Critique of parsimony analysis of endemicity as a method of historical biogeography

Aim Assess the value of parsimony analysis of endemism as either an a priori (cladistic) and an a posteriori (phylogenetic) method of historical biogeography. Location World‐wide. Methods Parsimony analysis of endemicity (PAE) and Brooks parsimony analysis (BPA). Results Parsimony analysis of endemicity is capable of finding correct and unambiguous area relationships only under scenarios of vicariance in combination with non‐response to vicariance or extinction. An empirical comparison between PAE and BPA, using the poeciliid fish genera Heterandria and Xiphophorus, demonstrates that PAE fails to document much of the historical complexity in this relatively simple system. Main conclusions The a priori assumptions of PAE are far more restrictive than those made by other a priori methods, limiting its utility as a method of cladistic biogeography. The inability of PAE to detect perfect vicariance or biogeographical histories involving dispersal, renders it unsuitable as a method of phylogenetic biogeography.     

An evaluation of new parsimony‐based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae

Aim Recently developed parametric methods in historical biogeography allow researchers to integrate temporal and palaeogeographical information into the reconstruction of biogeographical scenarios, thus overcoming a known bias of parsimony‐based approaches. Here, we compare a parametric method, dispersal–extinction–cladogenesis (DEC), against a parsimony‐based method, dispersal–vicariance analysis (DIVA), which does not incorporate branch lengths but accounts for phylogenetic uncertainty through a Bayesian empirical approach (Bayes‐DIVA). We analyse the benefits and limitations of each method using the cosmopolitan plant family Sapindaceae as a case study. Location World‐wide. Methods Phylogenetic relationships were estimated by Bayesian inference on a large dataset representing generic diversity within Sapindaceae. Lineage divergence times were estimated by penalized likelihood over a sample of trees from the posterior distribution of the phylogeny to account for dating uncertainty in biogeographical reconstructions. We compared biogeographical scenarios between Bayes‐DIVA and two different DEC models: one with no geological constraints and another that employed a stratified palaeogeographical model in which dispersal rates were scaled according to area connectivity across four time slices, reflecting the changing continental configuration over the last 110 million years. Results Despite differences in the underlying biogeographical model, Bayes‐DIVA and DEC inferred similar biogeographical scenarios. The main differences were: (1) in the timing of dispersal events – which in Bayes‐DIVA sometimes conflicts with palaeogeographical information, and (2) in the lower frequency of terminal dispersal events inferred by DEC. Uncertainty in divergence time estimations influenced both the inference of ancestral ranges and the decisiveness with which an area can be assigned to a node. Main conclusions By considering lineage divergence times, the DEC method gives more accurate reconstructions that are in agreement with palaeogeographical evidence. In contrast, Bayes‐DIVA showed the highest decisiveness in unequivocally reconstructing ancestral ranges, probably reflecting its ability to integrate phylogenetic uncertainty. Care should be taken in defining the palaeogeographical model in DEC because of the possibility of overestimating the frequency of extinction events, or of inferring ancestral ranges that are outside the extant species ranges, owing to dispersal constraints enforced by the model. The wide‐spanning spatial and temporal model proposed here could prove useful for testing large‐scale biogeographical patterns in plants.     

Divergence time uncertainty and historical biogeography reconstruction – an example from Urophylleae (Rubiaceae)

