Maximum Likelihood Ancestral State Reconstructions Research Articles

The systematics and evolution of the Sri Lankan rainforest land snail Corilla: New insights from RADseq-based phylogenetics

The stylommatophoran land-snail genus Corilla is endemic to Sri Lanka and India’s Western Ghats. On the basis of habitat distribution and shell morphology, the 10 extant Sri Lankan species fall into two distinct groups, lowland and montane. Here, we use phylogenetic analyses of restriction-site-associated DNA sequencing (RADseq) data and ancestral-state reconstructions of habitat association and shell morphology to clarify the systematics and evolution of Sri Lankan Corilla. Our dataset consists of 9 species of Corilla. Phylogenetic analyses were based on 88 assemblies (9,604–4,132,850 bp) generated by the RADseq assembler ipyrad, using four parameter combinations and different levels of missing data. Trees were inferred using a maximum likelihood (ML) approach. Ancestral states were reconstructed using maximum parsimony (MP) and ML approaches, with 1 binary state character analysed for habitat association (lowland vs montane) and 6 binary state characters analysed for shell morphology (shape, colour, lip width, length of upper palatal folds, orientation of upper palatal folds and collabral sculpture). Over a wide range of missing data (40–87 % missing individuals per locus) and assembly sizes (62,279–4,132,850 bp), nearly all trees conformed to one of two topologies (A and B), most relationships were strongly supported and total branch support approached the maximal value. Apart from the position of Corilla odontophora ‘south’, topologies A and B showed similar, well-resolved relationships at and above the species level. Our study agrees with the shell-based taxonomy of C. adamsi, C. beddomeae, C. carabinata, C. colletti and C. humberti (all maximally supported as monophyletic species). It shows that C. erronea and C. fryae constitute a single relatively widespread species (for which the valid name is C. erronea) and that the names C. gudei and C. odontophora each apply to at least two distinct, yet conchologically-cryptic species. The MP and ML ancestral-state reconstructions yielded broadly similar results and provide firm evidence that diversification in Sri Lankan Corilla has involved evolutionary convergence in the shell morphology of lowland lineages, with a pale shell and wide lip having evolved on at least two separate occasions (in C. carabinata and C. colletti) from montane ancestors having a dark, narrow-lipped shell.

Testing for a facultative locomotor mode in the acquisition of archosaur bipedality.

Bipedal locomotion is a defining characteristic of humans and birds and has a profound effect on how these groups interact with their environment. Results from extensive hominin research indicate that there exists an intermediate stage in hominin evolution—facultative bipedality—between obligate quadrupedality and obligate bipedality that uses both forms of locomotion. It is assumed that archosaur locomotor evolution followed this sequence of functional and hence character-state evolution. However, this assumption has never been tested in a broad phylogenetic context. We test whether facultative bipedality is a transitionary state of locomotor mode evolution in the most recent early archosaur phylogenies using maximum-likelihood ancestral state reconstructions for the first time. Across a total of seven independent transitions from quadrupedality to a state of obligate bipedality, we find that facultative bipedality exists as an intermediary mode only once, despite being acquired a total of 14 times. We also report more independent acquisitions of obligate bipedality in archosaurs than previously hypothesized, suggesting that locomotor mode is more evolutionarily fluid than expected and more readily experimented with in these reptiles.

Hip joint articular soft tissues of non-dinosaurian Dinosauromorpha and early Dinosauria: evolutionary and biomechanical implications for Saurischia

