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1.
Olivier Rieppel 《分类学与生物多样性》2013,11(1):9-19
This contribution analyses the primacy of classification over generalization, and the philosophy of total evidence that emerges from the relation of homology to character statements. Primary conjectures of homology are basic character statements, i.e. statements that predicate properties of organisms, properties that are instantiated by those organisms and/or their parts. Secondary conjectures of homology are embedded in a second‐level (metalinguistic) discourse that turns on the coherence or incoherence of those basic character statements relative to a hierarchy. The coherence or incoherence of character statements is a logical relation between statements, not a causal (historical) relation between organisms. The choice of the hypothesis of relationships that is supported by the largest set of coherent basic character statements is based on the empirical presupposition that the properties referred to by the set of coherent character statements are grounded in causally efficacious relations of inheritance and ontogeny, and co‐instantiated because they are inherited through common ancestry (Hennig's auxiliary principle). Unless that empirical presupposition is causally grounded, phylogeny reconstruction is of an inherently probabilistic nature, whether under parsimony or other models of analysis. The causal grounding of a coherent set of character statements typically seeks a link between character statements and causally efficacious generative mechanisms for morphological characters (as is defeasibly indicated by topology and connectivity), or secondary structure information for molecular characters. 相似文献
2.
James Mallet Nora Besansky Matthew W. Hahn 《BioEssays : news and reviews in molecular, cellular and developmental biology》2016,38(2):140-149
Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree‐like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control. 相似文献
3.
Samar O. Rabah Bikash Shrestha Nahid H. Hajrah Mumdooh J. Sabir Hesham F. Alharby Mernan J. Sabir Alawiah M. Alhebshi Jamal S.M. Sabir Lawrence E. Gilbert Tracey A. Ruhlman Robert K. Jansen 《植物分类学报:英文版》2019,57(1):1-14
Although past studies have included Passiflora among angiosperm lineages with highly rearranged plastid genomes (plastomes), knowledge about plastome organization in the genus is limited. So far only one draft and one complete plastome have been published. Expanded sampling of Passiflora plastomes is needed to understand the extent of the genomic rearrangement in the genus, which is also unusual in having biparental plastid inheritance and plastome‐genome incompatibility. We sequenced 15 Passiflora plastomes using either Illumina paired‐end or shotgun cloning and Sanger sequencing approaches. Assembled plastomes were annotated using Dual Organellar GenoMe Annotator (DOGMA) and tRNAscan‐SE. The Populus trichocarpa plastome was used as a reference to estimate genomic rearrangements in Passiflora by performing whole genome alignment in progressiveMauve. The phylogenetic distribution of rearrangements was plotted on the maximum likelihood tree generated from 64 plastid encoded protein genes. Inverted repeat (IR) expansion/contraction and loss of the two largest hypothetical open reading frames, ycf1 and ycf2, account for most plastome size variation, which ranges from 139 262 base pairs (bp) in P. biflora to 161 494 bp in P. pittieri. Passiflora plastomes have experienced numerous inversions, gene and intron losses along with multiple independent IR expansions and contractions resulting in a distinct organization in each of the three subgenera examined. Each Passiflora subgenus has a unique plastome structure in terms of gene content, order and size. The phylogenetic distribution of rearrangements shows that Passiflora has experienced widespread genomic changes, suggesting that such events may not be reliable phylogenetic markers. 相似文献
4.
Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus 下载免费PDF全文
Maria Aleksandra Bitner Bernard L. Cohen 《Zoological Journal of the Linnean Society》2015,173(2):486-504
We present five case studies among articulate (rhynchonelliform) brachiopods, i.e. of Rhynchonellida, Cancellothyridoidea, Terebratuloidea, Dyscolioidea, Laqueoidea, and various terebratulids with modified long‐loops, in an attempt to illustrate and better understand congruence and conflict between morpho‐classification and rDNA‐based molecular clade structure, having been prompted to address these issues by difficulties encountered when describing the newly collected brachiopod, E biscothyris bellonensis gen. et sp. nov. The five studies reveal dramatic conflict in the Rhynchonellida and Terebratuloidea/Dyscolioidea, good congruence in the Cancellothyridoidea and Laqueoidea, and fair congruence (albeit with weak phylogenetic signal) in the long‐looped terebratulids. We suggest that the leading cause of the observed conflict lies in the use of inadequately specific morphological characters and morpho‐classification. Phylogenetic systematic (cladistic) analyses of Rhynchonellida also conflict markedly with the rDNA gene tree, leading us to recognize that such analyses are not only conceptually circular (using morphological characters to assess a morphological classification) but also to propose that they are biased by the act of classification that necessarily precedes the identification of putatively homologous characters; when the prior classification does not reflect evolutionary history, phylogenetic analysis will do likewise. In addition, we propose that the brachiopod community has overlooked the significance of two sources of morphological homoplasy affecting brachiopod systematics: (1) the loss of co‐adapted genomic complexes caused by mass extinctions at the end of the Permian; and (2) the pervasive consequences of developmental integration and constraint resulting from the integrated roles of the outer mantle epithelium in shell deposition and growth that underly the determination of form and the shell‐based classification. © 2015 The Linnean Society of London 相似文献
5.
