ORCID Profile
0000-0002-9882-2111
Current Organisation
Macquarie University
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Palaeoecology | Ecology | Environmental Science and Management | Animal Systematics, Taxonomy And Phylogeny | Conservation and Biodiversity | Palaeoecology | Conservation And Biodiversity |
Information services not elsewhere classified | Expanding Knowledge in the Biological Sciences | Biological sciences | Earth sciences | Flora, Fauna and Biodiversity at Regional or Larger Scales | Expanding Knowledge in History and Archaeology
Publisher: Wiley
Date: 07-03-2019
Publisher: University of Chicago Press
Date: 05-2004
DOI: 10.1086/382898
Publisher: Wiley
Date: 14-02-2019
DOI: 10.1111/GEB.12892
Publisher: Proceedings of the National Academy of Sciences
Date: 12-08-2008
Abstract: The discipline-wide effort to database the fossil record at the occurrence level has made it possible to estimate marine invertebrate extinction and origination rates with much greater accuracy. The new data show that two biotic mechanisms have hastened recoveries from mass extinctions and confined ersity to a relatively narrow range over the past 500 million years (Myr). First, a drop in ersity of any size correlates with low extinction rates immediately afterward, so much so that extinction would almost come to a halt if ersity dropped by 90%. Second, very high extinction rates are followed by equally high origination rates. The two relationships predict that the rebound from the current mass extinction will take at least 10 Myr, and perhaps 40 Myr if it rivals the Permo-Triassic catastrophe. Regardless, any large event will result in a dramatic ecological and taxonomic restructuring of the biosphere. The data also confirm that extinction and origination rates both declined through the Phanerozoic and that several extinctions in addition to the Permo-Triassic event were particularly severe. However, the trend may be driven by taxonomic biases and the rates vary in accord with a simple log normal distribution, so there is no sharp distinction between background and mass extinctions. Furthermore, the lack of any significant autocorrelation in the data is inconsistent with macroevolutionary theories of periodicity or self-organized criticality.
Publisher: Elsevier BV
Date: 12-1996
Publisher: Springer Science and Business Media LLC
Date: 17-02-2020
Publisher: American Association for the Advancement of Science (AAAS)
Date: 20-09-2019
Abstract: Large mammals are at high risk of extinction globally. To understand the consequences of their demise for community assembly, we tracked community structure through the end-Pleistocene megafaunal extinction in North America. We decomposed the effects of biotic and abiotic factors by analyzing co-occurrence within the mutual ranges of species pairs. Although shifting climate drove an increase in niche overlap, co-occurrence decreased, signaling shifts in biotic interactions. Furthermore, the effect of abiotic factors on co-occurrence remained constant over time while the effect of biotic factors decreased. Biotic factors apparently played a key role in continental-scale community assembly before the extinctions. Specifically, large mammals likely promoted co-occurrence in the Pleistocene, and their loss contributed to the modern assembly pattern in which co-occurrence frequently falls below random expectations.
Publisher: Society for Sedimentary Geology
Date: 05-2011
Publisher: Geological Society of America
Date: 1998
Publisher: Wiley
Date: 29-09-2021
DOI: 10.1111/COBI.13811
Abstract: Conservation scientists are increasingly interested in the question of how extinction prunes the tree of life. This question is particularly important for Australian freshwater fishes because there is a broad mix of ∼300 old and young species, many of which are severely threatened. We used a complete species‐level phylogeny of Australian freshwater fishes to examine phylogenetic nonrandomness of extinction risk. We computed the potential loss of phylogenetic ersity by simulating extinction across the tree under a pattern weighted based on International Union for Conservation of Nature extinction risk category and compared this loss to projected ersity loss under a random null model of extinction. Finally, we calculated EDGE (evolutionary distinctiveness, global endangerment) scores for 251 freshwater and 60 brackish species and compiled a list of high‐priority species for conservation actions based on their extinction risk and evolutionary uniqueness. Extinction risk was not random and was clustered in both ersity cradles (recently ersifying, species‐rich clades, such as Galaxiidae and Percichthyidae) and museums (older, species‐poor groups, such as freshwater chondrichthyans). Clustered extinction made little difference to the average expected loss of phylogenetic ersity. However, the upper bound of loss was higher under a selective model of extinction, particularly when the counts of species lost were low. Thus, the loss of highly threatened species would diminish the tree of life more than a null model of randomly distributed extinction. High priority species included both widely recognized and charismatic ones, such as the Queensland lungfish ( Neoceratodus forsteri ), river sharks, and freshwater sawfishes, and lesser‐known species that receive less public attention, including the salamanderfish ( Lepidogalaxias salamandroides ), cave gudgeons, and many galaxiids, rainbowfishes, and pygmy perches.
Publisher: Wiley
Date: 26-05-2019
DOI: 10.1111/ECOG.04464
Publisher: Springer Science and Business Media LLC
Date: 28-09-2016
DOI: 10.1038/NCLIMATE3086
Publisher: Wiley
Date: 26-03-2018
Publisher: Cambridge University Press (CUP)
Date: 18-03-2016
DOI: 10.1017/PAB.2016.6
Abstract: Diet and body mass are highly important factors in mammalian ecology, and they have also proven to be powerful paleoecological indicators. Our previous research has proposed a new classification scheme for mammals with more dietary isions that emphasizes the primary resource in a given diet. We analyzed a database summarizing the dietary preferences of 139 species of marsupial and placental terrestrial mammals (including 14 orders) and their average body masses in order to explore whether this new classification better highlights ecomorphological differences between species. Additionally, the dietary ersity of every species in the data set was quantified by applying the inverse Simpson index to stomach content percentages. We observed a decrease in maximum dietary ersity with increasing body mass. Having lower requirements for energy and nutrients per unit of body weight or ecological advantages such as larger home ranges allows larger mammals to feed on less nutritive feeding resources (i.e., structural plant material). Our results also suggest that body-size ranges are different across dietary specializations. Smaller mammals ( kg) are mainly insectivores, granivores, or mixed feeders, while bigger animals ( kg) are usually either carnivores or herbivores that feed specifically on grasses and leaves. The medium-size range (1–30 kg) is mostly composed of frugivorous species that inhabit tropical and subtropical rain forests. Thus, the near absence of medium-sized mammals in open environments such as savannas can be linked to the decreasing density of fruit trees needed to support a pure frugivorous diet year-round. In other words, seasonality of precipitation prevents species from specializing on a totally frugivorous diet. Our results suggest that this new classification scheme correlates well with body mass, one of the most studied morphological variables in paleoecology and ecomorphology. Therefore, the classification should serve as a useful basis for future paleoclimatological studies.
