Invasive species and biodiversity crises: testing the link in the late devonian

During the Late Devonian Biodiversity Crisis, the primary driver of biodiversity decline was the dramatic reduction in speciation rates, not elevated extinction rates; however, the causes of speciation decline have been previously unstudied. Speciation, the formation of new species from ancestral populations, occurs by two primary allopatric mechanisms: vicariance, where the ancestral population is passively divided into two large subpopulations that later diverge and form two daughter species, and dispersal, in which a small subset of the ancestral population actively migrates then diverges to form a new species. Studies of modern and fossil clades typically document speciation by vicariance in much higher frequencies than speciation by dispersal. To assess the mechanism behind Late Devonian speciation reduction, speciation rates were calculated within stratigraphically constrained species-level phylogenetic hypotheses for three representative clades and mode of speciation at cladogenetic events was assessed across four clades in three phyla: Arthropoda, Brachiopoda, and Mollusca. In all cases, Devonian taxa exhibited a congruent reduction in speciation rate between the Middle Devonian pre-crisis interval and the Late Devonian crisis interval. Furthermore, speciation via vicariance is almost entirely absent during the crisis interval; most episodes of speciation during this time were due to dispersal. The shutdown of speciation by vicariance during this interval was related to widespread interbasinal species invasions. The lack of Late Devonian vicariance is diametrically opposed to the pattern observed in other geologic intervals, which suggests the loss of vicariant speciation attributable to species invasions during the Late Devonian was a causal factor in the biodiversity crisis. Similarly, modern ecosystems, in which invasive species are rampant, may be expected to exhibit similar shutdown of speciation by vicariance as an outcome of the modern biodiversity crisis.     

A molecular phylogeny of the neotropical butterfly genus Anartia (Lepidoptera: Nymphalidae)

While Anartia butterflies have served as model organisms for research on the genetics of speciation, no phylogeny has been published to describe interspecific relationships. Here, we present a molecular phylogenetic analysis of Anartia species relationships, using both mitochondrial and nuclear genes. Analyses of both data sets confirm earlier predictions of sister species pairings based primarily on genital morphology. Yet both the mitochondrial and nuclear gene phylogenies demonstrate that Anartia jatrophae is not sister to all other Anartia species, but rather that it is sister to the Anartia fatima-Anartia amathea lineage. Traditional biogeographic explanations for speciation across the genus relied on A. jatrophae being sister to its congeners. These explanations invoked allopatric divergence of sister species pairs and multiple sympatric speciation events to explain why A. jatrophae flies alongside all its congeners. The molecular phylogenies are more consistent with lineage divergence due to vicariance, and range expansion of A. jatrophae to explain its sympatry with congeners. Further interpretations of the tree topologies also suggest how morphological evolution and eco-geographic adaptation may have set species range boundaries.     

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.     

TERTIARY SPECIATION MODELS IN AUSTRALIAN ANURANS: MOLECULAR DATA CHALLENGE PLEISTOCENE SCENARIO

Similarities between frogs in the faunas of southwestern and southeastern Australia have long been viewed as indicators of close genetic relationships and recent (Pleistocene) divergences. We studied albumin evolution in 16 east-west species pairs of frogs representing six genera to assess the validity of these conclusions. Analysis of albumin evolution in western species of Heleioporus and some species of Litoria suggested recent speciation in these genera, with the closest sister groups occurring in the western and not among the eastern fauna. All divergences measured between eastern and western cognate species point to a Tertiary separation extending from the late Miocene to the early Oligocene. Micro-complement fixation studies provide an independent estimation of both genetic relationships between species pairs and the time of divergence of each species pair, allowing the testing of models of speciation and vicariance biogeography in a way not possible with earlier methodologies.     

Karyotypic diversity and speciation in Agrodiaetus butterflies

That chromosomal rearrangements may play an important role in maintaining postzygotic isolation between well-established species is part of the standard theory of speciation. However, little evidence exists on the role of karyotypic change in speciation itself--in the establishment of reproductive barriers between previously interbreeding populations. The large genus Agrodiaetus (Lepidoptera: Lycaenidae) provides a model system to study this question. Agrodiaetus butterflies exhibit unusual interspecific diversity in chromosome number, from n= 10 to n= 134; in contrast, the majority of lycaenid butterflies have n= 23/24. We analyzed the evolution of karyotypic diversity by mapping chromosome numbers on a thoroughly sampled mitochondrial phylogeny of the genus. Karyotypic differences accumulate gradually between allopatric sister taxa, but more rapidly between sympatric sister taxa. Overall, sympatric sister taxa have a higher average karyotypic diversity than allopatric sister taxa. Differential fusion of diverged populations may account for this pattern because the degree of karyotypic difference acquired between allopatric populations may determine whether they will persist as nascent biological species in secondary sympatry. This study therefore finds evidence of a direct role for chromosomal rearrangements in the final stages of animal speciation. Rapid karyotypic diversification is likely to have contributed to the explosive speciation rate observed in Agrodiaetus, 1.6 species per million years.     

