From forest fires to fisheries management: Anthropology,conservation biology,and historical ecology

Human‐environmental relationships have long been of interest to a variety of scientists, including ecologists, biologists, anthropologists, and many others. 1 , 2 In anthropology, this interest was especially prevalent among cultural ecologists of the 1970s and earlier, who tended to explain culture as the result of techno‐environmental constraints. 3 More recently researchers have used historical ecology, an approach that focuses on the long‐term dialectical relationship between humans and their environments, as well as long‐term prehuman ecological datasets. 4 - 7 An important contribution of anthropology to historical ecology is that anthropological datasets dealing with ethnohistory, traditional ecological knowledge, and human skeletal analysis, as well as archeological datasets on faunal and floral remains, artifacts, geochemistry, and stratigraphic analysis, provide a deep time perspective (across decades, centuries, and millennia) on the evolution of ecosystems and the place of people in those larger systems. Historical ecological data also have an applied component that can provide important information on the relative abundances of flora and fauna, changes in biogeography, alternations in food webs, landscape evolution, and much more.     

Bridging the gap between community ecology and historical biogeography: niche conservatism and community structure in emydid turtles

Historical (phylogenetic) biogeography and community ecology were once integrated as part of the broader study of organismal diversity, but in recent decades have become largely separate disciplines. This is unfortunate because many patterns studied by community ecologists may originate through processes studied by historical biogeographers and vice versa. In this study, we explore the causes of a geographic pattern of community structure (habitat use) in the emydid turtle assemblages of eastern North America, with more semi-terrestrial species of the subfamily Emydinae in the north and more aquatic species of Deirochelyinae in the south. Specifically, we address the factors that prevent northern emydines from invading southern communities. We test for competitive exclusion by examining patterns of range overlap, and test for the role of niche conservatism using analyses of climatic and physiological data based on a multilocus molecular phylogeny. We find no support for competitive exclusion, whereas several lines of evidence support the idea that niche conservatism has prevented northern emydines from dispersing into southern communities. Our results show how understanding the causes of patterns of historical biogeography may help explain patterns of community structure.     

Vagility: The Neglected Component in Historical Biogeography

The conceptual gap between ecological and historical biogeography is wide, although both disciplines are concerned with explaining how distributions have been shaped. A central aim of modern historical biogeography is to use a phylogenetic framework to reconstruct the geographic history of a group in terms of dispersals and vicariant events, and a number of analytical methods have been developed to do so. To date the most popular analytical methods in historical biogeography have been parsimony-based. Such methods can be classified into two groups based on the assumptions used. The first group assumes that vicariance between two areas creates common patterns of disjunct distributions across several taxa whereas dispersals and extinctions generate clade specific patterns. The second group of methods assumes that passive vicariance and within-area speciation have a higher probability of occurrence than active dispersal events and extinction. Typically, none of these methods takes into account the ecology of the taxa in question. I discuss why these methods can be potentially misleading if the ecology of the taxon is ignored. In particular, the vagility or dispersal ability of taxa plays a pivotal role in shaping the distributions and modes of speciation. I argue that the vagility of taxa should be explicitly incorporated in biogeographic analyses. Likelihood-based methods with models in which more realistic probabilities of dispersal and modes of speciation can be specified are arguably the way ahead. Although objective quantification will pose a challenge, the complete ignorance of this vital aspect, as has been done in many historical biogeographic analyses, can be dangerous. I use worked examples to show a simple way of utilizing such information, but better methods need to be developed to more effectively use ecological knowledge in historical biogeography.     

生态位模型的理论基础、发展方向与挑战

生态位模型是一个以生态位理论为基础的新兴研究领域.它通过采集研究对象的已知分布点及其相关的环境数据组成训练样本,利用数理统计或机器学习理论分析数据,构建特征函数表示物种在生态位空间的实际生态位.以生态位模型预测物种潜在分布地或计算物种间的生态位重叠等研究,在生态学、生物地理学和进化生物学研究中显得越来越重要.本文从生态位概念出发,详细解析了生态位模型的理论基础、相关的焦点争论、使用时的注意点以及可能的发展方向与面临的挑战,指出模型中要考虑人类活动对物种生态位的影响.希望本文所探讨的本领域最新的争论焦点能引起相关学者的关注与深入思考.     

