Is geographic variation within species related to macroevolutionary patterns between species?

The relationship between microevolution and macroevolution is a central topic in evolutionary biology. An aspect of this relationship that remains very poorly studied in modern evolutionary biology is the relationship between within-species geographic variation and among-species patterns of trait variation. Here, we tested the relationship between climate and morphology among and within species in the salamander genus Plethodon. We focus on a discrete colour polymorphism (presence and absence of a red dorsal stripe) that appears to be related to climatic distributions in a common, wide-ranging species (Plethodon cinereus). We find that this trait has been variable among (and possibly within) species for >40 million years. Furthermore, we find a strong relationship among species between climatic variation and within-species morph frequencies. These between-species patterns are similar (but not identical) to those in the broadly distributed Plethodon cinereus. Surprisingly, there are no significant climate-morphology relationships within most other polymorphic species, despite the strong between-species patterns. Overall, our study provides an initial exploration of how within-species geographic variation and large-scale macroevolutionary patterns of trait variation may be related.

Ecological radiation with limited morphological diversification in salamanders.

A major goal of evolutionary biology is to explain morphological diversity among species. Many studies suggest that much morphological variation is explained by adaptation to different microhabitats. Here, we test whether morphology and microhabitat use are related in plethodontid salamanders, which contain the majority of salamander species, and have radiated into a striking diversity of microhabitats. We obtained microhabitat data for 189 species that also had both morphometric and phylogenetic data. We then tested for associations between morphology and microhabitat categories using phylogenetic comparative methods. Associations between morphology and ecology in plethodontids are largely confined to a single clade within one subfamily (Bolitoglossinae), whereas variation in morphology across other plethodontids is unrelated to microhabitat categories. These results demonstrate that ecological radiation and morphological evolution can be largely decoupled in a major clade. The results also offer a striking contrast to lizards, which typically show close relationships between morphology and microhabitat.

Crest evolution in newts: implications for reconstruction methods, sexual selection, phenotypic plasticity and the origin of novelties.

The dorsal crest of newts (Salamandridae) is a novel, phenotypically plastic, sexually selected trait that may evolve in association with complex courtship behaviours. We estimated a near-comprehensive, time-calibrated phylogeny for salamandrids and analysed the evolution of their crests and display behaviour. Different models give conflicting reconstructions for crest evolution, showing that likelihood can estimate incorrect ancestral states with strong statistical support. The best-fitting model suggests that crests evolved once and were lost repeatedly, supporting the hypothesis that sexually selected traits may be frequently lost. We demonstrate the correlated evolution of crests and courtship behaviour and show that species with larger numbers of crest-related traits have larger repertoires of behaviours. We also show that phenotypically plastic morphological traits can be maintained over long macroevolutionary timescales (∼25-48 Myr). Finally, we use salamandrids to address how novel structures may arise, and support a model involving the expansion and subdivision of pre-existing structures.

Bridging the gap between community ecology and historical biogeography: niche conservatism and community structure in emydid turtles.

Historical (phylogenetic) biogeography and community ecology were once integrated as part of the broader study of organismal diversity, but in recent decades have become largely separate disciplines. This is unfortunate because many patterns studied by community ecologists may originate through processes studied by historical biogeographers and vice versa. In this study, we explore the causes of a geographic pattern of community structure (habitat use) in the emydid turtle assemblages of eastern North America, with more semi-terrestrial species of the subfamily Emydinae in the north and more aquatic species of Deirochelyinae in the south. Specifically, we address the factors that prevent northern emydines from invading southern communities. We test for competitive exclusion by examining patterns of range overlap, and test for the role of niche conservatism using analyses of climatic and physiological data based on a multilocus molecular phylogeny. We find no support for competitive exclusion, whereas several lines of evidence support the idea that niche conservatism has prevented northern emydines from dispersing into southern communities. Our results show how understanding the causes of patterns of historical biogeography may help explain patterns of community structure.

Testing for evolutionary trade-offs in a phylogenetic context: ecological diversification and evolution of locomotor performance in emydid turtles.

The evolution of ecological trade-offs is an important component of ecological specialization and adaptive radiation. However, the pattern that would show that evolutionary trade-offs have occurred between traits among species has not been clearly defined. In this paper, we propose a phylogeny-based definition of an evolutionary trade-off, and apply it to an analysis of the evolution of trade-offs in locomotor performance in emydid turtles. We quantified aquatic and terrestrial speed and endurance for up to 16 species, including aquatic, semi-terrestrial and terrestrial emydids. Emydid phylogeny was reconstructed from morphological characters and nuclear and mitochondrial DNA sequences. Surprisingly, we find that there have been no trade-offs in aquatic and terrestrial speed among species. Instead, specialization to aquatic and terrestrial habitats seems to have involved trade-offs in speed and endurance. Given that trade-offs between speed and endurance may be widespread, they may underlie specialization to different habitats in many other groups.

