Lauraceae are a diverse family of the Neotropical flora that have recently undergone extensive taxonomic changes in the delimitation of genera. Here we review 30 currently accepted Neotropical genera of Lauraceae based on the combination of vegetative and reproductive characters, with a focus on floral characters. We present an identification key, as well as diagnostic descriptions, number of species, distribution, and phylogenetic information for the accepted Neotropical genera.

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.

As it spread through time and into distinct areas of science-from comparative anatomy to evolutionary biology, cladistics, developmental and molecular biology-the homology concept has changed considerably, presenting various meanings. Despite many attempts at developing a comprehensive understanding of the concept, this context-sensitive notion of homology has been a subject of an ongoing debate. Inspired by that and following Kevin de Queiroz and Richard Mayden's view on species concept and delimitation, we presented in this article an attempt to systematize and advance the understanding of the homology problem. Our main goals were: (i) to present a comprehensive checklist of 'concepts of homology'; (ii) to identify which are really concepts with ontological definitions (theoretically rooted in structural correspondence and common ancestry), and which are, in fact, not concepts, but epistemological (empirical and methodological) criteria of homology delimitation; (iii) to provide a synonymy of the concepts and criteria of homology delimitation; (iv) to present a hierarchy of homology concepts within Hennig's hologenetic system; and (v) to endorse the adoption of a unified view of homology by treating homology as a correspondence of spatio-temporal properties (genetic, epigenetic, developmental and positional) at the level of the individual, species or monophyletic group. We found 59 'concepts of homology' in the literature, from which 34 were categorically treated as concepts, 17 as criteria of homology delimitation, Four were excluded from our treatment, and Müller's five concepts were rather treated as approaches to homology. Homology concepts and criteria were synonymized based on structural correspondence, replicability, common ancestry, genetic and epigenetic developmental causes, position and optimization. Regarding the synonymy, we conclusively recognized 21 different concepts of homology, and five empirical and four methodological criteria. Hierarchical ontological aspects of homology were systematized under Hennig's hologenetic system, based on the existence of ontogenetic, tokogenetic and phylogenetic levels of homology. The delimitation of tokogenetic and phylogenetic homologies depends on optimization criteria. The unified view of homology is discussed in the context of the ancestral angiosperm flower.

We propose and diagnose a new species of Ocotea (Lauraceae), O. mellosilvae. On the basis of morphological evidence, the species seems to be a member of the Ocotea notata group. We also present its morphological description, illustrations, distribution, habitat, phenology, and etymology.

I review the theory and practice behind as reported by Patterson (in: Joysey, Friday (eds) Problems of phylogenetic reconstruction, Academic Press, London, 1982) the criterion of conjunction in plant systematics and evolution, with a focus on: (1) de Pinna (Cladistics 7:367–394, 1991) analysis of homology in the cladistic framework; (2) Hawkins’ (in: Scotland, Pennington (eds) Homology and systematics: coding characters for phylogenetic analysis, Taylor and Francis, London, 2000) survey of character coding; (3) Sereno (Cladistics 23:565–587, 2007) view of neomorphic and transformational characters; (4) character coding and polymorphic taxa; and (5) the relationship between character coding and plant variation using examples cited by Hawkins (in: Scotland, Pennington (eds) Homology and systematics: coding characters for phylogenetic analysis, Taylor and Francis, London, 2000). I coin the term “Replicable homology,” in contrast to serial homology, to make reference to the presence of multiple copies of the same structure or part in the same organism. I conclude that by Patterson’s (in: Joysey, Friday (eds) Problems of phylogenetic reconstruction, Academic Press, London, 1982) criterion is an important tool in order to identify neomorphic characters and that it cannot be applied to transformational characters. Conventional coding is the appropriate way to code characters, whereas both conjunction and unifying coding should be abolished from character analysis, as they are in disagreement with the view that a single character state must contain a mutually exclusive condition in relation to other character states.

