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Figure 14. A in Stolidobranch ascidians from the tropical western Indian Ocean

Figure 14. A, Polycarpa gradata sp. nov. holotype. B, Polycarpa plantei sp. nov. specimens from Madagascar. C, Polycarpa pori sp. nov. D, Pyura gangelion sp. nov.

Figure 19 in Stolidobranch ascidians from the tropical western Indian Ocean

Figure 19. Polycarpa pori sp. nov.: A, specimen from the Red Sea ventrally opened. B, specimen from Madagascar, endocarps on the left body side are not figured. Scale bars: A = 5 mm, B = 1 cm.

Figure 11 in Stolidobranch ascidians from the tropical western Indian Ocean

Figure 11. Polycarpa argentata: A,B, both sides of a specimen removed from the tunic. C, specimen ventrally opened. D, detail of a polycarp. Scale bars: A,B,C = 1 cm, D = 0.5 mm.

Figure 28 in Stolidobranch ascidians from the tropical western Indian Ocean

Figure 28. Pyura mozambica sp. nov.: A, body ventrally opened. B,C, both sides of the body, the tunic removed. D, part of a gonad. Scale bars: A,B,C = 5 mm, D = 1 mm.

Figure 27 in Stolidobranch ascidians from the tropical western Indian Ocean

Figure 27. Siphonal spinules: A, Pyura gangelion; B, Pyura scortea; C, Pyura tongae; D, Microcosmus madagascariensis; E, Microcosmus pupa. Scale bars: A,C,D,E = 100 mm, B = 20 mm.

Figure 23 in Stolidobranch ascidians from the tropical western Indian Ocean

Figure 23. Cnemidocarpa hemprichi: A,B external view of the left and right sides of the body. C, internal view of the left side. D, part of the dorsal lamina. E, dorsal tubercle. F, apex of a gonad showing the testis vesicles. Scale bars: A,B,C = 1 cm, D = 1 mm, E, F = 2 mm.

Figure 22 in Stolidobranch ascidians from the tropical western Indian Ocean

Figure 22. Cnemidocarpa concha sp. nov.: A, large specimen ventrally opened, all endocarps not figured. B, detail of the posterior part of the right side with gonads and endocarps. C, oesophagus entrance and postendostylar appendix. Scale bars = 1 cm.

Figure 26 in Stolidobranch ascidians from the tropical western Indian Ocean

Figure 26. Styela meteoris sp. nov.: A. specimen ventrally opened. B,C, external view of the left and right sides of the body. D, gonad. Scale bars: A,B,C = 3 mm, D = 2 mm.

opencc-by-4.0Nov 2015View details →

FIGURE 12 in Three new Uroplectes (Scorpiones: Buthidae) with punctate metasomal segments from tropical central Africa

FIGURE 12. Habitus, dorsal aspect (A, C) and ventral aspect (B, D) of Uroplectes zambezicus, sp. nov. A, B. Holotype ♂ (AMNH), Zambezi River, Mozambique. C, D. Paratype ♀ (AMNH), same locality. Scale bars = 5 mm.

opencc-by-4.0Mar 2020View details →

Gut microbiota of wild arboreal and ground-feeding tropical primates

16S rRNA gene and ITS sequences from fecal samples of 12 groups of Udzungwa (Tanzania) red colobus Procolobus gordonorum (total number of samples: 89), and five groups of yellow baboon Papio cynocephalus (total number of samples: 69). The dataset consists of the following files: <ul> <li>16S_raw.tar: raw 16S rRNA gene sequences;</li> <li>16S_filtered.fasta.gz: merged, adapter trimmed and quality filtered 16S rRNA gene sequences;</li> <li>16S_ID.txt: 16S file ID to sample ID mapping;</li> <li>ITS_raw.tar: raw ITS sequences;</li> <li>ITS_filtered.fasta.gz: merged, adapter trimmed and quality filtered ITS sequences;</li> <li>ITS_ID.txt: ITS file ID to sample ID mapping;</li> <li>Metadata.tsv: sample metadata;</li> <li>Accessions.tsv: ENA project and sample accessions;</li> <li>Helminths.tsv: helminths abundances table.</li> </ul>

opencc-by-4.0Jul 2020View details →

ATASF: Tri-hourly anomaly of tropical atmospheric surface fluxes.

