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19 results for “species collapse”
Data from: Is a community state reachable, and why?, and Coexistence and collapse: an experimental investigation of the persistent communities of a protist species pool
<p>Deterministic models have difficulties to take into account stochasticity during community assembly. As a tool to circumvent this problem, we present a qualitative discreteevent model, where consequences of interspecific interactions are described as rules. This model provides a map of all possible future dynamics for a given system, which allows to exhaustively describe the possible pathways during an assembly process. Such a description does not rely on species traits details and is insensitive to stochastic effects. This allows to show that subsets of species are sometimes impossible to reach starting from larger sets of species, and therefore to question the reachability of community states during the system’s dynamics. Applying the model to an experimental dataset studying the collapse of protist communities, we obtain a very good theory-experiment agreement. We finally discuss what the notion of reachability can bring to community assembly.</p>
On the impermanence of species: The collapse of genetic incompatibilities in hybridizing populations
<p>Species pairs often become genetically incompatible during divergence, which is an important source of reproductive isolation. An idealized picture is often painted where incompatibility alleles accumulate and fix between diverging species. However, recent studies have shown both that incompatibilities can collapse with ongoing hybridization, and that incompatibility loci can be polymorphic within species. This paper suggests some general rules for the behavior of incompatibilities under hybridization. In particular, we argue that redundancy of genetic pathways can strongly affect the dynamics of intrinsic incompatibilities. Since fitness in genetically redundant systems is unaffected by introducing a few foreign alleles, higher redundancy decreases the stability of incompatibilities during hybridization, but also increases tolerance of incompatibility polymorphism within species. We use simulations and theories to show that this principle leads to two types of collapse: in redundant systems, exemplified by classical Dobzhansky-Muller incompatibilities, collapse is continuous and approaches a quasi-neutral polymorphism between broadly sympatric species, often as a result of isolation-by-distance. In non-redundant systems, exemplified by coevolution among genetic elements, incompatibilities are often stable, but can collapse abruptly with spatial traveling waves. As both types are common, the proposed principle may be useful in understanding the abundance of genetic incompatibilities in natural populations.</p>
FIGURE 8 in Late Pleistocene-Holocene amphibians from Okinawajima Island in the Ryukyu Archipelago, Japan: Reconfirmed faunal endemicity and the Holocene range collapse of forest-dwelling species
FIGURE 8. Fossils referred to Echinotriton andersoni. 1–4, postatlantal precaudal vertebra (one of 290 registered as RUMF-GF-04052) in anterior (1), left lateral (2), dorsal (3), and ventral (4) views; 5 and 6, atlas (one of 11 registered as RUMF-GF-04051) in anterior (5) and left lateral (6) views; 7, parietal-prootic-exoccipital (RUMF-GF-04047) in dorsal view; 8, right maxilla (one of 30 registered as RUMF-GF-04045) in lateral view; 9, right quadrate (one of five registered as RUMF-GF-04049) in dorsal view; 10, right dentary (one of 70 registered as RUMF-GF-04050) in medial view; 11, right rib (one of 181 registered as RUMF-GF-04053) in posterior view; 12, right humerus (one of 144 registered as RUMF-GF-04054) in lateral view; and 13, right femur (one of 163 registered as RUMF-GF-04055) in posterior view. Abbreviations: tro, trochanter; the others are the same as Figure 7. Scale bars equal 1 mm.
FIGURE 6 in Late Pleistocene-Holocene amphibians from Okinawajima Island in the Ryukyu Archipelago, Japan: Reconfirmed faunal endemicity and the Holocene range collapse of forest-dwelling species
FIGURE 6. Fossils referred to Buergeria japonica (1–4) and Rhacophorus viridis viridis (5–11). 1–3, right female humerus lacking the proximal part (YMHF-MA 010) in ventral (1), medial (2), and dorsal (3) views; 4, left ilium lacking most part of the crista dorsalis (RUMF-GF-04024) in lateral view; 5–7, left female humerus (one of seven registered as RUMF-GF-04025) in ventral (5), medial (6), and dorsal (7) views; 8–10, left male humerus (RUMF-GF-04027) in ventral (8), medial (9), and dorsal (10) views; and 11, pelvic girdle (fused right and left ilia [lacking anterior parts] with the ischium: RUMF-GF-04029) in left lateral view. Abbreviations: pre.acet, preacetabular zone; the others are the same as Figure 3. Arrows indicate the proximal ends of the crista paraventralis. Scale bars equal 1 mm.
