Genomic technologies have advanced rapidly in recent decades and have ushered in an exciting new era for the study of mammals. Mammalogists working with non-model species are now able to explore many new research areas that were unimaginable only a short time ago. For example, it is currently possible for individual researchers to sequence and assemble genomes for mammalian species of their choosing and to generate genome-wide DNA sequence data from hundreds of individuals simultaneously. Moreover, the miniaturization of both PCR and sequencing technology has created new opportunities for generating real-time DNA or RNA sequence data in the field. Here, we highlight emerging genomic technologies and associated methods that are providing exciting new research avenues for mammalogists in the fields of evolutionary genomics and ecology. Our aim is to not only provide a resource for novel experimental design, but also to provide a record of the current state of genomic applications as the American Society of Mammalogists enters a new century of discovery.

Marsupials and their fossil relatives, which collectively comprise Metatheria, have been of scientific interest for centuries, with many aspects of their evolution and systematics subject to intense research and debate. Here, we review progress over the last 25 years, which has included the description of many new species (modern and fossil), and major improvements in understanding of their phylogenetic relationships, as well as the overall evolutionary history and biogeography of Marsupialia (crown-clade) and Metatheria (total-clade). Significant advances have included the deployment of increasingly sophisticated molecular, morphological, and total evidence analyses, which have resolved most previously disputed relationships among and within the modern marsupial orders. A broad systematic consensus is now emerging, although several major areas of contention remain, particularly among fossil metatherians. New modern species continue to be described at an impressive rate, with almost 50 named in the last 25 years, and many more await discovery. There has also been an explosion in the discovery and description of fossil marsupials and non-marsupial metatherians (∼270 species), principally from Australasia and the Americas but also from Antarctica, Europe, and Asia. Most are represented by dental specimens only, but some consist of complete and well-preserved material, which has led to major improvements in our understanding of the evolution of cranial and postcranial morphology. Improvements in the fossil record and advances in methods for inferring divergence times have helped clarify when and where key events occurred in metatherian evolution, and the patterns of subclade diversification. We also have improved understanding of biogeographical relationships among metatherians on different landmasses. Despite enormous progress, numerous key uncertainties remain due to major gaps in the fossil record (e.g., Antarctica, Late Cretaceous, and early Paleogene of Australia) and a comparative lack of studies that directly combine molecular and fossil data. Future advances will largely depend on improvements in the fossil record and studies that better integrate neontological and paleontological evidence.

The order Chiroptera comprises all bat species and is the second-most diverse order of mammals. Organization of this diversity into well-delimited taxa embodying their evolutionary affinities remains challenging, particularly because the relationships among various groups at most taxonomic levels are not yet fully resolved. Historically, systematic questions were approached independently using tools and methodologies within researchers' individual expertise. With technological advances, this trend has shifted to more comprehensive analyses, merging independent datasets from various lines of research. Nevertheless, disagreements among phylogenetic relationships inferred from independent datasets, and derived from the complexity of modes of diversification and speciation, still preclude the achievement of a single, comprehensive, and stable classification framework for bats. In this context, integrative taxonomy uses complementarity among various disciplines to improve the outcome of hypothesis testing, which can be achieved by congruence or cumulation of datasets. Here, we provide a review of bat systematics, with emphasis on the instances where integrative taxonomy has proven to be crucial in delimitation of taxa. We focus on examples of true integration or integration using discrete data to support delimitation at different taxonomic levels. In addition, we discuss the difficulties associated with the integration of incongruent phylogenies, as well as how to incorporate information crucial to phylogenetic decisions from data not easily comparable to most common datasets. Our goal is to provide exemplar guidelines that can be useful to taxonomists for the creation of stable classifications without subjectivity and limitations of single datasets. Accordingly, we present a review of recent issues in chiropteran systematics, including comments on how the use of integrative taxonomy helped to solve them.

With almost 2,600 species, Rodentia is the most diverse order of mammals. Here, we provide an overview of changes in our understanding of the systematics of living rodents, including species recognition and delimitation, phylogenetics, and classification, with emphasis on the last three decades. Roughly, this corresponds to the DNA sequencing era of rodent systematics, but the field is undergoing a transition into the genomic era. At least 248 species were newly described in the period 2000–2017, including novelties such as the first living member of Diatomyidae and a murid species without molars (Paucidentomys vermidax), thus highlighting the fact that our understanding of rodent diversity is going through an age of discovery. Mito-nuclear discordance (including that resulting from mitochondrial introgression) has been detected in some of the few taxonomic studies that have assessed variation of two or more unlinked loci. As studies incorporate more loci, incomplete lineage sorting and introgression are likely to gain recognition as widespread phenomena in the near future. Molecular phylogenetics has had a major impact in rodent phylogeny and allowed the identification of three major rodent clades, here recognized as suborders: 1) the Hystricomorpha (sometimes referred as the Ctenohystrica) and including two infraorders, Hystricognathi and Ctenodactylomorphi; 2) the Sciuromorpha; and 3) the Supramyomorpha, a new suborder that comprises the infraorders Castorimorphi, Anomalurimorphi, and Myomorphi. In spite of the greater understanding and ensuing stability of rodent phylogeny gained during the last three decades, several major areas of the rodent tree remain unresolved or poorly supported. We expect that the analysis of genomic-scale data will help resolve those areas of the radiation of Rodentia that still remain poorly understood.

