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Data from: Moorean and Tahitian Partula tree snail survival after a mass extinction: new genomic insights using museum specimens
Natural history museum collections provide a biodiversity window into the past and are of particular importance to the study of extinction-impacted clades such as the Pacific Island tree snail family Partulidae. Deliberate introduction of the predatory rosy wolf snail Euglandina rosea in the late 20th century led to the extinction/extirpation of 55/61 Society Island Partulidae species. In this study, we phylogenomically investigated the inter-relationships of the three surviving Society Island valley Partula species: P. taeniata (Moorea), P. clara and P. hyalina (Tahiti). All three formed a distinct clade in earlier mitochondrial phylogenies. Using Next Generation Sequencing (NGS) double digested Restriction Associated DNA sequencing (ddRADseq), we found that 46-year-old lyophilized museum specimens produced similar numbers of reads, sequencing depth, and loci as 10-year old ethanol-preserved collections. Phylogenomic trees indicated that Tahitian P. clara and P. hyalina are the result of a single founding lineage from Moorea, contrasting previous mitochondrial results and clarifying the enigmatic taxonomic status of P. c. incrassa. Our study highlights the utility and viability of NGS techniques for museum specimens and their increased resolution of evolutionary patterns. Sampling will be expanded to include the remaining Society Island partulid taxa to further explore the evolutionary history of this radiation.
Data from: Coral reefs as drivers of cladogenesis: expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots
Diversification rates within four conspicuous coral reef fish families (Labridae, Chaetodontidae, Pomacentridae, Apogonidae) were estimated using Bayesian inference. Lineage through time plots revealed a possible late Eocene/early Oligocene cryptic extinction event coinciding with the collapse of the ancestral Tethyan/Arabian hotspot. Rates of diversification analysis revealed elevated cladogenesis in all families in the Oligocene/Miocene. Throughout the Miocene, lineages with a high percentage of coral reef associated taxa display significantly higher net diversification rates than expected. The development of a complex mosaic of reef habitats in the Indo-Australian Archipelago (IAA) during the Oligocene/Miocene appears to have been a significant driver of cladogenesis. Patterns of diversification suggest that coral reefs acted as a refuge from high extinction, as reef taxa are able to sustain diversification at high extinction rates. The IAA appears to support both cladogenesis and survival in associated lineages, laying the foundation for the Recent IAA marine biodiversity hotspot.
Data from: Ancient vicariance and climate-driven extinction explain continental-wide disjunctions in Africa: the case of the Rand Flora genus Canarina (Campanulaceae)
Transoceanic distributions have attracted the interest of scientists for centuries. Less attention has been paid to the evolutionary origins of 'continent-wide' disjunctions, in which related taxa are distributed across isolated regions within the same continent. A prime example is the 'Rand Flora' pattern, which shows sister taxa disjunctly distributed in the continental margins of Africa. Here, we explore the evolutionary origins of this pattern using the genus Canarina, with three species: C. canariensis, associated with the Canarian laurisilva, and C. eminii and C. abyssinica, endemic to the Afromontane region in East Africa, as case study. We infer phylogenetic relationships, divergence times and the history of migration events within Canarina using Bayesian inference on a large sample of chloroplast and nuclear sequences. Ecological niche modelling was employed to infer the climatic niche of Canarina through time. Dating was performed with a novel nested approach to solve the problem of using deep time calibration points within a molecular dataset comprising both above-species and population-level sampling. Results show C. abyssinica as sister to a clade formed by disjunct C. eminii and C. canariensis. Miocene divergences were inferred among species, whereas infraspecific divergences fell within the Pleistocene–Holocene periods. Although C. eminii and C. canariensis showed a strong genetic geographic structure, among-population divergences were older in the former than in the latter. Our results suggest that Canarina originated in East Africa and later migrated across North Africa, with vicariance and aridification-driven extinction explaining the 7000 km/7 million year divergence between the Canarian and East African endemics.
