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42 results for “Time to extinction”
How to render species comparable taxonomic units through deep time: A case study on intraspecific osteological variability in extant and extinct lacertid lizards
<p>Generally, the species is considered to be the only naturally occurring taxon. However, species recognized and defined using different species delimitation criteria cannot readily be compared, impacting studies of biodiversity through Deep Time. This comparability issue is particularly marked when comparing extant with extinct species because the only available data for species delimitation in fossils are derived from their preserved morphology, which is generally restricted to osteology in vertebrates. Here, we quantify intraspecific, intrageneric, and intergeneric osteological variability in extant species of lacertid lizards using pairwise dissimilarity scores based on a data set of 253 discrete osteological characters for 99 specimens referred to 24 species. Variability is always significantly lower intraspecifically than between individuals belonging to distinct species of a single genus, which is in turn significantly lower than intergeneric variability. Average values of intraspecific variability and associated standard deviations are consistent (with few exceptions), with an overall average within a species of 0.208 changes per character scored. Application of the same methods to six extinct lacertid species (represented by 40 fossil specimens) revealed that intraspecific osteological variability is inconsistent, which can at least in part be attributed to different researchers having unequal expectations of the skeletal dissimilarity within species units. Such a divergent interpretation of intraspecific and interspecific variability among extant and extinct species reinforces the incomparability of the species unit. Lacertidae is an example where extant species recognized and defined based on a number of delimitation criteria show comparable and consistent intraspecific osteological variability. Here, as well as in equivalent cases, application of those skeletal dissimilarity values to paleontological species delimitation potentially provides a way to ameliorate inconsistencies created by the use of morphology to define species.</p>
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>
Fig. 5 in Deep time extinction of largest insular ant predators and the first fossil Neoponera (Formicidae: Ponerinae) from Miocene age Dominican amber
Fig. 5 Size distribution of extant and extinct ant predators on Hispaniola. Principal component 1 derived from PCA of three morphometric traits across taxa. Fossil ants (yellow) exhibit larger body sizes than extant taxa (gray) on average and among extremes. Note: plot includes alate (queen) specimens, including the largest known fossil ant species, an undescribed Fulakora queen
Fig. 4 in Deep time extinction of largest insular ant predators and the first fossil Neoponera (Formicidae: Ponerinae) from Miocene age Dominican amber
Fig. 4 Morphospace of Hispaniolan predatory ants in fossil and extant communities. Morphometric data comprise head length, head width, and Weber's length across 35 extant and 26 fossil species
Fig. 1 in Deep time extinction of largest insular ant predators and the first fossil Neoponera (Formicidae: Ponerinae) from Miocene age Dominican amber
Fig. 1 Photomicrographs of Neoponera vejestoria sp. nov. (Holotype, MNHNSD FOS 18.01). A Head in frontal view. B Body in dorsal view. C Body in lateral view. Scale bars: A 1 mm; B, C 2 mm
Fig. 3 in Deep time extinction of largest insular ant predators and the first fossil Neoponera (Formicidae: Ponerinae) from Miocene age Dominican amber
Fig. 3 Principal component analysis morphospace of Neoponera ants according to species group. The sampling comprised 47 species represented by 12 linear morphological measurements. PC1 corresponds with the overall body size. Neoponera vejestoria is denoted with the blue star. The first five principal components of the Neoponera dataset make up 98% of the total variance. Principal component 1 comprises 84.14% of the variance; principal component 2 reflects the overall body shape, mainly in the pronotal width and petiolar dimensions (see Additional file 1: Fig. S4), comprising 5.61% of the variance
Timing and provenance of volcanic fluxes around the Permian-Triassic Boundary Mass Extinction in South China: U-Pb zircon geochronology, volcanic ash geochemistry and mercury isotopes
<p>The enclosed dataset contains all of the raw data supporting the results presented in the paper titled: <strong>"Timing and provenance of volcanic fluxes around the Permian-Triassic Boundary Mass Extinction in South China: U-Pb zircon geochronology, volcanic ash geochemistry and mercury isotopes". </strong></p> <p>The Excel data file contains four data sheets as follows: </p> <p>1. Table S1: This sheet contains the U-Pb output table from ETRedux. The data sheet contains all the U and Pb isotopic data generated for the current study.</p> <p>2. Table S2: This excel sheet contains the geochemical compositions of analyzed volcanic ash beds as well as LOI-normalized major element compositions of these ashes.</p> <p>3. Table S3: This excel sheet contains the other geochemical and isotope data for all analyzed samples. This includes Hg concentration and isotope compositions, TOC data, as well as major and trace element concentrations and ratios.</p> <p>4. a final table containing the analyzed Hg isotope compositions for the utilized standard reference materials - ETH Fluka, UM-Almaden, NIST 1632D and MESS-3.</p>
