Species Assemblages Research Articles

Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics.

Grapes are globally recognized as economically significant fruit trees. Among grape varieties, Thompson Seedless holds paramount influence for fresh consumption and for extensive applications in winemaking, drying, and juicing. This variety is one of the most efficient genotypes for grape genetic modification. However, the lack of a high-quality genome has impeded effective breeding efforts. Here, we present the high-quality reference genome of Thompson Seedless with all 19 chromosomes represented as 19 contiguous sequences (N50 = 27.1Mb) with zero gaps and prediction of all telomeres and centromeres. Compared with the previous assembly (TSv1 version), the new assembly incorporates an additional 31.5Mb of high-quality sequenced data with annotation of a total of 30 397 protein-coding genes. We also performed a meticulous analysis to identify nucleotide-binding leucine-rich repeat genes (NLRs) in Thompson Seedless and two wild grape varieties renowned for their disease resistance. Our analysis revealed a significant reduction in the number of two types of NLRs, TIR-NB-LRR (TNL) and CC-NB-LRR (CNL), in Thompson Seedless, which may have led to its sensitivity to many fungal diseases, such as powdery mildew, and an increase in the number of a third type, RPW8 (resistance to powdery mildew 8)-NB-LRR (RNL). Subsequently, transcriptome analysis showed significant enrichment of NLRs during powdery mildew infection, emphasizing the pivotal role of these elements in grapevine's defense against powdery mildew. The successful assembly of a high-quality Thompson Seedless reference genome significantly contributes to grape genomics research, providing insight into the importance of seedlessness, disease resistance, and color traits, and these data can be used to facilitate grape molecular breeding efforts.

MONITORING THE MANGROVES OF INDIAN SUNDARBANS USING GEOSPATIAL TECHNIQUES

Abstract. The world’s largest mangrove ecosystem Sundarbans lies in the southwestern part of the Ganges-Brahmaputra Delta. The health, function, and ecosystem services of the mangrove forest depend on the availability of freshwater flow within the deltaic system. The rivers, which used to feed the delta and nourish the mangrove ecosystem now stand disconnected from their upstream freshwater sources. The unavailability of freshwater restricts the growth of freshwater-loving mangroves and has the potential to affect the health of the existing mangroves limiting their ability to provide ecosystem services. Due to the high salinity, the natural reproduction of these valuable freshwater-loving floral species gradually got ceased. High salinity is considered a stress factor influencing the health, growth, productivity, and distribution of mangrove plants. In this circumstance, the main objective of the study is to monitor the spatiotemporal change of the mangrove ecosystem of Sundarbans in terms of species assemblage, floral diversity, biomass, canopy cover, forest health, etc. Remote sensing techniques and field measurements were used to perform an in-depth mangrove genus-level classification (Maximum Likelihood Classifier). To assess the plant species diversity, Shannon-Wiener Index was used in different plots of the Sundarbans to get an idea of the rich biodiversity of these coastal ecosystems. Different vegetation indices such as NDVI, OSAVI, SAVI, TDVI, etc. were estimated to assess the health of the mangrove forest. The biomass and carbon sequestration potential of the mangrove forest was assessed using field data and microwave remote sensing techniques. The result shows the declining trend of freshwater-loving mangroves from the central section of Sundarbans and an increasing trend of saline water-loving mangroves by replacing the others.

Impact of ports construction activities on structure, composition and diversity of fish population: case study of Tema, Ghana

Ports offer economic progress to many coastal developing countries. In view of the economic importance, the rising demand for maritime benefits requires the expansion of existing ports. However, marine ecosystems may become vulnerable to negative impact from the construction of these maritime structures. Therefore, the aim of the study was to establish the impact of Tema port expansion on the diversity and population structure of fish species. Data were collected quarterly from June 2018 to November 2021 through trawling fishing activities off the coast of Greater Accra, Ghana, and subsequently analysed using Primer 6 software. Sampling locations along the coast of Greater Accra included Vernon Bank (VNB), Disposal area (DSA) and Offshore Sakumono (OSK). The increased and reduced number of species at VNB and DSA, respectively, could be alluded to dredging and disposal of dredged spoils. Diversity indices at OSK site was higher than those observed in disturbed areas due to the absence of impact in this control area. Thus, it is recommended to conduct further studies on the assemblage of invasive species that migrated to the VNB during dredging activities, since these species can have severe economic impact on fishing activities of artisanal fishermen, especially at the local level.

