Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The Paleocene – Eocene mangroves of South-eastern Australia: spatial and temporal occurrences across four geological basins

The advent of the Paleocene-Eocene Thermal Maximum (PETM), a ~ 200 kyr period of global warming ca. 56 Ma, caused sea-levels to rise, transgressing near-coastal environments in South-eastern (SE) Australia over >55,000 km2. During the PETM, warming tropical climates may have extended south to ≥60°S paleolatitude. The PETM in SE Australia is corroborated primarily by stable carbon isotope chemostratigraphy and detailed palynology records in four geological basins. Previous work showed that, in addition to the globally recognised carbon isotope excursion, the PETM interval in coastal SE Australia can be identified using the dual occurrence of the tropical mangrove Nypa palm pollen (Spinizonocolpites prominatus) accompanied by thermophilic marine dinoflagellate cysts (mainly Apectodinium hyperacanthum). We here document a total of twenty-six Gippsland Basin wells that record this Nypa-A.hyperacanthum association in the earliest Eocene Kingfish Formation (Lower Malvacipollis diversus Zone). In the Bass Basin, eight wells record Nypa-A.hyperacanthum association within the Eastern View Group basal Koorkah Formation, or lower part of the Lower M. diversus Zone (earliest Eocene). In the Bass Basin a further thirteen wells with Nypa occurrences near the top of the Cormorant Formation are found, which might be associated with the longer-term warmth of the Early Eocene Climatic Optimum (EECO, ~53–49 Ma). Government bores and petroleum wells across the Otway Basin record the Nypa-A. hyperacanthum PETM association within the Pember Mudstone Lower M. diversus Zone in twenty-one bores. Nine horizons with Nypa occurrences occur within the Burrungule Member (EECO) at the top of the Dilwyn Formation. In western Tasmania, Nypa occurs in the Sorell Basin and Macquarie Harbour area within the Lower M. diversus Zone. Together, these observations show the remarkable extent of the mangrove-coasts that were established across the mid-high paleolatitudes in SE Australia during the warmest intervals of the Cenozoic, the PETM and EECO

A near‐field sea level record of East Antarctic Ice Sheet instability from 32 to 27 Myr

Fossil, facies, and isotope analyses of an early high‐paleolatitude (55°S) section suggests a highly unstable East Antarctic Ice Sheet from 32 to 27 Myr. The waxing and waning of this ice sheet from 140% to 40% of its present volume caused sea level changes of +25 m (ranging from ‐30 to +50 m) related to periodic glacial (100,000 to 200,000 years) and shorter interglacial events. The near‐field Gippsland sea level (GSL) curve shares many similarities to the far‐field New Jersey sea level (NJSL) estimates. However, there are possible resolution errors due to biochronology, taphonomy, and paleodepth estimates and the relative lack of lowstand deposits (in NJSL) that prevent detailed correlations with GSL. Nevertheless, the lateral variations in sea level between the GSL section and NJSL record that suggest ocean siphoning and antisiphoning may have propagated synchronous yet variable sea levels

Palaeogeographic, climatic and tectonic change in southeastern Australia: the Late Neogene evolution of the Murray Basin

The Murray Basin is a low-lying but extensive intracratonic depocentre in southeastern Australia, preserving an extraordinary record of Late Neogene sedimentation. New stratigraphic and sedimento-logic data allow the long-term evolution of the basin to be re-evaluated and suggest a significant role for: (1) tectonism in controlling basin evolution, and (2) progressive and step-wise climatic change beginning in the early Pleistocene. Tectonic change is associated with regional uplift, occurring at approximately the same rate from the early Pliocene until the present day, and possibly associated with changing mantle circulation patterns or plate boundary processes. This uplift led to the defeat and re-routing of the Murray River, Australia's major continental drainage system. Key to our interpretation is recognition of timing relationships between four prominent palaeogeographic features - the Loxton-Parilla Sands strandplain, the Gambier coastal plain, palaeo megalake Bungunnia and the Kanawinka Escarpment. Geomorphic and stratigraphic evidence suggest that during the Early Pliocene the ancestral Murray River was located in western Victoria, flowing south along the Douglas Depression. Relatively small amounts of regional uplift (<200 m) defeated this drainage system, dramatically changing the palaeogeography of southeastern Australia and forming Plio-Pleistocene megalake Bungunnia. At its maximum extent Lake Bungunnia covered more than 50,000 km(2), making it one of the largest known palaeo- or modern-lakes in an intracontinental setting. Magnetostratigraphic constraints suggest lake formation c. 2.4 Ma. The formation of Lake Bungunnia influenced the Pliocene coastal dynamics, depriving the coastline of a sediment source and changing the coastal system from a prograding strandline system to an erosional one. Erosion during this period formed the Kanawinka Escarpment, a palaeo sea-cliff and one of the most prominent and laterally extensive geomorphic features in southeastern Australia. Marine sediments c. 800 ka to c. 1.16 Ma represent the time of re-establishment of depositional coastal dynamics and of a permanent outlet for the Murray River. This age range is consistent with our best estimate of the age of the youngest lake Bungunnia sediments and points towards an early Pleistocene age for the demise of the lake system. The youngest Lake Bungunnia sediment, present on a number of distinct terraces, suggests that progressive, step-wise climatic change played a role in the demise of the lake. However, in order for the ancestral Murray River system to have been able to breach the pre-existing tectonic dam, it is likely that tectonic change and/or temporarily enhanced discharge was also significant. This scenario indicates that the modern Murray River has only been in existence for at most 700 ka. (C) 2010 Elsevier Ltd. All rights reserved

Microfossil, stable isotope, and facies of a near-continuous core from the Gippsland Basin

Fossil, facies, and isotope analyses of an early high-paleolatitude (55°S) section suggests a highly unstable East Antarctic Ice Sheet from 32 to 27 Myr. The waxing and waning of this ice sheet from 140% to 40% of its present volume caused sea level changes of ±25 m (ranging from -30 to +50 m) related to periodic glacial (100,000 to 200,000 years) and shorter interglacial events. The near-field Gippsland sea level (GSL) curve shares many similarities to the far-field New Jersey sea level (NJSL) estimates. However, there are possible resolution errors due to biochronology, taphonomy, and paleodepth estimates and the relative lack of lowstand deposits (in NJSL) that prevent detailed correlations with GSL. Nevertheless, the lateral variations in sea level between the GSL section and NJSL record that suggest ocean siphoning and antisiphoning may have propagated synchronous yet variable sea levels