Fossil wood of the Juglandaceae: Some questions of taxonomy,evolution, and phylogeny in the family based on wood anatomy

Some problems in the taxonomy of the Juglandaceae are discussed based on wood anatomy; the identification of fossil juglandaceous wood is considered. Data on fossil wood of the Juglandaceae are summarized; a key for identification of wood anatomy in modern and fossil Juglandaceae is compiled. Wood anatomical characters in members of the family are discussed in the light of major evolutionary trends in the secondary xylem of dicots, and a comparative characterization of members of the family is developed. A hypothesis is proposed that the subfamily Engelhardioideae is the most primitive member of the Juglandaceae based on wood anatomy, the tribe Juglandeae and subfamily Platycaryoideae are slightly more highly specialized, and the tribe Hicorieae is the most advanced. Evolutionary relationships between the members of the Juglandaceae are reviewed based on wood anatomy.     

Taxonomic and evolutionary implications of the Endosperm Balance Number hypothesis in potatoes

Summary The Endosperm Balance Number (EBN) hypothesis can explain to a considerable degree the crossability between tuber-bearing Solanum species. It has been shown to be genetically controlled and is dosage dependent. There is a good correlation between EBN and the postulated evolution and present taxonomy of potatoes. The primitive white stellate-flowered species from Mexico are 1EBN, and this condition is also found in species from South America with flowers of the same colour and shape. The evolution of a rotate corolla seems to be correlated with 2EBN. It is postulated that the 2EBN state arose as a reproductive isolating mechanism in South America. The taxonomic and evolutionary implications of the EBN hypothesis are discussed.     

Ontophylogenetic studies of the brachiopods of the order terebratulida

The patterns of ontophylogenetic change of the brachidium in Late Paleozoic, Mesozoic, and Cenozoic terebratulids are analyzed. The work of Russian specialists in establishing new evolutionary trends and working out terebratulid taxonomy on the basis of ontophylogenetic studies is discussed.     

PHYLOGENETIC ANALYSIS OF THE MARINE AND FRESHWATER THALAS-SIOSIROID DIATOMS

The thalassiosiroid centric diatoms are distinguished by at least one synapomorphy, the strutted process or fultoportula. Variously classified as a family (Thalassiosiraceae) or an order (Thalassiosirales) among centric diatoms, it is generally conceded that the group of several hundred fossil and living species is monophyletic as a whole. There are two ecological groups of thalassiosiroids, marine and freshwater. It has been hypothesized, based on an ecletic, non-rigorous, evolutionary taxonomy perspective that both the marine and freshwater ecological groups are also monophyletic, but this hypothesis has never been tested in a rigorous framework. Likewise, the freshwater thalassiosiroid species have been grouped into several genera and subgenera using an evolutionary taxonomic approach, but these hypotheses have not fully been tested using cladistic analysis. Focusing mainly on freshwater species, but including at least one representative of each marine genus and one representative from each of several proposed subgeneric groupings of the genus Thalassiosira , we scored morphological characters for fossil and living marine and freshwater Thalassiosiraceae to test these hypotheses. Our cladistic results provide strong support for monophyly for the freshwater group, but it seems unlikely that the marine group is monophyletic. The cladistic results are corroborated to greater or lesser degrees by the fossil record. The implications for evolution in the group and for taxon sampling in molecular studies we are conducting will be discussed.     

Phylogenetic taxonomy of the Cercosaurini (Squamata: Gymnophthalmidae), with new genera for species of Neusticurus and Proctoporus

The tribe Cercosaurini is one of the most poorly studied groups of the lizard family Gymnophthalmidae. Recent studies have suggested that two cercosauriine genera, Neusticurus and Proctoporus , are polyphyletic. The aim of the current study was to rectify the polyphyletic relationships and construct a phylogenetic taxonomy of the Cercosaurini that is congruent with evolutionary history. Neusticurus is divided into two genera, one of them new ( Potamites ), based on the clades recovered by molecular studies and previously discussed morphological data. Proctoporus is divided into three genera, one of which is new ( Petracola ), while an older name ( Riama ) is resurrected for another. All five genera are described and defined and taxonomic keys are presented. This study represents an important advance in rectifying the taxonomy of the Cercosaurini. Many other para- and polyphyletic genera remain in the Gymnophthalmidae and much future work on this group is warranted.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 405–416.     

