Ancestral Character State Reconstruction Research Articles

A Burmese amber fossil of <i>Radula</i> (Porellales, Jungermanniopsida) provides insights into the Cretaceous evolution of epiphytic lineages of leafy liverworts

Abstract. DNA-based divergence time estimates suggested major changes in the composition of epiphyte lineages of liverworts during the Cretaceous; however, evidence from the fossil record is scarce. We present the first Cretaceous fossil of the predominantly epiphytic leafy liverwort genus Radula in ca. 100 Myr old Burmese amber. The fossil's exquisite preservation allows first insights into the morphology of early crown group representatives of Radula occurring in gymnosperm-dominated forests. Ancestral character state reconstruction aligns the fossil with the crown group of Radula subg. Odontoradula; however, corresponding divergence time estimates using the software BEAST lead to unrealistically old age estimates. Alternatively, assignment of the fossil to the stem of subg. Odontoradula results in a stem age estimate of Radula of 227.8 Ma (95 % highest posterior density (HPD): 165.7–306.7) and a crown group estimate of 176.3 Ma (135.1–227.4), in agreement with analyses employing standard substitution rates (stem age 235.6 Ma (142.9–368.5), crown group age 183.8 Ma (109.9–289.1)). The fossil likely belongs to the stem lineage of Radula subg. Odontoradula. The fossil's modern morphology suggests that switches from gymnosperm to angiosperm phorophytes occurred without changes in plant body plans in epiphytic liverworts. The fossil provides evidence for striking morphological homoplasy in time. Even conservative node assignments of the fossil support older rather than younger age estimates of the Radula crown group, involving origins for most extant subgenera by the end of the Cretaceous and diversification of their crown groups in the Cenozoic.

Fossil evidence of eupolypod ferns in the mid-Cretaceous of Myanmar

Divergence time estimates based on DNA sequence variation of extant species suggest that eupolypod ferns were diverse already in the Cretaceous; however, fossil evidence to support this assumption remains exceedingly rare. Holttumopteris burmensis gen. et sp. nov., a fertile fern foliage fragment preserved in a piece of Albian–Cenomanian Burmese amber from Myanmar, is characterized by divided fertile leaves with catadromous, free lateral veins. Sporangia possess a vertical annulus interrupted by the sporangium stalk and contain monolete spores with a lophate perine. The sporangia occur clustered in discrete sori overarched by a laterally attached, reniform indusium. Reconstruction of ancestral character states suggests affinities of Holttumopteris to the Thelypteridaceae; however, several taxonomically relevant characters are not preserved. This discovery is nevertheless important because H. burmensis represents the first unequivocal fossil of a representative of the eupolypods from the middle Cretaceous.

Multiple innovations underpinned branching form diversification in mosses.

Summary Broad‐scale evolutionary comparisons have shown that branching forms arose by convergence in vascular plants and bryophytes, but the trajectory of branching form diversification in bryophytes is unclear. Mosses are the most species‐rich bryophyte lineage and two sub‐groups are circumscribed by alternative reproductive organ placements. In one, reproductive organs form apically, terminating growth of the primary shoot (gametophore) axis. In the other, reproductive organs develop on very short lateral branches. A switch from apical to lateral reproductive organ development is proposed to have primed branching form diversification.Moss gametophores have modular development and each module develops from a single apical cell. Here we define the architectures of 175 mosses by the number of module classes, branching patterns and the pattern in which similar modules repeat. Using ancestral character state reconstruction we identify two stages of architectural diversification.During a first stage there were sequential changes in the module repetition pattern, reproductive organ position, branching pattern and the number of module classes. During a second stage, vegetative changes occurred independently of reproductive fate.The results pinpoint the nature of developmental change priming branching form diversification in mosses and provide a framework for mechanistic studies of architectural diversification.

