Vertebrate ancient opsin photopigment spectra and the avian photoperiodic response

In mammals, photoreception is restricted to cones, rods and a subset of retinal ganglion cells. By contrast, non-mammalian vertebrates possess many extraocular photoreceptors but in many cases the role of these photoreceptors and their underlying photopigments is unknown. In birds, deep brain photoreceptors have been shown to sense photic changes in daylength (photoperiod) and mediate seasonal reproduction. Nonetheless, the specific identity of the opsin photopigment 'sensor' involved has remained elusive. Previously, we showed that vertebrate ancient (VA) opsin is expressed in avian hypothalamic neurons and forms a photosensitive molecule. However, a direct functional link between VA opsin and the regulation of seasonal biology was absent. Here, we report the in vivo and in vitro absorption spectra (λ(max) = ~490 nm) for chicken VA photopigments. Furthermore, the spectral sensitivity of these photopigments match the peak absorbance of the avian photoperiodic response (λ(max) = 492 nm) and permits maximum photon capture within the restricted light environment of the hypothalamus. Such a correspondence argues strongly that VA opsin plays a key role in regulating seasonal reproduction in birds.     

Vertebrate DNA transposon as a natural mutator: the medaka fish Tol2 element contributes to genetic variation without recognizable traces

DNA-based transposable elements, or DNA transposons, transpose in a cut-and-paste fashion, involving excision from the chromosome. If this process affects the function of a host gene and the excision rate is high, any gene associated with such an element would clearly be in a genetically "unstable" state, and there are many examples of unstable genes in various organisms. However, none have hitherto been reported in vertebrates. We here document the finding of an unstable mutant gene in the medaka fish, Oryzias latipes, a useful model animal for vertebrate genetics and evolutionary studies. In an inbred strain, excision of the Tol2 element inserted in a pigmentation gene occurs spontaneously, giving rise to different heritable phenotypes and new mutant genes that carry different excision footprint sequences. The phenotypic mutation rate is as high as 2% per gamete, representing a 1000-fold increase from spontaneous mutation rates so far determined with the same organism. With mutations caused by insertion, and then excision, of transposons, one can no longer recognize participation of transposons in their generation. Thus, the impact of DNA transposons on vertebrate genomes may be, and may have been, larger than commonly supposed.     

A mineralogical method to determine cyclicity in the taphonomic and diagenetic history of fossilized bones

The study of authigenic minerals within the voids of a fossilized bone can reveal its diagenetic history. When the order of precipitation of minerals is plotted on an Eh/pH diagram any cyclicity in the diagenetic history is revealed. If one cycle is displayed then it can be assumed that the bone has been found in its original bed of deposition; if two cycles or more are revealed then reworking or environmental change may have taken place. This is demonstrated in a case study of two bones from the Wealden Group (Lower Cretaceous) from the Isle of Wight, UK.     

Interpreting the origin of mammals: new approaches to the history of palaeontology

New sociological techniques in the history of science are described. Their value is illustrated by reinterpreting the diagnostic disputes which occurred following the first discovery of the Stonesfield mammals. It is concluded that contextual explanations are more sympathetic to early savants and more conducive to the integration of science and social history.     

文昌鱼—研究脊柱动物起源和进化的模式动物

长久以来,文昌鱼一直被认为和生活在约5亿年前的脊椎动物的直接祖先相似。由于文昌鱼在进化上的重要性,它在动物学研究史上发挥着关键作用,近100多年来,文昌鱼作为研究对象曾数次受到动物学界青睐或冷落,大约10年前,随着分子生物学技术应用于文昌鱼研究,又激发了动物学家对文昌鱼的研究兴趣,又一次出现在文昌鱼研究的高潮,并且一直持续至今,分子生物学研究结果表明,文昌鱼样生物可能是环节动物样动物和最早的脊椎动物之间的进化中间体,因此,文昌鱼在动物学研究史上好像绕了个大圈又回到了原处,在被忽视一段时间之后,又重新占据脊椎动物起源和进化研究中心舞台的位置,成为研究脊椎动物起源和进化的模式动物。     