Aim When hypotheses of historical biogeography are evaluated, age estimates of individual nodes in a phylogeny often have a direct impact on what explanation is concluded to be most likely. Confidence intervals of estimated divergence times obtained in molecular dating analyses are usually very large, but the uncertainty is rarely incorporated in biogeographical analyses. The aim of this study is to use the group Urophylleae, which has a disjunct pantropical distribution, to explore how the uncertainty in estimated divergence times affects conclusions in biogeographical analysis. Two hypotheses are evaluated: (1) long‐distance dispersal from Africa to Asia and the Neotropics, and (2) a continuous distribution in the boreotropics, probably involving migration across the North Atlantic Land Bridge, followed by isolation in equatorial refugia. Location Tropical and subtropical Asia, tropical Africa, and central and southern tropical America. Methods This study uses parsimony and Bayesian phylogenetic analyses of chloroplast DNA and nuclear ribosomal DNA data from 56 ingroup species, beast molecular dating and a Bayesian approach to dispersal–vicariance analysis (Bayes‐DIVA) to reconstruct the ancestral area of the group, and the dispersal–extinction–cladogenesis method to test biogeographical hypotheses. Results When the two models of geographic range evolution were compared using the maximum likelihood (ML) tree with mean estimates of divergence times, boreotropical migration was indicated to be much more likely than long‐distance dispersal. Analyses of a large sample of dated phylogenies did, however, show that this result was not consistent. The age estimate of one specific node had a major impact on likelihood values and on which model performed best. The results show that boreotropical migration provides a slightly better explanation of the geographical distribution patterns of extant Urophylleae than long‐distance dispersal. Main conclusions This study shows that results from biogeographical analyses based on single phylogenetic trees, such as a ML or consensus tree, can be misleading, and that it may be very important to take the uncertainty in age estimates into account. Methods that account for the uncertainty in topology, branch lengths and estimated divergence times are not commonly used in biogeographical inference today but should definitely be preferred in order to avoid unwarranted conclusions.     

Vicariance or long‐distance dispersal: historical biogeography of the pantropical subfamily Chrysophylloideae (Sapotaceae)

Aim Continental disjunctions in pantropical taxa have been explained by vicariance or long‐distance dispersal. The relative importance of these explanations in shaping current distributions may vary, depending on historical backgrounds or biological characteristics of particular taxa. We aimed to determine the geographical origin of the pantropical subfamily Chrysophylloideae (Sapotaceae) and the roles vicariance and dispersal have played in shaping its modern distribution. Location Tropical areas of Africa, Australasia and South America. Methods We utilized a recently published, comprehensive data set including 66 species and nine molecular markers. Bayesian phylogenetic trees were generated and dated using five fossils and the penalized likelihood approach. Distributional ranges of nodes were estimated using maximum likelihood and parsimony analyses. In both biogeographical and molecular dating analyses, phylogenetic and branch length uncertainty was taken into account by averaging the results over 2000 trees extracted from the Bayesian stationary sample. Results Our results indicate that the earliest diversification of Chrysophylloideae was in the Campanian of Africa c. 73–83 Ma. A narrow time interval for colonization from Africa to the Neotropics (one to three dispersals) and Australasia (a single migration) indicates a relatively rapid radiation of this subfamily in the latest Cretaceous to the earliest Palaeocene (c. 62–72 Ma). A single dispersal event from the Neotropics back to Africa during the Neogene was inferred. Long‐distance dispersal between Australia and New Caledonia occurred at least four times, and between Africa and Madagascar on multiple occasions. Main conclusions Long‐distance dispersal has been the dominant mechanism for range expansion in the subfamily Chrysophylloideae. Vicariance could explain South American–Australian disjunction via Antarctica, but not the exchanges between Africa and South America and between New Caledonia and Australia, or the presence of the subfamily in Madagascar. We find low support for the hypothesis that the North Atlantic land bridge facilitated range expansions at the Palaeocene/Eocene boundary.     

Systematics and biogeography of Rhodniini (Heteroptera: Reduviidae: Triatominae) based on 16S mitochondrial rDNA sequences