Instructing Liquid‐Liquid Phase Separation Inside Membranous Protocells

AbstractThe bottom‐up fabrication of compartmentalized cell‐like entities represents a promising avenue for reconstituting hierarchical organization within cells and emulating life‐like behaviors. Integrating the creation of semipermeable membranes and membraneless artificial organelles has recently garnered significant attention, aiming to achieve cytomimetic properties. We briefly describe the concept of liquid‐liquid phase separation and review approaches for the fabrication of cell‐sized membranous protocells (e. g., giant unilamellar vesicles, polymersomes and proteinosomes). Three strategies are emphasized for the construction of advanced cell‐like structures consisting of liquid‐like subcompartments enclosed by a membrane: (i) adsorption and assembly of organic or inorganic species onto the surface of preformed coacervate microdroplets; (ii) interfacial assembly of a lipid or polymer bilayer on the surface of an aqueous pool containing preformed microdroplets; and (ii) triggering phase separation within a preformed semipermeable membrane with chemical or physical stimuli. This review underscores the significance of the hierarchical organization of these synthetic cellular structures in mimicking cytomimetic functions, including transmembrane signaling, protocell communication, prototissue formation, and their compelling biomedical applications.

Beta‐diversity within coral atolls: Terrestrial species turnover increases with cyclone frequencies

AbstractAimAtolls are a widely distributed, common type of tropical ecosystem, each consisting of an annular coral reef and up to several hundred individual islets sitting on the reef platform. The small land areas and low elevation render the terrestrial communities susceptible to local extinctions from overwash and inundation due to tropical cyclones. Such recurring catastrophic disturbances should be expected to drive strong priority effects and historical contingency in species assembly, thus also promoting species turnover within atolls. This stands contradictory to the received wisdom of atolls consisting of numerous uniform, replicated island systems. We tested the hypothesis that the individual islets within an atoll exhibit compositional turnover and that this species turnover within atolls is related to cyclone frequency.LocationAtolls worldwide.Time PeriodPresent.Taxa StudiedVascular plants, reptiles, birds.MethodsWe compiled a global dataset at the level of islets for species presence/absence within atolls. We obtained long‐term (80 year) tropical cyclone frequency data for each atoll from the NOAA hurricane database and used Bayesian regression to estimate the effects of tropical cyclone frequency on species turnover within atolls.ResultsWe consistently measured high within‐atoll species turnover (i.e., between the individual islets within an atoll) on atolls worldwide. The degree of within‐atoll species turnover increases with increasing tropical cyclone frequency. Atolls that are more frequently hit by tropical cyclones show higher species turnover between their islets than those that occur outside the tropical cyclone belt.Main ConclusionsTropical cyclones are a significant driver of the community assemblages on atolls. These catastrophic disturbances promote a heterogenous atoll landscape, which challenges perceptions that the islets within an atoll are identical replicates of the entire atoll terrestrial community. Biodiversity surveys undertaken at the islet‐level (alpha‐diversity) might therefore not be representative of the entire atoll metacommunity (gamma) diversity.

The dynamic avifaunal assemblage of a fragmented urbanised habitat at Universiti Brunei Darussalam

Urbanisation reshapes ecosystems and fundamentally influences species assemblages. Urban habitats are also highly dynamic with changes taking place on both spatial and temporal scales. The campus of Universiti Brunei Darussalam is an example of an urban habitat consisting of a mosaic of green spaces, fragments of kerangas forest, planted native and ornamental plants as well as building infrastructure, roads and pathways. The aim of this study is to provide an insight into the bird assemblages found within the university campus. Two survey periods were conducted in 2006/2007 and in 2019/2020 using the line transect method. A total of 49 bird species belonging to 23 families and 10 orders were recorded in this study. No evidence of differences in species richness was observed between the two surveys after exclusion of migrants. Insectivores were the most species-rich followed by omnivores, granivores, carnivores and frugivores. As predicted, there was a higher number of non-forest dependent bird species than forest-dependent species. Vegetation cover was lower in 2007 than in 2019, but species composition was similar between the surveys, and the co-occurrence of bird species was random. Even though the bird diversity was considered depauperated, it was comprised of a wide range of species classified as residents, migrants and waterbirds, indicating their ability to tolerate urbanisation. More studies are required to confirm that bird species are surviving and reproducing in this urban habitat.

