Daniel R. Brooks

The nature of diversity : an evolutionary voyage of discovery

All living things on earth - from individual species to entire ecosystems - have evolved through time, and evolution is the acknowledged framework of modern biology. Yet many areas of biology have moved from a focus on evolution to much narrower perspectives. Daniel R. Brooks and Deborah A. McLennan argue that it is impossible to comprehend the nature of life on earth unless evolution - the history of organisms - is restored to a central position in research. They demonstrate how the phylogenetic approach can be integrated with ecological and behavioral studies to produce a richer and more complete picture of evolution. Clearly setting out the conceptual, methodological, and empirical foundations of their research program, Brooks and McLennan show how scientists can use it to unravel the evolutionary history of virtually any characteristic of any living thing, from behaviors to ecosystems. They illustrate and test their approach with examples drawn from a wide variety of species and habitats. The Nature of Diversity provides a powerful new tool for understanding, documenting, and preserving the worlds biodiversity. It is an essential book for biologists working in evolution, ecology, behavior, conservation, and systematics.

Parsimony Analysis in Historical Biogeography and Coevolution: Methodological and Theoretical Update

A unified methodology for parsimony analysis in studies of the co-speciation of clades that co-occur in ecological associations is presented.It incorporates two methodological prescriptions proposed by Wiley with a third, namely duplication of areas when members of single or multiple clades are differentially represented.

Advances in cladistics

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HISTORICAL ECOLOGY: A NEW APPROACH TO STUDYING THE EVOLUTION OF ECOLOGICAL ASSOCIATIONS

Historical ecology is presented as a complementary approach to evolutionary ecology. The prime distinction between the two approaches is the use of direct estimates of history in explanations by the former and of indirect estimates of history by the latter. Direct estimates of history are obtained by using phylogenetic systematics. They require analysis of many species simultaneously. Indirect estimates can be applied in individual cases and include such concepts as: (1) equating number of species in an ecological association with the age of the association; (2) equating the geographic range of a species with its age; and (3) equating the specificity of ecological interactions with the length of time species have been associated. Historical ecological methods have been applied in three general areas: (1) the historical context of geographic distribution patterns; (2) the historical context of ecological associations; and (3) the historical context of particular ecological life history traits. A unified quantitative approach allows historical ecological analysis for individual clades or aggregates of clades. Among the most interesting general conclusions that are forthcoming from the historical ecological perspective are those that differ from the evolutionary ecological view. These include: (1) ecological diversification lags behind morphological diversification historically; (2) degree of specificity is not a thoroughly reliable indicator of the age of an association; (3) resource tracking models of coevolution seem to include unacceptable assumptions; and (4) maximum competition scenarios are indistinguishable from random association scenarios. Future studies promise to be fruitful. A number of fundamental and general questions have held the attention of ecologists for over a century. Why are species distributed in the manner they are? Why are certain species associated with each other ecologically, and how long have such associations existed? And, why do certain species have the ecological life history traits they do, and under what circumstances did those traits emerge? In the past 125 years, biology has operated under an evolutionary paradigm, a stance that I think has been undeniably productive. The search for causal mechanisms responsible for observed attributes has concentrated on evolutionary, that is historical, mechanisms. In ecology, this has led to the emergence of the field called evolutionary ecology. In presenting what I will call historical ecology

How Specialists Can Be Generalists: Resolving the "Parasite Paradox" and Implications for Emerging Infectious Disease

The parasite paradox arises from the dual observations that parasites (broadly construed, including phy- tophagous insects) are resource specialists with restricted host ranges, and yet shifts onto relatively unrelated hosts are common in the phylogenetic diversification of parasite lineages and directly observable in ecological time. We synthe- size the emerging solution to this paradox: phenotypic flexibility and phylogenetic conservatism in traits related to resource use, grouped under the term ecological fitting, provide substantial opportunities for rapid host switching in changing environments, in the absence of the evolution of novel host-utilization capabilities. We discuss mechanisms behind ecological fitting, its implications for defining specialists and generalists, and briefly review empirical examples of host shifts in the context of ecological fitting. We conclude that host shifts via ecological fitting provide the fuel for the expansion phase of the recently proposed oscillation hypothesis of host range and speciation, and, more generally, the generation of novel combinations of interacting species within the geographic mosaic theory of coevolution. Finally, we conclude that taxon pulses, driven by climate change and large-scale ecological perturbation are drivers of biotic mixing and resultant ecological fitting, which leads to increased rates of rapid host switching, including the agents of Emerging Infectious Disease.