Trophic evolution in African citharinoid fishes (Teleostei: Characiformes) and the origin of intraordinal pterygophagy

The African freshwater suborder Citharinoidei (Characiformes) includes 110 species that exhibit a diversity of feeding modes comparable to those characteristic of more speciose groups such its sister, the Characoidei (2000+ species) or the distantly related Cichlidae (1600+ species). Feeding habits of the Citharinoidei range from generalist omnivores to highly specialized feeding modes including ectoparasitic fin-eating, i.e. pterygophagy. We examine diet preference evolution in the Citharinoidei using newly inferred multi-gene-based hypotheses of phylogenetic relationships for representatives of 12 of the 15 genera in the suborder. Ancestral character state reconstructions onto our best tree indicate that the three most-generalist diets - pelophage/planktivore, omnivore and invertivore - are also the most primitive conditions within the Citharinoidei. The feeding mode of the most recent common ancestor of the Citharinoidei was characterized by high uncertainty. The more specialized feeding habits - herbivory, piscivory and pterygophagy - originated later in the Citharinoidei, likely from invertivore ancestors and possibly across a short time period. Highly specialized fin eaters (Belonophago, Phago and Eugnatichthys) share a common origin along with a strict piscivore (Mesoborus) and an invertivore (Microstomatichthyoborus). The largely piscivorous, but facultative fin eater, Ichthyborus is not exclusively related to them. Our results demonstrate that overall diet preference transitions in the Citharinoidei were rare events with very few reversals or parallelisms, and that evolutionary shifts in trophic ecology have not played a major role in intraordinal diversification. This situation contrasts with other groups in which dietary transitions have played key roles in species diversification.

Phylogenetic analysis and evolution of morphological characters in Metrodorea and related species in Rutoideae (Rutaceae)

The aim of the study is to compare distinct morphological characters of Metrodorea (Rutaceae) with those of related genera, under a phylogenetic approach. Morphoanatomy of leaves was analyzed, and data concerning reproductive structures were compiled from the literature. We used available molecular sequences to recover a maximum likelihood tree, and we present a reconstruction of ancestral morphological character states made with the maximum likelihood criterion. The topologies obtained retrieve as synapomorphic characters of Metrodorea: aborted leaflets, vascularized intrapetiolar stipules, sinuous cell walls contour in the surface view of the epidermis, glandular trichomes on the adaxial and proximal region of the petiole, good development of areoles, muricate fruits, and valvate estivation of the corolla. The specific relationships within Metrodorea and between Metrodorea and other genera of Rutoideae are supported by characters as the location of crystals, type of adherence at leaf bases, and presence/absence of trichomes on the blade. The close relationship of Metrodorea and Raulinoa is strongly supported by several synapomorphies. Our data are mostly consistent with recent phylogenies, showing that the monophyly of Esenbeckia cannot be confirmed and that the clade Helietta-Balfourodendron (formerly included in another subfamily) is closely related to Raulinoa and Metrodorea (both part of Pilocarpinae) than to Pilocarpus itself. Possible relationships between these genera are discussed based on the morphological states found, and most of them supporting the hypothesis that Metrodorea is the sister group of Raulinoa.

Phylogeography and character evolution of Euphorbia sect. Aphyllis subsect. Macaronesicae (Euphorbiaceae)

AbstractThe Macaronesian species of Euphorbia sect. Aphyllis subsect. Macaronesicae are distributed in four of the five archipelagos of Macaronesia and two mainland enclaves in Portugal and Morocco. The aims of this study are to investigate the biogeographic history of this group with AFLP and cpDNA markers, and to identify taxonomic entities within subsect. Macaronesicae based on genetic data, characterize them morphologically and infer the evolution of their diagnostic characters based on the reconstruction of ancestral character states. A continuous spatial diffusion analysis of AFLP data implicated Tenerife (central Canary Islands) as the area of origin of the group, followed by colonization of other Canarian islands and other Macaronesian archipelagos. Two dispersal events back to the mainland were also inferred. Our phylogenetic network, neighbour‐joining clustering and Structure analyses of AFLP data demonstrated that species are genetically well delimited and suggested that they may have originated from a combination of allopatric speciation at broad scales (among islands) and fine scales (within islands), or possibly sympatric ecological speciation followed by more recent inter‐island dispersal events. Ancestral character state reconstructions of morphological characters suggested that the ancestor of subsect. Macaronesicae was adapted to arid or mesic habitats, and traits associated with adaptation to humid habitats were acquired later. The central Canary Islands harbour the highest species diversity of this group in the Archipelago, and the highest nuclear and plastid genetic diversity. With regards to taxonomy, phylogenetic analyses and neighbour‐joining clustering analyses based on AFLPs showed two clearly differentiated genetic groups, sister to each other, which correspond to the E. atropurpurea and E. lamarckii complexes formerly recognised based on morphology. Euphorbia aphylla is recovered as sister to the rest of the species, supporting its exclusion from the two complexes. Euphorbia tuckeyana is excluded from the E. lamarckii complex.

Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database.

The online resource http://www.plantrdnadatabase.com/ stores information on the number, chromosomal locations and structure of the 5S and 18S-5.8S-26S (35S) ribosomal DNAs (rDNA) in plants. This resource was exploited to study relationships between rDNA locus number, distribution, the occurrence of linked (L-type) and separated (S-type) 5S and 35S rDNA units, chromosome number, genome size and ploidy level. The analyses presented summarise current knowledge on rDNA locus numbers and distribution in plants. We analysed 2949 karyotypes, from 1791 species and 86 plant families, and performed ancestral character state reconstructions. The ancestral karyotype (2n=16) has two terminal 35S sites and two interstitial 5S sites, while the median (2n=24) presents four terminal 35S sites and three interstitial 5S sites. Whilst 86.57% of karyotypes show S-type organisation (ancestral condition), the L-type arrangement has arisen independently several times during plant evolution. A non-terminal position of 35S rDNA was found in about 25% of single-locus karyotypes, suggesting that terminal locations are not essential for functionality and expression. Single-locus karyotypes are very common, even in polyploids. In this regard, polyploidy is followed by subsequent locus loss. This results in a decrease in locus number per monoploid genome, forming part of the diploidisation process returning polyploids to a diploid-like state over time.

Ovule, Fruit, and Seed Development ofOrectanthe sceptrumand Its Systematic Relevance to Xyridaceae (Poales)

Premise of research. Orectanthe consists of only two species with a distribution limited to the Guayana Highlands, in locations where sample collection is challenging. The genus belongs to Abolbodoideae, one of the two subfamilies of Xyridaceae. The development of the ovule, fruit, and seed of Orectanthe sceptrum was studied using a comparative approach to provide useful information for the taxonomy and phylogeny of the family.Methodology. Flowers and fruits at different developmental stages were analyzed by light and scanning electron microscopy. Optimization of select characters on a previously published phylogeny was conducted to evaluate the evolution of some embryological characters in Poales. The seed weights of O. sceptrum and species of Abolboda and Xyris were measured for comparison.Pivotal results. Orectanthe sceptrum presents anatropous, tenuinucellate, and bitegmic ovules with a micropyle bounded by both integuments. The multilayered outer integument forms the seed wing, which is a unique feature of this genus. The development of megagametophyte is of the Polygonum type. The seed has a tanniferous hypostase, a starchy endosperm, and a reduced and undifferentiated embryo. The seed coat is composed of a tanniferous tegmen (endotegmen and exotegmen) and testa (endotesta and exotesta). The mechanical layer of the seed coat is the exotesta. The fruit has a sclerenchymatous exocarp. The ancestral character-state reconstructions show that anatropous, crassinucellate ovules, megagametophyte development of the Polygonum type, and nuclear endosperm are the ancestral conditions in Poales. Orthotropous, tenuinucellate ovules appear in the most recent common ancestor of the xyrid, restiid, and graminid clades. The seed weight of O. sceptrum is one to two orders of magnitude greater than the seed weight of Abolboda and Xyris species.Conclusions. Anatropous ovules and a seed coat formed by endotegmen, exotegmen, endotesta, and exotesta link Orectanthe to Abolboda (Abolbodoideae). Such characteristics are not found in Xyris (Xyridoideae), which is consistent with the subfamilial division. The presence of anatropous ovules in Abolbodoideae most likely represents a character reversal. The greater seed weight of O. sceptrum may explain the presence of wings in the seeds.

