Habitat breadth and geographic range predict diversity dynamics in marine Mesozoic bivalves

Paleobiology ◽  
10.1666/12047 ◽  
2013 ◽  
Vol 39 (3) ◽  
pp. 360-372 ◽  
Author(s):  
Sabine Nürnberg ◽  
Martin Aberhan
Keyword(s):  
Linear Models ◽  
Extinction Risk ◽  
Geographic Range ◽  
Independent Effect ◽  
Data Sets ◽  
Mass Extinctions ◽  
Mean Values ◽  
Extinction Rates ◽  
Habitat Breadth ◽  
Diversity Dynamics

Numerous environmental and intrinsic biotic factors have been sought to explain patterns in diversity and turnover. Using taxonomically vetted and sampling-standardized data sets of more than 50,000 taxonomic occurrences in the Paleobiology Database (PaleoDB) we tested whether habitat breadth predicts genus durations and diversity dynamics of marine Mesozoic bivalves, and whether this effect is independent of the well-known positive relationship between geographic range and longevity. We defined the habitat breadth of a genus as a function of its realized ranges in water depth, substrate type, and grain size of the substrate. Our analysis showed that mean values of extinction and origination rates are significantly higher for narrowly adapted genera compared to broadly adapted genera, with differences being evident in all analyzed stratigraphic intervals. Linear models showed that both geographic range and habitat breadth have an independent effect on genus durations and on diversity dynamics. These results reaffirm the role of geographic range and furthermore suggest that habitat breadth is an equally important key predictor of extinction risk and origination probability in Mesozoic marine bivalves. Habitat generalists, regardless of their geographic range, are generally less prone to extinction. Conversely, widely distributed genera that are more specialized may be more endangered than one would expect from their geographic range alone. Extinction rates tend to be higher for specialized genera in both background and mass extinctions, suggesting that wide habitat breadth universally buffers against extinction. The trajectories of origination rates through time differ from those of extinction rates. Whereas there is no pronounced ecological selectivity in origination in the Triassic and most of the Jurassic, Cretaceous origination rates are higher for specialized genera. This may best be explained by diversity-dependence. When diversity levels reach a critical point a further increase in diversity is achieved by elevated origination rates of more specialized forms.

scholarly journals Long-term differences in extinction risk among the seven forms of rarity

2012 ◽  
Vol 279 (1749) ◽  
pp. 4969-4976 ◽  
Author(s):  
Paul G. Harnik ◽  
Carl Simpson ◽  
Jonathan L. Payne
Keyword(s):  
Extinction Risk ◽  
Geographic Range ◽  
Primary Role ◽  
Marine Animals ◽  
Global Database ◽  
The Past ◽  
Geographic Range Size ◽  
Different Types ◽  
Habitat Breadth

Rarity is widely used to predict the vulnerability of species to extinction. Species can be rare in markedly different ways, but the relative impacts of these different forms of rarity on extinction risk are poorly known and cannot be determined through observations of species that are not yet extinct. The fossil record provides a valuable archive with which we can directly determine which aspects of rarity lead to the greatest risk. Previous palaeontological analyses confirm that rarity is associated with extinction risk, but the relative contributions of different types of rarity to extinction risk remain unknown because their impacts have never been examined simultaneously. Here, we analyse a global database of fossil marine animals spanning the past 500 million years, examining differential extinction with respect to multiple rarity types within each geological stage. We observe systematic differences in extinction risk over time among marine genera classified according to their rarity. Geographic range played a primary role in determining extinction, and habitat breadth a secondary role, whereas local abundance had little effect. These results suggest that current reductions in geographic range size will lead to pronounced increases in long-term extinction risk even if local populations are relatively large at present.

An analysis of the impacts of Cretaceous oceanic anoxic events on global molluscan diversity dynamics

Paleobiology ◽  
2019 ◽  
Vol 45 (02) ◽  
pp. 280-295 ◽  
Author(s):  
Nicholas A. Freymueller ◽  
Jason R. Moore ◽  
Corinne E. Myers
Keyword(s):  
Linear Models ◽  
Species Level ◽  
Extinction Rate ◽  
Extinction Rates ◽  
Anoxic Events ◽  
Molluscan Diversity ◽  
Extinction Events ◽  
Diversity Dynamics ◽  
The Impact ◽  
Stage Boundaries

