On the Selection and Analysis of Clades in Comparative Evolutionary Studies.

Researchers commonly present results of comparative studies of taxonomic groups. In this review, we criticize the focus on named clades, usually, comparably ranked groups such as families or orders, for comparative evolutionary analyses and question the general practice of using clades as units of analysis. The practice of analyzing sets of named groups persists despite widespread appreciation that the groups we have chosen to name are based on subjective human concerns rather than objective properties of nature. We demonstrate an effect of clade selection on results in one study and present some potential alternatives to selecting named clades for analysis that are relatively objective in clade choice. However, we note that these alternatives are only partial solutions for clade-based studies. The practice of analyzing named clades obviously is biased and problematic, but its issues portend broader problems with the general approach of employing clades as units of analysis. Most clade-based studies do not account for the nonindependence of clades, and the biological insight gained from demonstrating some pattern among a particular arbitrary sample of groups is arguable. [Clades; comparative biology; taxonomic groups.].

What constrains adaptive radiation? Documentation and explanation of under-evolved morphologies in Anolis lizards.

Adaptive radiations fill ecological and morphological space during evolutionary diversification. Why do some trait combinations evolve during such radiations, whereas others do not? 'Required' constraints of pleiotropy and developmental interaction frequently are implicated in explanations for such patterns, but selective forces also may discourage particular trait combinations. Here, we use a dataset of 351 species to demonstrate the dearth of some theoretically plausible trait combinations of limb, toe and tail length in Anolis lizards. For example, disproportionately few Anolis species display long limbs and short toes. We evaluate recovered patterns within three species of Anolis, and find that cladewide patterns are not evident at intraspecific levels. For example, within species, the combination of long limbs and short toes is not significantly rarer than long limbs and long toes. Differences in scale complicate inter- and intraspecific comparisons and disallow concrete conclusions of cause. However, the absence of the interspecific pattern at the intraspecific level is more compatible with selection favouring particular trait combinations than with 'required' forces dictating which trait combinations are available for selection. We also demonstrate the isometry of toe, tail and hindlimb length relative to body length between species but allometry in four of nine trait-body comparisons within species.

Phylogeography of a widespread lizard complex reflects patterns of both geographic and ecological isolation.

A primary challenge for modern phylogeography is understanding how ecology and geography, both contemporary and historical, shape the spatial distribution and evolutionary histories of species. Phylogeographic patterns are the result of many factors, including geology, climate, habitat, colonization history and lineage-specific constraints. Assessing the relative influences of these factors is difficult because few species, regions and environments are sampled in enough detail to compare competing hypotheses rigorously and because a particular phylogeographic pattern can potentially result from different evolutionary scenarios. The silky anoles (Anolis sericeus complex) of Central America and Mexico are abundant and found in all types of lowland terrestrial habitat, offering an excellent opportunity to test the relative influences of the factors affecting diversification. Here, we performed a range-wide statistical phylogeographic analysis on restriction site-associated DNA (RAD) markers from silky anoles and compared the phylogeographic patterns we recovered to historical and contemporary environmental and topographic data. We constructed niche models to compare niche overlap between sister lineages and conducted coalescent simulations to characterize how the major lineages of silky anoles have diverged. Our results revealed that the mode of divergence for major lineage diversification events was geographic isolation, resulting in ecological divergence between lineages, followed by secondary contact. Moreover, comparisons of parapatric sister lineages suggest that ecological niche divergence contributed to isolation by environment in this system, reflecting the natural history differences among populations in divergent environments.

Solitary ecology as a phenomenon extending beyond insular systems: exaptive evolution in Anolis lizards.

The mechanisms driving phenotypic evolution have been of interest to biologists since Darwin. Ecological release-wherein adaptive evolution occurs following relaxation of constraining selective pressures-and environmental filtering-wherein exaptive traits allow colonization of a new area-have been studied in several insular cases. Anolis lizards, which may exist in solitude or sympatry with multiple congeners, are an excellent system for evaluating whether ecological release and environmental filtering are associated with phenotypic shifts across phylogenetic and geographical scales. Insular solitary Anolis exhibit phenotypic differentiation in body size and sexual size dimorphism-SSD-through exaptive and adaptive evolution, respectively. But, the generality of these effects has not yet been addressed. Here, we analyse the evolution of body size and SSD relative to sympatry in mainland Anolis. We found that mainland species co-occurring with few congeners exhibit uniform body size and greater SSD relative to other random mainland assemblages, consistent with the insular solitary pattern. The locations of evolutionary shifts for both traits do not coincide with evolutionary transitions to decreased levels of sympatry. These results are consistent with exaptive environmental filtering but not adaptive ecological release. Future studies should be conducted at local scales to evaluate the role of these factors in the evolution of solitary existence in mainland and island species.