ABSTRACTDinosauromorphs evolved a wide diversity of hind limb skeletal morphologies, suggesting highly divergent articular soft tissue anatomies. However, poor preservation of articular soft tissues in fossils has hampered any follow-on functional inferences. We reconstruct the hip joint soft tissue anatomy of non-dinosaurian dinosauromorphs and early dinosaurs using osteological correlates derived from extant sauropsids and infer trends in character transitions along the theropod and sauropodomorph lineagues. Femora and pelves of 107 dinosauromorphs and outgroup taxa were digitized using 3D imaging techniques. Key transitions were estimated using maximum likelihood ancestral state reconstruction. The hips of dinosauromorphs possessed wide a disparity of soft tissue morphologies beyond the types and combinations exhibited by extant archosaurs. Early evolution of the dinosauriform hip joint was characterized by the retention of a prominent femoral hyaline cartilage cone in post-neonatal individuals, with the cartilage cone independently reduced within theropods and sauropodomorphs. The femur of Dinosauriformes possessed a fibrocartilage sleeve on the metaphysis, which surrounded a hyaline core. The acetabulum of Dinosauriformes possessed distinct labrum and antitrochanter structures. In sauropodomorphs, hip congruence was maintained by thick hyaline cartilage on the femoral head, whereas theropods relied on acetabular tissues such as ligaments and articular pads. In particular, the craniolaterally ossified hip capsule of non-Avetheropoda neotheropods permitted mostly parasagittal femoral movements. These data indicate that the dinosauromorph hip underwent mosaic evolution within the saurischian lineage and that sauropodomorphs and theropods underwent both convergence and divergence in articular soft tissues, correlated with transitions in body size, locomotor posture, and joint loading.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVPCitation for this article: Tsai, H. P., K. M. Middleton, J. R. Hutchinson, and C. M. Holliday. 2018. Hip joint articular soft tissues of non-dinosaurian Dinosauromorpha and early Dinosauria: evolutionary and biomechanical implications for Saurischia. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2017.1427593.

Phylogeny of the order Phyllachorales (Ascomycota, Sordariomycetes): among and within order relationships based on five molecular loci.

The order Phyllachorales (Pezizomycotina, Ascomycota) is a group of biotrophic, obligate plant parasitic fungi with a tropical distribution and high host specificity. Traditionally two families are recognised within this order: Phyllachoraceae and Phaeochoraceae, based mostly on morphological and host characteristics. Currently, the position of the order within the class Sordariomycetes is inconclusive, as well as the monophyly of the order, and its internal phylogenetic structure. Here we present a phylogeny of the order Phyllachorales based on sequence data of 29 species with a broad host range resulting from a wide geographical sampling. We inferred Maximum Likelihood and Bayesian phylogenies from data of five DNA regions: nrLSU rDNA, nrSSU rDNA, ITS rDNA, and the protein coding genes RPB2, and TEF1. We found that the order Phyllachorales is monophyletic and related to members of the subclass Sordariomycetidae within Sordariomycetes. Within the order, members of the family Phaeochoraceae form a monophyletic group, and the family Phyllachoraceae is split into two lineages. Maximum Likelihood ancestral state reconstructions indicate that the ancestor of Phyllachorales had a monocotyledonous host plant, immersed perithecia, and a black stroma. Alternative states of these characters evolved multiple times independently within the order. Based on our results we redefine the family Phyllachoraceae and propose the new family Telimenaceae with Telimena erythrinae as type species, resulting in three families in the order. Species of Telimena spp. occur in several monocotyledonous and eudicotyledonous host plants except Poaceae, and generally have enlarged black pseudostroma around the perithecia, a character not present in species of Phyllachoraceae.

Lower Ilium Evolution in Apes and Hominins.

Elucidating the pelvic morphology of the Pan-Homo last common ancestor (LCA) is crucial for understanding ape and human evolution. The pelvis of Ardipithecus ramidus has been the basis of controversial interpretations of the LCA pelvis. In particular, it was proposed that the lower ilium became elongate independently in the orangutan and chimpanzee clades, making these taxa poor analogues for the pelvis of the LCA. This study examines the variation in relative lower ilium height between and within living and fossil hominoid species (and other anthropoids), and models its evolution using available fossil hominoids as calibration points. We find nuanced differences in relative lower ilium height among living hominoids, particularly in regards to gorillas, which do not have elongate lower ilia (because they are likely to represent the plesiomorphic hominoid condition for this trait). We also show that differences in relative lower ilium height among hominoid taxa are not readily explained by differences in size between species. Our maximum likelihood ancestral state reconstructions support inferences that chimpanzees (Pan troglodytes in particular) and orangutans evolved their elongate lower ilia independently. We also find that the predicted lower ilium height of the Pan-Homo LCA is shorter than all great apes except gorillas. This study adds to a growing body of evidence that finds different regions of the body show different evolutionary histories in different hominoids, and underscores that the unique combinations of morphologies of each modern and fossil hominoid species should be considered when reconstructing the mosaic nature of the Pan-Homo LCA. Anat Rec, 300:828-844, 2017. © 2017 Wiley Periodicals, Inc.