Making the most of your host: the Metrosideros-feeding psyllids (Hemiptera, Psylloidea) of the Hawaiian Islands

The Hawaiian psyllids (Psylloidea, Triozidae) feeding on Metrosideros (Myrtaceae) constitute a remarkable radiation of more than 35 species. This monophyletic group has diversified on a single, highly polymorphic host plant species, Metrosideros polymorpha. Eleven Metrosideros-feeding species included in the Insects of Hawaii by Zimmerman are redescribed, and an additional 25 new species are described. Contrary to previous classifications that placed the Metrosideros-feeders in two genera, Trioza Foerster, 1848 and Kuwayama Crawford, 1911, all 36 named species are placed in Pariaconus Enderlein, 1926; and the relationship of this genus to other Pacific taxa within the family Triozidae, and other Austro-Pacific taxa feeding on host plants in Myrtaceae is clarified. The processes of diversification in Pariaconus include shifts in galling habit, geographic isolation within and between islands, and preferences for different morphotypes of the host plant. Four species groups are recognized: the bicoloratus and minutus groups are free-living or form pit galls, and together with the kamua group (composing all of the Kauai species) form a basal assemblage; the more derived closed gall species in the ohialoha group are found on all major islands except Kauai. The diversification of Pariaconus has likely occurred over several million years. Within island diversification is exemplified in the kamua group, and within species variation in the ohialoha group, but species discovery rates suggest this radiation remains undersampled. Mitochondrial DNA barcodes are provided for 28 of the 36 species. Genetic divergence, intraspecific genetic structure, and parallel evolution of different galling biologies and morphological traits are discussed within a phylogenetic framework. Outgroup analysis for the genus Pariaconus and ancestral character state reconstruction suggest pit-galling may be the ancestral state, and the closest outgroups are Palaearctic-Australasian taxa rather than other Pacific Metrosideros-feeders.

Inflorescence diversity in subtribe Eleusininae (Poaceae: Chloridoideae: Cynodonteae)

We studied the inflorescences of 112 members of tribe Chloridoideae subtribe Eleusininae from a morphological and evolutionary perspective to identify the most frequent types and to explore the evolutionary history of selected inflorescence associated characters. Six characters were scored on adult specimens and a principal coordinate analysis was conducted to identify inflorescence types. To investigate the evolution of inflorescences we regenerated the phylogeny of the subtribe and performed ancestral character state reconstructions using Maximum Parsimony. All species have panicles of spikelets with pyramidal, digitate or single-branched appearances. The number of primary branches varies widely among species, although some species have a single primary branch. The lack of terminal spikelet (truncation) and the similarity among primary branches of the inflorescence (homogenization) characterize the majority of the subtribe. In Eleusininae, the spikelet may be uni-, two- or multi-flowered. We found 13 inflorescence types in the group among 72 putative inflorescence forms. About 75% of the species can be divided to five different inflorescence types. Ancestral state reconstruction suggests an evolutionary direction towards simpler inflorescences with spikelets that contain 1–2 florets.

Mitochondrial phylogenomics illuminates the evolutionary history of Neuropterida.

Neuroptera (lacewings) and allied orders Megaloptera (dobsonflies, alderflies) and Raphidioptera (snakeflies) are predatory insects and together make up the clade Neuropterida. The higher-level relationships within Neuropterida have historically been widely disputed with multiple competing hypotheses. Moreover, the evolution of important biological innovations among various Neuropterida families, such as the origin, timing and direction of transitions between aquatic and terrestrial habitats of larvae, remains poorly understood. To investigate the origin and diversification of lacewings and their allies, we undertook phylogenetic analyses of mitochondrial genomes of all families of Neuropterida using Bayesian inference, maximum likelihood and maximum parsimony methods. We present a robust, fully resolved phylogeny and divergence time estimation for Neuropterida with strong statistical support for almost all nodes. Mitochondrial sequence data are typified by significant compositional heterogeneity across lineages, and parsimony and models assuming homogeneous rates did not recover Neuroptera as monophyletic. Only a model accounting for compositional heterogeneity (i.e. CAT-GTR) recovered all orders of Neuropterida as monophyletic. Significant findings of the mitogenomic phylogeny include recovering Raphidioptera as sister to Megaloptera plus Neuroptera. The sister family of all other lacewings are the dusty-wings (Coniopterygidae), rather than Nevrorthidae. Nevrorthidae are instead returned to their traditional position as the sister group of the spongilla-flies (Sisyridae) and closely related to Osmylidae. Our divergence time analysis indicates that the Mesozoic was indeed a 'golden age' for lacewings, with most families of Neuropterida diverging during the Triassic and Jurassic and all extant families present by the Early Cretaceous. Based on ancestral character state reconstructions of larval habitat we evaluate competing hypotheses regarding the life style of early neuropteridan larvae as either aquatic or terrestrial.

