Species Assemblages Research Articles

Vulnerability assessment of elasmobranch species to fisheries in coastal Kenya: Implications for conservation and management policies

Ecological Risk Assessment (ERA) of species is useful for making informed management decisions based on relative vulnerability of species to fisheries. Understanding the vulnerability of species to fishing gears is important for targeted management measures especially for species known to have delicate life-history strategies such as the elasmobranchs. Productivity and Susceptibility Analysis (PSA), an ERA approach, was applied to 61 elasmobranch species (32 shark and 29 ray species) to assess their relative vulnerability (low, medium and high) to fishing by artisanal, prawn trawl and tuna longline fisheries in Kenya’s coastal waters. Overall, results showed 28 % of rays and 31 % of sharks were highly vulnerable to the fisheries, with the pelagic longline tuna fishery having the largest proportions of rays (50 %) and sharks (54 %) being highly vulnerable. Most of the species were in the medium vulnerability category. Among the artisanal gears, only gillnets had species that were highly vulnerable to the fishery, while relatively fewer species (n = 9) of both sharks and rays were highly vulnerable to the prawn trawlers compared to those in the medium vulnerability category (n = 25). Seventeen species classified as High Vulnerability Species Assemblage (HVSA), were assessed to be at high risk of overfishing by different gears, and are recommended for management as a complex. Of the HVSA group, two species; Pseudoginglymostoma brevicaudatum and Rhina ancylostoma are classified by the IUCN Red List of Threatened Species as Critically Endangered (CR), while another four; Rhinoptera jayakari, Mobula birostris, Stegostoma tigrinum and Carcharhinus plumbeus are Endangered (EN), with the rest being either Vulnerable (Gymnura poecilura, Pastinachus ater, Pateobatis jenkinsii, Taeniurops meyeni, Triaenodon obsesus, Carcharhinus falciformis, and Carcharhinus carcharias), Near Threatened (Maculabatis ambigua, Mustelus mosis, Prionace glauca) or classified as Data Deficient (Pliotrema warreni). Although majority of the species have been placed in the medium vulnerability category, some of them are those that are threatened with extinction globally, calling for a more precautionary management approach. A validation approach has been used to mitigate the problems of PSAs associated with data quality and uncertainty around estimated vulnerability indices. More robust application of PSA will require continuous updating of life-history attributes to improve on sensitivity. A precautionary Shark and Ray Management Plan (SRMP) that takes into account the outputs of the PSA is recommended for management and conservation of the elasmobranch stocks in Kenya’s marine waters.

Single-colony MALDI mass spectrometry imaging reveals spatial differences in metabolite abundance between natural and cultured Trichodesmium morphotypes.

Trichodesmium, a globally significant N2-fixing marine cyanobacterium, forms extensive surface blooms in nutrient-poor ocean regions. These blooms consist of a dynamic assemblage of Trichodesmium species that form distinct colony morphotypes and are inhabited by diverse microorganisms. Trichodesmium colony morphotypes vary in ecological niche, nutrient uptake, and organic molecule release, differentially impacting ocean carbon and nitrogen biogeochemical cycles. Here, we assessed the poorly studied spatial abundance of metabolites within and between three morphologically distinct Trichodesmium colonies collected from the Red Sea. We also compared these results with two morphotypes of the cultivable Trichodesmium strain IMS101. Using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) coupled with liquid extraction surface analysis (LESA) tandem mass spectrometry (MS2), we identified and localized a wide range of small metabolites associated with single-colony Trichodesmium morphotypes. Our untargeted MALDI-MSI approach revealed 80 unique features (metabolites) shared between Trichodesmium morphotypes. Discrimination analysis showed spatial variations in 57 shared metabolites, accounting for 62% of the observed variation between morphotypes. The greatest variations in metabolite abundance were observed between the cultured morphotypes compared to the natural colony morphotypes, suggesting substantial differences in metabolite production between the cultivable strain IMS101 and the naturally occurring colony morphotypes that the cultivable strain is meant to represent. This study highlights the variations in metabolite abundance between natural and cultured Trichodesmium morphotypes and provides valuable insights into metabolites common to morphologically distinct Trichodesmium colonies, offering a foundation for future targeted metabolomic investigations.IMPORTANCEThis work demonstrates that the application of spatial mass spectrometry imaging at single-colony resolution can successfully resolve metabolite differences between natural and cultured Trichodesmium morphotypes, shedding light on their distinct biochemical profiles. Understanding the morphological differences between Trichodesmium colonies is crucial because they impact nutrient uptake, organic molecule production, and carbon and nitrogen export, and subsequently influence ocean biogeochemical cycles. As such, our study serves as an important initial assessment of metabolite differences between distinct Trichodesmium colony types, identifying features that can serve as ideal candidates for future targeted metabolomic studies.