Publisher: The Royal Society
Date: 22-08-2014
Abstract: Understanding the feeding behaviour of the species that make up any ecosystem is essential for designing further research. Mammals have been studied intensively, but the criteria used for classifying their diets are far from being standardized. We built a database summarizing the dietary preferences of terrestrial mammals using published data regarding their stomach contents. We performed multivariate analyses in order to set up a standardized classification scheme. Ideally, food consumption percentages should be used instead of qualitative classifications. However, when highly detailed information is not available we propose classifying animals based on their main feeding resources. They should be classified as generalists when none of the feeding resources constitute over 50% of the diet. The term ‘omnivore’ should be avoided because it does not communicate all the complexity inherent to food choice. Moreover, the so-called omnivore diets actually involve several distinctive adaptations. Our dataset shows that terrestrial mammals are generally highly specialized and that some degree of food mixing may even be required for most species.
Publisher: Geological Society of America
Date: 1998
Publisher: American Association for the Advancement of Science (AAAS)
Date: 10-11-2006
Abstract: Roopnarine et al . and Dietl and Vermeij do not challenge our results but argue that escalation can be seen only at fine scales. This claim diminishes the theory and needs to be tested, not asserted. Roopnarine et al . incorrectly presume that our data are dominated by carnivores. Dietl and Vermeij overlook the fact that in addition to having no effect on global ersity, escalation has no effect on occurrence frequency.
Publisher: Springer Science and Business Media LLC
Date: 19-07-2016
Abstract: The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of in idual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery.
Publisher: Cambridge University Press (CUP)
Date: 1992
DOI: 10.1017/S0094837300010873
Abstract: This paper presents a new means of interpreting the distribution of taxa among taxonomic lists. Traditionally, “similarity” indices have been used to compare lists, and “association” measures have been used to compare taxonomic distributions. It is argued that when s ling regimes are poorly understood, all similarity and association indices are unjustifiable. However, observations that taxa have overlapping ( conjunct ) or nonoverlapping ( disjunct ) distributions are universally meaningful. Because greater s ling can only increase the number of known conjunctions and because long lists serve as conjunctional Rosetta Stones, conjunction data sets can be far more reliable than the lists that generate them. One way to account for patterns of conjunction and disjunction is to create theoretical spaces composed of two distributional boundaries or edges for each taxon in each dimension. A parsimonious arrangement of edges implies distributions that always overlap when taxa are conjunct and infrequently overlap when taxa are disjunct. A procedure involving correspondence analysis is shown to minimize the number of implied disjunctions. The method is used to analyze a set of 271 Miocene large-mammal genus lists from the Great Plains region. Biostratigraphic and radiometric data demonstrate that the “best” arrangement of distributional edges is temporal and corresponds to an age-range chart. The edge sequence is calibrated to the radiometric time scale and used to compute a detailed genus-level ersity curve and to redefine the boundaries between Miocene Land-Mammal Ages and Subages in the Great Plains. Each of the Miocene Ages can be ided into two or three Subages. Diversity levels are apparently low throughout the Early Miocene and rise sharply during the Middle Miocene. Significant drops in ersity occurred at about 17.4, 11.6, 8.7, and 6.5 Ma. The base of the Barstovian corresponds to the base of the Middle Miocene, and the Clarendonian straddles the Middle-Late Miocene boundary.
Publisher: Cambridge University Press (CUP)
Date: 09-2015
DOI: 10.1017/PAB.2015.26
Abstract: A new turnover rate metric is introduced that combines simplicity and precision. Like the related three-timer and gap-filler equations, it involves first identifying a cohort of taxa s led in the time interval preceding the one of interest (call the intervals i 0 and i 1 ). Taxa s led in i 0 and i 1 are two-timers ( t 2 ) those s led in i 0 and i 2 but not i 1 are part-timers ( p ) and taxa s led only in either i 1 , i 2 , or i 3 are newly notated here as either s 1 , s 2 , or s 3 . The gap-filler extinction proportion can be reformulated as ( s 1 − s 3 )/ (t 2 + p) . The method proposed here is to substitute s 3 with the second-highest of the three counts when the expected ordering s 1 ≥ s 2 ≥ s 3 is violated. In simulation, this new estimator yields values that are highly correlated with those produced by the gap-filler equation but more precise. In particular, it rarely produces highly negative values even when s le sizes are quite small. It is mildly upwards biased when s ling is extremely poor and turnover rates are extremely low, but it is otherwise highly accurate. Ex les of Phanerozoic extinction rates for four major marine invertebrate groups are given to illustrate the method’s improved precision. Based on the results, the procedure is recommended for general use.
