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2,441 results for “Extinct”
The shape of phylogenies under phase-type distributed times to speciation and extinction
<p>Phylogenetic trees describe relationships between extant species, but beyond that their shape and their relative branch lengths can provide information on broader evolutionary processes of speciation and extinction. However, currently, many of the most widely used macro-evolutionary models make predictions about the shapes of phylogenetic trees that differ considerably from what is observed in empirical phylogenies. Here, we propose a flexible and biologically plausible macroevolutionary model for phylogenetic trees where times to speciation or extinction events are drawn from a Coxian phase-type (PH) distribution. First, we show that different choices of parameters in our model lead to a range of tree balances as measured by Aldous' $\beta$ statistic. In particular, we demonstrate that it is possible to find parameters that correspond well to empirical tree balance. Next, we provide a natural extension of the $\beta$ statistic to sets of trees. This extension produces less biased estimates of $\beta$ compared to using the median $\beta$ values from individual trees. Furthermore, we derive a likelihood expression for the probability of observing an edge-weighted tree under a model with speciation but no extinction. Finally, we illustrate the application of our model by performing both absolute and relative goodness-of-fit tests for two large empirical phylogenies (squamates and angiosperms) that compare models with Coxian PH distributed times to speciation with models that assume exponential or Weibull distributed waiting times. In our numerical analysis, we found that, in most cases, models assuming a Coxian PH distribution provided the best fit.</p>
Supplementary material: Does functional redundancy determine the ecological severity of a mass extinction event?
<p>Many authors have noted the apparent "decoupling" of the taxonomic and ecological severity of mass extinction events, with no widely accepted mechanistic explanation for this pattern having been offered. Here we test between two key factors that potentially influence ecological severity: biosphere entropy (a measure of functional redundancy), and the degree of functional selectivity (in terms of deviation from a pattern of random extinction with respect to functional entities). While theoretical simulations suggest that the Shannon entropy of a given community prior to an extinction event determines the expected outcome following a perturbation of a given magnitude, actual variation in Shannon entropy between major extinction intervals is insufficient to explain the observed variation in ecological severity. Within this information-theoretic framework, we show that it is the degree of functional selectivity which is expected to primarily determine the ecological impact of a given perturbation when levels of functional redundancy are not substantially different.</p>
Environmental stochasticity increases extinction risk to a greater degree in pollination specialists than in generalists
<p>Pollination sustains terrestrial food webs and agricultural systems and links the dynamics of interacting plant and pollinator species. Although environmental stochasticity is ubiquitous and can propagate through communities via species interactions in a way that increases extinction risk, it is unknown whether stochasticity affects species uniformly across pollination networks. In this paper, we introduce a stochastic dynamic model that makes novel use of the birth function and apply it to pollination networks of increasing size. We start with two- and four-species networks, in order to first illustrate the effects of stochasticity per se and then how those effects combine with specialization. We then describe the relationship between partner number and stochastic extinction risk in empirical networks with >20 species. In the 2-species network, increasing the variance of the stochastic term of the model increased the size of the region in parameter space where extinctions occur. In networks with 4 or more species, specialists were more vulnerable to extinction than generalists over a broad range of variances. Extinction risk in networks with >20 species declined nonlinearly with increasing mutualist partner number. Our results demonstrate the importance of including species interactions and stochasticity when using population-dynamic models to compare species' extinction risk. While models that omit either of these factors are likely to underestimate extinction risk, they disproportionately underestimate the vulnerability of specialists.</p>
Supplementary Data for: Shifts in food webs and niche stability shaped survivorship and extinction at the end-Cretaceous
<p>This compendium of files includes a list of statistical routines (Data S1) and cleaned fossil datasets from the Paleobiology Database (Data S2 to S3) for the <em>Science Avances</em> paper "<em>Shifts in food webs and niche stability shaped survivorship and extinction at the end-Cretaceous</em>". Data S1 and Data S2 can be opened in Microsoft Office and Data S3 can be imported in R using the <em>load()</em> command. Data S2 and S3 contain the same information (i.e., cleaned fossil datasets) but in different formats (<em>xlsx</em> vs. <em>RData</em>).</p> <p>Please, feel free to send an email to the maintainer Dr. Jorge García Girón (jogarg@unileon.es) if you face any trouble downloading, opening or using these files.</p>
1-3. Trionyx foveatus 4.Emys obscurus 5-7. Compsemys victus. 9-19 Crocodilus humilis. 20-23. Lepidotus occidentalis. 24-30 in Extinct vertebrata from the Judith River and Great Lignite formations of Nebraska.
1-3. Trionyx foveatus 4.Emys obscurus 5-7. Compsemys victus. 9-19 Crocodilus humilis. 20-23. Lepidotus occidentalis. 24-30 Mylognathus priscus
1-20. Trachodon mirabilis 21-48. Deinodon horridus 49-52. Palaeoscincus costatus 53-55 in Extinct vertebrata from the Judith River and Great Lignite formations of Nebraska.