The geographical pattern of speciation and floral diversification in the neotropics: the tribe sinningieae (gesneriaceae) as a case study

The geographical pattern of speciation and the relationship between floral variation and species ranges were investigated in the tribe Sinningieae (Gesneriaceae), which is found mainly in the Atlantic forests of Brazil. Geographical distribution data recorded on a grid system of 0.5 x 0.5 degree intervals and a near-complete species-level phylogenetic tree of Sinningieae inferred from a simultaneous analysis of seven DNA regions were used to address the role of geographical isolation in speciation. Geographical range overlaps between sister lineages were measured across all nodes in the phylogenetic tree and analyzed in relation to relative ages estimated from branch lengths. Although there are several cases of species sympatry in Sinningieae, patterns of sympatry between sister taxa support the predominance of allopatric speciation. The pattern of sympatry between sister taxa is consistent with range shifts following allopatric speciation, except in one clade, in which the overlapping distribution of recent sister species indicates speciation within a restricted geographical area and involving changes in pollinators and habitats. The relationship between floral divergence and regional sympatry was also examined by analyzing floral contrasts, phenological overlap, and the degree of sympatry between sister clades. Morphological contrast between flowers is not increased in sympatry and phenological divergence is more apparent between allopatric clades than between sympatric clades. Therefore, our results failed to indicate a tendency for sympatric taxa to minimize morphological and phenological overlap (geographic exclusion and/or character displacement hypotheses). Instead, they point toward adaptation in phenology to local conditions and buildup of sympatries at random with respect to flower morphology. Additional studies at a lower geographical scale are needed to identify truely coexisting species and the components of their reproductive isolation.     

Historical biogeography and speciation in the reef fish genus Haemulon (Teleostei: Haemulidae)

The high biodiversity of tropical marine hotspots has long intrigued evolutionary biologists and biogeographers. The genus Haemulon (grunts) is one of the most important (numerically, ecologically, and economically) reef fish groups in the New World and an excellent candidate to test hypotheses of speciation and diversity generation in the Greater Caribbean, the richest Atlantic biodiversity hotspot, as well as the eastern Pacific. To elucidate the phylogenetic relationships among the species of Haemulon, we obtained a combined total of 2639 base pairs from two mitochondrial genes (cytochrome b and cytochrome oxidase I), and two nuclear genes (TMO-4C4 and RAG2) from all nominal species. Parsimony, Maximum likelihood, and Bayesian analyses resulted in a well-resolved phylogeny with almost identical topologies. Previous phylogenetic hypotheses based on adult morphology, such as the close relationship among H. aurolineatum, H. boschmae, and H. striatum were not supported, whereas others using developmental characters, such as the relationship between H. plumieri and H. sciurus, were confirmed. Our data also indicate that the populations of the nominal H. steindachneri from the two sides of the Isthmus of Panama are genetically divergent at the species level in each ocean, and that the boga, Inermia vittata (family Inermiidae), belongs in the genus Haemulon. This evidence implies that there are 21 valid species of Haemulon, two more than previously recognized. The Amazon barrier and the Isthmus of Panama seem to have played roles in allopatric speciation of Haemulon. However, the majority of sister species pairs have completely overlapping distributions, indicating that vicariance is not the only process driving speciation in this genus. We conclude that both vicariance between biogeographic provinces, and ecological mechanisms of speciation within provinces contribute to species richness in the genus Haemulon.     

Sympatric speciation in birds is rare: insights from range data and simulations

Sympatric speciation is now accepted as theoretically plausible and a likely explanation for divergence in a handful of taxa, but its contribution to large-scale patterns of speciation remains contentious. A major problem is that it is difficult to differentiate between alternate scenarios of geographic speciation when species ranges have shifted substantially in the past. Previous studies have searched for a signal of the geographic mode of speciation by testing for a correlation between time since speciation and range overlap. Here we use simulations to show that the proportion of species showing zero or complete range overlap are more reliable indicators of the geography of speciation than is the correlation between time since speciation and overlap. We then apply these findings to the distributions of 291 pairs of avian sister species. Although 49% of pairs show some overlap in their ranges, our simulations show that this is not surprising under allopatric models of speciation. More revealingly, less than 2% show complete range overlap. Our simulations demonstrate that the observed patterns are most consistent with a model in which allopatric speciation is dominant but in which sympatric speciation is also present and contributes 5% of speciation events.     

