Early evolution of beetles regulated by the end-Permian deforestation

The end-Permian mass extinction (EPME) led to a severe terrestrial ecosystem collapse. However, the ecological response of insects—the most diverse group of organisms on Earth—to the EPME remains poorly understood. Here, we analyse beetle evolutionary history based on taxonomic diversity, morphological disparity, phylogeny, and ecological shifts from the Early Permian to Middle Triassic, using a comprehensive new data set. Permian beetles were dominated by xylophagous stem groups with high diversity and disparity, which probably played an underappreciated role in the Permian carbon cycle. Our suite of analyses shows that Permian xylophagous beetles suffered a severe extinction during the EPME largely due to the collapse of forest ecosystems, resulting in an Early Triassic gap of xylophagous beetles. New xylophagous beetles appeared widely in the early Middle Triassic, which is consistent with the restoration of forest ecosystems. Our results highlight the ecological significance of insects in deep-time terrestrial ecosystems.

Identifying the World’s Most At-Risk River Basins

Major river basins around the world, including the Amazon, may be hot spots for ecological shifts as the planet warms.

Early evolution of beetles regulated by the end-Permian deforestation

The end-Permian mass extinction (EPME) led to a severe terrestrial ecosystem collapse. However, the ecological response of insects—the most diverse group of organisms on Earth—to the EPME remains poorly understood. Here, we analyse beetle evolutionary history based on taxonomic diversity, morphological disparity, phylogeny, and ecological shifts from the Early Permian to Middle Triassic, using a comprehensive new data set. Permian beetles were dominated by xylophagous stem groups with a high diversity and disparity, which probably played an underappreciated role in the Permian carbon cycle. Our suite of analyses shows that Permian xylophagous beetles suffered a severe extinction during the EPME largely due to the collapse of forest ecosystems, resulting in an Early Triassic gap of xylophagous beetles. New xylophagous beetles appeared widely in the early Middle Triassic, which is consistent with the restoration of forest ecosystems. Our results highlight the ecological significance of insects in deep-time terrestrial ecosystems.

Pseudofinder: detection of pseudogenes in prokaryotic genomes

Prokaryotic genomes are generally gene dense and encode relatively few pseudogenes, or nonfunctional/inactivated remnants of genes. However, in certain contexts, such as recent ecological shifts or extreme population bottlenecks (such as those experienced by symbionts and pathogens), pseudogenes can quickly accumulate and form a substantial fraction of the genome. Identification of pseudogenes is, thus, a critical step for understanding the evolutionary forces acting upon, and the functional potential encoded within, prokaryotic genomes. Here, we present Pseudofinder, an open-source software dedicated to pseudogene identification and analysis. With Pseudofinder's multi-pronged, reference-based approach, we demonstrate its capacity to detect a wide variety of pseudogenes, including those that are highly degraded and typically missed by gene-calling pipelines, as well newly formed pseudogenes, which can have only one or a few inactivating mutations. Additionally, Pseudofinder can detect intact genes undergoing relaxed selection, which may indicate incipient pseudogene formation. Implementation of Pseudofinder in annotation pipelines will not only clarify the functional potential of sequenced microbes, but will also generate novel insights and hypotheses regarding the evolutionary dynamics of bacterial and archaeal genomes.

Towards co-creation: A design-led study of ecological shifts in the tidal margin.

<p><b>The ecological resilience of the intertidal margins of many cities is increasingly under pressure due to climatic shifts and urbanisation. As rising sea levels push the high-water mark landward, many coastal species are prevented from migrating inland due to natural or man-made barriers. This results in a phenomena known as ‘coastal squeeze’. </b></p> <p>Pauatahanui Inlet, Porirua supports a diverse ecosystem of aqua-fauna, micro invertebrates and wading birds that rely on the shallow saltmarsh habitat within the estuary. However, with sedimentation from the surrounding catchments slowly filling up the inlet along with and predicted tidal inundation from sea level rise, the future of this coastline is uncertain. </p> <p>Rather than attempting to solve or secure a fixed future for the coastline, as is the prevailing anthropocentric response, this design led research seeks to respond to these human induced pressures by working with the cyclical phenological processes and ecological interactions occurring within the harbour. The research ambition is to co-create a shared public tidal realm. </p> <p>This objective is tested through the design of a coastal boardwalk for the Pauatahanui Inlet. Unlike human-focused boardwalks, this infrastructure is designed with the capacity to adapt as the tidal edge shifts, in either direction, while facilitating movement for all forms of life to traverse the harbour. The research attempts to surpass perceived barriers between nature and culture with an emergent inquiry into the poetic nature of the site itself. Here landscape design practice is developed towards the creation of social capital as occurring between species, while ensuring the natural ecosystem (and the life it supports) has the capacity to adapt to potential climate related changes.</p>

Towards co-creation: A design-led study of ecological shifts in the tidal margin.

