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17 results for “Diversity-dependence”
Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification
One of the primary goals of macroevolutionary biology has been to explain general trends in long-term diversity patterns, including whether such patterns correspond to an up-scaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity-dependent diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time-dependence without diversity-dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time-dependent, but diversity-independent model that matches the expected diversity through time of a diversity-dependent model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity-dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity-dependence. We advocate that tests encompassing additional data, e.g., traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.
Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification
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Data and code for: Diversity-dependent diversification in the history of marine animals
<p>By comparing detrended estimates of diversity (taxonomic richness) and rates of origination, extinction, and net diversification, I show that, at the global scale over the course of the Phanerozoic Eon, rates of diversification and origination are negatively correlated with diversity. By contrast, extinction rates are only weakly correlated with diversity for the most part. These results hold for both genus- and species-level data and for many alternative analytical protocols. The asymmetry between extinction on the one hand and origination and net diversification, on the other hand, supports a model whereby extinction is largely driven by abiotic perturbations, with subsequent origination filling the void left by depleted diversity. Diversity-dependence is somewhat weaker, but still evident, if the initial Ordovician radiation or rebounds from major mass extinctions are omitted from analysis; thus, diversity-dependence is influenced, but not dominated, by these special intervals of Earth history. In the transition from Paleozoic to post-Paleozoic time, diversity-dependence of origination weakens while that of extinction strengthens; however, diversity-dependence of net diversification barely changes in strength. Despite nuances, individual clades largely yield results consistent with those for the aggregate data on all animals. On the whole, diversity-dependent diversification appears to be a pervasive factor in the macroevolution of marine animal life.</p>
Data and code for: Diversity-dependent diversification in the history of marine animals
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Data from: Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution
A long-standing hypothesis in adaptive radiation theory is that ecological opportunity constrains rates of phenotypic evolution, generating a burst of morphological disparity early in clade history. Empirical support for the early burst model is rare in comparative data, however. One possible reason for this lack of support is that most phylogenetic tests have focused on extant clades, neglecting information from fossil taxa. Here, I test for the expected signature of adaptive radiation using the outstanding 40-My fossil record of North American canids. Models implying time- and diversity-dependent rates of morphological evolution are strongly rejected for two ecologically important traits, body size and grinding area of the molar teeth. Instead, Ornstein–Uhlenbeck processes implying repeated, and sometimes rapid, attraction to distinct dietary adaptive peaks receive substantial support. Diversity-dependent rates of morphological evolution seem uncommon in clades, such as canids, that exhibit a pattern of replicated adaptive radiation. Instead, these clades might best be thought of as deterministic radiations in constrained Simpsonian subzones of a major adaptive zone. Support for adaptive peak models may be diagnostic of subzonal radiations. It remains to be seen whether early burst or ecological opportunity models can explain broader adaptive radiations, such as the evolution of higher taxa.
Explosive Cenozoic origin and diversity-dependent diversification dynamics shaped the evolution of Australian skipper butterflies
<p><span>Australia was predominantly tropical for most of the early Cenozoic, then transitioned to a cooler and drier climate in the Oligocene. In response to this increasing aridity, some lineages adapted to more xeric ecosystems, contracted, or became restricted to increasingly fragmented mesic refugia, or went extinct. Yet, the lack of macroevolutionary studies at a continental scale precludes a better understanding of Australian biodiversity patterns and processes during the Cenozoic. Here, we infer a robust dated phylogenomic tree for a radiation of Australian endemic butterflies, the Trapezitinae skippers, to test the impact of biotic and abiotic drivers on Cenozoic diversification dynamics in Australia. These butterflies originated during the Eocene (<em>ca</em>. 42 Ma) in the mesic biome of Australia. Trapezitinae exploded in diversity during a cool, dry period in the late Oligocene and early Miocene, then experienced a sharp deceleration in speciation. Xeric ecosystems appear to have been colonized more recently, supporting the hypothesis of arid and semi-arid biomes as evolutionary sinks. Temperature-dependent and phytophagy-dependent diversification models received little support. Instead, we find evidence for diversity-dependent processes with a declining diversification in Trapezitinae likely linked to limited ecological opportunities following a rapid initial burst of diversification.</span></p>
Explosive Cenozoic origin and diversity-dependent diversification dynamics shaped the evolution of Australian skipper butterflies
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Data from: Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution
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Data from: How reliably can we infer diversity-dependent diversification from phylogenies?
