Late Palaeozoic sequence stratigraphy and brachiopod faunas of the Tarim Basin, Northwest China

This thesis deals with the stratigraphy and brachiopod systematic palaeontology of the latest Devonian (Famennian) to Early Permian (Kungurian) sedimentary sequences of the Tarim Basin, NW China. Brachiopod faunas of latest Devonian and Carboniferous age have been published or currently in press in the course of the Ph.D candidature and are herein appendixed, while the Early Permian brachiopod faunas are systematically described in this thesis. The described Early Permian brachiopod faunas include 127 species, of which 29 are new and 12 indeterminate, and six new genera (subgenera) are proposed; Tarimella, Bmntonella, Marginifera (Arenaria), Marginifera (Nesiotia), Baliqliqia and Ustritskia. A new integrated brachiopod biostratigraphical zonation scheme is proposed, for the first time, for the latest Devonian-Early Permian sequences of the entire Tarim Basin on the basis of this study as well as previously published information (including the Candidate's own published papers). The scheme consists of twenty three brachiopod acm biozones, most of which replace previously proposed assemblage or assemblage zones. The age and distribution of these brachiopod zones within the Tarim Basin and their relationships with other important fossil groups are discussed. In terms of regional correlations and biostratigraphical affinities, the Late Devonian to Early Carboniferous brachiopod faunas of the Tarim Basin are closest to those from South China, while the Late Carboniferous faunas demonstrate strong similarities to coeval faunas from the Urals, central Asia, North China and South China. During the Asselian-Sakmarian, strong faunal links between the Tarim Basin and those of the Urals persisted, while at the same time links with central Asia, North China and South China weakened. On the other hand, during the Artinskian-Kungurian times, affinities of the Tarim faunas with the Urals/Russian Platform rapidly reduced, when those with peri-Gondwana (South Thailand, northern Tibet) and South China increased. Thirty lithofacies (or microfacies) types of four facies associations are recognised for the Late Devonian to early Permian sediments. Based on detailed lithostratigraphy, biostratigraphy and facies analysis, 23 third-order sequences belonging to four supcrsequences are identified for the Late Devonian to Early Permian successions, from which sea-level fluctuation curves are reconstructed. The sequence stratigraphical analysis reveals that four major regional regressions, each marking a distinct supersequence boundary, can be recognised; they correspond to the end-Serpukhovian, end-Moscovian, late Artinskian and end-Kungurian times, respectively. The development of these sequences is considered to have been formed and regulated by the interplay of both eustasy and tectonism. Using the system tract of a sequence as the mapping time unit, a succession of 47 palaeogeographical maps have been reconstructed through the Late Devonian to Early Permian. These maps reveal that the Tarim Basin was first immersed by southwest-directed (Recent geographical orientation) transgression in the late Famennian after the Caledonian Orogeny. Since then, the basin had maintained its geometry as a large, southwest-mouthed embayment until the late Moscovian when most areas were the uplifted above sea-level. The basin was flooded again in late Asselian-Artinskian times when a new transgression came from a large epicontinental sea lying to its northwest. Thereafter, marine deposition was restricted to local areas (southwestern and northwestern margins until the late Kungurian, while deposition of continental deposits prevailed and continued through the Middle and late Permian into the Triassic.

The Permian of Timor : stratigraphy, palaeontology and palaeography

The Permian of Timor in the Lesser Sunda Islands has attracted the attention of palaeontologists since the middle of the nineteenth century because of the richness, diversity and excellent state of preservation of its fauna. These abundant fossil data have been compiled and updated for the present account. The Permian rocks of Timor were deposited on the northern margin of Australia. At the present time the northern margin of Australia, in the region of Timor, is involved in a continent–arc collision, where Australia is colliding with the Banda Arcs. As a result of this collision, Permian rocks of the Australian margin have been disrupted by folding and faulting with the generation of mud-matrix mélange, and uplifted to form part of the island of Timor. Due to this tectonic disruption, it has proved difficult to establish a reliable stratigraphy for the Permian units on Timor, especially as the classic fossil collections were obtained largely from the mélange or purchased from the local people, and do not have adequate stratigraphic control. Detailed systematic, structural, stratigraphic and sedimentological studies since the 1960s have provided a firmer stratigraphic and palaeogeographic background for reconsideration of the significance of the classic fossil collections. Permian rocks on Timor belong either to a volcanic-carbonate sequence (Maubisse Formation), or to a clastic sequence (Atahoc and Cribas formations) in which volcanics are less prominent. The Permian sequences were deposited on Australian continental basement which was undergoing extension with spasmodic volcanic activity. Carbonates of the Maubisse Formation were deposited on horst blocks and volcanic edifices, while clastic sediments of the Atahoc and Cribas formations were deposited in grabens. The clastic sediments are predominantly fine-grained, derived from a distant siliciclastic source, and are interbedded with sediments derived from the volcanics and carbonates of adjacent horst blocks. Bottom conditions in the graben were often anoxic. In the present account, events on Timor during the Permian are related to the regional tectonic context, with the northward movement of Australia leading to the amelioration of the climate from sub-glacial to sub-tropical, together with the separation of crustal blocks from the northern Australian margin to form the Meso-Tethys.

