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opencc-zeroDec 2007View details →

FIG. 1 in A late Miocene leaf assemblage from Vrysses, western Crete, Greece, and its paleoenvironmental and paleoclimatic interpretation

FIG. 1. — Generalized map of the fossiliferous locations in Vrysses basin, western Crete (Greece).

opencc-by-4.0Dec 2006View details →

Fig. 1 in Effects of extended absence of flooding on the fish assemblages of three floodplain lagoons in the middle São Francisco River, Brazil

Fig. 1. Study area showing the location of the marginal lagoons.

opencc-by-4.0Sep 2004View details →

Fig. 1 in Spatial and temporal variation of benthic fish assemblages during the extreme drought of 1997-98 (El Niño) in the middle rio Negro, Amazonia, Brazil

Fig. 1. Study area in middle rio Negro basin (a) and detail of the sampling sites (b).

opencc-by-4.0Sep 2004View details →

Fig. 2 in Spatial and temporal variation of benthic fish assemblages during the extreme drought of 1997-98 (El Niño) in the middle rio Negro, Amazonia, Brazil

Fig. 2. River level during annual flood cycles. Large arrows denote dates of sampling expeditions.

opencc-by-4.0Jan 2009View details →

Figure 9 in An assemblage of early Oligocene lizards (Squamata) from the locality of Boutersem (Belgium), with comments on the Eocene-Oligocene transition

Figure 9. Necrosaurus sp., osteoderm, IRSNB R 250, previously BOU-AR-28-RS, dorsal view.

opencc-by-4.0Jan 2009View details →

Figure 7 in An assemblage of early Oligocene lizards (Squamata) from the locality of Boutersem (Belgium), with comments on the Eocene-Oligocene transition

Figure 7. Necrosaurus sp., fragment of maxilla, IRSNB R 248, previously BOU-AR-33-RS, medial view.

opencc-zeroSep 2021View details →

Temporal stability in species richness but reordering in species abundances within avian assemblages of a Tropical Andes conservation hot spot

As the pace of environmental change increases, there is an urgent need for quantitative data revealing the temporal dynamics of local communities in tropical areas. Here we quantify the stability of avian assemblages in the highly threatened, but poorly studied, Andean biodiversity hot spot. We evaluated the temporal variation in species richness and community composition of local bird assemblages in three habitat types (native forest, introduced forest, native shrub) using a unique, relatively long-term data series from Cajas National Park and Mazán Reserve in the Southern Andes of Ecuador. We sampled birds with mist nets using a standardized protocol over 11 years, from 2006 to 2016. Species richness remained stable over time across habitats, but community composition changed in the native forest. In particular, we observed taxonomic reordering in the native forest, in which the evenness in the distribution of abundances of taxa decreased over time. This finding is consistent with other studies where species richness remained constant over time while community composition changed. Our study highlights the value of long-term studies in the tropical Andes as we show that species composition of birds in a montane forest is changing, consistent with global trends in biodiversity change.

opencc-zeroSep 2021View details →

Data and R scripts from: Assemblage reorganisation of South African dragonflies due to climate change

Aim: Climate change is expected to cause large shifts in species assemblages such as dragonflies and damselflies (Insecta: Odonata). Here we assess the influence of environmental drivers of turnover on Odonata assemblages. Secondly, we map the predicted spatial variation in species composition, first as a gradient of assemblage similarity, and then as discrete bioregions delineating major areas of odonate endemism. Finally, we map the magnitude of expected change in species turnover in response to climate change under two emission scenarios. Location: South Africa Methods: We used a spatial database comprising of 164 species of odonates and 20 covariates, to explore changes in compositional turnover using generalised dissimilarity models. Bioregions were compiled through various clustering techniques. Results: Present-day odonate bioregions correspond to climatic zones and are clearly separated by transitional zones with rapid spatial turnover. Present odonate bioregions are projected to undergo extensive reorganisation by 2050 and 2070. Temporal turnover in species composition is expected to reach up to 80% in the large arid interior and 64% along the coast. Half of all South Africa's protected areas are likely to experience climate-induced changes to dragonfly bioregions in the near future. Main conclusions: Species assemblages are rapidly changing. This work highlights future shifts in climate will result in complex and non-linear responses in Odonata communities. With ongoing climate change, current odonate bioregions are predicted to expand while others will contract considerably in size within the next thirty years. The current demarcated protected areas may be inadequate to protect dragonflies as climates change. Odonata can be used to track forefronts of climate change, which will likely affect a larger array of taxa as well.