How lizards turn into snakes: a phylogenetic analysis of body-form evolution in anguid lizards.

One of the most striking morphological transformations in vertebrate evolution is the transition from a lizardlike body form to an elongate, limbless (snakelike) body form. Despite its dramatic nature, this transition has occurred repeatedly among closely related species (especially in squamate reptiles), making it an excellent system for studying macroevolutionary transformations in body plan. In this paper, we examine the evolution of body form in the lizard family Anguidae, a clade in which multiple independent losses of limbs have occurred. We combine a molecular phylogeny for 27 species, our morphometric data, and phylogenetic comparative methods to provide the first statistical phylogenetic tests of several long-standing hypotheses for the evolution of snakelike body form. Our results confirm the hypothesized relationships between body elongation and limb reduction and between limb reduction and digit reduction. However, we find no support for the hypothesized sequence going from body elongation to limb reduction to digit loss, and we show that a burrowing lifestyle is not a necessary correlate of limb loss. We also show that similar degrees of overall body elongation are achieved in two different ways in anguids, that these different modes of elongation are associated with different habitat preferences, and that this dichotomy in body plan and ecology is widespread in limb-reduced squamates. Finally, a recent developmental study has proposed that the transition from lizardlike to snakelike body form involves changes in the expression domains of midbody Hox genes, changes that would link elongation and limb loss and might cause sudden transformations in body form. Our results reject this developmental model and suggest that this transition involves gradual changes occurring over relatively long time scales.

Species delimitation in systematics: inferring diagnostic differences between species.

Species are fundamental units in studies of systematics, biodiversity and ecology, but their delimitation has been relatively neglected methodologically. Species are typically circumscribed based on the presence of fixed (intraspecifically invariant or non-overlapping) diagnostic morphological characters which distinguish them from other species. In this paper, we argue that determining whether diagnostic characters are truly fixed with certainty is generally impossible with finite sample sizes and we show that sample sizes of hundreds or thousands of individuals may be necessary to have a reasonable probability of detecting polymorphisms in diagnostic characters at frequencies approaching zero. Instead, we suggest that using a non-zero frequency cut-off may be a more realistic and practical criterion for character-based species delimitation (for example, allowing polymorphisms in the diagnostic characters at frequencies of 5% or less). Given this argument, we then present a simple statistical method to evaluate whether at least one of a set of apparently diagnostic characters is below the frequency cut-off. This method allows testing of the strength of the evidence for species distinctness and is readily applicable to empirical studies.

Adult colloid milium of the eyelid.

PURPOSE: To report a patient with bilateral upper and lower eyelid margin nodules that proved to be adult colloid milium. METHODS: After clinical study, biopsy specimens were obtained and analyzed histologically and ultrastructurally. RESULTS: Adult colloid milium can be diagnosed by clinicopathologic correlation. CONCLUSION: Adult colloid milium should be included in the differential diagnosis of eyelid margin nodules.

Normal cervical spine morphometry and cervical spinal stenosis in asymptomatic professional football players. Plain film radiography, multiplanar computed tomography, and magnetic resonance imaging.

Diagnosis of cervical spinal stenosis or instability rests on the objective findings depicted on static and dynamic radiographs. Before abnormal spinal morphometry can be determined, it is first necessary to establish normal values for the specific patient population being evaluated. Several studies have attempted to establish norms for plain film measurements of the cervical spine in children and adults, but few have applied consistent methods for generating precise measurements. The first part of this study established normal values for cervical spinal morphometry and segmental spinal motion in the elite athlete. The second part of this study determined the most accurate screening method for detecting cervical spinal stenosis. Three sagittal diameters of the cervical spinal canal were compared to determine which represented the smallest midline diameter on static and dynamic radiographs. The Torg ratio was also evaluated as a method to detect significant cervical spinal stenosis and was shown to have a high sensitivity but poor positive predictive value. The study clarified why the ratio yields a large number of false positive cases. From the results of this study, an algorithm has been developed for the evaluation of stenosis of the cervical spine in athletes.

Gastric linitis plastica metastatic to the uvea.

A 59-year-old man underwent total gastrectomy for diffuse, poorly differentiated gastric adenocarcinoma diagnosed as linitis plastica. Loss of vision in the right eye 5 months later due to extensive choroidal tumours was the first indication of metastatic disease. Radiologic studies showed multiple bony metastases. The blind, painful eye was enucleated. Pathological examination of the globe showed massive metastatic mucus-secreting adenocarcinoma of the choroid, with positive immunohistochemical staining for carcinoembryonic antigen (CEA) of the foci of the more highly differentiated neoplastic cells. The plasma CEA level had been normal. The patient died 3 months after enucleation from metastatic disease.

