Building a global alliance of biofoundries (vol 10, 2040, 2019)

The original version of this Comment contained errors in the legend of Figure 2, in which the locations of the fifteenth and sixteenth GBA members were incorrectly given as '(15) Australian Genome Foundry, Macquarie University; (16) Australian Foundry for Advanced Biomanufacturing, University of Queensland.'. The correct version replaces this with '(15) Australian Foundry for Advanced Biomanufacturing (AusFAB), University of Queensland and (16) Australian Genome Foundry, Macquarie University'. This has been corrected in both the PDF and HTML versions of the Comment

Triple jeopardy in the tropics: assessing extinction risk in Australia's freshwater biodiversity hotspot

© 2017 Dr. Matthew Charles Le FeuvreFreshwaters are the most degraded and imperiled ecosystem globally. Despite this high vulnerability, conservation efforts in freshwaters often lag behind those in terrestrial and marine ecosystems. In Australia this is particularly evident; despite high levels of river degradation, few freshwater fishes have had their conservation status assessed and only 14% of fishes are listed. Most listed species are restricted to southern Australia where rivers are particularly degraded. Northern Australia’s rivers are very diverse with many highly range restricted fishes. Yet almost no species are listed, despite potential vulnerability and an increasing number of threats across the north. Nowhere is this more evident than the Kimberley region in the north-west, where 49% of species are restricted to three or fewer rivers, and 10% are restricted to an area of <20 km2. Very little is known about the ecology of the region’s endemic fishes, so their vulnerability cannot be assessed. In my thesis I assess extinction risk in the freshwater fishes of the Kimberley using the triple jeopardy framework, that is whether they have small geographic ranges, low abundances and/or narrow ecological niches. Specifically I aim to (1) determine the relationships between range size, body size and abundance in all Australian freshwater fishes and (2) whether these relationships can be used to identify species at risk of extinction. I then determine whether (3) small ranged Kimberley endemics have narrow habitat, dietary or thermal niches compared to closely related widespread species and (4) synthesize these results to identify the fishes most at risk of extinction in the Kimberley. First, I test for a relationship between geographic range size and body size in all Australian freshwater fishes. I then investigate how this relationship varies with conservation status. I identify currently unlisted freshwater fishes that share traits with listed species and map their distribution, along with freshwater fish research effort, across Australia. I found a positive relationship between range size and body size. For a given body size, conservation listed species have a range less than one tenth the size of unlisted species. Based on this relationship, I identified 55 additional species that may be vulnerable to extinction. Most of these species are restricted to northern Australia where freshwater fishes are poorly known due to low research effort. Second, I test for abundance-geographic range size and abundance-body size relationships in Australian freshwater fishes and investigate how these relationships vary with conservation status. I identify and map currently unlisted freshwater fishes that are numerically rare, and combined with the results outlined above, map species with a double jeopardy risk of extinction. I found a negative body size-abundance relationship and no correlation between range size and abundance. Although relative abundance was a poor predictor of current conservation listing, I identified 59 consistently rare species. Twenty of these species (34%) currently suffer a double jeopardy risk of extinction and all were restricted to northern Australia. Third, using closely related widespread and endemic congeneric pairings of Kimberley freshwater fishes, I investigate whether endemic species have narrow dietary niches at any stage during their development. Using qualitative measures of habitat and presence/absence data, I also assess habitat specialization. Most range-restricted species have narrower ecological niches making them more vulnerable to extinction. Fourth I test the thermal performance of two pairs of congeneric species that are sympatric in the Drysdale River, with one widely distributed species and one range restricted species in each pair. In the Syncomistes pair, resting metabolic rate (RMR) was similar between species at low temperature but at higher temperatures the RMR of the widespread species was lower due to the onset of anaerobiosis. The range-restricted Syncomistes also has a higher critical thermal limit (CTL). In the Melanotaenia pair, the results were the opposite, with the widespread species having a higher CTL and RMR. The thermal performance of each species was related to their distribution within the catchment rather than their geographic range size, with the thermally sensitive species dominating the cooler, perennial downstream reaches, and the hardier species being more abundant in the hotter, more ephemeral upper catchment. Finally, I use the above information to assess the triple jeopardy extinction risk in the fishes of the Kimberley. Seventy-nine per cent of Kimberley endemic fishes are vulnerable on one or more axis, and two species had a triple jeopardy risk of extinction. The majority of vulnerable species are found in the remote rivers of the north-western Kimberley, but the most imperiled species (Hypseleotris kimberleyensis) is restricted to the heavily degraded Fitzroy River. My thesis shows that, despite fundamentally different environments, life histories and dispersal capacity, Australian freshwater fishes exhibit range size, body size and abundance relationships largely similar to terrestrial fauna. By identifying northern Australia as a hotspot of unrecognized vulnerable species, I provide an important context for guiding targeted research and informing future conservation management of Australia’s freshwater fishes. Combined with their small ranges and/or low abundance, the narrower niches of most Kimberley endemic species makes the region’s fishes particularly extinction prone. By identifying which endemic species are most vulnerable, my study provides specific information for targeting conservation efforts in the region. As the Kimberley and northern Australia more broadly are earmarked for major development, substantial effort is needed to effectively manage fish populations, design and manage developments with the environment as a major stakeholder and preserve remote rivers with high endemism and extinction risk. However, as northern Australia’s rivers are in good condition, with planning and research there is an excellent opportunity for proactive, properly informed freshwater conservation across the region