Diversity, Composition and Distribution Patterns of Spiders (Arachnida: Araneae) in Sand Forest, South Africa

ABSTRACTSpiders are the dominant representative of the top predator guild in many terrestrial ecosystems, but their diversity and distribution in forests in South Africa are still understudied. This study aimed to determine ground‐dwelling spider diversity, composition and distribution patterns in both sand forest and savanna (and their ecotone) using pitfall traps and to provide a spider species checklist for these three habitats in Phinda Private Game Reserve. A total of 410 individuals from 64 species and 21 families were recorded from the three habitat types. The Lycosidae family and Pardosa crassipalpis were the most dominant family and species. Spider abundances were similar between sand forest and the ecotone, but lower in savanna. However, species richness was similar across habitats. Spider species assemblages were similar between sand forest and the ecotone, but differed from the species assemblages in savanna. Spiders play an important role in food webs both below‐ and aboveground. Therefore, determining their diversity and distribution contributes to the overall understanding of the ecosystem in addition to promoting conservation efforts of key habitats such as the critically endangered sand forest.

A Review of the Arrival, Effects, and Management of Bagrada hilaris in South America: The Case of Chile

Biological invasions are partly defined by their ability to spread rapidly within invaded regions, posing threats to biodiversity and local species assemblages. The painted bug, Bagrada hilaris (Hemiptera, Pentatomidae) (Burmeister, 1835), originally described as being from India, is an important pest worldwide, mainly due to the serious economic losses incurred and the large number of zones invaded. Since its initial detection in Chile in 2016, the invasive and destructive paint bug has started its invasion to the east and invaded new areas in South America. Without adequate control methods, the insect may threaten brassica crop production, resulting in yield losses greater than 70% in recently infested areas. The extraordinarily wide range of the B. hilaris invasion has necessitated studies describing its biology and ecology, as well as highlighting the urgent need for effective and long-term management techniques. Hence, thoroughly revising the data on this pest in new areas that have been invaded, as well as in the area of origin, is expected to enable the development of management programs. This review incorporates information on B. hilaris in South America, including the invasion, ecology, and potential management approaches, which may allow for efficient integrated pest management, mainly in Chile. Lastly, researchers are expected to break the bottlenecks of some key issues, offering valuable perspectives for identifying strategies that warrant additional research as potential biological control agents for B. hilaris in South America, utilizing either augmentative or conservation biological control approaches, as well as semiochemicals and cultural practices.

Chromosome-level genome assembly of the sacoglossan sea slug Elysia timida (Risso, 1818)

BackgroundSequencing and annotating genomes of non-model organisms helps to understand genome architecture, the genetic processes underlying species traits, and how these genes have evolved in closely-related taxa, among many other biological processes. However, many metazoan groups, such as the extremely diverse molluscs, are still underrepresented in the number of sequenced and annotated genomes. Although sequencing techniques have recently improved in quality and quantity, molluscs are still neglected due to difficulties in applying standardized protocols for obtaining genomic data.ResultsIn this study, we present the chromosome-level genome assembly and annotation of the sacoglossan sea slug species Elysia timida, known for its ability to store the chloroplasts of its food algae. In particular, by optimizing the long-read and chromosome conformation capture library preparations, the genome assembly was performed using PacBio HiFi and Arima HiC data. The scaffold and contig N50s, at 41.8 Mb and 1.92 Mb, respectively, are approximately 30-fold and fourfold higher compared to other published sacoglossan genome assemblies. Structural annotation resulted in 19,904 protein-coding genes, which are more contiguous and complete compared to publicly available annotations of Sacoglossa with respect to metazoan BUSCOs. We found no evidence for horizontal gene transfer (HGT), i.e. no photosynthetic genes encoded in the sacoglossan nucleus genome. However, we detected genes encoding polyketide synthases in E. timida, indicating that polypropionates are produced. HPLC–MS/MS analysis confirmed the presence of a large number of polypropionates, including known and yet uncharacterised compounds.ConclusionsWe can show that our methodological approach helps to obtain a high-quality genome assembly even for a "difficult-to-sequence" organism, which may facilitate genome sequencing in molluscs. This will enable a better understanding of complex biological processes in molluscs, such as functional kleptoplasty in Sacoglossa, by significantly improving the quality of genome assemblies and annotations.

