Ancestral Area Analysis Research Articles

Evolution of the intercontinental disjunctions in six continents in the Ampelopsis clade of the grape family (Vitaceae).

BackgroundThe Ampelopsis clade (Ampelopsis and its close allies) of the grape family Vitaceae contains ca. 43 species disjunctly distributed in Asia, Europe, North America, South America, Africa, and Australia, and is a rare example to study both the Northern and the Southern Hemisphere intercontinental disjunctions. We reconstruct the temporal and spatial diversification of the Ampelopsis clade to explore the evolutionary processes that have resulted in their intercontinental disjunctions in six continents.ResultsThe Bayesian molecular clock dating and the likelihood ancestral area analyses suggest that the Ampelopsis clade most likely originated in North America with its crown group dated at 41.2 Ma (95% HPD 23.4 - 61.0 Ma) in the middle Eocene. Two independent Laurasian migrations into Eurasia are inferred to have occurred in the early Miocene via the North Atlantic land bridges. The ancestor of the Southern Hemisphere lineage migrated from North America to South America in the early Oligocene. The Gondwanan-like pattern of intercontinental disjunction is best explained by two long-distance dispersals: once from South America to Africa estimated at 30.5 Ma (95% HPD 16.9 - 45.9 Ma), and the other from South America to Australia dated to 19.2 Ma (95% HPD 6.7 - 22.3 Ma).ConclusionsThe global disjunctions in the Ampelopsis clade are best explained by a diversification model of North American origin, two Laurasian migrations, one migration into South America, and two post-Gondwanan long-distance dispersals. These findings highlight the importance of both vicariance and long distance dispersal in shaping intercontinental disjunctions of flowering plants.

Estimating ancestral ranges: testing methods with a clade of neotropical lizards (iguania: liolaemidae).

Establishing the ancestral ranges of distribution of a monophyletic clade, called the ancestral area, is one of the central objectives of historical biogeography. In this study, I used three common methodologies to establish the ancestral area of an important clade of Neotropical lizards, the family Liolaemidae. The methods used were: Fitch optimization, Weighted Ancestral Area Analysis and Dispersal-Vicariance Analysis (DIVA). A main difference from previous studies is that the areas used in the analysis are defined based on actual distributions of the species of Liolaemidae, instead of areas defined arbitrarilyor based on other taxa. The ancestral area of Liolaemidae found by Fitch optimization is Prepuna on Argentina, Central Chile and Coastal Peru. Weighted Ancestral Area Analysis found Central Chile, Coquimbo, Payunia, Austral Patagonia and Coastal Peru. Dispersal-Vicariance analysis found an ancestral area that includes almost all the areas occupied by Liolaemidae, except Atacama, Coquimbo and Austral Patagonia. The results can be resumed on two opposing hypothesis: a restricted ancestral area for the ancestor of Liolaemidae in Central Chile and Patagonia, or a widespread ancestor distributed along the Andes. Some limitations of the methods were identified, for example the excessive importance of plesiomorphic areas in the cladograms.

Phylogeny of a trans‐Wallacean radiation (Squamata, Gekkonidae,Gehyra) supports a single early colonization of Australia

Heinicke, M. P., Greenbaum, E., Jackman, T. R. & Bauer, A. M. Phylogeny of a trans‐Wallacean radiation (Squamata, Gekkonidae,Gehyra) supports a single early colonization of Australia. —Zoologica Scripta, 40, 584–602.The genusGehyra(34 species) is rare among squamate reptile radiations in spanning continents, extending from southeast Asia to Australia and Polynesia. Among the family Gekkonidae sensu stricto,Gehyrais the only genus that is species rich in Australia. We performed molecular phylogenetic, divergence timing, and ancestral area analyses to investigate the evolutionary and biogeographic history ofGehyra. Phylogenetic analyses resolveHemiphyllodactylusas the closest relative ofGehyra. Some data also linkPerochirusto this group, but previously suggested relationships with other morphologically similar genera of geckos are not supported. WithinGehyra, three geographically discrete clades are recovered, respectively, concentrated in Asia, the Pacific islands and Australia. Ancestral area analyses suggest thatGehyraoriginated in Asia, with a single colonization of Australia occurring in the mid‐Cenozoic. This date places the time ofGehyracolonization prior to those of other Australian gekkonid geckos, but after the near‐endemic pygopodoid geckos, a Gondwanan relictual group. Based on these dates, times of origin may best explain relative differences in species diversity among Australian gekkotans. In contrast, although originating earlier,Gehyrais less diverse in Asia than in Australia. This pattern may be explained by the long‐term presence of many competing, ecologically similar genera in Asia (e.g.Gekko,Hemidactylus,Lepidodactylus), whereas nearly all pygopodoids in Australia (the only gekkotans present at the time of colonization of Australia byGehyra) are ecologically distinct.