Fish distribution database

This file contains the freshwater fish species presence/absence data used in our analysis. The first column lists each of the rivers for which we had community data, while the remaining columns indicate the presence/absence of individual species coded as 1 = present, 0 = absent

In conversation

No abstract available

Data from: The Kimberley, north-western Australia, as a cradle of evolution and endemic biodiversity: an example using Grunters (Terapontidae)

Aim: To test two prominent, alternate hypotheses that provide explanations for the great accumulation of endemic species in the Kimberley bioregion in north-western Australia, using an extensively sampled, region wide phylogeny of northern Australia’s most speciose freshwater fish family, Terapontidae. Specifically, we test whether the Kimberley may act as (1) a “museum” accumulating taxa and endemic species over time or (2) a “cradle” of more recent diversification and neoendemism. Location: The Australian monsoonal tropics Taxon: Grunters (Terapontidae) Methods: We obtained a robust and well supported Bayesian phylogeny for the family using DNA sequences from mtDNA and nuclear gene regions. We performed molecular phylogenetic analyses using species tree methods including molecular dating analysis, ancestral range reconstruction, and diversification analysis. Results: Based on our phylogeny, the combined molecular clock estimates and likelihood-based historical biogeographic reconstructions suggest that terapontids recently transitioned into the Kimberley from the east during the late-Miocene. We found that 80% of Kimberley terapontids diversified within the Kimberley in the last 3 Ma. Further, diversification analyses identified a single significant shift in diversification rates ~1.4 Ma that corresponds with a change in global climate midway through the Pleistocene that was predominantly driven by speciation in the Kimberley. Main Conclusions: The weight of evidence suggests that the Kimberley has been a “cradle” of evolution for Terapontidae, rather than a “museum”. Our analysis provides strong evidence for a geologically recent transition of terapontids into the Kimberley from regions to the east during the late Miocene followed by a significant increase in speciation rates during the Pleistocene, driven by speciation in the Kimberley. The results provide important insight into the evolutionary and biogeographical processes that have shaped the regions unique biota, which will inform land managers working to protect and conserve both species and the processes responsible for generating and sustaining them

Terapontid_PosteriorTrees_10k

A posterior distribution of 10,000 trees sampled from the broader distribution used in the *BEAST analysi

The Optimal Design of a Distillation System for the Flexible Polygeneration of Dimethyl Ether and Methanol Under Uncertainty

Two process designs for the separation section of a flexible dimethyl ether and methanol polygeneration plant are presented, as well as an optimization method which can determine the optimal design under market uncertainty quickly and to global optimality without loss of model fidelity. The polygeneration plant produces a product mixture that is either mostly dimethyl ether or mostly methanol depending on market conditions by using a classic two-stage dimethyl ether production catalytic reaction route in which the second stage is bypassed when the market demand is such that methanol production is more favorable than dimethyl ether. The downstream distillation sequence is designed to purify the products to desired specifications despite the wide variability in feed condition that corresponds to the upstream reaction system operating either in DME-rich or methanol-rich mode. Because the optimal design depends on uncertain market conditions (realized as the percentage of the time in which the plant operates in either DME-rich or methanol-rich mode), this uncertainty is considered in the formulation of the optimal design problem. The results show that using one set of flexible distillation columns for two different objectives is superior to the “traditional” approach of using two different sets of distillation columns which are each optimized for one specific operating condition. Different approaches to design under uncertainty were considered, with a scenario-based two-stage stochastic formulation with a uniform distribution of the uncertain parameter recommended as the preferred formulation

Range restriction leads to narrower ecological niches and greater extinction risk in Australian freshwater fish

