Reconstructing ancestral ranges in historical biogeography: properties and prospects

Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, we review a selection of current methods for biogeographic analysis and discuss their respective properties. These methods include generalized parsimony approaches, weighted ancestral area analysis, dispersal-vicariance analysis, the dispersal--extinction--cladogenesis model and other maximum likelihood approaches, and Bayesian stochastic mapping of ancestral ranges, including a novel approach to inferring range evolution in the context of island biogeography. Some of these methods were developed specifically for problems of ancestral range reconstruction, whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral ranges. Methods for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed, but also in the various historical events that may change the ancestral ranges. We explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range estimation. Finally, we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.     

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.     

Comparative phylogeography as an integrative approach to historical biogeography

Phylogeography has become a powerful approach for elucidating contemporary geographical patterns of evolutionary subdivision within species and species complexes. A recent extension of this approach is the comparison of phylogeographic patterns of multiple co-distributed taxonomic groups, or 'comparative phylogeography.' Recent comparative phylogeographic studies have revealed pervasive and previously unrecognized biogeographic patterns which suggest that vicariance has played a more important role in the historical development of modern biotic assemblages than current taxonomy would indicate. Despite the utility of comparative phylogeography for uncovering such 'cryptic vicariance', this approach has yet to be embraced by some researchers as a valuable complement to other approaches to historical biogeography. We address here some of the common misconceptions surrounding comparative phylogeography, provide an example of this approach based on the boreal mammal fauna of North America, and argue that together with other approaches, comparative phylogeography can contribute importantly to our understanding of the relationship between earth history and biotic diversification.     

Phylogenetics of the allodapine bee genus Braunsapis: historical biogeography and long-range dispersal over water

Aim A previous study of the allodapine bee genus Braunsapis suggested an African origin, with dispersal events into Madagascar and Asia, and from Asia into Australia. We re‐examine the phylogeny of this genus, using an expanded set of taxa from Madagascar and Malawi and additional sequence data, in order to determine the number of dispersals and the timeframe over which they occurred. Location Africa, Madagascar, Malawi, Asia and Australia. Methods One nuclear (EF‐1α F2) and two mitochondrial (CO1 and Cyt b) gene regions were sequenced for 36 allodapine bee species (including members of the genera Braunsapis, Nasutapis, Allodape, Allodapula, and Macrogalea) and one ceratinine species (Ceratina japonica). We used Bayesian analyses to examine phylogenetic structure and a penalized likelihood approach to estimate approximate ages for key divergences in our phylogeny. Results Our analyses indicate a tropical African origin for Braunsapis in the early Miocene followed by very early dispersal into Asia and then a subsequent dispersal, following Asian diversification, into Australia during the late Miocene. There have also been two dispersals of Braunsapis from Africa to Madagascar and this result, when combined with phylogenetic and biogeographical data for other allodapines, suggests that these bees have the ability to cross moderately large ocean expanses. These dispersals may have been aided by the West Wind Drift, but rafting across the Mozambique Channel is also possible, and could be aided by the existence of developmental stages that require minimal or no feeding and by tolerance to sea water and spume. Accumulating evidence suggests that many biogeographical patterns in the southern hemisphere may be better explained by dispersal than by Gondwanan vicariance hypotheses. Our results add to this growing body of data and raise the possibility that some puzzling trans‐Indian Ocean distributions may also be explained by historical dispersal events across oceanic barriers that now seem insuperable.     

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.     

