Biology subjects

Couch, C.

Publications and source records attributed to Couch, C..

11 recordsLinked to original sources

bioRxiv2026

The builder's legacy: persistent reef structure creates a window for coral recovery after adult loss

Coral reef recovery depends on successful juvenile recruitment, yet which local factors govern early coral demography remains poorly resolved. Adult coral cover and reef structural complexity are widely hypothesized to regulate juvenile success, but their independent and interactive effects have not been mechanistically disentangled, nor has the relative role of living adult tissue versus persisting structural framework been clarified. Here, combining in situ coral size-structure surveys with high resolution photogrammetry across 405 reef segments spanning the main Hawaiian Islands, we quantify how adult cover and three-dimensional reef structure, measured as rugosity and fractal dimension, jointly shape juvenile coral densities. We reveal nonlinear relationships between juvenile density and adult cover, peaking at intermediate (~8%) coral cover, with fine-scale surface complexity and vertical relief exerting opposing influences across the cover gradient. Together, these reveal a structural legacy window in which reduced adult cover relaxes constraints on juvenile establishment while the three-dimensional habitat built by those adults persists. This decoupling of biological loss from structural loss creates a transient opportunity for population renewal, with intermediate-cover reefs supporting juveniles across the broadest range of structural configurations. More generally, our results show how the physical legacy of ecosystem engineers can continue to regulate population recovery after the organisms that create it have declined.

ecology↗

bioRxiv2025

Demographic insights for coral restoration

O_LICoral reef decline has prompted a global surge in reef restoration initiatives. The success of initiatives that aim to sustain coral populations or assemblages will depend on demographic principles. Restoration strategies generally follow two demographic pathways: supplemental approaches, which increase population numbers through the repeated addition of recruits, fragments, or adults, without fundamentally altering long-term population dynamics; and structural approaches, which enhance vital rates-growth, survival, or reproduction- through changes that modify the demographic processes governing population growth on a sustained basis, either extrinsically (e.g., herbivory, habitat protection) or intrinsically (e.g., assisted evolution). Some interventions, such as supplemental feeding, may temporarily improve vital rates but still function as supplemental approaches because benefits persist only while interventions continue. C_LIO_LIWe synthesized 28 coral matrix population models spanning morphologically diverse coral species from the Caribbean, Hawaii, and the Great Barrier Reef to quantify supplemental and structural changes needed to increase population growth. C_LIO_LIResults highlight two consistent demographic leverage points for which population growth was most sensitive: (1) survival of reproductive adults and (2) successful recruitment. Improving adult survival or recruitment by 20% through structural means produced a 5% increase in population growth rate across population on average, assuming the whole population was affected. By contrast through supplemental means, the same increase required [~]100 recruit outplants or 5-10 adult outplants per 1,000 individuals in a population annually. For large populations typical of restoration targets (105-107 individuals), this translates to 103 adult and 104 recruit outplants per year--levels rarely logistically or economically feasible. C_LIO_LIThese findings yield two key implications. First, supplemental interventions are inefficient for large populations and demand sustained, large-scale effort, even when they temporarily enhance growth or survival. Second, strategies enhancing vital rates across broad geographic areas represent the most effective means of boosting coral abundance, including habitat protection, alleviation of environmental stressors, and interventions which promote long-term survival and recruitment. Our demographic framework underscores that if the restoration goal is sustained increases in coral cover, success depends less on repeated supplements and more on interventions that produce lasting improvements in vital rates. C_LI

ecology↗

bioRxiv2025

Keetia tinka sp. nov. & K. kounounkan sp.nov. (Rubiaceae - Vanguerieae) new threatened forest climbers and shrubs of sandstone plateau of the Republic of Guinea.

