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Fig. 6 in Redescription of extinct New Zealand earthworm: (Schmarda, 1861) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae)

Fig. 6. Spermatheca in 8lhs in setal "a" line, with ventral nerve (ditto).

Fig. 2 in Extinction of Japan's first formally described earthworm (Horst, 1883) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae).

Fig. 2. von Siebold ca. 1820s (nl.wikipedia.org/wiki/Philipp_ Franz_von_Siebold CC-BY).

Fig. 1 in Redescription of extinct New Zealand earthworm: (Schmarda, 1861) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae)

Fig. 1. Schmarda's original figure (from Blakemore 2000b; fig. 105; 2012: fig. 12).

Fig. 4 in Redescription of extinct New Zealand earthworm: (Schmarda, 1861) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae)

Fig. 4. Deteriorating clitellum and ventrum pinned at 12–13 (ditto).

opencc-zeroMay 2024View details →

Data for: Reliable biogeography requires fossils: Insights from a new species-level phylogeny of extinct and living carnivores

A central objective of historical biogeography is to understand where clades originated and how they moved across space and over time. However, given the dynamic history of ecosystem changes in response to climate change and geologic events, the manifold long-distance dispersals over evolutionary timescales, and regional and global extinctions, it remains uncertain how reliable inferences based solely on extant taxa can be achieved. Using a novel species-level phylogeny of all known extant and extinct species of the mammalian order Carnivora and related extinct groups, we show that far more precise and accurate ancestral areas can be estimated by fully integrating extinct species into the analyses, rather than solely relying on extant species or identifying ancestral areas only based on the geography of the oldest fossils. Through a series of simulations, we further show that this conclusion is robust under realistic scenarios in which the unknown extinct taxa represent a biased subset of all extinct species. Our results highlight the importance of integrating fossil taxa into a phylogenetic framework to further improve our understanding of historical biogeography and reveal the dynamic dispersal and diversification history of carnivores.

opencc-zeroMay 2024View details →

The counteracting effects of human-driven speciation and extinction on mammal species richness and phylogenetic diversity

Human activities are causing massive increases in extinction rates, but may also lead to drastic increases in speciation rates – for example following the human-mediated spread of species to otherwise unreachable landmasses. The long-term net anthropogenic effects on biodiversity, therefore, remain uncertain. The aim of this paper is to assess the combined anthropogenic effects of extinctions and speciations on biodiversity over geological time scales. We estimate known anthropogenic and predicted future extinctions based on Red List categories from the International Union for Conservation of Nature. We infer potential anthropogenic speciations assuming that all introductions to isolated landmasses will over time evolve into distinct species. We then estimate changes in regional and global species richness and phylogenetic diversity due to these extinctions and speciations. We show that if all species introduced into new landmasses develop into new species, the number of anthropogenic speciation and extinctions eventually become similar. However, even after accounting for an anthropogenic increase in speciation, our estimates suggest recovery times for phylogenetic diversity of several million years. Our results highlight that while humans are causing drastic biodiversity losses, human-driven speciation could eventually counterbalance these losses in species numbers, while phylogenetic diversity at least within our simulation scenarios would remain permanently reduced. This conclusion, however, requires our pressures on biodiversity to cease soon and requires us to consider geological timescales rather than changes over this century.

opencc-by-4.0Feb 2024View details →

Unveiling the Milky Way dust extinction curve in 3D

We measure the extinction curves of 220 million stars with Gaia XP spectra and near-infrared photometry from 2MASS and WISE. We use a data-driven model that is developed from <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524.1855Z/abstract">Zhang et al. 2023</a>, with variable extinction curves, to determine stellar parameters and extinction curves simultaneously. For full details of our method, see our corresponding paper*. Here, we provide the resulting catalog of stellar parameters, our trained stellar model, and a few Python scripts that demonstrate how to interact with the catalog and model. See the <code>README.md</code> for more information. * Link of the paper will be posted here once available. Update on 05.04.2024: Uploaded the reference table <code>xi_Rv_ext_curve.h5</code>,  which was missing. Updated the script <code>plot_ext_curve.py</code> for a larger range of R(V) . Update on 17.05.2024: Uploaded preliminary maps in <code>Rv_map_new.h5</code>; Uploaded the script <code>example_query.py</code> for examples of querying the map, as well as code for generating sky-view and birds'-eye view pictures.