Phylogeny and biogeography of Caribbean mammals

Vicariance and dispersal hypotheses have been proposed over the last two hundred years to explain the distribution, diversity, and faunal composition of the Caribbean biota. Despite great advances in understanding the geological history of the region, recent biogeographical reviews have not used historical biogeographical methods. In this paper I review the taxonomy, distribution and phylogeny of all Cenozoic Caribbean non‐volant mammals and four bat lineages, and present reconciled trees for available phylogenies. Dates available from the fossil record and hypotheses of divergence based on molecular phylogenetic studies are also included in general assessments of fit between proposed geological models and Caribbean mammal diversification. The evidence posited in mammalian phylogenies does not add to the argument of dispersal vs. vicariance. One previously unidentified temporal pattern, the colonization of the Caribbean by South American mammals between the Palaeocene and the Middle Miocene, accounts for the distribution and phylogeny of the majority of lineages studied. Choloepodine and megalocnine sloths, hystricognath rodents, and primates all arrived during this window of colonization. Of these, megalocnine sloths, hystricognath rodents, Brachyphylla and allied bats, Stenodermatina bats, and primates fit the pattern of divergence from the mainland implied by the Gaarlandia hypothesis. Sloths, rodents and primates also roughly fit the timing of arrival to the Caribbean implied by Gaarlandia. The remaining taxa show contradictory dates of divergence according to molecular clock estimates, and no taxa fit the predicted timing and pattern of divergence among Antillean landmasses under the Gaarlandia model. Choloepodine sloths, murid rodents, insectivorans, mormoopids, and natalids show patterns of divergence from the mainland that are inconsistent with the Gaarlandia hypothesis and seem to require taxon‐specific biogeographical explanations. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81 , 373–394.     

Phylogeny and biogeography of the sharpshooters (Hemiptera: Cicadellidae: Cicadellinae)

Sharpshooters (Cicadellinae), a large subfamily of the Cicadellidae, exhibit a global distribution and a broad array of ecological preferences. To explore the phylogenetic relationships and roles of global historical, biotic and biogeographic processes in the diversification of sharpshooters, we analysed DNA sequence data from three mitochondrial and two nuclear genes for 243 taxa representing all Cicadellinae tribes, generic groups, regional faunas and data of geographic distributions of sharpshooter species compiled from online databases and available literature. The maximum likelihood (ML) and Bayesian inference (BI) analyses strongly support the monophyletic clade including Cicadellinae and Phereurininae. Divergence time estimates and biogeographic analyses suggest that sharpshooters originated in the Neotropical region or were more widespread in Gondwana during the Early Cretaceous and diversified through a combination of ancient vicariance and dispersal following the evolution of angiosperm-dominated habitats. The earliest divergence during the Cretaceous gave rise to Oriental and New World lineages, the latter of which subsequently dispersed into the Old World and gave rise to the diverse endemic fauna of Madagascar. The Oriental lineage shows high diversity and endemism in tropical Asia and the Pacific, with striking distributional discontinuities in Wallacea. These results suggest that a combination of environmental and evolutionary factors including continental-scale vicariance, long-distance dispersal and diversification of terrestrial microhabitats and host plants may explain the diversity of the modern sharpshooter fauna.     

The biogeography of Gunnera L.: vicariance and dispersal

Aim The genus Gunnera is distributed in South America, Africa and the Australasian region, a few species reaching Hawaii and southern Mexico in the North. A cladogram was used to (1) discuss the biogeography of Gunnera and (2) subsequently compare this biogeographical pattern with the geological history of continents and the patterns reported for other Southern Hemisphere organisms. Location Africa, northern South America, southern South America, Tasmania, New Zealand, New Guinea/Malaya, Hawaii, North America, Antarctica. Methods A phylogenetic analysis of twenty‐six species of Gunnera combining morphological characters and new as well as published sequences of the ITS region, rbcL and the rps16 intron, was used to interpret the biogeographical patterns in Gunnera. Vicariance was applied in the first place and dispersal was only assumed as a second best explanation. Results The Uruguayan/Brazilian Gunnera herteri Osten (subgenus Ostenigunnera Mattfeld) is sister to the rest of the genus, followed sequentially upwards by the African G. perpensa L. (subgenus Gunnera), in turn sister to all other, American and Australasian, species. These are divided into two clades, one containing American/Hawaiian species, the other containing all Australasian species. Within the Australasian clade, G. macrophylla Blume (subgenus Pseudogunnera Schindler), occurring in New Guinea and Malaya, is sister to a clade including the species from New Zealand and Tasmania (subgenus Milligania Schindler). The southern South American subgenus Misandra Schindler is sister to a clade containing the remaining American, as well as the Hawaiian species (subgenus Panke Schindler). Within subgenus Panke, G. mexicana Brandegee, the only North American species in the genus, is sister to a clade wherein the Hawaiian species are basal to all south and central American taxa. Main conclusions According to the cladogram, South America appears in two places, suggesting an historical explanation for northern South America to be separate from southern South America. Following a well‐known biogeographical pattern of vicariance, Africa is the sister area to the combined southern South America/Australasian clade. Within the Australasian clade, New Zealand is more closely related to New Guinea/Malaya than to southern South America, a pattern found in other plant cladograms, contradictory to some of the patterns supported by animal clades and by the geological hypothesis, respectively. The position of the Tasmanian G. cordifolia, nested within the New Zealand clade indicates dispersal of this species to Tasmania. The position of G. mexicana, the only North American species, as sister to the remaining species of subgenus Panke together with the subsequent sister relation between Hawaii and southern South America, may reflect a North American origin of Panke and a recolonization of South America from the north. This is in agreement with the early North American fossil record of Gunnera and the apparent young age of the South American clade.     

