A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages

Island systems have long been useful models for understanding lineage diversification in a geographic context, especially pertaining to the importance of dispersal in the origin of new clades. Here we use a well-resolved phylogeny of the flowering plant genus Cyrtandra (Gesneriaceae) from the Pacific Islands to compare four methods of inferring ancestral geographic ranges in islands: two developed for character-state reconstruction that allow only single-island ranges and do not explicitly associate speciation with range evolution (Fitch parsimony [FP; parsimony-based] and stochastic mapping [SM; likelihood-based]) and two methods developed specifically for ancestral range reconstruction, in which widespread ranges (spanning islands) are integral to inferences about speciation scenarios (dispersal-vicariance analysis [DIVA; parsimony-based] and dispersal-extinction-cladogenesis [DEC; likelihood-based]). The methods yield conflicting results, which we interpret in light of their respective assumptions. FP exhibits the least power to unequivocally reconstruct ranges, likely due to a combination of having flat (uninformative) transition costs and not using branch length information. SM reconstructions generally agree with a prior hypothesis about dispersal-driven speciation across the Pacific, despite the conceptual mismatch between its character-based model and this mode of range evolution. In contrast with narrow extant ranges for species of Cyrtandra, DIVA reconstructs broad ancestral ranges at many nodes. DIVA results also conflict with geological information on island ages; we attribute these conflicts to the parsimony criterion not considering branch lengths or time, as well as vicariance being the sole means of divergence for widespread ancestors. DEC analyses incorporated geological information on island ages and allowed prior hypotheses about range size and dispersal rates to be evaluated in a likelihood framework and gave more nuanced inferences about range evolution and the geography of speciation than other methods tested. However, ancestral ranges at several nodes could not be conclusively resolved, due possibly to uncertainty in the phylogeny or the relative complexity of the underlying model. Of the methods tested, SM and DEC both converge on plausible hypotheses for area range histories in Cyrtandra, due in part to the consideration of branch lengths and/or timing of events. We suggest that DEC model-based methods for ancestral range inference could be improved by adopting a Bayesian SM approach, in which stochastic sampling of complete geographic histories could be integrated over alternative phylogenetic topologies. Likelihood-based estimates of ancestral ranges for Cyrtandra suggest a major dispersal route into the Pacific through the islands of Fiji and Samoa, motivating future biogeographic investigation of this poorly known region.     

Prospects and challenges for parametric models in historical biogeographical inference

In historical biogeography, phylogenetic trees have long been used as tools for addressing a wide range of inference problems, from explaining common distribution patterns of species to reconstructing ancestral geographic ranges on branches of the tree of life. However, the potential utility of phylogenies for this purpose has yet to be fully realized, due in part to a lack of explicit conceptual links between processes underlying the evolution of geographic ranges and processes of phylogenetic tree growth. We suggest that statistical approaches that use parametric models to forge such links will stimulate integration and propel hypothesis-driven biogeographical inquiry in new directions. We highlight here two such approaches and describe how they represent early steps towards a more general framework for model-based historical biogeography that is based on likelihood as an optimality criterion, rather than having the traditional reliance on parsimony. The development of this framework will not be without significant challenges, particularly in balancing model complexity with statistical power, and these will be most apparent in studies of regions with many component areas and complex geological histories, such as the Mediterranean Basin.     

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.     

Reconstructing ancestral ranges in historical biogeography: properties and prospects

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

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.     

Conceptual and statistical problems with the DEC+J model of founder‐event speciation and its comparison with DEC via model selection