Flying shells: historical dispersal of marine snails across Central America

The geological rise of the Central American Isthmus separated the Pacific and the Atlantic oceans about 3 Ma, creating a formidable barrier to dispersal for marine species. However, similar to Simpson's proposal that terrestrial species can 'win sweepstakes routes'-whereby highly improbable dispersal events result in colonization across geographical barriers-marine species may also breach land barriers given enough time. To test this hypothesis, we asked whether intertidal marine snails have crossed Central America to successfully establish in new ocean basins. We used a mitochondrial DNA genetic comparison of sister snails (Cerithideopsis spp.) separated by the rise of the Isthmus. Genetic variation in these snails revealed evidence of at least two successful dispersal events between the Pacific and the Atlantic after the final closure of the Isthmus. A combination of ancestral area analyses and molecular dating techniques indicated that dispersal from the Pacific to the Atlantic occurred about 750 000 years ago and that dispersal in the opposite direction occurred about 72 000 years ago. The geographical distribution of haplotypes and published field evidence further suggest that migratory shorebirds transported the snails across Central America at the Isthmus of Tehuantepec in southern Mexico. Migratory birds could disperse other intertidal invertebrates this way, suggesting the Central American Isthmus may not be as impassable for marine species as previously assumed.

Major global radiation of corvoid birds originated in the proto-Papuan archipelago

A central paradigm in island biogeography has been the unidirectional "downstream" colonization of islands from continents (source to sink) based on the idea that less-diverse island communities are easier to invade than biologically more-diverse continental communities. Recently, several cases of "upstream" colonization (from islands to continents) have been documented, challenging the traditional view. However, all these cases have involved individual island species that have colonized mainland regions. Here, using molecular phylogenetic data, divergence time estimates, lineage diversity distributions, and ancestral area analyses, we reconstruct the spread of a species-rich (>700 species) passerine bird radiation (core Corvoidea) from its late Eocene/Oligocene origin in the emerging proto-Papuan archipelago north of Australia, including multiple colonizations from the archipelago to Southeast Asia. Thus, islands apparently provided the setting for the initiation of a major songbird radiation that subsequently invaded all other continents. Morphological and behavioral adaptations of the core Corvoidea as generalist feeders in open habitats, which facilitated dispersal and colonization, apparently evolved in the descendants of sedentary forest birds that invaded the proto-Papuan archipelago. The archipelago evidently provided islands of the right size, number, and proximity to continental areas to support the adaptation and diversification of vagile colonizers that went on to increase avian diversity on a global scale.

Morphological diversity and biogeography of procolophonids (Amniota: Parareptilia)

A recent phylogenetic analysis of procolophonid parareptiles is used as the basis for a study of morphological diversity (disparity) in these amniotes. Disparity values are compared in three groups of procolophonids (a paraphyletic series of basal taxa and two monophyletic sister groups: procolophonines and leptopleuronines), two ecophenotypic assemblages (one based upon inferred diet – non high-fibre versus high-fibre species; the other based upon cranial sculpture – non horned versus horned species), and two temporal assemblages (Lower Triassic versus Middle and Upper Triassic). The mean disparity values are comparable in the case of temporal and ecophenotypic assemblages. High-fibre species are marginally less disparate than non high-fibre species. The combined Middle and Upper Triassic species are slightly less disparate than Lower Triassic species. Finally, horned species are only slightly more disparate than non-horned species. The paraphyletic series of basal taxa and the leptopleuronines show similar disparity values, marginally higher than those for procolophonines. Phylogenetic analysis is also used to reconstruct the biogeographical history of procolophonids. Both ancestral area analysis and dispersal–vicariance analysis show that South Africa was the most likely ancestral area for procolophonids as a whole. North China – either as a single area or in combination with Russia or South Africa – was the most likely ancestral area for the leptopleuronine–procolophonine clade.

