PACT: an efficient and powerful algorithm for generating area cladograms

Aim To introduce and describe the functioning of a new algorithm, phylogenetic analysis for comparing trees (PACT), for generating area cladograms that provide accurate representation of information contained in taxon–area cladograms. Methods PACT operates in the following steps. Convert all phylogenies to taxon–area cladograms. Convert all taxon–area cladograms to Venn diagrams. Choose any taxon–area cladogram from the set of taxon–area cladograms to be analysed and determine its elements. This will be the template area cladogram. Select a second taxon–area cladogram. Determine its elements. Document which elements in the second tree occur in the template tree (denoted by ‘Y’) and which do not (denoted by ‘N’). Each ‘Y’ indicates a match with previous pattern and these are combined. Each ‘N’ is a new element and is attached to the template area cladogram at the node where it is linked with a Y. This requires two rules: (1) ‘Y + Y = Y’ (combine common elements) as long as they are connected at the same node; and (2) ‘Y + N = YN’ (add novel elements to the template area cladogram at the node where they first appear). Once the novel elements in the second taxon–area cladogram have been added to the template area cladogram, see if any of them can be further combined. This requires three additional rules: (1) ‘Y(Y? = Y(Y?’ (do not combine Y's if they are attached at different nodes on the template area cladogram); (2) ‘Y + YN = YN’ (Y is part of group YN); and (3) ‘YN + YN = YNN’ (Y is the same for each, but each N is different). Repeat for all available taxon–area cladograms. Results Three exemplars demonstrate that PACT provides the most accurate area cladograms for vicariance‐driven biotic diversification, dispersal‐driven biotic diversification and taxon pulse‐driven biotic diversification. PACT can also be used as an a priori method of biogeographical analysis. Main conclusions PACT embodies all the strong points and none of the weaknesses of previously proposed methods of historical biogeography. It is most useful as an a posteriori method, but it is also superior to all previous a priori methods because it does not specify costs, or weights or probabilities, or likelihoods of particular biogeographical processes a priori and is thus sensitive to clade‐specific historical contingencies.     

A historical biogeographical protocol for studying biotic diversification by taxon pulses

Aim To present a historical biogeographical protocol for distinguishing biotic diversification by taxon pulse radiations from biotic diversification by vicariance. Location Mexico and northern Central America. Methods Brooks Parsimony Analysis (BPA), phylogenetic inference, linear correlation analysis. Results The taxon pulse radiation of 33 clades in nine areas of endemism in Mesoamerica is based on nine episodes of biotic expansion from three areas, and six episodes of vicariance, involving four geographical splits. Nineteen per cent of speciation events are due to vicariance, 25% to peripheral isolates speciation and 56% are within‐area events. The species–area curve has a correlation coefficient (r²) of 0.47. Extinction events and species richness are highly correlated (r² = 0.75), but colonization events and species richness are poorly correlated (r² = 0.36), suggesting that colonization is not the main determinant of the species–area relationship. Colonization events are more poorly correlated with size of area (r² = 0.05) than are in situ speciation events (r² = 0.60). Colonization events and in situ events are poorly correlated (r² = 0.02). All areas of endemism have reticulated histories, and have acted as both sources and islands at various times. Main conclusions Taxon pulses can be distinguished from maximum vicariance using this protocol; refining it requires a method for generating area cladograms from complex data and incorporation of direct dating of evolutionary events.     

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.     

The historical biogeography of Scabiosa (Dipsacaceae): implications for Old World plant disjunctions

