Juvenile morphology: A clue to the origins of the most mysterious of mysticetes?

The origin of the pygmy right whale (Caperea marginata) has long been one of the most vexing conundrums of marine mammal evolution. The extremely disparate skeletal structure of Caperea and a patchy fossil record have left morphology and molecules at odds: whereas most morphological analyses ally Caperea with right whales (Balaenidae), most molecular studies instead suggest a close relationship with rorquals (Balaenopteridae) and grey whales (Eschrichtiidae). The morphological evidence supporting a Caperea-balaenid clade consists of several shared features of the skull and mandible, as traditionally observed in adult individuals. Here, we show that at least two of these features, the ascending process of the maxilla and the coronoid process, arise from substantially different precursors early during ontogeny and therefore likely do not represent genuine synapomorphies. Both of these juvenile morphologies have adult counterparts in the fossil record, thus indicating that the ontogenetic variation in the living species may be a genuine reflection of differing ancestral states. This new evidence contradicts previous morphological hypotheses on the origins of Caperea and may help to reconcile morphological and molecular evidence.     

Phylogeography of Australia’s king brown snake (Pseudechis australis) reveals Pliocene divergence and Pleistocene dispersal of a top predator

King brown snakes or mulga snakes (Pseudechis australis) are the largest and among the most dangerous and wide-ranging venomous snakes in Australia and New Guinea. They occur in diverse habitats, are important predators, and exhibit considerable morphological variation. We infer the relationships and historical biogeography of P. australis based on phylogenetic analysis of 1,249 base pairs from the mitochondrial cytochrome b, NADH dehydrogenase subunit 4 and three adjacent tRNA genes using Bayesian, maximum-likelihood, and maximum-parsimony methods. All methods reveal deep phylogenetic structure with four strongly supported clades comprising snakes from New Guinea (I), localities all over Australia (II), the Kimberleys of Western Australia (III), and north-central Australia (IV), suggesting a much more ancient radiation than previously believed. This conclusion is robust to different molecular clock estimations indicating divergence in Pliocene or Late Miocene, after landbridge dispersal to New Guinea had occurred. While members of clades I, III and IV are medium-sized, slender snakes, those of clade II attain large sizes and a robust build, rendering them top predators in their ecosystems. Genetic differentiation within clade II is low and haplotype distribution largely incongruent with geography or colour morphs, suggesting Pleistocene dispersal and recent ecomorph evolution. Significant haplotype diversity exists in clades III and IV, implying that clade IV comprises two species. Members of clade II are broadly sympatric with members of both northern Australian clades. Thus, our data support the recognition of at least five species from within P. australis (auct.) under various criteria. We discuss biogeographical, ecological and medical implications of our findings.Electronic Supplementary Material  Supplementary material is available in the online version of this article at     

The "Linh Duong" Pseudonovibos spiralis (Mammalia, Artiodactyla) is a new buffalo

The controversial phylogenetic position of the recently described South-East Asian endemic bovid, Pseudonovibos spiralis, was evaluated on the basis of phylogenetic analyses of originally obtained nearly complete 12S mitochondrial rDNA sequences for this species and Bubalus bubalis and 26 sequences of Bovidae from the Genbank using Cervus elaphus (Cervidae) as outgroup. In most of the phylogenetic analyses performed using PAUP 4.0 (maximum parsimony, maximum likelihood and neighbour-joining), Bovidae consisted of two major clades: Bovinae including the tribes Bovini, Tragelaphini and Boselaphini, and Antilopinae + Caprinae, incorporating all other bovids. In most trees P. spiralis fell within the buffalos (subtribe Bovina) between Bubalus and Syncerus. Therefore, our phylogenetic analyses of bovid mitochondrial 12S rRNA gene sequences suggest the close relationship of this enigmatic species with the buffalos and its placement within the subtribe Bovina.     