ATASF dataset is a product that contains the tri-hourly surface anomalies of the entire tropical region (180°W - 178.125°E/33.3328°S – 31.4281°N) of the heat fluxes and of the incident and reflected radiation. These are calculated from 20th Century Reanalysis V2c data provided by the NOAA/OAR/ESRL PSD, Boulder, Colorado, USA, from their Web site at <a href="http://www.esrl.noaa.gov/psd/">http://www.esrl.noaa.gov/psd/</a>. This product contains the variables: <ol> <li>Tri-hourly convective precipitation rate (kg m^{-2} s)</li> <li>Tri-hourly downward longwave radiation flux at surface (w m^{-2})</li> <li>Tri-hourly downward solar radiation flux at surface (w m^{-2})</li> <li>Tri-hourly upward longwave radiation flux at surface (w m^{-2})</li> <li>Tri-hourly upward solar radiation flux at surface (w m^{-2})</li> <li>Tri-hourly latent heat net flux at surface (w m^{-2})</li> <li>Tri-hourly sensible heat net flux at surface (w m^{-2})</li> </ol> All these 3D grids have a period of time from 1851-01-01 00:00:00 to 2014-12-31 21:00:00, with a spatial resolution of 1.875 x 1.904732 degrees. The objective of this dataset is to facilitate researchers to study the anomalies of these 7 parameters on the ocean surface during the occurrence of short and medium duration physical processes such as low pressures, cold fronts, hurricanes and others.

opencc-zeroSep 2021View details →

Active restoration fosters better recovery of tropical rainforest birds than natural regeneration in degraded forest fragments

<ol> <li>Ecological restoration has emerged as a key strategy for conserving tropical forests and habitat specialists, and monitoring faunal recovery using indicator taxa like birds can help assess restoration success. Few studies have examined, however, whether active restoration achieves better recovery of bird communities than natural regeneration, or how bird recovery relates to habitat affiliations of species in the community.</li> <li>In rainforests restored over the past two decades in a fragmented landscape (Western Ghats, India), we examined whether bird species richness and community composition recovery in 23 actively restored (AR) sites was significantly better than recovery in paired naturally regenerating (NR) sites, relative to 23 undisturbed benchmark (BM) rainforests. We measured 8 habitat variables and tested whether bird recovery tracked habitat recovery, whether rainforest and open-country birds showed contrasting patterns, and assessed species-level responses to restoration.</li> <li>We recorded 92 bird species in 460 point-count surveys. Rainforest bird species richness was highest in BM, intermediate in AR, and lowest in NR. Contrastingly, open-country bird species richness was least in BM, intermediate in AR, and highest in NR.</li> <li>Bird community composition varied significantly across treatment types with composition in AR in transition from NR to BM. Bird community dissimilarity between sites was positively related to dissimilarity in habitat structure and floristics, and geographic distance between sites. Variance partitioning indicated that structural and floristic dissimilarity explained 90% of the variation in community composition.</li> <li>Indicator species analysis revealed significant associations of 34 species with one or more treatment types. Species associated with BM and AR treatment types were all rainforest species, while only 38% of species associated with AR and NR treatment types were rainforest species.</li> <li> Synthesis and applications: We show that active restoration of degraded fragments benefits rainforest birds and reduces the infiltration of open-country birds, and highlight the importance of considering rainforest and open-country species separately. In human-modified tropical rainforest landscapes, active restoration of degraded fragments fosters partial recovery and complements protection of mature forests for bird conservation.</li> </ol>

opencc-zeroOct 2021View details →

Species ecology explains the various spatial components of genetic diversity in tropical reef fishes