Publisher: Wiley
Date: 11-2010
Publisher: Cambridge University Press (CUP)
Date: 2011
DOI: 10.1666/10022.1
Abstract: Phanerozoic trends in shell and life habit traits linked to postmortem durability were evaluated for the most common fossil brachiopod, gastropod, and bivalve genera in order to test for changes in taphonomic bias. Using the Paleobiology Database, we tabulated occurrence frequencies of genera for 48 intervals of ∼11 Myr duration. The most frequently occurring genera, cumulatively representing 40% of occurrences in each time bin, were scored for intrinsic durability on the basis of shell size, reinforcement (ribs, folds, and spines), life habit, and mineralogy. Shell durability is positively correlated with the number of genera in a time bin, but durability traits exhibit different temporal patterns across higher taxa, with notable offsets in the timing of changes in these traits. We find no evidence for temporal decreases in durability that would indicate taphonomic bias at the Phanerozoic scale among commonly occurring genera. Also, all three groups show a remarkable stability in mean shell size through the Phanerozoic, an unlikely pattern if strong size-filtering taphonomic megabiases were affecting the fossil record of shelly faunas. Moreover, small shell sizes are attained in the early Paleozoic in brachiopods and in the latest Paleozoic in gastropods but are steady in bivalves unreinforced shells are common to all groups across the entire Phanerozoic organophosphatic and aragonitic shells dominate only the oldest and youngest time bins and microstructures having high organic content are most common in the oldest time bins. In most cases, the timing of changes in durability-related traits is inconsistent with a late Mesozoic Marine Revolution. The post-Paleozoic increase in mean gastropod reinforcement occurs in the early Triassic, suggesting either an earlier appearance and expansion of durophagous predators or other drivers. Increases in shell durability hypothesized to be the result of increased predation in the late Mesozoic are not evident in the common genera examined here. Infaunal life habit does increase in the late Mesozoic, but it does not become more common than levels already attained during the Paleozoic, and only among bivalves does the elevated late Mesozoic level persist through the Holocene. These temporal patterns suggest control on the occurrence of durability-related traits by in idual evolutionary histories rather than taphonomic megabiases. Our findings do not mean taphonomic biases are absent from the fossil record, but rather that their effects apparently have had little net effect on the relative occurrence of shell traits generally thought to confer higher preservation potential over long time scales.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 12-05-2006
Abstract: Ecological interactions, such as predation and bioturbation, are thought to be fundamental determinants of macroevolutionary trends. A data set containing global occurrences of Phanerozoic fossils of benthic marine invertebrates shows escalatory trends in the relative frequency of ecological groups, such as carnivores and noncarnivorous infaunal or mobile organisms. Associations between these trends are either statistically insignificant or interpretable as preservational effects. Thus, there is no evidence that escalation drives macroecological trends at global and million-year time scales. We also find that taxonomic richness and occurrence data are cross-correlated, which justifies the traditional use of one as a proxy of the other.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 03-09-2010
Abstract: Although fossils can provide glimpses of evolution, the accuracy for predictions made on the basis of commonality among geographically and hierarchically distinct taxa is unknown. Alroy (p. 1191 see the Perspective by Marshall ) looked at the global marine fossil record and found that major taxonomic groups of animals have distinctive patterns of ersification and unpredictable responses to mass extinctions. Extrapolating from the current ongoing extinction event predicted a geologically rapid rebound of a number of species, although the future taxonomic composition of the marine biosphere could not be forecast.
Publisher: Cambridge University Press (CUP)
Date: 2000
DOI: 10.1666/0094-8373(2000)026<0319:UTDOTW>2.0.CO;2
Abstract: The study of evolutionary trends is one of the oldest and most intriguing topics in evolutionary biology and paleobiology (McNamara 1990). Workers since Cuvier, Lyell, and Owen have wanted to know if the fossil record demonstrates “progression” within temporal sequences of related organisms. Regardless of whether changes in the average values of morphological characters are progressive in any meaningful sense, these changes are still of great interest. In practice, questions about trends are most commonly framed by paleontologists in terms of “complexity” (however defined) or body size (McShea 1998a).
Publisher: The Royal Society
Date: 10-11-2021
Abstract: Latitudinal ersity gradients are among the most striking patterns in nature. Despite a large body of work investigating both geographic and environmental drivers, biogeographical provinces have not been included in statistical models of ersity patterns. Instead, spatial studies tend to focus on species–area and local–regional relationships. Here, we investigate correlates of a latitudinal ersity pattern in Australian coastal molluscs. We use an online database of greater than 300 000 specimens and quantify ersity using four methods to account for s ling variation. Additionally, we present a biogeographic scheme using factor analysis that allows for both gradients and sharp boundaries between clusters. The factors are defined on the basis of species composition and are independent of ersity. Regardless of the measure used, ersity is not directly explained by combinations of abiotic variables. Instead, transitions between regions better explain the observed patterns. Biogeographic gradients can in turn be explained by environmental variables, suggesting that environmental controls on ersity may be indirect. Faunas within provinces are homogeneous regardless of environmental variability. Thus, transitions between provinces explain most of the variation in ersity because small-scale factors are d ened. This explanation contrasts with the species-energy hypothesis. Future work should more carefully consider biogeographic gradients when investigating ersity patterns.
Publisher: Cold Spring Harbor Laboratory
Date: 23-09-2018
DOI: 10.1101/423780
Abstract: Unbiased time series of ersity dynamics are vital for quantifying the grand history of life. Applications include identifying ancient mass extinctions and inferring both biotic and abiotic controls on ersification rates. We introduce Dyn, a new R package that facilitates the calculation of taxonomic richness, extinction and origination rates from time-binned fossil s ling data. State-of-the-art s ling completeness metrics, counting protocols, and s ling standardisation functions permit the reconstruction of biologically meaningful time series. Additional functions permit the partitioning of turnover rates by trait and environmental affinity. We display Phanerozoic-scale ersity dynamics of marine invertebrates using the Dyn package. Using the core function and standard subs ling options, we revisit earlier assessments of declining extinction and origination rates over time and of equilibrial ersity dynamics to assess their methodological dependency. The modular and fast implementation of published methods ensures traceability, reproducibility, and comparability of future studies.
