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.     

The voice of historical biogeography

Historical biogeography is going through an extraordinary revolution concerning its foundations, basic concepts, methods, and relationships to other disciplines of comparative biology. There are external and internal forces that are shaping the present of historical biogeography. The external forces are: global tectonics as the dominant paradigm in geosciences, cladistics as the basic language of comparative biology and the biologist's perception of biogeography. The internal forces are: the proliferation of competing articulations, recourse to philosophy and the debate over fundamentals. The importance of the geographical dimension of life's diversity to any understanding of the history of life on earth is emphasized. Three different kinds of processes that modify the geographical spatial arrangement of the organisms are identified: extinction, dispersal and vicariance. Reconstructing past biogeographic events can be done from three different perspectives: (1) the distribution of individual groups (taxon biogeography) (2) areas of endemism (area biogeography), and (3) biotas (spatial homology). There are at least nine basic historical biogeographic approaches: centre of origin and dispersal, panbiogeography, phylogenetic biogeography, cladistic biogeography, phylogeography, parsimony analysis of endemicity, event-based methods, ancestral areas, and experimental biogeography. These nine approaches contain at least 30 techniques (23 of them have been proposed in the last 14 years). The whole practice and philosophy of biogeography depend upon the development of a coherent and comprehensive conceptual framework for handling the distribution of organisms and events in space.     

When phylogenetics met biogeography: Willi Hennig,Lars Brundin and the roots of phylogenetic and cladistic biogeography

Willi Hennig's (Beitr. Ent. 1960, 10, 15) Die Dipteren-Fauna von Neuseeland als systematisches und tiergeographisches Problem applied a phylogenetic approach to examine the distributional patterns exhibited by the Diptera of New Zealand. Hennig showed how phylogenetic trees may be used to infer dispersal, based on the progression and deviation rules, and also discussed the existence of vicariance patterns. The most important author who applied Hennig's phylogenetic biogeography was Lars Brundin, when analysing the phylogenetic relationships of two taxa of Chironomidae (Diptera) and using them to examine the biogeographic relationships of Australia, New Zealand, South America and South Africa. The relevance of Brundin's contribution was noted by several authors, as it began the cladistic or vicariance approach to biogeography, that implies the discovery of vicariance events shared by different monophyletic groups. Both phylogenetic and cladistic biogeography have a place in contemporary biogeography, the former for analysing taxon biogeography and the latter when addressing Earth or biota biogeography. The recent use of the term “phylogenetic biogeography” to refer to a posteriori methods of cladistic biogeography is erroneous and should be avoided.     

A likelihood framework for inferring the evolution of geographic range on phylogenetic trees

Abstract At a time when historical biogeography appears to be again expanding its scope after a period of focusing primarily on discerning area relationships using cladograms, new inference methods are needed to bring more kinds of data to bear on questions about the geographic history of lineages. Here we describe a likelihood framework for inferring the evolution of geographic range on phylogenies that models lineage dispersal and local extinction in a set of discrete areas as stochastic events in continuous time. Unlike existing methods for estimating ancestral areas, such as dispersal‐vicariance analysis, this approach incorporates information on the timing of both lineage divergences and the availability of connections between areas (dispersal routes). Monte Carlo methods are used to estimate branch‐specific transition probabilities for geographic ranges, enabling the likelihood of the data (observed species distributions) to be evaluated for a given phylogeny and parameterized paleogeographic model. We demonstrate how the method can be used to address two biogeographic questions: What were the ancestral geographic ranges on a phylogenetic tree? How were those ancestral ranges affected by speciation and inherited by the daughter lineages at cladogenesis events? For illustration we use hypothetical examples and an analysis of a Northern Hemisphere plant clade (Cercis), comparing and contrasting inferences to those obtained from dispersal‐vicariance analysis. Although the particular model we implement is somewhat simplistic, the framework itself is flexible and could readily be modified to incorporate additional sources of information and also be extended to address other aspects of historical biogeography.     

