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1. sFDvent: A global trait database for deep‐sea hydrothermal‐vent fauna

   https://doi.org/10.1111/geb.12975  

   Chapman, Abbie S. A. ; Beaulieu, Stace E. ; Colaço, Ana ; Gebruk, Andrey V. ; Hilario, Ana ; Kihara, Terue C. ; Ramirez‐Llodra, Eva ; Sarrazin, Jozée ; Tunnicliffe, Verena ; Amon, Diva J. ; et al ( July 2019 , Global Ecology and Biogeography)

   Traits are increasingly being used to quantify global biodiversity patterns, with trait databases growing in size and number, across diverse taxa. Despite growing interest in a trait‐based approach to the biodiversity of the deep sea, where the impacts of human activities (including seabed mining) accelerate, there is no single repository for species traits for deep‐sea chemosynthesis‐based ecosystems, including hydrothermal vents. Using an international, collaborative approach, we have compiled the first global‐scale trait database for deep‐sea hydrothermal‐vent fauna – sFDvent (sDiv‐funded trait database for theFunctionalDiversity ofvents). We formed a funded working group to select traits appropriate to: (a) capture the performance of vent species and their influence on ecosystem processes, and (b) compare trait‐based diversity in different ecosystems. Forty contributors, representing expertise across most known hydrothermal‐vent systems and taxa, scored species traits using online collaborative tools and shared workspaces. Here, we characterise the sFDvent database, describe our approach, and evaluate its scope. Finally, we compare the sFDvent database to similar databases from shallow‐marine and terrestrial ecosystems to highlight how the sFDvent database can inform cross‐ecosystem comparisons. We also make the sFDvent database publicly available online by assigning a persistent, unique DOI.

   Six hundred and forty‐six vent species names, associated location information (33 regions), and scores for 13 traits (in categories: community structure, generalist/specialist, geographic distribution, habitat use, life history, mobility, species associations, symbiont, and trophic structure). Contributor IDs, certainty scores, and references are also provided.

   Global coverage (grain size: ocean basin), spanning eight ocean basins, including vents on 12 mid‐ocean ridges and 6 back‐arc spreading centres.

   sFDvent includes information on deep‐sea vent species, and associated taxonomic updates, since they were first discovered in 1977. Time is not recorded. The database will be updated every 5 years.

   Deep‐sea hydrothermal‐vent fauna with species‐level identification present or in progress.

   .csv and MS Excel (.xlsx).

    

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2. Spatial, temporal and taxonomic scaling of richness in an eastern African large mammal community

   https://doi.org/10.1111/geb.12762  

   Du, Andrew ; Behrensmeyer, Anna K. ( October 2018 , Global Ecology and Biogeography)

   Ecological patterns and process change across spatial, temporal and taxonomic scales. This confounds comparisons between modern and fossil communities, which are sampled across very different scales, especially temporal ones. We use a recent bone dataset (i.e., “death assemblages”) from a modern ecosystem to explore spatial, temporal and taxonomic scaling in biodiversity assessments. Our ultimate goal is to create a model based on these scaling relationships to facilitate meaningful comparisons between modern and fossil communities.

   Amboseli National Park, southern Kenya.

   Mid‐1960 s to present day.

   Large mammals (>1 kg).

   We implemented a random placement null model and used model selection methods to investigate how species richness at Amboseli scales as a function of time and area [i.e., the species–time–area relationship (STAR) model]. We then analysed how the model coefficients change at different taxonomic scales (i.e., genus, family, order).

   In agreement with previous studies, we find species richness scales positively with time and area but with a negative interaction between the two. Rates of richness turnover decrease as taxonomic scale increases.