Phylogenetic studies of geographic range evolution are increasingly using statistical model selection methods to choose among variants of the dispersal‐extinction‐cladogenesis (DEC) model, especially between DEC and DEC+J, a variant that emphasizes “jump dispersal,” or founder‐event speciation, as a type of cladogenetic range inheritance scenario. Unfortunately, DEC+J is a poor model of founder‐event speciation, and statistical comparisons of its likelihood with DEC are inappropriate. DEC and DEC+J share a conceptual flaw: cladogenetic events of range inheritance at ancestral nodes, unlike anagenetic events of dispersal and local extinction along branches, are not modelled as being probabilistic with respect to time. Ignoring this probability factor artificially inflates the contribution of cladogenetic events to the likelihood, and leads to underestimates of anagenetic, time‐dependent range evolution. The flaw is exacerbated in DEC+J because not only is jump dispersal allowed, expanding the set of cladogenetic events, its probability relative to non‐jump events is assigned a free parameter, j, that when maximized precludes the possibility of non‐jump events at ancestral nodes. DEC+J thus parameterizes the mode of speciation, but like DEC, it does not parameterize the rate of speciation. This inconsistency has undesirable consequences, such as a greater tendency towards degenerate inferences in which the data are explained entirely by cladogenetic events (at which point branch lengths become irrelevant, with estimated anagenetic rates of 0). Inferences with DEC+J can in some cases depart dramatically from intuition, e.g. when highly unparsimonious numbers of jump dispersal events are required solely because j is maximized. Statistical comparison with DEC is inappropriate because a higher DEC+J likelihood does not reflect a more close approximation of the “true” model of range evolution, which surely must include time‐dependent processes; instead, it is simply due to more weight being allocated (via j) to jump dispersal events whose time‐dependent probabilities are ignored. In testing hypotheses about the geographic mode of speciation, jump dispersal can and should instead be modelled using existing frameworks for state‐dependent lineage diversification in continuous time, taking appropriate cautions against Type I errors associated with such methods. For simple inference of ancestral ranges on a fixed phylogeny, a DEC‐based model may be defensible if statistical model selection is not used to justify the choice, and it is understood that inferences about cladogenetic range inheritance lack any relation to time, normally a fundamental axis of evolutionary models.     

Fossil biogeography: a new model to infer dispersal,extinction and sampling from palaeontological data

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.     

A geography‐aware reconciliation method to investigate diversification patterns in host/parasite interactions

Cospeciation studies aim at investigating whether hosts and symbionts speciate simultaneously or whether the associations diversify through host shifts. This problem is often tackled through reconciliation analyses that map the symbiont phylogeny onto the host phylogeny by mixing different types of diversification events. These reconciliations can be difficult to interpret and are not always biologically realistic. Researchers have underlined that the biogeographic histories of both hosts and symbionts influence the probability of cospeciation and host switches, but up to now no reconciliation software integrates geographic data. We present a new functionality in the Mowgli software that bridges this gap. The user can provide geographic information on both the host and symbiont extant and ancestral taxa. Constraints in the reconciliation algorithm have been implemented to generate biologically realistic codiversification scenarios. We apply our method to the fig/fig wasp association and infer diversification scenarios that differ from reconciliations ignoring geographic information. In addition, we updated the reconciliation viewer SylvX to visualize ancestral character states on the phylogenetic trees and highlight parts of reconciliations that are geographically inconsistent when not accounting for geographic constraints. We suggest that the comparison of reconciliations obtained with and without such constraints can help solving ambiguities in the biogeographic histories of the partners. With the development of robust methods in historical biogeography, and the advent of next‐generation sequencing that leads to better‐resolved trees, a geography‐aware reconciliation method represents a substantial advance that is likely to be useful to researchers studying the evolution of biotic interactions and biogeography.     

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

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

The shape and temporal dynamics of phylogenetic trees arising from geographic speciation

Phylogenetic trees often depart from the expectations of stochastic models, exhibiting imbalance in diversification among lineages and slowdowns in the rate of lineage accumulation through time. Such departures have led to a widespread perception that ecological differences among species or adaptation and subsequent niche filling are required to explain patterns of diversification. However, a key element missing from models of diversification is the geographical context of speciation and extinction. In this study, we develop a spatially explicit model of geographic range evolution and cladogenesis, where speciation arises via vicariance or peripatry, and explore the effects of these processes on patterns of diversification. We compare the results with those observed in 41 reconstructed avian trees. Our model shows that nonconstant rates of speciation and extinction are emergent properties of the apportioning of geographic ranges that accompanies speciation. The dynamics of diversification exhibit wide variation, depending on the mode of speciation, tendency for range expansion, and rate of range evolution. By varying these parameters, the model is able to capture many, but not all, of the features exhibited by birth-death trees and extant bird clades. Under scenarios with relatively stable geographic ranges, strong slowdowns in diversification rates are produced, with faster rates of range dynamics leading to constant or accelerating rates of apparent diversification. A peripatric model of speciation with stable ranges also generates highly unbalanced trees typical of bird phylogenies but fails to produce realistic range size distributions among the extant species. Results most similar to those of a birth-death process are reached under a peripatric speciation scenario with highly volatile range dynamics. Taken together, our results demonstrate that considering the geographical context of speciation and extinction provides a more conservative null model of diversification and offers a very different perspective on the phylogenetic patterns expected in the absence of ecology.     