脊椎动物Sox基因家族的系统发生分析

脊椎动物Sox基因是一类高度保守的基因家族,它们编码一类转录因子,参与多种发育过程的调控,这个家族的共有特征是Sox蛋白具有一个约79个氨基酸,可与DNA特异结合的HMG盒区,该基因家族成员众多复杂,对它们的基因结构,功能及进化关系的研究有助于对该基因家族的全面认识,利用已克隆的全部脊椎动物全长核苷酸／蛋白质数据,对这些数据进行序列比对及进化树的构建,分析Sox基因家族成员的分类及分子进化模式。     

第四纪晚期中国大型哺乳动物古DNA研究进展

从古DNA视角探讨古代生物的遗传组成已有40多年历史。自2005年开始;随着高通量测序技术平台的开发应用及对小片段DNA分子提取能力的加强;古DNA研究跨入全新的深时古基因组时代;不仅解决了诸多生物谱系系统学问题;丰富了包括人类在内的多种生物的迁移、演化细节;而且启动了“全基因组-大数据-多物种”尺度研究生物对气候变化的分子响应;将古DNA研究涉及的样品年代从10万年以内拓展到近200万年前的早更新世。中国科学家近几年在东亚人群遗传演化和迁徙融合方面实现了诸多有影响力的突破;填补了现代人类演化进程中的重要“缺环”。相比而言;学界对除人类之外的脊椎动物古DNA研究关注度较低。本文回顾了第四纪晚期中国大型哺乳动物古DNA研究系列进展;分别总结了相关研究在揭示古代群体与现生群体的系统演化关系、古哺乳动物基因交流、动物种群对气候变化的分子响应等方面的研究突破;并对中国哺乳动物古基因组领域面临的机遇和挑战进行了展望。     

Endocranial morphology of Palaeocene Plesiadapis tricuspidens and evolution of the early primate brain

Expansion of the brain is a key feature of primate evolution. The fossil record, although incomplete, allows a partial reconstruction of changes in primate brain size and morphology through time. Palaeogene plesiadapoids, closest relatives of Euprimates (or crown-group primates), are crucial for understanding early evolution of the primate brain. However, brain morphology of this group remains poorly documented, and major questions remain regarding the initial phase of euprimate brain evolution. Micro-CT investigation of the endocranial morphology of Plesiadapis tricuspidens from the Late Palaeocene of Europe—the most complete plesiadapoid cranium known—shows that plesiadapoids retained a very small and simple brain. Plesiadapis has midbrain exposure, and minimal encephalization and neocorticalization, making it comparable with that of stem rodents and lagomorphs. However, Plesiadapis shares a domed neocortex and downwardly shifted olfactory-bulb axis with Euprimates. If accepted phylogenetic relationships are correct, then this implies that the euprimate brain underwent drastic reorganization during the Palaeocene, and some changes in brain structure preceded brain size increase and neocortex expansion during evolution of the primate brain.     

A dynamic history of gene duplications and losses characterizes the evolution of the SPARC family in eumetazoans

The vertebrates share the ability to produce a skeleton made of mineralized extracellular matrix. However, our understanding of the molecular changes that accompanied their emergence remains scarce. Here, we describe the evolutionary history of the SPARC (secreted protein acidic and rich in cysteine) family, because its vertebrate orthologues are expressed in cartilage, bones and teeth where they have been proposed to bind calcium and act as extracellular collagen chaperones, and because further duplications of specific SPARC members produced the small calcium-binding phosphoproteins (SCPP) family that is crucial for skeletal mineralization to occur. Both phylogeny and synteny conservation analyses reveal that, in the eumetazoan ancestor, a unique ancestral gene duplicated to give rise to SPARC and SPARCB described here for the first time. Independent losses have eliminated one of the two paralogues in cnidarians, protostomes and tetrapods. Hence, only non-tetrapod deuterostomes have conserved both genes. Remarkably, SPARC and SPARCB paralogues are still linked in the amphioxus genome. To shed light on the evolution of the SPARC family members in chordates, we performed a comprehensive analysis of their embryonic expression patterns in amphioxus, tunicates, teleosts, amphibians and mammals. Our results show that in the chordate lineage SPARC and SPARCB family members were recurrently recruited in a variety of unrelated tissues expressing collagen genes. We propose that one of the earliest steps of skeletal evolution involved the co-expression of SPARC paralogues with collagenous proteins.     

