Population collapse and retreat to fire refugia of the Tasmanian endemic conifer Athrotaxis selaginoides following the transition from Aboriginal to European fire management.

Untangling the nuanced relationships between landscape, fire disturbance, human agency, and climate is key to understanding rapid population declines of fire-sensitive plant species. Using multiple lines of evidence across temporal and spatial scales (vegetation survey, stand structure analysis, dendrochronology, and fire history reconstruction), we document landscape-scale population collapse of the long-lived, endemic Tasmanian conifer Athrotaxis selaginoides in remote montane catchments in southern Tasmania. We contextualized the findings of this field-based study with a Tasmanian-wide geospatial analysis of fire-killed and unburned populations of the species. Population declines followed European colonization commencing in 1802 ad that disrupted Aboriginal landscape burning. Prior to European colonization, fire events were infrequent but frequency sharply increased afterwards. Dendrochronological analysis revealed that reconstructed fire years were associated with abnormally warm/dry conditions, with below-average streamflow, and were strongly teleconnected to the Southern Annular Mode. The multiple fires that followed European colonization caused near total mortality of A. selaginoides and resulted in pronounced floristic, structural vegetation, and fuel load changes. Burned stands have very few regenerating A. selaginoides juveniles yet tree-establishment reconstruction of fire-killed adults exhibited persistent recruitment in the period prior to European colonization. Collectively, our findings indicate that this fire-sensitive Gondwanan conifer was able to persist with burning by Aboriginal Tasmanians, despite episodic widespread forest fires. By contrast, European burning led to the restriction of A. selaginoides to prime topographic fire refugia. Increasingly, frequent fires caused by regional dry and warming trends and increased ignitions by humans and lightning are breaching fire refugia; hence, the survival Tasmanian Gondwanan species demands sustained and targeted fire management.

Long-term survival after treatment of idiopathic lung lobe torsion in 80 cases.

OBJECTIVE: To report outcomes of dogs treated for lung lobe torsion (LLT) and to determine prognostic factors for survival. STUDY DESIGN: Retrospective multicenter study from four veterinary teaching hospitals. ANIMALS: Dogs (n = 80) with LLT. METHODS: Medical records were reviewed for clinical and histopathological findings. Long-term outcome was assessed with an owner questionnaire. Lung lobe torsion was classified as idiopathic or secondary on the basis of the etiology. RESULTS: The most represented breeds were pugs (47.5%) and sighthounds (16.2%). The cause of the LLT was considered primary in 77%, secondary in 21%, and unknown in 2% of dogs. Postoperative complications were recorded in 14% of dogs. Overall, 95% of dogs survived to discharge, and median follow-up was 1095 days (range, 7-3809). Owners assessed outcomes and quality of life as excellent in 93% and 89% of dogs, respectively. Primary LLT was associated with a longer survival (median not reached in the study) compared with secondary LLT (921 days; range, 7-2073; P = .001). CONCLUSION: Overall long-term survival after lung lobectomy for LLT was excellent. Primary LLT was associated with longer survival compared with secondary LLT. Long-term owner evaluation of clinical outcome for dogs undergoing lung lobectomy for LLT was considered excellent. CLINICAL IMPACT: Dogs with primary LLT undergoing lung lobectomy have a longer survival time compared with dogs with secondary LLT and have an excellent postoperative outcome.

Assigning clinical meaning to somatic and germ-line whole-exome sequencing data in a prospective cancer precision medicine study.

PURPOSE: Implementing cancer precision medicine in the clinic requires assessing the therapeutic relevance of genomic alterations. A main challenge is the systematic interpretation of whole-exome sequencing (WES) data for clinical care. METHODS: One hundred sixty-five adults with metastatic colorectal and lung adenocarcinomas were prospectively enrolled in the CanSeq study. WES was performed on DNA extracted from formalin-fixed paraffin-embedded tumor biopsy samples and matched blood samples. Somatic and germ-line alterations were ranked according to therapeutic or clinical relevance. Results were interpreted using an integrated somatic and germ-line framework and returned in accordance with patient preferences. RESULTS: At the time of this analysis, WES had been performed and results returned to the clinical team for 165 participants. Of 768 curated somatic alterations, only 31% were associated with clinical evidence and 69% with preclinical or inferential evidence. Of 806 curated germ-line variants, 5% were clinically relevant and 56% were classified as variants of unknown significance. The variant review and decision-making processes were effective when the process was changed from that of a Molecular Tumor Board to a protocol-based approach. CONCLUSION: The development of novel interpretive and decision-support tools that draw from scientific and clinical evidence will be crucial for the success of cancer precision medicine in WES studies.Genet Med advance online publication 26 January 2017.

