Selective Factors Associated with the Origin of Fur and Feathers

Conventional wisdom notwithstanding, fur and feathers are unlikelyto have arisen in direct association with elevated metabolicrates in early mammals, birds, or their ancestors. A completeinsulative fur coat probably appeared first in the earliestmammals long after mammalian ancestors (therapsids) had attainedmammalian, or near-mammalian, metabolic rates. The evolutionof feathers was unlinked to the evolution of modern avian metabolicrates since early, fully flighted birds (i.e., Archaeopteryx)retained an ectothermic metabolic status. Recent claims of "feathereddinosaurs" should be regarded with caution.     

Phylogenetic Origin of the Chloroplast*†

SYNOPSIS. The 16S ribosomal RNA of the chloroplast of Euglena gracilis strain Z has been characterized in terms of its 2-dimensional electrophoretic “fingerprint” (T1 ribonuclease). Over 100 spots were resolved on the “fingerprint” and each spot was characterized as to which RNA oligonucleotide fragment(s) it contained. When compared to similar analyses of prokaryotic 16S rRNAs and eukaryotic cytoplasmic 18S rRNAs, the chloroplast 16S rRNA was a typically prokaryotic RNA, but bore little if any relationship to eukaryotic 18S rRNAs. Therefore, the cistrons for chloroplast 16S rRNA are related to the equivalent prokaryotic cistrons, but, apparently, are not related to the equivalent eukaryotic cistrons. Among the organisms available for comparison, the Euglena chloroplast 16S rRNA appears most closely related to the 16S rRNA of the eukaryote, Porphyridium cruentum (a red alga), and at least distantly related to the 16S rRNAs of the blue-green algae and perhaps also to the bacilli.     

Origin of Ginkgo biloba L. Phylogenetic approach

A cladistic analysis on fossil and modern Gymnosperms (20 taxa) is presented and discussed with particular mention of Ginkgo biloba L. origin. The consensus tree obtained from 68 characters (59 informative characters) shows a monophyletic clade containing all plants bearing micropylate ovules ('Micropylophytes'). Medullosales appear at the base of this clade. Ginkgo forms the sister group of the Dicranophyllales + Coniferales. The obtained phylogeny implies that the Ginkgoales ancestor is to be found during the Upper Carboniferous.     

The Development of the Sauropsid Integument: A Contribution to the Problem of the Origin and Evolution of Feathers

Developmental anatomical data are insufficient to discuss plausibleintermediates between an ancestral, scaled, reptilian skin andappendage-bearing, avian skin. We also review adult tissue replacementand ubiquitous mechanisms underlying skin morphogenesis. Combiningdevelopmental data sensu lato with consideration of necessarybiological roles permits evaluation of major form/function trendsin skin evolution. New data on feathers reveal retention ofthe sauropsid synapomorphy of vertical alteration of - and ß-keratogenesis.By identifying roles that were obligatorily maintained throughoutevolution, we demonstrate constraints on hypothetical skin morphologiesin preavian taxa. We analyze feather origins as a problem ofemergence of complex form via modulations of morphogenesis.While existing data do not permit presentation of sequential,hypothetical, intermediates culminating in a plumage, the analysis:(1) implies that a protofeather and its follicle are most easilyderived from isolated, flattened, elongate, reptilian scales;(2) explains diversification of feather morphs from a contour-like"basic" feather and the similarity between feather and hairfollicles; and thus (3) reveals several developmental constraintson structures proposed as antecedent to avian feathers, whetherhypothetical constructs or palaeontological interpretations.Although these conclusions do not depend on any previous scenario,they are consistent with Regal's (1975) model and the limited,fossil evidence, especially that of the "basal archosaur" Longisquama.     

The Origin of Life in the Context of Inanimate Nature

Biophysics - Questions about the nature of life and the ability of living things to evolve are still attracting attention of scientists from different backgrounds. The idea that all living...     