Rapid maximum likelihood ancestral state reconstruction of continuous characters: A rerooting-free algorithm.

Ancestral state reconstruction is a method used to study the evolutionary trajectories of quantitative characters on phylogenies. Although efficient methods for univariate ancestral state reconstruction under a Brownian motion model have been described for at least 25 years, to date no generalization has been described to allow more complex evolutionary models, such as multivariate trait evolution, non‐Brownian models, missing data, and within‐species variation. Furthermore, even for simple univariate Brownian motion models, most phylogenetic comparative R packages compute ancestral states via inefficient tree rerooting and full tree traversals at each tree node, making ancestral state reconstruction extremely time‐consuming for large phylogenies. Here, a computationally efficient method for fast maximum likelihood ancestral state reconstruction of continuous characters is described. The algorithm has linear complexity relative to the number of species and outperforms the fastest existing R implementations by several orders of magnitude. The described algorithm is capable of performing ancestral state reconstruction on a 1,000,000‐species phylogeny in fewer than 2 s using a standard laptop, whereas the next fastest R implementation would take several days to complete. The method is generalizable to more complex evolutionary models, such as phylogenetic regression, within‐species variation, non‐Brownian evolutionary models, and multivariate trait evolution. Because this method enables fast repeated computations on phylogenies of virtually any size, implementation of the described algorithm can drastically alleviate the computational burden of many otherwise prohibitively time‐consuming tasks requiring reconstruction of ancestral states, such as phylogenetic imputation of missing data, bootstrapping procedures, Expectation‐Maximization algorithms, and Bayesian estimation. The described ancestral state reconstruction algorithm is implemented in the Rphylopars functions anc.recon and phylopars.

Molecular phylogeny, analysis of character evolution, and submersible collections enable a new classification of a diverse group of gobies (Teleostei: Gobiidae:Nes subgroup), including nine new species and four new genera

The Nes subgroup of the Gobiosomatini (Teleostei: Gobiiformes: Gobiidae) is an ecologically diverse clade of fishes endemic to the tropical western Atlantic and eastern Pacific oceans. It has been suggested that morphological characters in gobies tend to evolve via reduction and loss associated with miniaturization, and this, coupled with the parallel evolution of adaptations to similar microhabitats, may lead to homoplasy and ultimately obscure our ability to discern phylogenetic relationships using morphological characters alone. This may be particularly true for the Nes subgroup of gobies, where several genera that are diagnosed by ‘reductive characters’ have been shown to be polyphyletic. Here we present the most comprehensive phylogeny to date of the Nes subgroup using mitochondrial and nuclear sequence data. We then evaluate the congruence between the distribution of morphological characters and our molecular tree using maximum-likelihood ancestral state reconstruction, and test for phylogenetic signal in characters using Pagel's λ tree transformations (Nature, 401, 1999 and 877). Our results indicate that all of the characters previously used to diagnose genera of the Nes subgroup display some degree of homoplasy with respect to our molecular tree; however, many characters display considerable phylogenetic signal and thus may be useful in diagnosing genera when used in combination with other characters. We present a new classification for the group in which all genera are monophyletic and in most cases diagnosed by combinations of morphological characters. The new classification includes four new genera and nine new species described here, many of which were collected from rarely sampled deep Caribbean reefs using manned submersibles. The group now contains 38 species in the genera Carrigobius gen. nov., Chriolepis, Eleotrica, Gobulus, Gymneleotris, Nes, Paedovaricus gen. nov., Pinnichthys gen. nov., Psilotris, and Varicus. Lastly, we provide a key to all named species of the Nes subgroup along with photographs and illustrations to aid in identification.

Peculiar macrophagous adaptations in a new Cretaceous pliosaurid.