Glaciers, snow, and rain: Water source influences invertebrate community structure and secondary production across a hydrologically diverse subarctic landscape

AbstractThe melting cryosphere adds heterogeneity to the abiotic and biotic characteristics of many high latitude and montane rivers. However, climate change threatens the cryosphere's persistence in many regions. While existing research has explored the impacts of cryospheric loss on the diversity and structure of freshwater communities, implications for functional traits of communities, such as production of aquatic invertebrates, remain unresolved. Here, we quantified aquatic invertebrate community structure and secondary production in southeast Alaska (USA) streams that represent a meltwater to non‐meltwater gradient, including streams fed primarily by: (1) glacier‐melt, (2) snowmelt, (3) rainfall, and (4) a combination of these sources. We found alpha diversity was highest in the snow‐fed stream and lowest in the glacier‐fed stream. Annual secondary production was also lowest in the glacier‐fed stream (0.56 g ash‐free dry mass m−2), but 2–5 times higher in the other stream types primarily due to greater production of shared taxa that were found in all streams. However, despite low invertebrate diversity and productivity, the glacier‐fed stream hosted distinct species assemblages associated with unique cycles of stream flow, water temperature, turbidity, and nutrient concentrations, which contributed to higher beta diversity between streams. Our findings suggest that the loss of glacier‐melt contributions to rivers may result in increased freshwater invertebrate production but reduced beta diversity, which could have implications for community stability and the capacity of landscapes to support higher‐level consumers, including fishes.

Paleogeographic records of glacial and terminal glacial palynozones related to the Late Paleozoic Ice Age in the Brazilian portion of the Paraná Basin, Western Gondwana

Among the four palynozones established for the Pennsylvanian–Permian sedimentary succession of the Paraná Basin, two are related to the glacial (AcZ: Ahrensisporites cristatus and CmZ: Crucisaccites monoletus zones) and one is related to the following terminal glacial phase (VcZ: Vittatina costabilis Zone) in this portion of Gondwana. The AcZ and the CmZ are typically recognized within the basal and middle portions of the Itararé Group and the Aquidauana Formation, while the VcZ corresponds to the upper portions of both units. In this paper we present a palynostratigraphic analysis of all occurrences of these palynozones from 66 boreholes and 29 outcrops. Two paleogeographic maps are depicted showing the distribution of all sections where the palyonozones related to glacial and terminal glacial sections occur within the Itararé Group and the Aquidauana Formation. Glacial palynozones (AcZ and CmZ) are recognized from outcrops and boreholes from Santa Catarina, Paraná, São Paulo, Mato Grosso do Sul, Mato Grosso and Goiás states, encompassing the thickest portion of the Itararé Group and the Aquidauana Formation. The terminal glacial palynozone (VcZ) was recognized from several boreholes and outcrops, well distributed throughout the basin, from the Rio Grande do Sul, Santa Catarina, Paraná, São Paulo and Mato Grosso do Sul states. Reworked palynomorphs from Devonian and Mississippian strata found together with indigenous species in assemblages assigned to the glacial palynozones (AcZ and CmZ) are used herein as a tool for interpretation of the source area and as indicators of transport direction. As observed elsewhere in Gondwana, palynozones related to the glacial and terminal glacial phases present dominance of spores and monosaccate pollen grains, whereas those linked to the latter phase record the income and the quantitative increase of certain species indicative of progressive climate amelioration. Further sedimentary and stratigraphical aspects are also discussed.

In Search of Suitable Breeding Sites: Habitat Heterogeneity and Environmental Filters Determine Anuran Diversity of Western Madagascar

Environmental filtering shapes animal communities by preventing the colonization and persistence of certain species in a given habitat. More heterogenous environments are presumed to support a greater number of species and, consequently, increased species diversity, as environmental filters are also likely more heterogenous. Amphibians are especially sensitive to environmental influences due to distinct characteristics like permeable skin and low mobility. By analyzing the species richness and assemblage composition of tadpoles in 132 breeding ponds, we examined how the interplay of environmental variables shapes anuran species assemblages in breeding habitats of the dry forest of Western Madagascar. We found that environmental filtering is prevalent and habitat heterogeneity not only increases larval species richness but also alters species composition between these assemblages. Our study highlights the need for conserving heterogenous habitats to maintain local diversity. Furthermore, we recommend including multivariate modelling approaches to conservation efforts to acknowledge differences between specific habitats and beta diversity.