   We hypothesize that decreasing rates of turnover with increasing spatial and/or temporal scale are caused by taking progressively larger samples from a species pool that is changing at a slower rate relative to turnover at the scale of sampling. Because increasing area and time are simply alternative ways of uncovering the species pool, increased time‐averaging of communities results in a more spatially averaged ecological signal. Increasing taxonomic scale causes turnover rates to decrease because of how lower‐level taxa are aggregated into coarser, higher‐level ones. The STAR model presents a framework for extrapolating and comparing richness between small‐scale modern and large‐scale fossil communities, as well as a means to understand the general processes involved with changing scale.

    

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3. Weak but consistent abundance–occupancy relationships across taxa, space and time

   https://doi.org/10.1111/geb.13472  

   Ten Caten, Cleber ; Holian, Lauren ; Dallas, Tad ( March 2022 , Global Ecology and Biogeography)

   Abundance–occupancy relationships posit that more locally abundant species occupy more sites than less abundant species. Although widely supported, the occurrence and detection of abundance–occupancy relationships is sensitive to sampling and detection processes. Data from large‐scale standardized sampling efforts are key to address abundance–occupancy relationships. We aimed to use such a dataset to evaluate the occurrence of abundance–occupancy relationships across different spatial grains and over time for aquatic and terrestrial taxa.

   USA.

   2014–2019.

   Birds, mammals, beetles, ticks, fishes, macroinvertebrates and zooplankton.

   Species abundance and occupancy data were obtained from the National Ecological Observatory Network (NEON). Species mean abundance and occupancy (fraction of sampled locations that were occupied) were estimated for three different spatial grains (i.e., plot, site and domain) for all years sampled. Linear models were used to explore the consistency of interspecific abundance–occupancy relationships. The slope coefficients of these models were related to temporal and spatial variables and to species richness while controlling for taxa in a linear mixed‐effects model (LMM) framework.

   We found evidence for positive abundance–occupancy relationships across the three spatial grains and over time for all taxa we studied. However, our linear models had low explanatory power, suggesting that relationships, although general, were weak. Abundance–occupancy relationships were slightly stronger at the smallest spatial grain than at the largest spatial grain, but showed no detectable change over time for any taxa. Finally, species richness was not associated with the strength of these relationships.

   Together, our results suggest that positive interspecific abundance–occupancy relationships are fairly general but are not capable of explaining substantial variation in spatial patterns of abundance, and that other factors, such as species traits and niche, are also likely to influence these relationships.

    

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4. Frugivoria: A trait database for birds and mammals exhibiting frugivory across contiguous Neotropical moist forests

   https://doi.org/10.1111/geb.13716  

   Gerstner, Beth E. ; Bills, Patrick ; Zarnetske, Phoebe L. ( June 2023 , Global Ecology and Biogeography)

   Biodiversity in many areas is rapidly declining because of global change. As such, there is an urgent need for new tools and strategies to help identify, monitor and conserve biodiversity hotspots. This is especially true for frugivores, species consuming fruit, because of their important role in seed dispersal and maintenance of forest structure and health. One way to identify these areas is by quantifying functional diversity, which measures the unique roles of species within a community and is valuable for conservation because of its relationship with ecosystem functioning. Unfortunately, the functional trait information required for these studies can be sparse for certain taxa and specific traits and difficult to harmonize across disparate data sources, especially in biodiversity hotspots. To help fill this need, we compiled Frugivoria, a trait database containing ecological, life‐history, morphological and geographical traits for mammals and birds exhibiting frugivory. Frugivoria encompasses species in contiguous moist montane forests and adjacent moist lowland forests of Central and South America—the latter specifically focusing on the Andean states. Compared with existing trait databases, Frugivoria harmonizes existing trait databases, adds new traits, extends traits originally only available for mammals to birds also and fills gaps in trait categories from other databases. Furthermore, we create a cross‐taxa subset of shared traits to aid in analysis of mammals and birds. In total, Frugivoria adds 8662 new trait values for mammals and 14,999 for birds and includes a total of 45,216 trait entries with only 11.37% being imputed. Frugivoria also contains an open workflow that harmonizes trait and taxonomic data from disparate sources and enables users to analyse traits in space. As such, this open‐access database, which aligns with FAIR data principles, fills a major knowledge gap, enabling more comprehensive trait‐based studies of species in this ecologically important region.