Aim The tribe Rhodniini is one of six comprising the subfamily Triatominae (Heteroptera: Reduviidae), notorious as blood‐sucking household pests and vectors of Trypanosoma cruzi throughout Latin America. The human and economic cost of this disease in the American tropics is considerable, and these bugs are unquestionably of great importance to man. Studies of the evolution, phylogeny, biogeography, ecology, physiology and behaviour of the Rhodniini are needed to help improve existing Chagas’ disease control programmes. The objective of the study reported here was to propose biogeographical hypotheses to explain the modern geographical distribution of the species of Rhodniini. Location Neotropical region. Methods We employed mitochondrial rDNA sequences (16S) currently available in GenBank to align sequences of Rhodniini species using ClustalX. The analyses included 16S sequences from predatory reduviid subfamilies (Stenopodainae, Ectrichodiinae, Harpactorinae, Reduviinae and Salyavatinae) present in GenBank as an outgroup. Cladistic analysis used the program PAUP to derive trees based on maximum parsimony (MP) and maximum likelihood (ML). Known distribution data for Rhodniini species were obtained from reviews and plotted on maps of South and Central America using the program iMap. An area cladogram was derived from the cladistic result to show the historical connections among the studied taxa and the endemic areas. The program TreeMap (Jungle Edition) was used to deduce taxon–area associations where the optimal solutions to explain the biogeographical hypothesis of the Rhodniini in the Neotropics were those with lowest total cost. Results Parsimony and maximum‐likelihood analysis of 16S rDNA sequences included 14 species of Rhodniini, as well as five species of predatory Reduviidae representing five of the predatory subfamilies. Tanglegrams were used to show the relationship between the Neotropical areas of endemism and Rhodniini species. When TreeMap with codivergence (vicariance) events were weighted as 0 and duplication (sympatry), lineage losses (extinction) and host switching (dispersal) were all weighted as 1, 20 scenarios were found to explain the biogeographical history of Rhodniini in the Neotropical region. Twelve of the optimal solutions with the lowest total cost were used to explain the biogeography of the Rhodniini in the Neotropics. These optimal reconstructions require six vicariance events, 20 duplications (sympatry), at least three dispersals, and at least one extinction event. Main conclusions The Rhodniini have a complex biogeographical history that has involved vicariance, duplications (sympatry), dispersal and extinction events. The main geological events affecting the origin and diversification of the Rhodniini in the Neotropics were (1) uplift of the Central Andes in the Miocene or later, (2) break‐up of the Andes into three separate cordilleras (Eastern, Central and Western) in the Plio‐Pleistocene, (3) formation of a land corridor connecting South and North America in the Pliocene, and (4) uplift of the Serra do Mar and Serra da Mantiqueira mountain systems between the Oligocene and Pleistocene. The relationships and biogeographical history of the species of Rhodniini in the Neotropical region probably arose from the areas of endemism shown in our work.     

Distribution patterns and biogeographic analysis of Austral Polychaeta (Annelida)

Aim We investigate the biogeography of Austral Polychaeta (Annelida) using members of the families Eunicidae, Lumbrineridae, Oenonidae, Onuphidae, Serpulidae and Spionidae and Parsimony Analysis of Endemicity (PAE). We determine whether observed polychaete distribution patterns correspond to traditional shallow-water marine areas of endemism, estimate patterns of endemism and relationships between areas of endemism, and infer the biological processes that have caused these patterns. Location The study is concerned with extant polychaete taxa occupying shallow-water areas derived from the breakup of the Gondwana landmass (i.e. Austral areas). Methods Similarity was assessed using a significance test with Jaccard's indices. Areas not significantly different at 0.99 were combined prior to the PAE. Widespread species and genera (155 taxa) were scored for presence/absence for each area of endemism. PAE was used to derive hypotheses of area relationships. Hierarchical patterns in the PAE trees were identified by testing for congruence with patterns derived from cladistic biogeographic studies of other Gondwanan taxa and with geological evidence. Results The polychaete faunas of four area-pairs were not significantly different and the areas amalgamated: South-west Africa and South Africa, New Zealand South Island and Chatham Islands, Macquarie Island and Antipodean Islands, and West Antarctica and South Georgia. Areas with the highest levels of species endemism were southern Australia (67.0%), South-east South America (53.2%) and South Africa (40.4%). About 60% of species and 7.5% of genera occupied a single area of endemism. The remainder were informative in the PAE. Under a no long-distance dispersal assumption a single minimal-length PAE tree resulted (l=367; ci=0.42); under dispersal allowed, three minimal-length trees resulted (l=278; ci=0.56). In relation to the sister grouping of the New Zealand areas and Australia we find congruence between our minimal-length trees and those derived from a biogeographic study of land plants, and with area relationships predicted by the Expanding Earth Model. Main conclusions The polychaete distribution patterns in this study differ slightly from the classical areas of endemism, most notably in being broader, thereby bringing into question the value of using single provincial system for marine biogeographic studies. The Greater New Zealand region is found to be ‘monophyletic’ with respect to polychaetes, that is comprising a genuine biogeographical entity, and most closely related to the polychaete fauna of southern Australia. This finding is consistent with studies of land plants and with the Expanding Earth model, but disagrees with conventional geology and biogeographic hypothesis involving a ‘polyphyletic’ New Zealand. Both vicariance and concerted range expansion (=biotic dispersion) appear to have played important roles in shaping present-day distribution patterns of Austral polychaetes. Shallow-water ridge systems between the Australian and Greater New Zealand continental landmasses during the Tertiary are thought to have facilitated biotic dispersion.     