Incorporating functional traits with habitat maps: patterns of diversity in coastal benthic assemblages

Benthic species assemblages are groups of species that co-occur on the seafloor. Linking assemblages to physical environmental features allows for understanding and predicting their spatial distribution. Species identity and abundance are commonly quantified using a taxonomic approach to assess benthic diversity, yet functional traits that describe the behavior, life history, and morphology of a species may be equally or more important. Here, we investigate the biodiversity of five benthic species assemblages in relation to their habitat and environmental conditions in an Ecologically and Biologically Significant Area (EBSA) along Canada’s east coast, using both a taxonomic approach and biological traits analysis. Random Forest regression was applied to map spatial patterns of functional and taxonomic diversity metrics, including richness, Shannon index, and Rao’s quadratic entropy. We evaluate discrepancies between related taxonomic and trait measures, and the community-weighted mean of trait data was calculated to characterize each assemblage. Taxonomic and functional richness – representing the number of species and the species community volume in the trait space, respectively – showed similar spatial patterns. However, when considering diversity, which also accounts for the relative abundance and differences among species or traits, these patterns diverged. Taxonomically different assemblages exhibited similar trait compositions for two assemblages, indicating potential trait equivalencies, while one assemblage exhibited traits potentially indicating sensitivity to human activity. The taxonomic and functional metrics of richness and diversity were low close to the coast, which could be indicative of disturbance. Consideration of functional metrics can support spatial planning and prioritization for management and conservation efforts by assessing the sensitivity of traits to different stressors.

Functional traits mediate ant community assembly in a West African savannah-forest mosaic (Côte d'Ivoire)

African forest-savannah mosaics are complex landscapes holding mixtures of woody grasslands (savannah) and different forest systems (gallery forests and forest islands). In these landscapes, ants are highly diverse and perform essential ecosystem services, however, the assembly of ant communities in African forest-savannah mosaics is poorly understood. Here we showed the diversity and species overlap of ant communities in three habitats of the West African savannah and quantified the contribution of thermal tolerances and trophic ecology to community assembly. We investigated ant diversity in the West African Comoé National Park (Côte d'Ivoire) at 16 sites of three habitat types within a forest-savannah mosaic: continuous gallery forest, isolated forest islands and savannah. Across all sites, we collected a total of 91 species from 35 genera from three strata: trees, leaf litter, and soil. Additionally, we assessed differences in functional traits (trophic groups and thermal tolerance) between habitat types and strata. Though species richness was similar in all three habitats, there was a clear separation in species assemblages and functional traits between the two forest habitats and the savannah. Species assemblage shifts were primarily due to species turnover between savannah and forest habitats. In addition, the turnover in species assemblages from forests to savannah habitats was associated with a change in the thermal tolerance of species and in the proportion of trophobionts and predators. Forest and savannah habitats support distinct ant communities with different functional traits and contribute additively to the landscape-scale diversity of the West African ant fauna. Land-use and park management should focus on conserving both savannah and forest sites in tropical protected areas such as the Comoé National Park.

Interaction between three key species in the sea ice-reduced Arctic Barents Sea system.