The Structure of Rice Stemborer Assemblages: A Review of Species' Distributions, Host Ranges, and Interspecific Interactions.

This review describes global rice stemborer assemblages based on published species distributions, apparent host preferences, and reported shifts in assemblage composition in response to environmental factors. At least 56 moth (Lepidoptera: Crambidae, Pyralidae, Noctuidae) and fly (Diptera: Diopsidae, Chloropidae) species have been associated with rice; however, only 21 species are of potential, large-scale economic importance with a further 2 species of localized concern; most of the remaining species' associations with rice are based on dubious records without economic impacts on rice production. A list of stemborer-host associations indicates that rice stemborers are largely oligophagous on grasses (Poaceae), but a few species are polyphagous (also attacking Cyperaceae, Typhaceae, and some Eudicotyledon plants). Total stemborer abundance is determined by rice cropping patterns and management. Assemblage species richness is determined by geographical location, surrounding habitat (particularly as regards secondary and occasional species), and season. Evidence suggests that stemborer assemblage structure is largely determined through conditional interspecific competition. Regional assemblages typically include a single dominant lepidopteran species (primary species) that is largely restricted to rice and for which the climate is optimal; one or more secondary species that vary based on the age of rice attacked, rice anatomy, and the proximity to other habitats (including other crops); and occasional species that probably spill over from adjacent grasslands. The co-occurrence of lepidopteran with dipteran rice stemborers requires further research attention.

Strong temperature gradients in the ice age North Atlantic Ocean revealed by plankton biogeography

The cold Last Glacial Maximum, around 20,000 years ago, provides a useful test case for evaluating whether climate models can simulate climate states distinct from the present. However, because of the indirect and uncertain nature of reconstructions of past environmental variables such as sea surface temperature, such evaluation remains ambiguous. Instead, here we evaluate simulations of Last Glacial Maximum climate by relying on the fundamental macroecological principle of decreasing community similarity with increasing thermal distance. Our analysis of planktonic foraminifera species assemblages from 647 sites reveals that the similarity-decay pattern that we obtain when the simulated ice age seawater temperatures are confronted with species assemblages from that time differs from the modern. This inconsistency between the modern temperature dependence of plankton species turnover and the simulations arises because the simulations show globally rather uniform cooling for the Last Glacial Maximum, whereas the species assemblages indicate stronger cooling in the subpolar North Atlantic. The implied steeper thermal gradient in the North Atlantic is more consistent with climate model simulations with a reduced Atlantic meridional overturning circulation. Our approach demonstrates that macroecology can be used to robustly diagnose simulations of past climate and highlights the challenge of correctly resolving the spatial imprint of global change in climate models.

Elevational patterns of species richness and community structure of understorey birds in an East African montane forest

AbstractMt. Kasigau is the northeastern most of the Eastern Arc Mountains global hotspot and harbours some endemic and threatened species, but little is known about bird community changes along its elevational gradient. We assessed the relationship between bird biodiversity metrics, season, human disturbance, elevation and temperature using mist‐netting data collected bi‐annually over a 10‐year period. Birds were sampled along the mountain's elevational gradient at four elevation levels (858, 1104, 1321 and 1547 m). Bird richness, diversity and evenness decreased with increasing altitude in both dry and wet seasons. Bird abundance declined with increasing elevation for the lower three elevation levels but peaked at the highest elevation. All diversity metrics were higher in the wet season compared to the dry season across all the years. Elevation had a greater effect on species assemblages than season, disturbance and temperature. Temperature had significant effects on abundance, diversity and richness, while disturbance had significant effects on diversity, evenness and richness. We conclude that bird assemblages in Mt. Kasigau are strongly shaped by elevational changes, while temperature and disturbance constitute important factors influencing bird conservation in the face of global warming. Our study highlights that elevation, disturbance and temperature influence bird assemblages along tropical elevational gradients.