Aim To reconstruct the temporal and biogeographical history of Old World disjunctions in Scabiosa (Dipsacaceae) and the timing of diversification in the Mediterranean Basin, in order to evaluate the importance of biogeographical and climatological history (particularly the onset of a mediterranean climate) in shaping Scabiosa distributions. Location Europe and the Mediterranean Basin, southern Africa and eastern Asia. Methods This study uses maximum‐likelihood and Bayesian phylogenetic analyses of chloroplast DNA (atpB–rbcL, trnL–trnF, trnS–trnG, psbA–trnH) and nuclear ribosomal DNA [internal transcribed spacer (ITS) and external transcribed spacer (ETS)] from 24 out of c. 37 ingroup taxa, beast molecular dating, and the dispersal–extinction–cladogenesis method (Lagrange ) to reconstruct ancestral geographical ranges and the timing of diversification of the major clades of Scabiosa. Results Biogeographical and divergence time reconstructions showed that Scabiosa originated during the Miocene and diversified in Europe, followed by independent movements into Asia and Africa. Several of the major clades were inferred to have radiated sometime between the late Miocene and early Pleistocene, a timeframe that encompasses the onset of the mediterranean climate in Europe. More recent middle–late Pleistocene radiations in the Mediterranean Basin and southern Africa have played a large role in Scabiosa diversification. Main conclusions Members of Scabiosa appear to have capitalized on adaptations to montane and/or dry conditions in order to colonize similar habitats in different biogeographical regions. The formation of the East African Rift mountains is potentially of great importance in explaining the southward migration of Scabiosa. The initial diversification of Scabiosa in Europe during the Miocene is not consistent with the initiation of the mediterranean climate, but may instead be associated with increased aridity and the retreat of subtropical lineages during this time. However, the radiation of some of the major subclades within Scabiosa may have been associated with an emerging mediterranean climate. More recent and rapid radiations in both the Mediterranean Basin and southern Africa highlight the probable importance of Pleistocene climate fluctuations in Scabiosa diversification.     

Parsimony analysis of endemicity describes but does not explain: an illustrated critique

Aim To demonstrate that parsimony analysis of endemicity (PAE) is not analogous to a cladistic biogeographical analysis. Location We used six data sets from previously published studies from around the world. Methods In order to test the efficiency of PAE in recovering historical relationships among areas, we performed an empirical comparison of nodes recovered with PAE, primary Brooks parsimony analysis (BPA), and an event‐based method using three models (maximum codivergence, reconciled trees, and the default model of the treefitter program) for six data sets. We measured the performance of PAE in recovering historical area relationships by counting the number and examining the content of nodes recovered by PAE and by historical methods. The dispersal/vicariance ratio was calculated to assess the prevalence of dispersal or vicariance in each reconstruction and its relationship to the performance of PAE. Results Our results show that PAE recovers an average of 17.25% of historical nodes. PAE and BPA tend to provide similar results; however, in relation to the event‐based models, PAE performance was poor under all the tested scenarios. Although in some cases PAE reconstructions are more resolved than historical reconstructions, this does not necessarily mean that PAE produces more informative answers. These additional nodes correspond to unsupported statements that are based solely on the distributional data of taxa and not on their phylogenetic history. In other words, these nodes were not found by the historical methods, which take phylogenetics into account. The number of historical nodes recovered using PAE was in general negatively correlated with the dispersal/vicariance ratio. Main conclusions Our results show that PAE is unable to recover historical patterns and therefore does not fit into the current paradigm of historical biogeography. These findings raise doubts regarding conclusions derived from biogeographical studies that interpret PAE trees as area cladograms. We acknowledge that PAE aims to describe but does not explain the current distribution of organisms. It is therefore a useful tool in other biogeographical or ecological analyses for exploring the distribution of taxa or for establishing hypotheses of primary homology between areas.     

Assessing Modes of Speciation: Range Asymmetry and Biogeographical Congruence

Lynch [1989, in "Speciation and Its Consequences" (D. Otte and J. A. Endler, Eds.), pp. 527–553, Sinauer, Sunderland, MA, proposed a methodology for assessing the frequency of occurrence of various modes of initiating species formation, using a combination of phylogenetic relationships and relative size of geographic ranges for sister species and sister groups. Historical biogeography provides an alternative criterion for assessing modes of species formation. Species whose distributions conform to a general (replicated in multiple clades) pattern of area relationships are deemed to be the result of vicariance (including microvicariance) regardless of the details of current geographic range. Species exhibiting unique biogeographic distributions are the result of peripheral isolates speciation and postspeciation dispersal. Lineage duplications indicate sympatric speciation. An empirical assessment of this alternative approach was performed using the most recent phylogenetic trees and geographical distribution data on the Mesoamerican poeciliid fish comprising the genera Xiphophorus and Heterandria . The single area cladogram produced by secondary Brooks Parsimony Analysis indicates 3 vicariant events (accounting for seven extant species and the common ancestor of the northern swordtails, which are not further analyzed) and at least 13 episodes of peripheral isolates speciation. Two of the 10 areas considered in previous analyses are vicariant areas of endemism, 1 is historically unique due to a single episode of peripheral isolates speciation, and the remaining 7 have reticulated histories of speciation. The results corroborate inferences of speciation modes made by Lynch for the same data.     