Integrating multiple lines of evidence into historical biogeography hypothesis testing: a Bison bison case study

One of the grand goals of historical biogeography is to understand how and why species'' population sizes and distributions change over time. Multiple types of data drawn from disparate fields, combined into a single modelling framework, are necessary to document changes in a species''s demography and distribution, and to determine the drivers responsible for change. Yet truly integrated approaches are challenging and rarely performed. Here, we discuss a modelling framework that integrates spatio-temporal fossil data, ancient DNA, palaeoclimatological reconstructions, bioclimatic envelope modelling and coalescence models in order to statistically test alternative hypotheses of demographic and potential distributional changes for the iconic American bison (Bison bison). Using different assumptions about the evolution of the bioclimatic niche, we generate hypothetical distributional and demographic histories of the species. We then test these demographic models by comparing the genetic signature predicted by serial coalescence against sequence data derived from subfossils and modern populations. Our results supported demographic models that include both climate and human-associated drivers of population declines. This synthetic approach, integrating palaeoclimatology, bioclimatic envelopes, serial coalescence, spatio-temporal fossil data and heterochronous DNA sequences, improves understanding of species'' historical biogeography by allowing consideration of both abiotic and biotic interactions at the population level.     

The Sodium Hypochlorite Solution for the Removal of Lichen from Vertebrate Track Surfaces

The removal of extraneous biological materials from vertebrate ichnological specimens may be necessary if they have been exposed to subaerial processes in the field for long periods of time. It is not uncommon for fossil track specimens to be found nearly completely covered with lichen colonies, especially those recovered from alpine areas. This paper describes a technique using a sodium hypochlorite solution (bleach) to remove lichen from a track surface containing numerous avian prints and small theropod prints with skin impressions.     

Mitochondrial DNA phylogeography in northern grasshopper mice (Onychomys leucogaster) — the influence of Quaternary climatic oscillations on population dispersion and divergence

The details of mitochondrial DNA (mtDNA) phylogenetic structure of the northern grasshopper mouse Onychomys leucogaster were examined using populations from a postulated area of endemism that includes three arid regions (Colorado Plateaus, Interior Plains, and Wyoming Basins) in western North America. Fifteen tetra- and heptanucleotide restriction enzymes were used to assay restriction-site variation in a 2150-bp PCR-amplified fragment of mtDNA representing the ND2 and part of the COI gene regions. A total of 18 mtDNA haplotypes were detected. Although overall genetic divergence among these haplotypes was low (average = 1.1%), phylogeographic structuring was apparent. Notably, a clear phylogenetic split separated one group of haplotypes restricted to the Wyoming Basins from all others. This phylogenetic split was further corroborated by examination of nucleotide sequence variation from a 270-bp stretch of the mtDNA cytochrome b gene. Overall geographic and phylogenetic patterns suggest a complex history of geographic structuring and subsequent mixing of populations of grasshopper mice throughout the late Pleistocene. These patterns of variation are evaluated relative to alternative hypotheses about biotic responses to Quaternary climatic oscillations in western North American arid regions.     

转基因技术在果蝇及脊椎动物心脏基因研究中的应用

转基因技术是一项非常重要的生物工程新技术,主要应用于生产药物蛋白及异种器官移植,建立疾病基因模型,提高和改善家畜生产的产量和质量以及研究新基因的功能及表达调控.重点综述了几个新的转基因技术-UAS-Gal4系统,热休克启动子载体,RNAi技术,原核胚胎显微注射及基因敲除技术在研究果蝇及脊椎动物心脏基因中的应用.     

