Guang-Hui Xu

A revision of the Middle Triassic scanilepiform fish Fukangichthys longidorsalis from Xinjiang, China, with comments on the phylogeny of the Actinopteri

ABSTRACT The scanilepiform ray-finned fish Fukangichthys longidorsalis, from the Middle Triassic non-marine Kelamayi Formation of Xinjiang, China, was previously described incompletely, with many of its morphological characteristics unnoticed or misidentified. This study provides a revision of this problematic taxon based on an extensive reexamination of the original fossil material. Newly recognized anatomical information includes a plate-like quadratojugal, a triangular dermohyal, a wedge-shaped angular, two infraorbitals, three supraorbitals, fringing fulcra on the pectoral fins, and conical, acrodin-capped teeth in the jaws. Results of a phylogenetic analysis confirmed Fukangichthys as a scanilepiform within the Neopterygii, and provided new insights into the evolution of early actinopteran fishes. Cosmoptychius, previously regarded as the oldest stemgroup neopterygian, and Brachydegma, previously hypothesized to be the oldest halecomorph, are here reinterpreted as a stem-group actinopteran and a stem-group neopterygian, respectively. Additionally, Discoserra, previously hypothesized in a position close to the Holostei/Teleostei split, is now recovered in a clade with Ebenaqua, Bobasatrania and Platysomus gibbosus, and is therefore phylogenetically distant from crown neopterygians. As a consequence, fossil candidates for divergence time calibrations within the Actinopteri require reconsideration.

Global Transcriptome Analysis Reveals Acclimation-Primed Processes Involved in the Acquisition of Desiccation Tolerance in Boea hygrometrica

Boea hygrometrica resurrection plants require a period of acclimation by slow soil-drying in order to survive a subsequent period of rapid desiccation. The molecular basis of this observation was investigated by comparing gene expression profiles under different degrees of water deprivation. Transcripts were clustered according to the expression profiles in plants that were air-dried (rapid desiccation), soil-dried (gradual desiccation), rehydrated (acclimated) and air-dried after acclimation. Although phenotypically indistinguishable, it was shown by principal component analysis that the gene expression profiles in rehydrated, acclimated plants resemble those of desiccated plants more closely than those of hydrated acclimated plants. Enrichment analysis based on gene ontology was performed to deconvolute the processes that accompanied desiccation tolerance. Transcripts associated with autophagy and α-tocopherol accumulation were found to be activated in both air-dried, acclimated plants and soil-dried non-acclimated plants. Furthermore, transcripts associated with biosynthesis of ascorbic acid, cell wall catabolism, chaperone-assisted protein folding, respiration and macromolecule catabolism were activated and maintained during soil-drying and rehydration. Based on these findings, we hypothesize that activation of these processes leads to the establishment of an optimal physiological and cellular state that enables tolerance during rapid air-drying. Our study provides a novel insight into the transcriptional regulation of critical priming responses to enable survival following rapid dehydration in B. hygrometrica.

The oldest ionoscopiform from China sheds new light on the early evolution of halecomorph fishes.

The Halecomorphi are a major subdivision of the ray-finned fishes. Although living halecomorphs are represented solely by the freshwater bowfin, Amia calva, this clade has a rich fossil history, and the resolution of interrelationships among extinct members is central to the problem of understanding the origin of the Teleostei, the largest clade of extant vertebrates. The Ionoscopiformes are extinct marine halecomorphs that were inferred to have originated in the Late Jurassic of Europe, and subsequently dispersed to the Early Cretaceous of the New World. Here, we report the discovery of a new ionoscopiform, Robustichthys luopingensis gen. et sp. nov., based on eight well-preserved specimens from the Anisian (242–247 Ma), Middle Triassic marine deposits of Luoping, eastern Yunnan Province, China. The new species documents the oldest known ionoscopiform, extending the stratigraphic range of this group by approximately 90 Ma, and the geographical distribution of this group into the Middle Triassic of South China, a part of eastern Palaeotethys Ocean. These new data provide a minimum estimate for the split of Ionoscopiformes from its sister clade Amiiformes and shed new light on the origin of ionoscopiform fishes.