Data from: Ancient DNA from the extinct South American giant glyptodont Doedicurus sp. (Xenarthra: Glyptodontidae) reveals that glyptodonts evolved from Eocene armadillos
Glyptodonts were giant (some of them up to ~2400 kg), heavily armoured relatives of living armadillos, which became extinct during the Late Pleistocene/early Holocene alongside much of the South American megafauna. Although glyptodonts were an important component of Cenozoic South American faunas, their early evolution and phylogenetic affinities within the order Cingulata (armoured New World placental mammals) remain controversial. In this study, we used hybridization enrichment and high-throughput sequencing to obtain a partial mitochondrial genome from Doedicurus sp., the largest (1.5 m tall, and 4 m long) and one of the last surviving glyptodonts. Our molecular phylogenetic analyses revealed that glyptodonts fall within the diversity of living armadillos. Reanalysis of morphological data using a molecular 'backbone constraint' revealed several morphological characters that supported a close relationship between glyptodonts and the tiny extant fairy armadillos (Chlamyphorinae). This is surprising as these taxa are among the most derived cingulates: glyptodonts were generally large-bodied and heavily armoured, while the fairy armadillos are tiny (~9–17 cm) and adapted for burrowing. Calibration of our phylogeny with the first appearance of glyptodonts in the Eocene resulted in a more precise timeline for xenarthran evolution. The osteological novelties of glyptodonts and their specialization for grazing appear to have evolved rapidly during the Late Eocene to Early Miocene, coincident with global temperature decreases and a shift from wet closed forest towards drier open woodland and grassland across much of South America. This environmental change may have driven the evolution of glyptodonts, culminating in the bizarre giant forms of the Pleistocene.
Fossils, phylogenies, and the challenge of preserving evolutionary history in the face of anthropogenic extinctions
<p>Datasets and R scripts</p>
FIGURE 5 in A new and presumably extinct species of Ptychochromoides (Teleostei: Perciformes: Cichlidae) from central Madagascar
FIGURE 5. Scatterplot of sheared second and third PC scores of 13 logtransformed morphometric variables of Ptychochromoides betsileanus (n = 10; triangles), P. itasy (n = 3; squares), and Ptychochromoides sp (MNHN 1907104; n = 2; circles).
FIGURE 1 in A new and presumably extinct species of Ptychochromoides (Teleostei: Perciformes: Cichlidae) from central Madagascar
FIGURE 1. Map of Madagascar indicating recent or verifiable (Lake Itasy) collection localities for members of Ptychochromoides and Oxylapia polli.
FIGURES 13 in Polygyrid land snails, Vespericola (Gastropoda: Pulmonata), 4. A new and possibly extinct species from central California, U. S. A.
FIGURES 13. Vespericola ohlone Roth, sp. nov. Holotype, SBMNH 348128, Patterson's Willows, Alameda County, California. Top, apertural, and basal views of shell. Diameter (exclusive of outer lip) 14.5 mm; scale bar = 5 mm.
FIGURE 4 in A new and presumably extinct species of Ptychochromoides (Teleostei: Perciformes: Cichlidae) from central Madagascar
FIGURE 4. Ptychochromoides betsileanus, lectotype, BMNH 1882.2.25:69, adult male, 159.6 mm SL; Madagascar: Betsileo region. Right side illustrated due to damage to left side (image reversed).
FIGURE 6 in A new and presumably extinct species of Ptychochromoides (Teleostei: Perciformes: Cichlidae) from central Madagascar
FIGURE 6. Ptychochromoides vondrozo, holotype, UMMZ 235297, adult female, 182.0 mm SL; Madagascar: Fianarantsoa Province: Ramanara River. Right side illustrated due to distortion of specimen (image reversed). Photograph by Heok Hee Ng.
FIGURE 1 in New species amongst Sri Lanka's extinct shrub frogs (Amphibia: Rhacophoridae: Philautus)
FIGURE 1. Holotype female of Philautus pardus, 32.1 mm SVL, BMNH 1947.2.7.96. A. Dorsal view. B. Ventral view.
FIGURE 4 in New species amongst Sri Lanka's extinct shrub frogs (Amphibia: Rhacophoridae: Philautus)
FIGURE 4. Holotype female of Philautus maia, 44.6 mm SVL, BMNH 76.3.21.18. A. Illustration of eggs carried on venter in Günther (1876). B. Ventral view, showing depressions made by eggs. C. Lateral view, showing speckled pattern.