Among the seven shortfalls of biodiversity knowledge, the one that makes direct reference to phylogenetic information is the Darwinian shortfall, which embraces three components: “(1) the lack of fully resolved phylogenies for most groups of organisms; (2) the limited knowledge of branch lengths and difficulties in absolute time calibrations; and (3) unknown evolutionary models linking those phylogenies to ecological traits and the life-history variation” (Diniz-Filho et al. in Trends Ecol Evol 28:689–694, 2013). In order to overcome them, Diniz-Filho et al. (Trends Ecol Evol 28:689–694, 2013) emphasized the need to know the problems relative to phylogeny reconstruction, but they did not provide a clear comprehension of these problems. In the present article, I aim to comment on these problems in the context of the five epistemic stages of phylogenetic analysis. These are: (1) taxon sampling; (2) evidence; (3) homology assessment; (4) optimization methods; and (5) hypotheses formulation. A brief review of these stages is necessary to comprehend how complex is the use of phylogenetic hypotheses in ecology and conservation. I also provide additional and balanced solutions in an attempt to overcome the evolutionary shortfall.

A recent study using an extensive data set plus sophisticated analytical tools reconstructed a model of the ancestral angiosperm flower. Although attractive, it presents problems of homology assessment. We discuss its inconsistencies and endorse the use of a comparative model that integrates biological parameters as essential to elucidate floral evolution.

A new species of Ocotea (Lauraceae), O. aureotomentosa, is hypothesized and illustrated. We follow K. de Queiroz's view of a unified species concept and use morphological evidence to support our species hypothesis.

Journal of Systematics and EvolutionVolume 55, Issue 3 p. 225-230 Letter to the Editor Patterns of character evolution in phylogenies Leandro C. S. Assis, Corresponding Author Leandro C. S. Assis leandroassis@ufmg.br Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901 Brazil Author for Correspondence. E-mail: leandassis@gmail.com; leandroassis@ufmg.br.Search for more papers by this author Leandro C. S. Assis, Corresponding Author Leandro C. S. Assis leandroassis@ufmg.br Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901 Brazil Author for Correspondence. E-mail: leandassis@gmail.com; leandroassis@ufmg.br.Search for more papers by this author First published: 31 January 2017 https://doi.org/10.1111/jse.12241Citations: 3Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Citing Literature Volume55, Issue3May 2017Pages 225-230 RelatedInformation

In this metaphorical ‘composition’, I comment on nine ‘dissonant chords’ related to the drowning out of cladistic performance: (1) DNA-based phylogenetic hypotheses supported only by bootstrap values and without molecular synapomorphies; (2) the use of molecular data to the exclusion of morphological data, with the classification of clades diagnosed by morphological plesiomorphies plus bootstrap values; (3) neglect of the results of the congruence test and how they are interpreted; (4) the combination of character optimization using both model-based and parsimony methods, and its consequences; (5) the need to effectively integrate ontogeny and phylogeny; (6) the estimation of the ages of clades based on molecular-clock analyses; (7) the belief that new methods, theories, and hypotheses are more reliable than old ones, with the idea that model-based analyses achieve better results than parsimony analyses; (8) the false assumption of the irrelevance of classification; and (9) clashes amongst cladists themselves, who endorse distinct methods, philosophies, and theories. Finally, I present 10 ‘refrains’ in order to intensify the cladistic performance.

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Premise of research. The pantropical magnoliid family Lauraceae has an extensive macrofossil record that dates back to the Early Cretaceous. However, flower anatomy among extant species is relatively poorly known. We investigate flower structure and development in six Neotropical genera to elucidate the homologies of the floral parts, especially the prominent appendages that occur on the filaments of the inner fertile stamen whorl in some species.Methodology. We used SEM and LM to examine flower organization and development in 11 species of six genera (Aniba, Cryptocarya, Endlicheria, Licaria, Nectandra, Ocotea) and flower vasculature in two species (Cryptocarya moschata and Ocotea prolifera).Pivotal results. All the flowers examined are typical of Lauraceae: they are very small and possess two whorls of tepals that are similarly vascularized, with three bundles each (resembling bracteopetals), multiple androecium whorls, and a single carpel. Variation exists in some characters, especially in the androecium. A fourth (innermost) androecial whorl is present as staminodia in some species. The prominent stamen appendages are highly vascularized.Conclusions. The presence of three vascular bundles supplying both outer and inner tepals supports their potential homology as bracteotepals. Floral vasculature also indicates that the staminodia of the fourth androecial whorl are derived from stamens. A potential homology between the stamens and appendages remains debatable, because existing evidence is contradictory.