Out of southern Africa: Origin, biogeography and age of the Aizooideae (Aizoaceae)

The Aizooideae is an early-diverging lineage within the Aizoaceae. It is most diverse in southern Africa, but also has endemic species in Australasia, Eurasia and South America. We derived a phylogenetic hypothesis from Bayesian and Maximum Likelihood analyses of plastid DNA-sequences. We find that one of the seven genera, the fynbos-endemic Acrosanthes, does not belong to the Aizooideae, but is an ancient sister-lineage to the subfamilies Mesembryanthemoideae & Ruschioideae. Galenia and Plinthus are embedded inside Aizoon and Aizoanthemum is polyphyletic. The Namibian endemic Tetragonia schenckii is sister to Tribulocarpus of the Sesuvioideae. For the Aizooideae, we explored their possible age by means of relaxed Bayesian dating and used Bayesian Binary MCMC reconstruction of ancestral areas to investigate their area of origin. Early diversification occurred in southern Africa in the Eocene-Oligocene, with a split into a mainly African lineage and an Eurasian-Australasian-African-South American lineage. These subsequently radiated in the early Miocene. For Tetragonia, colonisation of Australasia via long-distance dispersal from Eurasia gave rise to the Australasian lineage from which there were subsequent dispersals to South America and Southern Africa. Despite the relatively old age of the Aizooideae, more than half the species have radiated since the Pleiocene, coinciding with the large and rapid diversification of the Ruschioideae. The lineage made up of Tetragonia schenckii &Tribulocarpus split from the remainder of the Sesuvioideae already in the mid Oligocene and its disjunct distribution between Namibia and north-east Africa may be the result of a previously wider distribution within an early Arid African flora. Our reconstruction of ancestral character-states indicates that the expanding keels giving rise to hygrochastic fruits originated only once, i.e. after the split of the Sesuvioideae from the remainder of the Aizoaceae and that they were subsequently lost many times. Variously winged and spiky fruits, adapted to dispersal by wind and animals, have evolved independently in the Aizooideae and the Sesuvioideae. There is then a greater diversity of dispersal systems in the earlier lineages than in the Mesembryanthemoideae and Ruschioideae, where dispersal is mainly achieved by rain.

Patterns of Phenotypic Variation in the Mouth Size of Lanternfishes (Teleostei: Myctophiformes)

Lanternfishes (Myctophiformes, ~260 species) are among the most abundant and species-rich groups of fishes endemic to the deep sea, and they play a major role in the oceanic ecosystem by transferring energy from shallower to deeper oceanic levels. Little is currently known regarding how lanternfishes have achieved such high species richness in the deep sea, and the majority of previous studies that have investigated diversification in this group have focused on bioluminescence. In this study, we investigate the variation in mouth size of lanternfishes in an effort to better understand potential mechanisms of speciation in this group, as previous studies have indicated that there is considerable variation in the size and biodiversity of prey items of lanternfishes. Geometric morphometrics were performed on 955 lanternfish specimens, and an ancestral character-state reconstruction was used to examine variation and evolution of mouth size in this group. We identify that mouth size in lanternfishes is highly ...

The complex evolutionary history of the tympanic middle ear in frogs and toads (Anura).

Most anurans possess a tympanic middle ear (TME) that transmits sound waves to the inner ear; however, numerous species lack some or all TME components. To understand the evolution of these structures, we undertook a comprehensive assessment of their occurrence across anurans and performed ancestral character state reconstructions. Our analysis indicates that the TME was completely lost at least 38 independent times in Anura. The inferred evolutionary history of the TME is exceptionally complex in true toads (Bufonidae), where it was lost in the most recent common ancestor, preceding a radiation of >150 earless species. Following that initial loss, independent regains of some or all TME structures were inferred within two minor clades and in a radiation of >400 species. The reappearance of the TME in the latter clade was followed by at least 10 losses of the entire TME. The many losses and gains of the TME in anurans is unparalleled among tetrapods. Our results show that anurans, and especially bufonid toads, are an excellent model to study the behavioural correlates of earlessness, extratympanic sound pathways, and the genetic and developmental mechanisms that underlie the morphogenesis of TME structures.