Lopingian (Late Permian) stratigraphy, sedimentation and palaeobiogeography in southern Tibet

Investigations of the Permian-Triassic sections and limestone blocks scattered in the Indus-Tsangbo Suture Zone in southern Tibet show widespread distribution of the Lopingian strata. The Lopingian deposits mostly contain rich brachiopod fossils and characteristic conodonts of the Mesogondolella shenz Zone of latest Changhsingian age in the topmost part. Brachiopod assemblages are largely comparable with those known from the upper Wargal and Chhidru Formations of the Salt Range, Pakistan, the Zewan Formation of Kashmir, the upper part of the Kuling Group in Spiti of India and the Hardman Formation of Western Australia. A revised Lopingian (Late Permian) age is proposed for the Selong Group and its equivalents in southern Tibet. The Lopingian deposits in southern Tibet can be grouped into three different sedimentary types, each of which reflects different sedimentary environments from coastal to continental shelfal settings on the northern peri-Gondwanan margin. The Qubu-type sequence represents marine coastal and proximal barrier-lagoon sediments during a gradual sea-level rise. Micaceous sandstone and shale of regressive origin, with abundant palynomorphs and acritarches, developed during the Late Lopingian sea-level lowstand, which is followed by a major rapid transgression at the very end of Permian. The Selong-type sequence in the Selong area consists of bioclastic limestone and calcareous shale in the lower part, and crinoid grainstone in the upper part. The latter part is believed to have been formed in a high-energy inner shelf shoal setting. The Chitichun-type sequence, sporadically distributed along the Indus-Tsangbo suture zone as small limestone blocks, consists of pure bioclastic sparite with the ammonoid Cyclolobus fauna. It is interpreted as the break-up products of sea-mounts and/or small isolated carbonate build-ups developed on the outer shelfal settings.

Revised stratigraphy of the Blanchetown Clay, Murray Basin: age constraints on the evolution of paleo Lake Bungunnia

Paleo Lake Bungunnia covered more than 40 000 km2 of southern Australia during the Plio-Pleistocene, although the age and origin of the lake remain controversial. The Blanchetown Clay is the main depositional unit and outcrop at Nampoo Station in far-western New South Wales provides the most continuous lacustrine section preserved in the basin. Here the Blanchetown Clay represents the maximum lake fill and comprises: (i) a basal well-sorted sand with interbedded clay (Chowilla Sand), representing initial flooding at the time of lake formation; (ii) a thick sequence of green-grey clay comprised dominantly of kaolinite and illite, with the apparently cyclic occurrence of illite interpreted to represent cool and dry glacial climatic intervals; and (iii) a 2.6 m-thick sequence of finely laminated silt and silty clay, here defined as the Nampoo Member of the Blanchetown Clay. New magnetostratigraphic data constrain the age of the oldest lake sediments to be younger than 2.581 Ma (Matuyama-Gauss boundary) and probably as young as 2.4 Ma. This age is significantly younger than the age of 3.2 Ma previously suggested for lake formation. The youngest Blanchetown Clay is older than 0.781 Ma (Brunhes-Matuyama boundary) and probably as old as 1.2 Ma. The Nampoo Station section provides a framework for the construction of a regional Plio-Pleistocene stratigraphy in the Murray Basin.

Reworked Devonian (Givetian-Frasnian) spores from a Permian glacially-derived sequence at Bacchus Marsh, Victoria

Emphanisporites rotatus McGregor emend. McGregor 1973 is a distinctive Devonian spore with a known primary source age range in Australia spanning the upper Givetian to early Frasnian (Middle to Late Devonian). This is the first record of the species from Victoria. It occurs as a reworked element in an Early Permian assemblage belonging to the Granularisporites confluens Zone derived from glacigene diamictite in the Bacchus Marsh area. As the predominant direction of Permian ice movement recorded in the Bacchus Marsh district was south-west to north-east, it is possible that the reworked spores were transported from Antarctica.