Two new species of Keetia are described from recent botanical collections for conservation management made in surviving submontane forest areas of the sandstone plateau areas of the Republic of Guinea. Keetia kounounkan Cheek & Simbiano is a shrub of the Kounounkan Plateau towards the border of Sierra Leone, so far with a single location in gallery forest. K. tinka Cheek & Simbiano is an evergreen rainforest climber of the main part of the Fouta Djalon Highlands with two locations both in degraded forest. Both species are described, illustrated and provisionally assessed for their conservation status, the first as Critically Endangered, the second as Endangered.

plant biology↗

bioRxiv2025

Traditional uses, population, threats and conservation of the bansouman or gingerbread plum Neocarya macrophylla (Chrysobalanaceae) in Republic of Guinea (West Africa)

The flora of the Republic of Guinea (West Africa) includes nearly 4000 vascular plants species, of which c. 10% have been documented to have local socio-economic uses. These socio-economic plants provide among others, foods, medicines, materials and a source of income for the people of Guinea. One example is the bansouman or gingerbread plum, Neocarya macrophylla (Chrysobalanaceae) which is locally valued for its large, delicious seeds (nuts), edible fruit flesh, and medicinal bark (among other medicinal parts). Through a field survey of 17 local communities adjacent to Neocarya populations and the Neocarya populations themselves (780 mature individuals measured), in seven of the ten Guinean prefectures from which the species is recorded, this study documents (1) the local names, harvesting methods, uses and seed sale prices at different points in the value chain, partitions the species by habitat, records perceived threats to trees, key elements of the population structure and relative frequency of Neocarya macrophylla in Guinea, (2) map and re assesses its global conservation status as Near Threatened using the 2012 IUCN Red List categories and criteria, and (3) construct a species conservation action plan. Analysis of our survey data suggests that the largest number of mature trees (75% of the total) is in the three northern prefectures (Gaoual, Koundara, Pita) at the western foot of the Fouta massif whence seeds are exported internationally. Trees mainly occurred in shrub savannah (45% of mature individuals), with lower numbers in three other habitats. Human set bush fires appear to be the most ubiquitous threat (55%) in Guinea, but sand quarrying (18%), agricultural conversion and debarking are also key threats. Natural regeneration levels seem low compared with data from Niger with juveniles (<1 m tall) less than 10 % of the number of mature, fruiting trees (> 11 cm circumference) recorded. This is the first study focused on Neocarya macrophylla in the Republic of Guinea. In contrast the species has been the subject of numerous other papers elsewhere in its range, and we document 14 studies from Niger alone in the last 15 years. While the species is well known as an important Indigenous Fruit Tree with multiple uses in some countries, it is currently not among the top 10 such species listed for Guinea. Compared with Nigeria where numerous other uses including industrial are derived from the species, Neocarya macrophylla appears under utilised in Guinea. We suggest that studies of the chemistry and nutritional value of the seeds of Guinean Neocarya are made, since there are indications that these differ between Guinea and e.g. Niger. Follow up studies to map tree distribution in Guinea in more detail, quantify tree density, fruit yield per tree and per Ha, and duration between germination and fruiting are advised. Field trials to select elite individuals are recommended. Development of a machine to extract seeds from the endocarp (decortication) is a priority as this is the major factor limiting wild harvesting and availability of seed for human consumption.

plant biology↗

bioRxiv2025

Laboratory transmission of Adult Salmon Enteritis and associated pathogens in juvenile Chinook Salmon (Oncorhynchus tshawytscha)

Adult Salmon Enteritis (ASE), characterized by severe ulcerative enteritis, has been linked to pre-spawn mortality (PSM) in spring Chinook Salmon (Oncorhynchus tshawytscha) in certain rivers in Oregon, USA. Catastrophic losses of spring Chinook Salmon have resulted from PSM, a significant threat to their population stability. Understanding the causes of ASE is therefore critical for mitigating PSM and supporting conservation. This study investigates the potential infectious etiology of ASE using a juvenile Chinook Salmon model. Fish were immunocompromised with dexamethasone implants, fasted, and exposed to intestinal tissues from ASE-affected adult Chinook. Histopathology of recipient fish revealed mid-intestinal lesions consistent with ASE. The microsporidium Enterocytozoon schreckii, which is observed in ASE-affected adults from rivers, was transmitted for the first time to juvenile Chinook Salmon, making E. schreckii a potential new pathogen of juvenile salmon. Additionally, intranuclear inclusions were identified in enterocytes by histopathology and viral particles were detected by electron microscopy in recipient fish. The study demonstrates that intestinal lesions consistent with ASE can be experimentally induced in juvenile Chinook Salmon through oral exposure to infected tissues, supporting an infectious etiology. Further research is needed to isolate specific pathogens, including viruses and E. schreckii, and to elucidate their roles in ASE development.