AbstractOceanic anoxic events (OAEs) are contemporaneous with 11 of the 18 largest Phanerozoic extinction events, but the magnitude and selectivity of their paleoecological impact remains disputed. OAEs are associated with abrupt, rapid warming and increased CO2flux to the atmosphere; thus, insights from this study may clarify the impact of current anthropogenic climate change on the biosphere. We investigated the influence of the Late Cretaceous Bonarelli event (OAE2; Cenomanian/Turonian stage boundary; ~94 Ma) on generic- and species-level molluscan diversity, extinction rates, and ecological turnover. Cenomanian/Turonian results were compared with changes across all Cretaceous stage boundaries, some of which are coincident with less severe OAEs. We found increased generic turnover, but not species-level turnover, associated with several Cretaceous OAEs. The absence of a species-level pattern may reflect species occurrence data that are too temporally coarse to robustly detect patterns. Five hypotheses of ecological selectivity relating anoxia to survivorship were tested across stage boundaries with respect to faunality, mobility, and diet using generalized linear models. Interestingly, benthic taxa were consistently selected against throughout the Cretaceous regardless of the presence or absence of OAEs. These results suggest that: (1) the Cenomanian/Turonian boundary (OAE2) was associated with a decline in molluscan diversity and increase in extinction rate that were significantly more severe than Cretaceous background levels; and (2) no differential ecological selectivity was associated with OAE-related diversity declines among the variables tested here.

scholarly journals A top-level model of case-based argumentation for explanation: Formalisation and experiments

2021 ◽  
pp. 1-36
Author(s):  
Henry Prakken ◽  
Rosa Ratsma
Keyword(s):  
Machine Learning ◽  
Decision Making ◽  
Linear Models ◽  
Evaluation Studies ◽  
Data Sets ◽  
Machine Learning Applications ◽  
Level Model ◽  
Similarities And Differences ◽  
Further Development ◽  
Case Based

This paper proposes a formal top-level model of explaining the outputs of machine-learning-based decision-making applications and evaluates it experimentally with three data sets. The model draws on AI & law research on argumentation with cases, which models how lawyers draw analogies to past cases and discuss their relevant similarities and differences in terms of relevant factors and dimensions in the problem domain. A case-based approach is natural since the input data of machine-learning applications can be seen as cases. While the approach is motivated by legal decision making, it also applies to other kinds of decision making, such as commercial decisions about loan applications or employee hiring, as long as the outcome is binary and the input conforms to this paper’s factor- or dimension format. The model is top-level in that it can be extended with more refined accounts of similarities and differences between cases. It is shown to overcome several limitations of similar argumentation-based explanation models, which only have binary features and do not represent the tendency of features towards particular outcomes. The results of the experimental evaluation studies indicate that the model may be feasible in practice, but that further development and experimentation is needed to confirm its usefulness as an explanation model. Main challenges here are selecting from a large number of possible explanations, reducing the number of features in the explanations and adding more meaningful information to them. It also remains to be investigated how suitable our approach is for explaining non-linear models.

scholarly journals Biological and extrinsic correlates of extinction risk in Chinese lizards

2021 ◽  
Author(s):  
Yuxi Zhong ◽  
Chuanwu Chen ◽  
Yanping Wang
Keyword(s):  
Body Size ◽  
Extinction Risk ◽  
Species Traits ◽  
Geographic Range ◽  
Range Size ◽  
Habitat Specialization ◽  
Mean Annual Precipitation ◽  
Mean Annual Temperature ◽  
Small Range ◽  
Extrinsic Factors

Abstract China is a country with one of the most species rich reptile faunas in the world. However, nearly a quarter of Chinese lizard species assessed by the China Biodiversity Red List are threatened. Nevertheless, to date, no study has explicitly examined the pattern and processes of extinction and threat in Chinese lizards. In this study, we conducted the first comparative phylogenetic analysis of extinction risk in Chinese lizards. We addressed the following three questions: 1) What is the pattern of extinction and threat in Chinese lizards? 2) Which species traits and extrinsic factors are related to their extinction risk? 3) How can we protect Chinese lizards based on our results? We collected data on ten species traits (body size, clutch size, geographic range size, activity time, reproductive mode, habitat specialization, habitat use, leg development, maximum elevation, and elevation range) and seven extrinsic factors (mean annual precipitation, mean annual temperature, mean annual solar insolation, normalized difference vegetation index (NDVI), human footprint, human population density, and human exploitation). After phylogenetic correction, these variables were used separately and in combination to assess their associations with extinction risk. We found that Chinese lizards with small geographic range, large body size, high habitat specialization, and living in high precipitation areas were vulnerable to extinction. Conservation priority should thus be given to species with the above extinction-prone traits so as to effectively protect Chinese lizards. Preventing future habitat destruction should also be a primary focus of management efforts because species with small range size and high habitat specialization are particularly vulnerable to habitat loss.

