Limits to randomness in paleobiologic models: the case of Phanerozoic species diversity

The question of how random, or unconstrained, paleobiologic models should be is examined with a case study: Signor's (1982, 1985) inverse calculation of levels of marine species diversity through the Phanerozoic. His calculation involved an ingenious model that estimated species numbers and species abundances in the world oceans of the past by correcting known numbers of fossil species for variations in sedimentary rocks available for sampling and in effort paleontologists might devote to sampling. The model proves robust to changes in possible shapes of species-abundance distributions, but it is sensitive to alterations in the assumption that paleontologists collect fossils at random. If it is assumed that ease of collecting varies with age of sediment (with the Cenozoic offering easy sampling) or that paleontologists tend to seek out rarer fossils, results of the inverse calculation change. In particular, the magnitude of the calculated Cenozoic diversity increase always declines from the factor of about seven as originally reported to something considerably smaller. This leaves open the problem of the magnitude of Cenozoic increase in marine species diversity, awaiting better empirical data and, perhaps, more exacting models, random or otherwise.     

Oxygen isotopic evidence for the depth stratification of tertiary and cretaceous planktic foraminifera

Oxygen isotope analyses of Tertiary and Cretaceous planktic foraminifera indicate that species have been stratified with respect to depth in the water column at least since Albian time. There is a relationship between morphology and depth habitat. Species with globigerine morphology have consistently occupied shallower depths than have species with globorotalid morphology. Biserially arranged species occupied both shallow and deep levels in the water column. On the average, it appears that ancient species with shallow habitats have been more susceptible to dissolution and have been preserved less well than species dwelling in deeper habitats. This relationship is similar to that observed for Recent planktic foraminifera. Comparison of carbon isotope ratios of adult and juvenile forms indicates that either the source of the carbon found in the shell or the carbon isotopic fractionations which occur during calcite secretion change during the development of individual foraminifera. The carbon isotopic ratios do not provide a reliable means for reconstructing the depth habitats of ancient species. Temperature-depth profiles for tropical Tertiary oceans have been reconstructed from the isotopic temperatures of planktic and benthic foraminifera. The vertical thermal structure of Oligocene oceans resembled that of modern oceans most closely. Those of Paleocene and Maastrichtian times differed most from that of modern oceans.     

Pennsylvanian phylloid algae interpreted as shallow-water xenophyophores

Xenophyophores, a group of agglutinated rhizopod protists, occur in nearly all the world's oceans at depths generally in excess of 1OOO m. In certain areas they dominate deep-sea, megafaunal communities. Their widespread distribution indicates a well-established adaptive radiation. Only one fossil analogue, however, has been proposed. This is Paleodictyon , a trace fossil that superficially resembles the Recent infaunal xenophyophore Occultammina profunda in morphology. The platy xenophyophore genus Psammina closely resembles certain late Palaeozoic fossils from northeastern Kansas that have been referred to as 'phylloid algae'. Here we compare modern xenophyophore structure with that of the fossil phylloids. By reconstructing the fossils, analysing their thin sections with polarized, blue, and ultraviolet light and subjecting them to Q-switched laser ablation, we conclude that certain phylloids could represent shallow-water xenophyophores. *** Phylloid algae, xenophyophores, motphology, reconstruction, laser ablation, Pennsylvanian.     

滇东北昭通箐门的泥盆纪珊瑚（二）——中泥盆世晚期的四射珊瑚

云南省昭通市东北郊箐门出露了一条比较完整的泥盆系浅海相地层剖面,下、中、上三个统均有出露,浅海底栖生物化石丰富,研究基础也相对较好,是研究滇东北地区泥盆纪地层的一条理想剖面。由于地层剖面比较长,沉积厚度比较大,此前我们已经描述了早泥盆世和中泥盆世早期的四射珊瑚,本文继续描述该剖面的中泥盆世晚期的地层及其四射珊瑚,讨论它们的地层划分、珊瑚群对比与古生物地理。至于晚泥盆世的珊瑚,由于篇幅的关系,我们拟另文继续描述。     

