Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis

In historical biogeography, model-based inference methods for reconstructing the evolution of geographic ranges on phylogenetic trees are poorly developed relative to the diversity of analogous methods available for inferring character evolution. We attempt to rectify this deficiency by constructing a dispersal-extinction-cladogenesis (DEC) model for geographic range evolution that specifies instantaneous transition rates between discrete states (ranges) along phylogenetic branches and apply it to estimating likelihoods of ancestral states (range inheritance scenarios) at cladogenesis events. Unlike an earlier version of this approach, the present model allows for an analytical solution to probabilities of range transitions as a function of time, enabling free parameters in the model, rates of dispersal, and local extinction to be estimated by maximum likelihood. Simulation results indicate that accurate parameter estimates may be difficult to obtain in practice but also show that ancestral range inheritance scenarios nevertheless can be correctly recovered with high success if rates of range evolution are low relative to the rate of cladogenesis. We apply the DEC model to a previously published, exemplary case study of island biogeography involving Hawaiian endemic angiosperms in Psychotria (Rubiaceae), showing how the DEC model can be iteratively refined from inspecting inferences of range evolution and also how geological constraints involving times of island origin may be imposed on the likelihood function. The DEC model is sufficiently similar to character models that it might serve as a gateway through which many existing comparative methods for characters could be imported into the realm of historical biogeography; moreover, it might also inspire the conceptual expansion of character models toward inclusion of evolutionary change as directly coincident, either as cause or consequence, with cladogenesis events. The DEC model is thus an incremental advance that highlights considerable potential in the nascent field of model-based historical biogeographic inference.     

Null models of geographic range size evolution reaffirm its heritability

Most models of allopatric speciation predict that the two daughter species will have range sizes different from each other's and potentially from that of their common ancestor. However, I find that this difference is less than that expected under a variety of null models of range evolution. Sister species' range values may therefore become more similar in the time following speciation. Greater-than-expected similarity (symmetry) has also been treated as a form of range size heritability. I therefore compare the results of this symmetry approach to a test for phylogenetic signal, using the range sizes of North American birds. I find that range size is heritable under both tests. I suggest that null models for range size heritability should be informed by an explicit model of evolution. Comparative methods may give erroneous results if they fail to take the unusual form of inheritance of range size into account.     

Population genetics and the evolution of geographic range limits in an annual plant

Abstract Theoretical models of species' geographic range limits have identified both demographic and evolutionary mechanisms that prevent range expansion. Stable range limits have been paradoxical for evolutionary biologists because they represent locations where populations chronically fail to respond to selection. Distinguishing among the proposed causes of species' range limits requires insight into both current and historical population dynamics. The tools of molecular population genetics provide a window into the stability of range limits, historical demography, and rates of gene flow. Here we evaluate alternative range limit models using a multilocus data set based on DNA sequences and microsatellites along with field demographic data from the annual plant Clarkia xantiana ssp. xantiana. Our data suggest that central and peripheral populations have very large historical and current effective population sizes and that there is little evidence for population size changes or bottlenecks associated with colonization in peripheral populations. Whereas range limit populations appear to have been stable, central populations exhibit a signature of population expansion and have contributed asymmetrically to the genetic diversity of peripheral populations via migration. Overall, our results discount strictly demographic models of range limits and more strongly support evolutionary genetic models of range limits, where adaptation is prevented by a lack of genetic variation or maladaptive gene flow.     