scholarly journals Geographic contingency, not species sorting, dominates macroevolutionary dynamics in an extinct clade of neogastropods (Volutospina; Volutidae)

Paleobiology ◽  
2021 ◽  
pp. 1-15
Author(s):  
Dana S. Friend ◽  
Brendan M. Anderson ◽  
Warren D. Allmon
Keyword(s):  
Middle Eocene ◽  
Ecological Factors ◽  
Geographic Range ◽  
Late Eocene ◽  
Range Size ◽  
Species Sorting ◽  
Extinction Rates ◽  
Geographic Range Size ◽  
Speciation Rates ◽  
Planktotrophic Larvae

Abstract Rates of speciation and extinction are often linked to many ecological factors, traits (emergent and nonemergent) such as environmental tolerance, body size, feeding type, and geographic range. Marine gastropods in particular have been used to examine the role of larval dispersal in speciation. However, relatively few studies have been conducted placing larval modes in species-level phylogenetic context. Those that have, have not incorporated fossil data, while landmark macroevolutionary studies on fossil clades have not considered both phylogenetic context and net speciation (speciation–extinction) rates. This study utilizes Eocene volutid Volutospina species from the U.S. Gulf Coastal Plain and the Hampshire Basin, U.K., to explore the relationships among larval mode, geographic range, and duration. Based on the phylogeny of these Volutospina, we calculated speciation and extinction rates in order to compare the macroevolutionary effects of larval mode. Species with planktotrophic larvae had a median duration of 9.7 Myr, which compared significantly to 4.7 Myr for those with non-planktotrophic larvae. Larval mode did not significantly factor into geographic-range size, but U.S. and U.K. species do differ, indicating a locality-specific component to maximum geographic-range size. Non-planktotrophs (NPTs)were absent among the Volutospina species during the Paleocene–early Eocene. The relative proportions of NPTs increased in the early middle Eocene, and the late Eocene was characterized by disappearance of planktotrophs (PTs). The pattern of observed lineage diversity shows an increasing preponderance of NPTs; however, this is clearly driven by a dramatic extinction of PTs, rather than higher NPT speciation rates during the late Eocene. This study adds nuance to paleontology's understanding of the macroevolutionary consequences of larval mode.

scholarly journals The effects of geographic range size and abundance on extinction during a time of “sluggish”’ evolution

Paleobiology ◽  
2020 ◽  
pp. 1-14
Author(s):  
Michelle M. Casey ◽  
Erin E. Saupe ◽  
Bruce S. Lieberman
Keyword(s):  
North American ◽  
Fossil Record ◽  
Extinction Risk ◽  
Geographic Range ◽  
Range Size ◽  
Late Paleozoic ◽  
The North ◽  
Geographic Range Size ◽  
The Relationship ◽  
Habitat Tracking

Abstract 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 spatiotemporal 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 before 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.

scholarly journals Quantifying geographic range measures and their utility as extinction risk proxies

2017 ◽  
Author(s):  
James Boyle
Keyword(s):  
Convex Hull ◽  
Sample Size ◽  
Cell Count ◽  
Spanning Tree ◽  
Minimum Spanning Tree ◽  
Extinction Risk ◽  
Geographic Range ◽  
Western Hemisphere ◽  
True Value ◽  
Latitudinal Range

Geographic range is used as a correlate of extinction risk for extant and extinct organisms across the fields of conservation and paleobiology. However, the exact method used to measure geographic range, the biases, and the limitations of each are rarely discussed explicitly despite their potential to impact conclusions. Here I examine and quantify properties of five commonly used measures of geographic range (convex hull area, maximum pairwise great circle distance, latitudinal range, longitudinal range, and cell count) along with a rarely used measure (minimum spanning tree distance) in the context of three datasets. A simulated dataset of two shapes with known areal limits, a paleontological occurrence dataset of pre-Cenozoic brachiopod genera from the Paleobiology Database (PBDB), and 50000 occurrence records of birds species in the western hemisphere from the eBird database. Simulated distributions indicate that when a distribution is simple (i.e. a rectangle) all measures are similarly accurate and precise at varying sample sizes and all measures converge toward the true value with increasing sample size. However, given a more complex distribution (i.e. horseshoe shape) the convex hull area becomes increasingly inaccurate as sample size increases even as it becomes more precise. Within the PBDB dataset the minimum spanning tree was heavily favored by Akaike Information Criterion as the most effective predictor of extinction risk. Analysis of the eBird data set indicated differences between IUCN Red List Categories were significant for all geographic range measures. Overall, these results suggest that for the purpose of categorical comparisons, such as those between victims and survivors of an extinction event, all six geographic range measures are interchangeable. However, the magnitude of the relationship between geographic range and extinction risk is strongly dependent on the choice of measure. Simple linear measures, such as latitudinal range, were relatively poor predictors while minimum spanning tree and cell count measures were strong predictors, especially after sampling was accounted for. The minimum spanning tree measure was found to perform at the same level or better than most other measures with the main drawback being that it is computationally expensive.