Population dynamics depend on trophic interactions that are affected by climate change. The rise in sea temperature is associated with the disappearance of sea ice in the Arctic. In the Arctic part of the Barents Sea, Atlantic cod, capelin and polar cod are three fish populations that interact and are confronted with climate-induced sea ice reductions. The first is a major predator in the system, while the last two are key species in Arctic and sub-Arctic ecosystems, respectively. There are still many unknowns regarding how predicted environmental change may influence the joint dynamics of these populations. Using time series from a 32 year long survey, we developed a state-space model that jointly modelled the dynamics of cod, capelin and polar cod. Using a hindcast scenario approach, we projected the effect of reduced sea ice on these populations. We show that the impact of sea ice reduction and concomitant sea temperature increase may lead to a decrease of polar cod abundance at the benefit of capelin but not of cod which may decrease, resulting in strong changes in the food web. Our analyses show that climate change in the Arcto-boreal system can generate different species assemblages and new trophic interactions, which is the knowledge needed for effective management measures.

Biogenic reef creation and biodiversity enhancement by an offshore longline mussel farm

As the mussel farming industry moves offshore, there is a need to fill evidence gaps on its ecological impacts. Over eight years, this research presents the results of a long-term monitoring study of the UK’s first large scale offshore mussel farm following a BACI (Before-After Control-Impact) approach to evaluate the temporal and spatial effects of the farm on benthic habitat and epibenthic species assemblages. Situated in historical fishing ground, the farm is located on a degraded seabed ecosystem dominated by soft sediment. After seven years of farming, damaged seabed increased its complexity, with biogenic reef being created (30 % increase). The structure is attracting a significantly increasing diversity and abundance of sessile, sedentary and mobile species to the area compared to control sites. The abundance and diversity of commercial species increased compared to far control sites and certain commercial species were exclusively recorded beneath the mussel headlines: Cancer pagurus, Maja squinado and Necora puber. Results are discussed through a three mechanisms framework: Species recruitment, settlement, and subsidy. Results from this study are crucial to support policymakers develope a sustainable offshore industry as part of the blue economy that can both produce sustainable protein and contribute to marine conservation objectives as ‘other effective area-based conservation measures’ (OECM). This study reports how low-trophic farming can support nature restoration and recovery.

Changes in Ground Beetle (Coleoptera: Carabidae) Species Assemblages after Removal of Red Pine (Pinus resinosa) Overstory on Dry Sand Prairie Sites in Michigan

Changes in Ground Beetle (Coleoptera: Carabidae) Species Assemblages after Removal of Red Pine (Pinus resinosa) Overstory on Dry Sand Prairie Sites in Michigan

Fish Species Assemblages and Diversity in Water Body Infested by Alien Species

Human is one of the mediators for non-native species invasion, especially in the aquatic ecosystem. Aquaculture and sport fishing activities are the main reasons for non-native fish introduction, especially in man-made habitats. In the present study, we determined the fish community between the invaded as opposed to pristine ecosystems in north Terengganu, Malaysia. The primary data was collected using hook and line, hand-held push net, cast net and gills net while secondary data were also utilised from published and unpublished data. The fish general information including functional traits and prey-predator relationship were obtained from literature and reliable online resources. The data were used to construct hypothetical diagrams and analyzed using taxonomic distinctness index. The fish community between the two habitats differ significantly in which the non-native fish invaded habitat has much lesser fish species richness than that of the pristine habitat. Taxonomic diversity between the two habitats also was markedly different. The non-native Cichla ocellaris added predation pressure to fish community in the lacustrine habitat as the apex predator and were proven to feed on the native fish fauna in the lake. We discuss the community structure in both habitats and explore the further impact of invasion by this invasive alien species on the native fish species. We conclude that the presence of Cichla ocellaris amplify pressure to native fish community in the man-made lake.

