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Data from: Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)
Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2-10 MY, yet over 6kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a subset of 60 loci in a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories in the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.
FIGURE 2. Ormosia altimontana A in A new species of Ormosia (Leguminosae, Papilionoideae, Sophoreae) from the Brazilian Atlantic Rain Forest
FIGURE 2. Ormosia altimontana A. Leaflets showing golden indument on the abaxial surface. B. Globose, red to orange seeds.
FIGURE 1. Ormosia altimontana A. fruiting branch. B. abaxial leaflet surface, showing the tomentose indument. C in A new species of Ormosia (Leguminosae, Papilionoideae, Sophoreae) from the Brazilian Atlantic Rain Forest
FIGURE 1. Ormosia altimontana A. fruiting branch. B. abaxial leaflet surface, showing the tomentose indument. C. seeds in hilar and lateral view. D. flower. E. standard petal. F. wing petal. G. keel petal. H. anthers, slightly dimorphic. I. dimorphic stamens. J. gynoecium. K. stigma. Branch and fruits (A–C) after M.P.M. de Lima 201. Flower (D–L) after H.C. de Lima 5515.
FIGURE 3 in A new species of Ormosia (Leguminosae, Papilionoideae, Sophoreae) from the Brazilian Atlantic Rain Forest
FIGURE 3. Principal Component Analysis of vegetative traits in O. altimontana, O friburgensis and O. ruddiana (See Appendix 1).
Figure 2 in Population dynamics, seasonality and sex ratio of twig-girdling beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) of an Atlantic rain forest in south-eastern Brazil
Figure 2. Mean (± SE) number of adult beetles of the tribe Onciderini found at the Serra do Japi during the period of adult activity (between October and May) from 2002 to 2006. (A) Species with peak abundance between December and February. (B) Species with peak abundance between January and March. (n = 5). An asterisk indicates significance among monthly abundances after Bonferroni correction (Friedman's ANOVA; p ≤ 0.013).
Figure 1 in Population dynamics, seasonality and sex ratio of twig-girdling beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) of an Atlantic rain forest in south-eastern Brazil
Figure 1. Rank-abundance pattern of adult beetles of the tribe Onciderini found at the Serra do Japi between December 2002 and December 2006. (n = 1113 individuals).
Figure 3 in Population dynamics, seasonality and sex ratio of twig-girdling beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) of an Atlantic rain forest in south-eastern Brazil
Figure 3. (A) Population fluctuation (number of individuals) of adult beetles of the tribe Onciderini found at the Serra do Japi between December 2002 and December 2006 (n = 1113 individuals). (B) Climate diagram for the Biological Reserve of the Serra do Japi at the same time period (data from a meteorological station approximately 8 km from the study site). The mean monthly temperature (◦ C) and rainfall (mm) are scaled to represent the potential evapotranspiration. Values inside each diagram indicate mean temperature (◦C) and total rainfall (mm) for each sampling year. Dry months are represented by dotted areas; humid months by the vertical lines and months with rain in excess of 100 mm are in solid black.
Figure 4 in Diet and feeding behaviour of the leaf-litter frog Ischnocnema henselii (Anura: Brachycephalidae) in Araucaria rain forests on the Serra Geral of Rio Grande do Sul, Brazil
Figure 4. Relationship between mouth width of hunting Ischnocnema henselii frogs and the volume of prey animals.
Figure 3 in Diet and feeding behaviour of the leaf-litter frog Ischnocnema henselii (Anura: Brachycephalidae) in Araucaria rain forests on the Serra Geral of Rio Grande do Sul, Brazil
Figure 3. Relationship between mouth width of hunting Ischnocnema henselii frogs and length of prey animals.
Figure 1 in Diet and feeding behaviour of the leaf-litter frog Ischnocnema henselii (Anura: Brachycephalidae) in Araucaria rain forests on the Serra Geral of Rio Grande do Sul, Brazil
Figure 1. Relationship between body size (snout–vent length) and weight in Ischnocnema henselii adults.