Character analysis in morphological phylogenetics: problems and solutions.

Many aspects of morphological phylogenetics are controversial in the theoretical systematics literature and yet are often poorly explained and justified in empirical studies. In this paper, I argue that most morphological characters describe variation that is fundamentally quantitative, regardless of whether they are coded qualitatively or quantitatively by systematists. Given this view, three fundamental problems in morphological character analysis (definition, delimitation, and ordering of character states) may have a common solution: coding morphological characters as continuous quantitative traits. A new parsimony method (step-matrix gap-weighting, a modification of Thiele's approach) is proposed that allows quantitative traits to be analyzed as continuous variables. The problem of scaling or weighting quantitative characters relative to qualitative characters (and to each other) is reviewed, and three possible solutions are described. The new coding method is applied to data from hoplocercid lizards, and the results show the sensitivity of phylogenetic conclusions to different scaling methods. Although some authors reject the use of continuous, overlapping, quantitative characters in phylogenetic analysis, quantitative data from hoplocercid lizards that are coded using the new approach contain significant phylogenetic structure and exhibit levels of homoplasy similar to those seen in data that are coded qualitatively.

Combining data sets with different phylogenetic histories.

The possibility that two data sets may have different underlying phylogenetic histories (such as gene trees that deviate from species trees) has become an important argument against combining data in phylogenetic analysis. However, two data sets sampled for a large number of taxa may differ in only part of their histories. This is a realistic scenario and one in which the relative advantages of combined, separate, and consensus analysis become much less clear. I propose a simple methodology for dealing with this situation that involves (1) partitioning the available data to maximize detection of different histories, (2) performing separate analyses of the data sets, and (3) combining the data but considering questionable or unresolved those parts of the combined tree that are strongly contested in the separate analyses (and which therefore may have different histories) until a majority of unlinked data sets support one resolution over another. In support of this methodology, computer simulations suggest that (1) the accuracy of combined analysis for recovering the true species phylogeny may exceed that of either of two separately analyzed data sets under some conditions, particularly when the mismatch between phylogenetic histories is small and the estimates of the underlying histories are imperfect (few characters, high homoplasy, or both) and (2) combined analysis provides a poor estimate of the species tree in areas of the phylogenies with different histories but gives an improved estimate in regions that share the same history. Thus, when there is a localized mismatch between the histories of two data sets, the separate, consensus, and combined analyses may all give unsatisfactory results in certain parts of the phylogeny. Similarly, approaches that allow data combination only after a global test of heterogeneity will suffer from the potential failings of either separate or combined analysis, depending on the outcome of the test. Excision of conflicting taxa is also problematic, in that doing so may obfuscate the position of conflicting taxa within a larger tree, even when their placement is congruent between data sets. Application of the proposed methodology to molecular and morphological data sets for Sceloporus lizards is discussed.

Does adding characters with missing data increase or decrease phylogenetic accuracy?

Missing data are a widely recognized nuisance factor in phylogenetic analyses, and the fear of missing data may deter systematists from including characters that are highly incomplete. In this paper, I used simulations to explore the consequences of including sets of characters that contain missing data. More specifically, I tested whether the benefits of increasing the number of characters outweigh the costs of adding missing data cells to a matrix. The results show that the addition of a set of characters with missing data is generally more likely to increase phylogenetic accuracy than decrease it, but the potential benefits of adding these characters quickly disappear as the proportion of missing data increases. Furthermore, despite the overall trend, adding characters with missing data does decrease accuracy in some cases. In these situations, the missing data entries are not themselves misleading, but their presence may mimic the effects of limited taxon sampling, which can positively mislead. Criteria are discussed for predicting whether adding characters with missing data may increase or decrease accuracy. The results of this study also suggest that accuracy can be increased to a surprising degree by (1) "filling the holes" in a data matrix as much as possible (even when relatively few taxa are missing data), and (2) adding fewer characters scored for all taxa rather than adding a larger number of characters known for fewer taxa. Missing data can also be eliminated from an analysis through the exclusion of incomplete taxa rather than incomplete characters, but this approach may reduce the usefulness of the analysis and (in some cases) the accuracy of the estimated trees.

The accuracy of methods for coding and sampling higher-level taxa for phylogenetic analysis: a simulation study.

