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1.
Ralf Britz Kevin W. Conway Lukas Rüber 《Zoological Journal of the Linnean Society》2014,172(3):556-615
We review the morphological and molecular evidence that Mayden & Chen recently used to infer that the developmentally truncated fish genus Paedocypris is not a member of the teleost order Cypriniformes or carp‐like fishes, but is ‘the basal sister group to all Cypriniformes’. This hypothesis contradicts several previous studies that used molecular sequence data or morphological characters. A review of the morphological characters that Mayden & Chen discussed and mapped onto their ‘simplified tree’ shows that these, analysed alone, rather support a close relationship of the cyprinids Sundadanio, Danionella, and Paedocypris. We also present four additional analyses of morphological data, which all contradict Mayden & Chen's result. Despite its highly reductive skeleton, posing a serious problem when analysing its phylogenetic position with skeletal characters, the presence in Paedocypris of the basioccipital masticatory plate is compelling evidence that it is a member of the Cyprinoidei (Cyprinidae plus Psilorhynchidae). Our reanalysis and exploration of their molecular sequence data shows that only a single gene, EGR3, of the six nuclear genes analysed by Mayden & Chen, is responsible for the position of Paedocypris as ‘the basal sister group to all Cypriniformes’. Three independent methods to visualize and analyse phylogenetic signal and conflict of data sets (phylogenetic networks, splits analysis methods or SAMS, and site‐wise likelihood analyses) reveal a high level of character conflict and noise in Mayden & Chen's data set. The ‘basal’ position of Paedocypris seems to be the outcome of the interplay of two long‐branch effects. We apply the same analytical methods to the data set from Rüber et al.'s molecular analysis of the phylogenetic position of Paedocypris and discuss our findings. We conclude that none of the molecular data sets compiled to date can establish the phylogenetic position of Paedocypris with confidence. Morphological data suggest that Paedocypris and Danionella are sister genera, and that their closest relative is Sundadanio, although the position of these three miniatures among cyprinoids is still unclear. © 2014 The Linnean Society of London 相似文献
2.
Species of the cyprinid genus Paedocypris are among the smallest and most developmentally truncated fishes and vertebrates. Our analysis of their skeletal structure reveals a puzzling combination of extreme developmental truncation and an increased morphological complexity in sexually dimorphic characters. The skeleton of Paedocypris is characterized by reduction and loss and resembles in many aspects that of a larval/early juvenile stage of its close relatives. We found 61 characters that have been affected by developmental truncation. A comparison with the skeletal development of a close relative, the zebrafish Danio rerio, demonstrates that the majority of the absent bones or skeletal structures in Paedocypris are those that appear late in the ossification trajectory of the zebrafish. Thus, their absence in Paedocypris seems to be due to the simple developmental truncation of terminal stages in the ossification sequence. Our study of the sexually dimorphic structures in Paedocypris demonstrates that predominantly the male exhibits the more complex state. In relation to the female, male Paedocypris uniquely possess a cleithrum with a pointed posterior process that covers the scapula laterally, and a more medially situated posterior flange that contacts the dorsal area of the coracoid; a massive and heavily ossified uppermost pectoral radial tightly bound to the scapula; thickened and enlarged three uppermost pectoral‐fin rays; a large triangular, dorsolaterally directed process on the outer arm of the massive os suspensorium; and a enlarged and shovel‐like anterodorsally directed basipterygium; and a hypertrophied first pelvic‐fin ray with additional anterior flanges that support keratinized pads of skin. Female Paedocypris show only one structure that is better developed than in males: the first proximal‐middle radial and the anteriormost fin ray of the dorsal fin are more massive and more heavily ossified. Although the function and biological role of these dimorphisms is still unknown, we hypothesize that they are related to a special reproductive behavior. Paedocypris is a prime example for the recent claim that miniaturization among cyprinids is associated with evolutionary novelty only in developmentally truncated miniatures and not in proportioned dwarfs. Paedocypris offers a strong challenge to Schindleria as the most extreme example of developmental truncation known among fishes. We highlight the difficulties that developmentally truncated taxa frequently pose to the resolution of their phylogenetic position and propose an approach to overcome this problem. Our phylogenetic comparison to determine the systematic position of Paedocypris among cyprinids reveals that it shares not only a number of unique absences, but also highly unusual progressive characters with Sundadanio and Danionella, two other Asian miniature cyprinids. We hypothesize that the three genera form a monophyletic group. We further found that Paedocypris and Danionella share a number of uniquely derived characters pointing to a sister group relationship of the two. J. Morphol., 2009. © 2008 Wiley‐Liss, Inc. 相似文献
3.
