Bones, Clones, and Biomes The History and Geography of Recent Neotropical Mammals
edited by Bruce D. Patterson and Leonora P. Costa
University of Chicago Press, 2012
Cloth: 978-0-226-64919-1 | Electronic: 978-0-226-64921-4
DOI: 10.7208/chicago/9780226649214.001.0001


As explorers and scientists have known for decades, the Neotropics harbor a fantastic array of our planet’s mammalian diversity, from capybaras and capuchins to maned wolves and mouse opossums to sloths and sakis. This biological bounty can be attributed partly to the striking diversity of Neotropical landscapes and climates and partly to a series of continental connections that permitted intermittent faunal exchanges with Africa, Antarctica, Australia, and North America. Thus, to comprehend the development of modern Neotropical mammal faunas requires not only mastery of the Neotropics’ substantial diversity, but also knowledge of mammalian lineages and landscapes dating back to the Mesozoic.

Bones, Clones, and Biomes offers just that—an exploration of the development and relationships of the modern mammal fauna through a series of studies that encompass the last 100 million years and both Central and South America. This work serves as a complement to more taxonomically driven works, providing for readers the long geologic and biogeographic contexts that undergird the abundance and diversity of Neotropical mammals. Rather than documenting diversity or distribution, this collection traverses the patterns that the distributions and relationships across mammal species convey, bringing together for the first time geology, paleobiology, systematics, mammalogy, and biogeography. Of critical importance is the book’s utility for current conservation and management programs, part of a rapidly rising conservation paleobiology initiative.


Bruce D. Patterson is the MacArthur Curator of Mammals at the Field Museum of Natural History in Chicago. Leonora P. Costa is associate professor in the Departamento de Ciências Biológicas at Universidade Federal do Espírito Santo, Vitória, Brazil.


“The new world tropics contain about a third of the known diversity of mammals, and this important work represents a modern synthesis of both paleontological and recent knowledge about the mammals of the region to better understand the current patterns of diversification and distribution. Our current understanding of plate tectonics, phylogenetic systematics, and huge advances in understanding the chronology of fossil mammal finds in South America argues that a synthesis such as that attempted here is timely.”
— Don E. Wilson, Smithsonian Institution

“Scientists have long recognized the value of South America as a grand evolutionary experiment. In this geologically and climatically turbulent region, long episodes of isolation from the rest of the world’s continents generated deeply divergent groups of endemic mammals, while plate tectonics dictated the sporadic infusion of new groups, generating new waves of diversification, adding new layers to the sequential accumulation of recent Neotropical mammal richness. In this compilation, the editors have brought paleontologists, geologists, molecular systematists, and biogeographers together to provide a much needed update on the unfolding story of recent Neotropical mammal diversity and diversification. This volume will be a welcomed addition to the libraries of a new generation of scientists seeking to unravel further the history of Neotropical mammal evolution in this fascinating and important region.”
— Brett R. Riddle, University of Nevada, Las Vegas

“This fascinating compilation provides a sorely needed modern synthesis of the impact of geology, history, evolution, and ecology on the distribution and biogeography of Neotropical mammals. Covering mammal evolutionary history and dispersal since its early origins, and spanning current geographical distribution and diversity from the West Indies and Central America to Amazonia, the Andes, and Patagonia, this remarkably informative volume will force readers to revise everything they thought they knew about Neotropical mammals.”
— Peter Meserve, Northern Illinois University

"An exploration of the development and relationships of the modern mammal fauna through a series of studies that encompass the last 100 million years and both Central and South America. This work serves as a complement to more taxonomically driven works, providing for readers the long geologic and biogeographical contexts that undergird the abundance and diversity of Neotropical mammals."
— Guardian

“Excellent maps, charts, and tables support clearly written text. Recommended.”
— E. Delson, CUNY Herbert H. Lehman College, Choice

“This excellent volume should . . . generate wide interest as an example of how to integrate science research across disciplines ranging from molecular genetics to paleontology as a means of exploring the dynamic history of a region. As both a synthesis of our current understanding and a user-friendly reference work (both taxonomic and subject indices are included), Bones,Clones, and Biomes will find broad use.”

