A genomic assessment of species boundaries and hybridization in a group of highly polymorphic anoles (distichus species complex)

Delimiting young species is one of the great challenges of systematic biology, particularly when the species in question exhibit little morphological divergence. Anolis distichus, a trunk anole with more than a dozen subspecies that are defined primarily by dewlap color, may actually represent several independent evolutionary lineages. To test this, we utilized amplified fragment length polymorphisms (AFLP) genome scans and genetic clustering analyses in conjunction with a coalescent‐based species delimitation method. We examined a geographically widespread set of samples and two heavily sampled hybrid zones. We find that genetic divergence is associated with a major biogeographic barrier, the Hispaniolan paleo‐island boundary, but not with dewlap color. Additionally, we find support for hypotheses regarding colonization of two Hispaniolan satellite islands and the Bahamas from mainland Hispaniola. Our results show that A. distichus is composed of seven distinct evolutionary lineages still experiencing a limited degree of gene flow. We suggest that A. distichus merits taxonomic revision, but that dewlap color cannot be relied upon as the primary diagnostic character.     

Testing the island effect in adaptive radiation: rates and patterns of morphological diversification in Caribbean and mainland Anolis lizards

Many of the classic examples of adaptive radiation, including Caribbean Anolis lizards, are found on islands. However, Anolis also exhibits substantial species richness and ecomorphological disparity on mainland Central and South America. We compared patterns and rates of morphological evolution to investigate whether, in fact, island Anolis are exceptionally diverse relative to their mainland counterparts. Quite the contrary, we found that rates and extent of diversification were comparable--Anolis adaptive radiation is not an island phenomenon. However, mainland and Caribbean anoles occupy different parts of morphological space; in independent colonizations of both island and mainland habitats, island anoles have evolved shorter limbs and better-developed toe pads. These patterns suggest that the two areas are on different evolutionary trajectories. The ecological causes of these differences are unknown, but may relate to differences in predation or competition among mainland and island communities.     

Testing ecological explanations for biogeographic boundaries

Barriers to dispersal and resulting biogeographic boundaries are responsible for much of life's diversity. Distinguishing the contribution of ecological, historical, and stochastic processes to the origin and maintenance of biogeographic boundaries, however, is a longstanding challenge. Taking advantage of newly available data and methods--including environmental niche models and associated comparative metrics--we develop a framework to test two possible ecological explanations for biogeographic boundaries: (1) sharp environmental gradients and (2) ribbons of unsuitable habitat dividing two highly suitable regions. We test each of these hypotheses against the null expectation that environmental variation across a given boundary is no greater than expected by chance. We apply this framework to a pair of Hispaniolan Anolis lizards (A. chlorocyanus and A. coelestinus) distributed on the either side of this island's most important biogeographic boundary. Integrating our results with historical biogeographic analysis, we find that a ribbon of particularly unsuitable habitat is acting to maintain a boundary between species that initially diverged on distinct paleo-islands, which merged to form present-day Hispaniola in the Miocene.     

Rodents of the Caribbean: origin and diversification of hutias unravelled by next-generation museomics

The Capromyidae (hutias) are endemic rodents of the Caribbean and represent a model of dispersal for non-flying mammals in the Greater Antilles. This family has experienced severe extinctions during the Holocene and its phylogenetic affinities with respect to other caviomorph relatives are still debated as morphological and molecular data disagree. We used target enrichment and next-generation sequencing of mitochondrial and nuclear genes to infer the phylogenetic relationships of hutias, estimate their divergence ages, and understand their mode of dispersal in the Greater Antilles. We found that Capromyidae are nested within Echimyidae (spiny rats) and should be considered a subfamily thereof. We estimated that the split between hutias and Atlantic Forest spiny rats occurred 16.5 (14.8–18.2) million years ago (Ma), which is more recent than the GAARlandia land bridge hypothesis (34–35 Ma). This would suggest that during the Early Miocene, an echimyid-like ancestor colonized the Greater Antilles from an eastern South American source population via rafting. The basal divergence of the Hispaniolan Plagiodontia provides further support for a vicariant separation between Hispaniolan and western islands (Bahamas, Cuba, Jamaica) hutias. Recent divergences among these western hutias suggest Plio-Pleistocene dispersal waves associated with glacial cycles.     