Effect of vagility potential on dispersal and speciation in rainforest insects

Explaining global patterns of species diversity is one of the most challenging objectives in biology. Most agree that complex interactions between historical and current processes are responsible for such patterns, although rigorous testing of possible mechanisms has proved difficult. Here we demonstrate that macropterous and flightless insects in the rainforests of north-eastern Australia have dispersed and speciated in similar manners. These results contradict the traditionally held assumption that differences in vagility potential would lead to significant differences in distributional patterns and speciation modes.     

Molecular phylogeny of the antitropical subgenus Goniistius (Perciformes: Cheilodactylidae: Cheilodactylus): evidence for multiple transequatorial divergences and non-monophyly

The subgenus Goniistius comprises eight species of marine nearshore fishes which are antitropically distributed. The molecular phylogeny of these and other cheilodactylids was reconstructed from cytochrome oxidase I and cytochrome b mitochondrial DNA sequences. The placement within Goniistius of the morphologically divergent species Cheilodactylus (G.) nigripes was not supported. The remaining seven species are sufficiently divergent from other cheilodactylids to be designated as a separate genus. The antitropical distribution oi Goniistius is the result of three transequatorial divergences, which occurred during two periods. Based on molecular clock calibrations, these periods are suggested to be the mid Miocene, and late Miocene to early Pliocene. It is not known in which direction or by which mechanism these transequatorial divergences occurred, although biogeographic hypotheses of Mesozoic or Pleistocene separations can be discounted. The degree of genetic divergence between North and South Pacific populations of C. (G.) mttatus Garrett indicates that they have undergone cryptic speciation.     

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.     

Molecular phylogeny of the endemic Philippine rodent Apomys (Muridae) and the dynamics of diversification in an oceanic archipelago

We analysed the phylogenetic relationships of ten of the 13 known species of the genus Apomys using DNA sequences from cytochrome b . Apomys, endemic to oceanic portions of the Philippine archipelago, diversified during the Pliocene as these oceanic islands arose de novo . Several of the speciation events probably took place on Luzon or Mindanao, the two largest, oldest, and most topographically complex islands. Only one speciation event is associated with vicariance due to Pleistocene sea-level fluctuation, and a Pleistocene diversification model in which isolation is driven by sea-level changes is inconsistent with the data. Tectonic vicariance is nearly absent from the Philippines, in which tectonic coalescence plays a significant role. Most speciation events (about two-thirds) are associated with dispersal to newly developed oceanic islands. The data imply that the species have persisted for long periods, measured in millions of years after their origins; further implications therefore are that faunal turnover is very slow, and persistence over geological time spans is more prominent than repeated colonization and extinction. Neither the equilibrium nor the vicariance model of biogeography adequately encompasses these results; a model incorporating colonization, extinction, and speciation is necessary and must incorporate long-term persistence to accommodate our observations.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80 , 699–715.     