— Joseph A. Cook, BioScience

“Editors Patterson and Costa fill a huge gap in the literature of Neotropical mammals with this up-to-date volume. . . . The book masterfully provides a synthesis of the evolutionary history and biogeographic patterns of recent mammals along with comprehensive coverage of past faunas. This well-executed combination of paleontology and neontology makes Bones, Clones, and Biomes a unique and timely contribution to historical biogeography. . . .  No biologist interested in organismal evolution in the New World should skip this volume, and it is a must-read for mammalogists.”
— Journal of Mammalogy

“I strongly recommend Bones, Clones, and Biomes to anyone interested in the recent or fossil mammals of the Neotropics, as well as to readers with a broader interest in the evolutionary history of mammalian faunas. You will be rewarded with a deeper understanding and appreciation of this fascinating fauna.”
— Journal of Vertebrate Paleontology


- Bruce D. Patterson, Leonora P. Costa
DOI: 10.7208/chicago/9780226649214.003.0001
[neotropical mammals, species, organisms, landscape, biomes, rainforests, biotic diversity]
The Neotropics are home to more than 1500 species of living mammals, almost 30% of all extant species. These charismatic organisms include remarkable animals found nowhere else on earth: armadillos and anteaters, capybaras and capuchins, maned wolves and mouse opossums, sloths and sakis. This biological bounty can be partly attributed to the striking diversity of Neotropical landscapes and biomes. The region supports lush rainforests (both temperate and tropical), parched deserts, sprawling savannas, thorny scrublands, alpine steppes, and towering peaks. A plethora of climatic and edaphic conditions accompanies and shape this biotic diversity. Another agency fostering its endemism has been South America's isolation as an island continent for much of the last 65 million years (Ma). However, unlike its Gondwana neighbor Australia, South America's history of isolation has been interrupted by a succession of continental connections that permitted intermittent faunal exchanges with Africa, Antarctica and Australia, and North America at different times. (pages 1 - 6)
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Part 1. The Geological Setting