The molecular evolution of the alcohol dehydrogenase locus and the phylogeny of Hawaiian Drosophila.

DNA sequences in the alcohol dehydrogenase genes of flies representing the major groups of Hawaiian Drosophila are used to clarify the relationships of these groups, among themselves and with mainland Drosophila. The topology of the tree derived from these sequences agrees with karyotypic and morphological data but disagrees, in part, with the results of an earlier study that used immunological comparisons between variants of a larval hemolymph protein. A time scale, derived from a comparison of closely related Hawaiian Drosophila species, provides divergence-time estimates that are substantially more recent than those obtained from the immunological studies, although they are still within the bounds set by fossil and biogeographical evidence. The two major lineages of Hawaiian Drosophila, the scaptomyzoids and the drosophiloids, are shown to be widely separated from one another. The scaptomyzoids appear to have diverged early in the history of the subgenus Drosophila, greater than 25 Mya. While hundreds of scaptomyzoid species are found in the Hawaiian archipelago, many fewer are found elsewhere around the world, suggesting that they could have originated outside Hawaii. The drosophiloid lineage is strictly endemic to Hawaii and originated little more than 10 Mya, according to the alcohol dehydrogenase molecular clock. Thus, Drosophila apparently inhabited the Hawaiian archipelago (greater than or equal to 5 Myr before the emergence of the oldest existing high island, Kauai, 5 Mya.     

Microhabitat use, diet, and performance data on the Hispaniolan twig anole, Anolis sheplani: pushing the boundaries of morphospace

Caribbean Anolis lizards are often cited as a textbook example of adaptive radiation. Similar morphologies (ecomorphs) have originated in similar ecological settings on different large islands in the West Indies. However, relatively little is known about one of the morphologically most specialized and divergent ecomorphs: the twig anoles. Here, we investigate aspects of morphology, dewlap size, locomotor and bite performance, structural habitat and diet of the poorly known twig anole, Anolis sheplani from Hispaniola. Few observations have previously been made of this species in its natural habitat, and few quantitative data on its natural history are available. A. sheplani is an extreme twig anole with respect to its morphology, performance capacities, and ecological niche. Males and females of this species do not differ from each other in body dimensions, performance or habitat use, but males do have a bigger dewlap than females. We present data for 25 individuals and compare them with data for other Greater Antillean anoles. It becomes apparent that twig anoles constitute a large component of the morphological, functional, and ecological diversity of Anolis lizards. Small twig anoles such as A. sheplani appear to be pushing the boundaries of morphospace and are thus crucial in our understanding of the evolution of phenotypic diversity.     

Egg rejection behavior in a population exposed to parasitism: Village Weavers on Hispaniola

In contrast to African Village Weavers (Ploceus cucullatus)that are parasitized by Diederik Cuckoos (Chrysococcyx caprius),introduced weavers on Hispaniola existed without parasitismfor at least 2 centuries until the arrival of the Shiny Cowbird(Molothrus bonariensis) in the 1970s. Cruz and Wiley (1989)found that Hispaniolan weavers had a lower rejection rate offoreign eggs than African populations. Subsequently, Robertand Sorci (1999) and Lahti (2005, 2006) found that acceptanceof dissimilar eggs is not characteristic of the species throughoutits Hispaniolan range. In 1999–2002, we studied egg rejectionin Hispaniolan weavers on a broad regional scale. Rejectionincreased as experimental eggs became increasingly differentfrom the host eggs. Rejection rates for mimetic eggs, differentcolor eggs, different-spotting eggs, and cowbird eggs was 23.2%,33.3%, 61.5%, and 85.3%, respectively, with higher rejectionof cowbird eggs in areas where cowbirds were observed. Althoughrejection is likely to have a genetic component, the differencescould be due to phenotypic plasticity. Plasticity in egg rejectionmay be expected, given the potential cost of rejection and thespatiotemporal distribution of cowbirds. Thus, egg rejectionhas not necessarily decreased in Hispaniolan weavers, but itmay act in a plastic manner, increasing where cowbirds are present.     