Pleistocene survival of an archaic dwarf baleen whale (Mysticeti: Cetotheriidae)

Pliocene baleen whale assemblages are characterized by a mix of early records of extant mysticetes, extinct genera within modern families, and late surviving members of the extinct family Cetotheriidae. Although Pleistocene baleen whales are poorly known, thus far they include only fossils of extant genera, indicating Late Pliocene extinctions of numerous mysticetes alongside other marine mammals. Here a new fossil of the Late Neogene cetotheriid mysticete Herpetocetus is reported from the Lower to Middle Pleistocene Falor Formation of Northern California. This find demonstrates that at least one archaic mysticete survived well into the Quaternary Period, indicating a recent loss of a unique niche and a more complex pattern of Plio–Pleistocene faunal overturn for marine mammals than has been previously acknowledged. This discovery also lends indirect support to the hypothesis that the pygmy right whale (Caperea marginata) is an extant cetotheriid, as it documents another cetotheriid nearly surviving to modern times.     

Natal departure timing from spatially varying environments is dependent of individual ontogenetic status

Natal departure timing represents one of the first crucial decisions for juveniles born in spatially varying environments that ultimately disappear, but our knowledge on its determinants is limited. The present study aimed at understanding the determinants of juvenile natal departure by releasing individually tagged juvenile pike (Esox lucius L.) with variable body size and trophic position in a temporary flooded grassland. Specifically, we investigated whether natal departure depends on individual competitive status (‘competition hypothesis’), physiological tolerance to environmental conditions (‘physiological hypothesis’) or individual trophic position and the spatial heterogeneity of trophic resources (‘trophic hypothesis’). The results indicated that departure timing was negatively correlated with body size at release, showing that the dominance status among competing individuals was not the main trigger of juvenile departure. A positive correlation between departure timing and individual body size at departure was observed, suggesting that inter-individual variability in physiological tolerance did not explain departure patterns. While individual growth performances were similar irrespective of the timing of natal departure, stable isotope analyses revealed that juveniles with higher trophic position departed significantly earlier than individuals with lower trophic position. Therefore, the trade-off driving the use of spatially varying environments was most likely dependent upon the benefits associated with energetic returns than the costs associated with inter-individual competition or physiological stress. This result highlighted how ontogeny, and particularly ontogenetic niche shift, can play a central role in juvenile’s decision to depart from natal habitats in a predatory species.     

Salt glands in the Jurassic metriorhynchid <Emphasis Type="Italic">Geosaurus</Emphasis>: implications for the evolution of osmoregulation in Mesozoic marine crocodyliforms

The presence of salt-excreting glands in extinct marine sauropsids has been long suspected based on skull morphology. Previously, we described for the first time the natural casts of salt-excreting glands in the head of the Jurassic metriorhynchid crocodyliform Geosaurus araucanensis from the Tithonian of the Vaca Muerta Formation in the Neuquén Basin (Argentina). In the present study, salt-excreting glands are identified in three new individuals (adult, a sub-adult and a juvenile) referable to the same species. New material provides significant information on the salt glands form and function and permit integration of evolutionary scenarios proposed on a physiological basis in extant taxa with evidence from the fossil record. G. araucanensis represents an advanced stage of the basic physiological model to marine adaptations in reptiles. G. araucanensis salt glands were hypertrophied. On this basis, it can be hypothesized that these glands had a high excretory capability. This stage implies that G. araucanensis (like extant pelagic reptiles, e.g. cheloniids) could have maintained constant plasma osmolality even when seawater or osmoconforming prey were ingested. A gradual model of marine adaptation in crocodyliforms based on physiology (freshwater to coastal/estuarine to estuarine /marine to pelagic life) is congruent with the phylogeny of crocodyliforms based on skeletal morphology. The fossil record suggests that the stage of marine pelagic adaptation was achieved by the Early Middle Jurassic. Salt gland size in the juvenile suggests that juveniles were, like adults, pelagic.     