Erratic rates of molecular evolution and incongruence of fossil and molecular divergence time estimates in Ostracoda (Crustacea)

Dating evolutionary origins of taxa is essential for understanding rates and timing of evolutionary events, often inciting intense debate when molecular estimates differ from first fossil appearances. For numerous reasons, ostracods present a challenging case study of rates of evolution and congruence of fossil and molecular divergence time estimates. On the one hand, ostracods have one of the densest fossil records of any metazoan group. However, taxonomy of fossil ostracods is controversial, owing at least in part to homoplasy of carapaces, the most commonly fossilized part. In addition, rates of evolution are variable in ostracods. Here, we report evidence of extreme variation in the rate of molecular evolution in different ostracod groups. This rate is significantly elevated in Halocyprid ostracods, a widespread planktonic group, consistent with previous observations that planktonic groups show elevated rates of molecular evolution. At the same time, the rate of molecular evolution is slow in the lineage leading to Manawa staceyi, a relict species that we estimate diverged approximately 500 million years ago from its closest known living relative. We also report multiple cases of significant incongruence between fossil and molecular estimates of divergence times in Ostracoda. Although relaxed clock methods improve the congruence of fossil and molecular divergence estimates over strict clock models, incongruence is present regardless of method. We hypothesize that this observed incongruence is driven largely by problems with taxonomy of fossil Ostracoda. Our results illustrate the difficulty in consistently estimating lineage divergence times, even in the presence of a voluminous fossil record.     

Ontogenetic systematics: The synthesis of taxonomy, phylogenetics, and evolutionary developmental biology

The main purpose of the present review is to draw attention to growing problems in the modern systematics and phylogenetics which are presently underestimated by the professional community. The dramatic reduction of the importance of ontogeny and morphology in phylogenetic studies of the second part of the 20th century is considered among the major factors of the modern taxonomic and evolutionary paradigm. The deep contradiction of modern approaches, which either merely consider systematics and phylogeny as genealogy or even in a neotypolgical manner irrespective of the evolutionary idea, is demonstrated. Thus, despite the widespread opinion that the evolutionary theory is the major basis for taxonomy, the processes, which in fact caused the origin and formation of the systematic hierarchy are often considered as redundant for the procedure of classification. In this respect, the classical, but well forgotten statement that evolution is a modification of ontogeny is specially highlighted. Tight relationships between evolution, ontogeny, systematics, and phylogenetics are prima facie obvious, but also presently underestimated, although the field of the evo-devo is continuously growing. Paradoxically, even despite the outburst of various molecular ontogenetic approaches, the commonly accepted evolutionary paradigm still lacks a general theory for changes in the shape of organisms. As a step towards the development of such a theory, a synthesis (or more exactly, resynthesis) of still largely independently developing major biological fields, i.e., ontogenetic and evolutionary studies, on the one hand, and traditional taxonomy, on the other hand, a new concept of ontogenetic systematics is proposed. The new concept is intended for integration of supposedly ??immobile?? traditional taxonomy with the dynamics, but predominantly considered as hypothetical, evolutionary field based on the process of ontogeny, which, in contrast to the evolution itself, can be observed in the real time. Therefore, it is concluded that, for instance, the evolution of the main group of living organisms Metazoa, is primarily the evolution of a very limited number of ontogenetic cycles that were formed as early as the Early Cambrian. A significant underestimation of cyclic properties of ontogeny in the evolution and systematics is shown. Using two model groups, echinoderms of the class Ophiuroidea and dorid nudibranch mollusks (Gastropoda: Doridacea), practical importance of the integrative approach developed here is demonstrated. The ??disruption?? of the ancestral ontogenetic cycle and further formation of a new descendant cycle (which implies some continuity of ancestral and descendant characters) is considered to be a major evolutionary pattern. The model proposed implies either progressive (addition of stages and characters) or regressive (reduction of already existing stages and structures) modification of ancestral taxon, the diagnosis of which corresponds to the model of its ontogenetic cycle. In the extreme cases of disruption of the ancestral ontogenetic cycle, adult characters of descendants are substituted by juvenile ancestral features, demonstrating paedomorphoses in the narrow sense. Within the framework of the approach proposed, the evolutionary and ontogenetic models of ancestral ontogenetic cycles of brittle stars and dorid nudibranchs are developed and discussed. Based on the original material of the extinct Paleozoic ophiuroid group Oegophiurida, the origin of key evolutionary novelties is discussed. A major conclusion of the present review is the high necessity of integration of new molecular data with already well-established taxonomic hierarchy and ontogenetic information as a basis for the development of the general theory of transformations of organisms, i.e., the theory of evolution in its true sense.     

Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance

The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g., cryptic species), differences in criteria of species concepts, lineages being in the early stages of the speciation or divergence process, and discordance between gene topologies (e.g., mitonuclear discordance). Here we use a taxonomically confounded species complex of toads in Central America that exhibits extensive mitonuclear discordance to test delimitation hypotheses. Our investigation integrates mitochondrial sequences, nuclear SNPs, morphology, and macroecological data to determine which taxonomy best explains the divergence and evolutionary relationships among these toads. We found that a three species taxonomy following the distributions of the nuclear SNP haplotypes offers the best explanation of the species in this complex based off of the integrated data types. Due to the taxonomic instability of this group, we also discuss conservation concerns in the face of improper taxonomic delimitation. Our study provides an empirical and integrative hypothesis testing framework to assess species delimitation hypotheses in the face of cryptic morphology and mitonuclear discordance and highlights the importance that a stable taxonomy has over conservation‐related actions.     

General protein patterns of muscle homogenates of some Lake Victoria haplochromines (Pisces: Cichlidae)

Cichlid fishes of the great East African lakes have been the subject of many evolutionary studies over the last decades. Over 100 haplochromine species have been described from Lake Victoria alone, many of which are endemic to that lake. Two recent studies, using enzyme electrophoresis, could not detect any genetic differentiation among the examined species. Consequently, it was concluded that the gene loci which were scored in these studies were not relevant to the genetic changes which occurred during speciation. Analyses of general protein electrophoretic patterns, however, does reveal differentiation on the supraspecific level. Three basic species groups can be discerned, each associated with ecological characteristics of these species such as diet and substratum. Implications for haplochromine evolution and taxonomy are discussed. Our data seem to support the hypothesis that trophic differentiation may have occurred within habitats, implying the possible importance of sympatric speciation in haplochromine evolution in Lake Victoria.     

591. EUPOMATIA LAURINA

Summary.  The evolutionary history, taxonomy, pollination biology and cultivation of Eupomatia laurina R. Br. (Eupomatiaceae ) are discussed. The species is illustrated with a painting and line drawings.     

The Species Concept as a Cognitive Tool for Biological Anthropology

Taxonomy is caught between the search for the “perfect” theory and an elusive biological variability. The lack of major advances in issues related to how “species” and other taxonomic categories are defined suggests that perhaps we should avoid excessively rigid formalism in this regard. The risk is a separation between elegant but useless theories and confusing applications of the taxonomic tools. Communication is one of the main functions of taxonomy, and stability one of the main parameters that taxonomy users should be sensitive to. An excess of stability may generate anachronistic consequences while continuous revisions may make the tool of taxonomy scarcely practical. The current tendency pushes toward more and more fragmentation of biologically valid taxa. While taxonomy specialists enjoy such challenges, many taxonomy users feel a bit nervous and discouraged when trying to use a tool that is constantly changing. Debates over taxonomy would seem particularly unrewarding for fields with limited samples and scarce biological diversity, such as palaeoanthropology. In this context, where the information available is rarely sufficient to supply consistent taxonomical evidence, there are frequently excessive efforts to create debate on species separations. The risk is that we maintain the debate on a purely theoretical level, or else we distrust a reliable use of taxonomy. A compromise (and recommended) choice between these two extremes would be to rely on shared and reasonable interpretations of homogeneous evolutionary units, without diving into fine‐grained issues that will remain, however, unresolved. Taxonomy should be a tool, not the goal, of the evolutionary biologist. Our mind needs discrete and recognizable objects to structure our perception of reality. There is no reason to expect that nature works the same way. Am. J. Primatol. 75:10‐15, 2013. © 2012 Wiley Periodicals, Inc.     

THE RELATIONSHIP BETWEEN EVOLUTIONARY THEORY AND PHYLOGENETIC ANALYSIS

The relationship between phylogenetic reconstruction and evolutionary theory is reassessed. It is argued here that phylogenies, and evolutionary principles, should be analysed initially as independently from each other as possible. Only then can they be used to test one another. If the phylogenies and evolutionary principles are totally consistent with one another, this consilience of independent lines of evidence increases confidence in both. If, however, there is a conflict, then one should assess the relative support for each hypothesis, and tentatively accept the more strongly supported one. We review examples where the phylogenetic hypothesis is preferred over the evolutionary principle, and vice versa, and instances where the conflict cannot be readily resolved. Because the analyses of pattern and process must initially be kept separate, the temporal order in which they are performed is unimportant. Therefore, the widespread methodology of always proceeding from cladogram to evolutionary ‘scenario’ cannot be justified philosophically. Such an approach means that cladograms cannot be properly tested against evolutionary principles, and that evolutionary ‘scenarios’ have no independent standing. Instead, we propose the ‘consilience’ approach where phylogenetic and evolutionary hypotheses are formulated independently from each other and then examined for agreement.     