Publisher: Elsevier BV
Date: 05-1995
Publisher: Informa UK Limited
Date: 12-09-2008
Publisher: Springer Science and Business Media LLC
Date: 09-03-2020
Publisher: Elsevier BV
Date: 10-2015
Publisher: American Association for the Advancement of Science (AAAS)
Date: 21-09-2001
Publisher: Proceedings of the National Academy of Sciences
Date: 16-02-2016
Publisher: No publisher found
Date: 1998
Publisher: Public Library of Science (PLoS)
Date: 25-01-2016
Publisher: American Association for the Advancement of Science (AAAS)
Date: 04-07-2008
Abstract: It has previously been thought that there was a steep Cretaceous and Cenozoic radiation of marine invertebrates. This pattern can be replicated with a new data set of fossil occurrences representing 3.5 million specimens, but only when older analytical protocols are used. Moreover, analyses that employ s ling standardization and more robust counting methods show a modest rise in ersity with no clear trend after the mid-Cretaceous. Globally, locally, and at both high and low latitudes, ersity was less than twice as high in the Neogene as in the mid-Paleozoic. The ratio of global to local richness has changed little, and a latitudinal ersity gradient was present in the early Paleozoic.
Publisher: Springer Science and Business Media LLC
Date: 18-02-2019
DOI: 10.1038/S41559-019-0811-8
Abstract: The fossil record provides one of the strongest tests of the hypothesis that ersity within local communities is constrained over geological timescales. Constraints to ersity are particularly controversial in modern terrestrial ecosystems, yet long-term patterns are poorly understood. Here we document patterns of local richness in Phanerozoic terrestrial tetrapods using a global data set comprising 145,332 taxon occurrences from 27,531 collections. We show that the local richness of non-flying terrestrial tetrapods has risen asymptotically since their initial colonization of land, increasing at most threefold over the last 300 million years. Statistical comparisons support phase-shift models, with most increases in local richness occurring: (1) during the colonization of land by vertebrates, concluding by the late Carboniferous and (2) across the Cretaceous/Paleogene boundary. In idual groups, such as mammals, lepidosaurs and dinosaurs also experienced early increases followed by periods of stasis often lasting tens of millions of years. Mammal local richness abruptly tripled across the Cretaceous/Paleogene boundary, but did not increase over the next 66 million years. These patterns are consistent with the hypothesis that ersity is constrained at the local-community scale.
Publisher: National Academies Press
Date: 22-12-2019
DOI: 10.17226/12501
Publisher: Cambridge University Press (CUP)
Date: 16-03-2020
DOI: 10.1017/PAB.2019.40
Abstract: The choice of measures used to estimate the richness of species, genera, or higher taxa is a crucial matter in paleobiology and ecology. This paper evaluates four methods called shareholder quorum subs ling, true richness estimated using a Poisson s ling model (TRiPS), squares, and the corrected first-order jackknife (cJ1). Quorum subs ling interpolates to produce a relative richness estimate, while the other three extrapolate to the size of the overall species pool. Here I use routine ecological data to show that squares and cJ1 pass several basic validation tests, but TRiPS does not. First, TRiPS estimates are insensitive to the shape of abundance distributions, being entirely predicted by total counts of species and of in iduals regardless of the details. Furthermore, TRiPS tends not to extrapolate at all when s ling is moderate or intense. Second, all three extrapolators yield lower values when they work with small uniform subs les of large raw inventories. The third test is a split-analyze-and-sum analysis: each inventory is ided between the most common and least common halves of the abundance distribution, the methods are applied to the half-inventories, and the estimates are summed. Squares and cJ1 perform well here, but TRiPS does not extrapolate as long as the full inventories are reasonably well-s led. It is otherwise not particularly accurate. The extrapolators are largely insensitive to the influence of abundance distribution evenness, as quantified using Pielou's J and a new index called the ratio of means. Quorum subs ling generally performs well, but it stumbles on the split-analyze-and-sum test and is confounded somewhat by evenness.
Publisher: Wiley
Date: 15-02-2019
Abstract: Integrons are genetic elements that promote rapid adaptation in bacteria by capturing exogenous, mobile gene cassettes. Recently, a subset of gene cassettes has facilitated the global spread of antibiotic resistance. However, outside clinical settings, very little is known about their ersity and spatial ecology. To address this question, we sequenced integron gene cassettes from soils s led across Australia and Antarctica. We recovered 44 970 open reading frames that encoded 27 215 unique proteins, representing an order of magnitude more cassettes than previous sequencing efforts. We found that cassettes have extremely high local richness, significantly greater than previously predicted, with estimates ranging from 4000 to 18 000 unique cassettes per 0.3 g of soil. We show that cassettes have a heterogeneous distribution across space, and that they exhibit rapid turnover with distance. Similarity between s les drops to between 0.1% and 10% at distances of as little as 100 m. Together, these data provide key insights into the ecology and size of the gene cassette metagenome.
Publisher: Research Square Platform LLC
Date: 22-09-2022
DOI: 10.21203/RS.3.RS-2054778/V1
Abstract: Ecological interactions help determine the distribution of species across landscapes and play crucial roles in ecosystem services such as pollination, seed dispersal, and pest control1. Human disturbances, particularly habitat alteration, have the potential to modify or erase ecological interactions2,3 and so jeopardise the processes they control. While ex les of interactions becoming rewired under human influence have been recorded, studies of this process for speciose assemblages at regional to continental scales are uncommon4 and obstructed by logistical difficulties2. The consequences for ecological communities and people are therefore poorly understood. Here we show that human habitat alteration is associated with a decrease in the spatial aggregation of Neotropical bat pairs and bird pairs that share similar dietary requirements. We find that groups of species pairs with similar vs. different diets have positive spatial associations on average, but pairs within dietary guilds have stronger associations than pairs with disparate diets when habitats are relatively intact. Our results suggest that species with similar resource requirements typically coexist in relatively intact natural settings. By contrast, exclusion becomes more common (though not dominant) when habitats are altered. Altered habitats thus fail to support the coexistence of erse competitive interactions, reversing patterns observed in the wild.