During the Middle and Late Jurassic, pliosaurid plesiosaurs evolved gigantic body size and a series of craniodental adaptations that have been linked to the occupation of an apex predator niche. Cretaceous pliosaurids (i.e. Brachaucheninae) depart from this morphology, being slightly smaller and lacking the macrophagous adaptations seen in earlier forms. However, the fossil record of Early Cretaceous pliosaurids is poor, concealing the evolution and ecological diversity of the group. Here, we report a new pliosaurid from the Late Hauterivian (Early Cretaceous) of Russia. Phylogenetic analyses using reduced consensus methods recover it as the basalmost brachauchenine. This pliosaurid is smaller than other derived pliosaurids, has tooth alveoli clustered in pairs and possesses trihedral teeth with complex serrated carinae. Maximum-likelihood ancestral state reconstruction suggests early brachauchenines retained trihedral teeth from their ancestors, but modified this feature in a unique way, convergent with macrophagous archosaurs or sphenacodontoids. Our findings indicate that Early Cretaceous marine reptile teeth with serrated carinae cannot be unequivocally assigned to metriorhynchoid crocodylomorphs. Furthermore, they extend the known diversity of dental adaptations seen in Sauropterygia, the longest lived clade of marine tetrapods.

Comparative Morphology and Evolution of Genital Papillae in a Genus of Darters (Percidae:Etheostoma)

A morphological study of female genital papillae of Etheostoma was conducted to examine the evolution of papillae as predicted by molecular phylogenies, and to examine correlations between papilla morphology and spawning behaviors and oviposition. Thirteen characters were used to describe variation in papillae in 128 species. Based on maximum likelihood ancestral state reconstructions, we corroborated several molecular phylogenetic hypotheses with morphology and developed hypotheses on several functional traits/adaptive traits and their associations with spawning behaviors. Papillar synapomorphies supported a close relationship between Allohistium and (Etheostoma + Nanostoma) + Ulocentra, a monophyletic Catonotus, and a sister-group relationship between E. vitreum and Boleosoma. Results suggest that the most recent common ancestor of Etheostoma buried eggs and had a simple tube with a distal, posteriorly oriented genital pore. All egg-burying species, except species of Nothonotus, have tube papillae that ...

Complete forelimb myology of the basal theropod dinosaur Tawa hallae based on a novel robust muscle reconstruction method.

The forelimbs of nonavian theropod dinosaurs have been the subject of considerable study and speculation due to their varied morphology and role in the evolution of flight. Although many studies on the functional morphology of a limb require an understanding of its musculature, comparatively little is known about the forelimb myology of theropods and other bipedal dinosaurs. Previous phylogenetically based myological reconstructions have been limited to the shoulder, restricting their utility in analyses of whole-limb function. The antebrachial and manual musculature in particular have remained largely unstudied due to uncertain muscular homologies in archosaurs. Through analysis of the musculature of extant taxa in a robust statistical framework, this study presents new hypotheses of homology for the distal limb musculature of archosaurs and provides the first complete reconstruction of dinosaurian forelimb musculature, including the antebrachial and intrinsic manual muscles. Data on the forelimb myology of a broad sample of extant birds, crocodylians, lizards, and turtles were analyzed using maximum likelihood ancestral state reconstruction and examined together with the osteology of the early theropod Tawa hallae from the Late Triassic of New Mexico to formulate a complete plesiomorphic myology for the theropod forelimb. Comparisons with previous reconstructions show that the shoulder musculature of basal theropods is more similar to that of basal ornithischians and sauropodomorphs than to that of dromaeosaurids. Greater development of the supracoracoideus and deltoideus musculature in theropods over other bipedal dinosaurs correlates with stronger movements of the forelimb at the shoulder and an emphasis on apprehension of relatively large prey. This emphasis is further supported by the morphology of the antebrachium and the intrinsic manual musculature, which exhibit a high degree of excursion and a robust morphology well-suited for powerful digital flexion. The forelimb myology of Tawa established here helps infer the ancestral conformation of the forelimb musculature and the osteological correlates of major muscle groups in early theropods. These data are critical for investigations addressing questions relating to the evolution of specialized forelimb function across Theropoda.