Biogeographical history of cuckoo‐shrikes (Aves: Passeriformes): transoceanic colonization of Africa from Australo‐Papua

AbstractAim Cuckoo‐shrikes and allies (Campephagidae) form a radiation of birds widely distributed in the Indo‐Pacific and Africa. Recent studies on the group have been hampered by poor taxon sampling, causing inferences about systematics and biogeography to be rather speculative. With improved taxon sampling and analyses within an explicit spatiotemporal framework, we elucidate biogeographical patterns of dispersal and diversification within this diverse clade of passerine birds.Location Africa, Asia, Australo‐Papua, the Pacific, the Philippines and Wallacea.Methods We use model‐based phylogenetic methods (MrBayes and garli) to construct a phylogenetic hypothesis of the core Campephagidae (Campephagidae with the exclusion of Pericrocotus). The phylogeny is used to assess the biogeographical history of the group with a newly developed Bayesian approach to dispersal–vicariance analysis (Bayes‐diva). We also made use of a partitioned beast analysis, with several calibration points taken from island ages, passerine mitochondrial substitution rates and secondary calibration points for passerine birds, to assess the timing of diversification and dispersal.Results We present a robust molecular phylogeny that includes all genera and 84% of the species within the core Campephagidae. Furthermore, we estimate divergence dates and ancestral area relationships. We demonstrate that Campephagidae originated in Australo‐Papua with a single lineage (Pericrocotus) dispersing to Asia early. Later, there was further extensive transoceanic dispersal from Australo‐Papua to Africa involving lineages within the core Campephagidae radiation.Main conclusions The phylogenetic relationships, along with the results of the ancestral area analysis and the timing of dispersal events, support a transoceanic dispersal scenario from Australo‐Papua to Africa by the core Campephagidae. The sister group to core Campephagidae, Pericrocotus, dispersed to mainland Asia in the late Oligocene. Asia remained uncolonized by the core Campephagidae until the Pliocene. Transoceanic dispersal is by no means an unknown phenomenon, but our results represent a convincing case of colonization over a significant water gap of thousands of kilometres from Australo‐Papua to Africa.

Implications of rbcL phylogeny for historical biogeography of genus Mercurialis L.: Estimating age and center of origin

The aim of this study was to address questions concerning the historical biogeography of the genus Mercurialis in the subfamily Acalyphoideae. Applying a molecular clock to obtained rbcL phylogeny, we estimated the minimal age of divergence of genus Mercurialis to ~65-66 Ma, placing it at the Cretaceous/Paleogene boundary. We used ancestral area analysis and dispersal-vicariance analysis to infer the center of origin of the genus. Contrary to previous hypothesis, our results show that Mercurialis originated in Indomalaya and migrated westward, while the Mediterranean area was most probably the center of ecological diversification and further speciation. Evolutionary events of vicariance and dispersals were reconstructed in a proposed scenario of divergence of Mercurialis within Acalyphoideae. .

Reconstructing ancestral ranges in historical biogeography: properties and prospects

Abstract 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.

Evolutionary divergence times in the Annonaceae: evidence of a late Miocene origin of Pseuduvaria in Sundaland with subsequent diversification in New Guinea

