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

Eocene-Oligocene coals of the Gippsland and Australo-Antarctic basins – Paleoclimatic and paleogeographic context and implications for the earliest Cenozoic glaciations

Australia's Gippsland Basin contains a semi-continuous Eocene-Oligocene (41.5–28.4 Ma) near-coastal coal record that formed adjacent to Pacific Ocean. Traralgon and Morwell Formation brown coals include 4 main seams (T2, T1, T0, M2). Coal seam palynology records show late Middle Eocene (T2) coals formed under megathermic conditions characterized by high-gymnosperm contents, Late Eocene (T1) coals formed under mesothermic conditions characterized by reduced-gymnosperm contents and earliest indications of palaeoclimate cooling. Earliest Oligocene T0 coal record (33.9–31.5 Ma) contains high-gymnosperm palynology profile, very similar to the T2 coals. The earliest indication of cooler climes only begins after this coal formed as indicated by low-gymnosperm high-Nothofagus (southern beech) pollen proportions. We suggest in Gippsland the earliest evidence for major glacial cooling (by inference the Oi1 event) be placed immediately above the T0 coal seam where Early to Late Oligocene Morwell Formation sands, clays and coals contain low counts of gymnosperms (< 10%) but high average proportions of Nothofagus (50%). This is the main definitive indicator that palaeoclimates had cooled between the Eocene and Oligocene. This agrees with the current ocean drilling position of the earliest (Oi1) glacial event shortly above the Eocene-Oligocene boundary. A number of contemporaneous Middle to Late Eocene brown coals occurred in near-coastal settings across 1200 km of southern Australia. Palaeogeographically, all these coal basins faced the Australo-Antarctic Gulf and have a much lower gymnosperm proportion (< 10%), low Nothofagus proportion (< 10%), but very high (non-Nothofagus) angiosperms proportion. This suggests a different climatic regime separated a cooler and wetter Gippsland Basin flora that responded to the cooler Proto-Ross Sea Gyre rotating around a wide Pacific Ocean, and a warm-wet climate associated with a warm proto-Leeuwin current of the Australo-Antarctic Gulf. © 2017 Elsevier B.V

Fire and Late Oligocene to Mid-Miocene peat mega-swamps of south-eastern Australia : A floristic and palaeoclimatic interpretation

This article is a presentation that formed part of the Ecological Society of Australia's annual symposium entitled "Fire in Australia : how was the biota prepared for human occupation". The Late Oligocene to Mid-Miocene (25-13million years ago) brown coals of the Gippsland Basin in southern Victoria, Australia, were deposited in peat mega-swamps, unlike any in the world at the present day. The swamps preserve a rich botanical suite of macro- and microfossils, many of which can be identified with plant genera and families present today in Australia, New Caledonia, New Zealand and New Guinea. The peat-forming environments also preserve evidence of past burning in the form of micro-charcoal as well as macro-charcoal, the latter being evident as regional lenses or layers of fusinite, generally in coals of the darkest colour termed dark lithotypes. The presence of micro-charcoal in dark and some other lighter lithotypes indicated that fires also burnt locally, although they may have been extinguished before regional-scale burning occurred. It is also feasible that some peat mega-swamp plant communities dominated by rainforest angiosperm plants may have been fire excluders and prevented widespread fires from developing. Pollen and macrofossil evidence is presented of a distinctive southern conifer and angiosperm flora with an open canopy, primarily associated with the darkest coals that formed in the wettest parts of the peat-forming environment. Elsewhere, swamp forests with a large rainforest component grew on swamps raised appreciably above the regional groundwater table in a structural context akin to the ombrogenous peats of tropical coastal Sumatra and Sarawak. These vegetation types were not fire prone, but may have occasionally burnt at a local scale or at forest margins. Evidence is presented for the existence of seasonal climatic conditions that would appear to have facilitated a drying-out of the peat swamps in the warmest months of the year. A mesothermal climate was invoked where mean annual precipitation was at least 1500mm, and possibly as much as 2000mm, and mean annual temperatures were ∼19°C. © 2013 CSIRO

Moderate levels of Eocene pCO2 indicated by Southern Hemisphere fossil plant stomata