Background
The genome sequence of the pufferfish Takifugu rubripes is an enormously useful tool in the molecular physiology of fish. Euryhaline fish that can survive both in freshwater (FW) and seawater (SW) are also very useful for studying fish physiology, especially osmoregulation. Recently we learned that there is a pufferfish, Takifugu obscurus, common name "mefugu" that migrates into FW to spawn. If T. obscurus is indeed a euryhaline fish and shares a high sequence homology with T. rubripes, it will become a superior animal model for studying the mechanism of osmoregulation. We have therefore determined its euryhalinity and phylogenetic relationship to the members of the Takifugu family. 相似文献4.
5.
Claudia Patricia Ornelas-García Omar Domínguez-Domínguez Ignacio Doadrio 《BMC evolutionary biology》2008,8(1):340
Background
Mesoamerica is one of the world's most complex biogeographical regions, mostly due to its complex geological history. This complexity has led to interesting biogeographical processes that have resulted in the current diversity and distribution of fauna in the region. The fish genus Astyanax represents a useful model to assess biogeographical hypotheses due to it being one of the most diverse and widely distributed freshwater fish species in the New World. We used mitochondrial and nuclear DNA to evaluate phylogenetic relationships within the genus in Mesoamerica, and to develop historical biogeographical hypotheses to explain its current distribution. 相似文献6.
Flavio Marchetto Serena Zaccara Frauke M Muenzel Walter Salzburger 《BMC evolutionary biology》2010,10(1):111
Background
Owing to its independence from the main Central European drainage systems, the Italian freshwater fauna is characterized by a high degree of endemicity. Three main ichthyogeographic districts have been proposed in Italy. Yet, the validity of these regions has not been confirmed by phylogenetic and population genetic analyses and a phylogeographic scenario for Italy's primary freshwater fish fauna is still lacking. Here, we investigate the phylogeography of the Italian vairone (Telestes muticellus). 相似文献7.
Background
The phylogenetic position and evolutionary relationships of Fusobacteria remain uncertain. Especially intriguing is their relatedness to low G+C Gram positive bacteria (Firmicutes) by ribosomal molecular phylogenies, but their possession of a typical gram negative outer membrane. Taking advantage of the recent completion of the Fusobacterium nucleatum genome sequence we have examined the evolutionary relationships of Fusobacterium genes by phylogenetic analysis and comparative genomics tools. 相似文献8.
Ruth?Tachezy Annabel?Rector Marta?Havelkova Elke?Wollants Pierre?Fiten Ghislain?Opdenakker A?Bennett?Jenson John?P?Sundberg Marc?Van Ranst
Background
An avian papillomavirus genome has been cloned from a cutaneous exophytic papilloma from an African grey parrot (Psittacus erithacus). The nucleotide sequence, genome organization, and phylogenetic position of the Psittacus erithacus papillomavirus (PePV) were determined. This PePV sequence represents the first complete avian papillomavirus genome defined. 相似文献9.
Rodolfo Pérez-Rodríguez Omar Domínguez-Domínguez Gerardo Pérez Ponce de León Ignacio Doadrio 《BMC evolutionary biology》2009,9(1):223
Background
The genus Algansea is one of the most representative freshwater fish groups in central Mexico due to its wide geographic distribution and unusual level of endemicity. Despite the small number of species, this genus has had an unsettled taxonomic history due to high levels of intraspecific morphological variation. Moreover, several phylogenetic hypotheses among congeners have been proposed but have had the following shortcomings: the use of homoplasious morphological characters, the use of character codification and polarisation methods that lacked objectivity, and incomplete taxonomic sampling. In this study, a phylogenetic analysis among species of Algansea is presented. This analysis is based upon two molecular markers, the mitochondrial gene cytochrome b and the first intron of the ribosomal protein S7 gene. 相似文献10.