POPULATION BIOLOGY OF THE TRANS-ARCTIC EXCHANGE: MtDNA SEQUENCE SIMILARITY BETWEEN PACIFIC AND ATLANTIC SEA URCHINS

MtDNAs from 2 protein coding regions comprising 576 base pairs were sequenced from 17 individual sea urchins of the species Strongylocentrotus pallidus collected from the north Pacific and north Atlantic oceans. Twelve of 17 individual sequences were identical. Two of these were further sequenced in a third, 441 base pair region, and were also found to be identical. We show how to interpret these results using a simplified Markov model of mtDNA evolution at silent sites. The model was calibrated using 3 urchin species with a published fossil record, and shows that identical S. pallidus mtDNAs in different oceans shared a common ancestor at most 90,000–150,000 years ago (95% confidence interval of upper limit of divergence). The Markov model, used to examine patterns of genetic distance within and between species, shows unexpected variation in the rate of base substitution. The rate of change of G's at fourfold sites is nearly 20 times greater than the rate of change of C's. At twofold sites, this range is less extreme, although purines consistently have a higher rate of change than pyrimidines. Striking genetic similarity and recent genetic exchange between oceans for these urchins is in marked contrast to most other trans-Arctic marine populations, which usually show morphological and genetic differentiation at the species or subspecies level. Recent fossil evidence shows that the north Atlantic and northeastern Pacific have been the scene of radical faunal changes during the Pliocene and Pleistocene. The genetic results presented here extend this conclusion to intraspecific patterns of genetic variability, and direct attention to the northwest Pacific where higher productivity and less environmental change may have left a heritage of greater marine genetic diversity.     

Insights from modeling studies on how climate change affects invasive alien species geography

Climate change and biological invasions are threatening biodiversity and ecosystem services worldwide. It has now been widely acknowledged that climate change will affect biological invasions. A large number of studies have investigated predicted shifts and other changes in the geographic ranges of invasive alien species related to climate change using modeling approaches. Yet these studies have provided contradictory evidence, and no consensus has been reached. We conducted a systematic review of 423 modeling case studies included in 71 publications that have examined the predicted effects of climate change on those species. We differentiate the approaches used in these studies and synthesize their main results. Our results reaffirm the major role of climate change as a driver of invasive alien species distribution in the future. We found biases in the literature both regarding the taxa, toward plants and invertebrates, and the areas of the planet investigated. Despite these biases, we found for the plants and vertebrates studied that climate change will more frequently contribute to a decrease in species range size than an increase in the overall area occupied. This is largely due to oceans preventing terrestrial invaders from spreading poleward. In contrast, we found that the ranges of invertebrates and pathogens studied are more likely to increase following climate change. An important caveat to these findings is that researchers have rarely considered the effects of climate change on transport, introduction success, or the resulting impacts. We recommend closing these research gaps, and propose additional avenues for future investigations, as well as opportunities and challenges for managing invasions under climate change.     

Fossil‐based comparative analyses reveal ancient marine ancestry erased by extinction in ray‐finned fishes

The marine‐freshwater boundary is a major biodiversity gradient and few groups have colonised both systems successfully. Fishes have transitioned between habitats repeatedly, diversifying in rivers, lakes and oceans over evolutionary time. However, their history of habitat colonisation and diversification is unclear based on available fossil and phylogenetic data. We estimate ancestral habitats and diversification and transition rates using a large‐scale phylogeny of extant fish taxa and one containing a massive number of extinct species. Extant‐only phylogenetic analyses indicate freshwater ancestry, but inclusion of fossils reveal strong evidence of marine ancestry in lineages now restricted to freshwaters. Diversification and colonisation dynamics vary asymmetrically between habitats, as marine lineages colonise and flourish in rivers more frequently than the reverse. Our study highlights the importance of including fossils in comparative analyses, showing that freshwaters have played a role as refuges for ancient fish lineages, a signal erased by extinction in extant‐only phylogenies.     

毛翅目化石研究进展

本文详细总结和回顾了世界毛翅目化石研究简史,列出已发表的化石种类名录、分布及年代,共37科、193属、661种(包括中国发现的4科9属15种),描述了不同地质时期主要毛翅目化石的分类单元和分布地区。简要介绍了毛翅目分类系统及系统发育、不同地质时期毛翅目化石的产地及时代。初步分析了目前该类群所存在的一些问题,并对今后的研究工作进行了展望。     

The Atapuerca human fossils

After 20 years of research, the Atapuerca sites have provided a large amount of archaeological and palaeontological remains. Human fossils have been found in three sites: Gran Dolina, galería and Sima de los Huesos. The Early Pleistocene human fossils from Gran Dolina have been ascribed to a new species,Homo antecessor, that represent the last common ancestor of Neandertals and modern humans. The Sima de los Huesos fossils and all the European Middle Pleistocene human fossils are the ancestors exclusively of the Neandertals, which evolved in Europe in conditions of geographic and genetic isolation.     

The geographical and bathymetrical distribution of the Fecampiidae (Turbellaria,Rhabdocoela)

All members of the Fecampiidae are endoparasites. Since 1964 when only four species were known, four new species and 11 cocoon types, made by as many unknown species, have been described.The Fecampiidae are distributed in all major oceans from shallow waters to more than 5000 m depth.     

