufficient to conclusively resolve the relationship between diversity and productivity, or that patterns are variable with mechanisms equally varied and complex. A more comprehensive survey of the ecological literature uncovered approximately 200 relationships, of which 30% were unimodal, 26% were positive linear, 12% were negative linear, and 32% were not significant. Categorization of studies with respect to geographic extent, ecological extent, taxonomic hierarchy, or energetic basis of productivity similarly yielded a heterogeneous distribution of relationships. Theoretical and empirical approaches increasingly suggest scale-dependence in the relationship between species richness and productivity; consequently, synthetic understanding may be contingent on explicit considerations of scale in analytical studies of productivity and diversity.

Allozyme polymorphisms have been the focus of studies of selection at single enzyme loci, and most involve the enzymes of central metabolism. DNA sequencing of enzyme loci has shown numerous examples of multiple amino acid polymorphisms segregating within electromorphs. The amino acid heterogeneity underlying many allozyme polymorphisms should confound analysis of functional differences and selection. Metabolic control theory proposed that pathways will be insensitive to functional changes in allozymes; however, there is evidence that many polymorphisms modulate fluxes. Studies of model systems have provided detailed evidence for selection acting on enzyme polymorphisms in metabolic genes. There is also evidence that regulatory changes are superimposed on structural changes. Codon bias implies that the functional differences encountered in allozyme studies should be detectable by natural selection; however, amino acid polymorphisms may also represent weakly deleterious mutations. Future studies should connect structural changes with effects on function and stability, and they should emphasize the multilocus nature of responses to selection.

Polymorphism, or variation within species, is common in all kinds of data and is the major focus of research on microevolution. However, polymorphism is often ignored by those who study macroevolution: systematists and comparative evolutionary biologists. Polymorphism may have a profound impact on phylogeny reconstruction, species-delimitation, and studies of character evolution. A variety of methods are used to deal with polymorphism in phylogeny reconstruction, and many of these methods have been extremely controversial for more than 20 years. Recent research has attempted to address the accuracy of these methods (their ability to estimate the true phylogeny) and to resolve these issues, using computer simulation, congruence, and statistical analyses. These studies suggest three things: that (a) the exclusion of polymorphic characters (as is commonly done in morphological phylogenetics) is unjustified and may greatly decrease accuracy relative to analyses that include these characters; (b) methods that incorporate frequency information on polymorphic characters tend to perform best, and (c) distance and likelihood methods designed for polymorphic data may often outperform parsimony methods. Although rarely discussed, polymorphism may also have a major impact on comparative studies of character evolution, such as the reconstruction of ancestral character states. Finally, polymorphism is an important issue in the delimitation of species, although this area has been somewhat neglected methodologically. The integration of within-species variation and microevolutionary processes into studies of systematics and comparative evolutionary biology is another example of the benefits of exchange of ideas between the fields of population genetics and systematics.

Flowing water has profound effects on a diverse array of ecological processes and patterns in streams and rivers. We propose a conceptual framework for investigating the multiple causal pathways by which flow influences benthic biota and focus particular attention on the local scales at which these organisms respond to flow. Flow (especially characteristics linked to the velocity field) can strongly affect habitat characteristics, dispersal, resource acquisition, competition, and predation; creative experiments will be needed to disentangle these complex interactions. Benthic organisms usually reside within the roughness layer, where the unique arrangement of sediment particles produces strongly sheared and highly three-dimensional flow patterns. Thus, accurate characterization of the local flow environments experienced by benthic organisms often requires the use of flow measurement technology with high spatial and temporal resolution. Because flow exhibits variation across a broad range of scales, it is also necessary to examine how organism-flow relationships at one scale are linked to those at others. Interdisciplinary approaches are needed in the study of physical-biological coupling; increased collaboration between ecologists and experts in fluid mechanics and hydraulic engineering is particularly desirable. A greater understanding of physical-biological coupling will not only yield deeper insights into the ecological organization of streams and rivers, it will also improve our ability to predict how flow alterations caused by various human activities affect these vital ecosystems.

The search for the origins of life and its presence beyond Earth is strengthened by new technology and by evidence that life tolerates extreme conditions and that planets are widespread. Astrobiologists learn how planets develop and maintain habitable conditions. They combine biological and information sciences to decipher the origins of life. They examine how biota, particularly microorganisms, evolve, at scales from the molecular to the biosphere level, including interactions with long-term planetary changes. Astrobiologists learn how to recognize the morphological, chemical, and spectroscopic signatures of life in order to explore both extraterrestrial samples and electromagnetic spectra reflected from extrasolar planets.