Phylogenetic inference and comparative evolution of a complex microsatellite and its flanking regions in carnivores

We sequenced locus Mel 08, with complex short repetitive motifs, in 24 carnivore species belonging to five different families in order to explore mutational changes in the region in the context of locus and species evolution. This non-coding locus includes up to four different parts or repetitive motifs showing size variability. The variability consists of repeat additions and deletions; substitutions, insertions and/or deletions creating interruptions in the repeat; and substitutions, insertions and deletions in the flanking regions. The locus has different repeat expansions in different carnivore subfamilies. We hypothesize that the complexity of this locus is due to a high mutation rate at an ancestral DNA sequence and, thus, prompts the emergence of repeats at mutational hotspots. High levels of homoplasy were evident, with nine electromorphs representing 28 haplotypes never shared across species. The variability in flanking regions was informative for phylogenetic inference and their evolutionary content. Tree topologies were congruent with relevant hypotheses on current conflicts in carnivore phylogenies, such as: (i) the monophyly of Lutrinae, (ii) the paraphyly of Mustelinae, (iii) the basal position of the Eurasian badger, Meles meles , in the Mustelidae, (iv) the classification of skunks as a separate family, Mephitidae, and (v) the placement of the red panda, Ailurus fulgens , as a monotypic family, Ailuridae, at a basal position in the Musteloidea.     

Interactions between soil habitat and geographic range location affect plant fitness

Populations are often found on different habitats at different geographic locations. This habitat shift may be due to biased dispersal, physiological tolerances or biotic interactions. To explore how fitness of the native plant Chamaecrista fasciculata depends on habitat within, at and beyond its range edge, we planted seeds from five populations in two soil substrates at these geographic locations. We found that with reduced competition, lifetime fitness was always greater or equivalent in one habitat type, loam soils, though early-season survival was greater on sand soils. At the range edge, natural populations are typically found on sand soil habitats, which are also less competitive environments. Early-season survival and fitness differed among source populations, and when transplanted beyond the range edge, range edge populations had greater fitness than interior populations. Our results indicate that even when the optimal soil substrate for a species does not change with geographic range location, the realized niche of a species may be restricted to sub-optimal habitats at the range edge because of the combined effects of differences in abiotic and biotic effects (e.g. competitors) between substrates.     

Phylogenetic relationships,evolution of broodcare behavior,and geographic speciation in the wrasse tribe Labrini

The family Labridae is a large assemblage of marine fish composed of about 580 species in 82 genera distributed in tropical and temperate marine waters around the world. Several subgroups, currently classified as tribes, have been identified in this large family, yet only a few phylogenetic analyses have been performed on labrid clades. We confirm monophyly of the labrid tribe Labrini and propose a phylogeny of the 23 species of the genera Acantholabrus, Centrolabras, Ctenolabrus, Labrus, Lappanella, Symphodus, Tautoga, and Tautogolabrus occurring in the eastern and western Atlantic and the Mediterranean. We analyzed a 577-bp segment of the mitochondrial 16S rDNA and a 506-bp segment of the mitochondrial control region in 22 species, for a total of up to 1069 bp per species. We used both parsimony and likelihood approaches under a variety of assumptions and models to generate phylogenetic hypotheses. The main features of the molecular phylogeny for the Labrini turned out to be the same for the two algorithms applied. The tree structure is similar to a previous, unpublished morphological phylogeny for a subset of labrine species. Estimated divergence times of the Labrini based on fossils and a molecular clock range from about 15 mya for the deepest splits to less than 1 mya for younger clades. Biogeographic patterns of the Symphodus species group and the genus Labrus are dominated by speciation events driven by the closing and opening of the Mediterranean Sea and periodic glaciation events during the past 1 million years. The Labrini are the only clade in the entire Labridae that exhibit nest-building and broodcare behavior. We use the phylogeny to show that similar broodcare behavior has evolved twice in the labrine fish and discuss scenarios for the evolution of broodcare from the diandric protogynous hermaphroditism found in ancestral labrines and many other wrasses.     