The historical assembly of continental biotas: Late Quaternary range-shifting, areas of endemism, and bio-geographic structure in the North American mammal fauna

A controversial question in biogeography and ecology involves the extent to which vicariance and dispersal interact to determine the structure of continental biotic assemblages, Accumulating evidence of" distributional changes during the past 40 000 yr (Late Quaternary) has suggested to ecologists that changes in geographic ranges during the Pleistocene were of sufficient magnitude to erode prior associations between earth and biotic evolution in continental biotas. This paper first argues that this question can only he addressed by examining the magnitude of Late Quaternary range-shifting at the spatial scale established within the framework of historical historical geography (e.g., areas of endemism) rather than that of ecology (e.g., local community assemblages); and second reassesses patterns of range-shifting in the FAUNMAP data base recording Late Quaternary distributions of North American mammals. At the scale of geo-morphological provinces. North American rodents have exhibited highly stable distributions during this time frame, suggesting that previous inferences drawn from analyses of stability at a local community scale are not relevant to questions of congruence between earth and biotic history at regional or continental scales, A comprehensive understanding of processes underlying the assembly of continental biotas still requires incorporation of biogeographic patterns developed well before episodes of Late Quaternary climatic turbulence.     

NOTHOFAGUS AND PACIFIC BIOGEOGRAPHY

Abstract — Gondwanan biogeography, particularly the relationships between southern South America, New Zealand, Australia, New Guinea and New Caledonia, has been much studied. Nothofagus is often used as the "test taxon", and many papers have been directed at using Nothofagus to explain Gondwanan biogeography. Cladistic biogeographers, working on plant material, have generally failed to find congruence among taxa expected from the southern Pacific disjunctions. New morphological and molecular data on the phytogeny of Nothofagus have re-opened the issue, and we analysed these data to construct a new hypothesis of the biogeography of the genus. We assembled all plant taxa for which we could find reasonably robust phylogenetic hypotheses, and sought a parsimonious biogeographical pattern common to all. Two analyses, based on different assumptions, produced the same general areacladogram. We use the general area-cladogram, in conjunction with the fossil record of Nothofagus to construct a historical scenario for the evolution of the genus. This scenario indicates extensive extinction, but also suggests that Australia has a more recent relationship to New Zealand than to southern South America. This is not congruent with the current geological theories, nor with the patterns evident from insect biogeography. We suggest that concordant dispersal is an unlikely explanation for this pattern, and propose that the solution might be found in alternative geological hypotheses.     

Biogeography and ecology: towards the integration of two disciplines

Although ecology and biogeography had common origins in the natural history of the nineteenth century, they diverged substantially during the early twentieth century as ecology became increasingly hypothesis-driven and experimental. This mechanistic focus narrowed ecology''s purview to local scales of time and space, and mostly excluded large-scale phenomena and historical explanations. In parallel, biogeography became more analytical with the acceptance of plate tectonics and the development of phylogenetic systematics, and began to pay more attention to ecological factors that influence large-scale distributions. This trend towards unification exposed problems with terms such as ‘community’ and ‘niche,’ in part because ecologists began to view ecological communities as open systems within the contexts of history and geography. The papers in this issue represent biogeographic and ecological perspectives and address the general themes of (i) the niche, (ii) comparative ecology and macroecology, (iii) community assembly, and (iv) diversity. The integration of ecology and biogeography clearly is a natural undertaking that is based on evolutionary biology, has developed its own momentum, and which promises novel, synthetic approaches to investigating ecological systems and their variation over the surface of the Earth. We offer suggestions on future research directions at the intersection of biogeography and ecology.     

Historical Biogeography: Evolution in Time and Space

Biogeography is the discipline of biology that studies the present and past distribution patterns of biological diversity and their underlying environmental and historical causes. For most of its history, biogeography has been divided into proponents of vicariance explanations, who defend that distribution patterns can mainly be explained by geological, tectonic-isolating events; and dispersalists, who argue that current distribution patterns are largely the result of recent migration events. This paper provides an overview of the evolution of the discipline from methods focused on finding general patterns of distribution (cladistic biogeography), to those that integrate biogeographic processes (event-based biogeography), to modern probabilistic approaches (parametric biogeography). The latter allows incorporating into biogeographic inference estimates of the divergence time between lineages (usually based on DNA sequences) and external sources of evidence, such as information on past climate and geography, the organism fossil record, or its ecological tolerance. This has revolutionized the discipline, allowing it to escape the dispersal versus vicariance dilemma and to address a wider range of evolutionary questions, including the role of ecological and historical factors in the construction of biomes or the existence of contrasting patterns of range evolution in animals and plants.     