opencc-zeroFeb 2020View details →

Worldwide bird assemblages across urban-wildland gradients

We gathered presence/absence and abundance data from published studies and reports for 319 well-characterized assemblages spanning 50 cities from Africa, Australia, Europe, North America and South America. We focused on cities with comparable survey data within urban habitats and in nearby natural habitat. The final dataset contains almost 10,000 records for 1507bird species, 66 of which are introduced (non-native) in at least one study region. Species abundance per unit area or unit time were available for 269 assemblages from 42 cities, comprising 1353 species. Following Newbold et al. (2015), we used published habitat descriptions to classify the intensity of human use in urban habitats for each assemblage: (1) highly urbanised environments mainly contain densely packed buildings with vegetation scarce or absent; (2) moderately urbanised environments are residential areas with single-family houses and associated gardens; and (3) little-urbanised environments have few buildings and abundant vegetation (e.g. urban parks). The habitats outside the city were assigned to either natural vegetation or rural habitat based on the description of the habitat given in the source paper. Standardised survey methods were used across habitats within each region.

opencc-zeroOct 2021View details →

Trait-habitat associations explain novel bird assemblages mixing native and alien species across New-Zealand landscapes

Aim: Species introductions have reshaped island faunas for the last 200 years, often threatening native biodiversity. Approximately equal numbers of native and alien species currently co-occur in the New Zealand avifauna, but they show distinct habitat use. Antagonistic interactions, habitat affinities and legacies of introduction history may concur to explain their segregation along habitat gradients. To investigate these processes, we explored how habitat, ecological traits and introduction history relate with the current composition of bird assemblages. Location: New Zealand Taxon: Birds Methods: We analysed 917 bird point counts spread along habitat and elevation gradients in the Canterbury region, South Island, and related 10 ecological traits to landscape composition using a three-table ordination method known as 'RLQ analysis', accounting for spatial autocorrelation and phylogeny. We tested whether alien species' positions in the RLQ were related to proxies of introduction history. Results: Eighteen endemic, 11 native and 19 alien species were distributed along a gradient from forest to open-habitat assemblages, in relation to foraging mode, nesting site and body size. A second gradient segregated species between native and exotic forests according to territoriality, sedentarity and diet. Traits accounted for the separation of native and alien bird species in forests, but not in open habitats. Phylogenetic signals emerged from the separation of native and alien species by forest type, and spatial structures suggested a landscape-level, rather than regional or local determinism. These correlations were independent of introduction history, although open-habitat assemblages tended to host alien species introduced later in time. Main conclusions: Habitat type and resource availability explain the spatial partitioning of New Zealand bird assemblages between native and alien species more consistently than competitive exclusion. We conclude that trait-mediated ecological differences among species have likely played a predominant role in species' segregation among landscapes, while maintaining endemic bird assemblages in native forests.

opencc-zeroOct 2021View details →

Size-driven preservational and macroecological biases in the latest Maastrichtian terrestrial vertebrate assemblages of North America