Abstract An updated inventory of Brazilian seed plants is presented and offers important insights into the country's biodiversity. This work started in 2010, with the publication of the Plants and Fungi Catalogue, and has been updated since by more than 430 specialists working online. Brazil is home to 32,086 native Angiosperms and 23 native Gymnosperms, showing an increase of 3% in its species richness in relation to 2010. The Amazon Rainforest is the richest Brazilian biome for Gymnosperms, while the Atlantic Rainforest is the richest one for Angiosperms. There was a considerable increment in the number of species and endemism rates for biomes, except for the Amazon that showed a decrease of 2.5% of recorded endemics. However, well over half of Brazillian seed plant species (57.4%) is endemic to this territory. The proportion of life-forms varies among different biomes: trees are more expressive in the Amazon and Atlantic Rainforest biomes while herbs predominate in the Pampa, and lianas are more expressive in the Amazon, Atlantic Rainforest, and Pantanal. This compilation serves not only to quantify Brazilian biodiversity, but also to highlight areas where there information is lacking and to provide a framework for the challenge faced in conserving Brazil's unique and diverse flora.

ABSTRACT The relation of homology is generally characterized as an identity relation, or alternatively as a correspondence relation, both of which are transitive. We use the example of the ontogenetic development and evolutionary origin of the gnathostome jaw to discuss identity and transitivity of the homology relation under the transformationist and emergentist paradigms respectively. Token identity and consequent transitivity of homology relations are shown to be requirements that are too strong to allow the origin of genuine evolutionary novelties. We consequently introduce the concept of compositional identity that is grounded in relations prevailing between parts (organs and organ systems) of a whole (organism). We recognize an ontogenetic identity of parts within a whole throughout the sequence of successive developmental stages of those parts: this is an intra‐organismal character identity maintained throughout developmental trajectory. Correspondingly, we recognize a phylogenetic identity of homologous parts within two or more organisms of different species: this is an inter‐species character identity maintained throughout evolutionary trajectory. These different dimensions of character identity—ontogenetic (through development) and phylogenetic (via shared evolutionary history)—break the transitivity of homology relations. Under the transformationist paradigm, the relation of homology reigns over the entire character (‐state) transformation series, and thus encompasses the plesiomorphic as well as the apomorphic condition of form. In contrast, genuine evolutionary novelties originate not through transformation of ancestral characters (‐states), but instead through deviating developmental trajectories that result in alternate characters. Under the emergentist paradigm, homology is thus synonymous with synapomorphy. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 578–587, 2015 . © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution published by Wiley Periodicals, Inc.

The present paper is mainly concerned with homology assessment through phylogenetic analyses. It raises a fundamental question: What are the epistemological differences between modern parsimony and model-based analyses in relation to homology assessment and phylogenetic inference? Although these methods usually achieve concordant topological results, they may generate discordant inferences of character evolution from the same datasets. This indicates that method selection has serious implications for evolutionary scenarios and classificatory arrangements. Notwithstanding that parsimony and model-based approaches use the Hennigian concepts of monophyly and synapomorphy, they employ different epistemological ways of dealing with the monophyly/synapomorphy relationship. Independently of their differences, these analyses should take into account all relevant evidence in support of the phylogenetic inferences. A focus on morphological homologues means that they must be included in data matrices, evaluated as part of the phylogenetic analysis, and cannot be ignored in calculation of the tree(s) length (parsimony), maximum-likelihood (maximum-likelihood), and posterior probabilities (Bayes).