Minute moss beetles in the Southern Hemisphere: Molecular phylogeny,historical biogeography and habitat shifts (Coleoptera: Hydraenidae)

Minute moss beetles (Hydraenidae) are one of the most speciose and widespread families of aquatic Coleoptera, with an estimated 4000 extant species, found in the majority of aquatic habitats from coastal rock pools to mountain streams and from the Arctic Circle to the Antarctic islands. Molecular phylogenetic works have improved our understanding of the evolutionary history of the megadiverse Hydraena, Limnebius and Ochthebius in recent years, but most genera in the family have not yet been included in any phylogenetic analyses, particularly most of those which are restricted to the Southern Hemisphere. Using a multimarker molecular matrix, sampling over 40% of described species richness and 75% of currently recognized genera, we infer a comprehensive molecular phylogeny of these predominantly Gondwanan Hydraenidae. Whilst the genera we focus on are morphologically diverse, and currently classified across all four hydraenid subfamilies, our phylogenetic analyses suggest that these Gondwanan genera may instead constitute a single clade. As a result of our findings, the African genus Oomtelecopon Perkins syn.n. is shown to nest within Coelometopon Janssens, the New Zealand Homalaena Ordish syn.n. and Podaena Ordish syn.n. are synonymised with Orchymontia Broun, and the South African Pterosthetops Perkins syn.n. is synonymised with Prosthetops Waterhouse, resulting in Pterosthetopini Perkins syn.n. being synonymised with Prosthetopini Perkins. Mesoceratops Bilton & Jäch gen.n. is erected to accommodate six former members of Mesoceration Janssens, which is shown to be polyphyletic. We propose the replacement name Orchymontia ordishi Jäch & Bilton nom.n. for Homalaena dilatata Ordish, 1984 (now a junior homonym); altogether 39 new combinations are proposed. Our Bayesian divergence times infer an origin for this ‘Gondwana group’ of genera in Africa plus Madagascar in the mid-Cretaceous and suggest that both vicariant and dispersal processes, together with extinctions, have shaped the biogeographic history of these beetles in the Southern Hemisphere during the Cretaceous, resulting in geographically conserved extant lineages. Finally, we reconstruct ancestral habitat shifts across our phylogeny, revealing numerous changes in habitat occupancy in these genera, including multiple origins of fully terrestrial, humicolous taxa in different regions.     

The other face of Lyell: historical biogeography in his Principles of geology

Although some excellent articles about Lyell's work have been published, they do not explicitly deal with Lyell's biogeographical conceptions. The purpose of this paper is to analyse Lyell's biogeographical model in terms of its own internal structure. Lyell tried to explain the distribution of organisms by appealing to a real cause (climate). However, he was aware that environmental conditions were clearly insufficient to explain the existence of biogeographical regions. Lyell's adherence to ecological determinism generated strong tensions within his biogeographical model. He shifted from granting a secondary weight to dispersal to assigning it a major role. By doing so, Lyell was led into an evident contradiction. A permanent tension in Lyell's ideas was generated by the prevalent explanatory pattern of his time. The explanatory model based on laws did not produce satisfactory results in biology because it did not deal with historical processes. We may conclude that the knowledge of organic distribution interested Lyell as long as it could be explained by the uniformitarian principles of his geological system. The importance of the second volume of the Principles of geology lies in its ample and systematic argumentation about the geographical distribution of organisms. Lyell established, independently from any theory about organic change, the first version of dispersalist biogeography.     