Publisher: Wiley
Date: 15-04-2019
DOI: 10.1111/GEB.12912
Publisher: Wiley
Date: 21-11-2016
Publisher: Springer Science and Business Media LLC
Date: 29-01-2016
DOI: 10.1038/NCOMMS10511
Abstract: Late Quaternary megafauna extinctions impoverished mammalian ersity worldwide. The causes of these extinctions in Australia are most controversial but essential to resolve, because this continent-wide event presaged similar losses that occurred thousands of years later on other continents. Here we apply a rigorous metadata analysis and new ensemble-hindcasting approach to 659 Australian megafauna fossil ages. When coupled with analysis of several high-resolution climate records, we show that megafaunal extinctions were broadly synchronous among genera and independent of climate aridity and variability in Australia over the last 120,000 years. Our results reject climate change as the primary driver of megafauna extinctions in the world’s most controversial context, and instead estimate that the megafauna disappeared Australia-wide ∼13,500 years after human arrival, with shorter periods of coexistence in some regions. This is the first comprehensive approach to incorporate uncertainty in fossil ages, extinction timing and climatology, to quantify mechanisms of prehistorical extinctions.
Publisher: Mary Ann Liebert Inc
Date: 03-2003
DOI: 10.1089/153110703321632462
Abstract: North American mammals experienced a major mass extinction at the Cretaceous/Tertiary (K/T) boundary that is tied unambiguously to the Chicxulub impact event. Immediately afterwards, there was an immense adaptive radiation that greatly expanded taxonomic ersity and the range of body sizes and ecological strategies. However, ties between later, Cenozoic impact events and specific episodes in mammalian evolution cannot be demonstrated. A time series of maximum known crater sizes within 1.0-million-year-long temporal bins is shown not to cross-correlate with five separate measures of taxonomic turnover rate, one measure of change in relative taxonomic composition, and four measures of change in body mass distributions. The lack of correlation persists even after excluding the volatile Paleocene mammalian data, adding dummy data to represent intervals without known craters, or lagging the time series against each other for up to 5 million years. Furthermore, the data fail to support broad-brush correspondences between ages of major (>20 km in diameter) craters and the timing of five key, post-K/T biotic transitions, including medium-sized extinction episodes during the late Paleocene and latest Miocene. The results challenge the idea that extraterrestrial impacts drive all, most, or even many extinction and radiation episodes in terrestrial organisms, and add to other evidence that natural, long-term biotic changes are often independent of changes in the physical environment.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 08-06-2001
Abstract: A computer simulation of North American end-Pleistocene human and large herbivore population dynamics correctly predicts the extinction or survival of 32 out of 41 prey species. Slow human population growth rates, random hunting, and low maximum hunting effort are assumed additional parameters are based on published values. Predictions are close to observed values for overall extinction rates, human population densities, game consumption rates, and the temporal overlap of humans and extinct species. Results are robust to variation in unconstrained parameters. This fully mechanistic model accounts for megafaunal extinction without invoking climate change and secondary ecological effects.
Publisher: The Royal Society
Date: 2017
Abstract: Extinction is a key feature of the evolutionary history of life, and assessments of extinction risk are essential for the effective protection of bio ersity. The goal in assembling this special issue of Biology Letters was to highlight problems and questions at the research frontier of extinction biology, with an emphasis on recent developments in the methodology of inferring the patterns and processes of extinction from a background of often noisy and sparse data. In selecting topics, we sought to illustrate how extinction is not simply a self-evident phenomenon, but the subject of a dynamic and quantitatively rigorous field of natural science, with practical applications to conservation.
Publisher: Cambridge University Press (CUP)
Date: 05-05-2016
DOI: 10.1017/PAB.2016.12
Abstract: Few methods exist that put a posterior probability on the hypothesis that a thing is gone forever given its sighting history. A recently proposed Bayesian method is highly accurate but aggressive, generating many near-zero or near-one probabilities of extinction. Here I explore a Bayesian method called the agnostic equation that makes radically different assumptions and is much more conservative. The method assumes that the overall prior probability of extinction is 50% and that slices of the prior are exponentially distributed across the time series. The conditional probability of the data given survival is based on a simple, long-known combinatorial expression that captures the chance all presences would fall at random before or within the last sighting’s interval ( L ) given that they could fall anywhere. The same equation is used to compute the conditional probability given extinction at the start of each interval i , that is, the chance that all sightings would fall before or within L given that none could equal or postdate i . The conditional probability is zero for all hypothesized extinction intervals through L . Bayes’s theorem is then used to compute the posterior extinction probability. It is noted that recycling the mean posterior for a population as a prior improves the method’s accuracy. The agnostic equation differs from an earlier, related one, because it explicitly includes a term to represent the hypothesis of survival, and it therefore does not assume that the species has necessarily gone extinct within the s ling window. Simulations demonstrate that the posterior extinction probabilities are highly accurate when considered as a suite but in idually indecisive, rarely approaching one. This property is advantageous whenever inferring extinction would have dangerous consequences. The agnostic method is therefore advocated in cases where conservative estimates are desired.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 15-03-2002
Abstract: A profound faunal reorganization occurred near the Paleocene/Eocene boundary, when several groups of mammals abruptly appeared on the Holarctic continents. To test the hypothesis that this event featured the dispersal of groups from Asia to North America and Europe, we used isotope stratigraphy, magnetostratigraphy, and quantitative biochronology to constrain the relative age of important Asian faunas. The extinct family Hyaenodontidae appeared in Asia before it did so in North America, and the modern orders Primates, Artiodactyla, and Perissodactyla first appeared in Asia at or before the Paleocene/Eocene boundary. These results are consistent with Asia being a center for early mammalian origination.
Publisher: Informa UK Limited
Date: 12-09-2007
Publisher: Cambridge University Press (CUP)
Date: 2011
Publisher: Wiley
Date: 03-2016
DOI: 10.1002/ECY.1321
Publisher: Proceedings of the National Academy of Sciences
Date: 05-2017
Abstract: Biologists believe that a major mass extinction is happening in the tropics. Destruction of forests is a key reason. However, there are no solid predictions of the percentage of species that will go extinct as more and more forests are disturbed. This paper provides estimates based on extrapolating the respective numbers of species in disturbed and undisturbed habitats. It uses a large global database of species inventories at particular sites. Trees and 10 groups of animals are analyzed. All the disturbed habitats put together include 41% fewer species than the undisturbed forests. This proportion varies among groups but is always substantial. Furthermore, disturbed local communities are dominated by widespread species such as rats and electric ants.