BackgroundPhylogenetic analyses of the Annonaceae consistently identify four clades: a basal clade consisting of Anaxagorea, and a small 'ambavioid' clade that is sister to two main clades, the 'long branch clade' (LBC) and 'short branch clade' (SBC). Divergence times in the family have previously been estimated using non-parametric rate smoothing (NPRS) and penalized likelihood (PL). Here we use an uncorrelated lognormal (UCLD) relaxed molecular clock in BEAST to estimate diversification times of the main clades within the family with a focus on the Asian genus Pseuduvaria within the SBC. Two fossil calibration points are applied, including the first use of the recently discovered Annonaceae fossil Futabanthus. The taxonomy and morphology of Pseuduvaria have been well documented, although no previous dating or biogeographical studies have been undertaken. Ancestral areas at internal nodes within Pseuduvaria are determined using dispersal-vicariance analysis (DIVA) and weighted ancestral area analysis (WAAA).ResultsThe divergence times of the main clades within the Annonaceae were found to deviate slightly from previous estimates that used different calibration points and dating methods. In particular, our estimate for the SBC crown (55.2-26.9 Mya) is much younger than previous estimates (62.5-53.1 ± 3.6 Mya and ca. 58.76 Mya). Early diversification of Pseuduvaria was estimated to have occurred 15-8 Mya, possibly associated with the 'mid-Miocene climatic optimum.' Pseuduvaria is inferred to have originated in Sundaland in the late Miocene, ca. 8 Mya; subsequent migration events were predominantly eastwards towards New Guinea and Australia, although several migratory reversals are also postulated. Speciation of Pseuduvaria within New Guinea may have occurred after ca. 6.5 Mya, possibly coinciding with the formation of the Central Range orogeny from ca. 8 Mya.ConclusionOur divergence time estimates within the Annonaceae are likely to be more precise as we used a UCLD clock model and calibrated the phylogeny using new fossil evidence. Pseuduvaria is shown to have dispersed from Sundaland after the late Miocene. The present-day paleotropical distribution of Pseuduvaria may have been achieved by long-distance dispersal, and speciation events might be explained by global climatic oscillations, sea level fluctuations, and tectonic activity.

Historical biogeography of Phymaturus (Iguania: Liolaemidae) from Andean and patagonian South America

Establishing the ancestral area of a group of organisms is one of the central objectives of historical biogeography. I applied three methods of ancestral area analysis, Fitch optimization, weighted ancestral area analysis and dispersal‐vicariance analysis (DIVA) to establish the ancestral area of the iguanian lizard genus Phymaturus. I then extended the analysis to hypothesize the ancestral area for Liolaemidae (Ctenoblepharys, Liolaemus and Phymaturus). The ancestral area for Phymaturus is Patagonia Central or Patagonia Central‐Cordillera Andina and Valle Central. For Liolaemidae, the ancestral area is Patagonia Central‐Coastal Perú, or Patagonia Central‐Patagonia Occidental‐Cordillera Andina and Valle Central‐Coastal Perú. The ancestral area of Phymaturus is congruent with previous studies, but the inclusion of Ctenoblepharys poses some questions regarding the distribution of the ancestor of the family.

Establishing a perimeter position: speciation around the Indian Ocean Basin

Historical biological interactions among peripheral landmasses on the periphery of the Indian Ocean Basin (IOB) are generally poorly understood. While interactions based on early Gondwanan vicariance have been used to explain present day lineage distributions, several recent studies have instead inferred dispersal across the IOB. This inference is often advanced because lineages under study have species inhabiting IOB islands. Here we examine the roles of continental vicariance vs. trans-IOB dispersal in the distribution of an avian genus found around the perimeter of the IOB. A molecular phylogeny does reveal evidence of a relationship that would require the inference of trans-IOB dispersal between eastern Africa and Sri Lanka. However, molecular clock data, ancestral area analyses and paleoclimatic reconstructions suggest that vicariance related to tropical forest expansion and retraction is more likely to have facilitated African-Asian interchange, with an initial colonization of Africa from Asia quickly followed by a recolonization of Asia. Subsequent dispersal from Asia to Sri Lanka and islands east of the Sunda Shelf are inferred; these latter islands were colonized in a stepping-stone fashion that culminated in colonization of the Sunda Shelf, and a recolonization of mainland Asia. We propose that circum-IOB distributions, which post-date early Gondwanan breakup, are most likely the result of continent-based vicariant events, particularly those events related to large-scale habitat alterations, and not trans-IOB dispersals.

Pliocene climatic change in insular Southeast Asia as an engine of diversification inFicedulaflycatchers