Molecular phylogenetic perspective on evolution of lizards of the Anolis grahami series

We report the results of phylogenetic analyses of 1447 bases of mitochondrial DNA sequence for 21 populations representing seven species of the Anolis grahami series (A. conspersus, A. garmani, A. grahami, A. lineatopus, A. opalinus, A. reconditus, and A. valencienni), six of which occur on Jamaica. These data include 705 characters that are phylogenetically informative according to parsimony. A parsimony analysis of these data combined with previously published allozymic data yields a single most parsimonious tree with strong support for monophyly of the A. grahami series, the sister-group relationship between Anolis lineatopus and A. reconditus and a clade composed of Anolis garmani, A. grahami, and A. opalinus. Based on DNA data alone, A. conspersus is nested within A. grahami. Haplotypes sampled from geographic populations of A. grahami, A. lineatopus, and A. opalinus are highly divergent (approximately 12-15% sequence difference on average for each species) and show similar phylogeographic patterns, suggesting that each of these currently recognized species may be a complex of species. Anolis valencienni also shows high sequence divergence among haplotypes from different geographic populations (approximately 8% sequence difference) and may contain cryptic species. Divergence among haplotypes within A. garmani is substantially lower (approximately 3% sequence difference), and phylogeographic patterns are significantly different from those observed in A. grahami, A. lineatopus and A. opalinus.     

Habitat use and ecological interactions of an introduced and a native species of Anolis lizard on Grand Cayman,with a review of the outcomes of anole introductions

Since its introduction ten years ago, Anolis sagrei has spread over much of Grand Cayman and is now more common in some habitats than the native anole, A. conspersus. Interspecific differences in body size, perch height, and microclimatic preference may have facilitated the colonization. Nonetheless, competition may be occurring between the species; comparisons with studies of habitat use prior to the arrival of A. sagrei indicate that in open habitats, where A. sagrei is now abundant, A. conspersus perches higher, but in closed habitats, where A. sagrei is absent, no change in perch height is evident. Review of data concerning 23 Anolis introductions indicates that the presence or absence of an ecologically similar native species may be an important determinant of colonization success or failure.     

The quick and the fast: the evolution of acceleration capacity in Anolis lizards

Although of prime ecological relevance, acceleration capacity is a poorly understood locomotor performance trait in terrestrial vertebrates. No empirical data exist on which design characteristics determine acceleration capacity among species and whether these design traits influence other aspects of locomotor performance. In this study we explore how acceleration capacity and sprint speed have evolved in Anolis lizards. We investigate whether the same or different morphological traits (i.e., limb dimensions and muscle mass) correlate with both locomotor traits. Within our sample of Anolis lizards, relative sprint speed and acceleration capacity coevolved. However, whereas the variation in relative acceleration capacity is primarily explained by the variation in relative knee extensor muscle mass, the variation in relative sprint speed is correlated to the variation in relative femur, tibia, and metatarsus length as well as knee extensor muscle mass. The fact that the design features required to excel in either performance trait partly overlap might explain the positive correlation between the variation in relative sprint speed and acceleration capacity. Furthermore, our data show how similar levels of sprint performance can be achieved through different morphological traits (limb segment lengths and muscle mass) suggesting that redundant mapping has potentially played a role in mitigating trade-offs.     

Phylogenetic analysis of European species of Proteocephalus (Cestoda: Proteocephalidea): compatibility of molecular and morphological data, and parasite-host coevolution.

The phylogeny of European species of the tapeworm genus Proteocephalus was studied, based on partial 18S rDNA and morphological data. The group was found to be monophyletic. The analysis showed a low informative value of available morphological characters in comparison with molecular data. The morphological matrix resulted in a poorly resolved tree which is, however, compatible with the topology (Proteocephalus osculatus (Proteocephalus torulosus (Proteocephalus macrocephalus, Proteocephalus filicollis) (Proteocephalus tetrastomus, Proteocephalus percae, Proteocephalus longicollis))) based on the 18S rDNA data. A comparison performed by the program TreeMap showed a lack of significant congruency between parasite and host phylogenies. Therefore, the distribution of species in their hosts appears to be independent of the phylogeny and it is likely to be a result of host-switching, rather than co-speciation events.     