Quarry rock reef design features influence fish assemblage structure across a systematically heterogenous restoration reef

To restore an area of temperate rocky-reef degraded by sedimentation, scour, and burial, a large quarry rock reef, the Palos Verdes Restoration Reef (PVR), was built with a heterogenous design including high relief elements intended to increase fish biomass productivity and support a diverse reef community. The replicated design features provide a unique opportunity to study the effects of reef design on fish habitat use patterns. To determine how submodule scale habitat features are associated with variation in the assemblage structure of eleven focal fish species on the PVR we conducted diver-operated stereo-video surveys on all 18 PVR modules 9–13 months after construction. The highest mean densities of most focal fish species and highest total fish densities were observed on high and medium-relief reef submodules and their adjacent ecotones positioned on the offshore sides or ends of modules. These included the most abundant species on the PVR, the zooplanktivorous Blacksmith (Chromis punctipinnis), as well as the fishery species Kelp Bass (Paralabrax clathratus) and California Sheephead (Bodianus pulcher). On the inshore side of parallel modules, the reef and ecotone transects on low and medium relief submodules exhibited the lowest total mean fish densities, and consistently lower mean focal fish species densities. Focal fish species assemblages also differed between the reef and sand-rock ecotone transects. Reef-resident planktivorous fishes likely contribute to reef primary and secondary productivity through consumer mediated nutrient transport and are an important consideration in restoration reef design. Future reef restoration designs should consider incorporating replicated heterogeneous design features including the placement of higher relief elements relative to shore and current patterns as a special consideration for providing habitat for planktivorous reef-resident fishes.

Rapid Monitoring of Aquatic Organism Biodiversity Based on Environmental DNA in a Medium-Sized Reservoir

Environmental DNA (eDNA) has emerged as a highly sensitive and efficient tool for the biomonitoring of aquatic ecosystems. In this study, we investigated fish and benthic species communities using eDNA techniques in a medium-sized reservoir (about 3 square kilometers) in Anhui, China. A total of 12 water samples and 11 sediment samples were analyzed by 12S and 18S primers, respectively. We analyzed the composition of species diversity and the effect of seven environmental factors using the Mantel test. A total of 42 fish taxa were present in the water samples, and 188 benthic taxa in the sediment samples. Species composition was different in disparate stations. We found that water temperature and salinity are pivotal factors influencing the composition of fish communities, while chlorophyll-a is a primary environmental determinant for benthic species assembly structures across different zones. Biodiversity information generated by eDNA techniques can be used to reflect the resource status of this reservoir. The relevant results will provide important scientific reference information for the development and exploitation of medium-sized reservoirs.

Boreal moss-microbe interactions are revealed through metagenome assembly of novel bacterial species

Moss-microbe interactions contribute to ecosystem processes in boreal forests. Yet, how host-specific characteristics and the environment drive the composition and metabolic potential of moss microbiomes is still poorly understood. In this study, we use shotgun metagenomics to identify the taxonomy and metabolic potential of the bacteria of four moss species of the boreal forests of Northern Québec, Canada. To characterize moss bacterial community composition and diversity, we assembled the genomes of 110 potentially novel bacterial species. Our results highlight that moss genus, species, gametophyte section, and to a lesser extent soil pH and soil temperature, drive moss-associated bacterial community composition and diversity. In the brown gametophyte section, two Stigonema spp. showed partial pathway completeness for photosynthesis and nitrogen fixation, while all brown-associated Hyphomicrobiales had complete assimilatory nitrate reduction pathways and many nearly complete carbon fixation pathways. Several brown-associated species showed partial to complete pathways for coenzyme M and F420 biosynthesis, important for methane metabolism. In addition, green-associated Hyphomicrobiales (Methylobacteria spp.) displayed potential for the anoxygenic photosystem II pathway. Overall, our findings demonstrate how host-specific characteristics and environmental factors shape the composition and metabolic potential of moss bacteria, highlighting their roles in carbon fixation, nitrogen cycling, and methane metabolism in boreal forests.

Impacts of phosphite treatment on Phytophthora community assemblages and inoculum abundances in Phytophthora-infected forest soil