Nathaniel M Evans Alberto Lindner Ekaterina V Raikova Allen G Collins Paulyn Cartwright 《BMC evolutionary biology》2008,8(1):139
Background
Polypodium hydriforme is a parasite with an unusual life cycle and peculiar morphology, both of which have made its systematic position uncertain. Polypodium has traditionally been considered a cnidarian because it possesses nematocysts, the stinging structures characteristic of this phylum. However, recent molecular phylogenetic studies using 18S rDNA sequence data have challenged this interpretation, and have shown that Polypodium is a close relative to myxozoans and together they share a closer affinity to bilaterians than cnidarians. Due to the variable rates of 18S rDNA sequences, these results have been suggested to be an artifact of long-branch attraction (LBA). A recent study, using multiple protein coding markers, shows that the myxozoan Buddenbrockia, is nested within cnidarians. Polypodium was not included in this study. To further investigate the phylogenetic placement of Polypodium, we have performed phylogenetic analyses of metazoans with 18S and partial 28S rDNA sequences in a large dataset that includes Polypodium and a comprehensive sampling of cnidarian taxa. 相似文献11.
Background
The chondrichthyan or cartilaginous fish (chimeras, sharks, skates and rays) occupy an important phylogenetic position as the sister group to all other jawed vertebrates and as an early lineage to diverge from the vertebrate lineage following two whole genome duplication events in vertebrate evolution. There have been few comparative genomic analyses incorporating data from chondrichthyan fish and none comparing genomic information from within the group. We have sequenced the complete Hoxa cluster of the Little Skate (Leucoraja erinacea) and compared to the published Hoxa cluster of the Horn Shark (Heterodontus francisci) and to available data from the Elephant Shark (Callorhinchus milii) genome project. 相似文献12.
Molecular Evidence on the Evolutionary and Biogeographical Patterns of European Cyprinids 总被引:21,自引:0,他引:21
The phylogenetic relationships of 106 European cyprinid taxa were determined based on the complete nucleotide sequence (1140
bp) of the mitochondrial cytochrome b gene. The molecular phylogeny was used (1) to revise the current systematics of European cyprinids, (2) to establish the
phylogenetic utility of traditional morphological characters that are widely used in Cyprinidae systematics, and (3) to discuss
alternative hypotheses on the biogeography of the family in Europe. The age of the major lineages within European cyprinids
was tentatively estimated with a molecular clock and showed full agreement with the fossil record of the group. Moreover,
the results provided unambiguous evidence for a close phylogenetic affinity of some Caucasian and Greek endemic cyprinid taxa
(e.g., B. capito and B. brachycephalus and Leuciscus keadicus, Barbus graecus, and B. albanicus, respectively) to Iberian and North African, but not Central European, cyprinids. The existence of such unexpected phylogenetic
relationships refutes the classical hypothesis on the biogeography of European cyprinids, which assumes a dispersal of the
cyprinid fauna from central Europe to southern Europe and northern Africa during the Miocene (and, hence, predicts a close
phylogenetic relationship of all Caucasian, Greek, Iberian, and North African cyprinids to central European taxa). Instead,
the existence of a Mediterranean realm independent of the central European route seems plausible based on the molecular evidence.
It is likely that the new biogeographical scenario proposed here might apply to other primary freshwater European animals
with low dispersal abilities, including fish, amphibians, and invertebrates.
Received: 2 February 1999 / Accepted: 16 March 1999 相似文献
13.
Background
The North American Agalinis are representatives of a taxonomically difficult group that has been subject to extensive taxonomic revision from species level through higher sub-generic designations (e.g., subsections and sections). Previous presentations of relationships have been ambiguous and have not conformed to modern phylogenetic standards (e.g., were not presented as phylogenetic trees). Agalinis contains a large number of putatively rare taxa that have some degree of taxonomic uncertainty. We used DNA sequence data from three chloroplast genes to examine phylogenetic relationships among sections within the genus Agalinis Raf. (= Gerardia), and between Agalinis and closely related genera within Orobanchaceae. 相似文献14.