Human-induced environmental changes are accelerating biodiversity loss. Identifying which life-history traits increase extinction risk is important to inform proactive conservation. While geographically or numerically rare species are typically more vulnerable, ecological specialization may also increase extinction risk particularly when associated with rarity. We investigate whether regionally endemic freshwater fishes have more specialized diets and habitat requirements than more widely distributed, closely related species. We then use this information to assess extinction risk. Using closely-related widespread and endemic congeneric pairings from the Kimberley region of north-western Australia, we investigate whether there are ontogenetic diet shifts in 13 species and if some of these ontogenetic trophic units (OTUs) have narrow dietary niches. Using qualitative measures of habitat and presence/absence data, we also assess habitat specialization in 32 species. Overall, range-restricted species had narrower ecological niches. Ontogenetic diet shifts existed in 12 of 13 species and range-restricted species were more specialized for some or all of their OTUs compared to their widespread congenerics. Endemic species had a higher degree of variance in habitat use compared to their widespread congenerics, showing they had more specialized habitat requirements. As specialization is linked to extinction risk, the narrow niche breadth of small-ranged endemic fishes makes them more vulnerable to extinction than more cosmopolitan species. As many endemics from the Kimberley region have small ranges and/or low abundances, they may have an increased risk of extinction. By identifying which endemic species have narrow ecological niches, our study provides essential information for targeting proactive conservation efforts

Strengthening the primary care workforce to deliver high-quality care for non-communicable diseases in refugee settings: lessons learnt from a UNHCR partnership.

Non-communicable disease (NCD) prevention and care in humanitarian contexts has been a long-neglected issue. Healthcare systems in humanitarian settings have focused heavily on communicable diseases and immediate life-saving health needs. NCDs are a significant cause of morbidity and mortality in refugee settings, however, in many situations NCD care is not well integrated into primary healthcare services. Increased risk of poorer outcomes from COVID-19 for people living with NCDs has heightened the urgency of responding to NCDs and shone a spotlight on their relative neglect in these settings. Partnering with the United Nations Refugee Agency (UNHCR) since 2014, Primary Care International has provided clinical guidance and Training of Trainer (ToT) courses on NCDs to 649 health professionals working in primary care in refugee settings in 13 countries. Approximately 2300 healthcare workers (HCW) have been reached through cascade trainings over the last 6 years. Our experience has shown that, despite fragile health services, high staff turnover and competing clinical priorities, it is possible to improve NCD knowledge, skills and practice. ToT programmes are a feasible and practical format to deliver NCD training to mixed groups of HCW (doctors, nurses, technical officers, pharmacy technicians and community health workers). Clinical guidance must be adapted to local settings while co-creating an enabling environment for health workers is essential to deliver accessible, high-quality continuity of care for NCDs. On-going support for non-clinical systems change is equally critical for sustained impact. A shared responsibility for cascade training-and commitment from local health partners-is necessary to raise NCD awareness, influence local and national policy and to meet the UNHCR's objective of facilitating access to integrated prevention and control of NCDs

Data from: A revision of the bioregionalisation of freshwater fish communities in the Australian Monsoonal Tropics

The Australian freshwater fish fauna is very unique, but poorly understood. In the Australian Monsoonal Tropics (AMT) biome of northern Australia, the number of described and candidate species has nearly doubled since the last attempt to analyse freshwater fish species composition patterns and determine a bioregionalisation scheme. Here, we utilise the most complete database of catchment‐scale freshwater fish distributions from the AMT to date to: (a) reanalyze spatial patterns of species richness, endemism and turnover of freshwater fishes; (b) propose a biogeographic regionalisation based on species turnover; (c) assess the relationship between species turnover and patterns of environmental change and historic drainage connectivity; and (d) identify sampling gaps. Biogeographic provinces were identified using an agglomerative cluster analysis of a Simpson's beta (βsim) dissimilarity matrix. A generalised dissimilarity model incorporating eighteen environmental variables was used to investigate the environmental correlates of species turnover. Observed and estimated species richness and endemism were calculated and inventory completeness was estimated based on the ratio of observed to estimated species richness. Three major freshwater fish biogeographic provinces and 14 subprovinces are proposed. These differ substantially from the current bioregionalisation scheme. Species turnover was most strongly influenced by environmental variables that are interpreted to reflect changes in terrain (catchment relief and confinement), geology and climate (runoff perenniality, stream density), and biotic responses to climate (net primary productivity). Past connectivity between rivers during low sea‐level events is also influential highlighting the importance of historical processes in explaining contemporary patterns of biodiversity in the AMT. The inclusion of 49 newly discovered species and candidate species only reinforced known focal points of species richness and endemism in the AMT. However, a number of key sampling gaps remain that need to be filled to fully characterise the proposed bioregionalisation