Many phylogenetic analyses, particularly morphological studies, use higher taxa (e.g., genera, families) rather than species as terminal taxa. This general approach requires dealing with interspecific variation among the species that make up the higher taxon. In this paper, I review different parsimony methods for coding and sampling higher taxa and compare their relative accuracies using computer simulations. Despite their widespread use, methods that involve coding higher taxa as terminals perform poorly in simulations, relative to splitting up the higher taxa and using species as terminals. Among the methods that use higher taxa as terminals, coding a taxon based on the most common condition among the included species (majority or modal coding) is generally more accurate than other coding methods, such as coding taxa as missing or polymorphic. The success of the majority method, and results of further simulations, suggest that in many cases "common equals primitive" within variable taxa, at least for low and intermediate rates of character change. The fixed-only method (excluding variable characters) performs very poorly, a result that is indirectly supported by analyses of published data for squamate reptiles. Sampling only a single species per higher taxon also yields low accuracy under many conditions. Along with recent studies of intraspecific polymorphism, the results of this study show the general importance of (1) including characters despite variation within taxa and (2) using methods that incorporate detailed information on the distribution of states within variable taxa.

War of the Iguanas: conflicting molecular and morphological phylogenies and long-branch attraction in iguanid lizards.

Recent studies based on different types of data (i.e., morphology, molecules) have found strongly conflicting phylogenies for the genera of iguanid lizards but have been unable to explain the basis for this incongruence. We reanalyze published data from morphology and from the mitochondrial ND4, cytochrome b, 12S, and 16S genes to explore the sources of incongruence and resolve these conflicts. Much of the incongruence centers on the genus Cyclura, which is the sister taxon of Iguana, according to parsimony analyses of the morphology and the ribosomal genes, but is the sister taxon of all other Iguanini, according to the protein-coding genes. Maximum likelihood analyses show that there has been an increase in the rate of nucleotide substitution in Cyclura in the two protein-coding genes (ND4 and cytochrome b), although this increase is not as clear when parsimony is used to estimate branch lengths. Parametric simulations suggest that Cyclura may be misplaced by the protein-coding genes as a result of long-branch attraction; even when Cyclura and Iguana are sister taxa in a simulated phylogeny, Cyclura is still placed as the basal member of the Iguanini by parsimony analysis in 55% of the replicates. A similar long-branch attraction problem may also exist in the morphological data with regard to the placement of Sauromalus with the Galápagos iguanas (Amblyrhynchus and Conolophus). The results have many implications for the analysis of diverse data sets, the impact of long branches on parsimony and likelihood methods, and the use of certain protein-coding genes in phylogeny reconstruction.

Phylogenetic analysis and intraspecific variation: performance of parsimony, likelihood, and distance methods.

Intraspecific variation is abundant in all types of systematic characters but is rarely addressed in simulation studies of phylogenetic method performance. We compared the accuracy of 15 phylogenetic methods using simulations to (1) determine the most accurate method(s) for analyzing polymorphic data (under simplified conditions) and (2) test if generalizations about the performance of phylogenetic methods based on previous simulations of fixed (nonpolymorphic) characters are robust to a very different evolutionary model that explicitly includes intraspecific variation. Simulated data sets consisted of allele frequencies that evolved by genetic drift. The phylogenetic methods included eight parsimony coding methods, continuous maximum likelihood, and three distance methods (UPGMA, neighbor joining, and Fitch-Margoliash) applied to two genetic distance measures (Nei's and the modified Cavalli-Sforza and Edwards chord distance). Two sets of simulations were performed. The first examined the effects of different branch lengths, sample sizes (individuals sampled per species), numbers of characters, and numbers of alleles per locus in the eight-taxon case. The second examined more extensively the effects of branch length in the four-taxon, two-allele case. Overall, the most accurate methods were likelihood, the additive distance methods (neighbor joining and Fitch-Margoliash), and the frequency parsimony method. Despite the use of a very different evolutionary model in the present article, many of the results are similar to those from simulations of fixed characters. Similarities include the presence of the "Felsenstein zone," where methods often fail, which suggests that long-branch attraction may occur among closely related species through genetic drift. Differences between the results of fixed and polymorphic data simulations include the following: (1) UPGMA is as accurate or more accurate than nonfrequency parsimony methods across nearly all combinations of branch lengths, and (2) likelihood and the additive distance methods are not positively misled under any combination of branch lengths tested (even when the assumptions of the methods are violated and few characters are sampled). We found that sample size is an important determinant of accuracy and affects the relative success of methods (i.e., distance and likelihood methods outperform parsimony at small sample sizes). Attempts to generalize about the behavior of phylogenetic methods should consider the extreme examples offered by fixed-mutation models of DNA sequence data and genetic-drift models of allele frequencies.