The resurrection of oceanic dispersal in historical biogeography

Geographical distributions of terrestrial or freshwater taxa that are broken up by oceans can be explained by either oceanic dispersal or vicariance in the form of fragmentation of a previously contiguous landmass. The validation of plate-tectonics theory provided a global vicariance mechanism and, along with cladistic arguments for the primacy of vicariance, helped create a view of oceanic dispersal as a rare phenomenon and an explanation of last resort. Here, I describe recent work that suggests that the importance of oceanic dispersal has been strongly underestimated. In particular, molecular dating of lineage divergences favors oceanic dispersal over tectonic vicariance as an explanation for disjunct distributions in a wide variety of taxa, from frogs to beetles to baobab trees. Other evidence, such as substantial gene flow among island populations of Anolis lizards, also indicates unexpectedly high frequencies of oceanic dispersal. The resurrection of oceanic dispersal is the most striking aspect of a major shift in historical biogeography toward a more even balance between vicariance and dispersal explanations. This new view implies that biotas are more dynamic and have more recent origins than had been thought previously. A high frequency of dispersal also suggests that a fundamental methodological assumption of many biogeographical studies--that vicariance is a priori a more probable explanation than dispersal--needs to be re-evaluated and perhaps discarded.     

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。     

Historical biogeography of some river basins in central Mexico evidenced by their goodeine freshwater fishes: a preliminary hypothesis using secondary Brooks parsimony analysis

Aims Our aim was to uncover and describe patterns of historical biogeography of the main river basins in central Mexico, based on a secondary Brooks parsimony analysis (BPA) of goodeine fishes, and to understand the processes that determine them with respect to the molecular clock of the goodeines and the geological events that have taken place in the region since the Miocene. Location The region covered in this study includes central Mexico, mostly the so‐called Mesa Central of Mexico, an area argued to be a transitional zone comprising several major river drainages from their headwaters at high elevations along the Transmexican Volcanic Belt to the coast of the Gulf of Mexico and the Pacific Ocean. Methods Based on a previous phylogenetic hypothesis regarding the Goodeidae, we built a data matrix using additive binary coding. First, we conducted a primary BPA to provide general explanations of the historical biogeography of Central Mexico. As ambiguity was found, a secondary BPA was conducted, and some areas were duplicated in order to explain the reticulated history of the area. Area cladograms were obtained by running a parsimony analysis. Instances of vicariance and non‐vicariance processes were described with reference to the cladogram obtained from secondary BPA. Results The study area was divided into 18 discrete regions. Primary BPA produced nine equally parsimonious cladograms with 129 steps, and a consistency index (CI) of 0.574. A strict consensus cladogram shows low resolution among some areas, but other area relationships are consistent. For secondary BPA, five of the 18 regions were duplicated (LEA, COT, AYU, CUT, PAN); one was triplicated (BAL); and one was quadruplicated (AME), suggesting that the pattern of distribution of species in these areas reflects multiple independent events. These areas correspond with the regions exhibiting the highest levels of diversification and the most complex geological history, and those for which river piracy events or basin connections have been proposed. The secondary BPA produced a single most parsimonious cladogram with 118 steps, and a CI of 0.858. This cladogram shows that none of the duplicated areas are nested together, reinforcing the idea of a reticulated history of the areas and not a single vicariant event. Main conclusions Although our results are preliminary and we cannot establish this as a general pattern, as the BPA is based on a single‐taxon cladogram, resolution obtained in the secondary BPA provides some insights regarding the historical biogeography of this group of fishes in river basins of central Mexico. Secondary BPA indicates that the historical biogeography of central Mexico, as shown by their goodeine freshwater fishes, is complex and is a result of a series of vicariant and non‐vicariant events such as post‐dispersal speciation and post‐speciation dispersal.     