Comparative Evolution of an Archetypal Adaptive Radiation: Innovation and Opportunity in Anolis Lizards.

Adaptive radiation is a widely recognized pattern of evolution wherein substantial phenotypic change accompanies rapid speciation. Adaptive radiation may be triggered by environmental opportunities resulting from dispersal to new areas or via the evolution of traits, called key innovations, that allow for invasion of new niches. Species sampling is a known source of bias in many comparative analyses, yet classic adaptive radiations have not been studied comparatively with comprehensively sampled phylogenies. In this study, we use unprecedented comprehensive phylogenetic sampling of Anolis lizard species to examine comparative evolution in this well-studied adaptive radiation. We compare adaptive radiation models within Anolis and in the Anolis clade and a potential sister lineage, the Corytophanidae. We find evidence for island (i.e., opportunity) effects and no evidence for trait (i.e., key innovation) effects causing accelerated body size evolution within Anolis. However, island effects are scale dependent: when Anolis and Corytophanidae are analyzed together, no island effect is evident. We find no evidence for an island effect on speciation rate and tenuous evidence for greater speciation rate due to trait effects. These results suggest the need for precision in treatments of classic adaptive radiations such as Anolis and further refinement of the concept of adaptive radiation.

A Phylogenetic, Biogeographic, and Taxonomic study of all Extant Species of Anolis (Squamata; Iguanidae).

Anolis lizards (anoles) are textbook study organisms in evolution and ecology. Although several topics in evolutionary biology have been elucidated by the study of anoles, progress in some areas has been hampered by limited phylogenetic information on this group. Here, we present a phylogenetic analysis of all 379 extant species of Anolis, with new phylogenetic data for 139 species including new DNA data for 101 species. We use the resulting estimates as a basis for defining anole clade names under the principles of phylogenetic nomenclature and to examine the biogeographic history of anoles. Our new taxonomic treatment achieves the supposed advantages of recent subdivisions of anoles that employed ranked Linnaean-based nomenclature while avoiding the pitfalls of those approaches regarding artificial constraints imposed by ranks. Our biogeographic analyses demonstrate complexity in the dispersal history of anoles, including multiple crossings of the Isthmus of Panama, two invasions of the Caribbean, single invasions to Jamaica and Cuba, and a single evolutionary dispersal from the Caribbean to the mainland that resulted in substantial anole diversity. Our comprehensive phylogenetic estimate of anoles should prove useful for rigorous testing of many comparative evolutionary hypotheses. [Anoles; biogeography; lizards; Neotropics; phylogeny; taxonomy].

The genome of the green anole lizard and a comparative analysis with birds and mammals.

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.

Comparison of natural and nonnative two-species communities of Anolis lizards.

Human-mediated colonizations present an informative model system for understanding assembly of organismal communities. However, it is unclear whether communities including naturalized species are accurate analogs of natural communities or unique combinations not present in nature. I compared morphology and phylogenetic structure of natural and naturalized two-species communities of Anolis lizards. Natural communities are phylogenetically clustered, whereas naturalized communities show no significant phylogenetic structure. This result likely reflects differences in colonization pools for these communities-that is, invasion from anywhere for naturalized communities but from proximal and thus phylogenetically close lineages in natural communities. Both natural and naturalized communities each include pairs of species that are significantly similar to each other in morphology, and both sets of communities are composed of species that possess traits of good colonizers. These similarities suggest that the formation of natural and naturalized communities may be at least partially governed by similar processes. Human-mediated invasions may be credibly viewed as modern incarnations of natural colonizations in this case.

Synonyms for some species of Mexican anoles (Squamata: Dactyloidae).

We studied type material and freshly collected topotypical specimens to assess the taxonomic status of five names associated with species of Mexican Anolis. We find A. schmidti to be a junior synonym of A. nebulosus, A. breedlovei to be a junior synonym of A. cuprinus, A. polyrhachis to be a junior synonym of A. rubiginosus, A. simmonsi to be a junior synonym of A. nebuloides, and A. adleri to be a junior synonym of A. liogaster.

Two new species of semiaquatic Anolis (Squamata: Dactyloidae) from Costa Rica.