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.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 235–246.     

The latitudinal,but not the longitudinal,geographic range positions of haematophagous ectoparasites demonstrate historical signatures

We tested whether geographic range position of fleas parasitic on small mammals in the Palearctic is affected by environmental niche conservatism or geographic range conservatism by measuring phylogenetic signal in range centroids and boundaries. We predicted that stronger phylogenetic signal in latitudinal than longitudinal range positions would indicate the important role of niche conservatism as a driver of the evolution of fleas’ geographic ranges. Phylogenetic signals in geographic range positions were measured across 120 species, as well as within five flea lineages (subfamily/family rank) of different evolutionary ages. To investigate the temporal pattern of the geographic range position’s evolution, we fitted the phylogenetic patterns in the geographic coordinates of range centroids and border extremes to four models of trait evolution. We consistently detected significant phylogenetic signals in the latitudes of the range centroids and the northern range borders. The latitudes of the southern range borders and the longitudes of the eastern/western borders demonstrated phylogenetic signals less often, whereas no signal was found for the longitudes of the range centroids. The phylogenetic signal in range position was more pronounced in younger lineages. The phylogenetic signal indices mainly suggested the evolution of range positions according to the Brownian motion model, whereas the best fit was often provided by the Orstein-Uhlenbeck model. This contradiction forced us to invoke a parsimonious explanation that the phylogenetic signal in range positions results from the interplay between the footprint of the speciation pattern and limited dispersal from the ancestral ranges.     

Molecular phylogeny of Solms‐laubachia (Brassicaceae) s.l., based on multiple nuclear and plastid DNA sequences,and its biogeographic implications

Abstract The Hengduan Mountains region of south‐west China is a noted biodiversity hotspot, but the geographic origins and historical assembly of its rich endemic flora, including the sky‐island species of Solms‐laubachia Muschl. (Brassicaceae), have been little studied. Previous molecular studies on the phylogeny of Solms‐laubachia showed it to be paraphyletic, leading to considerable expansion not only of its taxonomic limits, but also its geographic range, with the inclusion of taxa from outside the Hengduan region. However, these studies provided little resolution of interspecific relationships, preventing inferences about historical biogeography within the clade. In the present study, new sequence data from two nuclear genes (LEAFY and G3pdh) and two chloroplast intergenic spacers (petN–psbM and psbM–trnD) were combined with existing markers to increase phylogenetic signals. Phaeonychium villosum (Maxim.) Al‐Shehbaz was found to be nested within Solms‐laubachia s.l. In general, phylogenetic relationships appear to be a good predictor of geography, with the Hengduan Mountain endemics embedded in a paraphyletic grade of species from the western Himalayas and central Asia, but they also imply morphological homoplasy. Incongruence was detected between the nuclear and chloroplast gene trees, perhaps resulting from incomplete lineage sorting of ancestral polymorphisms. The crown age of Solms‐laubachia s.l. was estimated to be approximately 1.42–3.68 mya, using Bayesian relaxed molecular clock analysis. Historical biogeographic analysis using a parametric dispersal–extinction–cladogenesis model inferred central Asia and the western Himalayas as most probable ancestral range of Solms‐laubachia s.l., and estimated higher rates of eastward expansion than westward during the diversification of descendant lineages. In summary, our results suggest that Solms‐laubachia s.l. originated during the Pliocene in central Asia, and subsequently migrated eastward into the Hengduan Mountains, colonizing sky‐island, alpine scree‐slope habitats that may have provided novel ecological opportunity and accelerated speciation, ultimately establishing this region as the present center of diversity of the genus.     