Phylogenetic approaches in coevolution and biogeography

I review phylogenetic approaches to problems in coevolution and biogeography, illustrating with case studies. In coevolution, genealogical trees are essential in differentiating between ancient and recent associations, in identifying cospeciation events, and in studying host-switching patterns. Cospeciating associations are of particular interest because they allow powerful tests of molecular clocks and accurate comparison of evolutionary rates across groups of organisms. In biogeography, phylogenies can help reconstruct the distribution history of individual groups and identify past geological events that have affected the evolution of entire communities. Parsimony analysis in coevolution and biogeography should be based on identification of different types of events, each of which is associated with a specific cost. Similar event-based methods are applicable to coevolutionary and biogeographic inference, as well as in the mapping of gene trees onto organism trees. The discussed examples span a variety of organisms and spatiotemporal scales: primate pin worms, HIV, pocket gophers and their lice, aphids and their bacterial symbionts, gall wasps and their host plants, the root of the tree of life, the historical biogeography of the Holarctic, and the geographical origin of our own species.     

生物地理学的新认识及其方法在多样性保护中的应用

近年来,众多分子证据和古生物学证据的出现促进了对生物地理学领域一些关键问题(如,扩散和隔离)的理解,并达成了较为统一的认识:1)扩散和隔离都是解释生物地理学格局的重要假说,并可能同时影响了生物的分布格局;2)历史生物地理学和生态生物地理学不是截然割裂的,两者结合起来有助于从不同层次上理解生物地理和生物多样性格局;3)不同的生物地理学研究方法应相互补充以揭示复杂的生物地理过程。学科思想的演变也使得生物地理学研究内容发生变化,本文还综述了当今生物地理学所关注的科学问题,并重点论述了生物地理学方法在生物多样性保护中的应用。     

Fossil biogeography: a new model to infer dispersal,extinction and sampling from palaeontological data

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.     

Towards a panbiogeography of the seas

A contrast is drawn between the concept of speciation favoured in the Darwin–Wallace biogeographic paradigm (founder dispersal from a centre of origin) and in panbiogeography (vicariance or allopatry). Ordinary ecological dispersal is distinguished from founder dispersal. A survey of recent literature indicates that ideas on many aspects of marine biology are converging on a panbiogeographic view. Panbiogeographic conclusions supported in recent work include the following observations: fossils give minimum ages for groups and most taxa are considerably older than their earliest known fossil; Pacific/Atlantic divergence calibrations based on the rise of the Isthmus of Panama at 3 Ma are flawed; for these two reasons most molecular clock calibrations for marine groups are also flawed; the means of dispersal of taxa do not correlate with their actual distributions; populations of marine species may be closed systems because of self‐recruitment; most marine taxa show at least some degree of vicariant differentiation and vicariance is surprisingly common among what were previously assumed to be uniform, widespread taxa; mangrove and seagrass biogeography and migration patterns in marine taxa are best explained by vicariance; the Indian Ocean and the Pacific Ocean represent major biogeographic regions and diversity in the Indo‐Australian Archipelago is related to Indian Ocean/Pacific Ocean vicariance; distribution in the Pacific is not the result of founder dispersal; distribution in the south‐west Pacific is accounted for by accretion tectonics which bring about distribution by accumulation and juxtaposition of communities; tectonic uplift and subsidence can directly affect vertical distribution of marine communities; substantial parallels exist between the biogeography of terrestrial and marine taxa; biogeographically and geologically composite areas are tractable using panbiogeographic analysis; metapopulation models are more realistic than the mainland/island dispersal models used in the equilibrium theory of island biogeography; and regional biogeography is a major determinant of local community composition. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 84 , 675–723.     