Algorithms for Markov stochastic models

A survey of the main results of algorithmic studies of Markov processes and related stochastic models is shown. It consists of stationary solutions, transient solutions, first passage times, and multidimensional denumerable state Markov processes. In conclusion, some remarks on further works are presented.

Identification of a retroelement from the resurrection plant Boea hygrometrica that confers osmotic and alkaline tolerance in Arabidopsis thaliana.

Functional genomic elements, including transposable elements, small RNAs and non-coding RNAs, are involved in regulation of gene expression in response to plant stress. To identify genomic elements that regulate dehydration and alkaline tolerance in Boea hygrometrica, a resurrection plant that inhabits drought and alkaline Karst areas, a genomic DNA library from B. hygrometrica was constructed and subsequently transformed into Arabidopsis using binary bacterial artificial chromosome (BIBAC) vectors. Transgenic lines were screened under osmotic and alkaline conditions, leading to the identification of Clone L1-4 that conferred osmotic and alkaline tolerance. Sequence analyses revealed that L1-4 contained a 49-kb retroelement fragment from B. hygrometrica, of which only a truncated sequence was present in L1-4 transgenic Arabidopsis plants. Additional subcloning revealed that activity resided in a 2-kb sequence, designated Osmotic and Alkaline Resistance 1 (OAR1). In addition, transgenic Arabidopsis lines carrying an OAR1-homologue also showed similar stress tolerance phenotypes. Physiological and molecular analyses demonstrated that OAR1-transgenic plants exhibited improved photochemical efficiency and membrane integrity and biomarker gene expression under both osmotic and alkaline stresses. Short transcripts that originated from OAR1 were increased under stress conditions in both B. hygrometrica and Arabidopsis carrying OAR1. The relative copy number of OAR1 was stable in transgenic Arabidopsis under stress but increased in B. hygrometrica. Taken together, our results indicated a potential role of OAR1 element in plant tolerance to osmotic and alkaline stresses, and verified the feasibility of the BIBAC transformation technique to identify functional genomic elements from physiological model species.

A Middle Triassic thoracopterid from China highlights the evolutionary origin of overwater gliding in early ray-finned fishes

Gliding adaptations in thoracopterid flying fishes represent a remarkable case of convergent evolution of overwater gliding strategy with modern exocoetid flying fishes, but the evolutionary origin of this strategy was poorly known in the thoracopterids because of lack of transitional forms. Until recently, all thoracopterids, from the Late Triassic of Austria and Italy and the Middle Triassic of South China, were highly specialized ‘four-winged’ gliders in having wing-like paired fins and an asymmetrical caudal fin with the lower caudal lobe notably larger than the upper lobe. Here, we show that the new genus Wushaichthys and the previously alleged ‘peltopleurid’ Peripeltopleurus, from the Middle Triassic (Ladinian, 235–242 Ma) of South China and near the Ladinian/Anisian boundary of southern Switzerland and northern Italy, respectively, represent the most primitive and oldest known thoracopterids. Wushaichthys, the most basal thoracopterid, shows certain derived features of this group in the skull. Peripeltopleurus shows a condition intermediate between Wushaichthys and Thoracopterus in having a slightly asymmetrical caudal fin but still lacking wing-like paired fins. Phylogenetic studies suggest that the evolution of overwater gliding of thoracopterids was gradual in nature; a four-stage adaption following the ‘cranial specialization–asymmetrical caudal fin–enlarged paired fins–scale reduction’ sequence has been recognized in thoracopterid evolution. Moreover, Wushaichthys and Peripeltopleurus bear hooklets on the anal fin of supposed males, resembling those of modern viviparious teleosts. Early thoracopterids probably had evolved a live-bearing reproductive strategy.