Saproxylic beetles' morphological traits and higher trophic guilds indicate boreal forest naturalness

AbstractForests contribute to numerous ecosystem functions and services and contain a large proportion of terrestrial biodiversity, but they are being negatively impaced by anthropogenic activities. Forests that have never been clear‐cut and have old growth characteristics, termed “near‐natural,” often harbor different and richer species assemblages than managed forests. Alternative management strategies may be able to balance the needs of biodiversity with the demands of forestry, but evaluation efforts are limited by the challenges of measuring biodiversity. Species richness is frequently used as a simple measure of biodiversity, but research indicates that it may not adequately capture community‐level changes. Alternatively, trait‐based measures of biodiversity may prove to be useful, but research is lacking. In this paper, we use a large dataset that includes 339 obligate saproxylic beetle species collected over a decade in the boreal region throughout southern Norway to: (1) establish if there is a difference in beetle community composition between near‐natural and managed forests; and (2) determine which measures of beetle biodiversity best indicate forest naturalness. We arranged the sites in an ordination space and tested for differences in community composition between these forest types. We also tested different measures of biodiversity to determine which were the most predictive of forest naturalness. We found a clear difference in community composition between near‐natural and managed forests. Additionally, three measures of biodiversity were most predictive of forest naturalness: proportional abundance of predators, community weighted mean (CWM) of wing length, and CWM of body roundness. The probability that a forest was near‐natural increased with the proportional abundance of predators but decreased with CWM wing length and body roundness. Although species richness was higher in near‐natural forests, the effect was not significant. Overall, our findings underscore the conservation value of near‐natural forests and highlight the potential of several measures of biodiversity for determining forest quality.

Invertebrate fauna of the Albian–Lower Cenomanian deposits in the Fars and Isfahan provinces (Firuzabad and Fasakhod sections), Zagros Basin, Central Iran

The Albian- Cenomanian deposits of the Kazhdumi Formation at Zagros Basin (Firuzabad section and Central Iran (Fasakhod section), represents a carbonate sedimentary succession and contain rich and diverse invertebrate macro fauna. Detailed studies on about 200 specimens of invertebrate macro fauna revealed from two stratigraphic intervals led to recognition of 5 species of gastropods; (Liopeplum? sp., Columbellina sp., Cryptaulax? sp., Turritella? sp., Pleurotomaria sp.), 3 species of ammonites; (Knemiceras duberterti, Sphenodiscus sp., Knemiceras persicum), 10 species of bivalves assemblages; (Ceratostreon flabellatum, Cardium? sp., Exogyra (Costagyra) olisiponensis, Neithea (Neithea) quinquecostata, Trigonia sp., Buchia? sp., Cardium? sp., Pseudogyra sp., Ontaria? sp., Nucula? sp., Pleuromia? sp., 1 species of echinoids; Dorocidaris taouzensis with a prolific horizon of Notopocorystes xizangensis of raninoid crabs. The absence of large gastropods and bivalves fauna and abundance of suspension-feeders indicated instability of the substrate, shallow marine paleoenvironment.and a medium energy condition.

Additive, antagonistic and synergistic interactions of future climate and land use change on Theaceae species assemblages in China

While climate and land use change are commonly known to interactively affect biodiversity worldwide, their interactive effects have rarely been explored, hindering our understanding of the attribution of biodiversity change to each of these two drivers. Here, we used ensemble species distribution models to project the potential distribution of 200 Chinese Theaceae species in the 2070s under three types of climate and land use change scenarios: (1) dynamic climate and constant land use, (2) constant climate and dynamic land use and (3) dynamic climate and dynamic land use. We further assessed the single and combined effects of climate and land use change on Theaceae species assemblages in China, and their interactive effects (i.e., additive, antagonistic and synergistic effects) on species losses and gains. Our results revealed that the mean species richness is predicted to change ranging from − 3.43–0.07 species by the 2070 s in China and the predicted species turnover values range from 1.38% to 18.65%. Additive and antagonistic interactions would dominate species losses and gains in at least 26.54% and 30.17% of the study area, respectively, while synergistical interactions would only occur in < 9.14% of the study area. Moreover, there were significant negative correlations between the single effects of land use and climate change and their interactive effects. These findings highlight the importance of understanding the interactive effects of climate and land use change on biodiversity and will help to better minimize risks of future biodiversity loss and exploit opportunities provided by land use-climate change interactions.

The African mosquito-borne diseasosome: geographical patterns, range expansion and future disease emergence.