pathology↗

bioRxiv2024

Convolvulaceae of Guinea: taxonomy, conservation and useful plants

Convolvulaceae is a diverse and economically important plant family in Tropical Africa, including the crop sweet potato (Ipomoea batatas (L.) Lam.) and its wild relatives, morning glories (Ipomoea L.), bindweeds (Convolvulus L.), invasive weeds (e.g. Cuscuta L.) and several other species with food, medicinal, or traditional uses. A taxonomic treatment of Convolvulaceae for Guinea is here presented, including comprehensive morphological descriptions, identification keys to genera and species, distribution and ecological information, specimen data, and documentation of known uses. A total of 51 species belonging to 16 genera are documented, 38 of which are native, and 13 presumed introduced; 33 of these are used as medicine, 18 as ornamental, 12 as food and 15 with a range of other uses. Preliminary IUCN Red List assessments were carried out for 45 species for which there were no previous assessments All 45 preliminary conservation assessments were categorised as Least Concern for the global Red List, with 61% of native species having at least one occurrence point falling within protected areas.

plant biology↗

bioRxiv2024

Virectaria stellata (Sabiceeae Rubiaceae), a new sandstone cliff species from the Republic of Guinea with stellate hairs recorded for the first time in the Rubiaceae

Virectaria is a morphologically isolated genus of tropical African herbs or subshrubs, occurring from Senegal to Tanzania. Virectaria stellata, a new species from Guinea, is published. It is a perennial herb, with stems becoming creeping and rooting, to 60 cm long. Virectaria stellata has stellate hairs, recorded here for the first time in the family Rubiaceae. We hypothesize that the stellate hairs of this species result from horizontal gene flow from an Acanthaceae, most likely Barleria, due to their common and perhaps unique microstructure. Virectaria stellata is found in Forecariah and Kindia Prefectures in the Republic of Guinea. The species occurs in fissures in vertical sandstone rock at altitudes of 450 to 910 m, in sun or half-shade. An overview of sandstone endemic plant species in the vicinity of the new Virectaria is provided. No threats have been observed, therefore, Virectaria stellata is provisionally assessed here as Least Concern (LC).

plant biology↗

bioRxiv2023

A niche-adapted brain microbiome in salmonids at homeostasis

Ectotherms have long been known to have peculiar relationships with microorganisms. For instance, bacteria can be recovered from blood and internal organs of healthy teleost fish. However, until now, the presence of a microbial community in the healthy teleost brain has not been proposed. Here we report a living bacterial community in the brain of healthy salmonids. Brain bacterial loads in salmonids are comparable to those found in the spleen and 1000-fold lower than in the gut. Brain bacterial communities share >50% of their diversity with gut and blood bacterial communities. Using culturomics, we obtained 54 bacterial isolates from the brain of healthy rainbow trout. Comparative genomics uncovered unique niche adaptations associated with brain colonization and polyamine biosynthesis. In a natural system, salmonid brain microbiomes shift with the host life cycle, becoming dysbiotic in reproductively mature Chinook salmon, a species that undergoes reproductive death. Our study redefines the relationship between the teleost brain and bacterial microbiomes under physiological conditions. We posit that this symbiosis may endow salmonids with a direct mechanism to sense and respond to environmental microbes. One-Sentence SummarySalmonids have a brain-adapted, resident bacterial community

