Phylogeny of the hermit hummingbirds (trochilidae: Phaethornithinae)

A phylogeny of the hummingbirds of the genera Ramphodon, Eutoxeres, Glaucis, Threnetes, and Phaethornis is presented on the basis of external morphological characters. All 34 species of hermit hummingbirds are included in this study. Differences in 96 characters were examined with regard to their apomorphic (derived) or plesiomor‐phic (primitive) states, resulting in evolutionary trees drawn on the basis of cladistic principles. The most important results are: (1) “Ramphodon “ dohrnii is closer to Glaucis than to Ramphodon; (2) “Phaethornis” gounellei is the sister species to all Phaethornis and merits reevaluation as a separate genus, Anopetia; (3) Phaethornis philippii and P. koepckeae are the sister group to P. syrmatophorus, their straight bill having evolved independently of P. bourcieri; (4) the Phaethornis superciliosus/malaris species group includes P. longirostris as a third species; (5) Phaethornis subochraceus, P. pretrei, and P. augusti share a common ancestor, and (6) Phaethornis longuemareus (sensu Peters 1945) is polyphyletic, being comprised of four seperate species. Due to the lack of synapomorphies, the relationships of some species cannot be reliably determined on the basis of external morphological characters alone.     

Phylogeny,classification and nomenclature: a reply to F. Pleijel and G. W. Rouse

In systematics, the uncovering of monophyletic units, of sister group relationships and also of paraphyla is an important part of primary research. The hypotheses derived are thus subject to falsification and are subject to change. In contrast, classifications are a secondary step, as they are derived from such hypotheses. Classifications are based on different philosophies, which permit different solutions as to how results in the fields of taxonomy and phylogenetics can be transposed into a ‘system’. The function of classifications is at least partly utilitarian, and this is even more true for the names and principles of nomenclature. Nomenclature is simply a tool for information retrieval and for safeguarding understanding. Directly linking names and cladograms or nodes, respectively – making them subject to changes by falsification – would deliberately ignore the primary, strictly utilitarian function of long‐established principles of nomenclature and would endanger an instrument that functions almost perfectly. Approaches to introduce a so‐called PhyloCode should therefore not be pursued, as there is no chance at all that this kind of code could be generally accepted.     

Elastic instability model of rapid beak closure in hummingbirds

The hummingbird beak, specialized for feeding on floral nectars, is also uniquely adapted to eating flying insects. During insect capture the beak often appears to close at a rate that cannot be explained by direct muscular action alone. Here we show that the lower jaw of hummingbirds has a shape and compliance that allows for a controlled elastic snap. Furthermore, hummingbirds have the musculature needed to independently bend and twist the sides of the lower jaw. According to both our simple physical model and our elastic instability calculation, the jaw can be smoothly opened and then snapped closed through an appropriate sequence of bending and twisting actions by the muscles of the lower jaw.     

A specification of numerical taxonomy: Thermodynamical taxonomy

Thermodynamic taxonomy (ThT) is established from both a theoretical and pragmatical point of view. An application of thermodynamic taxonomy is given.     

The smallest avian genomes are found in hummingbirds

It has often been suggested that the genome sizes of birds are constrained relative to other tetrapods owing to the high metabolic demands of powered flight and the link between nuclear DNA content and red blood cell size. This hypothesis predicts that hummingbirds, which engage in energy-intensive hovering flight, will display especially constrained genomes even relative to other birds. We report genome size measurements for 37 species of hummingbirds that confirm this prediction. Our results suggest that genome size was reduced before the divergence of extant hummingbird lineages, and that only minimal additional reduction occurred during hummingbird diversification. Unlike in some other avian taxa, the small amount of variation observed within hummingbirds is not explained by variation in respiratory and flight-related parameters. Unexpectedly, genome size appears to have increased in four unrelated hummingbird species whose distributions are centred on humid forests of the upper-tropical elevational zone on the eastern slope of the Andes. This suggests that the secondary expansion of the genome may have been mediated by biogeographical and demographic effects.     

Implementation of a Markov model for phylogenetic trees

A recently developed mathematical model for the analysis of phylogenetic trees is applied to comparative data for 48 species. The model represents a return to fundamentals and makes no hypothesis with respect to the reversibility of the process. The species have been analysed in all subsets of three, and a measure of reliability of the results is provided. The numerical results of the computations on 17,296 triples of species are made available on the Internet. These results are discussed and the development of reliable tree structures for several species is illustrated. It is shown that, indeed, the Markov model is capable of considerably more interesting predictions than has been recognized to date.     