The dynamics of natural selection and vicariance in the Dominican anole: patterns of within-island molecular and morphological divergence

The larger islands of the Lesser Antilles are ecologically and geologically complex and are inhabited by single, but morphologically variable, Anolis species. Although earlier work has indicated that a large part of the morphological variation in Anolis oculatus from Dominica can be attributed to selection, a history of recurrent volcanic activity over the last few million years suggests that vicariance may have also played a significant role. We report a study of variation in the cytochrome b gene of mitochondrial DNA across the island to address this issue. We uncovered a very high degree of polymorphism, with an overall gene diversity of 0.97 and a nucleotide diversity of 0.04. Sequences, on average, differ by 3.82% and the maximum pairwise divergence (corrected for multiple hits) is 9.29%. Most haplotypes are restricted to single localities (a pattern not changed by increasing the sample size). Phylogenetic analysis revealed the presence of two distinct lineages on the island with strong phylogeographic structure. One of these is geographically restricted to a relatively small part of the central Caribbean coast. Sublineages were also discernible within the other more widely distributed lineage, but resolution within and support for these sublineages was poor. The phylogeographic pattern is not congruent with generalized body shape and scalation, but is significantly correlated with color pattern. Even when correcting for this lineage effect with partial Matrix correspondence tests, the relationship between color pattern and vegetation is reaffirmed, suggesting that although both vicariance and selection have played a role in the morphological differentiation of this species, selection for current environmental conditions has been more important. We discuss the causes of the phylogeographic structure in light of the volcanic history of the island and highlight the exceptional instance of congruence between all morphological character systems and lineage boundaries, which occurs at the transition between the northern and southern Caribbean ecotypes.     

Comparative variation of morphological and molecular evolution through geologic time: 28S ribosomal RNA versus morphology in echinoids.

The comparatively good fossil record of post-Palaeozoic echinoids allows rates of morphological change to be estimated over the past 260 million years and compared with rates of molecular evolution. Parsimony analysis of morphological data, based predominantly on skeletal characteristics, and parsimony, distance and maximum likelihood analyses of molecular data, from the first 380 bases from the 5' end of the 28S rRNA molecule, for 10 species of echinoid produce congruent phylogenies. The molecular sequence chosen is demonstrably far from saturation and sister groups have divergence times ranging from about 15 to 260 Ma. Parsimony analysis allows the great majority of molecular and morphological apomorphies to be placed in one of 18 independent geological time intervals, providing a direct measure of rates of evolution for periods in the geological past. Because most molecular fixed point mutations in our sequences cannot be polarized unambiguously by outgroup comparison (making the outgroup states effectively random), distance and parsimony analyses both tend spuriously to root the echinoid tree on the longest internal branch. A topology identical to that derived from morphological data is, however, obtained using Maximum Likelihood and also parsimony analysis where outgroup rooting is restricted to more conserved regions. This is taken as the correct topology for assessing rates of evolution. Overall, both morphological and molecular changes show a moderately strong correlation with time elapsed, but a weaker correlation with one another. Statistically significant differences in evolutionary rate are found between some, but not all, pair-wise comparisons of sister lineages for both molecular and morphological data. The molecular clock rate for echinaceans is three times faster than that for cidaroids and irregular echinoids. Spearman's rank correlation test, which requires only relative magnitude of changes to be known, suggests that morphological change has a slightly better correlation with time than does molecular change, averaged over all ten species. However, when just echinaceans are considered an extremely good correlation is found between the number of molecular changes and time elapsed, whereas morphological change remains poorly correlated. Thus, molecular rates approximate to a clocklike model within restricted echinoid clades, but vary significantly between clades. Averaging results over all echinoids produces a correlation that is no better than the correlation between morphological change and time elapsed.     