Joshua M Hull David P Mindell Sandra L Talbot Emily H Kay Hopi E Hoekstra Holly B Ernest 《BMC evolutionary biology》2010,10(1):224
Background
Phenotypic and molecular genetic data often provide conflicting patterns of intraspecific relationships confounding phylogenetic inference, particularly among birds where a variety of environmental factors may influence plumage characters. Among diurnal raptors, the taxonomic relationship of Buteo jamaicensis harlani to other B. jamaicensis subspecies has been long debated because of the polytypic nature of the plumage characteristics used in subspecies or species designations. 相似文献15.
Janet Yee Anita Tang Wei-Ling Lau Heather Ritter Dewald Delport Melissa Page Rodney D Adam Miklós Müller Gang Wu 《BMC molecular biology》2007,8(1):26
Background
Giardia intestinalis is a protist found in freshwaters worldwide, and is the most common cause of parasitic diarrhea in humans. The phylogenetic position of this parasite is still much debated. Histones are small, highly conserved proteins that associate tightly with DNA to form chromatin within the nucleus. There are two classes of core histone genes in higher eukaryotes: DNA replication-independent histones and DNA replication-dependent ones. 相似文献16.
Background
WTX is a novel gene mutated in a proportion of Wilms' tumors and in patients suffering from sclerosing bone dysplasia. On the molecular level WTX has been shown to act as an antagonist of canonical Wnt/β-catenin signaling in fish and mammals thus linking it to an essential pathway involved in normal development and cancer formation. Interestingly, WTX seems to also localize to an intranuclear component called paraspeckles. In spite of the growing interest of molecular biologists in WTX, little is known about its paralogs and its phylogenetic history. 相似文献17.
Kenneth M Noll Pascal Lapierre J Peter Gogarten Dhaval M Nanavati 《BMC evolutionary biology》2008,8(1):7
Background
The mal genes that encode maltose transporters have undergone extensive lateral transfer among ancestors of the archaea Thermococcus litoralis and Pyrococcus furiosus. Bacterial hyperthermophiles of the order Thermotogales live among these archaea and so may have shared in these transfers. The genome sequence of Thermotoga maritima bears evidence of extensive acquisition of archaeal genes, so its ancestors clearly had the capacity to do so. We examined deep phylogenetic relationships among the mal genes of these hyperthermophiles and their close relatives to look for evidence of shared ancestry. 相似文献18.
Background
In the studies incorporating worldwide sampling of A. thaliana populations, the samples from East Asia, especially from China, were very scattered; and the studies focused on global patterns of cpDNA genetic variation among accessions of A. thaliana are very few. In this study, chloroplast DNA sequence variability was used to infer phylogenetic relationships among Arabidopsis thaliana accessions from around the world, with the emphasis on samples from China. 相似文献19.
Ryan B MacDonald Mélanie Debiais-Thibaud Kyle Martin Luc Poitras Boon-Hui Tay Byrappa Venkatesh Marc Ekker 《BMC evolutionary biology》2010,10(1):157
Background
The phylogenetic position of the elephant shark (Callorhinchus milii ) is particularly relevant to study the evolution of genes and gene regulation in vertebrates. Here we examine the evolution of Dlx homeobox gene regulation during vertebrate embryonic development with a particular focus on the forebrain. We first identified the elephant shark sequence orthologous to the URE2 cis -regulatory element of the mouse Dlx1/Dlx2 locus (herein named CmURE2). We then conducted a comparative study of the sequence and enhancer activity of CmURE2 with that of orthologous regulatory sequences from zebrafish and mouse. 相似文献20.
Anna L. Haigh Marc Gibernau Olivier Maurin Paul Bailey Mónica M. Carlsen Alistair Hay Kevin Leempoel Catherine McGinnie Simon Mayo Sarah Morris Oscar Alejandro Pérez-Escobar Wong Sin Yeng Alejandro Zuluaga Alexandre R. Zuntini William J. Baker Félix Forest 《American journal of botany》2023,110(2):e16117