The First Enantiornithine Bird from the Upper Cretaceous of China

ABSTRACT. A new Late Cretaceous avian taxon, Parvavis chuxiongensis, gen. et sp. nov., is reported here based on an incomplete skeleton from Upper Cretaceous lake deposits in Yunnan Province, southern China. A phylogenetic analysis of 32 taxa and 242 morphological characters resulted in three most parsimonious trees, the strict consensus tree of which places Parvavis chuxiongensis within Enantiornithes. Histological study shows that the bones of Parvavis were composed of parallelfibered bone tissue without lines of arrested growth, and indicated that growth rate had slowed but had not stopped at any stage prior to death. The bones also lack the rough surface texture seen in juvenile birds. Therefore, the new bird was probably close to adult body size at the time of death. However, the specimen is surprisingly small, highlighting the wide range of body sizes in Upper Cretaceous enantiornithines. The new specimen also represents both the first known bird from the Upper Cretaceous of China and the first Mesozoic bird from the south of China, and thus extends the temporal and geographic range of Mesozoic birds in China.

A new saurichthyiform (Actinopterygii) with a crushing feeding mechanism from the Middle Triassic of Guizhou (China).

Background Equipped with an effective predatory feeding mechanism enhanced by large and sharp teeth, pointed snout and elongate body, saurichthyiform fishes are considered common fish-eaters in the early Mesozoic aquatic ecosystems. Additionally, because of the similar body plan across species, saurichthyiforms are also regarded evolutionally conservative, with few morphological and ecological changes during their long history. However, their phylogenetic affinity remains unclear as to whether they are chondrostean, neopterygian or stem-actinopteran, and likewise the intrarelationships of the group have rarely been explored. Methodology/Principal Findings Here we report a new saurichthyiform from the Middle Triassic of Guizhou, China, based on the well-preserved specimens including a 3-D braincase. The new taxon, Yelangichthys macrocephalus gen. et sp. nov., is unique among saurichthyiforms in having a peculiar neurocranium with a broad orbital tectum, paired posterior myodomes, a deep, transverse fossa in the posterodorsal part of the orbit, and a feeding mechanism structured for durophagy. Phylogenetic analysis places Yelangichthys gen. nov. at the most basal position in the Saurichthyiformes as the sister to Saurichthyidae, and a new family Yelangichthyidae is erected to include only Y. macrocephalus gen. et sp. nov. The monophyly of the Chondrostei comprising [Saurichthyiformes + Acipenseriformes] Birgeriiformes is supported, but not the monophyly of Saurichthys, the type genus of Saurichthyidae. With its outstanding osteological details, Yelangichthys gen. nov. greatly increases the neurocranial variations in saurichthyiforms, and its novel feeding structure suggests the consumption of hard-preys instead of fishes. Conclusions/Significance Our findings highlight the detailed osteology of a saurichthyiform braincase and its feeding design. We suggest that saurichthyiforms are closely allied to the Acipenseriformes. Saurichthyiforms were very diverse in the cranial osteology and they might have undergone a rapid evolutionary radiation via, for the new material here, transforming the feeding mechanism and thus exploiting the food resources unsuitable for other saurichthyiforms.

Taxonomic revision of Plesiofuro mingshuica from the Lower Triassic of northern Gansu, China, and the relationships of early neopterygian clades

ABSTRACT The ray-finned fish Plesiofuro mingshuica from the Triassic non-marine deposits of northern Gansu Province, China, was previously misidentified as a caturid halecomorph. This erroneous taxonomic assignment contributed to the misinterpretation of the age of the Plesiofuro-bearing fossil beds as Early Jurassic. Here, we provide a taxonomic revision of this problematic taxon based on a comparative study including over 500 new specimens. The revised description of Plesiofuro accommodates significant changes to the reconstruction of the snout, skull roof, cheek, circumorbital, and operculogular series, as well as the lower jaw. Results of a cladistic analysis incorporating these new data place Plesiofuro as a stem-group neopterygian. Additionally, phylogenetic results show that both ‘Perleidiformes’ and ‘Peltopleuriformes’ are paraphyletic, encompassing several independent stem-neopterygian subclades. As such, this study sheds new light on one of the least resolved areas of osteichthyan phylogeny: the so-called ‘subholosteans’ of the neopterygian total group.

First passage times for multidimensional denumerable state Markov processes

For a general multidimensional denumerable state Markov process with any initial state probability vector, the probability density function and its LS transform of the first passage time to a certain given state set are obtained and the algorithms for them are derived. It is proved that the resulting errors of the algorithms are both uniform in their respective arguments. Some numerical results are presented.