Water barriers and intra‐island isolation contribute to diversification in the insular Aethopyga sunbirds (Aves: Nectariniidae)

AbstractAimColonization and subsequent isolation across deep‐water barriers is thought to be the primary driver of diversification in insular birds. Shallow‐water barriers and intra‐island isolation are less well‐documented drivers of avian diversification. We examined the relative roles of different geographical barriers in the diversification of Aethopyga sunbirds, a widespread Southeast Asian genus that has its greatest diversity in the Philippine Archipelago.LocationPhilippines, Southeast Asia, Wallacea.MethodsWe reconstructed the phylogenetic relationships among Aethopyga sunbirds with mitochondrial and nuclear DNA sequences. Phylogeny was inferred using concatenated and coalescent frameworks, implemented in maximum likelihood and Bayesian analyses. We used maximum likelihood ancestral state reconstructions to examine the ancestral distribution and colonization history of Aethopyga. To determine whether the diversification at each node occurred within a continent, across a shallow‐water barrier, across a deep‐water barrier or within an island, we used a series of statements based on the phylogeny, current distribution of species and bathymetric reconstructions.ResultsAncestral state reconstructions inferred that the core Aethopyga ancestor was continental, and that the diversity of Aethopyga on oceanic islands is the result of three or four independent colonization events. Dispersal and subsequent isolation across deep‐water barriers was the most common mode of diversification in insular Aethopyga, although intra‐island isolation contributed to diversity, producing a small montane radiation within Mindanao. Analyses inferred only a single unequivocal event of diversification across a shallow‐water barrier. Deep molecular divergences between phenotypically distinct subspecies suggested that the taxonomy of Aethopyga is overly conservative and obscures biogeographical patterns. We recommend elevating five subspecies, all of which are endemic to the Philippines, to full species.Main conclusionsIn addition to corroborating the importance of isolation across deep‐water barriers, these data also underscore a potential role for additional isolating mechanisms in the generation of biodiversity on oceanic islands. A clade of four montane Aethopyga taxa evolved in situ within the Mindanao sky‐island system, an exception to the paradigm that birds do not diversify within the geographical confines of oceanic islands.

Combined Morphological and Molecular Phylogeny of the Clusioid Clade (Malpighiales) and the Placement of the Ancient Rosid MacrofossilPaleoclusia

Premise of research. The clusioid clade is a member of the large rosid order Malpighiales and contains ∼1900 species in five families: Bonnetiaceae, Calophyllaceae, Clusiaceae sensu stricto (s.s.), Hypericaceae, and Podostemaceae. Despite recent efforts to clarify their phylogenetic relationships using molecular data, no such data are available for several critical taxa, including especially Hypericum ellipticifolium (previously recognized in Lianthus), Lebrunia, Neotatea, Thysanostemon, and the second-oldest rosid fossil (∼90 Ma), Paleoclusia chevalieri. Here, we (i) assess congruence between phylogenies inferred from morphological and molecular data, (ii) analyze morphological and molecular data simultaneously to place taxa lacking molecular data, and (iii) use ancestral state reconstructions (ASRs) to examine the evolution of traits that have been important for circumscribing clusioid taxa and to explore the placement of Paleoclusia.Methodology. We constructed a morphological data set including 69 characters and 81 clusioid species (or species groups). These data were analyzed individually and in combination with a previously published molecular data set of four genes (plastid matK, ndhF, and rbcL and mitochondrial matR) using parsimony, maximum likelihood (ML), and Bayesian inference. We used ML ASRs to infer the evolution of morphological characters.Pivotal results. Our phylogeny inferred from morphology alone was poorly supported but largely in agreement with molecular data. Moreover, our combined analyses were much better supported and largely confirm taxonomic hypotheses regarding relationships of extant taxa newly included here. The extinct Paleoclusia was placed as a member of stem group Clusiaceae s.s. or within crown group Clusiaceae s.s. as sister to one of its two major subclades.Conclusions. Despite poor overall bootstrap support for the placement of Paleoclusia, ancestral character state reconstructions are generally in agreement with our placements. Our recommendation is that Paleoclusia be treated as either a minimum stem group or a crown group age constraint of Clusiaceae s.s.