Multiple intercontinental dispersals shaped the distribution area of Hordeum (Poaceae)

The grass genus Hordeum (Poaceae, Triticeae), comprising 31 species distributed in temperate and dry regions of the world, was analysed to determine the relative contributions of vicariance and long-distance dispersal to the extant distribution pattern of the genus. Sequences from three nuclear regions (DMC1, EF-G and ITS) were combined and analysed phylogenetically for all diploid (20 species) and two tetraploid Hordeum species and the outgroup Psathyrostachys. Ages of clades within Hordeum were estimated using a penalized likelihood analysis of sequence divergence. The sequence data resulted in an almost fully resolved phylogenetic tree that allowed the reconstruction of intrageneric migration routes. Hordeum evolved c. 12 million years ago in South-west Asia and spread into Europe and Central Asia. The colonization of the New World and South Africa involved at least six intercontinental exchanges during the last 4 million years (twice Eurasia-North America, North America-South America, twice South America-North America and Europe-South Africa). Repeated long-distance dispersal between the northern and southern hemisphere were important colonization mechanisms in Hordeum.     

Effects of mode of reproduction on genetic divergence over large spatial and temporal scales in intertidal snails of the genus Bembicium Philippi (Gastropoda: Littorinidae)

The littorine genus Bembicium , restricted to Australia and Lord Howe and Norfolk Islands, provides special opportunities to examine the effects of contrasting modes of development on genetic divergence over large spatial and temporal scales. Two species, Bembicium auratum and Bembicium nanum , have planktotrophic larvae, and large, overlapping geographical distributions, whereas the three direct developers, Bembicium vittatum , Bembicium melanostoma , and Bembicium flavescens , are geographical replacements. Phylogenetic analysis of genetic distances at 28 allozyme loci supported the current taxonomic treatment of the genus and monophyly of the direct developers. Both individually and as a clade, the direct developers showed substantially greater divergence than the species with planktotrophic larvae. Controlling for geographical distance and for particular sections of coastline, genetic subdivision within the direct developers was shown to be much higher than in the planktotrophs. Low levels of subdivision in B. auratum and B. nanum over distances of 4000–6800 km indicate maintenance of substantial genetic connectivity, independent of habitat and biogeographical history. By contrast, the direct developers show clear genetic impacts of their geographical histories. Despite extreme genetic subdivision within species, the direct developers B. vittatum and B. melanostoma have geographically coherent and complementary distributions, associated with biogeographical provinces. Thus, speciation appears to be driven by special biogeographical circumstances, rather than simply by genetic divergence of locally isolated populations.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 689–704.     

Radiating in a river: systematics, molecular genetics and morphological differentiation of viviparous freshwater gastropods endemic to the Kaek River, central Thailand (Cerithioidea, Pachychilidae)

Speciation in the context of adaptive radiation is regarded as a key process in the creation of biodiversity. While several lacustrine species flocks provide ideal models for elucidating the underlying evolutionary mechanisms, riverine radiations are both rarely known and studied. The Kaek River, a third‐order tributary of the Nan River and Chao Praya drainage in central Thailand, harbours an exceptional endemic species assemblage of morphologically distinct, viviparous pachychilid gastropods. Our systematic revision, combining a morphological and molecular genetics approach, reveals the sympatric existence of at least seven species of the genus Brotia that is widespread in rivers of South‐east Asia where usually only two species at the most coexist. At eight locations along a 100‐kilometre stretch of the Kaek River, we found the syntopic occurrence of two to three species that are separated by specific habitat preferences and exhibit trophic specialization in their radula morphology. Phylogenetic analyses (using MP, NJ, ML and Bayesian inference statistics) of partial COI and 16S sequence data of 17 samples from six species occurring sympatrically and parapatrically, respectively, in the Kaek River drainage (plus the type species B. pagodula as outgroup) indicate monophyly of all these endemic species. Brotia solemiana, which also occurs in the Loei River, a tributary of the Mekong drainage system, was found to be sister to all other Kaek River pachychilids. The distinctive morphotypes, proposed here to represent biospecies, do not show high levels of genetic variation consistent with long periods of reproductive isolation. This suggests a relatively recent origin of this intrariverine radiation and rapid morphological divergence in the Kaek River Brotia. Recent diversification combined with ecological separation and trophic specialization parallels conditions found, albeit on a more specious level, in the lacustrine species flock of the closely related pachychilid genus Tylomelania, which is endemic to ancient lakes on the Indonesian island of Sulawesi. We discuss and compare the allopatric and ecological aspects of speciation in this unique riverine radiation and outline a putative historical biogeography of the Kaek River species, employing the most recent geological and palaeohydrological data for Thailand. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82 , 275–311.     

