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Bivalve body size distribution through the Late Triassic mass extinction event
<p><span>The synergic relationship between physiology, ecology and evolutionary process makes the body size distribution (BSD) an essential component of the community ecology. Body size is highly susceptible to environmental change, and extreme upheavals, such as during a mass extinction event, could exert drastic changes on a taxon's BSD. It has been hypothesized that the Late Triassic mass extinction event (LTE) was triggered by intense global warming, linked to massive volcanic activity associated with the Central Atlantic Magmatic Province. We test the effects of the LTE on the BSD of fossil bivalve assemblages from three study sites spanning the Triassic/Jurassic boundary in the UK.</span> <span>Our results show that the effects of the LTE were rapid and synchronous across sites, and the BSDs of the bivalves record drastic changes associated with species turnover. No phylogenetic signal of size selectivity was recorded, although semi-infaunal species were apparently most susceptible to change. Each size class had the same likelihood of extinction during the LTE, which resulted in a platykurtic BSD with negative skew. The immediate post-extinction assemblage exhibits a leptokurtic BSD although with negatively skewed, where surviving species and newly appearing small-sized colonizers exhibit body sizes near the modal size. Recovery was relatively rapid (~100kyr), and larger bivalves began to appear during the Pre-Planorbis Zone, despite recurrent dysoxic/anoxic conditions. This study demonstrates how a mass extinction acts across the size spectrum in bivalves and shows how BSDs emerge from evolutionary and ecological processes.</span></p>
Distribution. Amazon and Orinoco basins from Venezuela to Paraguay and S Brazil. Formerly also Argentina and Uruguay, but now may be extinct there. in Mustelidae
Distribution. Amazon and Orinoco basins from Venezuela to Paraguay and S Brazil. Formerly also Argentina and Uruguay, but now may be extinct there.
Distribution. Throughout mainland SE Asia, from C & S Myanmar to W & SE Thailand, C & S Laos, Cambodia, C & S Vietnam, and Peninsular Malaysia; also present in Borneo, Sumatra, Java, Bali, Lombok, and several adjacent small islands. Most likely extinct from E Bangladesh, where it has not been reported for more than 40 years. Northern and western limits of its range are poorly known. in Manidae
Distribution. Throughout mainland SE Asia, from C & S Myanmar to W & SE Thailand, C & S Laos, Cambodia, C & S Vietnam, and Peninsular Malaysia; also present in Borneo, Sumatra, Java, Bali, Lombok, and several adjacent small islands. Most likely extinct from E Bangladesh, where it has not been reported for more than 40 years. Northern and western limits of its range are poorly known.
Subspecies and Distribution. C.l.liberiensisMorton,1849—Guinea,SierraLeone,Liberia,IvoryCoast. C. l. heslop: Corbet, 1969 — Nigeria (possibly extinct). in Hippopotamidae
Subspecies and Distribution. C.l.liberiensisMorton,1849—Guinea,SierraLeone,Liberia,IvoryCoast. C. l. heslop: Corbet, 1969 — Nigeria (possibly extinct).
Figure 4 in Recent mitochondrial lineage extinction in the critically endangered Javan rhinoceros
Figure 4. Neighbor-Joining network. The analysis of 14 modern and historical Javan and Indian rhinoceros mitochondrial DNA sequences was conducted using the 'Integer Neighbor-Joining' algorithm implemented in POPART. We used the partial D-loop region of 413 bp to maximize the number of available Javan rhino samples. 'Javan_annamiticus' represents the recently extinct (since 2010) Vietnamese subspecies Rhinoceros sondaicus annamiticus. Each circle represents a certain haplotype; smaller black circles indicate median vectors. Small black lines connecting branches between the haplotypes denote the number of mutation steps separating the haplotypes. Sample identities and regions of origin for the Javan rhinoceros samples are indicated next to each circle. Numbers in the legend indicate the number of sequences in each group.
Figure 3 in Recent mitochondrial lineage extinction in the critically endangered Javan rhinoceros
Figure 3. Bayesian phylogeny of the historical Javan rhinoceros mitochondrial DNA lineages, using the Indian rhino (Rhinoceros unicornis; GenBank ID: X97336) as the outgroup and including the partial (7606-bp-long) mitogenome of the Javan rhino sample collected in Bhutan (JR524). The blue bars represent the 95% highest posterior density (HPD) intervals of the divergence times. Node labels in bold show the Bayesian posterior probability (PP) values for the major clades. All specimens in the blue clade originated from Indonesia (apart from JR27, which has largely unknown 'Calcutta?' label) and are clearly divergent from the Bhutanese sample.