Phytophthora are causing declines in forest tree species worldwide and the chemical control treatment, phosphite, is the only treatment consistently shown to provide some protection to natural ecosystems from Phytophthora diseases. Phosphite inhibits Phytophthora growth and sporulation whilst boosting defence responses in the plant host. It is unclear, however, the extent of the impact of phosphite on Phytophthora species assemblages and inoculum abundances in soil around trees following treatment within natural ecosystems. In New Zealand, kauri (Agathis australis), an endemic and threatened foundation species, suffers from a dieback disease primarily caused by Phytophthora agathidicida. Phosphite is applied by trunk injection to kauri and has been shown to improve resin ‘bleed’ symptoms from basal trunk lesions and to promote recovery of thinned canopies. Phytophthora community and inoculum abundance were investigated in response to phosphite treatments at two field sites (Huia and Waitoki) in infected kauri stands in Auckland, New Zealand. At Huia, soil sampling and tree health surveying were conducted in November 2023 on trees treated with phosphite in 2012 as part of an earlier study. At Waitoki, the response to phosphite treatment was monitored 6 and 18 months following treatment. Phytophthora species were detected using soil baiting and metabarcoding of environmental DNA (eDNA) from soil and quantified with qPCR of root and soil DNA. Three species were detected with soil baiting (P. agathidicida, P. cinnamomi, and P. multivora) and two additional species with metabarcoding (P. pseudocryptogea, and an unknown clade 7 species similar to P. europaea). Phytophthora cinnamomi was the most abundant species, followed by P. agathidicida. Both species were more likely to occur together than by chance alone and were associated with declining tree health. The P. europaea-like species was in approximately 50% of the samples and was less likely to occur in roots with poorer health, or in association with P. agathidicida. The abundance of P. agathidicida inoculum was lower in the soil around the phosphite-treated trees than around the untreated control trees 1.5 years after treatment at Waitoki. Phosphite halted the lateral expansion of basal resin bleeds, and resin viscosity was reduced. Not only did phosphite treatments improve kauri dieback symptoms, but the phosphite treatments potentially had a direct impact on the epidemiology of the disease by reducing inoculum load around treated trees, with direct implications for disease management as an effective way to protect uninfected areas and minimise the spread of inoculum from infested zones.

Socioecological Resilience: Quantitative Assessment of the Impact of an Invasive Species Assemblage on a Lake Ecosystem

An invasive assemblage refers to a group of invasive species that coexist and interact within an ecosystem, significantly altering its dynamics, biodiversity, functions, and ecosystem services. Their presence in lakes can severely affect these ecosystems. The objective of this article is to present an assessment using indexes of socioecological resilience to the impact of an assemblage of two invasive species (P. clarkii and E. crassipes) in a lake ecosystem, the Fúquene Lagoon in Colombia. Socioecological resilience indexes (rating scale: 0.0–100%) are developed based on community perception within the area of influence of the lake ecosystem under study. Indexes are developed for each dimension of analysis (ecological, social, and economic) and include a global resilience index. Community perception is obtained through a survey according to the dimensions of analysis. The results of the comprehensive assessment using the developed indexes suggest significant vulnerability of the ecological (index = 37.7%) and social (index = 40.9%) resilience of the lake ecosystem to the invasive species assemblage. The low-risk perception and limited implementation of preventive measures accentuate this fragility. Although the economic dimension shows greater robustness (index = 56.9%), it is imperative to strengthen the adaptive capacity of the socioecological system to mitigate the adverse impacts of biological invasions and ensure the sustainability of the ecosystem (global resilience index = 45%). Assessing lake ecosystems’ recovery from invasive species requires a multidimensional approach, focusing on ecological, economic, and social factors to develop integrated management strategies for resilience and sustainability.

Fungal and beetle diversity in deciduous fine woody debris in spruce-dominated forests in relation to substrate quantity and quality

AbstractDeciduous fine woody debris (DFWD) is a common deadwood substrate type in boreal conifer-dominated forests, but it is usually present in low volumes, and its importance for deadwood dependent biodiversity is poorly understood. In this study, we investigated how DFWD-associated fungal and beetle diversity depends on local substrate availability and quality, and how species diversity differs between DFWD and coarse deciduous deadwood (birch logs) in boreal mixed spruce-dominated forests in southern Finland. We studied 25 forest plots (each 0.16 ha), measuring and sampling all pieces of DFWD with a diameter of 2–5 cm and minimum length of 50 cm. Wood-inhabiting fungi were surveyed from wood samples by DNA metabarcoding and saproxylic beetles were surveyed by bark sieving. Our results showed a clear positive relationship between DFWD abundance and the diversity of fungi and beetles. Tree species and decay class diversity were not important in explaining fungal and beetle diversity or community composition, possibly due to low degree of variation in DFWD quality among the study plots. DFWD hosted more diverse fungal assemblages than birch logs, including species of conservation concern, while no red-listed beetle species were observed on DFWD. Overall, species assemblages associated with fine and coarse deciduous deadwood were non-nested. Thus, DFWD represents a non-redundant complementary deadwood resource type alongside coarse deciduous deadwood in boreal forests.