1-20. Trachodon mirabilis 21-48. Deinodon horridus 49-52. Palaeoscincus costatus 53-55. Troodon formosus
Museum genomics reveals the hybrid origin of an extinct crater lake endemic
<p>Crater lake fishes are common evolutionary model systems, with recent studies suggesting a key role for gene flow in promoting rapid adaptation and speciation. However, the study of these young lakes can be complicated by human-mediated extinctions. Museum genomics approaches integrating genetic data from recently extinct species are therefore critical to understanding the complex evolutionary histories of these fragile systems. Here, we examine the evolutionary history of an extinct Southern Hemisphere crater lake endemic, the rainbowfish Melanotaenia eachamensis. We undertook comprehensive sampling of extant rainbowfish populations of the Atherton Tablelands of Australia alongside historical museum material to understand the evolutionary origins of the extinct crater lake population and the dynamics of gene flow across the ecoregion. The extinct crater lake species is genetically distinct from all other nearby populations due to historic introgression between two proximate riverine lineages, similar to other prominent crater lake speciation systems, but this historic gene flow has not been sufficient to induce a species flock. Our results suggest that museum genomics approaches can be successfully combined with extant sampling to unravel complex speciation dynamics involving recently extinct species.</p>
FIGURE 6 in New omomyoids (Euprimates, Mammalia) from the late Uintan of southern California, USA, and the question of the extinction of the Paromomyidae (Plesiadapiformes, Primates)
FIGURE 6. Micro-CT scan reconstructions of specimens of Walshina esmaraldensis gen. et sp. nov. generated using Avizo 7: 1: left M1, LACM 40198 (holotype), in occlusal view; 2: left M2, SDSNH 87336, in occlusal view; 3: lingual fragment of a left M2, SDSNH 87337, in occlusal view; 4: lingual fragment of a right M2, SDSNH 42268, in occlusal view; 5, 6, 9, 10: left M2, SDSNH 87332, in occlusal (5), buccal (6), mesial (9) and lingual (10) views; 7, 8, 11, 12: mesial fragment of a left M1, SDSNH 87331, in occlusal (7), buccal (8), mesial (11) and lingual (12) views; 13, 14, 17, 18: left M3, SDSNH 87334, in buccal (13), occlusal (14), lingual (17) and mesial (18) views; 15, 16, 19: distal fragment of a right M3, SDSNH 87335, in buccal (15), occlusal (16) and lingual (19) views.
FIGURE 5 in New omomyoids (Euprimates, Mammalia) from the late Uintan of southern California, USA, and the question of the extinction of the Paromomyidae (Plesiadapiformes, Primates)
FIGURE 5. Photographs taken with digital camera (1, 4-11) and Micro-CT scan reconstructions generated using Avizo 7 (2, 3). Walshina shifrae comb. nov. (1, 4, 7, 10) – 1: right M1, CM 15797 (holotype; mirrored), in occlusal view; 4: left M2, CM 15103, in occlusal view; 7: left M, CM 21637, in occlusal view; 10: left M; CM 15726, in occlusal view. 2 3 Walshina esmaraldensis gen. et sp. nov. (2, 5) – 2: left M1, LACM 40198 (holotype), in occlusal view; 5: left M2, SDSNH 62850, in occlusal view. Walshina mcgrewi comb. nov. (3, 6, 8, 9, 11) – 3: left M1, CM 15635 (holotype), in occlusal view; 6: left M2, CM15794, in occlusal view; 8, 9, 11: left mandibular fragment with M, CM 29005, in occlusal 2 (8), buccal (9), and lingual (11) views.
FIGURE 3 in New omomyoids (Euprimates, Mammalia) from the late Uintan of southern California, USA, and the question of the extinction of the Paromomyidae (Plesiadapiformes, Primates)
FIGURE 3. Reconstruction of western North America from 40 million years ago. Orange dot indicates the paleoposition of the sites discussed in this paper, whereas the red dot indicates the current relative position of the sites. The map is reproduced with R. Blakey's permission (Colorado Plateau Geosystems, Inc.).
FIGURE 2 in New omomyoids (Euprimates, Mammalia) from the late Uintan of southern California, USA, and the question of the extinction of the Paromomyidae (Plesiadapiformes, Primates)
FIGURE 2. Holotype of Trogolemur myodes, AMNH 12599 (Matthew, 1909: plate LII, figure 5). Right dentary with P2-M3. 1: occlusal view; 2: buccal view; 3: lingual view.
FIGURE 4 in New omomyoids (Euprimates, Mammalia) from the late Uintan of southern California, USA, and the question of the extinction of the Paromomyidae (Plesiadapiformes, Primates)
FIGURE 4. Environmental SEM images of four teeth of Walshina esmaraldensis gen. et sp. nov. 1: left M3, SDSNH 76276; 2: right M1, SDSNH 76337; 3: right M2, SDSNH 76338; 4: right M3, SDSNH 72583. All teeth are in occlusal view. Arrow indicates the location of the fovea.