Reducing the uncertainty in predictions of future climate change is one of today’s greatest scientific challenges, with many significant problems unsolved, including the relationship between pCO2 and global temperature. To better constrain these forecasts, it is meaningful to study past time intervals of global warmth, such as the Eocene (56.0–33.9 Ma), serving as climatic analogues for the future. Here we reconstructed pCO2 using the stomatal densities of a large fossil Lauraceae (laurel) leaf database from ten sites across the Eocene of Australia and New Zealand. We show that mostly moderate pCO2 levels of ∼450–600 ppm prevailed throughout the Eocene, levels that are considerably lower than the pCO2 forcing currently needed to recreate Eocene temperatures in climate models. Our data record significantly lower pCO2 than inferred from marine isotopes, but concur with previously published Northern Hemisphere Eocene stomatal proxy pCO2. We argue that the now globally consistent stomatal proxy pCO2 record for the Eocene is robust and that climate sensitivity was elevated and/or that additional climate forcings operated more powerfully than previously assumed.Additional funding from the Bolin Centre for Climate Research, Stockholm University</p

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 new perspective on Late Eocene and Oligocene vegetation and paleoclimates of South-eastern Australia

We present a composite terrestrial pollen record of latest Eocene through Oligocene (35.5–23 Ma) vegetation and climate change from the Gippsland Basin of south-eastern Australia. Climates were overwhelmingly mesothermic through this time period, with mean annual temperature (MAT) varying between 13 and 18 °C, with an average of 16 °C. We provide evidence to support a cooling trend through the Eocene–Oligocene Transition (EOT), but also identify three subsequent warming cycles through the Oligocene, leading to more seasonal climates at the termination of the Epoch. One of the warming episodes in the Early Oligocene appears to have also occurred at two other southern hemisphere sites at the Drake Passage as well as off eastern Tasmania, based on recent research. Similarities with sea surface temperature records from modern high southern latitudes which also record similar cycles of warming and cooling, are presented and discussed. Annual precipitation varied between 1200 and 1700 mm/yr, with an average of 1470 mm/yr through the sequence. Notwithstanding the extinction of Nothofagus sg. Brassospora from Australia and some now microthermic humid restricted Podocarpaceae conifer taxa, the rainforest vegetation of lowland south-eastern Australia is reconstructed to have been similar to present day Australian Evergreen Notophyll Vine Forests existing under the sub-tropical Köppen-Geiger climate class Cfa (humid subtropical) for most of the sequence. Short periods of cooler climates, such as occurred through the EOT when MAT was ~ 13 °C, may have supported vegetation similar to modern day Evergreen Microphyll Fern Forest. Of potentially greater significance, however, was a warm period in the Early to early Late Oligocene (32–26 Ma) when MAT was 17–18 °C, accompanied by small but important increases in Araucariaceae pollen. At this time, Araucarian Notophyll/Microphyll Vine Forest likely occurred regionally. © 2022 Elsevier B.V

Identification of the Paleocene-Eocene boundary in coastal strata in the Otway Basin, Victoria, Australia