An emerging synthesis between community ecology and evolutionary biology

A synthesis between community ecology and evolutionary biology is emerging that identifies how genetic variation and evolution within one species can shape the ecological properties of entire communities and, in turn, how community context can govern evolutionary processes and patterns. This synthesis incorporates research on the ecology and evolution within communities over short timescales (community genetics and diffuse coevolution), as well as macroevolutionary timescales (community phylogenetics and co-diversification of communities). As we discuss here, preliminary evidence supports the hypothesis that there is a dynamic interplay between ecology and evolution within communities, yet researchers have not yet demonstrated convincingly whether, and under what circumstances, it is important for biologists to bridge community ecology and evolutionary biology. Answering this question will have important implications for both basic and applied problems in biology.     

Phylogenetic Inferences Reveal a Large Extent of Novel Biodiversity in Chemically Rich Tropical Marine Cyanobacteria

Benthic marine cyanobacteria are known for their prolific biosynthetic capacities to produce structurally diverse secondary metabolites with biomedical application and their ability to form cyanobacterial harmful algal blooms. In an effort to provide taxonomic clarity to better guide future natural product drug discovery investigations and harmful algal bloom monitoring, this study investigated the taxonomy of tropical and subtropical natural product-producing marine cyanobacteria on the basis of their evolutionary relatedness. Our phylogenetic inferences of marine cyanobacterial strains responsible for over 100 bioactive secondary metabolites revealed an uneven taxonomic distribution, with a few groups being responsible for the vast majority of these molecules. Our data also suggest a high degree of novel biodiversity among natural product-producing strains that was previously overlooked by traditional morphology-based taxonomic approaches. This unrecognized biodiversity is primarily due to a lack of proper classification systems since the taxonomy of tropical and subtropical, benthic marine cyanobacteria has only recently been analyzed by phylogenetic methods. This evolutionary study provides a framework for a more robust classification system to better understand the taxonomy of tropical and subtropical marine cyanobacteria and the distribution of natural products in marine cyanobacteria.     

A monograph of the order Pyrosomatida (Tunicata, Thaliacea)

The taxonomy of the order Pyrosomatida is revised based on theexamination of over 300 samples from all parts of the worldoceans. The order consists of a single family (Pyrosomatidae),two subfamilies (Pyrostremmatinae and Pyrosomatinae), threegenera (Pyrostremma, Pyrosomdla and Pyrosoma) and 8 species(Pyrostremma spinosum, P. agassizi, Pyrosomella verticillata.P. operculata, Pyrosoma atlanticum, P. aherniosum, P. ovatumand P. godeauxi n.sp.). The species are briefly described anddata on their distribution are provided. A key to the speciesis given. A cladistic analysis of the distribution of relevantcharacter states is made and ideas on evolutionary developmentare put forward. Biogeographical data are summarized and inconjunction with that the likely modes of speciation in thisgroup are briefly discussed.     

Phylogeny and biogeography of the core babblers (Aves: Timaliidae)

The avian family Timaliidae is a species rich and morphologically diverse component of African and Asian tropical forests. The morphological diversity within the family has attracted interest from ecologists and evolutionary biologists, but systematists have long suspected that this diversity might also mislead taxonomy, and recent molecular phylogenetic work has supported this hypothesis. We produced and analyzed a data set of 6 genes and almost 300 individuals to assess the evolutionary history of the family. Although phylogenetic analysis required extensive adjustment of program settings, we ultimately produced a well-resolved phylogeny for the family. The resulting phylogeny provided strong support for major subclades within the family but extensive paraphyly of genera. Only 3 genera represented by more than 3 species were monophyletic. Biogeographic reconstruction indicated a mainland Asian origin for the family and most major clades. Colonization of Africa, Sundaland, and the Philippines occurred relatively late in the family's history and was mostly unidirectional. Several putative babbler genera, such as Robsonius, Malia, Leonardina, and Micromacronus are only distantly related to the Timaliidae.     

Rethinking the Synthesis Period in Evolutionary Studies

I propose we abandon the unit concept of “the evolutionary synthesis”. There was much more to evolutionary studies in the 1920s and 1930s than is suggested in our commonplace narratives of this object in history. Instead, four organising threads capture much of evolutionary studies at this time. First, the nature of species and the process of speciation were dominating, unifying subjects. Second, research into these subjects developed along four main lines, or problem complexes: variation, divergence, isolation, and selection. Some calls for ‹synthesis’ focused on these problem complexes (sometimes on one of these; other times, all). In these calls, comprehensive and pluralist compendia of plausibly relevant elements were preferred over reaching consensus about the value of particular formulae. Third, increasing confidence in the study of common problems coincided with methodological and epistemic changes associated with experimental taxonomy. Finally, the surge of interest in species problems and speciation in the 1930s is intimately tied to larger trends, especially a shifting balance in the life sciences towards process-based biologies and away from object-based naturalist disciplines. Advocates of synthesis in evolution supported, and were adapting to, these larger trends.