Phylogeny of Hypselodoris (Nudibranchia: Chromodorididae) with a review of the monophyletic clade of Indo-Pacific species, including descriptions of twelve new species

This work provides an account of the systematics and phylogeny of Hypselodoris . Aspects of the morphology of 42 species are described and the systematic status of an additional 11 species is discussed. Twelve new species are described: Hypselodoris alboterminata, H. bertschi, H. bollandi, H. fucata, H. iacula, H. insulana, H. krakatoa, H. paulinae, H. reidi, H. rudmani, H. violabranchia and H. zephyra. A phylogenetic analysis supports the monophyly of Hypselodoris and Risbecia . Two distinct clades of Hypselodoris are present. One contains species from the Atlantic and eastern Pacific while the other contains species limited to the Indo-Pacific tropics and adjacent temperate regions. Species from the Atlantic and eastern Pacific are bluish in body colour and have a plesiomorphically large receptaculum seminis while Indo-Pacific taxa are variably coloured and all have a minute receptaculum seminis. The distribution and size of mantle glands provides a wealth of morphological characters. With few exceptions, mantle glands vary in closely related species and are important for distinguishing members of smaller clades. Mantle gland distribution is therefore useful in identifying preserved material that is difficult to identify to species in the absence of the pigment of living specimens. Similar colour patterns found in sympatric species of Hypselodoris appear to be a result of both common descent and convergence between less closely related lineages. Biogeographic distributions of sister taxa provide several examples of vicariance. Examination of these cases shows that no single vicariant pattern is present, but vicariance appears to occur at the margins of the Indo-Pacific rather than centrally. Some vicariance occurs even within archipelagos such as the Hawaiian Islands. These cases largely refute the generality of the hypothesis of Springer (1982), that Pacific Plate and Australasian Plate endemic sister taxa should predominate.     

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.     

Speciation across the Tree of Life

Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.     

Molecular phylogenetics at the population/species interface in cave spiders of the southern Appalachians (Araneae:Nesticidae:Nesticus)

This paper focuses on the relationship between population genetic structure and speciation mechanisms in a monophyletic species group of Appalachian cave spiders (Nesticus). Using mtDNA sequence data gathered from 256 individuals, I analyzed patterns of genetic variation within and between populations for three pairs of closely related sister species. Each sister-pair comparison involves taxa with differing distributional and ecological attributes; if these ecological attributes are reflected in basic demographic differences, then speciation might proceed differently across these sister taxa comparisons. Both frequency-based and gene tree analyses reveal that the genetic structure of the Nesticus species studied is characterized by similar and essentially complete population subdivision, regardless of differences in general ecology. These findings contrast with results of prior genetic studies of cave-dwelling arthropods that have typically revealed variation in population structure corresponding to differences in general ecology. Species fragmentation through both extrinsic and intrinsic evolutionary forces has resulted in discrete, perhaps independent, populations within morphologically defined species. Large sequence divergence values observed between populations suggest that this independence may extend well into the past. These patterns of mtDNA genealogical structure and divergence imply that species as morphological lineages are currently more inclusive than basal evolutionary or phylogenetic units, a suggestion that has important implications for the study of speciation mechanisms.      

Influence of the geography of speciation on current patterns of coral reef fish biodiversity across the Indo‐Pacific

The role of speciation processes in shaping current biodiversity patterns represents a major scientific question for ecologists and biogeographers. Hence, numerous methods have been developed to determine the geography of speciation based on co‐occurrence between sister‐species. Most of these methods rely on the correlation between divergence time and several metrics based on the geographic ranges of sister‐taxa (i.e. overlap, asymmetry). The relationship between divergence time and these metrics has scarcely been examined in a spatial context beyond regression curves. Mapping this relationship across spatial grids, however, may unravel how speciation processes have shaped current biodiversity patterns through space and time. This can be particularly relevant for coral reef fishes of the Indo‐Pacific since the origin of the exceptional concentration of biodiversity in the Indo‐Australian Archipelago (IAA) has been actively debated, with several alternative hypotheses involving species diversification and dispersal. We reconstructed the phylogenetic relationships between three species‐rich families of coral reef fish (Chaetodontidae, Labridae, Pomacentridae) and calculated co‐occurrence metrics between closely related lineages of those families. We demonstrated that repeated biogeographic processes can be identified in present‐day species distribution by projecting co‐occurrence metrics between related lineages in a geographical context. Our study also evidence that sister‐species do not co‐occur randomly across the Indo‐Pacific, but tend to overlap their range within the IAA. We identified the imprint of two important biogeographic processes that caused this pattern in 48% of the sister‐taxa considered: speciation events within the IAA and repeated divergence between the Indian and Pacific Ocean, with subsequent secondary contact in the IAA.     