CladisticsVolume 30, Issue 1 p. 10-10 Letter to the EditorFree Access Species and tokogenetic homologies: 10 sutras Leandro C. S. Assis, Leandro C. S. Assis leandassis@gmail.com leandroassis@ufmg.br Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901 BrazilSearch for more papers by this author Leandro C. S. Assis, Leandro C. S. Assis leandassis@gmail.com leandroassis@ufmg.br Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901 BrazilSearch for more papers by this author First published: 04 June 2013 https://doi.org/10.1111/cla.12031Citations: 4AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Sir, According to Hall (1994), homology is at all levels of the biological hierarchy. According to Brower and de Pinna (2012), homology is equal to synapomorphy. According to Hennig (1966), phylogenetic relationships (monophyly) and tokogenetic relationships (reproductive community) relate to supraspecific and species taxa, respectively.11 Mishler and Theriot (2000), however, have treated species as monophyletic groups, thus using synapomorphies for species delimitation. Also according to Hennig (1966), synapomorphies delimit supraspecific taxa (monophyletic groups), whereas cohesion and isolation delimit species (tokogenetic groups).22 Meier and Willmann (2000) have proposed a modified version of Hennig's species concept. If synapomorphy delimits supraspecific taxa, and if synapomorphy is equal to homology, then homology cannot delimit species. If homology is at all levels of the biological hierarchy, is homology equivalent to synapomorphy? Would not synapomorphy be a kind of homology relative to supraspecific taxa?33 Müller (2003), Wägele (2004), Love (2007), and Assis (2013) have argued that homology and synapomorphy are not synonymous And what kind of homology would be relative to species? Tokogenetic homologies are at the level of species (tokogenetic relationships), whereas synapomorphies are at the level of supraspecific taxa (phylogenetic relationships). Tokogenetic homologies can be associated to any criteria of species delimitation. Notes 1 Mishler and Theriot (2000), however, have treated species as monophyletic groups, thus using synapomorphies for species delimitation. 2 Meier and Willmann (2000) have proposed a modified version of Hennig's species concept. 3 Müller (2003), Wägele (2004), Love (2007), and Assis (2013) have argued that homology and synapomorphy are not synonymous References Assis, L.C.S., 2013. Are homology and synapomorphy the same or different? Cladistics 29, 7– 9. Wiley Online LibraryWeb of Science®Google Scholar Brower, A.V.Z., de Pinna, M.C.C., 2012. Homology and errors. Cladistics 28, 529– 538. Wiley Online LibraryWeb of Science®Google Scholar B.K. Hall (Ed.), 1994. Homology: The Hierarchical Basis of Comparative Biology. Academic Press, San Diego, CA. CASPubMedGoogle Scholar Hennig, W., 1966. Phylogenetic Systematics. University of Illinois Press, Urbana, IL. PubMedWeb of Science®Google Scholar Love, A., 2007. Functional homology and homology of function: biological concepts and philosophical consequences. Biol. Philos. 22, 691– 708. CrossrefWeb of Science®Google Scholar Meier, R., Willmann, R., 2000. The Hennigian species concept. In Q.D. Wheeler, R. Meier (Eds.), Species Concepts and Phylogenetic Theory: A Debate. Columbia University Press, New York, pp. 30– 43. Google Scholar Mishler, B., Theriot, E., 2000. The phylogenetic species concept (sensu Mishler and Theriot). In Q.D. Wheeler, R. Meier (Eds.), Species Concepts and Phylogenetic Theory: A Debate. Columbia University Press, New York, pp. 44– 54. Google Scholar Müller, G.B., 2003. Homology: the evolution of morphological organization. In G.B. Müller, S.A. Newman (Eds.), Origination of Organismal Form: beyond the Gene in Developmental and Evolutionary Biology. MIT Press, Cambridge, MA, pp. 51– 69. Google Scholar Wägele, J.W., 2004. Hennig's phylogenetic systematics brought up to date. In D.M. Williams, P.L. Forey (Eds.), Milestones in Systematics. CRC Press, Boca Raton, FL, pp. 101– 126. CrossrefWeb of Science®Google Scholar Citing Literature Volume30, Issue1February 2014Pages 10-10 ReferencesRelatedInformation