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BACKGROUND: A general view in the study of pollination syndromes is that floral traits usually represent convergent floral adaptations to specific functional pollinator groups. However, the definition of convergence is elusive and contradictory in the literature. Is convergence the independent evolution of either the same trait or similar traits with the same function? A review of the concept of convergence in developmental biology and phylogenetic systematics may shed new light in studies of pollination syndromes. SCOPE: The aims of this article are (1) to explore the notion of convergence and other concepts (analogy, homoplasy and parallelism) within the theory and practice of developmental evolution and phylogenetic systematics; (2) to modify the definitions of syndromes in order to embrace the concepts of analogy and convergence; (3) to revisit the bat pollination syndrome in the context of angiosperm phylogeny, with focus on the showy 'petaloid' organs associated with the syndrome; (4) to revisit the genetic-developmental basis of flower colour; (5) to raise evolutionary hypotheses of floral evolution associated with the bat pollination syndrome; and (6) to highlight some of the current frontiers of research on the origin and evolution of flowers and its impact on pollination syndrome studies in the 21st century. CONCLUSIONS: The inclusion of the concepts of analogy and convergence within the concept of syndromes will constitute a new agenda of inquiry that integrates floral biology, phylogenetic systematics and developmental biology. Phyllostomid and pteropodid bat pollination syndrome traits in eudicots and monocots represent cases of analogous and convergent evolution. Pollination syndromes are a multivariate concept intrinsically related to the understanding of flower organogenesis and evolution. The formulation of hypotheses of pollination syndromes must consider the phylogenetic levels of universality for both plant and animal taxa, flower development, genetics, homology and evolution, and a clear definition of evolutionary concepts, including analogy, convergence, homoplasy and parallelism.

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Fungi show a high degree of morphological convergence. Regarded for a long time as an obstacle for phylogenetic studies, homoplasy has also been proposed as a source of information about underlying morphogenetic patterning mechanisms. The "local-activation and long-range inhibition principle" (LALIP), underlying the famous reaction-diffusion model proposed by Alan Turing in 1952, appears to be one of the universal phenomena that can explain the ontogenetic origin of seriate patterns in living organisms. Reproductive structures of fungi in the class Agaricomycetes show a highly periodic structure resulting in, for example, poroid, odontoid, lamellate or labyrinthic hymenophores. In this paper, we claim that self-organized patterns might underlie the basic ontogenetic processes of these structures. Simulations based on LALIP-driven models and covering a wide range of parameters show an absolute mutual correspondence with the morphospace explored by extant agaricomycetes. This could not only explain geometric particularities but could also account for the limited possibilities displayed by hymenial configurations, thus making homoplasy a direct consequence of the limited morphospace resulting from the proposed patterning dynamics.

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Cryptocladocera Bezzi, 1923 is a Neotropical genus of Tachinidae with remarkable multifissicorn antennae, previously composed of four species. A new species from Brazil, Cryptocladocera arnaudi Santis Alvarez-Garcia sp. nov., is described, illustrated and photographed herein. Cryptocladocera bezzii Arnaud, 1963 and Cryptocladocera mojingensis Arnaud, 1963 are proposed as junior synonyms of Cryptocladocera prodigiosa Bezzi, 1923, synn. nov. With these changes, Cryptocladocera is left with 3 species: C. arnaudi, C. pichilinguensis Arnaud, 1963 and C. prodigiosa. An updated key to the males of Cryptocladocera species is provided. Furthermore, C. prodigiosa is recorded for the first time for French Guiana and Brazil. Finally, the diversity and evolution of fissicorn antennae in tachinids are discussed.

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Understanding the evolution of biodiversity on Earth is a central aim in biology. Currently, various disciplines of science contribute to unravel evolution at all levels of life, from individual organisms to species and higher ranks, using different approaches and specific terminologies. The search for common origin, traditionally called homology, is a connecting paradigm of all studies related to evolution. However, it is not always sufficiently taken into account that defining homology depends on the hierarchical level studied (organism, population, and species), which can cause confusion. Therefore, we propose a framework to define homologies making use of existing terms, which refer to homology in different fields, but restricting them to an unambiguous meaning and a particular hierarchical level. We propose to use the overarching term "homology" only when "morphological homology," "vertical gene transfer," and "phylogenetic homology" are confirmed. Consequently, neither phylogenetic nor morphological homology is equal to homology. This article is intended for readers with different research backgrounds. We challenge their traditional approaches, inviting them to consider the proposed framework and offering them a new perspective for their own research.