Community structures and population dynamics of “Candidatus Accumulibacter” in activated sludges of wastewater treatment plants using ppk1 as phylogenetic marker

Candidatus Accumulibacter has been identified as dominant polyphosphate-accumulating organisms(PAOs) in enhanced biological phosphorus(P) removal(EBPR) from wastewater.This study revealed the relevance of community structure, abundance and seasonal population dynamics of Candidatus Accumulibacter to process operation of wastewater treatment plants(WWTPs) in China using ppk1 gene as phylogenetic marker. All sludge samples had properties of denitrifying P removal using nitrate as an electron acceptor.Accumulibacter abundance in the anaerobic-anoxic-oxic(A~2O) process was the highest(26%of total bacteria), and higher in winter than in summer with a better EBPR performance.Type-II was the dominant Accumulibacter in all processes, and type-I accounted for a small proportion of total Accumulibacter. The abundance of Clade-IIC as the most dominant clade reached 2.59 × 10~9 cells/g MLSS and accounted for 87.3% of total Accumulibacter. Clade IIC mainly contributed to denitrifying P removal. Clades IIA, IIC and IID were found in all processes, while clade-IIF was only found in oxidation ditch process through phylogenetic analysis. High proportion of clade IID to total Accumulibacter led to poor performance of aerobic P-uptake in inverted A~2O process. Therefore, Accumulibacter clades in WWTPs were diverse, and EBPR performance was closely related to the clade-level community structures and abundances of Accumulibacter.     

The evolutionary position of turtles revised

Consensus on the evolutionary position of turtles within the amniote phylogeny has eluded evolutionary biologists for more than a century. This phylogenetic problem has remained unsolved partly because turtles have such a unique morphology that only few characters can be used to link them with any other group of amniotes. Among the many alternative hypotheses that have been postulated to explain the origin and phylogenetic relationships of turtles, a general agreement among paleontologists emerged in favoring the placement of turtles as the only living survivors of the anapsid reptiles (those that lack temporal fenestrae in the skull). However, recent morphological and molecular studies have radically changed our view of amniote phylogenetic relationships, and evidence is accumulating that supports the diapsid affinities of turtles. Molecular studies favor archosaurs (crocodiles and birds) as the living sister group of turtles, whereas morphological studies support lepidosaurs (tuatara, lizards, and snakes) as the closest living relatives of turtles. Accepting these hypotheses implies that turtles cannot be viewed any longer as primitive reptiles, and that they might have lost the temporal holes in the skull secondarily rather than never having had them.     

A giant spider from the Jurassic of China reveals greater diversity of the orbicularian stem group

A large female spider, Nephila jurassica, was described from Middle Jurassic strata of north-east China and placed in the modern genus Nephila (family Nephilidae) on the basis of many morphological similarities, but, as with many ancient fossils, the single specimen lacked synapomorphies of the family (Selden et al. 2011). In order to test the placement within the nephilid phylogenetic tree, Kuntner et al. (2013) calibrated the molecular phylogeny using N. jurassica in three different scenarios based on inferred mitochondrial substitution rates. They concluded that N. jurassica fitted better as a stem orbicularian than a nephilid. Now, a giant male spider has been discovered at the same locality that yielded N. jurassica. The two sexes are considered conspecific based on their similar morphological features, size, and provenance. The male cannot be accommodated in Nephilidae because of its pedipalp morphology, so the new genus Mongolarachne and family Mongolarachnidae are erected for the species. Comparison with possibly related families show that Mongolarachnidae is most likely on the orbicularian stem, close to other cribellate orbicularians (e.g., Deinopoidea), which suggests a greater diversity of cribellate orbicularians during the Middle Jurassic.     

