Biogeography is a scientific discipline with a rich intellectual heritage extending back at least to the 18th century, and the discipline figured prominently in the development of ideas on evolution (see review in Lieberman, 2000). During the development of ideas on evolution, an important analogy was recognized between patterns of change in organisms across geographic space and patterns of change in organisms through geological time. For instance, Alfred Russel Wallace argued that, “If we now consider the geographical distribution of animals and plants upon the Earth, we shall find all the facts beautifully in accordance with, and readily explained by, the present hypothesis (Evolution). A country having species, genera, and whole families peculiar to it, will be the necessary result of its having been isolated for a long period…The phenomena of geological distribution are exactly analogous to those of geography. Closely related species are found associated in the same beds, and the change from species to species appears to have been as gradual in time as in space.” (Wallace, 1855 in Brooks, 1984, p. 75). Charles Darwin felt it was important enough to remark in the very introduction to his On the Origin of Species that, “…when on board H.M.S. ‘Beagle,’ as naturalist, I was much struck with certain facts in the distribution of the organic beings inhabiting South America, and in the geological relations of the present to the past inhabitants of that continent. These facts, as will be seen in the latter chapters of this volume, seemed to throw some light on the origin of species-that mystery of mysteries” (Darwin, 1859, p. 1).

Paleobiogeography is the discipline that aims to uncover correlations between Earth history (geological and climatic) change and evolution by focusing on how biotas evolve across geographic space. Phylogenetic biogeographic methods applied to fossil taxa, especially those methods based on a modified version of Brooks Parsimony Analysis, have shown potential for uncovering the relationship between Earth history change and evolution. Two processes have an important role in shaping the evolution of biotas across geographic space: these are vicariance and geodispersal. Approaches to biogeographic analysis in the fossil record have uncovered evidence linking some of the key episodes in the history of life, including the Cambrian radiation, to the major geological changes that were occurring at the time. They also have shown that in different time periods with different Earth history signatures the corresponding evolutionary and biogeographic signatures are different. Promising new areas in paleobiogeography include expanded application of phylogenetic approaches and the use of Geographic Information Systems.

Historical biogeography has recently experienced a significant advancement in three integrated areas. The first is the adoption of an ontology of complexity, replacing the traditional ontology of simplicity, or a priori parsimony; simple and elegant models of the biosphere are not sufficient for explaining the geographical context of the origin of species and their post-speciation movements, producing evolutionary radiations and complex multi-species biotas. The second is the development of a powerful method for producing area cladograms from complex data, especially cases of reticulated area relationships, without loss of information. That method, called Phylogenetic Analysis for Comparing trees (PACT), is described herein. The third element is the replacement of the model of maximum vicariance with the model called the Taxon Pulse hypothesis. PACT analysis of Hominoidea, Hyaenidae, and Proboscidea beginning in the Miocene, reveals that all three groups share a general episode of species formation in Africa in the early Miocene, followed by “out of Africa” expansion into Europe, Asia and North America, a second general episode of species formation in Asia in the mid-Miocene, followed by “out of Asia” expansion into Africa, Europe and North America. Finally, there were two additional “out of Africa” events during the late Miocene and into the Pliocene, the last one setting the stage for the emergence and spread of Homo. In addition to these shared episodes of vicariance and dispersal, each group exhibits clade-specific within-area and peripheral isolates speciation events. The complex history of dispersal and speciation over large areas exhibited by hominoids is part of a more general history of biotic diversification by taxon pulses.

Changing oxygen values in the past would have changed the potential for gene flow across higher elevations in terrestrial settings. In this brief review I discuss new work showing that intervals of low oxygen (essentially the late Permian through Middle Jurassic) should have caused extreme endemism among terrestrial animals and perhaps plants.

Lakes are important archives for continental records of paleoenvironmental as well as paleoclimatic change. They also record a unique macroevolutionary pattern that occurred when faunas invaded the continental realm. In order to document that pattern, we compiled a database of over ninety lake basins from the Neoproterozoic to the Permian. Each basin was evaluated based upon its sedimentology and paleontology and, where appropriate, was classified into one of three types: underfilled, balanced-filled, and overfilled, sensu Carroll and Bohacs (1999). The faunal elements from each were recorded at the species, generic, class, and phylum levels.

Looking at this critical time in lacustrine evolution, several patterns emerged. For the Neoproterozoic through Silurian time, there is a paucity of documented lake deposits and lake faunal records. Lakes during this time were oligotrophic and their nutrient cycling regimes were primitive. It is not until the establishment of land plants in the Silurian that lakes begin to respond with higher diversities and more complex physical and chemical conditions. During the Devonian-Carboniferous periods, diversity was on the rise as trophic levels became more complex. Globally, CO2 increased while marine Sr decreased, coinciding with the peaking of diversity within lakes. Most lakes of the Devonian and Carboniferous formed along continental margins or in tectonic basins with occasional connection to the marine realm. The faunas from these types of lakes were commonly comprised of mixed marine and freshwater elements and were far more diverse than other, more inland lakes. This “estuary effect” created a gateway or filter through which faunas invaded the continental realm.