Generating genomic data for 19 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diver- sity patterns from local to regional scales. We distinguish between the α, β and γ components of genetic diversity, which we subsequently link to six ecological traits. We find that the α and γ components of genetic diversity are strongly correlated so that species with a high total regional genetic diversity display systematically high local diversity. The α and γ diversity components are negatively associated with species abundance recorded using underwater visual surveys and positively with body size. Pelagic larval duration is found to be negatively related to genetic β diversity supporting its role as a dispersal trait in marine fishes. Deviation from the neutral theory of molecular evolution motivates further effort to understand the processes shaping genetic diversity and ultimately the diversification of the exceptional diversity of tropical reef fishes.

opencc-by-4.0Oct 2022View details →

OISSTv2 standardized daily SST in Eastern tropical Pacific

OISSTv2 standardized daily sea surface temperatures (SST) of 11 different 60x60 latitutde x longitude tiles in the eastern tropical Pacific. Time coverage: 1982-2021

opencc-by-4.0Oct 2022View details →

A deep learning dataset for underwater object detection of tropical freshwater fish species in northern Australia

This dataset includes 44,112 images with 82,904 bounding box annotations for 23 tropical freshwater fish taxa from northern Australia.  Images were derived from Remote Underwater Video (RUV) deployments in deep channel and shallow lowland billabongs, Kakadu National Park, Northern Territory Australia. RUV deployments were conducted during the <a href="https://www.dcceew.gov.au/science-research/supervising-scientist">Supervising Scientists</a> annual fish monitoring program in the 2016, 2017 and 2018 recessional flow period (dry season). More information can be found <a href="https://www.dcceew.gov.au/sites/default/files/documents/ss-atr-2020-21.pdf">here</a>. <ul> <li>All images are in .jpg format and are 1920x1080 in dimension.</li> <li>Bounding box annotations are in COCO format. </li> </ul> Two .zip files are included: <ul> <li><a href="https://zenodo.org/api/files/990412db-e633-4f82-9b32-6990ef439ccd/202210-KakaduFishAI-CompactModel.zip">202210-KakaduFishAI-CompactModel.zip</a>: includes compact model weights in tensorflow format (.pb) trained using Azure's Custom Vision platform. This model is suitable for edge devices due to its reduced size. Code is provided to use the compact model for inferencing. </li> <li> <a href="https://zenodo.org/api/files/990412db-e633-4f82-9b32-6990ef439ccd/202210-KakaduFishAI-TrainingData.zip">202210-KakaduFishAI-TrainingData.zip</a>: includes all images and one COCO (.json) file with annotations. </li> </ul> Fish taxa include:  <ol> <li>Ambassis agrammus</li> <li>Ambassis macleayi</li> <li>Amniataba percoides</li> <li>Craterocephalus stercusmuscarum</li> <li>Denariusa bandata</li> <li>Glossamia aprion</li> <li>Glossogobius spp.</li> <li>Hephaestus fuliginosus</li> <li>Lates calcarifer</li> <li>Leiopotherapon unicolor</li> <li>Liza ordensis</li> <li>Megalops cyprinoides</li> <li>Melanotaenia nigrans</li> <li>Melanotaenia splendida inornata</li> <li>Mogurnda mogurnda</li> <li>Nemetalosa erebi</li> <li>Neoarius spp.</li> <li>Neosilurus spp.</li> <li>Oxyeleotris spp.</li> <li>Scleropages jardinii</li> <li>Strongylura kreffti</li> <li>Syncomistes butleri</li> <li>Toxotes chatareus</li> </ol> If you use this data for your own deep learning project we'd love to hear about how you used this dataset: andrew.jansen@environment.gov.au.

opencc-zeroNov 2022View details →

High thermal tolerance in high elevation species and laboratory-reared colonies of tropical bumble bees