Figure 1 in Recent mitochondrial lineage extinction in the critically endangered Javan rhinoceros
Figure 1. Map of Javan rhino distribution in Southeast Asia, showing their approximate historical (yellow) and current (red) distribution (Fernando et al., 2006; Groves & Leslie, 2011). The green dots indicate the approximate locations of historical samples used in this study. Two samples with unknown locations are not mentioned on the plot (Table 1).
Figure 2 in Recent mitochondrial lineage extinction in the critically endangered Javan rhinoceros
Figure 2. Bayesian phylogeny of all available (N = 36) rhino whole mitochondrial DNA sequences (published + new sequences from this study). Two Equus mitochondrial DNA sequences were included as the outgroup. The blue bars represent the 95% highest posterior density (HPD) intervals of the divergence times. All branches within a species level have been collapsed to improve readability. Node labels in bold show the Bayesian posterior probability (PP) values for two nodes; the rest of the nodes had PP values of one. Geological time scale abbreviations: Q, Quaternary; Ple, Pleistocene; Pli, Pliocene. Extinct rhino lineages are shown with daggers after species names.
Distribution. Sulawesi and adjacent Is (Buton, Kabaena, Muna, Peleng, Lembeh, and on some of the Togian Is); thought to be extinct on Selayar I. Pigs have been widely domesticated through the Indonesian archipelago and beyond. This primarily involved the Eurasian Wild Pig (S. scrofa), but also S. celebensis, the only other species of pig successfully domesticated. Mitochondrial DNA studies of the dispersion of these domesticated forms agree on three major dispersal events, two involving S. scrofa and one S. celebensis. Evidence supports an early human-mediated translocation of S. celebensis to Flores and Timor and two later, separate human-mediated dispersals of domestic pig through islands of SE Asia into Oceania. In addition to Flores and Timor, S. celebensis is also thought to occur in its domesticated form on Halmahera, Lendu, Roti, and Savur Is, and even on Simeulue and Nias Is to the W of Sumatra and far from its island of origin, Sulawesi. In the Moluccas, and possibly elsewhere in this region, introduced S. celebensis are thought to have hybridized with other introduced pigs of S. scrofa derivation, and apparent hybrids between these species are now reported to survive on a number of islands, including Salawatti, Great Kei, Dobu, Seram, Ambon, Bacan, Ternate, Morotai, and New Guinea. It is also reported that in the 19" century the sows of domestic pigs in Sulawesi frequently mated with wild animals, after which they returned to their villages. in Suidae
Distribution. Sulawesi and adjacent Is (Buton, Kabaena, Muna, Peleng, Lembeh, and on some of the Togian Is); thought to be extinct on Selayar I. Pigs have been widely domesticated through the Indonesian archipelago and beyond. This primarily involved the Eurasian Wild Pig (S. scrofa), but also S. celebensis, the only other species of pig successfully domesticated. Mitochondrial DNA studies of the dispersion of these domesticated forms agree on three major dispersal events, two involving S. scrofa and one S. celebensis. Evidence supports an early human-mediated translocation of S. celebensis to Flores and Timor and two later, separate human-mediated dispersals of domestic pig through islands of SE Asia into Oceania. In addition to Flores and Timor, S. celebensis is also thought to occur in its domesticated form on Halmahera, Lendu, Roti, and Savur Is, and even on Simeulue and Nias Is to the W of Sumatra and far from its island of origin, Sulawesi. In the Moluccas, and possibly elsewhere in this region, introduced S. celebensis are thought to have hybridized with other introduced pigs of S. scrofa derivation, and apparent hybrids between these species are now reported to survive on a number of islands, including Salawatti, Great Kei, Dobu, Seram, Ambon, Bacan, Ternate, Morotai, and New Guinea. It is also reported that in the 19" century the sows of domestic pigs in Sulawesi frequently mated with wild animals, after which they returned to their villages.
Distribution. Palawan and associated Is (Calauit, Busuanga, Bacbac, Coron, Marily, Culion & Dumaran, Linapacan in the N, and Bugsuk, Balabac & Ramos in the S). Probably now extinct in Bulalacao. in Suidae
Distribution. Palawan and associated Is (Calauit, Busuanga, Bacbac, Coron, Marily, Culion & Dumaran, Linapacan in the N, and Bugsuk, Balabac & Ramos in the S). Probably now extinct in Bulalacao.