How to render species comparable taxonomic units through deep time: A case study on intraspecific osteological variability in extant and extinct lacertid lizards
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The shape of phylogenies under phase-type distributed times to speciation and extinction
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Supplementary information for: The effects of geographic range size and abundance on extinction during a time of 'sluggish' evolution
<p>Geographic range size and abundance are important determinants of extinction risk in fossil and extant taxa. However, the relationship between these variables and extinction risk has not been tested extensively during evolutionarily 'quiescent' times of low extinction and speciation in the fossil record. Here we examine the influence of geographic range size and abundance on extinction risk during the late Paleozoic (Mississippian–Permian), a time of 'sluggish' evolution when global rates of origination and extinction were roughly half those of other Paleozoic intervals. Analyses used spatio-temporal occurrences for 164 brachiopod species from the North American midcontinent. We found abundance to be a better predictor of extinction risk than measures of geographic range size. Moreover, species exhibited reductions in abundance prior to their extinction, but did not display contractions in geographic range size. The weak relationship between geographic range size and extinction in this time and place may reflect the relative preponderance of larger-ranged taxa, combined with the physiographic conditions of the region that allowed for easy habitat tracking that dampened both extinction and speciation. These conditions led to a prolonged period (19 – 25 Myr) during which standard macroevolutionary rules did not apply.</p>
Summary data for plots in: Eco-evolutionary extinction and recolonization dynamics reduce genetic load and increase time to extinction in highly inbred populations
<p>Understanding how genetic and ecological effects can interact to shape genetic loads within and across local populations is key to understanding ongoing persistence of systems that should otherwise be susceptible to extinction through mutational meltdown. Classic theory predicts short persistence times for metapopulations comprising small local populations with low connectivity, due to accumulation of deleterious mutations. Yet, some such systems have persisted over evolutionary time, implying the existence of mechanisms that allow metapopulations to avoid mutational meltdown. We first hypothesize a mechanism by which the combination of stochasticity in the numbers and types of mutations arising locally (genetic stochasticity), resulting in local extinction and recolonization through evolving dispersal, facilitates metapopulation persistence. We then test this mechanism using a spatially and genetically explicit individual-based model. We show that genetic stochasticity in highly structured metapopulations can result in local extinctions, which can favour increased dispersal, thus allowing recolonization of empty habitat patches. This causes fluctuations in metapopulation size and transient gene flow, which reduces genetic load and increases metapopulation persistence over evolutionary time. Our suggested mechanism and simulation results provide an explanation for the conundrum presented by the continued persistence of highly structured populations with inbreeding mating systems that occur in diverse taxa.</p>
Fig. 2 in Deep time extinction of largest insular ant predators and the first fossil Neoponera (Formicidae: Ponerinae) from Miocene age Dominican amber
Fig. 2 Artistic reconstruction of Neoponera vejestoria sp. nov. Artist: Minsoo Dong
Data from: Scaling of extinction time with habitat size across six orders of magnitude in experimental populations
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Summary data for plots in: Eco-evolutionary extinction and recolonization dynamics reduce genetic load and increase time to extinction in highly inbred populations
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Phylogenomics of sigmodontine rodents (Cricetidae: Sigmodontinae): Cloud forests and Pliocene extinction explain the timing and spread of an iconic South American radiation
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Supplementary information for: The effects of geographic range size and abundance on extinction during a time of ‘sluggish’ evolution
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Data from: Body-size trends of the extinct giant shark Carcharocles megalodon: a deep-time perspective on marine apex predators