   Ecological, life‐history, morphological and geographical traits.

   Neotropical countries (Mexico, Guatemala, Costa Rica, Panama, El Salvador, Belize, Nicaragua, Ecuador, Colombia, Peru, Bolivia, Argentina, Venezuela and Chile) with contiguous montane regions.

   IUCN spatial data: obtained February 2023, spanning range maps collated from 1998 to 2022. IUCN species data: obtained June 2019–September 2022. Newly included traits: span 1924 to 2023.

   Classes Mammalia and Aves; 40,074 species‐level traits; 5142 imputed traits for 1733 species (mammals: 582; birds: 1147) and 16 sub‐species (mammals).

   .csv; R.

    

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5. Late Holocene environmental change in Celestun Lagoon, Yucatan, Mexico

   https://doi.org/10.1007/s10933-021-00227-4  

   Hardage, Kyle ; Street, Joseph ; Herrera-Silveira, Jorge A. ; Oberle, Ferdinand K. J. ; Paytan, Adina ( December 2021 , Journal of Paleolimnology)

   Epikarst estuary response to hydroclimate change remains poorly understood, despite the well-studied link between climate and karst groundwater aquifers. The influence of sea-level rise and coastal geomorphic change on these estuaries obscures climate signals, thus requiring careful development of paleoenvironmental histories to interpret the paleoclimate archives. We used foraminifera assemblages, carbon stable isotope ratios (δ¹³C) and carbon:nitrogen (C:N) mass ratios of organic matter in sediment cores to infer environmental changes over the past 5300 years in Celestun Lagoon, Yucatan, Mexico. Specimens (> 125 µm) from modern core top sediments revealed three assemblages: (1) a brackish mangrove assemblage of agglutinatedMiliamminaandAmmotiumtaxa and hyalineHaynesina(2) an inner-shelf marine assemblage ofBolivina,Hanzawaia, andRosalina,and (3) a brackish assemblage dominated byAmmoniaandElphidium. Assemblages changed along the lagoon channel in response to changes in salinity and vegetation, i.e. seagrass and mangrove. In addition to these three foraminifera assemblages, lagoon sediments deposited since 5300 cal yr BP are comprised of two more assemblages, defined byArchaiasandLaevipeneroplis,which indicate marineThalassiaseagrasses, andTrichohyalus,which indicates restricted inland mangrove ponds. Our data suggest that Celestun Lagoon displayed four phases of development: (1) an inland mangrove pond (5300 BP) (2) a shallow unprotected coastline with marine seagrass and barrier island initiation (4900 BP) (3) a protected brackish lagoon (3000 BP), and (4) a protected lagoon surrounded by mangroves (1700 BP). Stratigraphic (temporal) changes in core assemblages resemble spatial differences in communities across the modern lagoon, from the southern marine sector to the northern brackish region. Similar temporal patterns have been reported from other Yucatan Peninsula lagoons and fromcenotes(Nichupte, Aktun Ha), suggesting a regional coastal response to sea level rise and climate change, including geomorphic controls (longshore drift) on lagoon salinity, as observed today. Holocene barrier island development progressively protected the northwest Yucatan Peninsula coastline, reducing mixing between seawater and rain-fed submarine groundwater discharge. Superimposed on this geomorphic signal, assemblage changes that are observed reflect the most severe regional wet and dry climate episodes, which coincide with paleoclimate records from lowland lake archives (Chichancanab, Salpeten). Our results emphasize the need to consider coastal geomorphic evolution when using epikarst estuary and lagoon sediment archives for paleoclimate reconstruction and provide evidence of hydroclimate changes on the Yucatan Peninsula.

    

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