An Asian Origin for Subtype IV BK Virus Based on Phylogenetic Analysis

Similarly to other members of the Polyomaviridae family, BK virus (BKV) is thought to have co-evolved with its human host. BKV has four subtypes that are distinguishable by immunological reactivity, with two (subtypes I and IV) being most prevalent in human populations. Subtype I is the major subtype worldwide, whereas subtype IV is prevalent in East Asia and Europe but rare in Africa. The geographic distribution pattern of subtype IV BKV is in apparent disagreement with the hypothesis that BKV co-evolved with humans, since subtype IV rarely occurs in Africa. To elucidate the origin of subtype IV, 53 complete subtype IV sequences derived from East Asians and Europeans were subjected to a detailed phylogenetic analysis using the maximum-likelihood and neighbor-joining methods. We identified six subgroups (a1, a2, b1, b2, c1, and c2) that formed a tree represented by the formula: “(a1, a2), ((b1, b2), (c1, c2)).” Interestingly, we found a close correlation between subtype IV subgroups and population geography; thus, all subgroups except c2 were prevalent in particular East Asian populations, with c2 occurring in both Europe and Northeast Asia. From these findings, we conclude that subtype IV of BKV now prevalent in modern humans is derived from a virus that infected ancestral Asians. We introduce two hypotheses to explain how ancestral Asians became infected with subtype IV BKV. [Reviewing Editor: Dr. Joshua Plotkin] Yuriko Nishimoto and Huai-Ying Zheng are two authors contributed equally to this article.     

Cross-Testing Adaptive Hypotheses: Phylogenetic Analysis and the Origin of Bird Flight

Adaptive scenarios in evolutionary biology have always beenbased on incremental improvements through a series of adaptivestages. But they have often been justified by appeal to assumptionsof how natural selection must work or by appeal to optimalityarguments or notions of evolutionary process. Cladistic methodology,though it cannot logically falsify hypotheses of process, provideshypotheses of evolutionary pattern independent of other considerationsand so provides a useful test of consilience with genealogy.I illustrate the cross-test of hypotheses of the evolution ofseveral functions and adaptations related to the origin of birdflight with independently derived phylogenetic analysis. Consiliencedoes not support ideas that the close ancestors of birds werearboreal or evolved flight from the trees, nor that they werephysiologically intermediate between typical reptiles and livingbirds, nor that feathers evolved for flight. Rather, the ancestorsof birds were terrestrial, they were fast-growing, active animals,and the original functions of feathers were in insulation andcoloration.     

基于trnL-F序列探讨杠板归Polygonum perfoliatum的系统位置

杠板归(Polygonum perfoliatum L.)的系统位置一直存在争议,文中以塔黄为外类群,采用最大简约法对杠板归及其近缘类群的trnL-F序列进行了系统发育分析,结果表明:(1)杠板归和刺蓼为姊妹群,自展分析的支持率为99%,分子证据支持杠板归归入刺蓼组,而没有必要单立组或属.(2)刺蓼组、春蓼组和头状蓼组植物聚在一起,自展支持率为100%,说明它们之间有很近的亲缘关系.     

Phylogenetic Origin of Phyllolobium with a Further Implication for Diversification of Astragalus in China

Astragalus is a species-rich genus occurring in the western arid habitats in China and its diversification and infrageneric relationships in this region remain unclear. In the present study, based on molecular data, we aim to (i) test whether Phyllolobium (previously treated as a subgenus Pogonophace in Astragalus ) should be warranted; and (ii) date the origin of Phyllolobium and probable diversification of Astragalus sensu stricto (s.s.). We sequenced five species from Phyllolobium first and collected all related sequences from the genus, Astragalus s.s and their close relatives ( Oxytropis and Caragana etc.). Our phylogenetic analyses suggested that all species of Phyllolobium comprise a monophyletic sister-group to genera of the subtribe Coluteinae. Molecular dating suggested that Phyllolobium and Astragalus s.s. originated around 8 and 10 million years ago. These two estimates are highly consistent with the intense uplifts of the Qinghai-Tibetan Plateau inferred from geological evidence. In addition, one section of Pogonophace (Sect. Robusti) was estimated to originate 2.5 million years ago and this section with a tendency for dry habitats seems to be evidence of Asian intensified aridity resulting from the intense uplift of the Qinghai-Tibetan Plateau.     

