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. 2015 Apr 21;112(16):4909-14.
doi: 10.1073/pnas.1409886112.

Fossils, phylogenies, and the challenge of preserving evolutionary history in the face of anthropogenic extinctions

Danwei Huang  1 , Emma E Goldberg  2 , Kaustuv Roy  3
Affiliations

Fossils, phylogenies, and the challenge of preserving evolutionary history in the face of anthropogenic extinctions

Danwei Huang et al. Proc Natl Acad Sci U S A. .

Abstract

Anthropogenic impacts are endangering many long-lived species and lineages, possibly leading to a disproportionate loss of existing evolutionary history (EH) in the future. However, surprisingly little is known about the loss of EH during major extinctions in the geological past, and thus we do not know whether human impacts are pruning the tree of life in a manner that is unique in the history of life. A major impediment to comparing the loss of EH during past and current extinctions is the conceptual difference in how ages are estimated from paleontological data versus molecular phylogenies. In the former case the age of a taxon is its entire stratigraphic range, regardless of how many daughter taxa it may have produced; for the latter it is the time to the most recent common ancestor shared with another extant taxon. To explore this issue, we use simulations to understand how the loss of EH is manifested in the two data types. We also present empirical analyses of the marine bivalve clade Pectinidae (scallops) during a major Plio-Pleistocene extinction in California that involved a preferential loss of younger species. Overall, our results show that the conceptual difference in how ages are estimated from the stratigraphic record versus molecular phylogenies does not preclude comparisons of age selectivities of past and present extinctions. Such comparisons not only provide fundamental insights into the nature of the extinction process but should also help improve evolutionarily informed models of conservation prioritization.

Keywords: bivalves; extinction; fossil record; phylogenetic diversity; phylogeny.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
A simple tree showing how the full branching history of a clade can be reduced to either stratigraphic ranges or a bifurcating phylogeny. A clade undergoes speciation (assumed here to be budding, with survival of the parent) and extinction, with nine lineages (A–I) surviving to the focal time (t = 0). The stratigraphic range and absolute age of each surviving species are determined by the time of its first appearance in the fossil record, without reference to species relationships. The bifurcating phylogeny is determined by the divergence times of surviving species relative to one another, without regard for their original times of speciation. Colors illustrate the four scenarios of age-dependent extinction at the focal time. Note that the oldest species differ—in both identity and age—between the absolute and relative age definitions, as do the youngest species. Thus, stratigraphic and phylogenetic diversity are differently affected by the loss of species.
Fig. 2.
Fig. 2.
PDexcess based on bifurcating phylogenies versus the corresponding SDexcess for the same extinction event under four age-biased extinction regimes. Individual colors depict extinction probability increasing linearly with absolute age (stratigraphic range) or with relative age (phylogenetic tip length) or decreasing linearly with absolute age or with relative age. Excess-over-random losses (see main text) are shown for four extinction intensities (m = 10, 30, 50, or 80%) and trees simulated with two pairs of speciation (λ) and extinction (μ) rates (ε = μ/λ = 0.2 or 0.8). (A) One thousand trees with ε = 0.8. (B) Largest quartile of trees (250) with ε = 0.8. (C) One thousand trees with ε = 0.2. (D) Largest quartile of trees (250) with ε = 0.2.
Fig. 3.
Fig. 3.
Taxon age selectivity under four age-biased extinction regimes plus a null model of random, age-independent extinction. (A–J) Bars represent the natural logarithm of the odds ratio (log-odds) based on a binomial logistic regression model. Log-odds are expected to be negative when extinction preferentially removes older taxa and positive when younger taxa are more likely to go extinct. Solid colors represent log-odds calculated based on absolute ages from stratigraphic ranges; shaded colors represent log-odds calculated using relative ages from bifurcating phylogenies. Shown are log-odds under four extinction intensities (m = 10, 30, 50, or 80%) for trees simulated with two pairs of speciation (λ) and extinction (μ) rates (ε = μ/λ = 0.2 or 0.8). Numbers above or below bars represent the proportions of trees that show a statistically significant effect of age on species survivorship.
Fig. 4.
Fig. 4.
Stratigraphic ranges (thick lines) and phylogenetic relationships (thin lines) of 89 Late Oligocene to Recent species of scallops (Pectinidae) known from California. The tree shown forms the backbone for generating 1,000 fully resolved Bayesian posterior trees used to analyze extinctions occurring at the Plio–Pleistocene transition, ∼2.5 Mya, which removed 25 of the 50 species present at that time. Species names and stratigraphic ranges are colored according to times of extinction relative to the Plio–Pleistocene transition.
See this image and copyright information in PMC

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