AbstractAims Insular Southeast Asia and adjacent regions are geographically complex, and were dramatically affected by both Pliocene and Pleistocene changes in climate, sea level and geology. These circumstances allow the testing of several biogeographical hypotheses regarding species distribution patterns and phylogeny. Avian species in this area present a challenge to biogeographers, as many are less hindered by barriers that may block the movements of other species. Widely distributed Southeast Asian avian lineages, of which there are many, have been generally neglected.Ficedulaflycatchers are distributed across Eurasia, but are most diverse within southern Asia and Southeast Asian and Indo‐Australian islands. We tested the roles of vicariance, dispersal and the evolution of migratory behaviours as mechanisms of speciation within theFicedulaflycatchers, with a focus on species distributed in insular Southeast Asia.Methods Using a published molecular phylogeny ofFicedulaflycatchers, we reconstructed ancestral geographical areas using dispersal vicariance analysis, weighted ancestral area analysis, and a maximum likelihood method. We evaluated the evolution of migratory behaviours using maximum likelihood ancestral character state reconstruction. Speciation timing estimates were calculated via local molecular clock methods.Results Ficedulaoriginated in southern mainland Asia,c. 6.5 Ma. Our analyses indicate that two lineages withinFicedulaindependently and contemporaneously colonized insular Southeast Asia and Indo‐Australia,c. 5 Ma. The potential impact of vicariance due to rising sea levels is difficult to assess in these early colonization events because the ancestral areas to these clades are reconstructed as oceanic islands. Within each of these clades, inter‐island dispersal was critical to species’ diversification across oceanic and continental islands. Furthermore, Pliocene and Pleistocene climatic change may have caused the disjunct island distributions between several pairs of sister taxa. Both vicariance and dispersal shaped the distributions of continental species.Main conclusions This study presents the first evaluation, forFicedula,of the importance of vicariance and dispersal in shaping distributions, particularly across insular Southeast Asia and Indo‐Australia. Although vicariant speciation may have initially separated the island clades from mainland ancestors, speciation within these clades was driven primarily by dispersal. Our results contribute to the emerging body of literature concluding that dynamic geological processes and climatic change throughout the Pliocene and Pleistocene have been important factors in faunal diversification across continental and oceanic islands.

Ancestral Area Analysis of Chaetodactylid Mites (Acari: Chaetodactylidae), with Description of a New Early Derivative Genus and Six New Species from the Neotropics

Distributions of chaetodactylid mites (Acari: Chaetodactylidae), obligate associates of long-tongued bees of the families Apidae and Megachilidae, largely correspond to those of their hosts. Early derivative lineages of mites (Centriacarus gen. n. and Roubikia) are restricted to the endemic Neotropical apid bee genera Centris and Roubikia, respectively. Phylogenetically derived mite lineages are worldwide in distribution: Sennertia species are associated with carpenter bees (Ceratina and Xylocopa), and Chaetodactylus species are associated with nine megachilid and five apid bee genera. In contrast, mites of the genus Achaetodactylus are known exclusively from African Ceratina hosts. Reconstruction of the historical biogeography of the group, including the newly described early derivative genus Centriacarus, is conducted for the first time. Present distribution and host associations of chaetodactylids can be best explained by host shifts and intercontinental dispersals of phylogenetically basal groups. The Neotropical region is most likely to have been the ancestral area of this mite family. We describe six new early derivative taxa from the Neotropics, the center of origin and a biodiversity hotspot for chaetodactylids: Centriacarus turbator sp. n. (ex Centris vittata; Brazil, Peru, Colombia, Panama, Mexico); Centriacarus guahibo sp. n. (ex Centris sp.; Venezuela); Roubikia officiosa sp. n. (ex Tetrapedia maura; Mexico); Roubikia imberba sp. n. (ex Tetrapedia sp., and cleptoparasites Coelioxoides waltheriae and C. exulans; Argentina); Chaetodactylus melitomae sp. n. (ex Melitoma marginella, M. segmentaria; Mexico, Honduras); and Chaetodactylus lassulus sp. n. (ex Trichothurgus dubius, T. herbsti; Chile).

Placing Biebersteiniaceae, a herbaceous clade of Sapindales, in a temporal and geographic context

Biebersteiniaceae comprise a single genus with four species of perennial herbs occurring from central Asia to Greece. A previous molecular phylogenetic study placed one of the species in an isolated position in Sapindales, while morphological studies had placed Biebersteinia in or near Geraniaceae, albeit doubtfully. We tested the monophyly and placement of the family with data from the chloroplast genes rbcL and atpB obtained for all four species, other major clades of Sapindales and outgroups for a total of up to 114 taxa. Parsimony, Bayesian, and likelihood analyses place Biebersteinia in Sapindales, possibly as sister to the other eight families. Strict and relaxed molecular clocks constrained with fossils of Biebersteinia and up to eight other Sapindales suggest that the Biebersteinia crown group diversified in the Oligocene and Miocene, while the stem lineage dates back to the Late Paleocene. Ages for other sapindalean families are earlier than those obtained in more sparsely sampled analyses, although estimates for Burseraceae agree surprisingly well. Ancestral area analyses suggest that Biebersteinia expanded from the eastern part of its range (i.e. Tibet and Inner Mongolia) to the west, although analyses are hampered by the unclear sister group relationships.