Mosquito-borne diseases (MBDs) threaten public health and food security globally. We provide the first biogeographic description of the African mosquito fauna (677 species) and the 151 mosquito-borne pathogens (MBPs) they transmit. While mosquito species richness agrees with expectations based on Africa's land surface, African arboviruses and mammalian plasmodia are more speciose than expected. Species assemblages of mosquitoes and MBPs similarly separate sub-Saharan Africa from North Africa, and those in West and Central Africa from eastern and southern Africa. Similarities between mosquitoes and MBPs in diversity and range size suggest that mosquitoes are key in delimiting the range of MBPs. With approximately 25% endemicity, approximately 50% occupying one to three countries and less than 5% occupying greater than 25 countries, the ranges of mosquitoes and MBPs are surprisingly small, suggesting that most MBPs are transmitted by a single mosquito species. Exceptionally widespread mosquito species feed on people and livestock, and most are high-altitude-windborne migrants. Likewise, widespread MBPs are transmitted among people or livestock by widespread mosquitoes, suggesting that adapting to people or livestock and to widespread mosquito species promote range expansion in MBPs. Range size may predict range expansion and emergence risk. We highlight key knowledge gaps that impede prediction and mitigation of future emergence of local and global MBDs.

Understory plant assemblage variations at different spatial scales: The case of Nothofagus forests in Tierra del Fuego

Understory vegetation is essential to forest functioning, integrity and provision of ecosystem services, but forest management often overlook understory conservation. As species distribution depends on many drivers, and diversity indicators varied with scales, it is difficult to define appropriate strategies for conservation, even in a single forest type. Moreover, many understory plant species occurred at both forests and non-forest ecosystems, and the assemblage could vary at sub-regional scales. Then, forest specialist species may not be similarly threatened in different ecosystem types or sub-regions. Therefore, we wonder if the variation of the understory plant assemblage of a single forest type at a sub-regional scale occurs in different forest types; how do vary the understory species assemblages compared to non-forest ecosystems at each sub-region; and how do vary the management effects on different forest types in a local scale within different sub-regions. For this, we studied understory vegetation richness and cover in three Nothofagus forest types and three non-forest ecosystems across four sub-regions of Tierra del Fuego, Argentina. We evaluated correlations, nestedness, relational patterns (by Non-metrical multidimensional scaling-NMS and Multi-response permutational procedure-MRPP) and Indicator Species Analysis-ISA, for 229 vascular plants distributed in 554 plots. Regarding local scale, we asssesed two main productive managements: timber harvesting in N. pumilio and livestock use in N. antarctica forests. Understory assemblages varied within each single forest type among different sub-regions (p < 0.033 for all MRPP), and different indicator plant species occurred at different geographic zones for two forest types (e.g., Adenocaulon chilensis in SE for N. pumilio forests, and Cotula scariosa in NW for N. antarctica forests), but not in forests with a nested understory distribution pattern (N. betuloides). Ecosystem types shared a high quantity of species (>40 %), except in SE zone. However, all ecosystem types significantly differed in every zone (p < 0.025), except grasslands and shrublands in NW (p = 0.165). Grasslands stand out as the species richest ecosystem in NW, SW and SE zones (between 62 and 123 spp.), highlighting their importance for conservation. Landscape heterogeneity emerged as an important mechanisms enriching species richness from neighbouring habitats, while in managed stands, resource availability seemed the main driver. Regarding the local scale, higher impacted by harvested condition in N. pumilio forests showed differences with less impacted conditions despite the zone, with some common indicator species (e.g., Taraxacum officinale). However, differences between aggregate retention and primary forests depends on the locality. Concerning N. antarctica forests, livestock homogeneizes the assemblages between zones, although indicator species remains different across zones, with dominance of exotics introduced for forage in NE (e.g., Poa pratensis). The presence of the same species in forests and non-forest ecosystems reduce the local extinction hazards in Tierra del Fuego. However, conservation strategies should be implemented at every sub-region. New natural reserves could be an alternative for conservation in zones without natural reserves, but complemented with land-sharing in managed forests. The consideration of potential differences among geographic zones could bring a more clear alternative to improve conservation at sub-regional scales where the same forest type cover large regions.