Subspecies and Distribution. H.m.meinertzhageniThomas,1904—EDRCongo,Rwanda,Burundi,Uganda,Kenya,SSudan,andEthiopia.IthasnotreliablybeenrecordedfromTanzania. H.m.woriensisBouet&Neuville,1930—discontinuouspresenceinGuinea,SierraLeone(?),Liberia,IvoryCoast,andGhana;possiblyalsoinGuineaBissau,andTogo. H. m. rimator Thomas, 1906 — SE Nigeria, W & SE Cameroon, Central African Republic, Gabon, Equatorial Guinea (extinct?), N Republic of the Congo, and N DR Congo. in Suidae
Subspecies and Distribution. H.m.meinertzhageniThomas,1904—EDRCongo,Rwanda,Burundi,Uganda,Kenya,SSudan,andEthiopia.IthasnotreliablybeenrecordedfromTanzania. H.m.woriensisBouet&Neuville,1930—discontinuouspresenceinGuinea,SierraLeone(?),Liberia,IvoryCoast,andGhana;possiblyalsoinGuineaBissau,andTogo. H. m. rimator Thomas, 1906 — SE Nigeria, W & SE Cameroon, Central African Republic, Gabon, Equatorial Guinea (extinct?), N Republic of the Congo, and N DR Congo.
Subspecies and Distribution. D.s.sumatrensisFischer,1814—SumatraandPeninsularMalaysia. D.s.harrissoniGroves,1965—Borneo. D. s. lasiotis Buckland, 1872 — South-east Asia (could be extinct). in Rhinocerotidae
Subspecies and Distribution. D.s.sumatrensisFischer,1814—SumatraandPeninsularMalaysia. D.s.harrissoniGroves,1965—Borneo. D. s. lasiotis Buckland, 1872 — South-east Asia (could be extinct).
Subspecies and Distribution. C.s.simumBurchell,1817—SEAngola,NENamibia,Botswana,Zimbabwe,SMozambique,Swaziland,SouthAfrica,andperhapsformerlyinextremeSWZambia. C. s. cottoni Lydekker, 1908 — historically present in S Chad, Central African Republic, S Sudan, NE DR Congo, and Uganda; last individuals occurred in DR Congo, but possibly extinct in the wild. The "Southern White Rhino," race simum, has been introduced into Kenya, Uganda, and Zambia. Especially vague range map for conservation reasons. in Rhinocerotidae
Subspecies and Distribution. C.s.simumBurchell,1817—SEAngola,NENamibia,Botswana,Zimbabwe,SMozambique,Swaziland,SouthAfrica,andperhapsformerlyinextremeSWZambia. C. s. cottoni Lydekker, 1908 — historically present in S Chad, Central African Republic, S Sudan, NE DR Congo, and Uganda; last individuals occurred in DR Congo, but possibly extinct in the wild. The "Southern White Rhino," race simum, has been introduced into Kenya, Uganda, and Zambia. Especially vague range map for conservation reasons.
Subspecies and Distribution. D.b.bicornisLinnaeus,1758—Namibia,W&SESouthAfrica. D.b.longipesZukowsky,1949—historicallyinNigeria,Cameroon,Chad,Sudan,andCentralAfricanRepublic(couldbeextinct). D. b. michaeli Zukowsky, 1965 — Kenya, Rwanda (could be extinct by now), and N Tanzania; historically also in Sudan, Ethiopia, and Uganda. D. b. minor Drummond, 1876 — C Tanzania, Zambia, Zimbabwe, Malawi, Botswana, and Mozambique (possibly extinct), to N and CE South Africa. Especially vague range map for conservation reasons. in Rhinocerotidae
Subspecies and Distribution. D.b.bicornisLinnaeus,1758—Namibia,W&SESouthAfrica. D.b.longipesZukowsky,1949—historicallyinNigeria,Cameroon,Chad,Sudan,andCentralAfricanRepublic(couldbeextinct). D. b. michaeli Zukowsky, 1965 — Kenya, Rwanda (could be extinct by now), and N Tanzania; historically also in Sudan, Ethiopia, and Uganda. D. b. minor Drummond, 1876 — C Tanzania, Zambia, Zimbabwe, Malawi, Botswana, and Mozambique (possibly extinct), to N and CE South Africa. Especially vague range map for conservation reasons.
Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow
<p><span>Steller's sea cow, an extinct sirenian and one of the largest Quaternary mammals, was described by Georg Steller in 1741 and eradicated by humans within 27 years. Here, we complement Steller's descriptions with paleogenomic data from 12 individuals. We identified convergent evolution between Steller's sea cow and cetaceans but not extant sirenians, suggesting a role of several genes in adaptation to cold environments. Among these are inactivations of lipoxygenase genes, which in humans and mouse models cause ichthyosis – a skin disease characterized by a thick, hyperkeratotic epidermis that recapitulates Steller's sea cows' reportedly bark-like skin. Finally, we found that Steller's sea cows' abundance was continuously declining for tens of thousands of years prior to their description, implying that environmental changes also contributed to their extinction.</span></p>
Distribution. Ryukyu Is (Amami-Oshima, Tokunoshima, Okinoerabujima, Okinawajima, Kumejima, Ishigakijima, and Iriomotejima). There is a record of one individual captured on Jeju I (South Korea) regarded as a vagrant as well as an old record from Kii Peninsula (Honshu), but it now to be extinct there. in Miniopteridae
Distribution. Ryukyu Is (Amami-Oshima, Tokunoshima, Okinoerabujima, Okinawajima, Kumejima, Ishigakijima, and Iriomotejima). There is a record of one individual captured on Jeju I (South Korea) regarded as a vagrant as well as an old record from Kii Peninsula (Honshu), but it now to be extinct there.