- Darin A. Croft
DOI: 10.7208/chicago/9780226649214.003.0002
[mammals, fossils, evolution, paleontology, South America]
South America's fossil record of mammals from the Cenozoic Era (the past 65 million years or so) is far from perfect. No fossils have yet been discovered from some intervals of this time span, whereas only one or a few poorly sampled localities represent others. South America's mammalian record pales in comparison to that of northern continents. South America probably has the best fossil record of mammals among southern hemisphere continents. The broad picture of mammal evolution on the continent has been known for more than half a century. The mammals of this continent evolved largely within the context of isolation, punctuated by rare episodes of waif dispersal and faunal interchange. This contrasts starkly with the history of mammal evolution on northern continents, in which episodes of faunal interchange were commonplace. Although the general context of evolving mammal communities in South America has been known for many years, remarkable advances have taken place in recent decades in virtually every aspect of mammalian paleontology. Scores of researchers have made these advances from South America and elsewhere using a variety of methods ranging from traditional to cutting edge. (pages 9 - 19)
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- Francisco J. Goin, Javier N. Gelfo, Laura Chornogubsky, Michael O. Woodburne, Thomas Martin
DOI: 10.7208/chicago/9780226649214.003.0003
[mammals, greenhouse, icehouse worlds, Patagonian fossil, water erosion, wind erosion]
This chapter offers a broad-stroke perspective on changing faunas and habitats of South America over the past 250 (million years) Ma. The observations are based primarily on the Patagonian fossil record, since it is the only region of the continent where nearly all major time intervals are represented. The excellent record in Patagonia is the result of fortuitous geological and climatic factors. For much of the Cenozoic, parts of Patagonia gradually accumulated water- and wind-borne sediments, conditions highly suitable for the preservation of teeth, bones, tracks, and other evidence of past life. Some of these sediments were sands and silts derived from the erosion of topographically higher areas, whereas others were ashes from volcanic eruptions. Water and wind erosion in Patagonia continuously expose new fossils. The chapter recognizes five main phases in the evolution of South American mammal faunas. (pages 20 - 50)
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- John J. Flynn, Reynaldo Charrier, Darin A. Croft, Andre R. Wyss
DOI: 10.7208/chicago/9780226649214.003.0004
[Cenozoic mammals, Andean faunas, mammal evolution, South America, biogeography, environments, tectonics]
This chapter shows that other areas of the Andes (Colombia and Bolivia in particular) have also produced significant collections of Cenozoic mammals. Smaller collections have come from the Andes of Ecuador and Peru. Most of these localities are north of the Tropic of Capricorn, well outside the traditionally well-sampled southern part of the continent. The only other mammal faunas known from this vast area of South America are a handful of lowland faunas from Brazil, Peru, and Venezuela. These low and middle latitude assemblages have provided critical insights into the development of Neotropical mammal communities. They are spread over tens of millions of years; however, they provide mere glimpses of habitats and communities rather than an integrated picture of evolving mammal faunas. Sampling thus remains a key issue in Neotropical paleomammalogy, especially in light of biogeographic hypotheses that recognize Patagonia as a region distinct from the rest of South America. Documenting new fossil mammal localities in low and intermediate latitudes is a priority for future research. (pages 51 - 75)
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- Sergio F. Vizcaíno, Guillermo H. Cassini, Néstor Toledo, M. Susana Bargo
DOI: 10.7208/chicago/9780226649214.003.0005
[mammalian herbivores, cenozoic faunas, ecosystems, paleocommunities, carnivorans, metatherian mammals]
This chapter examines how mammal body mass maxima and ranges have changed over the past 40 Ma. The study demonstrates that different taxonomic groups have occupied the role of largest herbivore during this interval, and indicates that the greatest diversity of large species was present in South America only 10,000 BP. This latter observation has important implications for the functioning of modern ecosystems and suggests that these paleocommunities were structured quite differently than those of today, a finding that echoes results of similar studies of other time intervals. The chapter adds to an expanding body of literature on diet, locomotion, body mass, and community structure that together have created a much more detailed picture of the life and times of extinct South American mammals. The absence of carnivorans (i.e., members of the order Carnivora) is a characteristic and intriguing feature of most South American paleocommunities. In their absence, the role of large, terrestrial, warm-blooded meat-eater (carnivore) was filled by metatherian mammals—specifically sparassodonts (borhyaenids and relatives)—as well as phorusrhacids, also known as terror birds, which were large to giant flightless birds with oversized heads and hooked beaks. (pages 76 - 101)
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- Francisco J. Prevosti, Leopoldo H. Soibelzon
DOI: 10.7208/chicago/9780226649214.003.0006
[carnivores, paleontological record, Cenozoic era, mega herbivores]
This chapter discusses the timing and pattern of carnivoran arrival and diversification in South America, as evidenced by the paleontological record. Although sampling deficiencies exist, the overall trend is one of staggered immigrations to South America followed by virtually unrestrained diversification (dampened only by a Quaternary extinction event). The last sparassodonts coexisted with the earliest South American carnivorans and there is no consensus regarding the role of carnivorans, if any, in their extinction. By any standard, however, the evolutionary success of carnivorans in the continent has been remarkable. The number of species presently inhabiting South America rivals the number of sparassodonts known from the entire Cenozoic. Modern South American ecosystems might still reflect the effects of the loss of these and other mega herbivores, and that this should be an area of further investigation. (pages 102 - 122)
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- Eduardo Eizirik
DOI: 10.7208/chicago/9780226649214.003.0007
[neotropical carnivores, morphological data, paleontology, Great American Biotic Interchange, carnivoran diversification, Neotropics]
This chapter addresses carnivoran diversification in the Neotropics by reviewing recent studies that employed molecular data sets for phylogenetic reconstructions and molecular dating. Most of the examples cover interfamilial and intergeneric splits, and discuss the implications of molecular-derived divergence dates for the interpretation of biogeographic patterns. In some cases, the discussion extends to intrageneric diversification, contrasting recent endemic clades (especially in the Felidae and Canidae) that show rapid divergences postdating the Great American Biotic Interchange (GABI) with others that have a more ancient history in the region. This is particularly the case with the Procyonidae, whose molecular dating analyses point not only to a much older origin than previously estimated, but also to splits between sister species that predate the GABI, contrary to traditional views on their historical biogeography. Overall, carnivores appear to be a remarkable group for investigating the diversity of biogeographic patterns and processes that characterize the history of the Neotropics, as diff erent clades have experienced disparate histories, with contrasting influences derived from the GABI. (pages 123 - 142)
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Part 2. Regional Patterns