FIGURE 7 in Late Pleistocene-Holocene amphibians from Okinawajima Island in the Ryukyu Archipelago, Japan: Reconfirmed faunal endemicity and the Holocene range collapse of forest-dwelling species
FIGURE 7. Fossils referred to Cynops ensicauda. 1–4, postatlantal precaudal vertebra (one of 108 registered as RUMF-GF-04039) in anterior (1), left lateral (2), dorsal (3), and ventral (4) views; 5 and 6, atlas (one of five registered as RUMF-GF-04038) in anterior (5) and left lateral (6) views; 7, parietal-prootic-exoccipital (RUMF-GF-04033) in dorsal view; 8, right maxilla (one of three registered as RUMF-GF-04032) in lateral view; 9, right dentary (one of nine registered as RUMF-GF-04037) in medial view; 10, right rib (one of 25 registered as RUMF-GF-04040) in posterior view; 11, right humerus (one of 85 registered as RUMF-GF-04041) in lateral view; and 12, right femur (one of 92 registered as RUMF-GF-04042) in posterior view. Abbreviations: con, condyle; diap, diapophyses; epi.pr, epipleural processes; neu.sp, neural spine; n.prep, notch for prearticular; parap, parapophyses; pos.pr, posterior process; subd.d, subdental ditch; zygap, zygapophyses. The arrow in 12 indicates the concavity (see text). Scale bars equal 1 mm.
FIGURE 2 in Late Pleistocene-Holocene amphibians from Okinawajima Island in the Ryukyu Archipelago, Japan: Reconfirmed faunal endemicity and the Holocene range collapse of forest-dwelling species
FIGURE 2. Photograph of the Sashiki Fissure (left) and schematic figure showing the structure of the fissure (right). In the right figure, broken lines represent the outline of the fissure behind rock, shaded areas represent studied sediments, and open circles represent the locations of the dating samples.
FIGURE 3 in Late Pleistocene-Holocene amphibians from Okinawajima Island in the Ryukyu Archipelago, Japan: Reconfirmed faunal endemicity and the Holocene range collapse of forest-dwelling species
FIGURE 3. Fossils referred to Limnonectes namiyei (1–4) and Babina holsti (5–11). 1–3, left female humerus lacking the proximal and distal parts and the crista ventralis (YMHF-MA 001) in ventral (1), medial (2) and dorsal (3) views; 4, left ilium lacking the anterior part (RUMF-GF-04000) in lateral view; 5–7, right female humerus (one of six registered as RUMF-GF-04003) in ventral (5), medial (6) and dorsal (7) views; 8–10, right male humerus lacking the proximal part (one of two registered as RUMF-GF-04004) in ventral (8), medial (9), and dorsal (10) views; and 11, right ilium lacking the anterior part (one of nine registered as RUMF-GF-04005) in lateral view. Abbreviations: acet, acetabulum; acet.m, acetabular margin; cr.dors, crista dorsalis; cr.lat, crista lateralis; cr.med, crista medialis; cr.par, crista paraventralis; cr.ven, crista ventralis; e.cap, eminentia capitata; ep.rad, epicondylus radialis; ep.ul, epicondylus ulnaris; fo.div, fossula dividens; il.sh, ilial shaft; ol.sc, olecranon scar; p.asc, pars ascendens; stm, spina tuberculi medialis; supr.fo, supracetabular fossa; tub.sup, tuber superior. Scale bars equal 5 mm.
FIGURE 1 in Late Pleistocene-Holocene amphibians from Okinawajima Island in the Ryukyu Archipelago, Japan: Reconfirmed faunal endemicity and the Holocene range collapse of forest-dwelling species
FIGURE 1. Maps of the Ryukyu Archipelago (1, 2) and Okinawajima Island (3). The map of Okinawajima shows topography, distribution of the Pleistocene limestone, and study sites. Geological data were obtained from Kizaki (1985).
FIGURE 4 in Late Pleistocene-Holocene amphibians from Okinawajima Island in the Ryukyu Archipelago, Japan: Reconfirmed faunal endemicity and the Holocene range collapse of forest-dwelling species
FIGURE 4. Fossils referred to Odorrana ishikawae (1–7) and Odorrana narina (8–14), 1–3, right female humerus (one of 10 registered as RUMF-GF-04009) in ventral (1), medial (2), and dorsal (3) views; 4–6, right male humerus (one of three registered as RUMF-GF-04010) in ventral (4), medial (5), and dorsal (6) views; 7, right ilium lacking the anterior part with part of the ischium (one of five registered as RUMF-GF-04011) in lateral view; 8–10, right female humerus (one of eight registered as RUMF-GF-04014) in ventral (8), medial (9), and dorsal (10) views; 11–13, right male humerus lacking the proximal part of the shaft and the distal part of the epicondylus ulnaris (RUMF-GF-04015) in ventral (11), medial (12), and dorsal (13) views; and 14, pelvic girdle (fused right and left ilia [lacking anterior parts] with the ischium and the pubis: RUMF-GF-04016) in right lateral view. Abbreviations are the same as Figure 3. Arrows indicate the proximal ends of the crista paraventralis. Scale bars equal 5 mm.