Molecular clocks keep dispersal hypotheses afloat: evidence for trans‐Atlantic rafting by rodents

Aim In order to resolve disputed biogeographical histories of biota with Gondwanan continental distributions, and to assess the null hypothesis of vicariance, it is imperative that a robust geological time‐frame be established. As an example, the sudden and coincident appearance of hystricognath rodents (Rodentia: Hystricognathi) on both the African and South American continents has been an irreconcilable controversy for evolutionary biologists, presenting enigmas for both Gondwanan vicariance and Late Eocene dispersal hypotheses. In an attempt to resolve this discordance, we aim to provide a more robust phylogenetic hypothesis and improve divergence‐date estimates, which are essential to assessing the null hypothesis of vicariance biogeography. Location The primary centres of distribution are in Africa and South America. Methods We implemented parsimony, maximum‐likelihood and Bayesian methods to generate a phylogeny of 37 hystricognath taxa, the most comprehensive taxonomic sampling of this group to date, on the basis of two nuclear gene regions. To increase phylogenetic resolution at the basal nodes, these data were combined with previously published data for six additional nuclear gene regions. Divergence dates were estimated using two relaxed‐molecular‐clock methods, Bayesian multidivtime and nonparametric rate smoothing. Results Our data do not support reciprocal monophyly of African and South American lineages. Indeed, Old World porcupines (i.e. Hystricomorpha) appear to be more closely related to New World lineages (i.e. Caviomorpha) than to other Old World families (i.e. Bathyergidae, Petromuridae and Thryonomyidae). The divergence between the monophyletic assemblage of South American lineages and its Old World ancestor was estimated to have occurred c. 50 Ma. Main conclusions Our phylogenetic hypothesis and divergence‐date estimates are strongly at odds with Gondwanan‐vicariance isolating mechanisms. In contrast, our data suggest that transoceanic dispersal has played a significant role in governing the contemporary distribution of hystricognath rodents. Molecular‐clock analyses imply a trans‐Tethys dispersal event, broadly confined to the Late Cretaceous, and trans‐Atlantic dispersal within the Early Eocene. Our analyses also imply that the use of the oldest known South American rodent fossil as a calibration point has biased molecular‐clock inferences.     

Marine dispersal as a pre‐requisite for Gondwanan vicariance among elements of the galaxiid fish fauna