Multiple environmental determinants of regional species richness and effects of geographic range size

Understanding patterns of species richness at broad geographic extents remains one of the most challenging yet necessary scientific goals of our time. Many hypotheses have been proposed to account for spatial variation in species richness; among them, environmental determinants have played a central role. In this study, we use data on regional bat species richness in the New World to study redundancy and complementarity of three environmental hypotheses: energy, heterogeneity and seasonality. We accomplish this by partitioning variation in species richness among components associated with unique and combined effects of variables from each hypotheses, and by partitioning the overall richness gradient into gradients of species with varying breadths of geographic distribution. These three environmental hypotheses explain most variation in the species richness gradient of all bats, but do not account for all positive spatial autocorrelation at short distances. Although environmental predictors are highly redundant, energy and seasonality explain different and complementary fractions of variation in species richness of all bats. On the other hand, heterogeneity variables contribute little to explain this gradient. However, results change dramatically when richness is estimated for groups of species with different sizes of geographic distribution. First, the amount of variation explained by environment decreases with a decrease in range size; this suggests that richness gradients of small‐ranged species can not be explained as easily as those of broadly distributed species, as has been implied by analyses that do not consider differences in range size among species. Second, the relative contribution of environmental predictors to explained variation also changes with change in range size. Seasonality and energy are good predictors of species with broad distributions, but they loose almost all explanatory power for richness of species with small ranges. In contrast, heterogeneity, which is a relatively poor predictor of richness of species with large ranges, becomes the main predictor of richness gradients of species with restricted distributions. This suggests that range size is a different dimension on which heterogeneity and other environmental characteristics are complementary to each other. Our results suggest that determinants of species richness gradients might be complex, or at least more complex than many studies have previously suggested.     

Phylogenetic evidence for pollinator-driven diversification of angiosperms

Since Darwin, the diversity of flowers has been attributed to selection by pollinators. Although pollinators commonly act as selective agents on floral traits, determining the extent to which they have influenced angiosperm diversification requires a historical perspective. Here we review recent studies that combine species-level phylogenies with pollinator data and show that pollinator shifts are common, being associated with at least a quarter of documented divergence events. However, shift frequency and directionality vary extensively, owing to variation in intrinsic factors such as floral features and phylogenetic history, as well as extrinsic factors such as interactions with local pollinator assemblages. Despite technical advances, phylogenies remain limited in their power to distinguish among various pollinator-driven evolutionary processes.     

The evolution and diversification of sleep

The evolutionary origins of sleep and its sub-states, rapid eye movement (REM) and non-REM (NREM) sleep, found in mammals and birds, remain a mystery. Although the discovery of a single type of sleep in jellyfish suggests that sleep evolved much earlier than previously thought, it is unclear when and why sleep diversified into multiple types of sleep. Intriguingly, multiple types of sleep have recently been found in animals ranging from non-avian reptiles to arthropods to cephalopods. Although there are similarities between these states and those found in mammals and birds, notable differences also exist. The diversity in the way sleep is expressed confounds attempts to trace the evolution of sleep states, but also serves as a rich resource for exploring the functions of sleep.     

Bayesian inference of character evolution

Much recent progress in evolutionary biology is based on the inference of ancestral states and past transformations in important traits on phylogenetic trees. These exercises often assume that the tree is known without error and that ancestral states and character change can be mapped onto it exactly. In reality, there is often considerable uncertainty about both the tree and the character mapping. Recently introduced Bayesian statistical methods enable the study of character evolution while simultaneously accounting for both phylogenetic and mapping uncertainty, adding much needed credibility to the reconstruction of evolutionary history.     