Mammals have played a foundational role in the explosive growth of phylogeography over the past 30 years that it has been a recognized discipline. Novel discoveries of geographic patterns and processes using phylogeographic approaches have integrated disciplines including biogeography, evolutionary biology, ecology, and conservation biology. Here, we use several approaches to survey the scope and influence of phylogeography, beginning with use of a well-studied family of North American rodents to contrast information content derived from DNA-based phylogeography versus a popular older method, allozyme electrophoresis, of assaying genetic variation within and among species across geography. We conclude that phylogeography has elevated the quality of insights attainable regarding, for example, the causal role of Earth history events in processes including lineage divergence, speciation, and adaptive evolution. Next, we use searches of the Web of Science with an array of terms that return information on molecular markers employed, numbers of individuals and localities examined, time frames investigated, historical processes and ways that species and biotas have responded to Earth history, design of phylogeographic studies (e.g., single-taxon versus comparative), and current gaps in taxonomic and geographic sampling. Highlighted results from phylogeographic assays include: an average of 3.3 cryptic lineages per taxonomic species in rodents; a bias in number of studies toward less-diverse biogeographic regions; and a relatively low number of mammalian genera studied. We conclude with predicted and recommended directions for future growth in mammalian phylogeography, including prospects for an increasing role of next generation-based genomics.

Ecophysiology is a relatively recent interdisciplinary field, and although active prior to the 75th anniversary of the American Society of Mammalogists (ASM), it has grown in breadth since then. This growth is in part a result of advances in technology that have reduced the size and improved the portability of key instrumentation, and also made sequencing of proteins and nucleic acids faster and less expensive. Here, we demonstrate the breadth of recent research on the ecophysiology of mammals, quantify the research activity of the past 25 years, and consider future research needs. Some of the most active areas of research have related to maintenance of homeostasis, associations of physiological traits with the evolution of varied life styles and life histories, and reproductive physiology. Key findings involve allometry and scaling, energetics and thermoregulation, phenotypic plasticity and epigenetics, and the importance of microbial symbionts. With respect to predictions of trends in mammalian ecophysiology, the strongest themes relate to conservation biology, in large part related to rapid climate change, habitat destruction, and other anthropogenic factors. How our mammalian fauna adapts (or not) to these changes will be of great interest, and has the potential to affect the science of mammalogy in the future.

Analysis of variation in whole-animal performance can shed light on causal connections between specific traits, integrated physiological capacities, and Darwinian fitness. Here, we review and synthesize information on naturally occurring variation in physiological performance capacities and how it relates to environmental adaptation in deer mice (Peromyscus maniculatus). We discuss how evolved changes in aerobic exercise capacity and thermogenic capacity have contributed to adaptation to high elevations. Comparative work on deer mice at high and low elevations has revealed evolved differences in aerobic performance capacities in hypoxia. Highland deer mice have consistently higher aerobic performance capacities under hypoxia relative to lowland natives, consistent with the idea that it is beneficial to have a higher maximal metabolic rate (as measured by the maximal rate of O₂ consumption, VO_2max) in an environment characterized by lower air temperatures and lower O₂ availability. Observed differences in aerobic performance capacities between highland and lowland deer mice stem from changes in numerous subordinate traits that alter the flux capacity of the O₂-transport system, the oxidative capacity of tissue mitochondria, and the relationship between O₂ consumption and ATP synthesis. Many such changes in physiological phenotype are associated with hypoxia-induced changes in gene expression. Research on natural variation in whole-animal performance forms a nexus between physiological ecology and evolutionary biology that requires insight into the natural history of the study species.