FIGURE 5 in Late Pleistocene-Holocene amphibians from Okinawajima Island in the Ryukyu Archipelago, Japan: Reconfirmed faunal endemicity and the Holocene range collapse of forest-dwelling species
FIGURE 5. Fossils referred to Rana ulma (1–7) and Microhyla okinavensis (8). 1–3, right female humerus (one of 176 registered as RUMF-GF-04019) in ventral (1), medial (2), and dorsal (3) views; 4–6, right male humerus (one of 87 registered as RUMF-GF-04020) in ventral (4), medial (5), and dorsal (6) views; 7, right ilium (one of 93 registered as RUMF-GF-04021) in lateral view; and 8, right ilium (one of two registered as RUMF-GF-04023) in lateral view. Abbreviations are the same as Figure 3. Arrows indicate the proximal ends of the crista paraventralis. Scale bars equal 1 mm.
On the impermanence of species: The collapse of genetic incompatibilities in hybridizing populations
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Data from: Population collapse of habitat-forming species in the Mediterranean: a long-term study of gorgonian populations affected by recurrent marine heatwaves
<p><span><span><span><span><span><span><span><span><span><span><span>Understanding the resilience of temperate reefs to climate change requires exploring the recovery capacity of their habitat-forming species from recurrent marine heatwaves (MHWs). Here, we show that, in a Mediterranean highly enforced Marine Protected Area established more than 40 years ago, habitat-forming octocoral populations that were firstly affected by a severe MHW in 2003 have not recovered after 15 years. Contrarily, they have followed collapse trajectories that have brought them to the brink of local ecological extinction. Since 2003, impacted populations of the red gorgonian <i>Paramuricea clavata</i> (Risso, 1826) and the red coral <i>Corallium rubrum</i> (Linnaeus, 1758) have followed different trends in terms of size structure, but a similar progressive reduction in density and biomass. Concurrently, recurrent MHWs were observed in the area during the 2003-2018 study period, which may have hindered populations recovery. The studied octocorals play a unique habitat-forming role in the coralligenous assemblages (i.e., reefs endemic to the Mediterranean Sea home to approximately 10% of its species). Therefore, our results underpin the great risk that recurrent MHWs pose for the long-term integrity and functioning of these emblematic temperate reefs.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Forest hoverfly community collapse: abundance and species richness drop over four decades
<p>To study abundance trends in hoverflies (Diptera: Syrphidae) in a Dutch forest, we monitored hoverflies over the course of 4 decades. Within the ‘Boeschoten’ forest the same permanent route of approximately 3 kilometres was inspected for the presence of hoverflies in the second half of the morning (10:00-13:00), for a duration of approximately 2 hours. The forest was included up to 30 meters from the route to obtain a complete inventory of the ecosystem; a complete list of all present hoverflies was aimed for each time. Monitoring was done only on sunny days, independent from temperature. All observed specimens have been counted and collected with an insect net, species and sex identified in the field, or preserved for identification later on (with e.g. Barendregt 1978; van der Goot 1981; Bot & van de Meutter 2019; Speight et al. 2020). While monitoring started in 1974, it was only from 1979 onwards that complete species lists were kept, and from 1982 onwards that the number of observed individuals per species was recorded. Boeschoten is an (extensively used) agricultural enclave within large mixed deciduous-coniferous forests in the center of The Netherlands, 40-50 m a.m.s., west of the village of Garderen (52º13'24"N, 5º40'31"E). The sandy soil is very dry and open water is only available in some small pools. The selected forest sections (ca. 20 ha) are partly dominated by <em>Quercus</em> for hundreds of years, partly former heathlands planted with <em>Pinus </em>and <em>Pseudotsuga </em>in the period 1900-1950. Locally, other tree species (<em>Fagus, Larix</em>) dominate; in the shrub layer <em>Sorbus, Amelanchier,</em> and <em>Rhamnus</em> are important. In the ground layer <em>Vaccinium myrtillus </em>dominates at many locations, next to some <em>Rubus </em>along paths. The forest did not change for at least 60 years in land use or management: only the trees matured further (no new planting) and in the ground layer the vegetation changed in some species after the period of intense acid rain around 1985, when <em>Galium saxatile </em>and <em>Deschampsia flexuosa </em>decreased and <em>Rubus </em>increased in abundance. In the surroundings of Boeschoten there are some smaller arable fields; 5 km to the south and west there is intensive livestock farming. </p> <p>The file ‘counts.csv’ contains the counts per species per monitoring day. The file contains the following variables:</p> <p>date: date of monitoring (in the second half of the morning)</p> <p>Baccha.elongata and next 104 variables:</p> <p> number of observed individuals of a particular species per day of monitoring. Species lists were not complete in 1974-1978, hence the NAs when a species was not recorded in that period. Systematic counting started in 1982. Presence before 1982 is indicated with a ‘1’, meaning ‘at least 1’.