- Sergio Solari, Paúl M. Velazco, Bruce D. Patterson
DOI: 10.7208/chicago/9780226649214.003.0008
[Neotropics, mammals, biome, taxonomy, hierarchical organization]
The Neotropics are home to roughly 1550 living species of mammals, 30% of all extant species, including groups found nowhere else on the Earth. This richness and uniqueness can be attributed to the amazing diversity of biomes in the Neotropics, including tropical rain forests, highland grasslands, deserts, savannas, and scrublands, many of them influenced to some degree by the Andes Mountains. In addition, the South American portion of the Neotropics was isolated during the late Mesozoic and most of the Cenozoic, interrupted by a sequence of continental connections that permitted faunal interchanges with Africa, Antarctica and Australia, and North America at different times. This chapter summarizes the distributions of living mammals at a general, gross scale, using a recent synopsis of mammal taxonomy and previously identified biogeographic units to identify general patterns reflected in the distributions of supraspecific groups. (pages 145 - 156)
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- Liliana M. Dávalos, Samuel T. Turvey
DOI: 10.7208/chicago/9780226649214.003.0009
[West Indian mammals, extinct, phylogenetic, population genetic, endemic lineages, pleistocene glacial cycles, biodiversity, Quaternary extinction]
The West Indian mammal fauna has played a key role in the development of biogeographic ideas for over a century, but a synthesis explaining regional patterns of mammal diversity and distribution in a historical framework has not emerged. Recent phylogenetic, population genetic, and radiocarbon dating studies of West Indian mammals explore the biological and historical drivers of colonization, speciation, and extinction in this region of endemism. A complete list of all its extant and extinct mammals is presented in this chapter. The mammalian biota is older than was earlier presumed, with many ancient endemic lineages, even among highly vagile organisms such as bats. Land bridges, Cenozoic eustatic sea-level changes and Pleistocene glacial cycles have been proposed to explain the colonization of the islands, but phylogenetic divergence analyses often conflict with the timing of these events and favor alternative biogeographic histories. The loss of West Indian biodiversity is incompletely understood, but new radiometric chronologies indicate that anthropogenic impacts rather than glacial-interglacial environmental changes are responsible for most Quaternary extinction and extirpation events involving land mammals. (pages 157 - 202)
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- Ana Laura Almendra, Duke S. Rogers
DOI: 10.7208/chicago/9780226649214.003.0010
[biogeography, mammals, biodiversity, nearctic, neotropical, phylogeographic, Pleistocene, Pliocene]
Central America contains a disproportionate amount of biodiversity owing to its complex topography and geologic history and its position between the Nearctic and Neotropical realms. The understanding of Central American faunas is far from complete and biogeographic and phylogeographic patterns for mammals are not well articulated, some conclusions are emerging from analyses of molecular data. For example, the actual biodiversity for mammals, particularly for rodents, is likely much higher than currently documented. The historical events and geographic features that have shaped Central America seem to have affected mammals and other groups in similar fashion. Mid and high elevation faunas are relatively diverse and contain higher levels of endemism than lowland faunas, although radiations have occurred among both lowland and montane taxa. Rodents exhibit more genetic structure than do bats, ungulates, and primates over comparable geographic sampling. In many cases, estimated levels of molecular divergence correspond to events that occurred in the early Pleistocene or late Pliocene. Unfortunately, continued and rapid change in land-use practices throughout Central America may preclude a complete and accurate reconstruction of the region's historical biogeography. (pages 203 - 229)
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- Burton K. Lim
DOI: 10.7208/chicago/9780226649214.003.0011