Mammals are imperiled worldwide. Threats to terrestrial species are primarily from habitat loss or modification, and in some instances from commercial, illegal, or unregulated hunting. Terrestrial species are negatively affected throughout the tropics from deforestation. Threats to marine mammals are related to harvest, strikes in shipping lanes, pollution, and depleted levels of food resources. Hazards to marine species are pronounced in the North Atlantic Ocean, North Pacific Ocean, and oceans and seas flanking southeastern Asia. Protected areas designed to conserve mammals often are too small, too few, poorly delimited or isolated, and too unreliably supported. The new conservation science proposes that human livelihoods be considered alongside traditional preservationist perspectives. For conservation outside of protected areas to succeed, the protection of wild mammals and their habitats should result in benefit to local people, especially in rural or poor communities. Concerns about declining populations of large mammals in North America during the late 19th and early 20th centuries resulted in the institution of regulations that contributed to the recovery of many populations. Today, in North America and Europe, wild populations are thriving and legal hunting is allowed for a number of mammals, something that is less common in many developing countries, where illegal killing remains a threat to conservation. Nevertheless, populations of large mammals are resilient to regulated hunting because of density-dependent processes that result in increased reproduction, survival, and growth rates. Unfortunately, hunting is unregulated for cultural and economic reasons over much of the Earth. We are beginning to see effects of climate change and invasive species on risk of extinction for many species. The future of mammals, however, is entwined ultimately with the size, growth, and resource demands of the human population.

The diverse functional roles of over 6,000 species of extant mammals that range in body size across eight orders of magnitude, from blue whales (Balaenoptera musculus) to tiny Etruscan shrews (Suncus etruscus), contribute to shaping Earth's ecosystems. Large mammalian herbivores (e.g., African elephants [Loxodonta africana], American bison [Bison bison], hippopotamuses [Hippopotamus amphibius]) and carnivores (e.g., wolves [Canis lupus], pumas [Puma concolor], sea otters [Enhydra lutris]) often have significant effects on primary producers in terrestrial, aquatic, and marine systems through nutrient cycling, energy flow, and the exertion of bottom-up and top-down processes. Small mammals, like bats, are important pollinators, dispersers of fruits, and consumers of arthropods, and others, especially rodents and primates, are important predators and dispersers of seeds. Many of these mammal-mediated processes occur simultaneously in the same ecosystem, and have significant effects on community structure of primary producers that in turn alter communities of other vertebrates and invertebrates. Many mammals also are ecosystem engineers (e.g., elephants, American beavers [Castor canadensis], porcupines [Erithezon dorsatum], prairie dogs [Cynomys spp.]) that create, significantly modify, or destroy habitat, and by doing so, they alter ecosystem structure and function and increase habitat heterogeneity and biodiversity. The extensive influence mammals have on ecosystems results in important services that contribute to human well-being, such as pollination, insect pest control, and bioturbation of soils. The rapid declines in abundance of many mammal populations and the associated increase in extinction risk raise conservation concerns for mammals. To maintain mammalian diversity and the critical ecosystem processes they provide, scientists need to mobilize concern for their status and strive for more effective and comprehensive conservation action. We provide insights and synthesis on the ecological role of mammals and highlight key research questions and future directions for their conservation.

The study of mammals has promoted the development and testing of many ideas in contemporary ecology. Here we address recent developments in foraging and habitat selection, source–sink dynamics, competition (both within and between species), population cycles, predation (including apparent competition), mutualism, and biological invasions. Because mammals are appealing to the public, ecological insight gleaned from the study of mammals has disproportionate potential in educating the public about ecological principles and their application to wise management. Mammals have been central to many computational and statistical developments in recent years, including refinements to traditional approaches and metrics (e.g., capture-recapture) as well as advancements of novel and developing fields (e.g., spatial capture-recapture, occupancy modeling, integrated population models). The study of mammals also poses challenges in terms of fully characterizing dynamics in natural conditions. Ongoing climate change threatens to affect global ecosystems, and mammals provide visible and charismatic subjects for research on local and regional effects of such change as well as predictive modeling of the long-term effects on ecosystem function and stability. Although much remains to be done, the population ecology of mammals continues to be a vibrant and rapidly developing field. We anticipate that the next quarter century will prove as exciting and productive for the study of mammals as has the recent one.

Disease ecology is a rapidly growing subdiscipline, and mammals and their parasites feature prominently in both historical and more recent research efforts. Nevertheless, the diversity of topics explored, and those not well explored, has not been systematically assessed. We conducted a systematic review of the published scientific literature in disease ecology of mammals and subjected the collection of original and review articles identified to a topic modeling approach, which is based on the words used in the published texts and their contexts (i.e., the frequency and strength of their semantic relationships with one another). In addition to concept maps identifying the most prominent research themes, we identified eight (not mutually exclusive) subcategories of studies, including experimental, theoretical, comparative, behavioral, immunological–microbiological, biogeographic–macroecological, vector-focused (e.g., mosquitoes), and disturbance-focused. The most prominent themes arising in review papers included the ecology of zoonotic diseases transmitted from non-human mammals, comparisons of pathogen prevalence between mammalian species, and pathogen discovery–disease surveillance studies, particularly of marine mammals and bats. For the original articles, the most prominent themes included ecology of rodent-transmitted viral and bacterial diseases and the population biology of zoonotic hosts. Most studies used comparative or descriptive approaches to investigate mammal–pathogen–disease relationships at a local scale, focusing on vector-borne diseases. Experimental, modeling, immunological, and behavioral approaches were strikingly underrepresented. Topics of strong conceptual importance, but that are underrepresented in the current literature, include: 1) the effects of the population density of mammalian hosts, and manipulations of density, on pathogen transmission; 2) macroecological studies that quantify effects of mammalian host species on parasite abundance and prevalence; and 3) effects of climate change on physiological and behavioral processes relevant to mammal–parasite interactions.