Speciation durations and Pleistocene effects on vertebrate phylogeography.

An approach applied previously to avian biotas is extended in this paper to other vertebrate classes to evaluate Pleistocene phylogeographic effects and to estimate temporal spans of the speciation process (speciation durations) from mitochondrial (mt) DNA data on extant taxa. Provisional molecular clocks are used to date population separations and to bracket estimates of speciation durations between minimum and maximum values inferred from genetic distances between, respectively, extant pairs of intraspecific phylogroups and sister species. Comparisons of genetic-distance trends across the vertebrate classes reveal the following: (i) speciation durations normally entail at least two million years on average; (ii) for mammals and birds, Pleistocene conditions played an important role in initiating phylogeographic differentiation among now-extant conspecific populations as well as in further sculpting pre-existing phylogeographic variety into many of today''s sister species; and (iii) for herpetofauna and fishes, inferred Pleistocene biogeographic influences on present-day taxa differ depending on alternative but currently plausible mtDNA rate calibrations.     

Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs

Though Pleistocene refugia are frequently cited as drivers of species diversification, comparisons of molecular divergence among sister species typically indicate a continuum of divergence times from the Late Miocene, rather than a clear pulse of speciation events at the Last Glacial Maximum. Community-scale inference methods that explicitly test for multiple vicariance events, and account for differences in ancestral effective population size and gene flow, are well suited for detecting heterogeneity of species' responses to past climate fluctuations. We apply this approach to multi-locus sequence data from five co-distributed frog species endemic to the Wet Tropics rainforests of northeast Australia. Our results demonstrate at least two episodes of vicariance owing to climate-driven forest contractions: one in the Early Pleistocene and the other considerably older. Understanding how repeated cycles of rainforest contraction and expansion differentially affected lineage divergence among co-distributed species provides a framework for identifying evolutionary processes that underlie population divergence and speciation.     

Marine radiations at small geographic scales: speciation in neotropical reef gobies (Elacatinus)

Studies of speciation in the marine environment have historically compared broad-scale distributions and estimated larval dispersal potential to infer the geographic barriers responsible for allopatric speciation. However, many marine clades show high species diversity in geographically restricted areas where barriers are not obvious and estimated dispersal potential should bring many sister taxa into contact. Genetic differentiation at small (separation < 1000 km) spatial scales could facilitate speciation by mechanisms other than the gradual accumulation of reproductive isolation during extended allopatry, such as ecological adaptation to local environmental conditions or the rapid evolution of genes tied to mate recognition, but the role of each of these possibilities has not been simultaneously explored for any species-rich marine taxon. Here, we develop a robust phylogenetic framework for 31 taxa from a species-rich group of Neotropical reef fishes (Gobiidae: Elacatinus) using 3230 bp from one mitochondrial and two nuclear gene regions. We use this framework to explore the contribution of large- and small-scale geographic isolation, ecological differentiation, and coloration toward the formation and maintenance of species. Although species of Elacatinus occur on both sides of the Isthmus of Panama, no sister species are separated by this barrier. Instead, our results indicate that sister taxa occur within oceans. Sister taxa usually differ by coloration, and more distantly related sympatric species frequently differ by resource use. This suggests that some combination of coloration and ecological differences may facilitate assortative mating at range boundaries or in sympatry. Overall, speciation in Elacatinus is consistent with a model of recurring adaptive radiations in stages taking place at small geographic scales.     