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

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

Remototrachyna, a newly recognized tropical lineage of lichens in the Hypotrachyna clade (Parmeliaceae, Ascomycota), originated in the Indian subcontinent

Biogeographical studies of lichens used to be complicated because of the large distribution ranges of many species. Molecular systematics has revitalized lichen biogeography by improving species delimitation and providing better information about species range limitations. This study focuses on the major clade of tropical parmelioid lichens, which share a chemical feature, the presence of isolichenan in the cell wall, and a morphological feature, microscopic pores in the uppermost layer. Our previous phylogenetic studies revealed that the largest genus in this clade, Hypotrachyna, is polyphyletic with a clade mainly distributed in South and East Asia clustering distant from the core of the genus. To divide the Hypotrachyna clade into monophyletic groups and to reevaluate morphological and chemical characters in a phylogenetic context, we sampled ITS, nuclear large subunit (nuLSU) and mitochondrial small subunit (mtSSU) rDNA sequences from 77 species. We are erecting the new genus Remototrachyna for a core group of 15 former Hypotrachyna species. The segregation of Remototrachyna from Hypotrachyna receives support from morphological and chemical data, as well from maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses of the DNA. We used a likelihood approach to study the geographic range evolution of Remototrachyna and Bulbothrix, which are sister groups. This analysis suggests that the ancestral range of Remototrachyna was restricted to India and that subsequent long-distance dispersal is responsible for the pantropical occurrence of two species of Remototrachyna.     

Phylogeny and Evolutionary Patterns in the Dwarf Crayfish Subfamily (Decapoda: Cambarellinae)

The Dwarf crayfish or Cambarellinae, is a morphologically singular subfamily of decapod crustaceans that contains only one genus, Cambarellus. Its intriguing distribution, along the river basins of the Gulf Coast of United States (Gulf Group) and into Central México (Mexican Group), has until now lacked of satisfactory explanation. This study provides a comprehensive sampling of most of the extant species of Cambarellus and sheds light on its evolutionary history, systematics and biogeography. We tested the impact of Gulf Group versus Mexican Group geography on rates of cladogenesis using a maximum likelihood framework, testing different models of birth/extinction of lineages. We propose a comprehensive phylogenetic hypothesis for the subfamily based on mitochondrial and nuclear loci (3,833 bp) using Bayesian and Maximum Likelihood methods. The phylogenetic structure found two phylogenetic groups associated to the two main geographic components (Gulf Group and Mexican Group) and is partially consistent with the historical structure of river basins. The previous hypothesis, which divided the genus into three subgenera based on genitalia morphology was only partially supported (P = 0.047), resulting in a paraphyletic subgenus Pandicambarus. We found at least two cases in which phylogenetic structure failed to recover monophyly of recognized species while detecting several cases of cryptic diversity, corresponding to lineages not assigned to any described species. Cladogenetic patterns in the entire subfamily are better explained by an allopatric model of speciation. Diversification analyses showed similar cladogenesis patterns between both groups and did not significantly differ from the constant rate models. While cladogenesis in the Gulf Group is coincident in time with changes in the sea levels, in the Mexican Group, cladogenesis is congruent with the formation of the Trans-Mexican Volcanic Belt. Our results show how similar allopatric divergence in freshwater organisms can be promoted through diverse vicariant factors.     

Ancestral inference and the study of codon bias evolution: implications for molecular evolutionary analyses of the Drosophila melanogaster subgroup

Reliable inference of ancestral sequences can be critical to identifying both patterns and causes of molecular evolution. Robustness of ancestral inference is often assumed among closely related species, but tests of this assumption have been limited. Here, we examine the performance of inference methods for data simulated under scenarios of codon bias evolution within the Drosophila melanogaster subgroup. Genome sequence data for multiple, closely related species within this subgroup make it an important system for studying molecular evolutionary genetics. The effects of asymmetric and lineage-specific substitution rates (i.e., varying levels of codon usage bias and departures from equilibrium) on the reliability of ancestral codon usage was investigated. Maximum parsimony inference, which has been widely employed in analyses of Drosophila codon bias evolution, was compared to an approach that attempts to account for uncertainty in ancestral inference by weighting ancestral reconstructions by their posterior probabilities. The latter approach employs maximum likelihood estimation of rate and base composition parameters. For equilibrium and most non-equilibrium scenarios that were investigated, the probabilistic method appears to generate reliable ancestral codon bias inferences for molecular evolutionary studies within the D. melanogaster subgroup. These reconstructions are more reliable than parsimony inference, especially when codon usage is strongly skewed. However, inference biases are considerable for both methods under particular departures from stationarity (i.e., when adaptive evolution is prevalent). Reliability of inference can be sensitive to branch lengths, asymmetry in substitution rates, and the locations and nature of lineage-specific processes within a gene tree. Inference reliability, even among closely related species, can be strongly affected by (potentially unknown) patterns of molecular evolution in lineages ancestral to those of interest.     

Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago

The extant endemic katydids (Orthoptera: Tettigoniidae) of the Hawaiian Archipelago include one to three species per high island and a single species on Nihoa, all currently placed in the genus Banza. These acoustic insects provide an excellent opportunity for investigating the evolution of reproductive isolation and speciation, but such studies require an understanding of phylogenetic relationships within the group. We use maximum parsimony, likelihood-based Bayesian inference, and maximum likelihood to infer phylogenetic relationships among these taxa, based on approximately 2kb of mitochondrial cytochrome oxidase I and cytochrome b. Our results strongly support two distinct high island clades: one clade ("Clade I") composed of species from Kauai, Oahu, Molokai, and Lanai and another clade ("Clade II") composed of species from Maui and Hawaii (Banza unica, from Oahu, may be basal to both these clades, but its placement is not well resolved). Within these clades, some inferred relationships are strongly supported, such as the sister status of B. kauaiensis (Kauai) and B. parvula (Oahu) within Clade I, but other relationships remain more ambiguous, such as the relative position of B. brunnea (Maui) within Clade II. Although a detailed reconstruction of the historical biogeography of the Hawaiian katydids is difficult, we use our genetic data combined with the known geological history of the Hawaiian Islands to set limits on plausible historical scenarios for diversification of this group. Beyond these historical biogeographic inferences, our results indicate possible cryptic speciation on both Oahu and Hawaii, as well as what may be unusually high average rates of nucleotide substitution. The present work sets the stage for future genetic and experimental investigations of this group.     

The Great American Biotic Interchange in frogs: multiple and early colonization of Central America by the South American genus Pristimantis (Anura: Craugastoridae)

The completion of the land bridge between North and South America approximately 3.5-3.1 million years ago (Ma) initiated a tremendous biogeographic event called the Great American Biotic Interchange (GABI), described principally from the mammalian fossil record. The history of biotic interchange between continents for taxonomic groups with poor fossil records, however, is not well understood. Molecular and fossil data suggest that a number of plant and animal lineages crossed the Isthmus of Panama well before 3.5 Ma, leading biologists to speculate about trans-oceanic dispersal mechanisms. Here we present a molecular phylogenetic analysis of the frog genus Pristimantis based on 189 individuals of 137 species, including 71 individuals of 31 species from Panama and Colombia. DNA sequence data were obtained from three mitochondrial (COI, 12S, 16S) and two nuclear (RAG-1 and Tyr) genes, for a total of 4074 base pairs. The resulting phylogenetic hypothesis showed statistically significant conflict with most recognized taxonomic groups within Pristimantis, supporting only the rubicundus Species Series, and the Pristimantis myersi and Pristimantis pardalis Species Groups as monophyletic. Inference of ancestral areas based on a likelihood model of geographic range evolution via dispersal, local extinction, and cladogenesis (DEC) suggested that the colonization of Central America by South American Pristimantis involved at least 11 independent events. Relaxed-clock analyses of divergence times suggested that at least eight of these invasions into Central America took place prior to 4 Ma, mainly in the Miocene. These findings contribute to a growing list of molecular-based biogeographic studies presenting apparent temporal conflicts with the traditional GABI model.     

Reconstructing ancestral ecologies: challenges and possible solutions

There are several ways to extract information about the evolutionary ecology of clades from their phylogenies. Of these, character state optimization and 'ancestor reconstruction' are perhaps the most widely used despite their being fraught with assumptions and potential pitfalls. Requirements for robust inferences of ancestral traits in general (i.e. those applicable to all types of characters) include accurate and robust phylogenetic hypotheses, complete species-level sampling and the appropriate choice of optimality criterion. Ecological characters, however, also require careful consideration of methods for accounting for intraspecific variability. Such methods include 'Presence Coding' and 'Polymorphism Coding' for discrete ecological characters, and 'Range Coding' and 'MaxMin Coding' for continuously variable characters. Ultimately, however, historical inferences such as these are, as with phylogenetic inference itself, associated with a degree of uncertainty. Statistically based uncertainty estimates are available within the context of model-based inference (e.g. maximum likelihood and Bayesian); however, these measures are only as reliable as the chosen model is appropriate. Although generally thought to preclude the possibility of measuring relative uncertainty or support for alternative possible reconstructions, certain useful non-statistical support measures (i.e. 'Sharkey support' and 'Parsimony support') are applicable to parsimony reconstructions.