Restriction-site variation of PCR-amplified chloroplast DNA regions and its implication for the evolution and taxonomy of Actinidia

 Twenty six restriction sites from five PCR-amplified chloroplast DNA sequences (rbcL, psbA, rpoB, and two spacers flanking the trnL gene) were mapped and analysed in 20 Actinidia taxa, encompassing all four sections into which the genus is divided. At least three species out of the 20 examined have been found to have originated through natural interspecific hybridisation on the basis of the discrepancy between morphological and biochemical traits and the cpDNA profiles of pairs of species. A widely reticulate evolution has therefore been postulated in Actinidia. Wagner and weighted parsimony analysis produced consensus trees that did not match the traditional taxonomy based on morphological characters. The molecular data clearly showed that some taxa, such as A. rufa and A. kolomikta, occupy a wrong position and most, if not all, of the traditional groups represented by sections and series are weakly supported, since they appear as polyphyletic. A. chinensis and A. deliciosa were confirmed to be very closely related. Since chloroplast DNA is paternally inherited in Actinidia, A. chinensis is a paternal progenitor, if not the only one, of A. deliciosa, the domesticated kiwifruit. Received: 18 August 1997 / Accepted: 6 October 1997     

Unique Reconstruction of Tree-Like Phylogenetic Networks from Distances Between Leaves

In this paper, a class of rooted acyclic directed graphs (called TOM-networks) is defined that generalizes rooted trees and allows for models including hybridization events. It is argued that the defining properties are biologically plausible. Each TOM-network has a distance defined between each pair of vertices. For a TOM-network N, suppose that the set X consisting of the leaves and the root is known, together with the distances between members of X. It is proved that N is uniquely determined from this information and can be reconstructed in polynomial time. Thus, given exact distance information on the leaves and root, the phylogenetic network can be uniquely recovered, provided that it is a TOM-network. An outgroup can be used instead of a true root.     

棕囊藻属的分类现状

棕囊藻属藻类生活史复杂、地理差异显著、游动单细胞个体微小,至今尚无明确的分类标准。在目前已报道的9个种中,Sournia(1988)认为只有两个种比较可靠,即形成胶群体的P.pouchetii(sensu lato)(包括P.globosa)和不形成胶群体的P.scrobiculata;一些学者将P.puchetii(sensu lato)进一步细分成P.pouchetii(sensu stricto)、P.globosa,P.antarctica等3种,为方便起见,多数学者将形成胶群体的棕囊藻定名为P.pouchetii,或写成未定种的形式Phaeocystis sp.棕囊藻属分类的混乱制约了相关研究的深入,解决棕囊藻分类混乱问题有赖于新的技术和方法的使用。     

Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs)

Summary RFLPs were used to study genome evolution and phylogeny in Brassica and related genera. Thirtyeight accessions, including 10 accessions of B. rapa (syn. campestris), 9 cultivated types of B. oleracea, 13 nine-chromosome wild brassicas related to B. oleracea, and 6 other species in Brassica and allied genera, were examined with more then 30 random genomic DNA probes, which identified RFLPs mapping to nine different linkage groups of the B. rapa genome. Based on the RFLP data, phylogenetic trees were constructed using the PAUP microcomputer program. Within B. rapa, accessions of pak choi, narinosa, and Chinese cabbage from East Asia constituted a group distinct from turnip and wild European populations, consistent with the hypothesis that B. rapa had two centers of domestication. A wild B. rapa accession from India was positioned in the tree between European types and East Asian types, suggesting an evolutionary pathway from Europe to India, then to South China. Cultivated B. oleracea morphotypes showed monophyletic origin with wild B. oleracea or B. alboglabra as possible ancestors. Various kales constitute a highly diverse group, and represent the primitive morphotypes of cultivated B. oleracea from which cabbage, broccoli, cauliflower, etc. probably have evolved. Cauliflower was found to be closely related to broccoli, whereas cabbage was closely related to leafy kales. A great diversity existed among the 13 collections of nine-chromosome wild brassicas related to B. oleracea, representing various taxonomic states from subspecies to species. Results from these studies suggested that two basic evolutionary pathways exist for the diploid species examined. One pathway gave rise to B. fruticulosa, B. nigra, and Sinapis arvensis, with B. adpressa or a close relative as the initial ancestor. Another pathway gave rise to B. oleracea and B. rapa, with Diplotaxis erucoides or a close relative as the initial ancestor. Raphanus sativus and Eruca sativus represented intermediate types between the two lineages, and might have been derived from introgression or hybridization between species belonging to different lineages. Molecular evidence for an ascending order of chromosome numbers in the evolution of Brassica and allied genera was obtained on the basis of RFLP data and phylogenetic analysis.     

Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs)

Summary Restriction fragment length polymorphisms (RFLPs) of nuclear DNAs have been used to explore the origin and evolution of the six cultivated Brassica species. Extensive RFLP variation was found at the species, subspecies and variety levels. Based on RFLP data from Brassica and related genera, a detailed phylogenetic tree was generated using the PAUP microcomputer program, which permits a quantitative analysis of the interrelationships among Brassica species. The results suggested that 1) B. nigra originated from one evolutionary pathway with Sinapis arvensis or a close relative as the likely progenitor, whereas B. campestris and B. oleracea came from another pathway with a possible common ancestor in wild B. oleracea or a closely related nine chromosome species; 2) the amphidiploid species B. napus and B. juncea have evolved through different combinations of the diploid morphotypes and thus polyphyletic origins may be a common mechanism for the natural occurrence of amphidiploids in Brassica; 3) the cytoplasm has played an important role in the nuclear genome evolution of amphidiploid species when the parental diploid species contain highly differentiated cytoplasms. A scheme for the origins of diploid and amphidiploid species is depicted based on evidence gathered from nuclear RFLP analysis, cpDNA RFLP analysis, cytogenetic studies and classical taxonomy.     

A problem in morganucodontid taxonomy (Mammalia)

During the past three decades knowledge of the earliest mammals has greatly increased through study of specimens of morganucodontids of Late Triassic and Early Jurassic age discovered in Africa, Asia and Europe. Communication of the results of diis research has been and continues to be impaired by disputes over the validity or content of the genera Eozostrodon Parrington and Morganucodon Kiihne. On the basis of the limited data available and in the interest of stability of nomenclature, Eozostrodon parvus is the appropriate name for the morganucodontid represented in the fauna preserved in fissure fillings in Holwell Quarry, England. Its diagnostic dental morphology is not duplicated in the extensive samples of the most abundant morganucodontid known from Wales for which the name Morganucodon watsoni is appropriate. Although generic reference of these species is a moot point, recognition of separate species is warranted and, with other data, points to a diverse assemblage of morganucodontids forming part of the base of a prototherian radiation.     

生物谱系命名法规简评

基于林奈命名法和林奈分类系统的生物分类系统已经存在250多年并仍然为广大生物学工作者使用,由此产生的国际动物、植物、细菌的命名法规亦执行了100年(1905年,国际植物命名法规第1版产生),并在不断修订.随着分类方法的不断进步,林奈分类系统的一些缺陷逐渐显露,一种被称为生物谱系命名法规(PhyloCode)的新的命名法出现在人们眼前.这种基于系统发育系统学的命名法规一经问世就引起诸多争论,但是,作为一种新的命名法规,无论与传统的命名法规融合还是独立发展,对于已有的分类系统都是一个新的机遇和挑战.     

Hominids' taxonomy. Three levels of discussion

Paleoanthropology plays a significant role in the study of man and the research of his past. As we all know, the anthropologists in the last century followed the alternative trends of multiplying and reducing the number of taxonomic names. The present paper presents three different levels of taxonomic discussion concerning fossil hominids. These levels belong to different orders: empirical, theoretical and psychological, and they do not exist in isolation from each other. On the contrary, they are connected and interdependent. It shall also be argued that taxonomic controversies described below arise from both objective and subjective factors.     

Biodiversity and a taxonomy of Chilean taxonomists

The Chilean taxonomic community is reduced, with the largest fraction of taxonomists devoted to well known groups, such as vertebrates. Some invertebrates and plant taxa have no Chilean taxonomist working on them, all factors that hamper the inventory of the Chilean biota.     

A darwinian species definition and its implications

A review of the vast literature on the epistemology and ontology of “species” is far beyond the capacity of both the writer and the length‐allotment of this essay, limiting it to a somewhat dogmatic presentation of personal opinions, few of them original. Also prohibited by the prescribed word limit is an account of species concepts considered but not adopted; in many cases, their omission does not do justice to their intellectual content.     

根瘤菌多样性和系统发育研究的多相分类体系及其进展

近年来对新的根瘤菌资源的不断发掘及现代分子生物学技术的发展和应用使根瘤菌分类研究有了突破性进展。多相分类通过综合获取信息,多种方法相互印证、互为补充,推进了根瘤菌的表型、遗传型和系统发育三方面的发展,从而较全面地反映根瘤菌的生物多样性特征,是根瘤菌多样性研究工作中常常采用的技术手段。文中主要阐述了根瘤菌多相分类体系中的主要方法及现代根瘤菌系统发育地位的研究和进展。     

中国木灵藓科植物的分类研究概况

木灵藓科(Orthotrichaceae)是世界性藓类植物大科,本文综述了该科植物在中国早期和现代的分类研究概况,在此基础上,对中国木灵藓科植物研究意义和研究趋势进行了展望。     

The taxonomy of the genusFrankia

Summary A discussion covering the problems ofFrankia taxonomy was held at the Frankia Workshop in Wageningen, September 4–6, 1983. It was agreed that the genusFrankia can be satisfactorily defined, but that solid criteria for species determination are not now available and that use of specific names should be avoided for the present.