470-Million-year-old black corals from China

Phosphatic (possibly secondarily phosphatised) remains of antipatharian coralla, previously unknown in the fossil record, occur abundantly in the early Ordovician Fenxiang Formation in the Hubei Province, southern China. Probably two species (and genera) are represented, which differ in spinosity of branches. The more spinose one, Sinopathes reptans, has its lateral spines bearing regular, longitudinally arranged costellae. The early Floian geological age of this finding, about 470?Ma, supports predictions on the timing of anthozoan phylogeny derived from the molecular phylogenetic evidence. Black corals (Antipatharia) are basal to the scleractinians in the Hexacorallia clade, being more derived than sea anemones and the Zoantharia. Based on calibration of the molecular clock with Mesozoic data, the first split of lineages within the scleractinian hexacorals was proposed to take place approximately 425 million years ago. This implies that the origin of Antipatharia should precede this date. They have not been known in the fossil record because of unmineralised skeleton composed primarily of laminar chitin complexed with a protein. Unlike all recent species, the encrusting basal part of the colony dominated in the Ordovician ones and only occasionally erect branches developed, rather chaotically ramified. This presumably plesiomorphic trait seems consistent with ancient geological age and suggests that some problematic fossils from the Late Cambrian may be their, even less-derived, relatives.     

The European land leech: biology and DNA-based taxonomy of a rare species that is threatened by climate warming

The European land leech Xerobdella lecomtei was discovered in 1868 and is one of the rarest animals on Earth. During the 1960s, several individuals of these approx. 40 mm long, cold-adapted terrestrial annelids that inhabit the moist soils of birch forests around Graz, Austria, were investigated. Only one original research paper has been published on the biology of this species. Between 2001 and 2005, we re-investigated the morphology of preserved specimens and searched for living individuals in their natural habitat that appeared to be intact. We found only one juvenile individual (length approx. 10 mm), indicating that this local leech population became largely extinct over the past four decades. The feeding behaviour of our ‘lonesome George of the annelids’ was studied and is described here in detail. After its death, the Xerobdella individual was used for chemical extraction and molecular studies (deoxyribonucleic acid [DNA] barcoding, based on one gene, the mitochondrial cytochrome c oxidase subunit I). In addition, novel DNA barcodes for a land leech from Madagascar and a recently discovered species from Europe were obtained. Our phylogenetic tree shows that X. lecomtei is not a member of the tropical land leeches (family Haemadipsidae), as previously thought, but represents a separate line of descent (family Xerobdellidae). The decline of the local leech population around Graz correlates with a rise in average summer temperatures of +3°C between 1961 and 2004. This warming led to a drastic reduction in the moisture content of the soil where X. lecomtei lives. We suggest that human-induced climate change without apparent habitat destruction can lead to the extinction of populations of cold-adapted species that have a low colonization ability.     

MUCT短程硝化和反硝化除磷系统中Candidatus Accu- mulibacter的代谢活性和菌群结构

采用实现亚硝酸型硝化的MUCT工艺处理低C/N实际生活污水,在短程硝化的基础上实现反硝化除磷.研究短程硝化建立与破坏过程中,亚硝酸盐积累率的变化对系统除磷性能及Candidatus Accumulibacter菌群结构的影响.结果表明:MUCT除磷以反硝化除磷为主,平均反硝化除磷率高达88%.磷去除率与亚硝酸盐积累率具有很好的正相关性.短程硝化阶段磷的平均去除率比全程硝化阶段高30%以上,证明了亚硝酸盐更适合作为低C/N比污水反硝化除磷的电子受体.以多聚磷酸盐激酶基因(ppk1)作为遗传标记,采用实时荧光定量PCR方法考察不同亚硝酸盐积累率下Accumulibacter的丰度、各主要进化分支的菌群结构和相对丰度.当系统处于全程硝化状态时,存在少量以硝酸盐为电子受体的Acc-I型反硝化聚磷菌,低于总Accumulibacter的5%;当系统进入短程硝化状态后,Acc-I逐渐消失.运行期间以亚硝酸盐作为电子受体进行反硝化除磷的Acc-IID始终是优势聚磷菌,达到总Accumulibacter的92%以上,甚至接近100%,保证了亚硝酸型反硝化除磷的稳定运行,亚硝酸盐浓度是影响其丰度变化的重要因素.     