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Bayesian analysis of morphological data is becoming increasingly popular mainly (but not only) because it allows for time-calibrated phylogenetic inference using relaxed morphological clocks and tip dating whenever fossils are available. As with molecular data, recent studies have shown that modeling among-character rate variation (ACRV) in morphological matrices greatly improves phylogenetic inference. In a likelihood framework this may be accomplished, for instance, by employing a hidden Markov model to assign characters to rate categories drawn from a (discretized) $\Gamma$ distribution and/or by partitioning data sets according to rate heterogeneity and estimating per-partition branch lengths, conditioned on a single topology. While the first approach is available in many phylogenetic analysis software, there is still no clear consensus on how to partition data, except perhaps in the simplest cases (e.g., "by codon" partitioning of coding sequences). Additionally, there is a trade-off between improvement in likelihood scores and the number of free parameters in the analysis, which rises quickly with the number of partitions. This trade-off may be dealt with by employing statistics that penalize overfitting of complex models, such as Akaike or Bayesian information criteria, or the more recently introduced stepping-stone method for marginal likelihood approximation. We applied the latter to three distinct matrices of discrete morphological data and demonstrated that sorting characters by homoplasy scores (obtained from implied weighting parsimony analysis) outperformed other partitioning strategies (anatomically-based and PartitionFinder2). The method was in fact so efficient in segregating characters by rates of evolution that no within-partition ACRV modeling was necessary, while among-partition rate variation was adequately accommodated by rate multipliers. We conclude that partitioning by homoplasy is a powerful and easy-to-implement strategy to address ACRV in complex data sets. We provide some guidelines focusing on morphological matrices, although this approach may be also applicable to molecular data sets.

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BACKGROUND: Members of the Bacillus genus have been isolated from a variety of environments. However, the relationship between potential metabolism and the niche from which bacteria of this genus have been isolated has not been extensively studied. The existence of a monophyletic aquatic Bacillus group, composed of members isolated from both marine and fresh water has been proposed. Here, we present a phylogenetic/phylogenomic analysis to investigate the potential relationship between the environment from which group members have been isolated and their evolutionary origin. We also carried out hierarchical clustering based on functional content to test for potential environmental effects on the genetic content of these bacteria. RESULTS: The phylogenetic reconstruction showed that Bacillus strains classified as aquatic have evolutionary origins in different lineages. Although we observed the presence of a clade consisting exclusively of aquatic Bacillus, it is not comprised of the same strains previously reported. In contrast to phylogeny, clustering based on the functional categories of the encoded proteomes resulted in groups more compatible with the environments from which the organisms were isolated. This evidence suggests a detectable environmental influence on bacterial genetic content, despite their different evolutionary origins. CONCLUSION: Our results suggest that aquatic Bacillus species have polyphyletic origins, but exhibit convergence at the gene content level.

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Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed "hemiplasy." The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti.

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BACKGROUND: Homoplasy affects demographic inference estimates. This effect has been recognized and corrective methods have been developed. However, no studies so far have defined what homoplasy metrics best describe the effects on demographic inference, or have attempted to estimate such metrics in real data. Here we study how homoplasy in chloroplast microsatellites (cpSSR) affects inference of population expansion time. cpSSRs are popular markers for inferring historical demography in plants due to their high mutation rate and limited recombination. RESULTS: In cpSSRs, homoplasy is usually quantified as the probability that two markers or haplotypes that are identical by state are not identical by descent (Homoplasy index, P). Here we propose a new measure of multi-locus homoplasy in linked SSR called Distance Homoplasy (DH), which measures the proportion of pairwise differences not observed due to homoplasy, and we compare it to P and its per cpSSR locus average, which we call Mean Size Homoplasy (MSH). We use simulations and analytical derivations to show that, out of the three homoplasy metrics analyzed, MSH and DH are more correlated to changes in the population expansion time and to the underestimation of that demographic parameter using cpSSR. We perform simulations to show that Approximate Bayesian Computation (ABC) can be used to obtain reasonable estimates of MSH and DH. Finally, we use ABC to estimate the expansion time, MSH and DH from a chloroplast SSR dataset in Pinus caribaea. To our knowledge, this is the first time that homoplasy has been estimated in population genetic data. CONCLUSIONS: We show that MSH and DH should be used to quantify how homoplasy affects estimates of population expansion time. We also demonstrate how ABC provides a methodology to estimate homoplasy in population genetic data.

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PREMISE OF THE STUDY: Pentaclethra and Dimorphandra (Leguminosae) have long been considered a possible enigmatic link between caesalpinioids and mimosoids because they both have an imbricate calyx and heteromorphic androecium, floral features that are rare among mimosoids but common among caesalpinioids. This study compared the developing flowers of Dimorphandra mollis and Pentaclethra macroloba to determine whether the shared floral conditions also have the same ontogenetic origin. METHODS: Buds of different sizes and flowers were processed for surface (scanning electron microscopy) and histological (light microscopy) examination. KEY RESULTS: The floral meristem initiates five sepal primordia in a modified helical order in both species. The median sagittal sepal is adaxial. The overlap of the sepals during elongation culminates with the formation of the imbricate calyx. Heteromorphic androecia arise in the intermediate stages of development. In P. macroloba, the fertile pollen-bearing stamens are antesepalous, robust and short, and the anthers carry a robust apical gland; the staminodes are long and white with a vestigial apical gland. In contrast, in D. mollis the fertile pollen-bearing stamens are antepetalous without glands and as long as the staminodes. The staminodes are thinner with an expanded apical region. CONCLUSIONS: The imbricate calyx and the heteromorphic androecium in the studied species originated via distinct pathways, favoring the hypothesis of homoplasy of these conditions. The pathways observed in P. macroloba are more similar to those observed in caesalpinioids than to those observed in mimosoids, indicating that although the floral development differs between the species studied, it supports the basal placement of Pentaclethra among mimosoids.

