Detecting shifts in diversity limits from molecular phylogenies: what can we know?

McInnes, Lynsey; Purvis, Andy

doi:10.1098/rspb.2011.0241

Cited by 20 publications

(18 citation statements)

References 61 publications

(136 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…McInnes et al [125] have also discussed the inadequacies of molecular phylogenies for detecting ancient diversification shifts. By contrast, Morlon et al [126] have shown that diversification dynamics inferred from molecular phylogenies can be concordant with the fossil record if rate variation through time and among major taxonomic groups is taken into account.…”

Section: Discussionmentioning

confidence: 99%

Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

et al. 2012

View full text Add to dashboard Cite

Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71–63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event (“Grande Coupure”) at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.

show abstract

Section: Discussionmentioning

confidence: 99%

Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

et al. 2012

View full text Add to dashboard Cite

show abstract

“…We argue that diversity dependence again plays a key role, in both types of shift. The clade-wide rate shifts occur when external factors create new ecological opportunities for all lineages (McInnes et al 2011), for instance, climate change (Ezard et al 2011) or tectonic movement (e.g., cetaceans diversifying more rapidly due to restructuring of the oceans; Steeman et al 2009). These external factors, in creating more niche space, most likely affect the clade-level carrying capacity rather than the intrinsic speciation rate or extinction rate.…”

Section: A Coherent Framework For Adaptive Radiationsmentioning

confidence: 99%

A Conceptual and Statistical Framework for Adaptive Radiations with a Key Role for Diversity Dependence

Etienne

Haegeman

2012

The American Naturalist

117

142

View full text Add to dashboard Cite

In this article we propose a new framework for studying adaptive radiations in the context of diversity-dependent diversification. Diversity dependence causes diversification to decelerate at the end of an adaptive radiation but also plays a key role in the initial pulse of diversification. In particular, key innovations (which in our definition include novel traits as well as new environments) may cause decoupling of the diversity-dependent dynamics of the innovative clade from the diversity-dependent dynamics of its ancestral clade. We present a likelihood-based inference method to test for decoupling of diversity dependence using molecular phylogenies. The method, which can handle incomplete phylogenies, identifies when the decoupling took place and which diversification parameters are affected. We illustrate our approach by applying it to the molecular phylogeny of the North American clade of the legume tribe Psoraleeae (47 extant species, of which 4 are missing). Two diversification rate shifts were previously identified for this clade; our analysis shows that the first, positive shift can be associated with decoupling of two Pediomelum subgenera from the other Psoraleeae lineages, while we argue that the second, negative shift can be attributed to speciation being protracted. The latter explanation yields nonzero extinction rates, in contrast to previous findings. Our framework offers a new perspective on macroevolution: new environments and novel traits (ecological opportunity) and diversity dependence (ecological limits) cannot be considered separately.

show abstract

“…It has the limitation of not distinguishing whether differences in diversification are due to speciation or extinction (this may be inferred, in cases). Estimating diversification rates from species-level phylogenies has greater power to detect the effect of a candidate trait on diversification, and estimating speciation and extinction rates has the advantage of directly distinguishing between those two mechanisms (though the power to do so is often limited; (Rabosky and McCune 2010;McInnes et al 2011;Morlon et al 2011). The two latter approaches have the disadvantage of focusing on a single candidate trait.…”

Section: Introductionmentioning

confidence: 99%

Ecological Marginalization Facilitated Diversification in Conifers

2015

View full text Add to dashboard Cite

Species selection occurs when species traits influence speciation or extinction. But it is often difficult to demonstrate a net effect of traits on diversification, for example due to balancing effects of extinction and speciation. We tested if, since conifers lost their former status of dominant land plants to angiosperm trees, their extant diversity shows a signature of traits conferring resistance to extinction. We compared extant species richness across conifer genera in relation to phenotypic and ecological traits predicted to affect speciation and/or extinction, in two geographic regions that experienced distinct regimes of extinction and species turnover (the northern vs. southern hemispheres). Species richness had low phylogenetic signal across conifer genera, and species-rich genera were not older than species-poor ones, indicating intrinsic differences in diversification. High-altitude genera, which are ecologically more dissimilar to angiosperm trees, were more species-rich, suggesting that distinctiveness from angiosperm competitors facilitated conifer diversification. This effect seems more due to increased speciation than to reduced extinction, because it was unique to northern hemisphere genera, where rates of extinction and species turnover have been higher than in the south. We found no strong evidence that resistance to extinction was the main mechanism of species selection in conifers. Instead, having a marginal ecological niche relative to angiosperm competitors facilitated diversification in conifers, likely due to increased speciation. Resistance to extinction may nonetheless have been important in certain ancient lineages, and we discuss suggestive results for traits that may explain the endurance of such lineages.

show abstract

Detecting shifts in diversity limits from molecular phylogenies: what can we know?

Cited by 20 publications

References 61 publications

Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

A Conceptual and Statistical Framework for Adaptive Radiations with a Key Role for Diversity Dependence

Ecological Marginalization Facilitated Diversification in Conifers

Contact Info

Product

Resources

About