The end-Cretaceous (K/Pg) mass-extinction event is the most recent and well-understood of the "Big Five" and triggered establishment of modern terrestrial ecosystem structure. Despite the depth of research into this event, our knowledge of upper Maastrichtian terrestrial deposits globally relies primarily on assemblage-level data limited to a few well-sampled formations in North America, the Hell Creek and Lance formations. These assemblages disproportionally affect our interpretations of this important interval. Multiple investigations have quantified diversity patterns within these assemblages, but the potential effect of formation-level size-dependent taphonomic biases and their implications on extinction dynamics remains unexplored. Here, the relationship between taphonomy and body size of the Hell Creek and Lance formation dinosaurs and mammals are quantitatively analyzed. Small-bodied dinosaur taxa (< 70 kg) are consistently less complete, unlikely to be articulated, and delayed in their description relative to their large-bodied counterparts. Family-level abundance (particularly skeletons) is strongly tied to body mass, and the relative abundance of juveniles of large-bodied taxa similarly is underrepresented. Mammals show similar but non significant trends. The results are remarkably similar to those from the Campanian-aged Dinosaur Park Formation, suggesting a widespread strong taphonomic bias against the preservation of small taxa, which will result in their seemingly depauperate diversity within the assemblage. This taphonomically skewed view of diversity and abundance of small-bodied taxa amidst our best late Maastrichtian samples has significant implications for understanding speciation and extinction dynamics (e.g., size-dependent extinction selectivity) across the K/Pg Boundary.

opencc-by-4.0Oct 2021View details →

Data for deJonge et al. - Characterizing an invasion assemblage: first comparison of insect communities on native and introduced subspecies of Phragmites australis in Ontario, Canada

Data for deJonge et al. publication "Characterizing an invasion assemblage: first comparison of insect communities on native and introduced subspecies of Phragmites australis in Ontario, Canada". Data are produced from a 2016-2017 survey of 28 geographically paired sites across Ontario, Canada containing introduced Phragmites australis ssp. australis or native Phragmites australis ssp. americanus. The dataset includes for each site basic descriptions of site characteristics (e.g., latitude, stem density), the stem attack rate (% of live stems containing at least one insect) of fourteen insect taxa, and alpha-diversity indices calculated from the attack rates ("FullSiteData" tab). It also includes basic presence and absence data for each taxon across the fourteen sites of each subspecies ("Presence-AbsenceData" tab), and paired differences between native and introduced sites in alpha- and beta-diversity indices, and stem attack rates by taxon ("PairedData(Native-Introduced)" tab).

Geomorphology variables predict fish assemblages for forested and endorheic rivers

This dataset contains data from field collections described in the paper: "Shields, R., Pyron, M., Arsenault, E., Thorp, J., Minder, M., Artz, C., Costello, J., Otgonganbat, A., Mendsaikhan, B., Maasri., A. (2022) Geomorphology variables predict fish assemblages for forested and endorheic rivers. Ecology and Evolution. ECE-2021-08-01367". Stream fishes are restricted to specific environments with appropriate habitats for feeding and reproduction. Interactions between streams and surrounding landscapes influence the availability and type of fish habitat, nutrient concentrations, suspended solids, and substrate composition. Valley width and gradient are geomorphological variables that influence the frequency and intensity that a stream interacts with the surrounding landscape. For example, in constrained valleys, canyon walls are steeply-sloped and valleys are narrow, limiting the movement of water into riparian zones. Wide valleys have long, flat floodplains that are inundated with high discharge. We tested for differences in fish assemblages with geomorphology variation among streams in US and Mongolia montane forested and endorheic ecoregions. Montane rivers of Mongolia are pristine and have few invasive species, compared to montane rivers of the western US. Sites where we collected were defined as geomorphologically unique river segments (i.e., functional process zones; FPZs) using an automated ArcGIS-based tool. This tool extracts geomorphic variables at the valley and catchment scales and uses them to cluster stream segments based on their similarity. We collected a representative fish sample from replicates of FPZs. Then, we used constrained ordinations to determine if river geomorphology could predict fish assemblage variation. Our constrained ordination approach using geomorphology to predict fish assemblages resulted in significance using fish taxonomy and traits in several watersheds. The watersheds where constrained ordinations were not successful were next analyzed with unconstrained ordinations to examine patterns among fish taxonomy and traits with geomorphology variables. US and Mongolia montane river fish assemblages varied with geomorphology variables including river elevation, gradient, valley width, channel sinuosity, valley slope, and annual precipitation. These results provide evidence that fish assemblages respond similarly and strongly to geomorphic variables on two continents. We recommend increased conservation of river ecosystems of the US and Mongolia, to prevent further degradation.