Deciphering primate phylogeny from macromolecular specificities

A problem in deciphering primate phylogeny, morphological convergence between different evolutionary lines, can be overcome by species comparisons of proteins, macromolecules with specificities closely linked to the genetic code in DNA. Various chemical, electrophoretic, and immunological data on serum and tissue proteins in primates are reviewed with respect to their phylogenetic significance. Much of this data deals with protein specificities in the Hominoidea and depicts a particularly close genetic relationship between man and the African apes. Hominoidea, Cercopithecoidea, Ceboidea, and Lorisoidea are characterized by their proteins as monophyletic or natural taxa, even though the conventional subdivisions within several of these superfamilies are not in complete accord with the protein analyses. The protein evidence supports the conventional grouping of Cercopithecoidea with Hominoidea in the infraorder Catarrhini and the grouping of Catarrhini and Platyrrhini (Ceboidea) in the suborder Anthropoidea. Lemuroidea and Lorisoidea appear to be closer to one another than to either Tupaioidea or Anthropoidea and closer to the Anthropoidea than to the Tupaioidea. Comparisons of primate DNA's by Hoyer and coworkers are demonstrating genetic affinities among primates which agree with those deduced from the comparison of protein specificities. Species differences and similarities in the relative amounts of different protein macromolecules reflect the grade relationships of primates, but, unlike the comparisons of amino-acid sequences or antigenic specificities, are not reliable indicators of phyletic affinities. Data on the ratios of M(uscle) to H(eart) type lactate dehydrogenase in a series of primate brains provides a biochemical example of the concept that there are “lower” (primitive) and “higher” (advanced) grades of evolutionary development among the extant primates.     

Character displacement in the midst of background evolution in island populations of Anolis lizards: A spatiotemporal perspective

Negative interactions between species can generate divergent selection that causes character displacement. However, other processes cause similar divergence. We use spatial and temporal replication across island populations of Anolis lizards to assess the importance of negative interactions in driving trait shifts. Previous work showed that the establishment of Anolis sagrei on islands drove resident Anolis carolinensis to perch higher and evolve larger toepads. To further test the interaction's causality and predictability, we resurveyed a subset of islands nine years later. Anolis sagrei had established on one island between surveys. We found that A. carolinensis on this island now perch higher and have larger toepads. However, toepad morphology change on this island was not distinct from shifts on six other islands whose Anolis community composition had not changed. Thus, the presence of A. sagrei only partly explains A. carolinensis trait variation across space and time. We also found that A. carolinensis on islands with previously established A. sagrei now perch higher than a decade ago, and that current A. carolinensis perch height is correlated with A. sagrei density. Our results suggest that character displacement likely interacts with other evolutionary processes in this system, and that temporal data are key to detecting such interactions.     

Detection of a novel sequence change in the major form of alpha-MSH isolated from the intermediate pituitary of the reptile, Anolis carolinensis.

Intermediate pituitaries of the reptile, Anolis carolinensis, were separately pulse labeled with [3H]Trp and [3H]Tyr. The major form of alpha-MSH was purified by immunoprecipitation and isolated by reverse phase HPLC. Tryptic peptide analysis indicated that the [3H]Trp-labeled C-terminal fragment of Anolis alpha-MSH had the same retention time as mammalian ACTH(9-13) amide; however, the [3H]Tyr-labeled N-terminal fragment did not coelute with either mammalian ACTH(1-8) or N-acetyl-ACTH(1-8). Purification of alpha-MSH from 76 Anolis intermediate pituitaries confirmed that a sequence change had occurred in the N-terminal region of Anolis alpha-MSH. The tissues were acid extracted and purified by Sephadex G-25 chromatography and reverse phase HPLC to yield 4.5 micrograms of purified Anolis alpha-MSH for amino acid composition analysis and automated Edman degradation sequence analysis. The major form of Anolis alpha-MSH is nonacetylated and has the following novel primary sequence: Ser-Tyr-Ala-Met-Glu-His-Phe-Arg-Trp-Gly-Lys-Pro(Val-amide). The presence of Val-amide was verified by immunological analysis, tryptic peptide analysis and amino acid composition analysis.     