microbiology↗

bioRxiv2023

CRISPR-based diagnostics detects invasive insect pests

Rapid identification of organisms is essential across many biological and medical disciplines, from understanding basic ecosystem processes and how organisms respond to environmental change, to disease diagnosis and detection of invasive pests. CRISPR-based diagnostics offers a novel and rapid alternative to other identification methods and can revolutionize our ability to detect organisms with high accuracy. Here we describe a CRISPR-based diagnostic developed with the universal cytochrome-oxidase 1 gene (CO1). The CO1 gene is the most sequenced gene among Animalia, and therefore our approach can be adopted to detect nearly any animal. We tested the approach on three difficult-to-identify moth species (Keiferia lycopersicella, Phthorimaea absoluta, and Scrobipalpa atriplicella) that are major invasive pests globally. We designed an assay that combines recombinase polymerase amplification (RPA) with CRISPR for signal generation. Our approach has a much higher sensitivity than other real time-PCR assays and achieved 100% accuracy for identification of all three species, with a detection limit of up to 120 fM for P. absoluta and 400 fM for the other two species. Our approach does not require a lab setting, reduces the risk of cross-contamination, and can be completed in less than one hour. This work serves as a proof of concept that has the potential to revolutionize animal detection and monitoring.

genetics↗

bioRxiv2020

An analysis of Species Conservation Action Plans in Guinea

To achieve conservation success, we need to support the recovery of threatened species. Yet, <5% of plant species listed as threatened on the IUCN Red List have Species Conservation Action Plans (CAPs). If we are to move from a Red List to a Green List for threatened plant species, CAPs need to be devised and implemented. Guinea is one of the most botanically diverse countries in West Africa. Recent research found that nearly 4000 vascular plants occur in Guinea, a 30% increase from previous estimates. 273 of these plant species are now assessed as threatened with global extinction. There is increasing pressure on the environment from the extractive industry and a growing population. In parallel with implementation of an Important Plant Area programme in Guinea, CAPs were developed for 20 threatened plant species. These plans elaborate conservation efforts needed first to safeguard threatened species both in situ and ex situ and then to support their recovery. We document the approach used to assemble the Species Conservation Action Plans, and we discuss the importance of having up to date field information, IUCN Red List assessments, and use of a collaborative approach. The need for these plans is increasingly important with recent calculations suggesting a third of African plants are threatened with extinction. This paper outlines initial detailed plant conservation planning in Guinea and offers a template for conservation practitioners in other tropical African countries to follow.

ecology↗

bioRxiv2018

Deep structural brain lesions associated with consciousness impairment early after haemorrhagic stroke

BackgroundThe significance of deep structural lesions on level of consciousness early after intracerebral haemorrhage (ICH) is largely unknown.\n\nMethodsWe studied a consecutive series of patients with spontaneous ICH that underwent MRI within 7 days of the bleed. We assessed consciousness by testing for command following from time of MRI to hospital discharge, and determined 3-months functional outcomes using the Glasgow Outcome Scale-Extended (GOS-E). ICH and oedema volumes, intraventricular haemorrhage (IVH), and midline shift (MLS) were quantified. Presence of blood and oedema in deep brain regions previously implicated in consciousness were assessed. A machine learning approach using logistic regression with elastic net regularization was applied to identify parameters that best predicted consciousness at discharge controlling for confounders.\n\nResultsFrom 158 ICH patients that underwent MRI, 66% (N=105) were conscious and 34% (N=53) unconscious at the time of MRI. Almost half of unconscious patients (49%, N= 26) recovered consciousness by ICU discharge. Focal lesions within subcortical structures predicted persistent impairment of consciousness at discharge together with MLS, IVH, and ICH and oedema volumes (AUC 0.74; 95%-CI 0.73-0.75). Caudate nucleus, midbrain peduncle, and pontine tegmentum were implicated as critical structures. Unconscious patients predicted to recover consciousness had better 3-month functional outcomes than those predicted to remain unconscious (35% vs 0% GOS-E [≥]4; p-value=0.02).\n\nConclusionMRI lesions within key subcortical structures together with measures reflecting the mass effect of the haemorrhage (lesion volumes, IVH, MLS) obtained within one week of ICH can help predict early recovery of consciousness and 3-month functional outcome.

neuroscience↗