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56 results for “African rainforest”
Data from: Exploring rainforest diversification using demographic model testing in the African foam-nest treefrog (Chiromantis rufescens)
Aim: Species with wide distributions spanning the African Guinean and Congolian rainforests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rainforest species, the African Foam-nest Treefrog (Chiromantis rufescens). Location: Guinean and Congolian rainforests, West and Central Africa. Taxon: Chiromantis rufescens. Methods: We collected mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data for 130 samples of Chiromantis rufescens. After estimating population structure and inferring species trees using coalescent methods, we tested demographic models to evaluate alternative population divergence histories that varied with respect to gene flow, population size change, and periods of isolation and secondary contact. Species distribution models were used to identify regions of climatic stability that could have served as forest refugia since the Last Interglacial. Results: Population structure within Chiromantis rufescens resembles the major biogeographic regions of the Guinean and Congolian forests. Coalescent-based phylogenetic analyses provide strong support for an early divergence between the western Upper Guinean forest and the remaining populations. Demographic inferences support diversification models with gene flow and population size changes even in cases where contemporary populations are currently allopatric, which provides support for forest refugia and barrier models. Species distribution models suggest that forest refugia were available for each of the populations throughout the Pleistocene. Main conclusions: Considering historical demography is essential for understanding population diversification, especially in complex landscapes such as those found in the Guineo-Congolian forest. Population demographic inferences help connect patterns of genetic variation to diversification model predictions. The diversification history of Chiromantis rufescens was shaped by a variety of processes, including vicariance from river barriers, forest fragmentation, and adaptive evolution along environmental gradients.
Fig. 4 in The anuran fauna in a protected West African rainforest and surrounding agricultural systems
Fig. 4. Selected amphibian species from Taï National Park and surrounding agroforestry systems. (A) Conraua alleni inhabits rainforest streams. (B) Ptychadena cf. aequiplicata is a typical inhabitant of primary forest. (C) Chiromantis rufescens breeds in puddles along forest roads and stagnant ponds and puddles in the forest. (D) Arthroleptis cf. poecilonotus (a complex of at least two species) occurs in primary and degraded forest, and is particularly abundant in agroforestry systems. (E) Amnirana galamensis is a typical inhabitant of African savannas and was detected for the first time in the Taï area. (F) Ptychadena mascareniensis is a very abundant frog in rice fields.
Fig. 2 in The anuran fauna in a protected West African rainforest and surrounding agricultural systems
Fig. 2. The different habitats in and around Taï National Park which were surveyed for amphibians. (A) and (B) near primary forest; (C) cocoa plantation; (D) rubber plantation; (E) heavily degraded forest edge; (F) rice field.
Fig. 3 in The anuran fauna in a protected West African rainforest and surrounding agricultural systems
Fig. 3. Species accumulation curve (triangles) and estimated amphibian species richness (Chao 2, squares; and Jack-knife 1, circles) of the Taï National Park and surrounding agroforestry system. The mean values of 500 random runs of the daily species lists are given. A daily species list comprised the presence/absence records collected during seven hours of sampling (four hours during daylight, and three hours during night) on one plot by two people for a total of 14 person-hours.
Fig. 1 in The anuran fauna in a protected West African rainforest and surrounding agricultural systems
Fig. 1. Locations of the 32 study plots in the Taï National Park and surrounding agroforestry systems (see Appendix 1 for the plot list and habitat descriptions). Inset figure: position of Taï National Park in Côte d'Ivoire.
Data from: Exploring rainforest diversification using demographic model testing in the African foam-nest treefrog (Chiromantis rufescens)
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Data from: Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens)
The little greenbul, a common rainforest passerine from sub-Saharan Africa, has been the subject of long-term evolutionary studies to understand the mechanisms leading to rainforest speciation. Previous research found morphological and behavioural divergence across rainforest–savannah transition zones (ecotones), and a pattern of divergence with gene flow suggesting divergent natural selection has contributed to adaptive divergence and ecotones could be important areas for rainforests speciation. Recent advances in genomics and environmental modelling make it possible to examine patterns of genetic divergence in a more comprehensive fashion. To assess the extent to which natural selection may drive patterns of differentiation, here we investigate patterns of genomic differentiation among populations across environmental gradients and regions. We find compelling evidence that individuals form discrete genetic clusters corresponding to distinctive environmental characteristics and habitat types. Pairwise FST between populations in different habitats is significantly higher than within habitats, and this differentiation is greater than what is expected from geographic distance alone. Moreover, we identified 140 SNPs that showed extreme differentiation among populations through a genomewide selection scan. These outliers were significantly enriched in exonic and coding regions, suggesting their functional importance. Environmental association analysis of SNP variation indicates that several environmental variables, including temperature and elevation, play important roles in driving the pattern of genomic diversification. Results lend important new genomic evidence for environmental gradients being important in population differentiation.