Comparisons of dental morphology in river stingrays (Chondrichthyes: Potamotrygonidae) with new fossils from the middle Eocene of Peruvian Amazonia rekindle debate on their evolution

Endemic South American river stingrays (Potamotrygonidae), which include the most diversified living freshwater chondrichthyans, were conspicuously absent from pre-Neogene deposits in South America despite the fact that recent phylogenetic analyses strongly suggest an older origination for this clade. To date, the rare representatives of this family were mostly represented by ambiguous isolated remains. Here, we report 67 isolated fossil teeth of a new obligate freshwater dasyatoid (Potamotrygon ucayalensis nov. sp) from the fossiliferous level CTA-27 (Yahuarango Formation), near Contamana, in the Peruvian Amazonia. We assigned this sample to a new representative of Potamotrygon by comparison with numerous fresh jaws of living specimens of Potamotrygonidae, thus providing the first detailed review of dental morphology for this poorly understood clade. These new fossils fill a long stratigraphic gap by extending the family range down to the middle Eocene (～41 Mya). Moreover, the relative modernity and diversity in tooth morphology among Eocene freshwater stingrays (including Potamotrygon ucayalensis nov. sp. and coeval North American dasyatoids) indicate that the hypothetically marine ancestor of potamotrygonids probably invaded the rivers earlier than in the middle Eocene. The first potamotrygonids and affiliates were possibly more generalized and less endemic than now, which is consistent with an opportunistic filling of vacated ecospace.     

Phylogeny of Collembola based on cuticular compounds:inherent usefulness and limitation of a character type

The phylogeny of Collembola, originally discussed from a morphological point of view, has more recently benefited from novel insights brought by molecular analyses. Both morphological and molecular characters produced a well-resolved phylogenetic hypothesis including all orders, most families, and a large number of genera. However, several conflicting points exist between molecular and morphological data, and new characters are clearly needed to resolve these inconsistencies. In this study the usefulness of a new character type not previously used in the phylogenetic study of Collembola was tested: the epicuticular chemical compounds. Our phylogenetic analysis was based on 380 compounds from 26 Collembola species. The results show good resolution for terminal branches but not for internal nodes. This is probably due to the partial involvement of epicuticular lipids in ecological functions such as water conservation and sexual attraction. Thus, this character type is appropriate for reconstructing phylogenetic relationships among recently diversified groups. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

First ceratosaurian dinosaur from Australia

The basal theropod dinosaur clade Ceratosauria, and its subclade Abelisauroidea, is characteristic of late Mesozoic terrestrial vertebrate faunas in western Gondwana (South America, Africa, Madagascar, and India) and Europe. Yet unambiguous records of ceratosaurs have hitherto been absent from Australia, where the theropod assemblage appears to include several typically Laurasian clades. Here, we report the first evidence of ceratosaurs (and potentially abelisauroids) from eastern Gondwana––a diagnostic astragalocalcaneum from the Aptian (121–125?Ma) of Victoria, Australia. Ceratosauria thus occurred in both western and eastern Gondwana during the Early Cretaceous. This fossil adds to the poorly known dinosaur fauna of Australia, a major clade of basal theropods, emphasising that its mid-Cretaceous theropod diversity was surprisingly cosmopolitan despite relative geographic isolation, including clades that have been thought to be typical of both Gondwana and Laurasia––Ceratosauria, Spinosauridae, Carcharodontosauria, Tyrannosauroidea, and Deinonychosauria. Such a contemporaneous association of theropod clades is unknown from other Gondwanan continents and questions the views that the late Mesozoic dinosaur fauna of Australia was dominated by Gondwanan or Laurasian elements, extreme isolation, relictualism, and/or novelty as a ‘centre of origin’. The cosmopolitan theropod fauna of Australia probably reflects the global distribution of these clades early in their history, prior to significant continental breakup.     