Assessing congruence of opportunistic records and systematic surveys for predicting Hispaniolan mammal species distributions

Comparative assessment of the relative information content of different independent spatial data types is necessary to evaluate whether they provide congruent biogeographic signals for predicting species ranges. Opportunistic occurrence records and systematically collected survey data are available from the Dominican Republic for Hispaniola’s surviving endemic non‐volant mammals, the Hispaniolan solenodon (Solenodon paradoxus) and Hispaniolan hutia (Plagiodontia aedium); opportunistic records (archaeological, historical and recent) exist from across the entire country, and systematic survey data have been collected from seven protected areas. Species distribution models were developed in maxent for solenodons and hutias using both data types, with species habitat suitability and potential country‐level distribution predicted using seven biotic and abiotic environmental variables. Three different models were produced and compared for each species: (a) opportunistic model, with starting model incorporating abiotic‐only predictors; (b) total survey model, with starting model incorporating biotic and abiotic predictors; and (c) reduced survey model, with starting model incorporating abiotic‐only predictors to allow further comparison with the opportunistic model. All models predict suitable environmental conditions for both solenodons and hutias across a broadly congruent, relatively large area of the Dominican Republic, providing a spatial baseline of conservation‐priority landscapes that might support native mammals. Correlation between total and reduced survey models is high for both species, indicating the substantial explanatory power of abiotic variables for predicting Hispaniolan mammal distributions. However, correlation between survey models and opportunistic models is only moderately positive. Species distribution models derived from different data types can provide different predictions about habitat suitability and conservation‐priority landscapes for threatened species, likely reflecting incompleteness and bias in spatial sampling associated with both data types. Models derived using both opportunistic and systematic data must therefore be applied critically and cautiously.     

Adaptive radiation in Lesser Antillean lizards: molecular phylogenetics and species recognition in the Lesser Antillean dwarf gecko complex, Sphaerodactylus fantasticus

The time associated with speciation varies dramatically among lower vertebrates. The nature and timing of divergence is investigated in the fantastic dwarf gecko Sphaerodactylus fantasticus complex, a nominal species that occurs on the central Lesser Antillean island of Guadeloupe and adjacent islands and islets. This is compared to the divergence in the sympatric anole clade from the Anolis bimaculatus group. A molecular phylogenetic analysis of numerous gecko populations from across these islands, based on three mitochondrial DNA genes, reveals several monophyletic groups occupying distinct geographical areas, these being Les Saintes, western Basse Terre plus Dominica, eastern Basse Terre, Grand Terre, and the northern and eastern islands (Montserrat, Marie Galante, Petite Terre, Desirade). Although part of the same nominal species, the molecular divergence within this species complex is extraordinarily high (27% patristic distance between the most divergent lineages) and is compatible with this group occupying the region long before the origin of the younger island arc. Tests show that several quantitative morphological traits are correlated with the phylogeny, but in general the lineages are not uniquely defined by these traits. The dwarf geckos show notably less nominal species-level adaptive radiation than that found in the sympatric southern clade of Anolis bimculatus , although both appear to have occupied the region for a broadly similar period of time. Nevertheless, the dwarf gecko populations on Les Saintes islets are the most morphologically distinct and are recognized as a full species ( Sphaerodactylus phyzacinus ), as are anoles on Les Saintes ( Anolis terraealtae ).     

Weak founder effect signal in a recent introduction of Caribbean Anolis

Species introductions provide a rare opportunity to study rapid evolutionary and genetic processes in natural systems, often under novel environmental pressures. Few empirical studies have been able to characterize genetic founder effects associated with demographic bottlenecks at the earliest stages of species introductions. This study utilizes prior mitochondrial DNA information which identifies the putative source population for a recently established ( c . 7 years between import and sampling) species introduction. We investigated the evidence for a founder effect in a highly successful introduction of a Puerto Rican Anolis species that has established itself on Dominica to the localized exclusion of the native, endemic anole. Five highly polymorphic microsatellite loci were used to explore the partitioning of genetic diversity within and between native source, native nonsource, and introduced populations of Anolis cristatellus . Group comparisons reveal significantly lower allelic richness and expected heterozygosity in introduced populations compared to native populations; however, tests for heterozygosity excess relative to allelic richness failed to provide consistent evidence for a founder effect within introduced populations. Significant levels of within-population genetic variation were present in both native and introduced populations. We suggest that aspects of the reproductive ecology of Anolis (high fecundity, sperm storage and multiple paternity) offer an important mechanism by which genetic variation may be maintained following demographic bottlenecks and founder events in some squamate taxa.