FIGURE 3. A in New species amongst Sri Lanka's extinct shrub frogs (Amphibia: Rhacophoridae: Philautus)
FIGURE 3. A. Factor scores (no rotation) of principal components analysis of mensural data of Philautus pardus (square), P. viridis (rhombus), P. stuarti (star), and P. variabilis (circle) (females represented by open symbols, males by solid symbols). B. Canonical variables plot of discriminant function analysis of sizeadjusted residuals (the 95% confidence ellipses are centered on the centroid of each species).
FIGURE 2 in New species amongst Sri Lanka's extinct shrub frogs (Amphibia: Rhacophoridae: Philautus)
FIGURE 2. Holotype female of Philautus pardus, 32.1 mm SVL, BMNH 1947.2.7.96. A. Lateral view of head. B. Dorsal view of head. C. Left hand. D. Left foot. E. Diagrammatic representation of leftfoot webbing. Scale bars = 1 mm.
FIGURE 5 in New species amongst Sri Lanka's extinct shrub frogs (Amphibia: Rhacophoridae: Philautus)
FIGURE 5. Holotype female of Philautus maia, 44.6 mm SVL, BMNH 76.3.21.18. A. Lateral aspect of head. B. Thigh, showing reticulated pattern. C. Left hand. D. Left foot. E. Diagrammatic representation of leftfoot webbing. Scale bars = 1 mm.
FIGURE 6. A in New species amongst Sri Lanka's extinct shrub frogs (Amphibia: Rhacophoridae: Philautus)
FIGURE 6. A. Factor scores (no rotation) of principal components analysis of mensural data of P. m a i a (square), P. reticulatus (circle), P. lunatus (rhombus) and P. papillosus (star) (females represented by open symbols, males by solid symbols). B. Canonical variables plot of discriminant function analysis of sizeadjusted residuals (the 95% confidence ellipse is centered on the centroid).
FIGURES 1–4. 1–3 Spatiator martensi n in Spatiator martensi n. sp., a second species of the extinct spider family Spatiatoridae in Eocene Baltic amber (Araneae)
FIGURES 1–4. 1–3 Spatiator martensi n. sp., ♂ holotype in Baltic amber; 1 outline of the body, lateral aspect. Reconstruction from dorsal and oblique aspects. Only a single eye is drawn; 2–3 right pedipalpus, dorsal and ventral aspect. Normal (thin) setae are not drawn. 4 Spatiator praeceps Petrunkevitch 1942, ♂, in Baltic amber, ventral aspect of the right pedipalpus. C = conductor, E = embolus, M = emulsion, S = sperm duct. Scales: 1, 1.0 mm; 2–4, 0.2 mm.
FIGURE 5. Spatiator martensi n in Spatiator martensi n. sp., a second species of the extinct spider family Spatiatoridae in Eocene Baltic amber (Araneae)
FIGURE 5. Spatiator martensi n. sp. (Spatiatoridae), fossil ♂ in Baltic amber, dorsal aspect. Body length 4.3 mm.
FIGURE 15 in A taxonomic revision of Atelopus pachydermus, and description of two new (extinct?) species of Atelopus from Ecuador (Anura: Bufonidae)
FIGURE 15. Manus (A) and pes (B), in ventral view, of female Atelopus onorei from Río Chipla, Provincia Azuay (QCAZ 1868). The arrow designates the Sesamoid I. Stippled areas are bone; cartilage shown in dark gray. Broken line indicates missing phalanx. Scale = 2 mm.
FIGURE 14 in A taxonomic revision of Atelopus pachydermus, and description of two new (extinct?) species of Atelopus from Ecuador (Anura: Bufonidae)
FIGURE 14. Skeletal features of female Atelopus onorei from Río Chipla, Provincia Azuay (QCAZ 1868). (A) ventral view of hyobranchium, (B) dorsal view of vertebral column and pelvic girdle, and (C) ventral view of pectoral girdle. Scale = 5 mm.
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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.