Historical biogeography and phenotype‐phylogeny of Chroodiscus (lichenized Ascomycota: Ostropales: Graphidaceae)

Aim To analyse the historical biogeography of the lichen genus Chroodiscus using a phenotype‐based phylogeny in the context of continental drift and evolution of tropical rain forest vegetation. Location All tropical regions (Central and South America, Africa, India, Southeast Asia, north‐east Australia). Methods We performed a phenotype‐based phylogenetic analysis and ancestral character state reconstruction of 14 species of the lichen genus Chroodiscus, using paup * and mesquite ; dispersal–vicariance analysis (DIVA) and dispersal–extinction–cladogenesis (DEC) modelling to trace the geographical origin of individual clades; and ordination and clustering by means of pc‐ord , based on a novel similarity index, to visualize the biogeographical relationships of floristic regions in which Chroodiscus occurs. Results The 14 species of Chroodiscus show distinctive distribution patterns, with one pantropical and one amphi‐Pacific taxon and 12 species each restricted to a single continent. The genus comprises four clades. DIVA and DEC modelling suggest a South American origin of Chroodiscus in the mid to late Cretaceous (120–100 Ma), with subsequent expansion through a South American–African–Indian–Southeast Asian–Australian dispersal route and late diversification of the argillaceus clade in Southeast Asia. Based on the abundance of extant taxa, the probability of speciation events in Chroodiscus is shown to be extremely low. Slow dispersal of foliicolous rain forest understorey lichens is consistent with estimated phylogenetic ages of individual species and with average lengths of biological species intervals in fungi (10–20 Myr). Main conclusions The present‐day distribution of Chroodiscus can be explained by vicariance and mid‐distance dispersal through the interconnection or proximity of continental shelves, without the need for recent, trans‐oceanic long‐distance dispersal. Phylogenetic reconstruction and age estimation for Chroodiscus are consistent with the ‘biotic ferry’ hypothesis: a South American origin and subsequent eastward expansion through Africa towards Southeast Asia and north‐eastern Australia via the Indian subcontinent. The present‐day pantropical distributions of many clades and species of foliicolous lichens might thus be explained by eastward expansion through continental drift, along with the evolution of modern rain forests starting 120 Ma, rather than by the existence of a hypothetical continuous area of pre‐modern rain forest spanning South America, Africa and Southeast Asia during the mid and late Cretaceous.     

A tale of North and South America: time and mode of dispersal of the amphitropical genus Munroa (Poaceae,Chloridoideae)

Plant disjunctions have provided some of the most intriguing distribution patterns historically addressed by biogeographers. We evaluated the three hypotheses that have been postulated to explain these patterns [vicariance, stepping‐stone dispersal and long‐distance dispersal (LDD)] using Munroa, an American genus of grasses with six species and a disjunct distribution between the desert regions of North and South America. The ages of clades, cytology, ancestral characters and areas of distribution were investigated in order to establish relationships among species, to determine the time of divergence of the genus and its main lineages, and to understand further the biogeographical and evolutionary history of this genus. Bayesian inference recovered the North American M. pulchella as sister species to the rest. Molecular dating and ancestral area analyses suggest that Munroa originated in North America in the late Miocene–Pliocene (7.2 Mya; 8.2–6.5 Mya). Based on these results, we postulate that two dispersal events modelled the current distribution patterns of Munroa: the first from North to South America (7.2 Mya; 8.2–6.5 Mya) and the second (1.8 Mya; 2–0.8 Mya) from South to North America. Arid conditions of the late Miocene–Pliocene in the Neogene and Quaternary climatic oscillations in North America and South America were probably advantageous for the establishment of populations of Munroa. We did not find any relationship between ploidy and dispersal events, and our ancestral character analyses suggest that shifts associated with dispersal and seedling establishment, such as habit, reproductive system, disarticulation of rachilla, and shape and texture of the glume, have been important in these species reaching new areas. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 110–125.