Phylogenetic Analyses of the Core Antenna Domain: Investigatingthe Origin of Photosystem I

Phototrophy, the conversion of light to biochemical energy, occurs throughout the Bacteria and plants, however, debate continues over how different phototrophic mechanisms and the bacteria that contain them are related. There are two types of phototrophic mechanisms in the Bacteria: reaction center type 1 (RC1) has core and core antenna domains that are parts of a single polypeptide, whereas reaction center type 2 (RC2) is composed of short core proteins without antenna domains. In cyanobacteria, RC2 is associated with separate core antenna proteins that are homologous to the core antenna domains of RC1. We reconstructed evolutionary relationships among phototrophic mechanisms based on a phylogeny of core antenna domains/proteins. Core antenna domains of 46 polypeptides were aligned, including the RC1 core proteins of heliobacteria, green sulfur bacteria, and photosystem I (PSI) of cyanobacteria and plastids, plus core antenna proteins of photosystem II (PSII) from cyanobacteria and plastids. Maximum likelihood, parsimony, and neighbor joining methods all supported a single phylogeny in which PSII core antenna proteins (PsbC, PsbB) arose within the cyanobacteria from duplications of the RC1-associated core antenna domains and accessory antenna proteins (IsiA, PcbA, PcbC) arose from duplications of PsbB. The data indicate an evolutionary history of RC1 in which an initially homodimeric reaction center was vertically transmitted to green sulfur bacteria, heliobacteria, and an ancestor of cyanobacteria. A heterodimeric RC1 (=PSI) then arose within the cyanobacterial lineage. In this scenario, the current diversity of core antenna domains/proteins is explained without a need to invoke horizontal transfer.This article contains online-only supplementary material.Reviewing Editor: Dr. W. Ford Doolittle     

鸽源冠状病毒核衣壳基因克隆及分子进化分析

目前最新研究发现,冠状病毒除能感染鸡、火鸡外,也能感染孔雀、鹧鸪、海鸟、灰雁、野鸭、野鸽等多种禽类[4-5]。2005年初笔者从以呼吸锣音、上呼吸道粘液异常增多、气管壁出血、胰脏肿大充出血和肺脏出现肉样病变为主要特征的病鸽中分离到1株病毒,通过形态学观察、动物回归试验     

鸽源冠状病毒核衣壳基因克隆及分子进化分析

目前最新研究发现, 冠状病毒除能感染鸡、火鸡外,也能感染孔雀、鹧鸪、海鸟、灰雁、野鸭、野鸽等多种禽类[4-5].2005年初笔者从以呼吸锣音、上呼吸道粘液异常增多、气管壁出血、胰脏肿大充出血和肺脏出现肉样病变为主要特征的病鸽中分离到1株病毒,通过形态学观察、动物回归试验、鸡胚接种试验、血凝特性试验等证实为冠状病毒,暂命为PSH[2].本研究对PSH N基因进行了克隆和序列分析,其目的一方面是为揭示该病毒N结构基因的变异特点和该病毒的遗传演化规律;另一方面为进一步研制出快速诊断试剂和安全有效的基因工程疫苗及防治鸽源冠状病毒病奠定良好的基础.     

A Genomic and Phylogenetic Perspective on Endosymbiosis and Algal Origin

Accounting for the diversity of photosynthetic eukaryotes is an important challenge in microbial biology. It has now become clear that endosymbiosis explains the origin of the photosynthetic organelle (plastid) in different algal groups. The first plastid originated from a primary endosymbiosis, whereby a previously non-photosynthetic protist engulfed and enslaved a cyanobacterium. This alga then gave rise to the red, green, and glaucophyte lineages. Algae such as the chlorophyll c-containing chromists gained their plastid through secondary endosymbiosis, in which an existing eukaryotic alga (in this case, a rhodophyte) was engulfed. Another chlorophyll c-containing algal group, the dinoflagellates, is a member of the alveolates that is postulated to be sister to chromists. The plastid in these algae has followed a radically different path of evolution. The peridinin-containing dinoflagellates underwent an unprecedented level of plastid genome reduction with the ca. 16 remaining genes encoded on 1–3 gene minicircles. In this short review, we examine algal plastid diversity using phylogenetic and genomic methods and show endosymbiosis to be a major force in algal evolution. In particular, we focus on the evolution of targeting signals that facilitate the import of nuclear-encoded photosynthetic proteins into the plastid.     