Early Oligocene Calocedrus (Cupressaceae) from the Maoming Basin,South China,and its paleogeographic and paleoclimatic implications

The genus Calocedrus Kurz is characterized by flattened branches covered with decussate and dimorphic leaves. In this study, we describe fossil foliage of Calocedrus discovered in the Shangcun Formation (early Oligocene) of the Maoming Basin, South China. The fossils have wedge‐shaped branchlet segments and scale‐like strongly dimorphic leaves, similar to the fossil species Calocedrus lantenoisi (Laurent) Tao. There have been no detailed studies of the morphological features and cuticle structures of C. lantenoisi. Therefore, a newly emended diagnosis of the species C. lantenoisi is given based on a detailed study of leaf morphology and cuticular characters exhibited by the Maoming fossils. This is one of the earliest fossil records of Calocedrus in the world, providing additional evidence for the early biogeographic history of this genus and supporting the inference that eastern Asian Calocedrus is primitive among all the living species. The extant species of Calocedrus are mainly distributed in mountainous regions. On the basis of the “nearest living relative” analysis, we propose that the Maoming Basin was adjacent to a mountainous region during the early Oligocene.     

Examining affinities of the Taung child by developmental simulation

As a well-preserved juvenile and the type specimen of Australopithecus africanus, the Taung child figures prominently in taxonomic, ontogenetic, and phylogenetic analyses of fossil hominins. Despite general agreement about allocation of Sterkfontein and Makapansgat fossils to this species, limited morphological comparisons have been possible between these adult specimens and the juvenile Taung. Here, we used developmental simulation to estimate the adult form of the Taung child, and directly compare its morphology to that of other fossil hominins. Specimens were represented by 50 three-dimensional landmarks superimposed by generalized Procrustes analysis. The simulation process applied developmental trajectories from extant hominine species to the Taung fossil in order to generate its adult form. Despite differences found in the developmental patterns of these modern species, simulations tested on extant juveniles-transforming them into "adults" using trajectories from other species-revealed that these differences have negligible impact on adult morphology. This indicates that morphology already present by occlusion of the first permanent molar is the primary determinant of adult form, thereby supporting use of extant trajectories to estimate the morphology of an extinct species. The simulated Taung adult was then compared to other adult fossils. As these comparisons required assumptions about the pattern and magnitude of developmental change, additional analyses were performed to evaluate these two parameters separately. Results of all analyses overwhelmingly rejected the possibility that the Taung child was a juvenile robust australopith, but were consistent with the hypothesis that the Taung and Sterkfontein fossils are conspecific. Between Sts 5 and Sts 71, the latter is more likely to resemble the adult form of the Taung child.     

A phylogenetic hypothesis for Crocodylus (Crocodylia) based on mitochondrial DNA: evidence for a trans-Atlantic voyage from Africa to the New World

The phylogenetic relationships among extant species of Crocodylus (Crocodylia) have been inconsistently resolved by previous systematic studies. Here we used nearly complete mitochondrial (mt) genomes (～16,200 base pairs) for all described Crocodylus species, eight of which are new to this study, to derive a generally well-supported phylogenetic hypothesis for the genus. Model-based analyses support monophyly of all Asian+Australian species and paraphyly of Crocodylus niloticus (Nile crocodile) with a monophyletic New World clade nested within this species. Wild-caught Nile crocodiles from eastern populations group robustly with the four New World species to the exclusion of Nile crocodiles from western populations, a result that is also favored by parsimony analyses and by various subpartitions of the overall mt dataset. The fossil record of Crocodylus extends back only to the Late Miocene, while the earliest fossils assigned to C. niloticus and to New World Crocodylus are Pliocene. Therefore, in combination with paleontological evidence, mt DNA trees imply a relatively recent migration of Crocodylus from Africa to the Americas, a voyage that would have covered hundreds of miles at sea.     

Paleobiological Perspectives on Early Eukaryotic Evolution

Eukaryotic organisms radiated in Proterozoic oceans with oxygenated surface waters, but, commonly, anoxia at depth. Exceptionally preserved fossils of red algae favor crown group emergence more than 1200 million years ago, but older (up to 1600–1800 million years) microfossils could record stem group eukaryotes. Major eukaryotic diversification ∼800 million years ago is documented by the increase in the taxonomic richness of complex, organic-walled microfossils, including simple coenocytic and multicellular forms, as well as widespread tests comparable to those of extant testate amoebae and simple foraminiferans and diverse scales comparable to organic and siliceous scales formed today by protists in several clades. Mid-Neoproterozoic establishment or expansion of eukaryophagy provides a possible mechanism for accelerating eukaryotic diversification long after the origin of the domain. Protists continued to diversify along with animals in the more pervasively oxygenated oceans of the Phanerozoic Eon.Eukaryotic organisms have a long evolutionary history, recorded, in part, by conventional and molecular fossils. For the Phanerozoic Eon (the past 542 million years), eukaryotic evolution is richly documented by the skeletons (and, occasionally, nonskeletal remains) of animals, as well as the leaves, stems, roots, and reproductive organs of land plants. Phylogenetic logic, however, tells us that eukaryotes must have a deeper history, one that began long before the first plant and animal fossils formed. To what extent does the geological record preserve aspects of deep eukaryotic history, and can the chemistry of ancient sedimentary rocks elucidate the environmental conditions under which the eukaryotic cell took shape?     