[biogeography, mammals, guianas, species, Miocene, South America]
The Guianas of northern South America consist of French Guiana, Suriname, Guyana, and southeastern Venezuela (states of Delta Amacuro, Bolivar, and Amazonas). There are 284 species representing 12 orders of terrestrial mammals documented from the Guianas. Over half of the species (147) are bats, with rodents accounting for about 20 percent and other orders each representing less than 10 percent of the mammalian species. The Guiana plateau (〉500 m elevation) is the most prominent biogeographic feature. It has influenced diversification of mammals in this region by fostering endemism and functioning as a geographic barrier. Within South America, the ancient Guiana Shield has acted as a stable core area for range expansions from both the Andes and the Amazon during periods of environmental change beginning in the Miocene. (pages 230 - 258)
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- Cibele R. Bonvicino, Marcelo Weksler
DOI: 10.7208/chicago/9780226649214.003.0012
[organisms, biographic, geotectonic, mammals, Pliocene]
Recent work on the phylogeographic patterns of Amazonian organisms and a better understanding of the geologic history of the region have enabled scientists to specify and test the spatial, temporal, and phylogenetic predictions of these biogeographic models. Four main causal factors have been postulated, and their expectations and predictions are reviewed here: Firstly, the role of rivers as barriers to species dispersal is evident, but their role as primary agents of speciation is still unclear. Secondly, geotectonic changes associated with uplift of the central Andes and increase in global sea levels produced gradual submersion of western Amazonia, creating the wetland system known as Lake Pebas. The effects of marine incursions have been associated with diversification of several organisms, but no mammalian phylogenetic pattern has been effectively linked to Lake Pebas. Thirdly, the genetic structure of rodents and frogs in Western Amazonia is correlated with the location and orientation of the Iquitos Paleoarch, an ancient drainage barrier that survived until the Pliocene. Fourthly, several variations of refugia in response to Quaternary climatic fluctuations are not supported by genetic studies of small mammals. The knowledge of the biogeographic processes leading to patterns within Amazonia is still incomplete, as the mammalian fauna of this vast region and the spatial and temporal genetic patterns of most of its species remain poorly known. (pages 259 - 282)
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- Leonora P. Costa, Yuri L. R. Leite
DOI: 10.7208/chicago/9780226649214.003.0013
[vertebrates, biodiversity, biogeography, phylogeographic, Atlantic Forest]
The Atlantic Forest is one of the world's 32 biodiversity hotspots, reflecting its high levels of plant and animal richness, endemism, and threats. Traditional biogeographic studies, based mainly on plants and other vertebrate groups, such as lizards, have long pointed out the singularities of this area, as well as provided indications of a marked distinction between north and south components in the Atlantic Forest. Phylogeographic studies have documented and reinforced the general pattern of southern and northern components for many taxonomic groups, including rodents, marsupials, carnivores, and xenarthrans, as well as for other vertebrates, such as lizards, birds, snakes, and frogs. There are striking phylogeographic breaks within the Atlantic Forest, most of them represented by northern and southern components that converge at 20°S latitude, suggesting a common vicariant event. However, it remains to be determined when and where the Atlantic Forest phylogroups were isolated, what events were responsible for their isolation, and how the different groups responded to such events. (pages 283 - 306)
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- Ana Paula Carmignotto, Mario de Vivo, Alfredo Langguth
DOI: 10.7208/chicago/9780226649214.003.0014
[mammals, biomes, grasslands, savannas, Pleistocene, South America]