A reassessment of Hemizygia and Syncolostemon (Ocimeae—Lamiaceae)

The relationships between Hemizygia and Syncolostemon are investigated. Parsimony analyses of morphological data and sequences of the trnL intron, trnL‐trnF intergenic spacer and the rps16 intron were carried out separately and in combination. All analyses largely show strong support for the two genera as a monophyletic group; neither genus as currently circumscribed is monophyletic. They are herein merged under the earliest name Syncolostemon. The clade can be diagnosed by the presence of fused anterior stamens. Bremer’s ancestral area analysis method suggests that the Afroalpine and Afromontane archipelago‐like Regional Centre of Endemism may be the ancestral area for Syncolostemon s.l.

Review of generic limits of the tiger moth genera Virbia Walker and Holomelina Herrich-Schäffer (Lepidoptera: Arctiidae: Arctiinae) and their biogeography

A phylogeny for Holomelina and Virbia was constructed based on adult morphology. This study included 42 of the 70 recognized species in Holomelina and Virbia, two new species, and two elevated synonyms (H. marginata Druce and V. inversia Edwards). The following outgroups were chosen from the Arctiini: Arachnis picta Packard, Hypercompe permaculata Packard, Paracles fusca Walker, Phragmatobia fuliginosa (Linneaus), Pyrrarctia isabella (J. E. Smith), and Spilosoma virginica (Fabricius). Fifty-eight characters (195 states) were described and scored, including several newly discovered characters of the male and female abdomen and genitalia. Three male character systems, the shape and orientation of the basiphallus; the shape, orientation and ornamentation of the endophallus; and the pattern of sclerotization of the eighth male sternite, were important diagnostic characters for smaller clades and species. The maximum parsimony analysis of all taxa with 100 randomized repetitions yielded 779 trees with a length (L) of 1698, a consistency index (CI) of 0.41 and a retention index (RI) of 0.65. Holomelina species were placed in two clades, an H. aurantiaca clade and an H. opella clade that was paraphyletic with respect to Virbia. The ingroup clade comprised of Holomelina and Virbia species was supported by eleven synapomorphies and a Bremer index higher than fifteen. The decay of this node was greater than 10. Taxon jack-knife analyses revealed that results were sensitive to the inclusion of two outgroup species, A. picta and P. fuliginosa. When either was removed the relationships of ingroup taxa became unresolved. When the analysis was restricted to species which represented by both males and females, we recovered an ingroup consisting of Holomelina and Virbia species, but the strict consensus of 123 trees (L = 1356, CI = 0.47, RI = 0.65) resulted in a polytomy of smaller clades. Neither analysis recovered a reciprocally monophyletic Holomelina and Virbia. We place Holomelina as a junior generic synonym of Virbia and provide a species checklist for Virbia. Biogeographic areas were scored from distribution information in a specimen-level database consisting of over 12,000 specimens. The following eight areas were recognized: A. western USA and Canada, B. central USA and Canada, C. eastern USA and Canada, D. southwestern USA and Mexico, E. central America, F. western South America, G. eastern and central South America, and H. highlands of northern South America. A weighted ancestral area analysis was used to determine ancestral areas for five major ingroup clades. We propose replacing the name “probability index” (PI) of Bremer with the term “Weighted Area Index (WAI)” because the PI of Bremer is not based on a statistical distribution and the term is misleadingWe determined that the ancestral area for Virbia was most likely the southwestern United States and Mexico. The species distributed in North America north of Mexico represent a composite fauna with a minimum of two dispersal events from Mexico into the northern latitudes. In contrast, the South American fauna appears to have a single origin.