Data from: The fifth review of Birds of Conservation Concern in the United Kingdom, Channel Islands and Isle of Man and second IUCN Red List assessment of extinction risk of birds for Great Britain
<p>The fifth review of <i>Birds of Conservation Concern</i> (<i>BoCC5</i>) in the UK, Channel Islands and Isle of Man assessed and assigned 245 species to updated Red, Amber and Green lists of conservation concern and showed a continuing decline in the status of our bird populations. In total, 70 species (29% of those assessed) are now on the Red list, up from 36 species in the first review in 1996. Since the last review, in 2015, Golden Oriole <i>Oriolus oriolus</i> has been lost as a breeding species. Eleven species have been moved to the Red list, while only six species moved from Red to Amber. Newly Red-listed species include Common Swift <i>Apus apus</i>, Common House Martin <i>Delichon urbicum</i>, Greenfinch <i>Chloris chloris</i> and the globally threatened Leach's Storm-petrel <i>Hydrobates leucorhous</i>. There has been no improvement in the overall status of species associated with farmland and upland, or Afro-Palearctic migrants; indeed, more such species have been Red-listed. Concerns over the status of our wintering wildfowl and wader populations have also increased. As a direct result of targeted conservation action, White-tailed Eagle <i>Haliaeetus albicilla</i> moves from Red to Amber.</p> <p>We also present a review of the separate, and distinct, second IUCN Regional Red List assessment of extinction risk for Great Britain, which show that 46% of 235 regularly occurring species, and 43% of 285 separate breeding and non-breeding populations, are assessed as being threatened with extinction from Great Britain.</p>
Figure 10 in Taxonomy, phylogeny, and diversity of the extinct Lesser Antillean rice rats (Sigmodontinae: Oryzomyini), with description of a new genus and species
Figure 10. Maxillary and mandibular tooth rows and cranial elements of Pennatomys nivalis gen. et sp. nov. A–C, maxillary tooth rows. A, FLMNH-EAP 05270001 (St. Eustatius). B, NHM M 82456 (Nevis) (reversed for comparison). C, FLMNH-EAP 05270002 (St. Eustatius). D–G, mandibular tooth rows. D, NHM M 82452 (holotype: Nevis). E, NHM M 82460 (Nevis). F, FLMNH-EAP 05270003 (St. Eustatius) (reversed for comparison). G, FLMNH-EAP 05270004 (St. Eustatius) (reversed for comparison). H–I, maxilla, FLMNH-EAP 05270002 (St. Eustatius). J, mandible, labial view, FLMNH-EAP 05270003 (St. Eustatius). K, paired frontals, FLMNH-EAP 05270005 (St. Eustatius). Scale bars: 1 mm.
Figure 11 in Taxonomy, phylogeny, and diversity of the extinct Lesser Antillean rice rats (Sigmodontinae: Oryzomyini), with description of a new genus and species
Figure 11. Phylogenetic relationships of West Indian oryzomyines. Consensus cladogram of four most-parsimonious trees (tree length, L = 1245; consistency index, CI = 0.37; retention index, RI = 0.64) of combined molecular (Irbp) and morphological characters. Jackknife (> 50%) and Bremer (> 1) nodal support indices are shown above and below branches, respectively. Clades A, B, C, and D are the same as those recovered by Weksler (2006). Out-groups include Peromyscus maniculatus (Neotominae), Nyctomys sumichrasti (Tylomyinae), and Delomys sublineatus, Thomasomys baeops, and Wiedomys pyrrhorhinos (Sigmodontinae). Oryzomyine generic taxonomy follows that of Weksler et al. (2006).
Figure 8 in Taxonomy, phylogeny, and diversity of the extinct Lesser Antillean rice rats (Sigmodontinae: Oryzomyini), with description of a new genus and species
Figure 8. Dorsal, lateral, and ventral views of Oligoryzomys victus skin (NHM 97.12.26.1). Scale bar: 2 cm.
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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.
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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.
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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.