Vagility across Vanessa (Lepidoptera: Nymphalidae): mobility in butterfly species does not inhibit the formation and persistence of isolated sister taxa

Allopatric speciation is thought to occur in the absence of gene flow, thereby suggesting that widespread vagile species might be less likely to generate restricted sister taxa because of a lack of isolation. The butterfly genus Vanessa provides an ideal test of this concept, as it contains some of the most cosmopolitan and vagile species of butterflies on the planet, as well as some highly restricted taxa. Given the age of these groups, this arrangement offers a special opportunity to examine the relationship between vagility and phylogeny in generating novel taxa; specifically, does the vagility of some lineages impede allopatric speciation, leaving restricted clades more speciose? A phylogenetic hypothesis is proposed for all species belonging to the butterfly genus Vanessa based on DNA sequences from one mitochondrial and eight nuclear gene regions. The resulting topology shows very little conflict among gene regions, with five well‐supported clades corresponding to morphologically consistent species groups. The data very strongly indicate a polyphyletic genus Antanartia, and thus to preserve monophyly two species previously assigned to Antanartia are transferred to Vanessa, Vanessa hippomene comb.n. and Vanessa dimorphica comb.n. , resulting in a total of 22 species placed in Vanessa. A biogeographical analysis shows that in many cases the most geographically restricted species are sister to geographically widespread species, suggesting dispersal and allopatric speciation. Surprisingly, in almost all cases the divergences between widespread and restricted species are quite old (>5 Ma), suggesting long‐term isolation and stability of both vagile and sedentary species, despite the high (even intercontinental) vagility of many extant species and, by extension, ancestral species. The biogeography of Vanessa suggests that species vagility and allopatry do not fully explain the forces governing cladogenesis in this remarkable genus.     

Trans-oceanic and endemic origins of the small minnow mayflies (Ephemeroptera, Baetidae) of Madagascar

We investigated the relative importance of dispersal and vicariance in forming the Madagascar insect fauna, sequencing approximately 2300bp from three rRNA gene regions to investigate the phylogeny of Afrotropical small minnow mayflies (Ephemeroptera: Baetidae). Six lineages contained trans-oceanic sister taxa, and variation in genetic divergence between sister taxa revealed relationships that range from very recent dispersal to ancient vicariance. Dispersal was most recent and frequent in species that spend the larval stage in standing water, adding to evidence that these evolutionarily unstable habitats may select for ecological traits that increase dispersal in insects. Ancestral state likelihood analysis suggested at least one Afrotropical lineage had its origin in Madagascar, demonstrating that unidirectional dispersal from a continental source may be too simplistic. We conclude that the Malagasy mayfly fauna should be considered in a biogeographical context that extends beyond Madagascar itself, encompassing trans-oceanic dispersal within multiple lineages.     

Out of the Andes: patterns of diversification in clearwing butterflies

Global biodiversity peaks in the tropical forests of the Andes, a striking geological feature that has likely been instrumental in generating biodiversity by providing opportunities for both vicariant and ecological speciation. However, the role of these mountains in the diversification of insects, which dominate biodiversity, has been poorly explored using phylogenetic methods. Here we study the role of the Andes in the evolution of a diverse Neotropical insect group, the clearwing butterflies. We used dated species-level phylogenies to investigate the time course of speciation and to infer ancestral elevation ranges for two diverse genera. We show that both genera likely originated at middle elevations in the Andes in the Middle Miocene, contrasting with most published results in vertebrates that point to a lowland origin. Although we detected a signature of vicariance caused by the uplift of the Andes at the Miocene–Pliocene boundary, most sister species were parapatric without any obvious vicariant barrier. Combined with an overall decelerating speciation rate, these results suggest an important role for ecological speciation and adaptive radiation, rather than simple vicariance.     

Vagility: The Neglected Component in Historical Biogeography

The conceptual gap between ecological and historical biogeography is wide, although both disciplines are concerned with explaining how distributions have been shaped. A central aim of modern historical biogeography is to use a phylogenetic framework to reconstruct the geographic history of a group in terms of dispersals and vicariant events, and a number of analytical methods have been developed to do so. To date the most popular analytical methods in historical biogeography have been parsimony-based. Such methods can be classified into two groups based on the assumptions used. The first group assumes that vicariance between two areas creates common patterns of disjunct distributions across several taxa whereas dispersals and extinctions generate clade specific patterns. The second group of methods assumes that passive vicariance and within-area speciation have a higher probability of occurrence than active dispersal events and extinction. Typically, none of these methods takes into account the ecology of the taxa in question. I discuss why these methods can be potentially misleading if the ecology of the taxon is ignored. In particular, the vagility or dispersal ability of taxa plays a pivotal role in shaping the distributions and modes of speciation. I argue that the vagility of taxa should be explicitly incorporated in biogeographic analyses. Likelihood-based methods with models in which more realistic probabilities of dispersal and modes of speciation can be specified are arguably the way ahead. Although objective quantification will pose a challenge, the complete ignorance of this vital aspect, as has been done in many historical biogeographic analyses, can be dangerous. I use worked examples to show a simple way of utilizing such information, but better methods need to be developed to more effectively use ecological knowledge in historical biogeography.