Phylogenetic diversification of the globin gene superfamily in chordates

Phylogenetic reconstructions provide a means of inferring the branching relationships among members of multigene families that have diversified via successive rounds of gene duplication and divergence. Such reconstructions can illuminate the pathways by which particular expression patterns and protein functions evolved. For example, phylogenetic analyses can reveal cases in which similar expression patterns or functional properties evolved independently in different lineages, either through convergence, parallelism, or evolutionary reversals. The purpose of this article is to provide a robust phylogenetic framework for interpreting experimental data and for generating hypotheses about the functional evolution of globin proteins in chordate animals. To do this, we present a consensus phylogeny of the chordate globin gene superfamily. We document the relative roles of gene duplication and whole-genome duplication in fueling the functional diversification of vertebrate globins, and we unravel patterns of shared ancestry among globin genes from representatives of the three chordate subphyla (Craniata, Urochordata, and Cephalochordata). Our results demonstrate the value of integrating phylogenetic analyses with genomic analyses of conserved synteny to infer the duplicative origins and evolutionary histories of globin genes. We also discuss a number of case studies that illustrate the importance of phylogenetic information when making inferences about the evolution of globin gene expression and protein function. Finally, we discuss why the globin gene superfamily presents special challenges for phylogenetic analysis, and we describe methodological approaches that can be used to meet those challenges.     

Host specificity and geographic range in haematophagous ectoparasites

A negative interspecific correlation between the degree of habitat specialization and the size of a species' geographic range has been documented for several free living groups of organisms, providing support for the niche breadth hypothesis. In contrast, practically nothing is known about the geographic range sizes of parasitic organisms and their determinants. In the context of the niche breadth hypothesis, parasites represent ideal study systems, because of the well documented variation in host specificity among parasite species. Here, we investigated the relationship between host specificity (a measure of niche breadth) and geographic range size among flea species parasitic on small mammals, using data from seven distinct geographical regions. Two measures of host specificity were used: the number of host species used by a flea species, and a measure of the average taxonomic distance between the host species used by a flea; the latter index provides an evolutionary perspective on host specificity. After correcting for phylogenetic influences, and using either of our two measures of host specificity, the degree of host specificity of fleas was negatively correlated with the size of their geographic range in all seven regions studied here, with only one minor exception. Overall, these results provide strong support for the niche breadth hypothesis, although other explanations cannot be ruled out.     

The evolution and diversification of Dicers in plants

Most multicellular organisms regulate developmental transitions by microRNAs, which are generated by an enzyme, Dicer. Insects and fungi have two Dicer-like genes, and many animals have only one, yet the plant, Arabidopsis, has four. Examining the poplar and rice genomes revealed that they contain five and six Dicer-like genes, respectively. Analysis of these genes suggests that plants require a basic set of four Dicer types which were present before the divergence of mono- and dicotyledonous plants ( approximately 200 million years ago), but after the divergence of plants from green algae. A fifth type of Dicer seems to have evolved in monocots.     

Phylogenetic autocorrelation and heritability of geographic range size,shape and position of fiddler crabs,genus Uca (Crustacea,Decapoda)

The aim of this study was to evaluate the levels of phylogenetic heritability of the geographical range size, shape and position for 88 species of fiddler crabs of the world, using phylogenetic comparative methods and simulation procedures to evaluate their fit to the neutral model of Brownian motion. The geographical range maps were compiled from literature, and range size was based on the entire length of coastline occupied by each species, and the position of each range was calculated as its latitudinal and longitudinal midpoint. The range shape of each species was based in fractal dimension (box‐counting technique). The evolutionary patterns in the geographical range metrics were explored by phylogenetic correlograms using Moran’s I autocorrelation coefficients, autoregressive method (ARM) and phylogenetic eigenvector regression (PVR). The correlograms were compared with those obtained by simulations of Brownian motion processes across phylogenies. The distribution of geographical range size of fiddler crabs is right‐skewed and weak phylogenetic autocorrelation was observed. On the other hand, there was a strong phylogenetic pattern in the position of the range (mainly along longitudinal axis). Indeed, the ARM and PVR evidenced, respectively, that ca. 86% and 91% of the longitudinal midpoint could be explained by phylogenetic relationships among the species. The strong longitudinal phylogenetic pattern may be due to vicariant allopatric speciation and geographically structured cladogenesis in the group. The traits analysed (geographical range size and position) did not follow a Brownian motion process, thus suggesting that both adaptive ecological and evolutionary processes must be invoked to explain their dynamics, not following a simple neutral inheritance in the fiddler‐crab evolution.