The disjunct distributions of morphologically similar plants between eastern Asia and eastern North America have fascinated botanists and biogeographers since the Linnaean era. This biogeographic pattern is currently recognized by the disjunct distributions of some species, approximately 65 genera, and a few closely related genera in these two widely separated areas. Early workers treated many disjuncts as conspecific, but most were later recognized as intercontinental species pairs. Recent phylogenetic studies confirm affinities between many of the disjunct taxa but also indicate that the disjunct pairs of species are rarely each other's closest relatives. Instead, a pattern of further diversification of species on one or both continents is commonly found. Phylogenetic, molecular, geologic, and fossil data all support the hypothesis that the eastern Asian and eastern North American disjunct distributions are relicts of the maximum development of temperate forests in the northern hemisphere during the Tertiary. Fossil and geologic evidence supports multiple origins of this pattern in the Tertiary, with both the North Atlantic and the Bering land bridges involved. In many genera of flowering plants, current estimates of divergence times using molecular and fossil data suggest that the disjunct patterns were established during the Miocene. Morphological stasis, evidenced by the minimal morphological divergence of species after a long time of separation, must have occurred in some of the disjunct groups in the north temperate zone.

The discovery that DNA survives in ancient remains and can be amplified by the polymerase chain reaction has added a direct temporal dimension to evolutionary studies. Initial reports suggested that the time period open to investigation was vast, extending back into the Cretaceous period. However, attempts to replicate of results involving DNA purported to be over a million years old have not succeeded. Theoretical studies suggest that DNA is unlikely to survive intact more than about 100,000 years. However, even over this time period, the evolutionary questions that can be addressed are far reaching and include systematics, paleoecology, the origin of diseases, and evolutionary processes at the population level.

Inbreeding depression critically influences both mating system evolution and the persistence of small populations prone to accumulate mutations. Under some circumstances, however, inbreeding will tend to purge populations of enough deleterious recessive mutations to reduce inbreeding depression (ID). The extent of purging depends on many population and genetic factors, making it impossible to make universal predictions. We review 52 studies that compare levels of ID among species, populations, and lineages inferred to differ in inbreeding history. Fourteen of 34 studies comparing ID among populations and species found significant evidence for purging. Within populations, many studies report among-family variation in ID, and 6 of 18 studies found evidence for purging among lineages. Regression analyses suggest that purging is most likely to ameliorate ID for early traits (6 studies), but these declines are typically modest (5–10%). Meta-analyses of results from 45 populations in 11 studies reveal no significant overall evidence for purging, but rather the opposite tendency, for more selfing populations to experience higher ID for early traits. The likelihood of finding purging does not vary systematically with experimental design or whether early or late traits are considered. Perennials are somewhat less likely to show purging than annuals (2 of 10 vs. 7 of 14). We conclude that although these results doubtless reflect variation in population and genetic parameters, they also suggest that purging is an inconsistent force within populations. Such results also imply that attempts to deliberately reduce the load via inbreeding in captive rearing programs may be misguided. Future studies should examine male and female fitness traits over the entire life cycle, estimate mating histories at all levels (i.e. population and families within populations), report data necessary for meta-analysis, and statistically test for purging of genetic loads.

Domesticated plant taxa cannot be regarded as evolutionarily discrete from their wild relatives. Most domesticated plant taxa mate with wild relatives somewhere in the world, and gene flow from crop taxa may have a substantial impact on the evolution of wild populations. In a literature review of the world's 13 most important food crops, we show that 12 of these crops hybridize with wild relatives in some part of their agricultural distribution. We use population genetic theory to predict the evolutionary consequences of gene flow from crops to wild plants and discuss two applied consequences of crop-to-wild gene flow–the evolution of aggressive weeds and the extinction of rare species. We suggest ways of assessing the likelihood of hybridization, introgression, and the potential for undesirable gene flow from crops into weeds or rare species.

Interspecific hybridization can disrupt normal resistance of plant and animal species to their parasites. Resistance to parasites is affected by hybridization in the following ways: no difference between hybrids and parentals, additivity, hybrid susceptibility, and dominance to susceptibility. Similar patterns were seen across host taxa. Responses of different parasite species vary widely to the same hybrid host, which indicates diverse genetic effects of interspecific hybridization on resistance. Differences between field and common garden or laboratory studies suggest that environmental factors in hybrid zones influence the patterns seen in the field. Based on recent studies of hybrid-parasite interactions, three avenues of future research will provide a more complete understanding of the roles of hybrids and the roles of parasites in host evolution. First, the relationship between inheritance of putative resistance mechanisms of hosts and responses of parasites needs study using analyses of recombinant progenies. Second, the interaction among environmental variation in hybrid zones, resistance mechanisms, responses of parasites, and the impact of parasites on host fitness needs experimental analysis using reciprocal transplant experiments in hybrid zones. Finally, the role of hybrids in the community structure and interactions of parasites needs study.