Mammalian community ecology asks how interacting biotic and abiotic processes at local and regional scales shape community assembly. Throughout the 100-year history of the American Society of Mammalogists (ASM), mammalogists laid the foundation for studying community assembly by documenting presence and abundance of mammals across different sites through time. During the past 50 years, mammalian community ecology has matured due to long-term studies, new perspectives, and advanced analytical approaches. From an initial focus on local communities and ecological time frames, community ecologists now integrate regional processes and evolutionary time frames. Examination of patterns of assembly expanded from taxonomic diversity derived from species identity and abundance to incorporate phylogenetic and functional diversity. Arid-land small mammal and island systems provide natural laboratories to examine community assembly. Worldwide, small-mammal communities in arid lands exhibit several general trends including low α-diversity, greater β-diversity, and structures comprising core and transient species. Despite broad similarities in ecological conditions, the relative dominance of proximate processes structuring communities varies between regions due to differences in factors such as small-mammal lineages and predictability of resource pulses. Island studies reveal how island size and isolation affect species composition, and how processes of community assembly and disassembly are often simplified, compared to the situation in mainland communities. Recent approaches document the contributions of speciation on, and dispersal to and between islands, to patterns of community assembly. Islands also serve as models of how humans affect mammal communities. Land use practices were altering ecosystems before the founding of ASM, and these changes have accelerated over the last 100 years. Habitat conversion and degradation combined with climate change are redefining mammal communities globally. We discuss the need to apply our understanding of community ecology in efforts to restore ecological function, structure, and composition to stem potentially large losses in mammalian diversity.

Recognition of the Anthropocene epoch formally acknowledges the pervasive and increasingly dominant effects of human activities on the world's biomes. A defining characteristic of the Anthropocene is habitat conversion (land-use change) for agricultural and urbanized land uses. Within this context, landscape ecology is of critical importance as it examines the influence of spatial heterogeneity on ecological patterns and processes at spatial and temporal extents that are larger than those traditionally studied in ecology. The application of landscape ecological approaches to mammalian populations, communities, and metacommunities began in and has increased steadily since the 1990s. Non-volant small mammals or bats are often the focus of landscape studies of communities, whereas carnivores or artiodactyls are commonly the focus of population-level studies cast within the domains of conservation or wildlife management. Research on the landscape ecology of mammals has primarily been conducted in Europe and North America, but with increasing frequency has been explored on other continents. Mammalian research has contributed significantly to the development of landscape ecology, demonstrating that responses to landscape structure are often taxon-, scale-, or context-dependent. Future research should consider hierarchical approaches that are scale-sensitive, with explicit linkage to contemporary hypotheses, thereby advancing theoretical understanding and informing management and conservation action.

Mammalian biodiversity exhibits strong geographic gradients that correspond to variation in the physical environment (habitat, area, climate, and landforms) and reflect biogeographic processes that have unfolded over millennia. Principal among these patterns are the species–area relationship, as well as latitudinal, elevational, and topographic gradients. We review these gradients for mammalian assemblages of today and over geologic time. Contemporary gradients are for the most part general. Nonetheless, variation across different phylogenetic and ecological subsets of continental mammalian faunas illuminates the multifactorial, historical nature of biodiversity gradients in terms of the diversification history of clades, variation in resources that support species with different ecological traits, and changes in landscapes over time. Accordingly, future work should integrate modern and historical patterns of taxonomic richness with phylogenetic and functional diversity of different clades and ecological subsets of continental faunas. Changes in global climate and land use are disrupting the integrity of biogeographic patterns. Insights from the study of gradients of mammalian biodiversity should address the challenges of conservation in a rapidly changing world.

The field of macroecology has made many contributions to our understanding of mammalian ecology and evolution through its use of big data and the examination of statistical patterns that emerge. Here, we review the advances in three areas of mammalian macroecology: 1) spatial and temporal patterns of assemblage structure and space use, 2) the processes and constraints underlying the evolution of body size and life history, and 3) advances in understanding and predicting loss of biodiversity. We highlight the important role that studies of mammals have played in the advancement of macroecological theories and patterns, and note that both mammalogy and macroecology are richer because of this linkage.