<p><b>The ecological resilience of the intertidal margins of many cities is increasingly under pressure due to climatic shifts and urbanisation. As rising sea levels push the high-water mark landward, many coastal species are prevented from migrating inland due to natural or man-made barriers. This results in a phenomena known as ‘coastal squeeze’. </b></p> <p>Pauatahanui Inlet, Porirua supports a diverse ecosystem of aqua-fauna, micro invertebrates and wading birds that rely on the shallow saltmarsh habitat within the estuary. However, with sedimentation from the surrounding catchments slowly filling up the inlet along with and predicted tidal inundation from sea level rise, the future of this coastline is uncertain. </p> <p>Rather than attempting to solve or secure a fixed future for the coastline, as is the prevailing anthropocentric response, this design led research seeks to respond to these human induced pressures by working with the cyclical phenological processes and ecological interactions occurring within the harbour. The research ambition is to co-create a shared public tidal realm. </p> <p>This objective is tested through the design of a coastal boardwalk for the Pauatahanui Inlet. Unlike human-focused boardwalks, this infrastructure is designed with the capacity to adapt as the tidal edge shifts, in either direction, while facilitating movement for all forms of life to traverse the harbour. The research attempts to surpass perceived barriers between nature and culture with an emergent inquiry into the poetic nature of the site itself. Here landscape design practice is developed towards the creation of social capital as occurring between species, while ensuring the natural ecosystem (and the life it supports) has the capacity to adapt to potential climate related changes.</p>

Exposure to foreign gut microbiota can facilitate rapid dietary shifts

Dietary niche is fundamental for determining species ecology; thus, a detailed understanding of what drives variation in dietary niche is vital for predicting ecological shifts and could have implications for species management. Gut microbiota can be important for determining an organism’s dietary preference, and therefore which food resources they are likely to exploit. Evidence for whether the composition of the gut microbiota is plastic in response to changes in diet is mixed. Also, the extent to which dietary preference can be changed following colonisation by new gut microbiota from different species is unknown. Here, we use Drosophila spp. to show that: (1) the composition of an individual’s gut microbiota can change in response to dietary changes, and (2) ingestion of foreign gut microbes can cause individuals to be attracted to food types they previously had a strong aversion to. Thus, we expose a mechanism for facilitating rapid shifts in dietary niche over short evolutionary timescales.

Importance of Interkingdom Interactions Among Oral Microbiome Towards Caries Development – A Review

The human microbiome plays a crucial role in health and disease conditions. These microbiomes constitute a structured, coordinated microbial network throughout the human body. The oral cavity harbors one of the extensively diverse bacteria in the human system. Although many studies emphasize bacteriome and its interaction with the host system, very little attention is given to candidate phyla radiation (CPR), fungal components, and its interkingdom interaction in the oral microecology even with advanced techniques. The interkingdom interactions among caries causing microbes trigger the pathogenesis of bacterial diseases and cause ecological shifts and affect the host system. Studying the complex relations among the diverse oral microbiome and its host, especially CPR phyla and fungi, would give a holistic view of the caries etiology. This review provides evidence on the interkingdom interaction that establishes a complex community that could help predict future oral and systemic diseases.

A novel system for intensive Diadema antillarum propagation as a step towards population enhancement

The long-spined sea urchin Diadema antillarum was once an abundant reef grazing herbivore throughout the Caribbean. During the early 1980s, D. antillarum populations were reduced by > 93% due to an undescribed disease. This event resulted in a lack of functional reef herbivory and contributed to ongoing ecological shifts from hard coral towards macroalgae dominated reefs. Limited natural recovery has increased interest in a range of strategies for augmenting herbivory. An area of focus has been developing scalable ex situ methods for rearing D. antillarum from gametes. The ultimate use of such a tool would be exploring hatchery origin restocking strategies. Intensive ex situ aquaculture is a potentially viable, yet difficult, method for producing D. antillarum at scales necessary to facilitate restocking. Here we describe a purpose-built, novel recirculating aquaculture system and the broodstock management and larval culture process that has produced multiple D. antillarum cohorts, and which has the potential for practical application in a dedicated hatchery setting. Adult animals held in captivity can be induced to spawn year-round, with some evidence for annual and lunar periodicity. Fecundity and fertilization rates are both consistently very high, yet challenges persist in both late stage larval development and early post-settlement survival. Initial success was realized with production of 100 juvenile D. antillarum from ~ 1200 competent larvae. While the system we describe requires a significant level of investment and technical expertise, this work advances D. antillarum culture efforts in potential future hatchery settings and improves the viability of scalable ex situ production for population enhancement.