Seed morphology of Ricotia (Brassicaceae) and its phylogenetic and systematic implication

In the present study, macro- and micromorphological characters of seeds in Ricotia L. (9 species and 30 accessions) were examined by light (LM) and scanning electron microscopy (SEM) to evaluate the taxonomic relevance of these traits. Four main seed surface types were detected (papillate, reticulate, reticulate-papillate and undulate) in Ricotia. In order to address the evolution of selected seed characters, ancestral character state reconstruction analysis was performed. The results indicate that the lack of wing and the reticulate surface are ancestral states for Ricotia. Finally, mapping of seed shape characters (but not the seed surface microsculpturing) among Ricotia species is concordant with current phylogenetic concepts of Ricotia.

Phylogenetic relationships of Darwin’s “Mr. Arthrobalanus”: The burrowing barnacles (Cirripedia: Acrothoracica)

The barnacles of the superorder Acrothoracica are small, burrowing, epibiotic, and dioecious (large female with dwarf male) crustaceans largely found in the carbonate sediments and skeletons of marine invertebrates. The acrothoracicans represent the Cirripedia with the most plesiomorphic characters and have prominently featured in phylogenetic speculations concerning these crustaceans. Traditionally, Acrothoracica was divided into two main orders, Pygophora and Apygophora. The Apygophora had uniramus cirri and no anus. The Pygophora had biramus terminal cirri and an anus and was further divided into two families, Lithoglyptidae and Cryptophialidae. Kolbasov (2009) revised the superorder Acrothoracica on the basis of morphological examinations of females, dwarf males, and cyprids and rearranged the acrothoracican species into two new orders, Lithoglyptida and Cryptophialida. The present study is the first attempt to reconstruct the phylogenetic relationships of acrothoracican barnacles by sequencing two mitochondrial (cytochrome C oxidase I and 16S ribosomal DNA) and two nuclear (18S ribosomal DNA and histone H3) markers of 8 of the 11 genera comprising 23 acrothoracican species. All monophylies of the eight acrothoracican genera sampled in this study were strongly supported. The deep interfamilial relationship constructed is consistent with the recent morphological phylogenetic relationship proposed by Kolbasov, Newman, and Høeg (Kolbasov, 2009) that Cryptophialidae (order Cryptophialida) is the sister group to all other acrothoracicans (order Lithoglyptida). According to an ancestral character state reconstruction analysis, the posterior lobes of females; armament of opercular bars, attachment stalk, lateral projections of the body, and aperture slits in dwarf males; and habitat use appear to have phylogenetic importance.

Tyrosine Hydroxylation in Betalain Pigment Biosynthesis Is Performed by Cytochrome P450 Enzymes in Beets (Beta vulgaris).

Yellow and red-violet betalain plant pigments are restricted to several families in the order Caryophyllales, where betacyanins play analogous biological roles to anthocyanins. The initial step in betalain biosynthesis is the hydroxylation of tyrosine to form L-DOPA. Using gene expression experiments in beets, yeast, and Arabidopsis, along with HPLC/MS analysis, the present study shows that two novel cytochrome P450 (CYP450) enzymes, CYP76AD6 and CYP76AD5, and the previously described CYP76AD1 can perform this initial step. Co-expressing these CYP450s with DOPA 4,5-dioxygenase in yeast, and overexpression of these CYP450s in yellow beets show that CYP76AD1 efficiently uses L-DOPA leading to red betacyanins while CYP76AD6 and CYP76AD5 lack this activity. Furthermore, CYP76AD1 can complement yellow beetroots to red while CYP76AD6 and CYP76AD5 cannot. Therefore CYP76AD1 uniquely performs the beet R locus function and beets appear to be genetically redundant for tyrosine hydroxylation. These new functional data and ancestral character state reconstructions indicate that tyrosine hydroxylation alone was the most likely ancestral function of the CYP76AD alpha and beta groups and the ability to convert L-DOPA to cyclo-DOPA evolved later in the alpha group.

WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States.

Premise of the study:Reconstructions of ancestral character states are among the most widely used analyses for evaluating the morphological, cytological, or ecological evolution of an organismic lineage. The software application Mesquite remains the most popular application for such reconstructions among plant scientists, even though its support for automating complex analyses is limited. A software tool is needed that automates the reconstruction and visualization of ancestral character states with Mesquite and similar applications.Methods and Results:A set of command line–based Python scripts was developed that (a) communicates standardized input to and output from the software applications Mesquite, BayesTraits, and TreeGraph2; (b) automates the process of ancestral character state reconstruction; and (c) facilitates the visualization of reconstruction results.Conclusions:WARACS provides a simple tool that streamlines the reconstruction and visualization of ancestral character states over a wide array of parameters, including tree distribution, character state, and optimality criterion.

Complex Evolutionary and Genetic Patterns Characterize the Loss of Scleral Ossification in the Blind Cavefish Astyanax mexicanus.

The sclera is the tough outer covering of the eye that provides structural support and helps maintain intraocular pressure. In some fishes, reptiles, and birds, the sclera is reinforced with an additional ring of hyaline cartilage or bone that forms from scleral ossicles. Currently, the evolutionary and genetic basis of scleral ossification is poorly understood, especially in teleost fishes. We assessed scleral ossification among several groups of the Mexican tetra (Astyanax mexicanus), which exhibit both an eyed and eyeless morph. Although eyed Astyanax surface fish have bony sclera similar to other teleosts, the ossicles of blind Astyanax cavefish generally do not form. We first sampled cavefish from multiple independent populations and used ancestral character state reconstructions to determine how many times scleral ossification has been lost. We then confirmed these results by assessing complementation of scleral ossification among the F1 hybrid progeny of two cavefish populations. Finally, we quantified the number of scleral ossicles present among the F2 hybrid progeny of a cross between surface fish and cavefish, and used this information to identify quantitative trait loci (QTL) responsible for this trait. Our results indicate that the loss of scleral ossification is common–but not ubiquitous–among Astyanax cavefish, and that this trait has been convergently lost at least three times. The presence of wild-type, ossified sclera among the F1 hybrid progeny of a cross between different cavefish populations confirms the convergent evolution of this trait. However, a strongly skewed distribution of scleral ossicles found among surface fish x cavefish F2 hybrids suggests that scleral ossification is a threshold trait with a complex genetic basis. Quantitative genetic mapping identified a single QTL for scleral ossification on Astyanax linkage group 1. We estimate that the threshold for this trait is likely determined by at least three genetic factors which may control the severity and onset of lens degeneration in cavefishes. We conclude that complex evolutionary and genetic patterns underlie the loss of scleral ossification in Astyanax cavefish.

Phylogenetic analysis reveals an evolutionary transition from internal to external brooding in Epiactis Verrill (Cnidaria: Anthozoa: Actiniaria) and rejects the validity of the genus Cnidopus Carlgren.

Reproductive behaviors in the sea anemone genus Epiactis provide an opportunity for investigating the evolution of reproductive phenomena such as brooding and sex allocation (hermaphroditic vs. gonochoric) in a group of closely related and easily accessible species. However, given its broad geographic distribution, the striking diversity in reproductive behaviors, and the lack of synapomorphy for the genus, the monophyly of Epiactis is questionable. Here we perform phylogenetic analyses to test the monophyly of Epiactis and the validity of Cnidopus, which consists entirely of species once assigned to Epiactis. We use the large number of brooding species in Epiactis to investigate evolutionary patterns in brooding modes and characteristics associated with them. We find a monophyletic group of North Pacific Epiactis species: this group includes the type species of the genus and species that brood internally or externally, and that are hermaphroditic or gonochoric. Based on the results, we reject the genus Cnidopus because its circumscription renders Epiactis sensu stricto paraphyletic. Ancestral character state reconstruction indicates that in the North Pacific, externally brooding species evolved from internally brooding ancestors and that sex allocation is highly labile. Species relationships in Epiactis and Aulactinia appear to conform to geographic patterns more strongly than to taxonomic hypotheses. Contrary to expectations based on other invertebrates, we fail to find a strong correlation between brooding and hermaphroditism.