Rapid recovery of boreal rove beetle (Staphylinidae) assemblages 16 years after variable retention harvest

Post-harvest recovery of biodiversity is one of the important goals in modern forestry. A variable retention (VR) approach has been of particular interest in North America because it promotes rapid faunal recovery while minimizing the negative lasting impacts of logging on the natural fauna. We studied responses of rove beetles (Coleoptera: Staphylinidae) to a broad range of retention harvests (2, 10, 20, 50, and 75 % retention) in comparison to uncut controls as part of the Ecosystem Management Emulating Natural Disturbance (EMEND) experiment in the boreal mixedwood forest of western Canada. We sampled beetles using pitfall traps 1, 2, 11, and 16 years post-harvest in replicated (n=3) stands representing four cover types (deciduous-dominated, deciduous with spruce understory, mixed, and coniferous-dominated). We collected 74,263 individuals distributed across 99 species (excluding Aleocharinae). Estimated species richness was highest in clear-cuts until year 11, but by year 16 species richness was similar among treatments. Species composition initially varied strongly in relation to the intensity of harvest treatments, but overall variation decreased with time, and by year 16, species composition overlapped among most treatment combinations. Assemblages recovered more quickly in early successional (deciduous-dominated) than in late successional (mixed and conifer-dominated) stands. Overall, our results show that rove beetle assemblages in stands harvested to all VR prescriptions converged more rapidly toward those in fire-origin mature stands than did assemblages in clear-cuts over the first 16 years post-harvest. Thus, it demonstrates that even modest levels of forest retention can facilitate the recovery of staphylinid assemblages in managed landscapes.

Data for: Determinants of resource use in lizard assemblages from the Neotropical semiarid Caatinga

Non-sessile animals could partition the use of resources in different axes, reducing the effects of competition and allowing coexistence. Here, we investigated the spatial and trophic niche dimensions in four lizard assemblages in the Neotropical semiarid Caatinga to investigate the determinants of resource use and the extent which lizards partition their niches. We sampled each lizard assemblage once, for ten days, in the dry season of 2017 and 2018. In two lizard assemblages, we detected non-random niche overlap patterns that were higher or lower than expected by chance. The high niche overlap patterns suggests that either there is intense current competition for available microhabitats or an abundance of microhabitats. The lower niche overlap may be influenced by the presence of species adapted to sandy habitats (psamophilous), suggesting that spatial partitioning detected has historical basis, which is supported by the pPCA results and by the lack of patterns in the realized niche distribution of species across niche space. We detected trophic niche partitioning in three lizard assemblages. In one assemblage, we discovered random spatial and trophic niche overlap patterns, revealing that competition is not a determining factor in the structure of that assemblage. In fact, phylogenetic effects were predominantly the main determinants of resource use in the four studied lizard assemblages. Arid and semiarid habitats cover about one third of land surface of the world. Comparisons between our findings and those from other regions of the world may aid identify general trends in the lizard ecology of dry environments.

opencc-by-4.0Nov 2022View details →

The ecological memory of fish assemblages in agroecosystems with different history of landscape changes

Here, we presented the data (local, past and response) and R code (models_Zeni et al.) we used to investigate the relationship between past land use changes and instream habitat (explanatory variables) and fish biodiversity patterns (response variables) in streams from different regions in Brazil.

Data from: Metamorphism as the cause of bone alteration in the Jarrow assemblage (Langsettian, Pennsylvanian) of Ireland