FIGURE 1. The late Wasatchian paromomyid Phenacolemur citatus. 1 in New omomyoids (Euprimates, Mammalia) from the late Uintan of southern California, USA, and the question of the extinction of the Paromomyidae (Plesiadapiformes, Primates)
FIGURE 1. The late Wasatchian paromomyid Phenacolemur citatus. 1: USGS 6573 (original fossil), right maxilla with P3-M2. 2-4: USGS 21712 (cast), left dentary with P4-M3 in occlusal (2), buccal (3), and lingual (4) views.
FIGURE 7 in New omomyoids (Euprimates, Mammalia) from the late Uintan of southern California, USA, and the question of the extinction of the Paromomyidae (Plesiadapiformes, Primates)
FIGURE 7. Hypothesis of relationships of Walshina gen. nov. in the context of the Order Primates. Strict consensus cladogram based on data modified from Holroyd and Strait (2008), including the addition of seven newly-coded trogolemurins (Trogolemur amplior, Tr. fragilis, Tr. leonardi, Sphacorhysis burntforkensis, Walshina esmaraldensis gen. et sp. nov., W. mcgrewi comb. nov., and W. shifrae comb. nov.), a microchoerine (Melaneremia bryanti), and three anaptomorphins (Anemorhysis sublettensis, An. wortmani, and An. natronensis). Trogolemurins are marked in blue.
Fig. 1. Type RNHL 1809 in Extinction of Japan's first formally described earthworm (Horst, 1883) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae).
Fig. 1. Type RNHL 1809 of Amynthas japonicus in Leiden (courtesy of J. Bleeker Sept., 2016). This is the only known specimen and image of this Japanese species (cf. M. sieboldi – http://www. geocities.jp/at_mocha/mimizu/sieboldi-3.html).
Fig. 3 in Extinction of Japan's first formally described earthworm (Horst, 1883) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae).
Fig. 3. Historical Nagasaki (with Dejima island) around the time of collection (from Siebold's Nippon, 1897; archive.org/ details/nipponarchivzur00siebgoog Wikipedia CC-BY).
Regional and local factors interact to shape colonization and extinction dynamics of invasive Hydrilla verticillata in a patchy landscape
<p>Understanding the response of species to global change requires disentangling the drivers of their distributions across landscapes. Colonization and extinction processes, shaped by the interplay of landscape-level and local patch-level factors, are key determinants of these distributions. However, disentangling the influence of these factors, when larger-scale processes manifest at local scales, remains a challenge. We addressed this challenge by investigating the colonization and extinction dynamics of the aquatic plant, <em>Hydrilla verticillata</em>, in a complex riverine rock pool system. This system, with hundreds of rock pools experiencing varying flooding frequencies, provided a natural laboratory to examine how a single landscape-level disturbance can differentially impact colonization and extinction depending on local patch characteristics to shape species distributions. Using five years of data across over 500 sites and more than 5,000 surveys, we employed dynamic occupancy models to model colonization, extinction, and changes in <em>Hydrilla</em> patch occupancy while accounting for imperfect detection. Our results revealed that larger, infrequently flooded pools closer to the river were more likely to be colonized. In contrast, local extinction of Hydrilla was more likely in smaller pools closer to the river that flooded frequently. These findings underscore the importance of considering context-dependence in species distribution models. The same landscape-level disturbance (flooding) had opposing effects on colonization and extinction, with the direction and magnitude of these effects varying with local patch characteristics. Our study highlights the need for integrating local and landscape-level factors, and considering how larger-scale processes play out at the patch level, to understand the complex dynamics that shape species distributions.</p>
Fig. 4 in Morphological and molecular description of Ixodes woyliei n. sp. (Ixodidae) with consideration for co-extinction with its critically endangered marsupial host
Fig. 4 Scanncng electron mccrographs of Ixodes woyliei n. sp. Female. a Spurs on coxae. b Spcracular plate. c Tarsus I. d Haller's organ. Scale-bars: a, 200 μm; b, c, 50 μm; d, 15 μm
Fig. 8 in Morphological and molecular description of Ixodes woyliei n. sp. (Ixodidae) with consideration for co-extinction with its critically endangered marsupial host
Fig. 8 Scanncng electron mccrographs of Ixodes woyliei. Nsmph, legs and spcracular plate. a Spurs on coxae. b Spcracular plate. c Tarsus I. d Haller's organ. Scale-bars: a, c, 100 μm; b, 20 μm; d, 10 μm
Fig. 7 in Morphological and molecular description of Ixodes woyliei n. sp. (Ixodidae) with consideration for co-extinction with its critically endangered marsupial host
Fig. 7 Scanncng electron mccrographs of Ixodes woyliei n. sp. Nsmph. a Gnathosoma, dorsal vcew. b Gnathosoma, ventral vcew. c Hspostome. Scale-bars: a, b = 40 μm; c, 10 μm
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