</p> <p>observer: initials of the person responsible for a day of monitoring. AB = Aat Barendregt, TZ = Theo Zeegers, WS = Wouter van Steenis.</p> <p>temp: mean temperature in degrees Celsius between 10:00 and 13:00 (i.e. during the general time of monitoring) on the day of monitoring, based on hourly data from KNMI weather station Deelen.</p> <p>sun: mean proportion of time with direct sunlight between 10:00 and 13:00 (i.e. during the general time of monitoring) at the day of monitoring, based on hourly data from KNMI weather station Deelen.</p> <p>precip: total amount of precipitation in millimeters between 10:00 and 13:00 (i.e. during the general time of monitoring) at the day of monitoring, based on hourly data from KNMI weather station Deelen.</p> <p>relhumid: mean relative humidity (percentage) between 10:00 and 13:00 (i.e. during the general time of monitoring) at the day of monitoring, based on hourly data from KNMI weather station Deelen.</p> <p>T30d: mean temperature in degrees Celsius in the 30 days preceding the day of monitoring, based on daily data from KNMI weather station Deelen.</p> <p>S30d: mean proportion of time with direct sunlight in the 30 days preceding the day of monitoring, based on daily data from KNMI weather station Deelen.</p> <p>P30d: mean amount of precipitation (in millimeters) per day in the 30 days preceding the day of monitoring, based on daily data from KNMI weather station Deelen.</p> <p>Tapr: mean temperature in April of the year of monitoring, based on daily data from KNMI weather station Deelen.</p> <p>Sapr: mean proportion of time with direct sunlight in April of the year of monitoring, based on daily data from KNMI weather station Deelen.</p> <p>Papr: mean amount of precipitation (in millimeters) per day in April of the year of monitoring, based on daily data from KNMI weather station Deelen.</p> <p>seasonScore: day-of-the-year-specific GAM prediction of the total abundance of hoverflies, rescaled between 0 and 1</p>
Figure 4. ITS1 gene tree. Terminal tips have been collapsed for visualization purposes. Nodes are labelled with ultrafast bootstrap support. A in Hidden in the hills: phylogeny of the freshwater mussel genus Alasmidonta (Bivalvia: Unionidae) and description of a new species
Figure 4. ITS1 gene tree. Terminal tips have been collapsed for visualization purposes. Nodes are labelled with ultrafast bootstrap support. A full tree is available in the Supporting Information (File S1). The scale is in substitutions per site.
Data from: Population collapse of habitat-forming species in the Mediterranean: a long-term study of gorgonian populations affected by recurrent marine heatwaves
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Data from: Species collapse via hybridization in Darwin's tree finches
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Data from: Animal personality in a foundation species drives community divergence and collapse in the wild
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Data from: Hybridization, species collapse, and species reemergence after disturbance to premating mechanisms of reproductive isolation
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Population collapse of habitat-forming species in the Mediterranean: a long-term study of gorgonian populations affected by recurrent marine heatwaves
<p>This dataset contains the data and code associated to the manuscript "Population collapse of habitat-forming species in the Mediterranean: a long-term study of gorgonian populations affected by recurrent marine heatwaves."</p> <p>Understanding the resilience of temperate reefs against the increasingly frequent marine heatwaves (MHWs) requires exploring the recovery capacity of their key habitat-forming species. Here, we show that, in a Mediterranean highly enforced Marine Protected Area established more than 40 years ago, the habitat-forming octocoral populations that were affected by the 2003-MHW have not recovered after 15 years. Contrarily, they have followed collapse trajectories that have brought them to the brink of local ecological extinction. Since 2003, impacted populations of the red gorgonian Paramuricea clavata (Risso, 1826) and the red coral Corallium rubrum (Linnaeus, 1758) have followed different trends in terms of size structure, but a similar progressive reduction in density and biomass. Concurrently, recurrent MHWs were observed in the area during the 2003-2018 study period, what may have hindered any chance of populations recovery. Since Mediterranean habitat-forming octocorals play a unique role in the functioning of coralligenous assemblages, our results underpin the great risk that recurrent MHWs pose for the long-term integrity and functioning of these emblematic temperate reefs.</p>
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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)
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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.