Accounting for spatiotemporal sampling variation in joint species distribution models

Abstract Estimating relative abundance is critical for informing conservation and management efforts and for making inferences about the effects of environmental change on populations. Freshwater fisheries span large geographic regions, occupy diverse habitats and consist of varying species assemblages. Monitoring schemes used to sample these diverse populations often result in populations being sampled at different times and under different environmental conditions. Varying sampling conditions can bias estimates of abundance when compared across time, location and species, and properly accounting for these biases is critical for making inferences. We develop a joint species distribution model (JSDM) that accounts for varying sampling conditions due to the environment and time of sampling when estimating relative abundance. The novelty of our JSDM is that we explicitly model sampling effort as the product of known quantities based on time and gear type and an unknown functional relationship to capture seasonal variation in species life history. We use the model to study relative abundance of six freshwater fish species across the state of Minnesota, USA. Our model enables estimates of relative abundance to be compared both within and across species and lakes, and captures the inconsistent sampling present in the data. We discuss how gear type, water temperature and day of the year impact catchability for each species at the lake level and throughout a year. We compare our estimates of relative abundance to those obtained from a model that assumes constant catchability to highlight important differences within and across lakes and species. Synthesis and applications: Our method illustrates that assumptions relating indices of abundance to observed catch data can greatly impact model inferences derived from JSDMs. Specifically, not accounting for varying sampling conditions can bias inference of relative abundance, restricting our ability to detect responses to management interventions and environmental change. While our focus is on freshwater fisheries, this model architecture can be adopted to other systems where catchability may vary as a function of space, time and species.

When Do Traits Tell More Than Species about a Metacommunity? A Synthesis across Ecosystems and Scales.

AbstractLinking species traits with the variation in species assemblages across habitats has often proved useful for developing a more mechanistic understanding of species distributions in metacommunities. However, summarizing the rich tapestry of a species in all of its nuance with a few key ecological traits can also lead to an abstraction that provides less predictability than when using taxonomy alone. As a further complication, taxonomic and functional diversities can be inequitably compared, either by integrating taxonomic-level information into the calculation of how functional aspects of communities vary or by detecting spurious trait-environment relationships. To remedy this, we here synthesize analyses of 80 datasets on different taxa, ecosystems, and spatial scales that include information on abundance or presence/absence of species across sites with variable environmental conditions and the species' traits. By developing analyses that treat functional and taxonomic diversity equitably, we ask when functional diversity helps to explain metacommunity structure. We found that patterns of functional diversity explained metacommunity structure and response to environmental variation in only 25% of the datasets using a multitrait approach but up to 59% using a single-trait approach. Nevertheless, an average of only 19% (interquartile range = 0%-29%) of the traits showed a significant signal across environmental gradients. Species-level traits, as typically collected and analyzed through functional diversity patterns, often do not bring predictive advantages over what the taxonomic information already holds. While our assessment of a limited advantage of using traits to explain variation in species assemblages was largely true across ecosystems, traits played a more useful role in explaining variation when many traits were used and when trait constructs were more related to species' status, life history, and mobility. We propose future research directions to make trait-based approaches and data more helpful for inference in metacommunity ecology.

Chromosome-scale genomes of commercially important mahoganies, Swietenia macrophylla and Khaya senegalensis

Mahogany species (family Meliaceae) are highly valued for their aesthetic and durable wood. Despite their economic and ecological importance, genomic resources for mahogany species are limited, hindering genetic improvement and conservation efforts. Here we perform chromosome-scale genome assemblies of two commercially important mahogany species: Swietenia macrophylla and Khaya senegalensis. By combining 10X sequencing and Hi-C data, we assemble high-quality genomes of 274.49 Mb (S. macrophylla) and 406.50 Mb (K. senegalensis), with scaffold N50 lengths of 8.51 Mb and 7.85 Mb, respectively. A total of 99.38% and 98.05% of the assembled sequences are anchored to 28 pseudo-chromosomes in S. macrophylla and K. senegalensis, respectively. We predict 34,129 and 31,908 protein-coding genes in S. macrophylla and K. senegalensis, respectively, of which 97.44% and 98.49% are functionally annotated. The chromosome-scale genome assemblies of these mahogany species could serve as a vital genetic resource, especially in understanding the properties of non-model woody plants. These high-quality genomes could support the development of molecular markers for breeding programs, conservation efforts, and the sustainable management of these valuable forest resources.