Figure 5 in Diet and feeding behaviour of the leaf-litter frog Ischnocnema henselii (Anura: Brachycephalidae) in Araucaria rain forests on the Serra Geral of Rio Grande do Sul, Brazil
Figure 5. Prey items as found in the stomachs of adult Ischnocnema henselii frogs and composition of the litter fauna in the frogs' habitat.
Post‐agriculture rain forest succession on a tropical Pacific island
<p>We surveyed the tree and seedling community in 34 vegetation plots in mature and >50 y old secondary lowland rain forest on the Polynesian island of Tutuila, American Samoa. The main data set includes original data from the tree surveys as well as all repeat surveys of seedling plots. We also include all R code and data sets used in analyses, including soil and environmental data, species by plot matrices for NMDS, and processed data used for survival analysis.</p>
FIGURE 24 in Three new genera of large marsh beetles (Coleoptera: Scirtidae) from Valdivian temperate rain forests of southern South America
FIGURE 24. Distribution of Mucronotus gen. nov. A) M. enigmaticus sp. nov. (blue dots) and M. patagonicus sp. nov. (red dots); B) M. schwabei (Pic); C) M. valdivianus sp. nov.; D) M. velutinus (Solier).
FIGURE 21 in Three new genera of large marsh beetles (Coleoptera: Scirtidae) from Valdivian temperate rain forests of southern South America
FIGURE 21. Mucronotus velutinus (Solier), male. A) terminal segments and genitalia; B) penis; C) tegmen; D) sternite VIII; E) sternite IX; F) tergite VIII; G) tergite IX. Scale bar = 0.5 mm.
FIGURE 20 in Three new genera of large marsh beetles (Coleoptera: Scirtidae) from Valdivian temperate rain forests of southern South America
FIGURE 20. Mucronotus valdivianus sp. nov., female. A) genital tract; B) bursal sclerite. Abbreviations: bscl—bursal sclerite, bsl—bursella, gla—gland. Scale bars = 1.0 mm (A), 0.5 mm (B).
FIGURE 17 in Three new genera of large marsh beetles (Coleoptera: Scirtidae) from Valdivian temperate rain forests of southern South America
FIGURE 17. Mucronotus schwabei (Pic), male. A) penis; B) tegmen; C) sternite VIII; D) sternite IX; E) tergite VIII; F) tergite IX. Scale bar = 0.5 mm.
FIGURE 16 in Three new genera of large marsh beetles (Coleoptera: Scirtidae) from Valdivian temperate rain forests of southern South America
FIGURE 16. Mucronotus patagonicus sp. nov., male. A) terminal segments and genitalia; B) penis; C) tegmen; D) left paramere, close-up; E) sternite VIII; F) sternite IX; G) tergite VIII; H) tergite IX. Scale bar = 0.5 mm.
FIGURE 15 in Three new genera of large marsh beetles (Coleoptera: Scirtidae) from Valdivian temperate rain forests of southern South America
FIGURE 15. Mucronotus enigmaticus sp. nov., female. A) genital tract; B) bursal sclerite. Abbreviations: bscl—bursal sclerite, bsl—bursella, gla—gland. Scale bars = 1.0 mm (A), 0.5 mm (B).
FIGURE 13. Mucronotus gen. nov., pronotum. A in Three new genera of large marsh beetles (Coleoptera: Scirtidae) from Valdivian temperate rain forests of southern South America
FIGURE 13. Mucronotus gen. nov., pronotum. A) M. enigmaticus sp. nov., male; B) M. enigmaticus sp. nov., female; C) M. patagonicus sp. nov., male, D) M. schwabei (Pic), male, E) M. valdivianus sp. nov., male, F) M. velutinus (Solier), male.
FIGURE 11 in Three new genera of large marsh beetles (Coleoptera: Scirtidae) from Valdivian temperate rain forests of southern South America
FIGURE 11. Mucronotus gen. nov., ventral portion of head, prosternum and mesoventrite. A) M. schwabei (Pic); B) M. velutina (Solier).
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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.