A PRELIMINARY PHYLOGENETIC AND BIOGEOGRAPHIC ANALYSIS OF THE DYAKIIDAE (GASTROPODA: STYLOMMATOPHORA) AND A BIOGEOGRAPHIC ANALYSIS OF OTHER SUNDALAND TAXA

Abstract — The phylogeny of the Dyakiidae, an early diverging lineage of the Limacoidea sensu lalo , is reconstructed. In the Dyakiidae a unique transformation series of different genital accessory organs, the so-called "stimulators", is preserved which is an important argument for the hypothesis that the different stimulator types of the Stylommatophora are homologous. The biogeographic distribution patterns of the genera of the Dyakiidae are summarized and the ancestral areas of the major clades are analysed. The analysis of the area cladograms of the Dyakiidae and of several butterfly and heteroptera genera occurring in Sundaland revealed neither a general pattern of relationship between the areas of endemism in Sundaland, nor a general pattern of relationship between Sundaland and other areas. The area cladogram of the rather immobile Dyakiidae endemic to Sundaland might reflect older events than the area cladograms of the more mobile and widespread butterfly and plant bug genera. The general incompatibility of the area cladograms involving Sundaland taxa suggests that dispersal across barriers has played a major role in the historical biogeography of the analysed groups and challenges the hypothesis of vicariance biogeography that the distribution patterns of organisms are largely due to the fragmentation of an ancestral biota.     

Use of dispersal–vicariance analysis in biogeography – a critique

Aim Analytical methods are commonly used to identify historical processes of vicariance and dispersal in the evolution of taxa. Currently, dispersal–vicariance analysis implemented in the software diva is the most widely used method. Despite some recognized shortcomings of the method, it has been treated as error‐free in many cases and used extensively as the sole method to reconstruct histories of taxa. In light of this, an evaluation of the limitations of the method is needed, especially in relation to several newer alternatives. Methods In an approach similar to simulation studies in phylogenetics, I use hypothetical taxa evolving in specific geological scenarios and test how well diva reconstructs their histories. Results diva reconstructs histories accurately when evolution has been simple; that is, where speciation is driven mainly by vicariance. Ancestral areas are wrongly identified under several conditions, including complex patterns of dispersals and within‐area speciation events. Several potentially serious drawbacks in using diva for inferences in biogeography are discussed. These include the inability to distinguish between contiguous range expansions and across‐barrier dispersals, a low probability of invoking extinctions, incorrect constraints set on the maximum number of areas by the user, and analysing the ingroup taxa without sister groups. Main conclusions Most problems with inferences based on diva are linked to the inflexibility and simplicity of the assumptions used in the method. These are frequently invalid, resulting in spurious reconstructions. I argue that it might be dangerous to rely solely on diva optimization to infer the history of a group. I also argue that diva is not ideally suited to distinguishing between dispersal and vicariance because it cannot a priori take into account the age of divergences relative to the timing of barrier formation. I suggest that other alternative methods can be used to corroborate the findings in diva , increasing the robustness of biogeographic hypotheses. I compare some important alternatives and conclude that model‐based approaches are promising.     

Titi monkey biogeography: Parallel Pleistocene spread by Plecturocebus and Cheracebus into a post‐Pebas Western Amazon

Titi monkeys, subfamily Callicebinae, are a diverse, species‐rich group of Neotropical primates with an extensive range across South America. Their distribution in space and time makes them an interesting primate model for addressing questions of Neotropical historical biogeography. Our aim was to reconstruct the biogeographic history of Callicebinae to better understand their diversification patterns and the history of their colonisation of South America since the late Miocene. We reconstructed a time‐calibrated phylogeny of 19 titi species under Bayesian inference using two mitochondrial and 11 nuclear loci. Species were assigned across eight Neotropical areas of endemism, and statistical biogeographic methods implemented in BioGeoBEARS were employed to estimate ancestral areas using 12 biogeographic models. Our results indicate that the most recent common ancestor to extant titi monkeys was widespread from the present‐day Andean foothills in the Colombian Amazon, through the wet and dry savannas of Bolivia and Brazil, to the southern Atlantic forest of eastern Brazil. Genus‐level divergences were characterised by vicariance of ancestral range in the late Miocene. Species‐level diversification in Cheracebus and the Plecturocebus moloch group occurred as they spread across the Amazon in the Pleistocene and were largely characterised by a sequential, long‐distance “island‐hopping” dispersal model of speciation from a narrow area of origin through jump dispersal across rivers. This study comprises the first large‐scale investigation of the evolutionary history of titi monkeys in the context of Amazonian and South American historical biogeography and sheds light on the processes that generated the great diversity found among Callicebinae.     