The Pattern and Timing of Diversification of Philippine Endemic Rodents: Evidence from Mitochondrial and Nuclear Gene Sequences

The 22 genera and 64 species of rodents (Muridae: Murinae) distributed in the Philippine Islands provide a unique opportunity to study patterns and processes of diversification in island systems. Over 90% of these rodent species are endemic to the archipelago, but the relative importance of dispersal from the mainland, dispersal within the archipelago, and in situ differentiation as explanations of this diversity remains unclear, as no phylogenetic hypothesis for these species and relevant mainland forms is currently available. Here we report the results of phylogenetic analyses of the endemic Philippine murines and a wide sampling of murine diversity from outside the archipelago, based on the mitochondrial cytochrome b gene and the nuclear-encoded IRBP exon 1. Analysis of our combined gene data set consistently identified five clades comprising endemic Philippine genera, suggesting multiple invasions of the archipelago. Molecular dating analyses using parametric and semiparametric methods suggest that colonization occurred in at least two stages, one ca. 15 Mya, and another 8 to 12 million years later, consistent with the previous recognition of "Old" and "New" endemic rodent faunas. Ancestral area analysis suggests that the Old Endemics invaded landmasses that are now part of the island of Luzon, whereas the three New Endemic clades may have colonized through either Mindanao, Luzon, or both. Further, our results suggest that most of the diversification of Philippine murines took place within the archipelago. Despite heterogeneity between nuclear and mitochondrial genes in most model parameters, combined analysis of the two data sets using both parsimony and likelihood increased phylogenetic resolution; however, the effect of data combination on support for resolved nodes was method dependent. In contrast, our results suggest that combination of mitochondrial and nuclear data to estimate relatively ancient divergence times can severely compromise those estimates, even when specific methods that account for rate heterogeneity among genes are employed. [Biogeography; divergence date estimation; mitochondrial DNA; molecular systematics; Murinae; nuclear exon; Philippines; phylogeny.].

Molecular phylogenetics and biogeography of Lepus in Eastern Asia based on mitochondrial DNA sequences

In spite of several classification attempts among taxa of the genus Lepus, phylogenetic relationships still remain poorly understood. Here, we present molecular genetic evidence that may resolve some of the current incongruities in the phylogeny of the leporids. The complete mitochondrial cytb, 12S genes, and parts of ND4 and control region fragments were sequenced to examine phylogenetic relationships among Chinese hare taxa and other leporids throughout the World using maximum parsimony, maximum likelihood, and Bayesian phylogenetic reconstruction approaches. Using reconstructed phylogenies, we observed that the Chinese hare is not a single monophyletic group as originally thought. Instead, the data infers that the genus Lepus is monophyletic with three unique species groups: North American, Eurasian, and African. Ancestral area analysis indicated that ancestral Lepus arose in North America and then dispersed into Eurasia via the Bering Land Bridge eventually extending to Africa. Brooks Parsimony analysis showed that dispersal events followed by subsequent speciation have occurred in other geographic areas as well and resulted in the rapid radiation and speciation of Lepus. A Bayesian relaxed molecular clock approach based on the continuous autocorrelation of evolutionary rates along branches estimated the divergence time between the three major groups within Lepus. The genus appears to have arisen approximately 10.76 MYA (± 0.86 MYA), with most speciation events occurring during the Pliocene epoch (5.65 ± 1.15 MYA ∼ 1.12 ± 0.47 MYA).

Historical biogeography and the evolution of the latitudinal gradient of species richness in the Papionini (Primata: Cercopithecidae)

We apply historical biogeography techniques to the macaques, baboons and their relatives (Primata: Papionini) and relate the inferred history of range shifts, and associated evolutionary events, to the latitudinal distribution of extant species, which is strongly tropical. The results of reversible parsimony, weighted ancestral area and dispersal-vicariance analyses all agree that Central Africa was part of the range of the ancestor of the tribe. Tropical regions with high current species richness (Central Africa, South-east Asia, Indonesia) have: (1) had a relatively long history of occupation, (2) experienced both a greater number and a greater average rate of speciation events and (3) given rise to more dispersal events to other regions. However, nested sister-taxon comparisons across the tribe show no overall association between differences in latitude and differences in rates of cladogenesis. Our historical reconstructions are largely consistent with previous hypotheses and fossil data, and suggest that both the passage of time since colonization and rates of cladogenesis have enhanced tropical species richness. Historical biogeography may thus considerably aid understanding of this and other spatial problems in macroecology.