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Pitheciids, one of the major radiations of New World monkeys endemic to South and Central America, are distributed in the Amazon and Orinoco basins, and include Callicebus, Cacajao, Chiropotes, and Pithecia. Molecular phylogenetics strongly support pitheciid monophyly, whereas morphological analyses infer a range of phylogenies including a sister relationship between Aotus and Callicebus. We collected geometric morphometric cranial data from pitheciids and Aotus, and used cranial data for distance-based phylogenetic analysis and tests of phylogenetic signal. Phylogenetic analyses of pitheciids were repeated with Lagothrix, Callimico, and Saimiri outgroups for Procrustes shape with and without Aotus based on the whole cranium and six anatomical regions. All phylogenetic signal tests were significant, and tree lengths were shortest and had the least morphological change over the phylogeny for Procrustes residuals from the cranial base and palate. The majority of phylogenetic analyses of Procrustes shape for pitheciids without Aotus supported the molecular phylogeny, and with Aotus included the majority inferred an Aotus-Callicebus clade, although three analyses with Callimico as outgroup supported the molecular phylogeny. The morphological similarity of Aotus and Callicebus is likely a mix of plesiomorphy, allometry, and homoplasy, and future phylogenetic inference of living and extinct platyrrhine taxa should consider the impact of these factors alongside outgroup selection and cranial region.

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Helicoidea is a diverse group of land snails with a global distribution. While much is known regarding the relationships of helicoid taxa, comparatively little is known about the evolution of the mitochondrial genome in the superfamily. We sequenced two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 representing the first such data from the helicoid family Polygyridae, and used them in an evolutionary analysis of mitogenomic gene order. We found the mitochondrial genome of Praticolella mexicana to be 14,008 bp in size, possessing the typical 37 metazoan genes. Multiple alternate stop codons are used, as are incomplete stop codons. Mitogenome size and nucleotide content is consistent with other helicoid species. Our analysis of gene order suggested that Helicoidea has undergone four mitochondrial rearrangements in the past. Two rearrangements were limited to tRNA genes only, and two involved protein coding genes.

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PREMISE OF THE STUDY: Morphologically diverse clades are useful for detecting adaptive morphological evolution. Each of their variants may have evolved once or several times, suggesting that their repeated appearance may be due to environmental pressures. The North American Manihot species are an excellent system to detect possible adaptations and to assess the effect of mono- or polyphyly on classification. With 20 species, this group includes growth forms from tuberous herbs to trees. The monophyly of this group and its relationship with the economically important M. esculenta were tested for the first time with complete sampling of North American species. METHODS: We carried out maximum likelihood and Bayesian phylogenetic analyses on a matrix of 3662 bp from chloroplast (psbA-trnH, trnL-trnF) and nuclear loci (PEPC and two paralogous copies of G3pdh). We included all North American Manihot species, Manihotoides pauciflora, and published sequences from 34 South American species. KEY RESULTS: Our results support monophyly of the North American Manihot group. Its taxonomic sections are paraphyletic, and three to four growth forms evolved repeatedly. Manihotoides pauciflora is nested within North American Manihot species. Some PEPC and G3pdh clones grouped with clones of other species and not with clones from their own species. CONCLUSIONS: North and South American Manihot species are sister clades. Paraphyly of North American sections suggests that taxonomic revision is warranted. The position of Manihotoides pauciflora confirms that Manihotoides should remain subsumed within Manihot. Most growth forms likely evolved repeatedly in this group. The behavior of PEPC and G3pdhNA clones is probably due to incomplete lineage sorting.

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The utility of microsatellites (SSRs) in reconstructing phylogenies is largely confined to studies below the genus level, due to the potential of homoplasy resulting from allele size range constraints and poor SSR transferability among divergent taxa. The eucalypt genus Corymbia has been shown to be monophyletic using morphological characters, however, analyses of intergenic spacer sequences have resulted in contradictory hypotheses- showing the genus as either equivocal or paraphyletic. To assess SSR utility in higher order phylogeny in the family Myrtaceae, phylogenetic relationships of the bloodwood eucalypts Corymbia and related genera were investigated using eight polymorphic SSRs. Repeat size variation using the average square and Nei's distance were congruent and showed Corymbia to be a monophyletic group, supporting morphological characters and a recent combination of the internal and external transcribed spacers dataset. SSRs are selectively neutral and provide data at multiple genomic regions, thus may explain why SSRs retained informative phylogenetic signals despite deep divergences. We show that where the problems of size-range constraints, high mutation rates and size homoplasy are addressed, SSRs might resolve problematic phylogenies of taxa that have diverged for as long as three million generations or 30 million years.