We describe two new species of Draconura-clade semiaquatic anoles from the central Pacific versant of Costa Rica. The two new species are similar to Anolis aquaticus in external appearance and ecology but differ from this species in male dewlap coloration and scalation. Anolis robinsoni sp. nov. and A. riparius sp. nov. differ from each other mainly in male dewlap color. All three species are distinct according to diagnostic morphological traits and a phylogenetic analysis of mitochondrial DNA sequences (669 bases of COI gene). We discuss the distribution and ecology of Anolis aquaticus and the new species.

Developing a community-based genetic nomenclature for anole lizards.

BACKGROUND: Comparative studies of amniotes have been hindered by a dearth of reptilian molecular sequences. With the genomic assembly of the green anole, Anolis carolinensis available, non-avian reptilian genes can now be compared to mammalian, avian, and amphibian homologs. Furthermore, with more than 350 extant species in the genus Anolis, anoles are an unparalleled example of tetrapod genetic diversity and divergence. As an important ecological, genetic and now genomic reference, it is imperative to develop a standardized Anolis gene nomenclature alongside associated vocabularies and other useful metrics. RESULTS: Here we report the formation of the Anolis Gene Nomenclature Committee (AGNC) and propose a standardized evolutionary characterization code that will help researchers to define gene orthology and paralogy with tetrapod homologs, provide a system for naming novel genes in Anolis and other reptiles, furnish abbreviations to facilitate comparative studies among the Anolis species and related iguanid squamates, and classify the geographical origins of Anolis subpopulations. CONCLUSIONS: This report has been generated in close consultation with members of the Anolis and genomic research communities, and using public database resources including NCBI and Ensembl. Updates will continue to be regularly posted to new research community websites such as lizardbase. We anticipate that this standardized gene nomenclature will facilitate the accessibility of reptilian sequences for comparative studies among tetrapods and will further serve as a template for other communities in their sequencing and annotation initiatives.

A new giant anole (Squamata: Iguanidae: Dactyloinae) from southwestern Ecuador.

We describe a new species of Anolis lizard from the Pacific slopes of the Andes of southwestern Ecuador at elevations between 3721,000 m. The new species belongs to the Dactyloa clade and may be distinguished from other Anolis by size, external anatomy, mitochondrial DNA divergence, and dewlap color. Based on phylogenetic analyses of mitochondrial and nuclear DNA sequence data, we found that the new species is sister to A. fraseri in a clade composed primarily of large Dactyloid species. The new species is known from a protected area in southern Ecuador, Buenaventura Reserve, which suggests that at least some its populations are well protected.

Does breeding season variation affect evolution of a sexual signaling trait in a tropical lizard clade?

Sexually selected traits can be expected to increase in importance when the period of sexual behavior is constrained, such as in seasonally restricted breeders. Anolis lizard male dewlaps are classic examples of multifaceted signaling traits, with demonstrated intraspecific reproductive function reflected in courtship behavior. Fitch and Hillis found a correlation between dewlap size and seasonality in mainland Anolis using traditional statistical methods and suggested that seasonally restricted breeding seasons enhanced the differentiation of this signaling trait. Here, we present two tests of the Fitch-Hillis Hypothesis using new phylogenetic and morphological data sets for 44 species of Mexican Anolis. A significant relationship between dewlap size and seasonality is evident in phylogenetically uncorrected analyses but erodes once phylogeny is accounted for. This loss of strong statistical support for a relationship between a key aspect of dewlap morphology and seasonality also occurs within a species complex (A. sericeus group) that inhabits seasonal and aseasonal environments. Our results fail to support seasonality as a strong driver of evolution of Anolis dewlap size. We discuss the implications of our results and the difficulty of disentangling the strength of single mechanisms on trait evolution when multiple selection pressures are likely at play.

The existence and evolution of morphotypes in Anolis lizards: coexistence patterns, not adaptive radiations, distinguish mainland and island faunas.