Bumble bees are key pollinators with some species reared in captivity at a commercial scale, but with significant evidence of population declines and with alarming predictions of substantial impacts under climate change scenarios. While studies on the thermal biology of temperate bumble bees are still limited, they are entirely absent from the tropics where the effects of climate change are expected to be greater. Herein we test if bees' thermal tolerance decreases with elevation and if the stable optimal conditions used in laboratory-reared colonies reduces their thermal tolerance. We assessed changes in the lower (CTMin) and upper (CTMax) critical thermal limits of four species at two elevations (2600 and 3600 m) in the Colombian Andes, examined the effect of body size, and evaluated the thermal tolerance of wild caught and laboratory-reared individuals of B. pauloensis. We also compiled information on bumble bees' thermal limits and assessed potential predictors for broad-scale patterns. We found that CTMin decreased with increasing elevation while CTMax was similar between elevations. CTMax was slightly higher (0.84 °C) in laboratory-reared than in wild-caught bees while CTMin was similar, and CTMin decreased with increasing body size while CTMax did not. Latitude is a good predictor for CTMin only while annual mean temperature, maximum and minimum temperatures of the warmest and coldest months are good predictors for both CTMin and CTMax. The stronger response in CTMin with increasing elevation, and similar CTMax, supports Brett's heat-invariant hypothesis, which has been documented in other taxa. Andean bumble bees appear to be about as heat tolerant as those from temperate areas, suggesting that other aspects besides temperature (e.g., water balance) might be more determinant environmental factors for these species. Laboratory-reared colonies are adequate surrogates for addressing questions on thermal tolerance and global warming impacts.

opencc-zeroNov 2022View details →

Demographic study of a tropical epiphytic orchid with stochastic simulations of hurricanes, herbivory, episodic recruitment, and logging

In a time of global change, having an understanding of the nature of biotic and abiotic factors that drive a species' range may be the sharpest tool in the arsenal of conservation and management of threatened species. However, such information is lacking for most tropical and epiphytic species due to the complexity of life history, the roles of stochastic events, and the diversity of habitat across the span of a distribution. In this study, we conducted repeated censuses across the core and peripheral range of Trichocentrum undulatum, a threatened orchid that is found throughout the island of Cuba (species core range) and southern Florida (the northern peripheral range). We used demographic matrix modeling as well as stochastic simulations to investigate the impacts of herbivory, hurricanes, and logging (in Cuba) on projected population growth rates (𝜆 and 𝜆s) among sites.

opencc-by-4.0Dec 2022View details →

Dataset for Nature Geoscience: Acceleration of a large deep-seated tropical landslide due to urbanisation feedbacks

This archive file contains datafiles used in the manuscript: 'Acceleration of a large deep-seated tropical landslide due to urbanisation feedbacks' [https://doi.org/10.1038/s41561-022-01073-3]. It contains historical aerial orthomosaics, UAS DSM and orthomosaics, shapefiles, deformation maps, etc. for Funu landslide.

opencc-zeroNov 2022View details →

Initiation of speciation across multiple dimensions in a rock-restricted, tropical lizard

Population isolation and concomitant genetic divergence, resulting in strong phylogeographic structure, is a core aspect of speciation initiation. If and how speciation then proceeds and ultimately completes depends on multiple factors that mediate reproductive isolation, including divergence in genomes, ecology, and mating traits. Here we explored these multiple dimensions in two young (Plio-Pleistocene) species complexes of gekkonid lizards (Heteronotia) from the Kimberley–Victoria River regions of tropical Australia. Using mtDNA screening and exon capture phylogenomics, we show that the rock-restricted H. planiceps exhibits exceptional fine-scale phylogeographic structure compared to the co-distributed habitat generalist H. binoei. This indicates pervasive population isolation and persistence in the rock-specialist, and thus a high rate of speciation initiation across this geographically complex region, with levels of genomic divergence spanning the "grey zone" of speciation. Proximal lineages of H. planiceps were often separated by different rock substrates suggesting a potential role for ecological isolation; however, phylogenetic incongruence and historical introgression were inferred between one such pair. Eco-morphological divergence among lineages within both H. planiceps and H. binoei was limited, except that limestone-restricted lineages of H. planiceps tended to be larger than rock-generalists. By contrast, among-lineage divergence in the chemical composition of epidermal pore secretions (putative mating trait) exceeded eco-morphology in both complexes, but with less trait overlap among lineages in H. planiceps. This system — particularly the rock-specialist H. planiceps — highlights the role of multidimensional divergence during incipient speciation, with divergence in genomes, eco-morphology, and chemical signals all at play at very fine spatial scales.