Aim The aim of this study was to determine the contributions of Gondwanan vicariance and marine dispersal to the contemporary distribution of galaxiid fishes. This group has been central in arguments concerning the roles of dispersal and vicariance in the Southern Hemisphere, as some taxa have marine life history stages through which transoceanic dispersal may have been facilitated, yet other galaxiids are entirely restricted to freshwaters. Location Southern Hemisphere land masses of Gondwanan derivation. Methods Biogeographic hypotheses of Gondwanan vicariance and marine dispersal were tested using four lines of evidence: (1) concordance of species–area phylogenetic relationships, (2) molecular estimates of lineage divergence times with a priori expectations based on plate tectonics, (3) reconstructions of ancestral dispersal capabilities, and (4) reconstructions of distribution inheritance scenarios (using the dispersal–extinction–cladogenesis model to infer historical ranges and dispersal and extinction events). Results Phylogenetic relationships were reconstructed from 4531 mitochondrial and nuclear nucleotide characters, and 181 morphological characters, across 53 of the 56 presently recognized species. Phylogenetic relationships were generally well resolved and supported among galaxiids using the combined dataset, and conflicting relationships between molecular and morphological datasets typically received low topological support from either or both datasets. Transoceanic disjunctions were exhibited at 16 nodes, but only three pre‐dated relevant continental fragmentation events; furthermore, ancestral distribution inheritance scenarios for two of these nodes reflected cladogenesis within, rather than between, Gondwanan land masses, and ancestral marine dispersal capability could not be rejected for all three. Instead, the four lines of evidence surveyed suggest that Gondwanan vicariance occurred twice, but in both instances was preceded by marine dispersal between land masses, and in at least one instance was initiated by the cessation of marine dispersal subsequent to continental fragmentation. Main conclusions Gondwanan vicariance appears to have been preceded by marine dispersal in the few instances where it may explain contemporary galaxiid distribution, such that these biogeographic mechanisms may sometimes have a synergistic relationship.     

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.     

Evidence for Gondwanan vicariance in an ancient clade of gecko lizards

Aim Geckos (Reptilia: Squamata), due to their great age and global distribution, are excellent candidates to test hypotheses of Gondwanan vicariance against post‐Gondwanan dispersal. Our aims are: to generate a phylogeny of the sphaerodactyl geckos and their closest relatives; evaluate previous phylogenetic hypotheses of the sphaerodactyl geckos with regard to the other major gecko lineages; and to use divergence date estimates to inform a biogeographical scenario regarding Gondwanan relationships and assess the roles of vicariance and dispersal in shaping the current distributions of the New World sphaerodactyl geckos and their closest Old World relatives. Location Africa, Asia, Europe, South America, Atlantic Ocean. Methods We used parsimony and partitioned Bayesian methods to analyse data from five nuclear genes to generate a phylogeny for the New World sphaerodactyl geckos and their close Old World relatives. We used dispersal–vicariance analysis to determine ancestral area relationships among clades, and divergence times were estimated from the phylogeny using nonparametric rate smoothing. Results We recovered a monophyletic group containing the New World sphaerodactyl genera, Coleodactylus, Gonatodes, Lepidoblepharis, Pseudogonatodes and Sphaerodactylus, and the Old World Gekkotan genera Aristelliger, Euleptes, Quedenfeldtia, Pristurus, Saurodactylus and Teratoscincus. The dispersal–vicariance analysis indicated that the ancestral area for this clade was North Africa and surrounding regions. The divergence between the New World spaherodactyl geckos and their closest Old World relative was estimated to have occurred c. 96 Myr bp . Main conclusions Here we provide the first molecular genetic phylogenetic hypothesis of the New World sphaerodactyl geckos and their closest Old World relatives. A combination of divergence date estimates and dispersal–vicariance analysis informed a biogeographical scenario indicating that the split between the sphaerodactyl geckos and their African relatives coincided with the Africa/South America split and the opening of the Atlantic Ocean. We resurrect the family name Sphaerodactylidae to represent the expanded sphaerodactyl clade.     

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.     

When simplicity is not parsimonious: a priori and a posteriori methods in historical biogeography