Community structure and environmental drivers of offshore hard-bottom reef fishes in the northern Gulf of Mexico

Abstract Understanding patterns in community structure in large marine ecosystems is necessary for advancing community- and ecosystem-based approaches to marine fisheries management. We analyzed data from a large-scale, fishery-independent video survey to quantify the structure of reef fish communities on offshore hard-bottom reef habitats in the northern Gulf of Mexico (nGOM). A novel aspect of this work is that all species visualized on videos were identified and enumerated over a 13-year period, which allowed for a comprehensive analysis of fish community structure. We observed a total of 243 fish species from 54 families and 14 orders. Species richness and biodiversity varied considerably across the nGOM and were highest in regions that harbor extensive coral reef habitat (south Florida, Louisiana-Texas shelf). Multivariate analyses identified 12 species assemblages, with important fishery species and species of concern (i.e. IUCN-listed) occurring in the largest identified assemblages. One assemblage composed mostly of large-bodied fishery species accounted for 45% by number and 89% by weight of all fish observed. Species assemblages were most strongly associated with depth, temperature, and substrate composition, with weaker associations with the amount of attached algae and vertical relief, while species richness was positively correlated with bottom water temperature. In general, large-scale bathymetric and hydrographic factors (e.g. depth, temperature) were more important than local topographic structure and biogenic habitat in structuring reef fish communities at the spatial scales (i.e.1000 km) considered here. Our results advance ecosystem-based approaches to fisheries management by providing a basis for incorporating multispecies spatial dynamics into the monitoring and assessment of hard-bottom reef fish communities in the nGOM.

A call to integrate non‐visual functions of pigments and their interactions with visual functions to understand global change impacts on visual systems

Abstract Animal coloration serves a variety of visually related functions in nature (e.g. mate choice, aposematism and camouflage) but the pigments in integumentary tissues such as skin, scales and feathers may also serve functions unrelated to the visual environment (e.g. temperature regulation, detoxification and pollutant protection). Our understanding of the significance of the non‐visual functions of animal integumentary pigments, as well as how they interact with the visually related functions to shape animal visual systems, remains limited. Furthermore, due to their important roles in shaping species interactions and mediating interactions in the environment, animal colour traits are likely to be impacted by global change (e.g. increased temperatures, altered habitat quality and quantity, increased environmental stochasticity, pollutants and novel species assemblages). Considering the effects of global change on both visual and non‐visual functions is important for understanding whether the selection is acting directly on the pigment or on coloration. Since changing the trait distributions can then lead to changes in visual systems, we advocate for studies to consider all potential functions of integumentary pigments, both visual and non‐visual functions and their interaction. Towards this goal, we first highlight common functions of pigments with a focus on non‐visual functions across animal systems. Then we synthesize our current understanding of how global change can impact pigmentation and discuss factors that can modify the interactions between climate change and pigment function. Lastly, we discuss how changes in colour traits can impact visual systems and provide an example using amphibians and their responses to climate change as a model. Read the free Plain Language Summary for this article on the Journal blog.

SVbyEye: A visual tool to characterize structural variation among whole-genome assemblies.

We are now in the era of being able to routinely generate highly contiguous (near telomere-to-telomere) genome assemblies of human and nonhuman species. Complex structural variation and regions of rapid evolutionary turnover are being discovered for the first time. Thus, efficient and informative visualization tools are needed to evaluate and directly observe structural differences between two or more genomes. We developed SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence alignments along with various functionalities to process alignments in PAF format. The tool facilitates the characterization of complex structural variants in the context of sequence homology helping resolve the mechanisms underlying their formation. SVbyEye is available at https://github.com/daewoooo/SVbyEye.