Predictive mapping of tree species assemblages in an African montane rainforest
<p>Conservation of mountain ecosystems can benefit from knowledge of habitats and their distribution patterns. This benefit is particularly true for diverse ecosystems with high conservation values such as the "Afromontane" rainforests. We mapped the vegetation of one such forest: the rugged Bwindi Impenetrable Forest, Uganda—a World Heritage Site known for its many restricted-range plants and animal taxa including several iconic species. Given variation in elevation, terrain and human impacts across Bwindi, we hypothesised that these factors influence the composition and distribution of tree species. To test this, detailed surveys were carried out using stratified random sampling. We established 289 georeferenced sample sites (each with 15 trees ≥20 cm dbh) ranging from 1,320 to 2,467 m a.s.l. and measured 4,335 trees comprising 89 species that occurred in four or more sample sites. These data were analysed against twenty-one digitally mapped biophysical variables using various analytical techniques including non-metric multidimensional scaling (NMDS) and random forests. We identified six tree species assemblages with distinct compositions. Among the biophysical variables, elevation had the strongest correlation with the ordination (r<sup>2</sup>=0.5; <em>p</em><0.001). The "out-of-bag" (OOB) estimate of the error rate for the best final model was 50.7% meaning that nearly half of the variation was accounted for using a limited set of variables. We demonstrate that it is possible to predict the spatial pattern of such a forest based on sampling across a highly complex landscape. Such methods offer accurate mapping of composition that can guide conservation.</p>
Strong habitat-specific phenotypic plasticity but no genome-wide differentiation across a rainforest gradient in an African butterfly
<p>Habitat-specific thermal responses are well documented in various organisms and likely determine the vulnerability of populations to climate change. However, the underlying roles of genetics and plasticity that shape such habitat-specific patterns are rarely investigated together. Here we examined the thermal plasticity of the butterfly <em>Bicyclus</em> <em>dorothea</em> originating from rainforest and ecotone habitats in Cameroon under common garden conditions. We also sampled wild-caught butterflies from forest and ecotone sites and used RADseq to explore genome-wide population differentiation. We found differences in the level of phenotypic plasticity across habitats. Specifically, ecotone populations exhibited greater sensitivity in wing eyespot features with variable development temperatures relative to rainforest populations. Known adaptive roles of wing eyespots in <em>Bicyclus</em> species suggest that this morphological plasticity is likely under divergent selection across environmental gradients. However, we found no distinct population structure of genome-wide variation between habitats, suggesting high levels of ongoing gene flow between habitats is homogenizing most parts of the genome.</p>
Data from: Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens)
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Predictive mapping of tree species assemblages in an African montane rainforest
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Strong habitat-specific phenotypic plasticity but no genome-wide differentiation across a rainforest gradient in an African butterfly
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Data from: Testing alternative hypotheses for evolutionary diversification in an African songbird: rainforest refugia versus ecological gradients
Geographic isolation in rainforest refugia and local adaptation to ecological gradients may both be important drivers of evolutionary diversification. However, their relative importance and the underlying mechanisms of these processes remain poorly understood because few empirical studies address both putative processes in a single system. A key question is to what extent is divergence in signals that are important in mate and species recognition driven by isolation in rainforest refugia or by divergent selection across ecological gradients? We studied the little greenbul, Andropadus virens, an African songbird, in Cameroon and Uganda, to determine whether refugial isolation or ecological gradients better explain existing song variation. We then tested whether song variation attributable to refugial or ecological divergence was biologically meaningful using reciprocal playback experiments to territorial males. We found that much of the existing song variation can be explained by both geographic isolation and ecological gradients, but that divergence across the gradient, and not geographic isolation, affects male response levels. These data suggest that ecologically divergent traits, independent of historical isolation during glacial cycles, can promote reproductive isolation. Our study provides further support for the importance of ecology in explaining patterns of evolutionary diversification in ecologically diverse regions of the planet.
Data from: Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers
The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the pygmy phenotype in the Batwa, a rainforest hunter-gatherer population from Uganda (east central Africa). The identified genomic regions have multiple attributes that provide supporting evidence of genuine association with the pygmy phenotype, including enrichments for SNPs previously associated with stature variation in Europeans and for genes with growth hormone receptor and regulation functions. To test adaptive evolutionary hypotheses, we computed the haplotype-based integrated haplotype score (iHS) statistic and the level of population differentiation (FST) between the Batwa and their agricultural neighbors, the Bakiga, for each genomic SNP. Both |iHS| and FST values were significantly higher for SNPs within the Batwa pygmy phenotype-associated regions than the remainder of the genome, a signature of polygenic adaptation. In contrast, when we expanded our analysis to include Baka rainforest hunter-gatherers from Cameroon and Gabon (west central Africa) and Nzebi and Nzime neighboring agriculturalists, we did not observe elevated |iHS| or FST values in these genomic regions. Together, these results suggest adaptive and at least partially convergent origins of the pygmy phenotype even within Africa, supporting the hypothesis that small body size confers a selective advantage for tropical rainforest hunter-gatherers but raising questions about the antiquity of this behavior.