Despite using the same null hypothesis, a priori and a posteriori approaches in historical biogeography differ fundamentally. Methods such as Component Analysis (CA) and Reconciled Tree Analysis (RTA) may eliminate or modify input data in order to maximize fit to the null hypothesis, by invoking assumptions 1 and 2. Methods such as Brooks Parsimony Analysis (BPA) modify the null hypothesis, if necessary, to maintain the integrity of the input data, as required by assumption 0. Two exemplars illustrate critical empirical differences between CA/RTA and BPA: (1) CA rather than BPA may select the incorrect general area cladogram for a set of data (2) BPA, not RTA, provides the most parsimonious interpretation of all available data and (3) secondary BPA, proposed in 1990, applied to data sets for which dispersal producing areas with reticulate histories is most parsimonious, provides biologically realistic interpretations of area cladograms. These observations lead to the conclusion that BPA and CA/RTA are designed to implement different research programmes based on different conceptual frameworks. BPA is designed to assess the biogeographic context of speciation events, whereas CA/RTA are designed to find the best fitting pattern of relationships among areas based on the taxa that inhabit them. Unique distributional elements and reticulate (hybrid) histories of areas are essential for explaining complex histories of speciation. The conceptual framework for BPA, thus, assumes biogeographical complexity, relying on parsimony as an explanatory tool to summarize complex results, whereas CA/RTA assumes biogeographical simplicity, assuming conceptual parsimony a priori .     

Historical biogeography of New World emballonurid bats (tribe Diclidurini): taxon pulse diversification

Aim To reconstruct the biogeographical history of New World emballonurid bats (tribe Diclidurini). Although bats are the second most species‐rich order of mammals, they have not contributed substantially to our understanding of the historical biogeography of mammals in the Neotropics because of a poor fossil record. In addition, being the only group of mammals that fly, bats typically have large distributions with relatively few species endemic to restricted areas that are amenable to vicariant biogeographical approaches. Location Central and South America. Methods Phylogenetic analysis for comparing trees (PACT) is a new algorithm that incorporates all spatial information from taxon area cladograms into a general area cladogram. There were nine biogeographical areas identified in Central and South America for New World emballonurid bats. Molecular dating was used to incorporate the temporal aspect of historical biogeography. This method was compared with dispersal–vicariance analysis (DIVA), which assumes vicariance as the default mode of speciation. Results Of the 45 speciation events in a fully resolved phylogeny, eight that were hypothesized by DIVA as vicariance were considered by PACT as two peripheral isolations and six within‐area events. DIVA was less parsimonious because it required six more post‐speciation dispersal events in addition to the 73 hypothesized by PACT. DIVA reconstructed a widely distributed ancestor, suggesting that most dispersal events occurred earlier, whereas the ancestral area for PACT based on character optimization was the Northern Amazon, suggesting that dispersal events were more recent phenomena. Main conclusions The general area cladogram from PACT indicated that within‐area events, and not vicariance, provide the major mode of speciation for New World emballonurid bats. There was no biological evidence supporting or rejecting sympatric speciation in New World emballonurid bats. However, the geological history, combined with fluctuations in temperature and sea level, suggested within‐area speciation in a changing and heterogeneous environment in the Northern Amazon during the Miocene. This scenario is similar to the taxon‐pulse hypothesis of biotic diversification, which posits repeated episodes of range expansions and contractions from a stable core area such as the Guiana Shield within the Northern Amazon.     

Exploring the Afromontane centre of endemism: Kniphofia Moench (Asphodelaceae) as a floristic indicator

Aim The genus Kniphofia contains 71 species with an African–Malagasy distribution, including one species from Yemen. The genus has a general Afromontane distribution. Here we explore whether Kniphofia is a floristic indicator of the Afromontane centre of endemism and diversity. The South Africa Centre of diversity and endemism was explored in greater detail to understand biogeographical patterns. Location Africa, Afromontane Region, southern Africa, Madagascar and Yemen. Methods Diversity and endemism for the genus were examined at the continental scale using a chorological approach. Biogeographical patterns and endemism in the South Africa Centre were examined in greater detail using chorology, phenetics, parsimony analysis of endemicity (PAE) and mapping of range‐restricted taxa. Results Six centres of diversity were recovered, five of which are also centres of endemism. Eight subcentres of diversity are proposed, of which only two are considered subcentres of endemism. The South Africa Centre is the most species‐rich region and the largest centre of endemism for Kniphofia. The phenetic analysis of the South Africa Centre at the full degree square scale recovered three biogeographical areas that correspond with the subcentres obtained from the chorological analysis. The PAE (at the full degree square scale) and the mapping of range‐restricted taxa recovered two and six areas of endemism (AOEs), respectively. These latter two approaches produced results of limited value, possibly as a result of inadequate collecting of Kniphofia species. Only two AOEs were identified by PAE and these are embedded within two of the six AOEs recovered by the mapping of range‐restricted taxa. All the above AOEs are within the three subcentres found by chorological and phenetic analysis (at the full degree square scale) for the South Africa Centre. Main conclusions The centres for Kniphofia broadly correspond to the Afromontane regional mountain systems, but with some notable differences. We regard Kniphofia as a floristic indicator of the Afromontane Region sensu lato. In southern Africa, the phenetic approach at the full‐degree scale retrieved areas that correlate well with those obtained by the chorological approach.     