Within- and among-genus components of size evolution during mass extinction, recovery, and background intervals: a case study of Late Permian through Late Triassic foraminifera

Paleobiology ◽  
2012 ◽  
Vol 38 (4) ◽  
pp. 627-643 ◽  
Author(s):  
Brianna L. Rego ◽  
Steve C. Wang ◽  
Demir Altiner ◽  
Jonathan L. Payne
Keyword(s):  
Mass Extinction ◽  
Extinction Risk ◽  
Maximum Size ◽  
Size Reduction ◽  
Late Triassic ◽  
Mass Extinctions ◽  
Late Permian ◽  
Biotic Recovery ◽  
Size Evolution ◽  
Selective Extinction

One of the best-recognized patterns in the evolution of organismal size is the tendency for mean and maximum size within a clade to decrease following a major extinction event and to increase during the subsequent recovery interval. Because larger organisms are typically thought to be at higher extinction risk than their smaller relatives, it has commonly been assumed that size reduction mostly reflects the selective extinction of larger species. However, to our knowledge the relative importance of within- and among-lineage processes in driving overall trends in body size has never been compared quantitatively. In this study, we use a global, specimen-level database of foraminifera to study size evolution from the Late Permian through Late Triassic. We explicitly decompose size evolution into within- and among-genus components. We find that size reduction following the end-Permian mass extinction was driven more by size reduction within surviving species and genera than by the selective extinction of larger taxa. Similarly, we find that increase in mean size across taxa during Early Triassic biotic recovery was a product primarily of size increase within survivors and the extinction of unusually small taxa, rather than the origination of new, larger taxa. During background intervals we find no strong or consistent tendency for extinction, origination, or within-lineage change to move the overall size distribution toward larger or smaller sizes. Thus, size stasis during background intervals appears to result from small and inconsistent effects of within- and among-lineage processes rather than from large but offsetting effects of within- and among-taxon components. These observations are compatible with existing data for other taxa and extinction events, implying that mass extinctions do not influence size evolution by simply selecting against larger organisms. Instead, they appear to create conditions favorable to smaller organisms.

On Bayesian model selection for INGARCH models viatrans-dimensional Markov chain Monte Carlo methods

2021 ◽  
pp. 1471082X2110347
Author(s):  
Panagiota Tsamtsakiri ◽  
Dimitris Karlis
Keyword(s):  
Time Series ◽  
Model Selection ◽  
Bayesian Model ◽  
Linear Models ◽  
Simulation Experiment ◽  
Mean Values ◽  
The Past ◽  
Competing Models ◽  
Selection For ◽  
Log Linear

There is an increasing interest in models for discrete valued time series. Among them, the integer autoregressive conditional heteroscedastic (INGARCH) is a model that has found several applications. In the present article, we study the problem of model selection for this family of models. Namely we consider that an observation conditional on the past follows a Poisson distribution where its mean depends on its past mean values and on past observations. We consider both linear and log-linear models. Our purpose is to select the most appropriate order of such models, using a trans-dimensional Bayesian approach that allows jumps between competing models. A small simulation experiment supports the usage of the method. We apply the methodology to real datasets to illustrate the potential of the approach.

Analyzing the Relationship between Diagnosis and the Cost of Diabetic Patients

2010 ◽  
pp. 173-196
Author(s):  
Xiao Wang
Keyword(s):  
Data Analysis ◽  
Data Warehouse ◽  
Chronic Condition ◽  
Linear Models ◽  
Diabetic Patients ◽  
Data Sets ◽  
Exploratory Data ◽  
The Cost ◽  
The Relationship ◽  
Total Charges

The purpose of this study is to examine the relationship between the diagnosis and the cost of patient care for those with diabetes in Medicare. In this analysis, the author used data sets about outpatient claim, inpatient claim as well as beneficiary demography information for the year 2004, all of which were taken from the Chronic Condition Data Warehouse provided by the Centers for Medicare and Medicaid. The author analyzed the cases for diabetic inpatients and outpatients by different methods. For outpatient analysis, exploratory data analysis and linear models were used .The results show that the total charges for diagnoses are reduced considerably for payment. The distribution of the total charges follows a Gamma distribution. The output of the generalized linear model demonstrates that only 15 out of the top 20 primary treatments for charges are statistically significant to the expenditures on outpatients.

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