Publisher: Cambridge University Press (CUP)
Date: 1994
DOI: 10.1017/S0094837300012677
Abstract: The fundamental goal of biochronology is ordering taxonomic first and last appearance events. The most useful biochronologic data are of the form “the first appearance event of one taxon predates the last appearance event of a second taxon” (FAE LAE). FAE LAE data sets are unusually reliable because they converge on a unique solution with greater s ling. The fact that the FAE of one taxon i the LAE of another taxon j always can be inferred either if i is found lower than j in a stratigraphic section, or if i and j co-occur in at least one taxonomic list. Thus, FAE LAE data accurately synthesize two disparate sources of information: routine biostratigraphic observations and taxonomic lists that may have no stratigraphic context. Appearance event ordination, the new method introduced here, is intended to summarize FAE LAE data. The algorithm is founded on the following parsimony criterion: arrangements of FAEs and LAEs should always imply FAE i LAE j when this is known, and otherwise imply LAE j FAE i whenever possible. The technique differs from others related to correspondence analysis in its use of FAE LAE data and explicit definition as a parsimony method. The algorithm is even more unique in that it uses different subsets of FAE i LAE j statements at each iterative step, converging on separate sets of scores for the FAEs and LAEs. After arranging either the FAEs or the LAEs on the basis of their scores, the other set of scores can be discarded and the best arrangement of the remaining events can be inferred directly. An analysis of the Plio-Pleistocene mammalian record in the Lake Turkana region is used to illustrate the method. Biochronologic resolution on the order of 0.2-1.5 m.y. is achieved. The Turkana species lists by themselves demonstrate enough FAE i LAE j relationships to resolve the basic biochronologic pattern, but stratigraphic information is still of great use.
Publisher: Proceedings of the National Academy of Sciences
Date: 05-10-2015
Abstract: It is hard to know how many species have gone extinct so far because it is difficult to prove that something not seen recently is really gone forever. This paper uses a new, highly conservative statistical method to infer the number of extinct hibian and reptile species across the world. Frogs are of particular concern because an invasive fungus has recently caused many populations to collapse. The data are lists of specimens in museum collections. The method provides sensible results when the data are randomized or artificial extinctions are imposed. It suggests that about 200 frog extinctions have occurred and hundreds more will be lost over the next century, so we are on pace to create a mass extinction.
Publisher: Informa UK Limited
Date: 02-11-2012
Publisher: Springer Science and Business Media LLC
Date: 22-06-2021
DOI: 10.1186/S12862-021-01863-0
Abstract: The orogeny of the eastern Mediterranean region has substantially affected ecological speciation patterns, particularly of mountain-dwelling species. Mountain vipers of the genus Montivipera are among the paramount ex les of Mediterranean neo-endemism, with restricted ranges in the mountains of Anatolia, the Levant, Caucasus, Alborz, and Zagros. Here we explore the phylogenetic and ecological ersification of Montivipera to reconstruct its ecological niche evolution and biogeographic history. Using 177 sequences of three mitochondrial genes, a dated molecular phylogeny of mountain vipers was reconstructed. Based on 320 occurrence points within the entire range of the genus and six climatic variables, ecological niches were modelled and used to infer ancestral niche occupancy. In addition, the biogeographic history and ancestral states of the species were reconstructed across climate gradients. Dated phylogenetic reconstruction revealed that the ancestor of mountain vipers split into two major clades at around 12.18 Mya followed by multiple vicariance events due to rapid orogeny. Montivipera colonised coastal regions from a mountain-dwelling ancestor. We detected a highly complex ecological niche evolution of mountain vipers to temperature seasonality, a variable that also showed a strong phylogenetic signal and high contribution in niche occupation. Raising mountain belts in the Eastern Mediterranean region and subsequent remarkable changes in temperature seasonality have led to the formation of important centres of ersification and endemism in this bio ersity hotspot. High rates of niche conservatism, low genetic ersity, and segregation of ranges into the endemic distribution negatively influenced the adaptive capacity of mountain vipers. We suggest that these species should be considered as evolutionary significant units and priority species for conservation in Mediterranean mountain ecosystems.
Publisher: Cambridge University Press (CUP)
Date: 2023
DOI: 10.1017/EXT.2023.2
Abstract: Extinction is a new open-access journal focused on the patterns and processes underlying the loss of bio ersity. It aims to inform conservation efforts, with a broad spatial and temporal scope. Extinction biology – the scientific study of species loss – has a long history and has recently become a more interdisciplinary and integrated field. This journal offers a unique, synthetic forum in which to present cutting-edge research and discuss its implications. This includes ecological, molecular, paleontological, and social perspectives, based on empirical data, theory, and modelling, to understand extinction processes. By tackling the big challenges, the research published in Extinction will be valuable for researchers and practitioners concerned with extinction and its role in shaping the history and future of life on Earth.
Publisher: Wiley
Date: 03-03-2015
DOI: 10.1111/COBI.12471
Abstract: Captive breeding of mammals in zoos is the last hope for many of the best-known endangered species and has succeeded in saving some from certain extinction. However, the number of managed species selected is relatively small and focused on large-bodied, charismatic mammals that are not necessarily under strong threat and not always good candidates for reintroduction into the wild. Two interrelated and more fundamental questions go unanswered: have the major breeding programs succeeded at the basic level of maintaining and expanding populations, and is there room to expand them? I used published counts of births and deaths from 1970 to 2011 to quantify rates of growth of 118 captive-bred mammalian populations. These rates did not vary with body mass, contrary to strong predictions made in the ecological literature. Most of the larger managed mammalian populations expanded consistently and very few programs failed. However, growth rates have declined dramatically. The decline was predicted by changes in the ratio of the number of in iduals within programs to the number of mammal populations held in major zoos. Rates decreased as the ratio of in iduals in programs to populations increased. In other words, most of the programs that could exist already do exist. It therefore appears that debates over the general need for captive-breeding programs and the best selection of species are moot. Only a concerted effort could create room to manage a substantially larger number of endangered mammals.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 05-1998
DOI: 10.1126/SCIENCE.280.5364.731
Abstract: Body mass estimates for 1534 North American fossil mammal species show that new species are on average 9.1% larger than older species in the same genera. This within-lineage effect is not a s ling bias. It persists throughout the Cenozoic, accounting for the gradual overall increase in average mass (Cope's rule). The effect is stronger for larger mammals, being near zero for small mammals. This variation partially explains the unwavering lower size limit and the gradually expanding mid-sized gap, but not the sudden large increase in the upper size limit, at the Cretaceous-Tertiary boundary.