Homology and phylogeny and their automated inference

The analysis of the ever-increasing amount of biological and biomedical data can be pushed forward by comparing the data within and among species. For example, an integrative analysis of data from the genome sequencing projects for various species traces the evolution of the genomes and identifies conserved and innovative parts. Here, I review the foundations and advantages of this "historical" approach and evaluate recent attempts at automating such analyses. Biological data is comparable if a common origin exists (homology), as is the case for members of a gene family originating via duplication of an ancestral gene. If the family has relatives in other species, we can assume that the ancestral gene was present in the ancestral species from which all the other species evolved. In particular, describing the relationships among the duplicated biological sequences found in the various species is often possible by a phylogeny, which is more informative than homology statements. Detecting and elaborating on common origins may answer how certain biological sequences developed, and predict what sequences are in a particular species and what their function is. Such knowledge transfer from sequences in one species to the homologous sequences of the other is based on the principle of 'my closest relative looks and behaves like I do', often referred to as 'guilt by association'. To enable knowledge transfer on a large scale, several automated 'phylogenomics pipelines' have been developed in recent years, and seven of these will be described and compared. Overall, the examples in this review demonstrate that homology and phylogeny analyses, done on a large (and automated) scale, can give insights into function in biology and biomedicine.     

城市污水处理厂Candidatus Accumulibacter的菌群结构及定量分析

Candidatus Accumulibacter是污水生物除磷系统中的优势聚磷菌.本研究采用编码聚合磷酸盐激酶的功能基因(polyphosphate kinase 1gene,ppk1)作为遗传标记,对9个污水处理厂共12个活性污泥样品中Accumulibacter的进化枝水平的丰度及其菌群结构进行了研究.实时定量PCR(Quantitative PCR,QPCR)的结果显示,Accumulibacter的6个进化枝(IA、IIA、IIB、IIC、IID、IIF)均存在于12个污泥样品中.A2O及其改良工艺中总Accumulibacter丰度最高,达到总菌的22.77%.所有样品中Accumulibacter均以Type-II为主,其中,IIC、IID的丰度均达到了108cells·g-1(以MLSS计),占Accumulibacter的平均比例分别为75.34%和14.87%,是污水处理厂中的优势聚磷菌.分支IA丰度最低,占总Accumulibacter比例平均只有0.32%.系统发育分析结果显示,每个样品中Accumulibacter分支多样化,均含有IIA、IIC、IID分支.QPCR和系统发育分析都证实了生物除磷效果与Accumulibacter的群落结构密切相关,除磷效果不好可能和IID占总Accumulibacter比例较高有关.     

A molecular phylogenetic analysis of the neotropical dart-poison frog genus Phyllobates (Amphibia: Dendrobatidae)

 A phylogenetic analysis of the Neotropical dart-poison frogs, genus Phyllobates, was performed based on mitochondrial cytochrome b sequences. Members of Phyllobates from South and Central America were found to form each an evolutionary lineage. Among the South American lineage, species with uniform dorsal coloration as adults form a derived monophyletic clade. Received: 26 June 2000 / Accepted in revised form: 8 November 2000     

Phylogeny of cooperatively breeding cuckoos (Cuculidae,Crotophaginae) based on mitochondrial gene sequences

The Crotophaginae is a subfamily of New World cuckoos comprising the monotypic genus Guira and three ani species (Crotophaga). All exhibit a rare form of cooperative breeding known as plural female joint-nesting, whereby two or more females lay eggs in a single nest. I reconstructed the phylogeny of Crotophaginae using the mitochondrial genes cytochrome oxidase I, II, and III, ATPase 6 and 8, and cytochrome b. The subfamily was monophyletic, implying a single origin of cooperative breeding in New World cuckoos. Crotophaga was also monophyletic with Guira as its sister taxon. Within Crotophaga, the smooth-billed (C. ani) and groove-billed (C. sulcirostris) anis formed the internal clade with the greater ani (C. major) basal to this pair. This phylogeny is consistent with differences in reproductive patterns and social organization exhibited by crotophagine cuckoos, and will serve as a framework for future study of the evolution of cooperative breeding in this subfamily.