A molecular phylogeny of black-tyrants (Tyrannidae:Knipolegus) reveals strong geographic patterns and homoplasy in plumage and display behavior

ABSTRACT. We present the first molecular phylogenetic hypothesis for Knipolegus (black-tyrants), a widespread genus of South American tyrant-flycatchers, based on nuclear and mitochondrial DNA sequences. Bayesian and maximum-likelihood analyses support three clades within Knipolegus, one confined to northern South America, one confined to southeast Brazil, and one confined to the Southern Cone and southern Andes. Within each clade, two or more species are broadly sympatric or parapatric, overlapping in general distribution but differing in habitat specialization. Maximum-likelihood ancestral state reconstructions using an equal-rate stochastic model support a single origin of austral migration in the southern group. Contrasting with these strong geographic patterns, ancestral state reconstructions of plumage and display evolution were more complex, with multiple inferred character-state changes. Ancestral state reconstructions suggest a sexually dimorphic ancestor of Knipolegus, and sexually similar pluma...

Evolution of anatomical and physiological specialization in the compound eyes of stomatopod crustaceans

Stomatopod crustaceans have complex and diverse visual systems. Among their many unique features are a specialized ommatidial region (the midband) that enables the eye to have multiple overlapping visual fields, as well as sets of spectral filters that are intercalated at two levels between tiers of photoreceptors involved in polychromatic color vision. Although the physiology and visual function of stomatopod eyes have been studied for many years, how these unique visual features originated and diversified is still an open question. In order to investigate how stomatopods have attained the current complexity in visual function, we have combined physiological and morphological information (e.g. number of midband rows, number of filters in the retina, and the spectral properties of filters) with new phylogenetic analyses of relationships among species based on nucleotide sequence data from two nuclear (18S and 28S rDNA) and two mitochondrial [16S and cytochrome oxidase I (COI)] genes. Based on our recovered phylogenetic relationships among species, we propose two new superfamilies within the Stomatopoda: Hemisquilloidea and Pseudosquillodea. Maximum likelihood ancestral state reconstructions indicate that ancestral stomatopod eyes contained six midband rows and four intrarhabdomal filters, illustrating that the visual physiological complexity originated early in stomatopod evolutionary history. While the two distal filters contain conservative sets of filter pigments, the proximal filters show more spectral diversity in filter types, particularly in midband row 2, and are involved in tuning the color vision system to the photic environment. In particular, a set of related gonodactyloid families (Gonodactylidae, Protosquillidae, Takuidae) inhabiting shallow, brightly lit coral reef waters contain the largest diversity of filter pigments, which are spectrally placed relative to the underlying photoreceptors to take advantage of the broad spectrum of light available in the environment.

Evolution of lamina anatomy in the palm family (Arecaceae)

The unique properties of tree building in Arecaceae strongly constrain their architectural lability. Potentially compensating for this limitation, the extensive diversification of leaf anatomical structure within palms involves many characters whose alternate states may confer disparate mechanical or physiological capabilities. In the context of a recent global palm phylogeny, we analyzed the evolution of 10 such lamina anatomical characters and leaf morphology of 161 genera, conducting parsimony and maximum likelihood ancestral state reconstructions, as well as tests of correlated evolution. Lamina morphology evolves independently from anatomy. Although many characters do optimize as synapomorphic for major clades, anatomical evolution is highly homoplasious. Nevertheless, it is not random: analyses indicate the recurrent evolution of different cohorts of correlated character states. Notable are two surface layer (epidermis and hypodermis) types: (1) a parallel-laminated type of rectangular epidermal cells with sinuous anticlinal walls, with fibers present in the hypodermis and (2) a cross-laminated type of hexagonal cells in both layers. Correlated with the cross-laminated type is a remarkable decrease in the volume fraction of fibers, accompanied by changes in the architecture and sheath cell type of the transverse veins. We discuss these and other major patterns of anatomical evolution in relation to their biomechanical and ecophysiological significance.

Gene Duplication Is an Evolutionary Mechanism for Expanding Spectral Diversity in the Long-Wavelength Photopigments of Butterflies