Establishing a Framework for a Natural Area Taxonomy

The identification of areas of endemism is essential in building an area classification, but plays little role in how natural areas are discovered. Rather area monophyly, derived from cladistics, is essential in the discovery of natural area classifications or area taxonomy. We propose Area Taxonomy to be a new sub-discipline of historical biogeography, one that can be revised and debated, and which has its own area nomenclature. Separately to area taxonomy, we outline how natural areas may be discovered by transcribing the concepts of homology and monophyly from biological systematics to historical biogeography, in the form of area homologues, area homologies and area monophyly.     

A critique of 'countryside biogeography' as a guide to research in human‐dominated landscapes

Proliferation of redundant terms in ecology and conservation slows progress and creates confusion. ‘Countryside biogeography’ has been promoted as a new framework for conservation in production landscapes, so may offer a replacement for other concepts used by landscape ecologists. We conducted a systematic review to assess whether the 'countryside biogeography' concept provides a distinctive framing for conservation in human‐dominated landscapes relative to existing concepts. We reviewed 147 papers referring to countryside biogeography and 81 papers that did not. These papers were divided into categories representing three levels of use of countryside biogeography concepts (strong, weak, cited only) and two categories that did not use countryside biogeography at all but used similar concepts including fragmentation and matrix. We revealed few distinctions among groups of papers. Countryside biogeography papers made more frequent use of the terms 'ecosystem services', 'intensification' and 'land sparing' compared with non‐countryside biogeography papers. Papers that did not refer to countryside biogeography sampled production areas (e.g. farms) less often, and this related to their focus on habitat specialist species for which patch‐matrix assumptions were reasonable. Countryside biogeography offers a conceptual wrapper rather than a distinctive framework for advancing research in human‐modified landscapes. This and similar wrappers such as ‘conservation biogeography’ and ‘agricultural biogeography’ risk creating confusion among new researchers, and can prevent clear communication about research. To improve communication, we recommend using the suite of well‐established terms already applied to conservation in human‐modified landscapes rather than through an interceding conceptual wrapper.     

生态位分化与森林群落物种多样性维持研究展望

一直以来,生态学家和进化生物学家对森林群落物种多样格局及其形成机制持有不同的观点。虽然Robert Ricklefs将进化和生态过程整合的观点已经被群落生态学家广泛接受,但是区域物种进化历史以及局域群落微进化过程是否能够影响群落生态学过程以及这些过程如何影响群落结构和动态还有待商榷。经典的生态位理论同时强调了种间和种内生态位分化对群落多样性维持的影响。但是生态学家普遍认为种间差异足以代表群落内个体间的相互作用关系,并且由于进化过程导致的种内分化往往涉及较长的时间尺度,因此,虽然种内差异是自然选择的重要材料,物种对环境的适应性进化过程所导致的种内分化对群落构建的影响往往被生态学家所忽视。为此,通过回顾种间和个体生态位分化的研究历史,对两类研究分别进行简要阐述,强调在今后的群落生态学研究中需要考虑个体分化对局域群落构建的影响。     

Ecological and evolutionary genetics of Arabidopsis

The crucifer Arabidopsis thaliana has been the subject of intense research into molecular and developmental genetics. One of the consequences of having this wealth of physiological and molecular data available, is that ecologists and evolutionary biologists have begun to incorporate this model system into their studies. Current research on A. thaliana and its close relatives ably illustrates the potential for synergy between mechanistic and organismal biology. On the one hand, mechanistically oriented research can be placed in an historical context, which takes into account the particular phylogenetic history and ecology of these species. This helps us to make sense of redundancies, anomalies and sub-optimalities that would otherwise be difficult to interpret. On the other hand, ecologists and evolutionary biologists now have the opportunity to investigate the physiological and molecular basis for the phenotypic changes they observe. This provides new insight into the mechanisms that influence evolutionary change.     

Ecophylogenetics: advances and perspectives

Ecophylogenetics can be viewed as an emerging fusion of ecology, biogeography and macroevolution. This new and fast-growing field is promoting the incorporation of evolution and historical contingencies into the ecological research agenda through the widespread use of phylogenetic data. Including phylogeny into ecological thinking represents an opportunity for biologists from different fields to collaborate and has provided promising avenues of research in both theoretical and empirical ecology, towards a better understanding of the assembly of communities, the functioning of ecosystems and their responses to environmental changes. The time is ripe to assess critically the extent to which the integration of phylogeny into these different fields of ecology has delivered on its promise. Here we review how phylogenetic information has been used to identify better the key components of species interactions with their biotic and abiotic environments, to determine the relationships between diversity and ecosystem functioning and ultimately to establish good management practices to protect overall biodiversity in the face of global change. We evaluate the relevance of information provided by phylogenies to ecologists, highlighting current potential weaknesses and needs for future developments. We suggest that despite the strong progress that has been made, a consistent unified framework is still missing to link local ecological dynamics to macroevolution. This is a necessary step in order to interpret observed phylogenetic patterns in a wider ecological context. Beyond the fundamental question of how evolutionary history contributes to shape communities, ecophylogenetics will help ecology to become a better integrative and predictive science.     