The early history of lake faunas is one of opportunity and amelioration. The feedback loops created by the establishment of vascular plants altered the nutrient cycle on land and in lakes. All trophic levels were established early but became increasingly complex throughout the Paleozoic, as roles changed and faunal elements became established. Groups invading the continents via the “estuary effect” did so numerous times before establishing themselves permanently. This was linked with the episodic reestablishment in marine-freshwater connections along these continental margins. In general, the macroevolutionary history of lake faunas demonstrates a dramatically different diversification pattern than that of the marine, and further study is necessary to understand the intricacies of these patterns and whether or not they continue through the Mesozoic and Cenozoic eras.

Mapping geographic ranges of species and higher taxa using Geographic Information Systems (GIS) produces quantitative data on spatial and temporal changes in geographic ranges. The primary advantage of GIS analysis is that it has the capacity to utilize large amounts of occurrence data of species to produce quantitatively constrained geographic range reconstructions that are amenable to statistical analysis. The basic steps in GIS range reconstruction are database assembly (including taxonomic, geographic, and stratigraphic information for each specimen), mapping of localities of species on modern continental configuration, rotation of occurrence data of species onto paleocontinental reconstructions, and reconstructions of geographic ranges. GIS analysis of ranges of species has been used to assess faunal dynamics of the Late Devonian Biodiversity Crisis, and three case studies are presented here. In these case studies, GIS-derived ranges of species are used to assess the relationship of biogeography with sea level, speciation and extinction rates, mass extinction survival, speciation mode, and invasive history of taxa. These case studies represent a subset of the potential for GIS analyses to examine paleontological patterns and contribute to improving understanding of the interaction between paleobiogeography, paleoecology, and evolution in the fossil record.

Biogeographical barriers serve to limit the geographic range of a species, be it in the ocean or on land. Land barriers to marine migration and marine barriers to land migration are the most easily determined from the geological record; however, temperature can be invoked in both situations. Physiographic features such as mountain ranges can restrict land organisms, and shallow marine organisms may not be able to cross oceans of great depth. Barriers can allow the passage of organisms by three means, in order of greater restriction to migration: 1) corridors; 2) filters; and 3) sweepstakes routes. Examples from the fossil record and recent are given of barriers to marine and continental organisms and their means of overcoming those barriers.

Recent molecular analyses of the traditional scleractinian suborder Faviina have revealed a new Atlantic clade of reef corals, which disagrees with traditional classification. The new clade contradicts long-held notions of Cenozoic diversification being concentrated in the Pacific, and of Atlantic species bearing close evolutionary relationships with Pacific species. In the present paper, we outline an approach for integrating molecular, morphologic, and fossil data, which will allow future examination of the timing and phylogenetic context of the divergence of the new Atlantic clade. Our analyses are preliminary and focus on 17 genetically characterized species within the new Atlantic clade. The molecular dataset consists of 630 base pairs from the COI gene and 1143 base pairs from the cytB gene. The morphologic dataset consists of 25 traditional morphologic characters (86 states) in 57 species (23 extant and 32 extinct). Phylogenetic analyses are first performed separately on the molecular and morphologic (extant taxa only) datasets. Subsequent phylogenetic analyses involve adding fossil taxa to the morphologic dataset and performing a combined analysis for extant taxa.

The results of both molecular and morphologic phylogenetic analyses disagree with traditional classification. They also disagree with each other, indicating the two datasets provide different phylogenetic signals and are informative at different taxonomic levels. Molecular trees for the mitochondrial genes analyzed have higher bootstrap support for deeper nodes in the tree; morphologic trees have higher bootstrap support near branch tips. The addition of fossils to the morphologic dataset does not improve resolution within phylogenetic trees, but it does indicate that all of the major subclades within the new Atlantic clade originated prior to middle Eocene time. The pulse of origination associated with Plio-Pleistocene faunal turnover involved speciation within well-established clades. Examination of the geographic distributions of the taxa within each of the four resulting trees indicates that the origin of the Brazilian reef coral fauna involved more than one separate dispersal event or that the fauna may be descended from a larger Mio-Pliocene Atlantic (Caribbean to Brazil) species pool, portions of which have subsequently become extinct. Because of the complex nature of scleractinian evolution (involving possible hybridization), we advocate using a phylogenetic approach that compares multiple independent datasets, including datasets that are currently being developed for new microstructural characters.

The biogeography of Madagascar is a subject of deep fascination due both to its long isolation from other land masses and to its intrinsic geological complexity. Here, I describe the geological and biological idiosyncrasies of Madagascar, as well as some of the methods that can potentially be applied toward understanding the present distribution of Malagasy mammals, their ancestral origins, and the mechanisms by which they came to occupy Madagascar. Given the potential enormity of the subject, this contribution is provided more in the spirit of provocation than explanation.

Frequent and repeated climate fluctuations of the late Quaternary serve as a “natural experiment” for the response of species to environmental change. Analysis of the FAUNMAP database documents individualistic shifts in the geographic distributions for late Quaternary mammals. However, because the individualistic response is not necessarily random and because many species share similar niche parameters, it is possible that some species appear to form coherent groups of core species. In reality their dispersals are individualistic with regard to rate and timing. The individualistic response of mammals, as well as that of other organisms, has created late Quaternary communities without modern analogues. This concept has profound implications for the design of biological reserves and for land use management with respect to future global climate change. However, the relevance of non-analogue mammal communities has been challenged by Alroy (1999), who claims that non-analogue associations were not common in the Quaternary and that they appeared to occur in both the Pleistocene and Holocene. Reexamination of his analysis shows that he employed a different definition for non-analogue faunas and that his methods of analyses created artificially low counts of non-analogue communities and consequently an underestimate of their importance.