ECOLOGICAL FITTING AS A DETERMINANT OF THE COMMUNITY STRUCTURE OF PLATYHELMINTH PARASITES OF ANURANS

Host-parasite associations are assumed to be ecologically specialized, tightly coevolved systems driven by mutual modification in which host switching is a rare phenomenon. Ecological fitting, however, increases the probability of host switching, creating incongruences between host and parasite phylogenies, when (1) specialization on a particular host resource is a shared characteristic of distantly related parasites, and (2) the resource being tracked by the parasite is widespread among many host species. We investigated the effect of ecological fitting on structuring the platyhelminth communities of anurans from a temperate forest and grassland in the United States and tropical dry and wet forests in Mexico and Costa Rica. The six communities all exhibit similar structure in terms of the genera and families inhabiting the frogs. Parasite species richness is highly correlated with the amount of time a host spends in association with aquatic habitats, a conservative aspect of both parasite and host natural history, and determined in a proximal sense by host mobility and diet breadth. The pattern of parasite genera and families within host genera across the regions examined is consistent with the prediction that ecological fitting by phylogenetically conservative species, coupled with historical accidents of speciation and dispersal, should be evidenced as a nested-subset structure; the shared requirement for aquatic habitats of tadpoles provides a baseline assemblage to which other parasite taxa are added as a function of adult host association with aquatic habitats. We conclude that parasite communities are structured by both ecological fitting and coevolution (mutual modification), the relative influences of which are expected to vary among different communities and associations.

Phylogenetic approaches in ecology

This paper argues that many ecological studies could benefit greatly from a phylogenetic approach. For this purpose, cladistics is an appropriate method to reconstruct phylogeny. Case studies from seven research topics in ecology are reviewed. In all studies, historical explanations have played a central role, and mostly, cladograms have been used. Connections to statistical methods for estimating quantitative variation among taxa are discussed. A phylogenetic base would greatly strengthen both problem formulation and analysis. This is true for population studies as well as for all areas where adaptational explanations are invoked; single species studies as well as comparative studies or coevolution studies. Three cladistic procedures useful in ecological research are briefly described. Ecology and systematics have much to offer each other and it is a challenge to bring the two fields together.

Phylogeny and biodiversity: Conserving our evolutionary legacy

Historical ecological studies provide information about the origins of species in an area and the origins of traits characterizing the interactions between those species and their environment. Incorporating this evolutionary information into conservation policies will broaden the base of options for making effective decisions about the preservation of biodiversity.

Theories and methods in different approaches to phylogenetic systematics

Abstract— Systematic techniques may be viewed as symbolic languages which have both surface structure (measures of descriptive adequacy) and deep structure (measures of explanatory adequacy). Phylogenetic systematics is not theory‐neutral because its deep structure embodies evolutionary assumptions. Pattern cladistics stands in relationship to phylogenetic systematics as a part to a whole and is indistinguishable from phylogenetic systematics unless an artificial dichotomy between surface structure and deep structure is maintained. Direct observation of ontogeny as a means of polarizing characters also stands as a part to a whole relative to outgroup comparisons. Direct observation of ontogeny does not resolve any cases that outgroup comparison fails to resolve, and outgroup comparison does resolve some cases where direct observation fails.

Entropy and information in evolving biological systems

Integrating concepts of maintenance and of origins is essential to explaining biological diversity. The unified theory of evolution attempts to find a common theme linking production rules inherent in biological systems, explaining the origin of biological order as a manifestation of the flow of energy and the flow of information on various spatial and temporal scales, with the recognition that natural selection is an evolutionarily relevant process. Biological systems persist in space and time by transfor ming energy from one state to another in a manner that generates structures which allows the system to continue to persist. Two classes of energetic transformations allow this; heat-generating transformations, resulting in a net loss of energy from the system, and conservative transformations, changing unusable energy into states that can be stored and used subsequently. All conservative transformations in biological systems are coupled with heat-generating transformations; hence, inherent biological production, or genealogical proesses, is positively entropic. There is a self-organizing phenomenology common to genealogical phenomena, which imparts an arrow of time to biological systems. Natural selection, which by itself is time-reversible, contributes to the organization of the self-organized genealogical trajectories. The interplay of genealogical (diversity-promoting) and selective (diversity-limiting) processes produces biological order to which the primary contribution is genealogical history. Dynamic changes occuring on times scales shorter than speciation rates are microevolutionary; those occuring on time scales longer than speciation rates are macroevolutionary. Macroevolutionary processes are neither redicible to, nor autonomous from, microevolutionary processes.