The Evolution of Feathers*

Existing hypotheses on the evolution of feathers are reviewed with the assumptions that feather evolved from reptilian scales and that pennaceous feathers evolved before downy feathers. Observations with a scanning electron microscope demonstrate that basic to the structure of pennaceous feathers is the lamelliform structure of barbules, the planes of which are oriented at right angles to the plane of the feather vane. Thus the structure of the vane is more open than generally realized. The airtight vane of flight feathers is assumed a later specialization. Most of the existing hypotheses assume that the feather acts as a relatively solid barrier between the skin of the bird and the exterior and they are therefore not in agreement with the actual structure of feathers. A hypothesis is needed which explains the adaptive value of a pennaceous feather being porous. The hypothesis is put foward that feathers evolved due to selection for a water-repellent integument. For purely physical reasons a porous surface repels water drops more strongly than does a solid surface of the same material. Physicists have pointed out that the structure of feathers conforms closely with the theoretical requirements for water-repellency. Possibly feathers started to evolve on reptiles living at the seashore, where the main advantage of increased water-repellency was to reduce cooling from evaporation of water off a wet integument.     

A Phylogenetic Study of the Origin of the Domestic Pig Estimated from the Near-Complete mtDNA Genome

The near-complete pig mtDNA genome sequence (15,997 bp) was determined from two domestic pigs (one Chinese Meishan and one Swedish Landrace) and two European wild boars. The sequences were analyzed together with a previously published sequence representing a Swedish domestic pig. The sequences formed three distinct clades, denoted A, E1, and E2, with considerable sequence divergence between them (0.8–1.2%). The results confirm our previous study (based on the sequence of the cytochrome B gene and the control region only) and provide compelling evidence that domestication of pigs must have occurred from both an Asian and a European subspecies of the wild boar. We estimated the time since the divergence of clade A (found in Chinese Meishan pigs) and E1 (found in European domestic pigs) at about 900,000 years before present, long before domestication about 9000 years ago. The pattern of nucleotide substitutions among the sequences was in good agreement with previous interspecific comparisons of mammalian mtDNA; the lowest substitution rates were observed at nonsynonymous sites in protein-coding genes, in the tRNA and rRNA genes, while the highest rates were observed at synonymous sites and in the control region. The presence of Asian clade A in some major European breeds (Large White and Landrace) most likely reflects the documented introgression of Asian germplasm into European stocks during the 18th and 19th centuries. The coexistence of such divergent mtDNA haplotypes for 100+ generations is expected to lead to the presence of recombinant haplotypes if paternal transmission and recombination occur at a low frequency. We found no evidence of such recombination events in the limited sample studied so far. Received: 19 April 2000; Accepted: 15 November 2000     

The Origin and Evolution of tRNA Inferred from Phylogenetic Analysis of Structure

The evolutionary history of the two structural and functional domains of tRNA is controversial but harbors the secrets of early translation and the genetic code. To explore the origin and evolution of tRNA, we reconstructed phylogenetic trees directly from molecular structure. Forty-two structural characters describing the geometry of 571 tRNAs and three statistical parameters describing thermodynamic and mechanical features of molecules quantitatively were used to derive phylogenetic trees of molecules and molecular substructures. Trees of molecules failed to group tRNA according to amino acid specificity and did not reveal the tripartite nature of life, probably due to loss of phylogenetic signal or because tRNA diversification predated organismal diversification. Trees of substructures derived from both structural and statistical characters support the origin of tRNA in the acceptor arm and the hypothesis that the top half domain composed of acceptor and pseudouridine (TΨC) arms is more ancient than the bottom half domain composed of dihydrouridine (DHU) and anticodon arms. This constitutes the cornerstone of the genomic tag hypothesis that postulates tRNAs were ancient telomeres in the RNA world. The trees of substructures suggest a model for the evolution of the major functional and structural components of tRNA. In this model, short RNA hairpins with stems homologous to the acceptor arm of present day tRNAs were extended with regions homologous to TΨC and anticodon arms. The DHU arm was then incorporated into the resulting three-stemmed structure to form a proto-cloverleaf structure. The variable region was the last structural addition to the molecular repertoire of evolving tRNA substructures. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.