Grasses through space and time: An overview of the biogeographical and macroevolutionary history of Poaceae

Grasses are widespread on every continent and are found in all terrestrial biomes. The dominance and spread of grasses and grassland ecosystems have led to significant changes in Earth′s climate, geochemistry, and biodiversity. The abundance of DNA sequence data, particularly chloroplast sequences, and advances in placing grass fossils within the family allows for a reappraisal of the family′s origins, timing, and geographic spread and the factors that have promoted diversification. We reconstructed a time-calibrated grass phylogeny and inferred ancestral areas using chloroplast DNA sequences from nearly 90% of extant grass genera. With a few notable exceptions, the phylogeny is well resolved to the subtribal level. The family began to diversify in the Early–Late Cretaceous (crown age of 98.54 Ma) on West Gondwana before the complete split between Africa and South America. Vicariance from the splitting of Gondwana may be responsible for the initial divergence in the family. However, Africa clearly served as the center of origin for much of the early diversification of the family. With this phylogenetic, temporal, and spatial framework, we review the evolution and biogeography of the family with the aim to facilitate the testing of biogeographical hypotheses about its origins, evolutionary tempo, and diversification. The current classification of the family is discussed with an extensive review of the extant diversity and distribution of species, molecular and morphological evidence supporting the current classification scheme, and the evidence informing our understanding of the biogeographical history of the family.     

Historical biogeography of the endemic Campanulaceae of Crete

Aim The clade Campanulaceae in the Cretan area is rich in endemics, with c. 50% of its species having restricted distributions. These species are analysed in the context of a larger phylogeny of the Campanulaceae. Divergence times are calculated and hypotheses of vicariance and dispersal are tested with the aim of understanding whether Cretan lineages represent remnants of an older continental flora. Location The Cretan area: Crete and the Karpathos Islands (Greece). Methods We obtained chloroplast DNA sequence data from rbcL, atpB and matK genes for 102 ingroup taxa, of which 18 are from the Cretan area, 11 are endemics, and two have disjunct, bi‐regional distributions. We analysed the data using beast , a Bayesian approach that simultaneously infers the phylogeny and divergence times. We calibrated the tree by placing a seed fossil in the phylogeny, and used published age estimates as a prior for the root. Results The phylogenetic reconstruction shows that all Campanula species fall within a well‐supported campanuloid clade; however, Campanula is highly polyphyletic. The Cretan endemics do not form a monophyletic group, and species are scattered throughout the campanuloid clade. Therefore, the Cretan taxa did not evolve following a single vicariance or dispersal event. Most Cretan lineages represent remnants of an older continental flora, with the exception of one clade that radiated in situ after island isolation, and one lineage that appears to have arrived by dispersal. Main conclusions Most Cretan species were present in the islands at the time of their isolation, and very little long‐distance dispersal to Crete and diversification within Crete has occurred since then. Endemism is probably driven by loss of species on the mainland after island isolation. Species on the islands may have been more widespread in the past, but they are now restricted to often inaccessible areas, probably as a result of human pressure.     

Evidence and hypothesis in biogeography

Evidence can provide support for or against a particular biogeographical hypothesis. Treating a hypothesis as if it were evidence or an empirical observation confounds many biogeographical analyses. We focus on two recent publications that address, in part, the evolution of the biota of Sulawesi, the large Indonesian island in the centre of the Indo‐Australian Archipelago. Many biogeographical explanations are hampered by invoking simple notions of mechanism or process – dispersal and vicariance – or constraints, such as dispersal from a centre of origin, and, in so doing, dismiss more complex geological phenomena such as emergent volcanoes within island chains or composite areas as irrelevant. Moreover, they do not search for, therefore never discover, biogeographical patterns that may better explain the distribution of biota through time.