U-Series dating of Liujiang hominid site in Guangxi,Southern China

It has been established that modern humans were living in the Levant and Africa ca. 100ka ago. Hitherto, this has contrasted with the situation in China where no unequivocal specimens of this species have been securely dated to more than 30ka. Here we present the results of stratigraphic studies and U-series dating of the Tongtianyan Cave, the discovery site of the Liujiang hominid, which represents one of the few well-preserved fossils of modern Homo sapiens in China. The human fossils are inferred to come from either a refilling breccia or a primarily deposited gravel-bearing sandy clay layer. In the former case, which is better supported, the fossils would date to at least approximately 68ka, but more likely to approximately 111-139ka. Alternatively, they would be older than approximately 153ka. Both scenarios would make the Liujiang hominid one of the earliest modern humans in East Asia, possibly contemporaneous with the earliest known representatives from the Levant and Africa. Parallel studies on other Chinese localities have provided supporting evidence for the redating of Liujiang, which may have important implications for the origin of modern humans.     

蜉蝣目化石的研究进展

回顾了世界蜉蝣目化石研究简史,列出已发表的化石种类名录、分布及年代,共40科、124属、218种,其中包括中国的8属13种;描述了不同地质时期主要蜉蝣化石的分类单元和分布地区.简要介绍了蜉蝣分类系统及系统发育、稚虫食性、与其它昆虫的关系和古生态等方面的研究成果.在本文的第2部分,初步分析了目前该类群所存在的一些问题,并对今后的研究工作进行了展望.     

Paleozoic Protein Fossils Illuminate the Evolution of Vertebrate Genomes and Transposable Elements

Genomes hold a treasure trove of protein fossils: Fragments of formerly protein-coding DNA, which mainly come from transposable elements (TEs) or host genes. These fossils reveal ancient evolution of TEs and genomes, and many fossils have been exapted to perform diverse functions important for the host’s fitness. However, old and highly degraded fossils are hard to identify, standard methods (e.g. BLAST) are not optimized for this task, and few Paleozoic protein fossils have been found. Here, a recently optimized method is used to find protein fossils in vertebrate genomes. It finds Paleozoic fossils predating the amphibian/amniote divergence from most major TE categories, including virus-related Polinton and Gypsy elements. It finds 10 fossils in the human genome (eight from TEs and two from host genes) that predate the last common ancestor of all jawed vertebrates, probably from the Ordovician period. It also finds types of transposon and retrotransposon not found in human before. These fossils have extreme sequence conservation, indicating exaptation: some have evidence of gene-regulatory function, and they tend to lie nearest to developmental genes. Some ancient fossils suggest “genome tectonics,” where two fragments of one TE have drifted apart by up to megabases, possibly explaining gene deserts and large introns. This paints a picture of great TE diversity in our aquatic ancestors, with patchy TE inheritance by later vertebrates, producing new genes and regulatory elements on the way. Host-gene fossils too have contributed anciently conserved DNA segments. This paves the way to further studies of ancient protein fossils.     

中更新世晚期中国古人类化石的形态多样性及其演化意义

近年对许家窑、许昌、华龙洞、澎湖、夏河、哈尔滨等人类化石开展的系统研究,引发了学界对中更新世晚期人类演化及分类的不同认识。基于对相关中国人类化石形态特征的分析,作者提出这一时期中国人类化石形态特征表现为四种类型：1）以中更新世晚期人类共有特征为主;2）以原始特征为主;3）以现代特征为主;4）独特形态组合。多数化石形态特征表现为前三种类型,而许昌和许家窑这种以硕大的头骨和巨大颅容量构成的独特形态组合在其他同时期化石还没有发现。化石形态的多样性提示,不同类型的中更新世晚期中国古人类对现代人的形成贡献不同。作者认为在该时期的人类化石形态多样性规律还未阐明的情况下,将具有混合或镶嵌特征的相关人类化石归入分类地位不确定的人群较为合适。     

中国直翅目昆虫化石研究现状

截至目前,中国古昆虫学家已研究了分布于中国14省区的50件直翅目化石标本,发表新属38个,新种48个.通过图表提供了我国已发现的直翅目化石名录并介绍了其分布和年代.直翅目化石的研究对昆虫的起源、昆虫与植物的协同演化及古气候的演变等研究提供线索.中国已发现的直翅目化石主要分布于辽、冀、内蒙古三省区,其地质时代大部分为中生代.提出了在化石研究中存在的问题.