A protocol for temporal calibration of general area cladograms

Aim To describe a protocol for incorporating a temporal dimension into historical biogeographical analysis, while maintaining the essential independence of all datasets, involving the generation of general area cladograms. Location Global. Methods General area cladograms (GACs) are a reconstruction of the evolutionary history of a set of areas and unrelated clades within those areas. Nodes on a GAC correspond to speciation events in a group of taxa; general nodes are those at which multiple unrelated clades speciate. We undertake temporal calibration of GACs using molecular clock estimates of splitting events between extant taxa as well as first appearance data from the fossil record. We present two examples based on re‐analysis of previously published data: first, a temporally calibrated GAC generated from secondary Brooks parsimony analysis (BPA) of six extant bird clades from the south‐west of North America using molecular clock estimates of divergence times; and second, an analysis of African Neogene mammals based on a phylogenetic analysis for comparing trees (PACT) analysis. Results A hypothetical example demonstrates how temporal calibration reveals potentially critical information about the timing of both unique and general events, while also illustrating instances of incongruence between dates generated from molecular clock estimates and fossils. For the African Neogene mammal dataset, our analysis reveals that most mammal clades underwent geodispersal associated with the Neogene climatic optimum (c. 16 Ma) and vicariant speciation in central Africa correlated with increased aridity and cooler temperatures around 2.5 Ma. Main conclusions Temporally calibrated GACs are valuable tools for assessing whether coordinated patterns of speciation are associated with large‐scale climatic or tectonic phenomena.     

Distribution patterns of the genus Pacifigorgia (Octocorallia: Gorgoniidae): track compatibility analysis and parsimony analysis of endemicity

Aim We analysed the distribution patterns of the eastern Pacific octocoral genus Pacifigorgia and deduced its ancestral distribution to determine why Pacifigorgia is absent from the Gulf of Mexico, the Caribbean of central America, and the Antilles. We also examined the current patterns of endemism for Pacifigorgia to look for congruence between hot spots of endemism in the genus and generally recognized areas of endemism for the eastern Pacific. Location The tropical eastern Pacific and western Atlantic, America. Methods We used track compatibility analysis (TCA) and parsimony analysis of endemicity (PAE) to derive ancestral distribution patterns and hot spots of endemism, respectively. Distributional data for Pacifigorgia were gathered from several museum collections and from fieldwork, particularly in the Pacific of Costa Rica and Panama. Results A single generalized track joined the three main continental eastern Pacific biogeographical provinces and the western Atlantic. This track can be included within a larger eastern Atlantic–eastern Pacific transoceanic track that may be the oldest transoceanic track occurring in the region. PAE results designate previously recognized eastern Pacific biogeographical provinces as Pacifigorgia hot spots of endemism. The number of endemic species, which for other taxonomic groups is similar among the eastern Pacific provinces, is higher in the Panamic province for Pacifigorgia. Main conclusions We propose that the absence of Pacifigorgia from the Gulf of Mexico, the Caribbean of central America, and the Antilles is the result of an ancient absence of the genus from these areas rather than the consequence of a major, recent, extinction episode. The Cortez province and the Mexican province appear together as a result of either non‐response to vicariance or dispersal across the Sinaloan Gap. We posit that the Central American Gap acts as a barrier that separates the Panamic province from the northern Cortez–Mexican province.