Publisher: California Digital Library (CDL)
Date: 07-09-2022
DOI: 10.21425/F5FBG56553
Publisher: Wiley
Date: 02-2015
DOI: 10.1890/14-0471.1
Abstract: Pairwise similarity coefficients are downward biased when s les only record presences and s ling is partial. A simple but forgotten index proposed by Stephen Forbes in 1907 can help solve this problem. His original equation requires knowing the number of species absent in both s les that could have been present. It is proposed that this count should simply be ignored and that the coefficient should be adjusted using a simple heuristic correction. Four analyses show that the corrected equation outperforms the Dice and Simpson indices, which are highly correlated with many others. In two-s le simulations, similarity is almost always closer to the assumed value when the species pool size and s ling intensity are varied, regardless of whether the underlying abundance distribution is uniform, log-normal, or geometric. The index is also much more robust when s ling is unequal. An analysis of bat s les from peninsular Malaysia buttresses these conclusions. The corrected coefficient also indicates that local assemblages of North American mammals are random subs les of larger species pools by returning similarity of values of around 1, and it suggests a more consistent relationship between biome-scale comparisons and local-scale comparisons. Finally, it yields a better-dispersed pattern when the biome-scale inventories are ordinated. If these results are generalizable, then the new and old equation should see wide application, potentially taking the place of the two most commonly used alternatives (the interrelated Dice and Jaccard indices) whenever s ling is incomplete.
Publisher: The Royal Society
Date: 08-04-2020
Abstract: There is no consensus about how terrestrial bio ersity was assembled through deep time, and in particular whether it has risen exponentially over the Phanerozoic. Using a database of 60 859 fossil occurrences, we show that the spatial extent of the worldwide terrestrial tetrapod fossil record itself expands exponentially through the Phanerozoic. Changes in spatial s ling explain up to 67% of the change in known fossil species counts, and these changes are decoupled from variation in habitable land area that existed through time. Spatial s ling therefore represents a real and profound s ling bias that cannot be explained as redundancy. To address this bias, we estimate terrestrial tetrapod ersity for palaeogeographical regions of approximately equal size. We find that regional-scale ersity was constrained over timespans of tens to hundreds of millions of years, and similar patterns are recovered for major subgroups, such as dinosaurs, mammals and squamates. Although the Cretaceous/Palaeogene mass extinction catalysed an abrupt two- to three-fold increase in regional ersity 66 million years ago, no further increases occurred, and recent levels of regional ersity do not exceed those of the Palaeogene. These results parallel those recovered in analyses of local community-level richness. Taken together, our findings strongly contradict past studies that suggested unbounded ersity increases at local and regional scales over the last 100 million years.
Publisher: Wiley
Date: 10-2018
DOI: 10.1111/ELE.13152
Abstract: Are communities limited by biotic interactions, or are they random draws from regional species pools? One way to tell is to compare total species counts in geographic regions to average counts in ecological s les falling within those regions. If species richness is limited regionally, then the relationship should be curvilinear even in a log‐log space. Global sets of s les including trees and 10 groups of animals are analysed to test this hypothesis. Most relationships are indeed curvilinear. To explain these patterns, a simple model is proposed that invokes biotic interaction‐limited speciation or immigration rates combined with extinction or extirpation rates that fall as the number of occupied patches increases. Local and regional richness come into balance as the rates trade off, causing global richness to also be limited. Surprisingly, however, the data for trees break the pattern, suggesting that the great adaptive radiation of seed plants may still be unfolding.
Publisher: The Royal Society
Date: 10-02-2016
Abstract: During the Pleistocene, Australia and New Guinea supported a rich assemblage of large vertebrates. Why these animals disappeared has been debated for more than a century and remains controversial. Previous synthetic reviews of this problem have typically focused heavily on particular types of evidence, such as the dating of extinction and human arrival, and have frequently ignored uncertainties and biases that can lead to misinterpretation of this evidence. Here, we review erse evidence bearing on this issue and conclude that, although many knowledge gaps remain, multiple independent lines of evidence point to direct human impact as the most likely cause of extinction.
Publisher: Oxford University Press (OUP)
Date: 05-2003
Publisher: American Association for the Advancement of Science (AAAS)
Date: 04-09-2015
Abstract: Findings of a new, low-dominance distribution of terrestrial abundance: the double geometric.
Publisher: Proceedings of the National Academy of Sciences
Date: 15-05-2001
Abstract: Global ersity curves reflect more than just the number of taxa that have existed through time: they also mirror variation in the nature of the fossil record and the way the record is reported. These s ling effects are best quantified by assembling and analyzing large numbers of locality-specific biotic inventories. Here, we introduce a new database of this kind for the Phanerozoic fossil record of marine invertebrates. We apply four substantially distinct analytical methods that estimate taxonomic ersity by quantifying and correcting for variation through time in the number and nature of inventories. Variation introduced by the use of two dramatically different counting protocols also is explored. We present s ling-standardized ersity estimates for two long intervals that sum to 300 Myr (Middle Ordovician-Carboniferous Late Jurassic-Paleogene). Our new curves differ considerably from traditional, synoptic curves. For ex le, some of them imply unexpectedly low late Cretaceous and early Tertiary ersity levels. However, such factors as the current emphasis in the database on North America and Europe still obscure our view of the global history of marine bio ersity. These limitations will be addressed as the database and methods are refined.