opencc-zeroJun 2024View details →

A global map of species at risk of extinction due to natural hazards

An often-overlooked question of the biodiversity crisis is how natural hazards contribute to species extinction risk. To address this issue, we explored how four natural hazards: earthquakes, hurricanes, tsunamis, and volcanoes, overlapped with the distribution ranges of amphibians, birds, mammals, and reptiles that have either narrow distributions or populations with few mature individuals. To assess which species are at risk from these natural hazards, we combined the frequency and magnitude of each natural hazard to estimate a probability of impact. We considered species at risk if they overlapped with regions where any of the four natural hazards historically occurred (n = 3,722). Those species with at least a quarter of their range subjected to a high probability of impact were considered at high risk (n = 2,001) of extinction due to natural hazards. In total, 834 reptiles, 617 amphibians, 302 birds, and 248 mammals were at high risk and they were mainly distributed on islands and in the tropics. Hurricanes (n = 983) and earthquakes (n = 868) affected the most species, while tsunamis (n = 272), and volcanoes (n = 171) affected considerably fewer. The region with the highest number of species at high risk was the Pacific Ring of Fire, especially due to volcanoes, earthquakes and tsunamis, while hurricane-related high-risk species were concentrated in the Caribbean Sea, Gulf of Mexico, and northwestern Pacific Ocean. Our study provides important information regarding the species at risk due to natural hazards and can help guide conservation attention and efforts to safeguard their survival.

opencc-by-4.0May 2024View details →

All-sky three-dimensional dust density and extinction Maps of the Milky Way out to 2.8 kpc

Three-dimensional dust density maps are crucial for understanding the structure of the interstellar medium of the Milky Way and the processes that shape it. However, constructing these maps requires large datasets and the methods used to analyse them are computationally expensive and difficult to scale up. As a result it is has only recently become possible to map kiloparsec-scale regions of our Galaxy at parsec-scale grid sampling. We present all-sky three-dimensional dust density and extinction maps of the Milky Way out to 2.8~kpc in distance from the Sun using the fast and scalable Gaussian Process algorithm Dustribution. The sampling of the three-dimensional map is $l,b,d = 1^{\circ} \times1^{\circ} \times 1.7$~pc. The input extinction and distance catalogue contains 120 million stars with photometry and astrometry from Gaia DR2, 2MASS and AllWISE. This combines the strengths of optical and infrared data to probe deeper into the dusty regions of the Milky Way. We compare our maps with other published 3D dust maps. All maps quantitatively agree at the $0.001$~mag~pc$^{-1}$ scale with many qualitatively similar features, although each map also has its own features. We recover Galactic features previously identified in the literature. Moreover, we also see a large under-density that may correspond to an inter-arm or -spur gap towards the Galactic Centre.   Here we provide the full dataset generated from Dustribution covering the full sky out to 2.8 kpc. We provide the 3D dust extinction and density files as well the l,b,d coordinate grid that the data is presented in.    The data in each file is as follows: <ul> <li>lbdGrid_l_bounds.pkl.npy: The boundaries of the grid cells of the merged map in l (degrees). Numpy array of size 881.</li> <li>lbdGrid_b_bounds.pkl.npy: The boundaries of the grid cells of the merged map in b (degrees). Numpy array of size 273.</li> <li>lbdGrid_d_bounds.pkl.npy: The boundaries of the grid cells of the merged map in d (pc). Numpy array of size 1644.</li> <li>Density_Median_lbd.pkl.npy: The median of 100 density samples of the merged map (mag pc^-1). Treat this as the estimate of the density. Numpy array of size (880, 272, 1644)</li> <li>Density_16P_lbd.pkl.npy: The 16th percentile of the density of the merged map (mag pc^-1). Treat median-16p as the estimate of the lower uncertainty on the density. Numpy array of size (880, 272, 1644)</li> <li>Density_84P_lbd.pkl.npy: The 84th percentile of the density of the merged map (mag pc^-1). Treat 84p-median as the estimate of the upper uncertainty on the density. Numpy array of size (880, 272, 1644) </li> <li>Ext_Median_lbd.pkl.npy: The median of the integral of 100 sample maps at each cell in the merged map (mag). Treat this as the estimate of the extinction in each cell. Numpy array of size (880, 272, 1644). </li> <li>Ext_16P_lbd.pkl.npy: The 16th percentile of the integral of 100 sample maps at each cell in the merged map (mag). Treat median-16p as the estimate of the lower uncertainty on the extinction in each cell. Numpy array of size (880, 272, 1644)</li> <li>Ext_84P_lbd.pkl.npy: The 84th percentile of the integral of 100 sample maps at each cell in the merged map (mag). Treat 84p-median as the estimate of the upper uncertainty on the extinction in each cell. Numpy array of size (880, 272, 1644)</li> <li>read_and_plot.ipynb: a short jupyter notebook demonstrating how to read in the data files, with some quick examples of plotting them.</li> </ul>

opencc-by-4.0Feb 2017View details →

Fig. 1 in Morphological and molecular description of Ixodes woyliei n. sp. (Ixodidae) with consideration for co-extinction with its critically endangered marsupial host