Colonization of and radiation in South America by butterflies in the subtribe Phyciodina (Lepidoptera: Nymphalidae)

The historical biogeography of insects in South America is largely unknown, as dated phylogenies have not been available for most groups. We have studied the phylogenetic relationships and historical biogeography of a subtribe of butterflies, Phyciodina in the family Nymphalidae, based on one mitochondrial gene (COI) and two nuclear gene regions (EF-1alpha and wingless). The subtribe comprises 89 species mainly found in tropical South America, with a few species in North America and the Greater Antilles. We find that the enigmatic genus Antillea is sister to the rest of Phyciodina, and suggest that it should be included in the subtribe. Several genera are found to be polyphyletic or nested within another genus, and are proposed to be synonymised. These are Dagon, Castilia, Telenassa and Janatella, which we propose should be synonymised with Eresia. Brazilian "Ortilia" form an independent lineage and require a new genus name. The diversification of Phyciodina has probably taken place over the past about 34 MYA. The ancestral phyciodine colonised South America from North America through a possible landspan that connected the Greater Antilles to South America about 34MYA. A vicariance event left the ancestral Antillea on the Greater Antilles, while the ancestral 0e on South America colonised the Guyanan Shield and soon after the Brazilian Shield. We hypothesise that the Brazilian Shield was an important area for the diversification of Phyciodina. From there, the ancestor of Anthanassa, Eresia and Tegosa colonised NW South America, where especially Eresia diversified in concert with the rising of the Andes beginning about 20 MYA. Central America was colonised from NW South America about 15 MYA by the ancestors of Anthanassa and Phyciodes. Our study is the first to use a dated phylogeny to study the historical biogeography of a group of South American species of butterflies.     

Human biogeography: evidence of our place in nature

Focusing on human biogeography as a research endeavour may make sense to biogeographers, but in the academic world generally this particular scholarly niche has long been filled by other rival disciplines such as sociology, human ecology, geography, anthropology and archaeology. It may be true that having so many ways of looking at ourselves as a species is a good thing, but it can also be argued that this academic fragmentation of effort has often nurtured the commonplace view that we as a species are 'above' or 'not part of' what plain folks call the 'natural world'. Here I review the historical and basic intellectual ingredients of what might be (but often isn't) called human biogeography. I offer a case study drawn from my research work on the Sepik coast of Papua New Guinea. This research illustrates how adopting an explicitly biogeographical approach to human diversity can lead to unexpected insights into the character and history of human settlement in this part of the world. One benefit of having a field with this explicit orientation might be that the conservation of biodiversity would make more sense to more people.     

A call for a new paradigm of island biogeography

MacArthur and Wilson’s equilibrium theory of island biogeography quickly became the paradigm of the field in the 1960s and has strongly influenced this and other disciplines of ecology and conservation biology for the past three decades. Recently, however, a growing number of ecologists have begun to question whether the theory remains a useful paradigm for modern ecology. We now have a much better appreciation for the complexity of nature and we study patterns that span a very broad range in spatial, temporal and ecological scales. At such scales, assumptions that communities are in equilibrium, that species, islands and intervening landscapes or seascapes are equivalent or homogeneous with respect to factors influencing immigration and extinction, and that in situ speciation can be overlooked become very tenuous. With this in mind, this and other papers of this special feature discuss the principal, conceptual shortcomings of the equilibrium theory and offer some modifications or alternatives to the theory that we hope will eventually lead to a more comprehensive understanding of the forces structuring insular communities.     

Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis

In historical biogeography, model-based inference methods for reconstructing the evolution of geographic ranges on phylogenetic trees are poorly developed relative to the diversity of analogous methods available for inferring character evolution. We attempt to rectify this deficiency by constructing a dispersal-extinction-cladogenesis (DEC) model for geographic range evolution that specifies instantaneous transition rates between discrete states (ranges) along phylogenetic branches and apply it to estimating likelihoods of ancestral states (range inheritance scenarios) at cladogenesis events. Unlike an earlier version of this approach, the present model allows for an analytical solution to probabilities of range transitions as a function of time, enabling free parameters in the model, rates of dispersal, and local extinction to be estimated by maximum likelihood. Simulation results indicate that accurate parameter estimates may be difficult to obtain in practice but also show that ancestral range inheritance scenarios nevertheless can be correctly recovered with high success if rates of range evolution are low relative to the rate of cladogenesis. We apply the DEC model to a previously published, exemplary case study of island biogeography involving Hawaiian endemic angiosperms in Psychotria (Rubiaceae), showing how the DEC model can be iteratively refined from inspecting inferences of range evolution and also how geological constraints involving times of island origin may be imposed on the likelihood function. The DEC model is sufficiently similar to character models that it might serve as a gateway through which many existing comparative methods for characters could be imported into the realm of historical biogeography; moreover, it might also inspire the conceptual expansion of character models toward inclusion of evolutionary change as directly coincident, either as cause or consequence, with cladogenesis events. The DEC model is thus an incremental advance that highlights considerable potential in the nascent field of model-based historical biogeographic inference.     

Deep genealogies and the mid-peninsular seaway of Baja California

Geological forces and long-term climate changes can have profound effects on species. Such effects may be manifested in the pattern and magnitude of genealogical diversity, as revealed by mitochondrial DNA (mtDNA) lineages. The relative importance of the different forces on a regional biota must be evaluated along with a good understanding of geological and climatological history. The peninsula of Baja California of north-western Mexico is one area where both geology and climate have affected the historical biogeography of the regional biota. Molecular studies based on the genealogical relationships among mtDNA lineages have contributed greatly towards elucidating the historical biogeography of Baja California. Perhaps most noticeably, numerous concordant breaks in mtDNA genealogies half-way along the peninsula suggest a vicariant history in which the mid-peninsula was temporarily submerged. This vicariant explanation has recently been criticized, as no conclusive geological evidence exists for a continuous submergence of the mid-peninsula. As an alternative, a scenario based on climatological factors has been suggested. Here we discuss the validity of the hypothesized mid-peninsular vicariance event and the climate-based alternative in explaining the concordant genealogical breaks. We argue that, despite the significant changes in climate brought about by the glacial cycles throughout the Quaternary, a vicariant history involving a mid-peninsular seaway remains the most parsimonious explanation of the observed patterns in mtDNA genealogies.     

Diversity and biogeography of marine actinobacteria

The actinomycetes, although not all the Actinobacteria, are easy to isolate from the marine environment. However, their ecological role in the marine ecosystem is largely neglected and various assumptions meant there was little incentive to isolate strains for search and discovery of new drugs. However, the marine environment has become a prime resource in search and discovery for novel natural products and biological diversity, and marine actinomycetes turn out to be important contributors. Similarly, striking advances have been made in marine microbial ecology using molecular techniques and metagenomics, and actinobacteria emerge as an often significant, sometimes even dominant, environmental clade. Both approaches - cultivation methods and molecular techniques - are leading to new insights into marine actinobacterial biodiversity and biogeography. Very different views of actinobacterial diversity emerge from these, however, and the true extent and biogeography of this are still not clear. These are important for developing natural product search and discovery strategies, and biogeography is a hot topic for microbial ecologists.     

Dispersal is fundamental to biogeography and the evolution of biodiversity on oceanic islands

Vicariance biogeography emerged several decades ago from the fusion of cladistics and plate tectonics, and quickly came to dominate historical biogeography. The field has since been largely constrained by the notion that only processes of vicariance and not dispersal offer testable patterns and refutable hypotheses, dispersal being a random process essentially adding only noise to a vicariant system. A consequence of this thinking seems to have been a focus on the biogeography of continents and continental islands, considering the biogeography of oceanic islands less worthy of scientific attention because, being dependent on stochastic dispersal, it was uninteresting. However, the importance of dispersal is increasingly being recognized, and here we stress its fundamental role in the generation of biodiversity on oceanic islands that have been created in situ , never connected to larger land masses. Historical dispersal patterns resulting in modern distributions, once considered unknowable, are now being revealed in many plant and animal taxa, in large part through the analysis of polymorphic molecular markers. We emphasize the profound evolutionary insights that oceanic island biodiversity has provided, and the fact that, although small in area, oceanic islands harbour disproportionately high biodiversity and numbers of endemic taxa. We further stress the importance of continuing research on mechanisms generating oceanic island biodiversity, especially detection of general, non-random patterns of dispersal, and hence the need to acknowledge oceanic dispersal as significant and worthy of research.