Butterfly long-wavelength (L) photopigments are interesting for comparative studies of adaptive evolution because of the tremendous phenotypic variation that exists in their wavelength of peak absorbance (lambda(max) value). Here we present a comprehensive survey of L photopigment variation by measuring lambda(max) in 12 nymphalid and 1 riodinid species using epi-microspectrophotometry. Together with previous data, we find that L photopigment lambda(max) varies from 510-565 nm in 22 nymphalids, with an even broader 505- to 600-nm range in riodinids. We then surveyed the L opsin genes for which lambda(max) values are available as well as from related taxa and found 2 instances of L opsin gene duplication within nymphalids, in Hermeuptychia hermes and Amathusia phidippus, and 1 instance within riodinids, in the metalmark butterfly Apodemia mormo. Using maximum parsimony and maximum likelihood ancestral state reconstructions to map the evolution of spectral shifts within the L photopigments of nymphalids, we estimate the ancestral pigment had a lambda(max) = 540 nm +/- 10 nm standard error and that blueshifts in wavelength have occurred at least 4 times within the family. We used ancestral state reconstructions to investigate the importance of several amino acid substitutions (Ile17Met, Ala64Ser, Asn70Ser, and Ser137Ala) previously shown to have evolved under positive selection that are correlated with blue spectral shifts. These reconstructions suggest that the Ala64Ser substitution has indeed occurred along the newly identified blueshifted L photopigment lineages. Substitutions at the other 3 sites may also be involved in the functional diversification of L photopigments. Our data strongly suggest that there are limits to the evolution of L photopigment spectral shifts among species with only one L opsin gene and that opsin gene duplication broadens the potential range of lambda(max) values.

A Genomic Fossil Reveals Key Steps in Hemoglobin Loss by the Antarctic Icefishes

Antarctic icefishes are the only vertebrates that do not have hemoglobin and erythrocytes in their blood. These startling phenotypes are associated in several icefish species with deletions of juvenile and adult globin loci, which in red-blooded teleosts are typically composed of tightly linked pairs of alpha- and beta-globin genes. It is unknown if the loss of hemoglobin expression in icefishes was the direct result of such deletions or if other mutational events compromised globin chain synthesis prior to globin gene loss. In this study, we show that 15 of the 16 icefish species have lost the adult beta-globin gene but retain a truncated alpha-globin pseudogene. Surprisingly, a phylogenetically derived icefish species, Neopagetopsis ionah, possesses a complete, but nonfunctional, adult alphabeta-globin complex. This cluster contains 2 distinct beta-globin pseudogenes whose phylogenetic origins span the entire Antarctic notothenioid radiation, consistent with an origin via introgression. Maximum likelihood ancestral state reconstruction supports a scenario of icefish globin gene evolution that involves a single loss of the transcriptionally active adult alphabeta-globin cluster prior to the diversification of the extant species in the clade. Through lineage sorting of ancestral polymorphism, 2 types of alleles became fixed in the clade: 1) the alpha-globin pseudogene of the majority of species and 2) the inactive alphabeta-globin complex of N. ionah. We conclude that the globin pseudogene complex of N. ionah is a "genomic fossil" that reveals key intermediate steps on the pathway to loss of hemoglobin expression by all icefish species.

NICHE EVOLUTION AND ADAPTIVE RADIATION: TESTING THE ORDER OF TRAIT DIVERGENCE

In the course of an adaptive radiation, the evolution of niche parameters is of particular interest for understanding modes of speciation and the consequences for coexistence of related species within communities. We pose a general question: In the course of an evolutionary radiation, do traits related to within-community niche differences (alpha niche) evolve before or after differentiation of macrohabitat affinity or climatic tolerances (beta niche)? Here we introduce a new test to address this question, based on a modification of the method of independent contrasts. The divergence order test (DOT) is based on the average age of the nodes on a tree, weighted by the absolute magnitude of the contrast at each node for a particular trait. The comparison of these weighted averages reveals whether large divergences for one trait have occurred earlier or later in the course of diversification, relative to a second trait; significance is determined by bootstrapping from maximum-likelihood ancestral state reconstructions. The method is applied to the evolution of Ceanothus, a woody plant group in California, in which co-occurring species exhibit significant differences in a key leaf trait (specific leaf area) associated with contrasting physiological and life history strategies. Co-occurring species differ more for this trait than expected under a null model of community assembly. This alpha niche difference evolved early in the divergence of two major subclades within Ceanothus, whereas climatic distributions (beta niche traits) diversified later within each of the subclades. However, rapid evolution of climate parameters makes inferences of early divergence events highly uncertain, and differentiation of the beta niche might have taken place throughout the evolution of the group, without leaving a clear phylogenetic signal. Similar patterns observed in several plant and animal groups suggest that early divergence of alpha niche traits might be a common feature of niche evolution in many adaptive radiations.