Fig. 1 Locatcons of Bettongia penicillata populatcons where samples were obtacned

opencc-zeroJun 2024View details →

Data from: Elevated human impact on islands increases the introduction and extinction status of native insular reptiles

In the Anthropocene, the ranges of introduced species are expanding, while extinction-prone species are contracting. Introductions and extinctions are caused by how species respond to human impacts, but it is unknown why the ranges of some species expand and some contract. Here, we test whether this opposite response of human impact is due to introduced and extinction-prone species falling at opposite ends of geographic, evolutionary, or ecological trait continua. We constructed a database of native range maps, traits, phylogenetic relationships, and the introduction and extinction-prone status of squamate reptiles with ranges native to the Western Hemisphere. Across >3,000 snake and lizard species (88% of known native squamates), 142 had been introduced elsewhere and 483 were extinction-prone (i.e., vulnerable, endangered, critically endangered, extinct in the wild, extinct). To explain variation in status, we first tested if the same human-impacted regions in the Americas contained the native ranges of species of either status. Second, we tested for phylogenetic signal in species status. Finally, we tested the explanatory power of multiple trait continua. The native ranges of introduced and extinction-prone reptiles were clustered in island regions with high human impact vs. mainland regions with lower human impact. Phylogenetic signal was weak for status, but introduced and extinction-prone species were clustered in different clades. All geographic and ecological traits that explained each status supported the opposite ends hypothesis. Introduced species had larger, edgier ranges, while extinction-prone species had smaller, simpler ranges. Introduced species were mostly herbivorous/omnivorous, while extinction-prone species were mostly carnivorous. Introduced species produced larger clutches, while extinction-prone species had smaller body sizes. In the Anthropocene, the naive ranges of introduced and extinction-prone species are in the same human-impacted regions where trait continua, having opposite effects, determine whether species ranges expand or contract in the continuing face of global change.

opencc-zeroJul 2024View details →

Archival mitogenomes identify invasion by the Batrachochytrium dendrobatidis CAPE lineage caused an African amphibian extinction in the wild

Outbreaks of emerging infectious diseases are influenced by local biotic and abiotic factors, with host declines occurring when conditions favour the pathogen. Deterioration in the population of the microendemic Tanzanian Kihansi spray toad (Nectophrynoides asperginis) occurred after the construction of a hydropower dam, implicating habitat modification in this species decline. Population recovery followed habitat augmentation, however a subsequent outbreak of chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd) led to the spray toads extinction in the wild. We show using spatiotemporal surveillance and mitogenome assembly of Bd from archived toad mortalities that the outbreak was caused by invasion of the BdCAPE lineage and not the panzootic lineage BdGPL. Molecular dating reveals an emergence of BdCAPE across Southern Africa overlapping with the timing of the spray toads extinction. That our post-outbreak surveillance of co-occurring amphibian species in the Udzungwa Mountains shows widespread infection by BdCAPE yet no signs of ill-health or decline suggests these other species can tolerate Bd when environments are stable. We conclude that, despite transient success in mitigating the impact caused by dams' construction, invasion by BdCAPE caused the ultimate die-off that led to the extinction of the Kihansi spray toad.

opencc-by-4.0Jun 2015View details →

Fig. 2 in Short communications Extinct or not extinct: the case of the Chalcides ocellatus (Squamata: Scincidae) population from the Park of the ex Bourbonic Royal Palace of Portici (Naples, Italy)

Fig. 2 - Ranina sp. (MSNM i28047), "Serre di Rapolano" (Siena). (x 1.5).

opencc-by-4.0Jun 2015View details →

Fig. 2 in Short communications Extinct or not extinct: the case of the Chalcides ocellatus (Squamata: Scincidae) population from the Park of the ex Bourbonic Royal Palace of Portici (Naples, Italy)

Fig. 2 - Study site.

opencc-by-4.0Jun 2015View details →

Fig. 1 in Short communications Extinct or not extinct: the case of the Chalcides ocellatus (Squamata: Scincidae) population from the Park of the ex Bourbonic Royal Palace of Portici (Naples, Italy)

Fig. 1 - Adult specimen of Chalcides ocellatus recently found at Portici (Naples).

opencc-by-4.0Dec 2015View details →

Fig. 1 in Past, present and future of host‾parasite co-extinctions

Fig. 1. Cumulative number of documented species extinctions according to IUCN (2014).

Fig. 30 in Synopsis of the extinct Batrachia, Reptilia and Aves of North America

Fig. 30.

Fig. 33 in Synopsis of the extinct Batrachia, Reptilia and Aves of North America

Fig. 33.

Fig. 32 in Synopsis of the extinct Batrachia, Reptilia and Aves of North America

Fig. 32.

Fig.31 in Synopsis of the extinct Batrachia, Reptilia and Aves of North America

Fig.31.