Slowdowns in lineage accumulation in phylogenies suggest that speciation rates decline as diversity increases. Likelihood methods have been developed to detect such diversity dependence. However, a thorough test of whether such approaches correctly infer diversity dependence is lacking. Here, we simulate phylogenetic branching under linear negative diversity-dependent and diversity-independent models and estimate from the simulated phylogenies the maximum-likelihood parameters for three different conditionings – on survival of the birth–death process given the crown age, on tree size (N) and on tree size given the crown age. We report the accuracy of recovering the simulation parameters and the reliability of the model selection based on the χ2 likelihood ratio test. Parameter estimate accuracy: Conditioning on survival given the crown age yields a severe bias of the carrying capacity K towards N and an upward bias of the speciation rate, particularly in clades where diversity-dependent feedbacks are still weak (N « K). Conditioning on N yields an overestimate of K and an underestimate of speciation rate, particularly when saturation has been reached. Dual conditioning yields relatively unbiased parameter estimates on average, but the deviation from the true value for any single estimate may be large. Model selection reliability: The frequency of incorrectly rejecting a diversity-independent model when the simulation was diversity-independent (type I error) differs substantially from the significance level α used in the likelihood ratio test, rendering the likelihood ratio test inappropriate. The frequency of correctly rejecting the diversity-independent model when the simulation was diversity-dependent (power) is larger when the clade is closer to equilibrium and for conditioning on crown age. We conclude that conditioning on crown age has the best statistical properties overall, but caution that parameter estimates may be biased. To assess parameter uncertainty in future studies of diversity dependence on real data, we recommend parametric bootstrapping, examination of the likelihood surface and comparison of estimates across the types of conditioning. To assess model selection reliability, we discourage the use of the χ2 likelihood ratio test or AIC (which are equivalent in this case), but recommend a likelihood ratio test based on parametric bootstrap. We illustrate this method for the diversification of Dendroica warblers.
Data from: Diversity-dependent evolutionary rates in early Paleozoic zooplankton
The extent to which biological diversity affects rates of diversification is central to understanding macroevolutionary dynamics, yet no consensus has emerged on the importance of diversity-dependence of evolutionary rates. Here we analyse the species-level fossil record of early Paleozoic graptoloids, documented with high temporal resolution, to test directly whether rates of diversification were influenced by levels of standing diversity within this major clade of marine zooplankton. To circumvent the statistical regression-to-the-mean artefact, whereby higher- and lower-than-average values of diversity tend to be followed by negative and positive diversification rates, we construct a non-parametric, empirically scaled, diversity-independent null model by randomizing the observed diversification rates with respect to time. Comparing observed correlations between diversity and diversification rate to those expected from this diversity-independent model, we find evidence for negative diversity-dependence, accounting for up to 12% of the variance in diversification rate, with maximal correlation at a temporal lag of ~1 million years. Diversity-dependence persists throughout the Ordovician and Silurian, despite a major increase in the strength and frequency of extinction and speciation pulses in the Silurian. In contrast to some previous work, we find that diversity-dependence affects rates of speciation and extinction nearly equally on average, although subtle differences emerge when we compare the Ordovician and Silurian.
Data from: Detecting local diversity-dependence in diversification
Whether there are ecological limits to species diversification is a hotly debated topic. Molecular phylogenies show slowdowns in lineage accumulation, suggesting that speciation rates decline with increasing diversity. A maximum likelihood method to detect diversity-dependent diversification from phylogenetic branching times exists, but it assumes that diversity-dependence is a global phenomenon and therefore ignores that the underlying species interactions are mostly local, and not all species in the phylogeny co-occur locally. Here, we explore whether this maximum likelihood method based on the non-spatial diversity-dependence model can detect local diversity-dependence, by applying it to phylogenies, simulated with a spatial stochastic model of local-diversity-dependent speciation, extinction and dispersal between two local communities. We find that type I errors (falsely detecting diversity-dependence) are low, and the power to detect diversity-dependence is high when dispersal rates are not too low. Interestingly, when dispersal is high the power to detect diversity-dependence is even higher than in the non-spatial model. Moreover, estimates of intrinsic speciation rate, extinction rate and ecological limit strongly depend on dispersal rate. We conclude that the non-spatial diversity-dependent approach can be used to detect diversity-dependence in clades of species that live in not too disconnected areas, but parameter estimates must be interpreted cautiously.
Data from: Limited by the roof of the world: mountain radiations of Apollo swallowtails controlled by diversity-dependence processes
Mountainous areas comprise a substantial part of the world species richness, but the evolutionary origins and diversification of this biodiversity remain elusive. Diversification may result from differences in clade age (longer time to diversify), net diversification rates (faster speciation rate), or carrying capacities (number of niches). The likelihood of these macroevolutionary scenarios was assessed for six clades of Apollo swallowtails (Parnassius) that diversified mainly in the Himalayan-Tibetan region. The analyses suggest that neither the clade age, nor the speciation rate could explain the mountain butterfly diversification. Instead diversity-dependence models were strongly supported for each group. Models further estimated clades' carrying capacities that approximate the current number of species, indicating that diversity equilibrium is reached (or close to be). The results suggest that diversification of mountain butterflies was controlled by ecological limits, which governed the number of niches, and provide macroevolutionary justification for regarding mountains as islands.
Data from: Diversity-dependent evolutionary rates in early Paleozoic zooplankton
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Data from: Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees
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Data from: Detecting local diversity-dependence in diversification
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Data from: Limited by the roof of the world: mountain radiations of Apollo swallowtails controlled by diversity-dependence processes
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Data from: How reliably can we infer diversity-dependent diversification from phylogenies?
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