Publisher: Cambridge University Press (CUP)
Date: 2014
DOI: 10.1666/13036
Abstract: Paleobiologists have used many different methods for estimating rates of origination and extinction. Unfortunately, all equations that consider entire age ranges are distorted by the Pull of the Recent, the Signor-Lipps effect, and simple edge effects. Attention has been paid recently to an equation of Foote's that considers counts of taxa either crossing the bottom and top of an interval or crossing one boundary but not the other. This generalized boundary-crosser (BC) method has important advantages but is still potentially subject to the major biases. The only published equation that circumvents all of them is the three-timer (3T) log ratio, which does so by focusing on a four-interval moving window. Although it is highly accurate it is noisy when turnover rates are very high or s ling is very poor. More precise values are yielded by a newly derived equation that uses the same counts. However, it also considers taxa s led in a window's first and fourth intervals but missing from the third (i.e., gap-fillers). Simulations show that the 3T, gap-filler (GF), and BC equations yield identical values when s ling and turnover are uniform through time. When applied to Phanerozoic-scale marine animal data, 3T and GF agree well but the BC rates are systematically lower. The apparent reason is that (1) long-ranging but infrequently s led genera are less likely to be split up by taxonomists and (2) the BC equation overweights taxa with long ranges. Thus, BC rates pertain more to rare genera that are likely to represent large clades whereas GF rates pertain more to actual species-level patterns. Given these results, all published turnover rates based either on genus-level data or on age ranges must be reconsidered because they may reflect taxonomic practices more strongly than the species-level dynamics of interest to biologists.
Publisher: Cambridge University Press (CUP)
Date: 24-02-2015
DOI: 10.1017/PAB.2014.21
Abstract: Multivariate methods such as cluster analysis and ordination are basic to paleoecology, but the messy nature of fossil occurrence data often makes it difficult to recover clear patterns. A recently described faunal similarity index based on the Forbes coefficient improves results when its complement is employed as a distance metric. This index involves adding terms to the Forbes equation and ignoring one of the counts it employs (that of species found in neither of the s les under consideration). Analyses of simulated data matrices demonstrate its advantages. These matrices include large and small s les from two partially overlapping species pools. In a cluster analysis, the widely used Dice coefficient and the Euclidean distance metric both create groupings that reflect s le size, the Simpson index suggests large differences that do not exist, and the corrected Forbes index creates groupings based strictly on true faunal overlap. In a principal coordinates analysis (PCoA) the Forbes index almost removes the s le-size signal but other approaches create a second axis strongly dominated by s le size. Meanwhile, species lists of late Pleistocene mammals from the United States capture biogeographic signals that standard ordination methods do recover, but the adjusted Forbes coefficient spaces the points out more sensibly. Finally, when biome-scale lists for living mammals are added to the data set and extinct species are removed, correspondence analysis misleadingly separates out the biome lists, and PCoA based on the Dice coefficient places them to the edge of the cloud of fossil assemblage data points. PCoA based on the Forbes index places them in more reasonable positions. Thus, only the adjusted Forbes index is able to recover true biological patterns. These results suggest that the index may be useful in analyzing not only paleontological data sets but any data set that includes species lists having highly variable lengths.
Publisher: Proceedings of the National Academy of Sciences
Date: 12-03-2002
Abstract: Estimates of bio ersity in both living and fossil groups depend on raw counts of currently recognized named species, but many of these names eventually will prove to be synonyms or otherwise invalid. This difficult bias can be resolved with a simple “flux ratio” equation that compares historical rates of invalidation and revalidation. Flux ratio analysis of a taxonomic data set of unrivalled completeness for 4,861 North American fossil mammal species shows that 24–31% of currently accepted names eventually will prove invalid, so ersity estimates are inflated by 32–44%. The estimate is conservative compared with one obtained by using an older, more basic method. Although the degree of inflation varies through both historical and evolutionary time, it has a minor impact on previously published background origination and extinction rates. Several lines of evidence suggest that the same bias probably affects more poorly studied, hyper erse living groups such as fungi and insects. If so, then current estimates of total global ersity could be revised downwards to as low as 3.5–10.5 million species.
Publisher: Cambridge University Press (CUP)
Date: 2014
DOI: 10.1666/13074
Abstract: Determining whether a species has gone extinct is a central problem in both paleobiology and conservation biology. Past literature has mostly employed equations that yield confidence intervals around the endpoints of temporal ranges. These frequentist methods calculate the chance of not having seen a species lately given that it is still alive (a conditional probability). However, any reasonable person would instead want to know the chance that a species is extinct given that it has not been seen (the posterior probability). Here, I present a simple Bayesian equation that estimates posteriors. It uninterestingly assumes that the s ling probability equals the frequency of sightings within the range. It interestingly sets the prior probability of going extinct during any one time interval (E) by assuming that extinction is an exponential decay process and there is a 50% chance a species has gone extinct by the end of its observed range. The range is first adjusted for unders ling by using a routine equation. Bayes' theorem is then used to compute the posterior for interval 1 (ε 1 ), which becomes the prior for interval 2. The following posterior ε 2 again incorporates E because extinction might have happened instead during interval 2. The posteriors are called “creeping-shadow-of-a-doubt values” to emphasize the uniquely iterative nature of the calculation. Simulations show that the method is highly accurate and precise given moderate to high s ling probabilities and otherwise conservative, robust to random variation in s ling, and able to detect extinction pulses after a short lag. Improving the method by having it consider clustering of sightings makes it highly resilient to trends in s ling. Ex le calculations involving recently extinct Costa Rican frogs and Maastrichtian ammonites show that the method helps to evaluate the status of critically endangered species and identify species likely to have gone extinct below some stratigraphic horizon.
Publisher: Cambridge University Press (CUP)
Date: 12-1994
Publisher: Oxford University Press (OUP)
Date: 09-1994
Start Date: 05-2010
End Date: 12-2014
Amount: $788,800.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2021
End Date: 12-2023
Amount: $391,000.00
Funder: Australian Research Council
View Funded Activity