A preliminary study of 16S rRNA sequence variation in Australia Macrobrachium shrimps (Palaemonidae: Decapoda) reveals inconsistencies in their current classification

The systematic relationships among Australian palaemonid shrimps have been the subject of speculation for some time. A preliminary phylogenetic study was undertaken to clarify the relationships of five species, Macrobrachium intermedium (Stimpson), M. australiense (Holthuis), M. atactum (Riek), M. rosenbergii (de Man) and Palaemon serenus (Heller), using 16S rRNA mitochondrial gene sequences. Phylogenetic analyses indicated inconsistencies with the current classification in two respects. First, M. intermedium formed a very well-supported clade with P. serenus distinct from M. australiense, M. atactum and M. rosenbergii. Second, the two species from inland Australia, M. australiense and M. atactum, showed a high level of genetic similarity over a substantial geographic range, suggesting that they may represent conspecific populations. The taxonomic and biogeographic implications of these findings for Macrobrachium in Australia are discussed.

Large-scale biological sequence assembly and alignment by using computing grid

Large-scale sequence assembly and alignment are fundamental parts of biological computing. However, most of the large-scale sequence assembly and alignment require intensive computing power and normally take very long time to complete. To speedup the assembly and alignment process, this paper parallelizes the Euler sequence assembly and pair-wise/multiple sequence assembly, two important sequence assembly methods, and takes advantage of Computing Grid which has a colossal computing capacity to meet the large-scale biological computing demand.

Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): a novel gene order revealed

The complete mitochondrial DNA sequence was determined for the Australian freshwater crayfish Cherax destructor (Crustacea: Decapoda: Parastacidae). The 15,895-bp genome is circular with the same gene composition as that found in other metazoans. However, we report a novel gene arrangement with respect to the putative arthropod ancestral gene order and all other arthropod mitochondrial genomes sequenced to date. It is apparent that 11 genes have been translocated (ND1, ND4, ND4L, Cyt b, srRNA, and tRNAs Ser(UGA), Leu(CUN), Ile, Cys, Pro, and Val), two of which have also undergone inversions (tRNAs Pro and Val). The ‘duplication/random loss’ mechanism is a plausible model for the observed translocations, while ‘intramitochondrial recombination’ may account for the gene inversions. In addition, the arrangement of rRNA genes is incompatible with current mitochondrial transcription models, and suggests that a different transcription mechanism may operate in C. destructor.

Mitochondrial DNA sequence and gene organization in the Australian Blacklip Abalone Haliotis rubra (Leach)

The complete mitochondrial DNA of the blacklip abalone Haliotis rubra (Gastropoda: Mollusca) was cloned and 16,907 base pairs were sequenced. The sequence represents an estimated 99.85% of the mitochondrial genome, and contains 2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes found in other metazoan mtDNA. An AT tandem repeat and a possible C-rich domain within the putative control region could not be fully sequenced. The H. rubra mtDNA gene order is novel for mollusks, separated from the black chiton Katharina tunicata by the individual translocations of 3 tRNAs. Compared with other mtDNA regions, sequences from the ATP8, NAD2, NAD4L, NAD6, and 12S rRNA genes, as well as the control region, are the most variable among representatives from Mollusca, Arthropoda, and Rhynchonelliformea, with similar mtDNA arrangements to H. rubra. These sequences are being evaluated as genetic markers within commercially important Haliotis species, and some applications and considerations for their use are discussed.

Mining sequential causal patterns with user-specified skeletons in multi-sequence of event data

The approaches proposed in the past for discovering sequential patterns mainly focused on single sequential data. In the real world, however, some sequential patterns hide their essences among multi-sequential event data. It has been noted that knowledge discovery with either user-specified constraints, or templates, or skeletons is receiving wide attention because it is more efficient and avoids the tedious selection of useful patterns from the mass-produced results. In this paper, a novel pattern in multi-sequential event data that are correlated and its mining approach are presented. We call this pattern sequential causal pattern. A group of skeletons of sequential causal patterns, which may be specified by the user or generated by the program, are verified or mined by embedding them into the mining engine. Experiments show that this method, when applied to discovering the occurring regularities of a crop pest in a region, is successful in mining sequential causal patterns with user-specified skeletons in multi-sequential event data.

A computational framework for nucleic acid sub-sequence identification

Identification of nucleic acid sub-sequences within larger background sequences is a fundamental need of the biology community. The applicability correlates to research studies looking for homologous regions, diagnostic purposes and many other related activities. This paper serves to detail the approaches taken leading to sub-sequence identification through the use of hidden Markov models and associated scoring optimisations. The investigation of techniques for locating conserved basal promoter elements correlates to promoter thus gene identification techniques. The case study centred on the TATA box basal promoter element, as such the background is a gene sequence with the TATA box the target. Outcomes from the research conducted, highlights generic algorithms for sub-sequence identification, as such these generic processes can be transposed to any case study where identification of a target sequence is required. Paths extending from the work conducted in this investigation have led to the development of a generic framework for the future applicability of hidden Markov models to biological sequence analysis in a computational context.