Lloyd BD 《Molecular ecology》2003,12(7):1895-1911
Short-tailed bats Mystacina tuberculata were widespread throughout the forest that dominated prehuman New Zealand, but extensive deforestation has restricted them to scattered populations in forest fragments. In a previous study, the species' intraspecific phylogeny was investigated using multiple mitochondrial gene sequences. Six phylogroups were identified with estimated divergences of 0.93-0.68 Ma. In the current study, the phylogeographical structure and demographic history of the phylogroups were investigated using control region sequences modified by removing homoplasic sites. Phylogeographical structure in the North Island was generally consistent with an isolation-by-distance dispersal model. Coalescent-based analyses (i.e. mismatch distributions, skyline plots, lineage dispersal analysis and nested clade analysis) indicated that the three phylogroups found in central and southern North Island expanded before the last glacial maximum, presumably during interstadials when Nothofagus forest was most extensive. Genetic structure within a central North Island hybrid zone was consistent with range expansion from separate refugia following reforestation after catastrophic volcanic eruptions. Phylogeographical structure in the South Island was consistent with southern populations originating during rapid southward range expansion from refugia in northern South Island following postglacial reforestation of the South Island 10-9 kya. 相似文献
6.
Arnold EN 《Journal of morphology》2002,252(2):145-169
Differences in surface structure (ober-hautchen) of body scales of lacertid lizards involve cell size, shape and surface profile, presence or absence of fine pitting, form of cell margins, and the occurrence of longitudinal ridges and pustular projections. Phylogenetic information indicates that the primitive pattern involved narrow strap-shaped cells, with low posteriorly overlapping edges and relatively smooth surfaces. Deviations from this condition produce a more sculptured surface and have developed many times, although subsequent overt reversals are uncommon. Like variations in scale shape, different patterns of dorsal body microornamentation appear to confer different and conflicting performance advantages. The primitive pattern may reduce friction during locomotion and also enhances dirt shedding, especially in ground-dwelling forms from moist habitats. However, this smooth microornamentation generates shine that may compromise cryptic coloration, especially when scales are large. Many derived features show correlation with such large scales and appear to suppress shine. They occur most frequently in forms from dry habitats or forms that climb in vegetation away from the ground, situations where dirt adhesion is less of a problem. Microornamentation differences involving other parts of the body and other squamate groups tend to corroborate this functional interpretation. Microornamentation features can develop on lineages in different orders and appear to act additively in reducing shine. In some cases different combinations may be optimal solutions in particular environments, but lineage effects, such as limited reversibility and different developmental proclivities, may also be important in their genesis. The fine pits often found on cell surfaces are unconnected with shine reduction, as they are smaller than the wavelengths of most visible light. 相似文献
7.