The Jarrow assemblage is a Lagerstätte of Pennsylvanian tetrapods and fish preserved in the Leinster Coalfield, Ireland. Fossils from this site have an interesting taphonomy that is not observed in other Pennsylvanian coal swamp assemblages. The bone material of the Jarrow tetrapods has undergone alteration and eventual coalification – causing specimens to become poorly defined from the surrounding coal matrix. Bone alteration at Jarrow has traditionally been linked to early diagenesis. Here a multi-analytical approach, combining X-ray scanning electron microscopy, cathodoluminescence, micro-computed tomography and laser ablation quadrupole inductively coupled plasma mass spectrometry, is used to investigate the origin of alteration within the Jarrow fossil specimens. Original bone morphology is no longer present, being replaced by bituminous material and sphalerite surrounded by tabular apatite (a morphology atypical of bone apatite). Direct U-Pb dating of this recrystallised apatite provides an age of 302 ± 11.4 Ma. In recrystallised apatite, zonation in halogen elements, variably positive and negative Eu-anomalies and depletion in LREE suggest an influence of hydrothermal fluids sourced during the maturation of the Leinster Coalfield. A new taphonomic model for the Jarrow assemblage is proposed: alteration of primary fossil bone occurred primarily due to burial heating of the Leinster Coalfield caused by Variscan deformation. Bone apatite was dissolved and then recrystalised as tabular crystals in a void followed by the mineralisation of sphalerite and bituminous material within the bone giving the Jarrow assemblage fossils their unique appearance.

Spatial heterogeneity in benthic foraminiferal assemblages track regional impacts of paleoenvironmental change across Cretaceous OAE2

The impact of global climate events on local ecosystems can vary spatially. Understanding this heterogeneity can illuminate which environments will be most impacted and the proximal drivers of ecosystem responses. Cenomanian-Turonian marine deposits of the Western Interior Seaway (WIS) record paleoceanographic changes associated with transgression and the onset of Oceanic Anoxic Event 2 (OAE2). They provide an ideal setting to study basinwide paleoecological responses during a global perturbation. Here, we integrate benthic foraminiferal assemblages from before, during, and after OAE2 via multivariate ordination analysis to examine spatial patterns in faunal responses across the western United States on a common scale and to interrogate a previously defined faunal marker used for basin-wide correlation, the Benthonic Zone (BZ). We identify oxygenation and organic matter quality as primary and secondary controls of variation across the 10 stratigraphic records and use this variation to infer paleoenvironmental changes. Stratigraphic trends reveal, in contrast to previous studies, deoxygenation at the onset of OAE2. They also reveal temporal patterns in oxygenation and productivity consistent with the gradual northward migration of a southern water mass into the WIS. This spatial heterogeneity hinders the use of the BZ in biostratigraphy because assemblages change in response to diachronous environmental change, and thus timing of the BZ with respect to OAE2 is not consistent across the basin. Our study demonstrates that regional processes can overshadow ecosystem responses to global events and underscores the importance of considering how changes in the position of water masses impact the expression of global biogeochemical perturbations.

CT data for: Insight into the evolutionary assemblage of cranial kinesis from a Cretaceous bird

The independent movements and flexibility of various parts of the skull, called cranial kinesis, is an evolutionary innovation that is found in living vertebrates only in some squamates and crown birds and is considered to be a major factor underpinning much of the enormous phenotypic and ecological diversity of living birds, the most diverse group of extant amniotes. Compared to the postcranium, our understanding of the evolutionary assemblage of the characteristic modern bird skull has been hampered by sparse fossil records of early cranial materials, with competing hypotheses regarding the evolutionary development of cranial kinesis among early members of the avialans. Here, a detailed three-dimensional reconstruction of the skull of the Early Cretaceous enantiornithine Yuanchuavis kompsosoura allows for its in-depth description, including elements that are poorly known among early diverging avialans but are central to deciphering the mosaic assembly of features required for modern avian cranial kinesis. Our reconstruction of the skull shows evolutionary and functional conservation of the temporal and palatal regions by retaining the ancestral theropod dinosaurian configuration within the skull of this otherwise derived and volant bird. Geometric morphometric analysis of the palatine suggests that loss of the jugal process represents the first step in the structural modifications of this element leading to the kinetic crown bird condition. The mixture of plesiomorphic temporal and palatal structures together with a derived avialan rostrum and postcranial skeleton encapsulated in Yuanchuavis manifests the key role of evolutionary mosaicism and experimentation in early bird diversification.