Cerrado and Caatinga are neighboring open biomes of tropical South America, but their vegetation, soil, and climate characteristics render them distinctive formations. Despite these differences, their mammal faunas are largely shared. The gallery, semideciduous, and deciduous forests contribute importantly to the species richness of these faunas, which together with the open habitats such as grasslands, savannas, and shrubby caatinga; enhance the overall species richness and high regional diversity of these formations. However, distinct histories of the open and forested formations are evident in mammal species distributions. The disjunct distribution of some arboreal mammals in the eastern Amazon and northern Atlantic rain forests, together with Pleistocene records of arboreal mammals in present-day areas of the Caatinga, reveal that this biome was not always an open, semiarid area but once constituted a forested formation. The higher number of endemic species of the Cerrado together with species shared with the Chaco (contrasted with the lower richness and endemism of the Caatinga) suggests the long-term persistence of open habitats in present-day areas of the Cerrado. (pages 307 - 350)
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- Bruce D. Patterson, Sergio Solari, Paúl M. Velazco
DOI: 10.7208/chicago/9780226649214.003.0015
[Andes, biogeography, forests, mammal, biota, taxa]
The development of the Andes has indelibly marked the divergence of many tropical lowland taxa with basal splits into trans-Andean and cis-Andean components. Besides defining the limits of various lowland centers of endemism, the Andes house several very distinctive biotas of their own—the arid Western Slope, alpine communities including páramo, jalca, and puna extending onto the Altiplano, and moist forested communities on the Eastern Versant of the northern and central Andes reaching into northwestern Argentina. These biotas seem to be historically as well as ecologically distinctive. Speciation appears to have been recent and rapid on the Eastern Versant and in the Altiplano, while the Western Slope biota has a more relictual character. In some cases, Andean radiations are rooted in the tropical lowlands while in others, lowland radiations seem to be derived from Andean (or proto-Andean) ancestry. Few Andean mammals are well studied, but residents of the middle elevations of the Eastern Slope are especially poorly known. Middle-elevation faunas are highly diverse, show substantial degrees of endemism, and their species may be critical to developing accurate historical reconstructions of groups with widespread Neotropical distributions. Sampling these habitats should therefore be a high priority for future surveys. (pages 351 - 378)
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- Enrique P. Lessa, Guillermo D'Elía, Ulyses F. J. Pardiñas
DOI: 10.7208/chicago/9780226649214.003.0016
[mammals, biogeography, phylogeography, habitats]
The Patagonian–Fuegian region comprises areas of Argentinean monte, Patagonian steppe and grasslands, and Valdivian temperate and Magellanic sub polar forests. Although the area was affected by the glacial cycles of the Neogene, glacial sheets were typically much more limited in South America than in northern continents. This chapter reviews the distributional, phylogenetic, phylogeographic, and population genetic information on the composition and historical biogeography of mammals in the region. Although many species are likely relatively recent colonizers of the region, distributional and phylogenetic data provide several examples of endemic species and others that likely resulted from local diversification. Phylogeographic analyses provide additional indications of differentiation within the region. Phylogeographic breaks divide species distributions by latitude rather than between major habitats. Population genetic analyses reveal several cases of demographic expansion, all of which can be assigned to the late Pleistocene (i.e., the last 500,000 years). However, very few of these can be attributed to events postdating the Last Glacial Maximum. The current mammalian fauna of Patagonia and Tierra del Fuego is the result of a complex mix of local fragmentation, differentiation, and colonization from lower latitudes. (pages 379 - 398)
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Taxonomic Index

Subject Index