Detailed, stratigraphically well-constrained environmental reconstructions are available for Paleocene and Eocene strata at a range of sites in the southwest Pacific Ocean (New Zealand and East Tasman Plateau; ETP) and Integrated Ocean Discovery Program (IODP) Site U1356 in the south of the Australo-Antarctic Gulf (AAG). These reconstructions have revealed a large discrepancy between temperature proxy data and climate models in this region, suggesting a crucial error in model, proxy data or both. To resolve the origin of this discrepancy, detailed reconstructions are needed from both sides of the Tasmanian Gateway. Paleocene-Eocene sedimentary archives from the west of the Tasmanian Gateway have unfortunately remained scarce (only IODP Site U1356), and no well-dated successions are available for the northern sector of the AAG. Here we present new stratigraphic data for upper Paleocene and lower Eocene strata from the Otway Basin, southeast Australia, on the (north)west side of the Tasmanian Gateway. We analyzed sediments recovered from exploration drilling (Latrobe-1 drill core) and outcrop sampling (Point Margaret) and performed high-resolution carbon isotope geochemistry of bulk organic matter and dinoflagellate cyst (dinocyst) and pollen biostratigraphy on sediments from the regional lithostratigraphic units, including the Pebble Point Formation, Pember Mudstone and Dilwyn Formation. Pollen and dinocyst assemblages are assigned to previously established Australian pollen and dinocyst zonations and tied to available zonations for the SW Pacific. Based on our dinocyst stratigraphy and previously published planktic foraminifer biostratigraphy, the Pebble Point Formation at Point Margaret is dated to the latest Paleocene. The globally synchronous negative carbon isotope excursion that marks the Paleocene-Eocene boundary is identified within the top part of the Pember Mudstone in the Latrobe-1 borehole and at Point Margaret. However, the high abundances of the dinocyst Apectodinium prior to this negative carbon isotope excursion prohibit a direct correlation of this regional bio-event with the quasi-global Apectodinium acme at the Paleocene-Eocene Thermal Maximum (PETM; 56Ma). Therefore, the first occurrence of the pollen species Spinizonocolpites prominatus and the dinocyst species Florentinia reichartii are here designated as regional markers for the PETM. In the Latrobe-1 drill core, dinocyst biostratigraphy further indicates that the early Eocene (∼56-51Ma) sediments are truncated by ∼ 10Myr long hiatus overlain by middle Eocene (∼ 40Ma) strata. These sedimentary archives from southeast Australia may prove key in resolving the model-data discrepancy in this region, and the new stratigraphic data presented here allow for detailed comparisons between paleoclimate records on both sides of the Tasmanian Gateway

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

Identification of the Paleocene-Eocene boundary in coastal strata in the Otway Basin, Victoria, Australia

Detailed, stratigraphically well-constrained environmental reconstructions are available for Paleocene and Eocene strata at a range of sites in the southwest Pacific Ocean (New Zealand and East Tasman Plateau; ETP) and Integrated Ocean Discovery Program (IODP) Site U1356 in the south of the Australo-Antarctic Gulf (AAG). These reconstructions have revealed a large discrepancy between temperature proxy data and climate models in this region, suggesting a crucial error in model, proxy data or both. To resolve the origin of this discrepancy, detailed reconstructions are needed from both sides of the Tasmanian Gateway. Paleocene-Eocene sedimentary archives from the west of the Tasmanian Gateway have unfortunately remained scarce (only IODP Site U1356), and no well-dated successions are available for the northern sector of the AAG. Here we present new stratigraphic data for upper Paleocene and lower Eocene strata from the Otway Basin, southeast Australia, on the (north)west side of the Tasmanian Gateway. We analyzed sediments recovered from exploration drilling (Latrobe-1 drill core) and outcrop sampling (Point Margaret) and performed high-resolution carbon isotope geochemistry of bulk organic matter and dinoflagellate cyst (dinocyst) and pollen biostratigraphy on sediments from the regional lithostratigraphic units, including the Pebble Point Formation, Pember Mudstone and Dilwyn Formation. Pollen and dinocyst assemblages are assigned to previously established Australian pollen and dinocyst zonations and tied to available zonations for the SW Pacific. Based on our dinocyst stratigraphy and previously published planktic foraminifer biostratigraphy, the Pebble Point Formation at Point Margaret is dated to the latest Paleocene. The globally synchronous negative carbon isotope excursion that marks the Paleocene-Eocene boundary is identified within the top part of the Pember Mudstone in the Latrobe-1 borehole and at Point Margaret. However, the high abundances of the dinocyst Apectodinium prior to this negative carbon isotope excursion prohibit a direct correlation of this regional bio-event with the quasi-global Apectodinium acme at the Paleocene-Eocene Thermal Maximum (PETM; 56Ma). Therefore, the first occurrence of the pollen species Spinizonocolpites prominatus and the dinocyst species Florentinia reichartii are here designated as regional markers for the PETM. In the Latrobe-1 drill core, dinocyst biostratigraphy further indicates that the early Eocene (∼56-51Ma) sediments are truncated by ∼ 10Myr long hiatus overlain by middle Eocene (∼ 40Ma) strata. These sedimentary archives from southeast Australia may prove key in resolving the model-data discrepancy in this region, and the new stratigraphic data presented here allow for detailed comparisons between paleoclimate records on both sides of the Tasmanian Gateway