The evolution of distinct ecologies and correlated morphologies ("ecomorphs," in combination) among similar species allows sympatric occupation of diverse microhabitats. Particular ecomorphs may evolve repeatedly, that is, convergently, as separate lineages arrive at similar solutions. Caribbean Anolis lizards (anoles) are a classic ecomorph system, particularly well-studied for the diverse morphotypes resulting from adaptive radiations. But few studies have analyzed the equally species-diverse mainland Anolis. Here, we use clustering analyses of nine traits for 336 species of Anolis to objectively identify morphological groups (morphotypes). We analyze the presence of recovered morphotypes on mainland and islands in general and relative to the composition of 76 mainland and 91 island anole assemblages. We test for evolutionary convergence of morphotypes within and between mainland and island environments by mapping our recovered morphotypes onto recent phylogenetic estimates and by analyzing four of our measured traits using program SURFACE. We find that particular morphotypes tend to be restricted to either mainland or island environments. Morphotype diversity and convergence are not concentrated within either island or mainland environments. Morphotype content of assemblages differs between mainland and island areas, with island assemblages displaying greater numbers of morphotypes than mainland assemblages. Taken with recent research, these results suggest a restructuring of one of the classic adaptive radiation stories and a reconsideration of research concerning island-mainland faunal differences. Island radiations of anoles are unexceptional relative to mainland radiations with regard to species count, rates of speciation and phenotypic evolution, morphotype diversity, and rates of convergence. But local island assemblage appear to be more diverse than mainland assemblages. The explanation for this assemblage disparity may reside in one of the classic hypothesized island-mainland environmental differences (i.e., greater numbers of predators/competitors/environmental complexity on the mainland). Similarity between mainland and island anole radiations may indicate exceptional evolution in the anole clade overall or ordinary evolution in an extraordinarily studied clade.

Convergent exaptation and adaptation in solitary island lizards.

Independent evolutionary lineages often display similar characteristics in comparable environments. Three kinds of historical hypotheses could explain this convergence. The first is adaptive and evolutionary: nonrandom patterns may result from analogous evolutionary responses to shared conditions. The second explanation is exaptive and ecological: species may be filtered by their suitability for a particular type of environment. The third potential explanation is a null hypothesis of random colonization from a historically nonrandom source pool. Here we demonstrate that both exaptation and adaptation have produced convergent similarity in different size-related characters of solitary island lizards. Large sexual size dimorphism results from adaptive response to solitary existence; uniform, intermediate size results from ecological filtering of potential colonizers. These results demonstrate the existence of deterministic exaptive convergence and suggest that convergent phenomena may require historical explanations that are ecological as well as evolutionary.

Test of Von Baer's law of the conservation of early development.

One of the oldest and most pervasive ideas in comparative embryology is the perceived evolutionary conservation of early ontogeny relative to late ontogeny. Karl Von Baer first noted the similarity of early ontogeny across taxa, and Ernst Haeckel and Charles Darwin gave evolutionary interpretation to this phenomenon. In spite of a resurgence of interest in comparative embryology and the development of mechanistic explanations for Von Baer's law, the pattern itself has been largely untested. Here, I use statistical phylogenetic approaches to show that Von Baer's law is an unnecessarily complex explanation of the patterns of ontogenetic timing in several clades of vertebrates. Von Baer's law suggests a positive correlation between ontogenetic time and amount of evolutionary change. I compare ranked position in ontogeny to frequency of evolutionary change in rank for developmental events and find that these measures are not correlated, thus failing to support Von Baer's model. An alternative model that postulates that small changes in ontogenetic rank are evolutionarily easier than large changes is tentatively supported.

A study of the utility of convergent characters for phylogeny reconstruction: do ecomorphological characters track evolutionary history in Anolis lizards?

The reconstruction of phylogeny requires homologous similarities across species. Characters that have been shown to evolve quickly or convergently in some species are often considered to be poor phylogenetic markers. Here I evaluate the phylogenetic utility of a set of morphological characters that are correlated with ecology and have been shown to evolve convergently in Anolis lizards in the Greater Antilles. Results of randomization tests suggest that these "ecomorph" characters are adequate phylogenetic markers, both for Anolis in general and for the Greater Antillean species for which ecomorphological convergence was originally documented. Explanations for this result include the presence of ecomorphologically similar species within evolutionary radiations within islands, some monophyly of ecomorphs across islands, and the existence of several species that defy ecomorphological characterization but share phylogenetic similarity in some ecomorph characters.

Anolis marsupialis Taylor 1956, a valid species from southern Pacific Costa Rica (Reptilia, Squamata, Dactyloidae).

The examination of the holotype of Anolis marsupialis Taylor 1956 along with recently collected specimens reveals that A. marsupialis is a valid species. It differs from its closest congeners A. humilis Peters 1863 and A. quaggulus Cope 1885, in male dewlap coloration, scalation, body size, and hemipenial morphology. These findings are supported by preliminary molecular genetic analysis. 

A test for patterns of modularity in sequences of developmental events.

This study presents a statistical test for modularity in the context of relative timing of developmental events. The test assesses whether sets of developmental events show special phylogenetic conservation of rank order. The test statistic is the correlation coefficient of developmental ranks of the N events of the hypothesized module across taxa. The null distribution is obtained by taking correlation coefficients for randomly sampled sets of N events. This test was applied to two datasets, including one where phylogenetic information was taken into account. The events of limb development in two frog species were found to behave as a module.