Hall BK 《Biological reviews of the Cambridge Philosophical Society》2003,78(3):409-433
Homology is at the foundation of comparative studies in biology at all levels from genes to phenotypes. Homology is similarity because of common descent and ancestry, homoplasy is similarity arrived at via independent evolution. However, given that there is but one tree of life, all organisms, and therefore all features of organisms, share some degree of relationship and similarity one to another. That sharing may be similarity or even identity of structure and the sharing of a most recent common ancestor--as in the homology of the arms of humans and apes--or it may reflect some (often small) degree of similarity, such as that between the wings of insects and the wings of birds, groups whose shared ancestor lies deep within the evolutionary history of the Metazoa. It may reflect sharing of entire developmental pathways, partial sharing, or divergent pathways. This review compares features classified as homologous with the classes of features normally grouped as homoplastic, the latter being convergence, parallelism, reversals, rudiments, vestiges, and atavisms. On the one hand, developmental mechanisms may be conserved, even when a complete structure does not form (rudiments, vestiges), or when a structure appears only in some individuals (atavisms). On the other hand, different developmental mechanisms can produce similar (homologous) features. Joint examination of nearness of relationship and degree of shared development reveals a continuum within an expanded category of homology, extending from homology --> reversals --> rudiments --> vestiges --> atavisms --> parallelism, with convergence as the only class of homoplasy, an idea that turns out to be surprisingly old. This realignment provides a glimmer of a way to bridge phylogenetic and developmental approaches to homology and homoplasy, a bridge that should provide a key pillar for evolutionary developmental biology (evo-devo). It will not, and in a practical sense cannot, alter how homoplastic features are identified in phylogenetic analyses. But seeing rudiments, reversals, vestiges, atavisms and parallelism as closer to homology than to homoplasy should guide us toward searching for the common elements underlying the formation of the phenotype (what some have called the deep homology of genetic and/or cellular mechanisms), rather than discussing features in terms of shared or independent evolution. 相似文献
8.
Patterns of linkage disequilibrium, homoplasy, and incompatibility are difficult to interpret because they depend on several factors, including the recombination process and the population structure. Here we introduce a novel model-based framework to infer recombination properties from such summary statistics in bacterial genomes. The underlying model is sequentially Markovian so that data can be simulated very efficiently, and we use approximate Bayesian computation techniques to infer parameters. As this does not require us to calculate the likelihood function, the model can be easily extended to investigate less probed aspects of recombination. In particular, we extend our model to account for the bias in the recombination process whereby closely related bacteria recombine more often with one another. We show that this model provides a good fit to a data set of Bacillus cereus genomes and estimate several recombination properties, including the rate of bias in recombination. All the methods described in this article are implemented in a software package that is freely available for download at http://code.google.com/p/clonalorigin/. 相似文献
9.
Katz PS 《Philosophical transactions of the Royal Society of London. Series B, Biological sciences》2011,366(1574):2086-2099
The complexity of nervous systems alters the evolvability of behaviour. Complex nervous systems are phylogenetically constrained; nevertheless particular species-specific behaviours have repeatedly evolved, suggesting a predisposition towards those behaviours. Independently evolved behaviours in animals that share a common neural architecture are generally produced by homologous neural structures, homologous neural pathways and even in the case of some invertebrates, homologous identified neurons. Such parallel evolution has been documented in the chromatic sensitivity of visual systems, motor behaviours and complex social behaviours such as pair-bonding. The appearance of homoplasious behaviours produced by homologous neural substrates suggests that there might be features of these nervous systems that favoured the repeated evolution of particular behaviours. Neuromodulation may be one such feature because it allows anatomically defined neural circuitry to be re-purposed. The developmental, genetic and physiological mechanisms that contribute to nervous system complexity may also bias the evolution of behaviour, thereby affecting the evolvability of species-specific behaviour. 相似文献
10.
JOSEPH H. WILLIAMS ROBERT T. MCNEILAGE MATTHEW T. LETTRE MACKENZIE L. TAYLOR 《Botanical journal of the Linnean Society. Linnean Society of London》2010,162(4):581-593
An important aspect of the evolution of carpel closure, or angiospermy, is the relationship between pollen tube growth patterns and internalization of the pollen‐tube pathway. True carpel closure, involving postgenital fusion of inner carpel margins, is inferred to have arisen once within the ancient order Nymphaeales, in the common ancestor of Nymphaeaceae. We studied pollen tube development, from pollination to fertilization, in a natural population of Nymphaea odorata, using hand pollinations and timed flower collections. Pollen germinates in stigmatic secretions within 15 min and pollen tubes enter subdermal transmitting tissue within an hour, following wide intercellular spaces towards the zone of postgenital fusion. At the zone of fusion they turn downwards to grow in narrow spaces between interlocked cells and then wander freely to ovules within ovarian secretions. The pollen‐tube pathway is 2–6 mm long and upper ovules are first penetrated 2.5 h after pollination. Pollen tubes grow at rates of approximately 1 mm/h whether in stigmatic fluid, transmitting tissues or ovarian secretions. Pollen‐tube pathways are structurally diverse across Nymphaeales, yet their pollen tubes have similar morphologies and rapid growth rates. This pattern suggests pollen tube growth innovations preceded and were essential for the evolution of complete carpel closure. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162 , 581–593. 相似文献