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.     

Adapting generalized frequency coding to use colour spectra in the determination of phylogenetic relationships: an example with hummingbirds

We introduce a methodology to perform phylogenetic analyses on bird taxa using parsimony based on plumage colour characters obtained as spectra. The generalized frequency coding method was adapted to transform continuous colour spectral data into discrete variables. As an example of the application of the methodology, we analysed two species of the hummingbird genus Campylopterus and all species of the genera Anthracothorax and Eulampis , which occur in South and Central America and the Caribbean islands. The genus Topaza was used as an outgroup because of its basal position within the hummingbirds. The results were mostly in accordance with both traditional morphological as well as molecular analyses indicating that there is phylogenetic information in plumage colours measured in an integral and objective way and that the new method is appropriate for phylogenetic analyses at this lower taxonomic level.     

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.     

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.     

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.     

黄曲霉和米曲霉的多相鉴定方法

【背景】黄曲霉(Aspergillus flavus)和米曲霉(Aspergillus oryzae)形态特征相近,基因组高度相似,较难区分。【目的】旨在总结一套准确鉴别二者的分类方法。【方法】利用22株标准菌株对传统形态学、产毒培养基、酶联免疫毒素检测、系统发育分析、产毒基因检测等5种鉴别方法分别进行验证。【结果】各鉴定方法的结果存在异同,单一的鉴定方法容易出现假阴性或假阳性结果。【结论】利用单一方法区分黄曲霉和米曲霉具有潜在风险,多相鉴定方法可以准确鉴别二者。     

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     

A phylogenomic resolution for the taxonomy of Aegean green lizards

Lacerta pamphylica and Lacerta trilineata are two currently recognized green lizard species with a historically problematic taxonomy. In cases of tangled phylogenies, next-generation sequencing and double-digest restriction-site-associated DNA protocols can provide a wealth of genomic data and resolve difficult taxonomic issues. Here, we generated genome-wide SNPs and mitochondrial sequences, and applied molecular species delimitation approaches to provide a stable taxonomy for the Aegean green lizards. Mitochondrial gene trees, genetic cluster delimitation and population structure analyses converged into recognizing the populations of (a) L. pamphylica, (b) east Aegean islands, Anatolia and Thrace (diplochondrodes lineage), (c) central Aegean islands (citrovittata), and (d) remaining Balkan populations and islands (trilineata), as separate clusters. Phylogenomic analyses revealed a split into two major clades, east and west of the Aegean Barrier, unambiguously showing a sister–clade relationship between pamphylica and diplochondrodes, rendering L. trilineata paraphyletic. Species delimitation models were tested in a Bayesian framework using the genomic SNPs: lumping all populations into a single ‘species’ had the lowest likelihood but the current taxonomy was also outperformed by all other models. All lines of evidence support the Pamphylian green lizard as a valid species; thus, east Aegean L. trilineata should also be considered a distinct species under the name Lacerta diplochondrodes. Finally, evidence from the mitochondrial and nuclear genomes is overwhelmingly in favour of recognizing the morphologically distinct Cycladian green lizards as a distinct species. We propose their elevation to full species under the name Lacerta citrovittata. All remaining insular and continental populations of the Balkan Peninsula represent the species L. trilineata.     

Overview of the taxonomy of zooxanthellate Scleractinia

Coral taxonomy has entered a historical phase where nomenclatorial uncertainty is rapidly increasing. The fundamental cause is mandatory adherence to historical monographs that lack essential information of all sorts, and also to type specimens, if they exist at all, that are commonly unrecognizable fragments or are uncharacteristic of the species they are believed to represent. Historical problems, including incorrect subsequent type species designations, also create uncertainty for many well‐established genera. The advent of in situ studies in the 1970s revealed these issues; now molecular technology is again changing the taxonomic landscape. The competing methodologies involved must be seen in context if they are to avoid becoming an additional basis for continuing nomenclatorial instability. To prevent this happening, the International Commission on Zoological Nomenclature (ICZN) will need to focus on rules that consolidate well‐established nomenclature and allow for the designation of new type specimens that are unambiguous, and which include both skeletal material and soft tissue for molecular study. Taxonomic and biogeographic findings have now become linked, with molecular methodologies providing the capacity to re‐visit past taxonomic decisions, and to extend both taxonomy and biogeography into the realm of evolutionary theory. It is proposed that most species will ultimately be seen as operational taxonomic units that are human rather than natural constructs, which in consequence will always have fuzzy morphological, genetic, and distribution boundaries. The pathway ahead calls for the integration of morphological and molecular taxonomies, and for website delivery of information that crosses current discipline boundaries. © 2013 The Author. Zoological Journal of the Linnean Society published by John Wiley & Sons Ltd. on behalf of The Linnean Society of London     

Patterns of territorial space use by Shining Sunbeams (Aglaeactis cupripennis), tropical montane hummingbirds

For many territorial hummingbirds, habitat use is influenced primarily by the interaction between resource acquisition and non-foraging behaviors such as territory advertisement and defense. Previous research has highlighted the importance of foraging-associated habitat features like resource density and distribution in determining the space-use patterns of hummingbirds. Less is known, however, about how habitat selection associated with non-foraging behaviors influences space use by territorial species. We used radio telemetry to examine patterns of territorial space use by Shining Sunbeams (Aglaeactis cupripennis) in high Andean montane forests near Manu National Park, Peru, and Bosque Comunal “El Carmen” near Chordeleg, Ecuador. We quantified within-territory habitat characteristics related to resource acquisition and non-foraging behaviors such as territory advertisement and defense. We found that Shining Sunbeams showed high use of core areas in territories where foraging effort was relatively low. We found no relationship, however, between the position of core areas and habitat characteristics associated with territory defense, predator avoidance, or other non-foraging behaviors. We also found no relationship between use of non-core areas and habitat use based on resource acquisition. Thus, patterns of territorial space use by Shining Sunbeams may be characterized by core areas not determined by foraging behavior. Further studies examining territorial behaviors and the influence of intrusion pressure will help identify the underlying determinants of territory space use by this and other species of Andean hummingbirds.     

Male-like ornamentation in female hummingbirds results from social harassment rather than sexual selection

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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.     

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。     

Complex coevolution of wing,tail, and vocal sounds of courting male bee hummingbirds

Phenotypic characters with a complex physical basis may have a correspondingly complex evolutionary history. Males in the “bee” hummingbird clade court females with sound from tail‐feathers, which flutter during display dives. On a phylogeny of 35 species, flutter sound frequency evolves as a gradual, continuous character on most branches. But on at least six internal branches fall two types of major, saltational changes: mode of flutter changes, or the feather that is the sound source changes, causing frequency to jump from one discrete value to another. In addition to their tail “instruments,” males also court females with sound from their syrinx and wing feathers, and may transfer or switch instruments over evolutionary time. In support of this, we found a negative phylogenetic correlation between presence of wing trills and singing. We hypothesize this transference occurs because wing trills and vocal songs serve similar functions and are thus redundant. There are also three independent origins of self‐convergence of multiple signals, in which the same species produces both a vocal (sung) frequency sweep, and a highly similar nonvocal sound. Moreover, production of vocal, learned song has been lost repeatedly. Male bee hummingbirds court females with a diverse, coevolving array of acoustic traits.