The loss of the lower temporal arcade in diapsid reptiles

The fossil record of diapsid reptiles does not provide conclusive evidence that the loss of the lower temporal arcade is correlated with the development of streptostyly. Analysis of the structure of the external jaw adductor in extant lizards results in the formulation of an alternative hypothesis to explain the loss of the lower temporal arcade in lepidosaurs. Extant lizards show the development of a posteroventral portion of the superficialis layer (lb) of the external adductor, which invades the lateral surface of the lower jaw, thus escaping the original confines of the external adductor. The development and expansion of a posteroventral lb muscle would have to be correlated with the loss of at least the posterior portion of the lower temporal arcade. Fossil lepidosaurs such as Clevosaurus, Prolacerta and Macrocnemus show the reduction of the lower temporal arcade from back to front, which is consistent with the hypothesis of the development of a posteroventral lb muscle.     

Representations of the Natural System in the Nineteenth century

‘The Natural System’ is the abstract notion of the order in living diversity. The richness and complexity of this notion is revealed by the diversity of representations of the Natural System drawn by ornithologists in the Nineteenth Century. These representations varied in overall form from stars, to circles, to maps, to evolutionary trees and cross-sections through trees. They differed in their depiction of affinity, analogy, continuity, directionality, symmetry, reticulation and branching, evolution, and morphological convergence and divergence. Some representations were two-dimensional, and some were three-dimensional; n-dimensional representations were discussed but never illustrated. The study of diagrammatic representations of the Natural System is made difficult by the frequent failure of authors to discuss them in their texts, and by the consequent problem of distinguishing features which carried meaning from arbitrary features and printing conventions which did not. Many of the systematics controversies of the last thirty years have their roots in the conceptual problems which surrounded the Natural System in the late 1800s, problems which were left unresolved when interest in higher-level systematics declined at the turn of this century. From the symposium ‘Making Sense of Science Making Diagrams’, held at the History, Philosophy, and Social Studies of Biology meeting, London, Ontario, 1989.     

Tracing the genetic origin of Europe's first farmers reveals insights into their social organization

Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today''s Hungary. However, the genetic background of the LBK genesis is yet unclear. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (seventh/sixth millennia BC) from the Carpathian Basin and southeastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early southeastern European and Carpathian Basin farming cultures on Central European populations of the sixth–fourth millennia BC. Comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through southeastern Europe and the Carpathian Basin into Central Europe. However, our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting a system of patrilineal descent and patrilocal residential rules among the early farmers.     

History of Ichnology: The Correspondence Between the Reverend Henry Duncan and the Reverend William Buckland and the Discovery of the First Vertebrate Footprints

The Reverend Henry Duncan (1774–1846), clergyman, philosopher, writer, politician, archeologist, poet, educator, social reformer, and the founder of savings banks, was indeed a Man for All Seasons. In 1824, while Minister of the Church of Scotland at Ruthwell, Dumfriesshire, he was presented with a slab of red sandstone from the Corncockle Muir quarry in Annandale, exhibiting a set of footprints on it. Although Duncan felt from the start that he was dealing with the tracks of an animal, he wrote to the Reverend William Buckland, Reader in Mineralogy and Geology at the University of Oxford, to solicit his opinion on the origin of these curious markings. Buckland was at first skeptical, but after receiving casts of the markings from Duncan, he became convinced that they did in fact represent footprints. Duncan and Buckland maintained a correspondence about the footprints, and on January 7, 1828, Duncan described the Corncockle Muir footprints to the Royal Society of Edinburgh and quoted Buckland's findings. Duncan's paper was not published by the Society until 1831, but it aroused considerable interest—“Footsteps before the Flood”!—and was reported in several newspapers. This was the first scientific report of a fossil track; although a schoolboy, Pliny Moody, had found fossil footprints in Connecticut in 1802, they were not scientifically described until 1836. The Scottish tracks are now considered to be not reptilian but of synapsid origin and the rocks containing them are now known to be of Permian age.