Oncologists' and cancer patients' views on whole-exome sequencing and incidental findings: results from the CanSeq study.

PURPOSE: Although targeted sequencing improves outcomes for many cancer patients, it remains uncertain how somatic and germ-line whole-exome sequencing (WES) will integrate into care. METHODS: We conducted surveys and interviews within a study of WES integration at an academic center to determine oncologists' attitudes about WES and to identify lung and colorectal cancer patients' preferences for learning WES findings. RESULTS: One-hundred sixty-seven patients (85% white, 58% female, mean age 60) and 27 oncologists (22% female) participated. Although oncologists had extensive experience ordering somatic tests (median 100/year), they had little experience ordering germ-line tests. Oncologists intended to disclose most WES results to patients but anticipated numerous challenges in using WES. Patients had moderately low levels of genetic knowledge (mean 4 correct out of 7). Most patients chose to learn results that could help select a clinical trial, pharmacogenetic and positive prognostic results, and results suggesting inherited predisposition to cancer and treatable noncancer conditions (all ≥95%). Fewer chose to receive negative prognostic results (84%) and results suggesting predisposition to untreatable noncancer conditions (85%). CONCLUSION: The majority of patients want most cancer-related and incidental WES results. Patients' low levels of genetic knowledge and oncologists' inexperience with large-scale sequencing present challenges to implementing paired WES in practice.Genet Med 18 10, 1011-1019.

Macroecology of Australian Tall Eucalypt Forests: Baseline Data from a Continental-Scale Permanent Plot Network.

Tracking the response of forest ecosystems to climate change demands large (≥1 ha) monitoring plots that are repeatedly measured over long time frames and arranged across macro-ecological gradients. Continental scale networks of permanent forest plots have identified links between climate and carbon fluxes by monitoring trends in tree growth, mortality and recruitment. The relationship between tree growth and climate in Australia has been recently articulated through analysis of data from smaller forest plots, but conclusions were limited by (a) absence of data on recruitment and mortality, (b) exclusion of non-eucalypt species, and (c) lack of knowledge of stand age or disturbance histories. To remedy these gaps we established the Ausplots Forest Monitoring Network: a continental scale network of 48 1 ha permanent plots in highly productive tall eucalypt forests in the mature growth stage. These plots are distributed across cool temperate, Mediterranean, subtropical and tropical climates (mean annual precipitation 850 to 1900 mm per year; mean annual temperature 6 to 21°C). Aboveground carbon stocks (AGC) in these forests are dominated by eucalypts (90% of AGC) whilst non-eucalypts in the understorey dominated species diversity and tree abundance (84% of species; 60% of stems). Aboveground carbon stocks were negatively related to mean annual temperature, with forests at the warm end of the temperature range storing approximately half the amount of carbon as forests at the cool end of the temperature range. This may reflect thermal constraints on tree growth detected through other plot networks and physiological studies. Through common protocols and careful sampling design, the Ausplots Forest Monitoring Network will facilitate the integration of tall eucalypt forests into established global forest monitoring initiatives. In the context of projections of rapidly warming and drying climates in Australia, this plot network will enable detection of links between climate and growth, mortality and carbon dynamics of eucalypt forests.

Effects of high-severity fire drove the population collapse of the subalpine Tasmanian endemic conifer Athrotaxis cupressoides.

Athrotaxis cupressoides is a slow-growing and long-lived conifer that occurs in the subalpine temperate forests of Tasmania, a continental island to the south of Australia. In 1960-1961, human-ignited wildfires occurred during an extremely dry summer that killed many A. cupressoides stands on the high plateau in the center of Tasmania. That fire year, coupled with subsequent regeneration failure, caused a loss of ca. 10% of the geographic extent of this endemic Tasmanian forest type. To provide historical context for these large-scale fire events, we (i) collected dendroecological, floristic, and structural data, (ii) documented the postfire survival and regeneration of A. cupressoides and co-occurring understory species, and (iii) assessed postfire understory plant community composition and flammability. We found that fire frequency did not vary following the arrival of European settlers, and that A. cupressoides populations were able to persist under a regime of low-to-mid severity fires prior to the 1960 fires. Our data indicate that the 1960 fires were (i) of greater severity than previous fires, (ii) herbivory by native marsupials may limit seedling survival in both burned and unburned A. cupressoides stands, and (iii) the loss of A. cupressoides populations is largely irreversible given the relatively high fuel loads of postfire vegetation communities that are dominated by resprouting shrubs. We suggest that the feedback between regeneration failure and increased flammability will be further exacerbated by a warmer and drier climate causing A. cupressoides to contract to the most fire-proof landscape settings.