Correlating early evolution of parasitic platyhelminths to Gondwana breakup

Investigating patterns and processes of parasite diversification over ancient geological periods should involve comparisons of host and parasite phylogenies in a biogeographic context. It has been shown previously that the geographical distribution of host-specific parasites of sarcopterygians was guided, from Palaeozoic to Cainozoic times, mostly by evolution and diversification of their freshwater hosts. Here, we propose phylogenies of neobatrachian frogs and their specific parasites (Platyhelminthes, Monogenea) to investigate coevolutionary processes and historical biogeography of polystomes and further discuss all the possible assumptions that may account for the early evolution of these parasites. Phylogenetic analyses of concatenated rRNA nuclear genes (18S and partial 28S) supplemented by cophylogenetic and biogeographic vicariance analyses reveal four main parasite lineages that can be ascribed to centers of diversity, namely Australia, India, Africa, and South America. In addition, the relationships among these biogeographical monophyletic groups, substantiated by molecular dating, reflect sequential origins during the breakup of Gondwana. The Australian polystome lineage may have been isolated during the first stages of the breakup, whereas the Indian lineage would have arisen after the complete separation of western and eastern Gondwanan components. Next, polystomes would have codiverged with hyloid sensu stricto and ranoid frog lineages before the completion of South American and African plate separation. Ultimately, they would have undergone an extensive diversification in South America when their ancestral host families diversified. Therefore, the presence of polystome parasites in specific anuran host clades and in discrete geographic areas reveals the importance of biogeographic vicariance in diversification processes and supports the occurrence and radiation of amphibians over ancient and recent geological periods.     

Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event

The fossil record has been used to support the origin and radiation of modern birds (Neornithes) in Laurasia after the Cretaceous-Tertiary mass extinction event, whereas molecular clocks have suggested a Cretaceous origin for most avian orders. These alternative views of neornithine evolution are examined using an independent set of evidence, namely phylogenetic relationships and historical biogeography. Pylogenetic relationships of basal lineages of neornithines, including ratite birds and their allies (Palaleocognathae), galliforms and anseriforms (Galloanserae), as well as lineages of the more advanced Neoves (Gruiformes, (Capimulgiformes, Passeriformes and others) demonstrate pervasive trans-Antarctic distribution patterns. The temporal history of the neornithines can be inferred from fossil taxa and the ages of vicariance events, and along with their biogeographical patterns, leads to the conclusion that neornithines arose in Gondwana prior to the Cretaceous Tertiary extinction event.     

历史生物地理学进展

生物地理学研究动植物的地理分布。历史生物地理学重建生物区系历史。分替理论的复兴动摇了散布理论的上百年统治。最近10年主要是分替理论推动了历史生物地理学,出现了多个途径——种系发生物地理学、分支分替生物地理学、特有性的俭吝分析和泛生物地理学。岛屿生物地理学理论有了改进和严格的实验检验;庇所学说产生了新的模型。最后就我国如何发展生物地理学提出了对策措施。     

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.     

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.     

Genome-wide genetic variation coupled with demographic and ecological niche modeling of the dusky-footed woodrat (Neotoma fuscipes) reveal patterns of deep divergence and widespread Holocene expansion across northern California

Understanding how species have responded to past climate change may help refine projections of how species and biotic communities will respond to future change. Here, we integrate estimates of genome-wide genetic variation with demographic and niche modeling to investigate the historical biogeography of an important ecological engineer: the dusky-footed woodrat, Neotoma fuscipes. We use RADseq to generate a genome-wide dataset for 71 individuals from across the geographic distribution of the species in California. We estimate population structure using several model-based methods and infer the demographic history of regional populations using a site frequency spectrum-based approach. Additionally, we use ecological niche modeling to infer current and past (Last Glacial Maximum) environmental suitability across the species’ distribution. Finally, we estimate the directionality and possible spatial origins of regional population expansions. Our analyses indicate this species is subdivided into three regionally distinct populations, with the deepest divergence occurring ~1.7 million years ago across the modern-day San Francisco-Bay Delta region; a common biogeographic barrier for the flora and fauna of California. Our models of environmental suitability through time coincide with our estimates of population expansion, with relative long-term stability in the southern portion of the range, and more recent expansion into the northern end of the range. Our study illustrates how the integration of genome-wide data with spatial and demographic modeling can reveal the timing and spatial extent of historic events that determine patterns of biotic diversity and may help predict biotic response to future change.Subject terms: Evolutionary genetics, Molecular evolution     

Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis

Diapensiaceae (Ericales) are a small family of about 15 species. Within this clade, two species are broadly distributed throughout the Northern Hemisphere, whereas the remaining species have a disjunct distribution between eastern North America and eastern Asia. To address patterns and processes of diversification in Diapensiaceae, we conducted biogeographic analyses and inferred shifts in the ecological niche across the phylogeny of the clade. Although Diapensiaceae have been the focus of multiple phylogenetic and biogeographic studies, previous studies have been taxonomically limited. This study has greatly improved the phylogenetic underpinning for Diapensiaceae with the most inclusive taxonomic sampling thus far, employing both nuclear and plastid gene sequence data for at least one sample per species in the family. Our estimates indicate that genera of Diapensiaceae variously diverged in the Eocene, Oligocene, and early to mid‐Miocene. The biogeographic analysis suggests that the probable ancestor of the Diapensiaceae crown clade originated in the Nearctic, with vicariance events contributing to the current distribution of the disjunct taxa. Ecological niche, when considered in a phylogenetic context, was observed to be clustered on the basis of biogeographic realm. In general, a greater ecological overlap was found at younger nodes and a greater niche divergence was found among distantly related species. Diversification in Diapensiaceae appears to have been shaped by both large‐scale biogeographic factors, such as vicariance, and divergence in an ecological niche among closely related species.     

A mitochondrial phylogeny of the rainforest skink genus Saproscincus, Wells and Wellington (1984)

The phylogenetic relationships and historical biogeography of 10 currently described rainforest skinks in the genus Saproscincus were investigated using mitochondrial protein-coding ND4 and ribosomal RNA 16S genes. A robust phylogeny is inferred using both maximum likelihood and Bayesian analysis, with all inter-specific nodes strongly supported when datasets are combined. The phylogeny supports the recognition of two major lineages (northern and southern), each of which comprises two divergent clades. Both northern and southern lineages have comparably divergent representatives in mid-east Queensland (MEQ), providing further molecular evidence for the importance of two major biogeographic breaks, the St. Lawrence gap and Burdekin gap separating MEQ from southern and northern counterparts respectively. Vicariance associated with the fragmentation and contraction of temperate rainforest during the mid-late Miocene epoch underpins the deep divergence between morphologically conservative lineages in at least three instances. In contrast, one species, Saproscincus oriarus, shows very low sequence divergence but distinct morphological and ecological differentiation from its allopatric sister clade within Saproscincus mustelinus. These results suggest that while vicariance has played a prominent role in diversification and historical biogeography of Saproscincus, divergent selection may also be important.     

Biogeography: An Emerging Cornerstone for Understanding Prokaryotic Diversity,Ecology, and Evolution

New questions about microbial ecology and diversity combined with significant improvement in the resolving power of molecular tools have helped the reemergence of the field of prokaryotic biogeography. Here, we show that biogeography may constitute a cornerstone approach to study diversity patterns at different taxonomic levels in the prokaryotic world. Fundamental processes leading to the formation of biogeographic patterns are examined in an evolutionary and ecological context. Based on different evolutionary scenarios, biogeographic patterns are thus posited to consist of dramatic range expansion or regression events that would be the results of evolutionary and ecological forces at play at the genotype level. The deterministic or random nature of those underlying processes is, however, questioned in light of recent surveys. Such scenarios led us to predict the existence of particular genes whose presence or polymorphism would be associated with cosmopolitan taxa. Furthermore, several conceptual and methodological pitfalls that could hamper future developments of the field are identified, and future approaches and new lines of investigation are suggested.