The extinct shark Carcharocles megalodon is one of the largest marine apex predators ever to exist. Nonetheless, little is known about its body-size variations through time and space. Here, we studied the body-size trends of C. megalodon through its temporal and geographic range to better understand its ecology and evolution. Given that this species was the last of the megatooth lineage, a group of species that shows a purported size increase through time, we hypothesized that C. megalodon also displayed this trend, increasing in size over time and reaching its largest size prior to extinction. We found that C. megalodon body-size distribution was left-skewed (suggesting a long-term selective pressure favoring larger individuals), and presented significant geographic variation (possibly as a result of the heterogeneous ecological constraints of this cosmopolitan species) over geologic time. Finally, we found that stasis was the general mode of size evolution of C. megalodon (i.e., no net changes over time), contrasting with the trends of the megatooth lineage and our hypothesis. Given that C. megalodon is a relatively long-lived species with a widely distributed fossil record, we further used this study system to provide a deep-time perspective to the understanding of the body-size trends of marine apex predators. For instance, our results suggest that (1) a selective pressure in predatory sharks for consuming a broader range of prey may favor larger individuals and produce left-skewed distributions on a geologic time scale; (2) body-size variations in cosmopolitan apex marine predators may depend on their interactions with geographically discrete communities; and (3) the inherent characteristics of shark species can produce stable sizes over geologic time, regardless of the size trends of their lineages.
Data from: Explaining high-diversity death assemblages: undersampling of the living community, out-of-habitat transport, time-averaging of rare taxa, and local extinction
Molluscan benthic assemblages provide unique opportunities for understanding both spatial and temporal patterns of biodiversity. Species richness in the shell remains found at a site (i.e. the death assemblage) is typically several times higher than in the counterpart living assemblage, reflecting a complex history of settlement, dissemination and decomposition post-mortem. We used high-density temporal and spatial sampling (>37'000 individuals representing 196 taxa) of a shallow (5-8 m) nearshore sandy habitat off the coast of south-east Sardinia (Italy, Mediterranean Sea) to study the factors responsible for differences in the relative diversity of living and death assemblages. We found that death assemblages at all sites were considerably more diverse than living communities (1.5-3.5x more dead than living taxa after sample-size standardization), with 78% of all taxa solely recovered as empty shells, resulting in low live-dead agreement. By carefully filtering the raw data and combining them with habitat information extracted from the literature, we disentangled the major causes of this discordance and quantified their individual effects. Increased dead diversities could not be attributed to undersampling of the living community, but instead resulted from three phenomena of decreasing importance: the post-mortem, out-of-habitat transport of non-indigenous taxa (57% of dead-only taxa were allochthonous), the time-averaged presence of rare indigenous taxa (40% of dead-only taxa), and the likely local extirpation of a small number of species (3% of dead-only taxa). Our approach demonstrates how ecological inferences based on death assemblages can be improved by restricting analyses to demonstrably indigenous taxa, and highlights how mollusc shell remains can be used to provide information over both ecological and evolutionary timescales.
Data from: Modeling time to population extinction when individual reproduction is autocorrelated
In nature, individual reproductive success is seldom independent from year to year, due to factors such as reproductive costs and individual heterogeneity. However, population projection models that incorporate temporal autocorrelations in individual reproduction can be difficult to parameterize, particularly when data are sparse. We therefore examine whether such models are necessary to avoid biased estimates of stochastic population growth and extinction risk, by comparing output from a matrix population model that incorporates reproductive autocorrelations to output from a standard age-structured matrix model that does not. We use a range of parameterizations, including a case study using moose data, treating probabilities of switching reproductive class as either fixed or fluctuating. Expected time to extinction from the two models is found to differ by only small amounts (under 10%) for most parameterizations, indicating that explicitly accounting for individual reproductive autocorrelations is in most cases not necessary to avoid bias in extinction estimates.
Distribution. Endemic to C & S Italy, as far N as Umbria. Presumably extinct in Sicily where it was recorded for the last time in 1885. in Talpidae
Distribution. Endemic to C & S Italy, as far N as Umbria. Presumably extinct in Sicily where it was recorded for the last time in 1885.
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