Can extinction rates be estimated without fossils?

Paradis, Emmanuel

doi:10.1016/j.jtbi.2004.02.018

Cited by 58 publications

(69 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our results add to a growing body of evidence that larger bodied animals are more susceptible to extinction. The lack of significance for historical patterns of extinction may indicate that methods to detect extinction rates from extant species are severely compromised in statistical power [10,11,18,48,49,53]. Intriguingly, we found some evidence that speciation rates appear to increase with body mass in primates (see also [50]).…”

Section: Discussionmentioning

confidence: 74%

“…It could be that higher threat categories among largebodied primates have resulted only from anthropogenic effects in the present. Alternatively, the tests may have failed to detect differences because available methods to estimate historical extinction rates suffer from low statistical power ( [10], see also [11,18,48,49,52,53]). Using simulations, for example, Maddison et al [10] showed that the power to detect variation in speciation rates is relatively high (power for speciation in simulations of 500 species was approx.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Primate extinction risk and historical patterns of speciation and extinction in relation to body mass

et al. 2010

View full text Add to dashboard Cite

Body mass is thought to influence diversification rates, but previous studies have produced ambiguous results. We investigated patterns of diversification across 100 trees obtained from a new Bayesian inference of primate phylogeny that sampled trees in proportion to their posterior probabilities. First, we used simulations to assess the validity of previous studies that used linear models to investigate the links between IUCN Red List status and body mass. These analyses support the use of linear models for ordinal ranked data on threat status, and phylogenetic generalized linear models revealed a significant positive correlation between current extinction risk and body mass across our tree block. We then investigated historical patterns of speciation and extinction rates using a recently developed maximumlikelihood method. Specifically, we predicted that body mass correlates positively with extinction rate because larger bodied organisms reproduce more slowly, and body mass correlates negatively with speciation rate because smaller bodied organisms are better able to partition niche space. We failed to find evidence that extinction rates covary with body mass across primate phylogeny. Similarly, the speciation rate was generally unrelated to body mass, except in some tests that indicated an increase in the speciation rate with increasing body mass. Importantly, we discovered that our data violated a key assumption of sample randomness with respect to body mass. After correcting for this bias, we found no association between diversification rates and mass.

show abstract

Section: Discussionmentioning

confidence: 74%

Section: Discussionmentioning

confidence: 99%

Primate extinction risk and historical patterns of speciation and extinction in relation to body mass

et al. 2010

View full text Add to dashboard Cite

show abstract

“…Because estimates of extinction rates on phylogenies of extant taxa from these and similar methods (e.g. QuaSSE) have large variances and bias, they must be interpreted with caution without additional data from the fossil record [69,[71][72][73][74].…”

Section: Resultsmentioning

confidence: 99%

The role of ecological opportunity in shaping disparate diversification trajectories in a bicontinental primate radiation

Tran

2014

Proc. R. Soc. B.

View full text Add to dashboard Cite

Exceptional species and phenotypic diversity commonly are attributed to ecological opportunity (EO). The conventional EO model predicts that rates of lineage diversification and phenotypic evolution are elevated early in a radiation only to decline later in response to niche availability. Foregut fermentation is hypothesized to be a key innovation that allowed colobine monkeys (subfamily Colobinae), the only primates with this trait, to successfully colonize folivore adaptive zones unavailable to other herbivorous species. Therefore, diversification rates also are expected to be strongly linked with the evolution of traits related to folivory in these monkeys. Using dated molecular phylogenies and a dataset of feeding morphology, I test predictions of the EO model to evaluate the role of EO conferred by foregut fermentation in shaping the African and Asian colobine radiations. Findings from diversification methods coupled with colobine biogeographic history provide compelling evidence that decreasing availability of new adaptive zones during colonization of Asia together with constraints presented by dietary specialization underlie temporal changes in diversification in the Asian but not African clade. Additionally, departures from the EO model likely reflect iterative diversification events in Asia.

show abstract

“…Obviously, any incorporation of fossil data to phylogenetic inference will improve our ability to understand diversity dynamics (20,21,(34)(35)(36), and our likelihood expressions can be modified to incorporate some types of fossil information (SI Results). However, we have shown here that molecular phylogenies alone can recover diversity dynamics that are consistent with the fossil record.…”

Section: Discussionmentioning

confidence: 99%

Reconciling molecular phylogenies with the fossil record

Morlon

Parsons

Plotkin

2011

Proc. Natl. Acad. Sci. U.S.A.

354

669

View full text Add to dashboard Cite

Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record. According to the fossil record, species frequently go extinct, and many clades experience periods of dramatic diversity loss. However, most analyses of molecular phylogenies fail to identify any periods of declining diversity, and they typically infer low levels of extinction. This striking inconsistency between phylogenies and fossils limits our understanding of macroevolution, and it undermines our confidence in phylogenetic inference. Here, we show that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies. To make this inference, we derive an analytic expression for the likelihood of a phylogeny that accommodates scenarios of declining diversity, time-variable rates, and incomplete sampling; we show that this likelihood expression reliably detects periods of diversity loss using simulation. We then study the cetaceans (whales, dolphins, and porpoises), a group for which standard phylogenetic inferences are strikingly inconsistent with fossil data. When the cetacean phylogeny is considered as a whole, recently radiating clades, such as the Balaneopteridae, Delphinidae, Phocoenidae, and Ziphiidae, mask the signal of extinctions. However, when isolating these groups, we infer diversity dynamics that are consistent with the fossil record. These results reconcile molecular phylogenies with fossil data, and they suggest that most extant cetaceans arose from four recent radiations, with a few additional species arising from clades that have been in decline over the last ∼10 Myr.I nferring rates of speciation and extinction and the resulting pattern of diversity over geological time scales is one of the most fundamental but challenging questions in biodiversity studies (1-4). Traditionally, biologists have relied on the fossil record to study long-term diversity dynamics (4-7). However, many groups, including terrestrial insects, birds, and plants, lack an adequate fossil record. Methods have therefore been developed to estimate speciation and extinction rates and test hypotheses about the mechanisms governing diversification using phylogenies of extant species reconstructed from molecular data (1,(8)(9)(10)(11)(12)(13)(14). These methods have raised the possibility of inferring diversity dynamics for groups that lack a detailed fossil record.Given the large number of taxonomic groups that lack fossil data, approaches that rely on extant taxa alone are critically important. However, recent studies have highlighted major inconsistencies between the diversity dynamics inferred from phylogenies and those dynamics inferred from the fossil record (4,11,15). For example, the fossil record clearly shows that the diversity of cetaceans has declined over the last 10 Myr (4, 16), whereas two recent phylogeny-based maximum likelihood analyses of this group would suggest that cetacean diversity has been expanding (17, 18). More generally, phylogeny-bas...

show abstract

Can extinction rates be estimated without fossils?

Cited by 58 publications

References 26 publications

Primate extinction risk and historical patterns of speciation and extinction in relation to body mass

Primate extinction risk and historical patterns of speciation and extinction in relation to body mass

The role of ecological opportunity in shaping disparate diversification trajectories in a bicontinental primate radiation

Reconciling molecular phylogenies with the fossil record

Contact Info

Product

Resources

About