Data from: Two new species of long-fingered frogs of the genus Cardioglossa (Anura: Arthroleptidae) from Central African rainforests
We describe two new frog species of Cardioglossa (Family Arthroleptidae) from Central Africa. The new species are found in the rainforests of western-central Democratic Republic of the Congo and the Republic of the Congo near the Gabonese border, respectively. We demonstrate that these species are morphologically and genetically distinct from each other and all other species of Cardioglossa. Both new species lack the dorsal hour-glass pattern present in many species of the genus, but they can be distinguished from each other and related species by distinctive colour patterns on their lateral surfaces and extremities. Both new species most closely resemble C. gratiosa, which occurs in the Atlantic coastal forests extending from Cameroon through Gabon. The new species can be differentiated from C. gratiosa by the absence of black transverse bars on all limbs or by distinctive lateral colouration. Analysis of mitochondrial ribosomal 16S DNA sequences reveals low to moderate levels (1.9–7.5%) of divergence between these new species and closely related species of Cardioglossa. The floodplains of the Congo and Ubangi Rivers may be important geographic barriers for many of these species. The occurrence of these two new lowland species in the Congo Basin reveals that the distribution and diversity of Cardioglossa in this region was underestimated. In addition, we elevate C. nigromaculata inornata to species-level status, based in part on newly available colour photographs from 1950 of specimens from the only known locality.
FIGURE 1 in A new species of African diurnal dwarf geckos (Gekkonidae: Lygodactylus) from the Lower Guinea rainforest
FIGURE 1: Habitats and geographical distribution of Lygodactylus lobeke sp. nov. on a hybrid map of the major vegetation divisions (Sayre et al. 2013) and 1 arc-second elevation map across tropical Africa (NASA 2000). Photos of habitats from (a) type locality (holotype) near Goumela, southeastern Cameroon, and (b) second locality (paratype) near Sanga Wanda, Mayombe National Park, Cabinda Province, Angola. Photographs by B.R. (a) and J.L-R. (b).
FIGURE 4 in A new species of African diurnal dwarf geckos (Gekkonidae: Lygodactylus) from the Lower Guinea rainforest
FIGURE 4: Lygodactylus lobeke sp. nov. type material in preservative. a) to d) female holotype (ZSM 56/2024): a) dorsal and b) ventral views; c) dorsal view of head, d) ventral view of (regenerated) tail tip. e) to h) male paratype (FKH 1259): e) dorsal and f) ventral views; g) dorsal view of head, h) ventral view of (regenerated) tail tip. Photographs by B.R. (a–d) and P. VP. (e–h).
FIGURE 3 in A new species of African diurnal dwarf geckos (Gekkonidae: Lygodactylus) from the Lower Guinea rainforest
FIGURE 3: Lygodactylus lobeke sp. nov. in life. (a) Chin and (c) precloacal region and proximal part of the tail of the female holotype. Precloacal region with 9 precloacal spots, corresponding to the precloacal pores in the male specimen. Arrowheads in (c) mark row of precloacal scales with spots. Original part of tail with double row of enlarged subcaudal scales, two of which are marked with circles. Inset: same, contrast enhanced. (b) Chin and (d) precloacal region and pseudo-escutcheon (yellow scales) of the male paratype. Precloacal region with 9 precloacal pores. Arrowheads in (d) mark row of precloacal pores. Photographs by B.R. (a, c) and P.VP. (b, d).
FIGURE 6 in A new species of African diurnal dwarf geckos (Gekkonidae: Lygodactylus) from the Lower Guinea rainforest
FIGURE 6: Lygodactylus lobeke sp. nov. female holotype in life: 'Mood dependent' colorations. (a) and (b) 'distress' coloration (compare coloration shortly after capture, see Fig. 2a); (c) 'neutral' coloration; (d) 'display' coloration; (e) 'pyjamas' coloration (resting at night on a leaf). Photographs by B.R.
FIGURE 2 in A new species of African diurnal dwarf geckos (Gekkonidae: Lygodactylus) from the Lower Guinea rainforest
FIGURE 2: Lygodactylus lobeke sp. nov. in life, shortly after capture. Female holotype: lateral (a) and dorsal views (b). Male paratype: lateral (c) and dorsal views (d). Photographs of holotype: ambient light, analog (Kodachrome 200) (2002), photographs of paratype: flash, digital (Canon EOS 6D Mark II) (2023). Photographs by B.R. (a, b) and P.VP. (c, d).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.