The influence of functional traits on species survivorship has been evaluated in various contexts in both modern and ancient ecosystems, but an important direction for research is to integrate datasets that include both extinct and extant taxa. This approach can provide a more reliable understanding of the effects of functional traits on macroecological and macroevolutionary dynamics. Knowledge of the links between individual traits and survivorship is crucial for developing accurate extinction risk predictive models.
Here we test the impact of numerous functional traits on the survival and extinction of species through time, using bivalve and gastropod species from the rich fossil record of the western Atlantic over the last ~3 million years, along with the associated extant biota. We also compare the impact of these organismic traits on survival relative to a group level trait: geographic distribution. Analyses use a dataset of 12 functional traits including life habit, feeding behavior and basal metabolic rate (BMR), for 115 species from 36 families. Traits were observed and measured from specimens in the collections of the Paleontological Research Institution, Florida Museum of Natural History, and University of Kansas, as well as surveys of the literature and online databases such as the Neogene Marine Biota of Tropical America (NMITA).
Results derived from Principal Coordinates Analysis (PCoA) show there is a clear distinction between extinct and extant species, overall, when comparing them based on life habit, maximum body size, shell composition and BMR. Most traits showed little direct relation with survival, except BMR and associated maximum body size, supporting the Metabolic Theory of Ecology. Since many functional traits do not explain survival, their function may be mis- or over-interpreted, and traits posited to represent important organismic adaptations may not play a prominent role in long-term species survival, especially during the major climate changes over the last ~ 3 million years. Some traits do show significant interactions, and these were more fully explored using additional multivariate analyses. The relative importance of geographic range size suggests group-level characters may be the primary determinant of extinction patterns over macroevolutionary time scales.
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Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families
Analyses of evolutionary dynamics depend on how phylogenetic data are time-scaled. Most analyses of extant taxa assume a purely bifurcating model, where nodes are calibrated using the daughter lineage with the older first occurrence in the fossil record. This contrasts with budding, where nodes are calibrated using the younger first occurrence. Here, we use the extensive fossil record of bivalve molluscs for a large-scale evaluation of how branching models affect macroevolutionary analyses. We time-calibrated 91% of nodes, ranging in age from 2.59 to 485 Ma, in a phylogeny of 97 extant bivalve families. Allowing budding-based calibrations minimizes conflict between the tree and observed fossil record, and reduces the summed duration of inferred ‘ghost lineages’ from 6.76 billion years (Gyr; bifurcating model) to 1.00 Gyr (budding). Adding 31 extinct paraphyletic families raises ghost lineage totals to 7.86 Gyr (bifurcating) and 1.92 Gyr (budding), but incorporates more information to date divergences between lineages. Macroevolutionary analyses under a bifurcating model conflict with other palaeontological evidence on the magnitude of the end-Palaeozoic extinction, and strongly reduce Cenozoic diversification. Consideration of different branching models is essential when node-calibrating phylogenies, and for a major clade with a robust fossil record, a budding model appears more appropriate.
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- Award ID(s):
- 2049627
- NSF-PAR ID:
- 10326277
- Date Published:
- Journal Name:
- Proceedings of the Royal Society B: Biological Sciences
- Volume:
- 288
- Issue:
- 1964
- ISSN:
- 0962-8452
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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SUMMARY Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, has been common throughout the evolutionary history of plants, particularly in various lineages of flowering plants. However, phylogenomic studies have also highlighted the challenges of disentangling signals of ancient hybridization from other sources of genomic conflict (in particular, incomplete lineage sorting). Here, we provide a critical review of ancient hybridization in vascular plants, outlining well‐documented cases of ancient hybridization across plant phylogeny, as well as the challenges unique to documenting ancient versus recent hybridization. We provide a definition for ancient hybridization, which, to our knowledge, has not been explicitly attempted before. Further documenting the extent of deep reticulation in plants should remain an important research focus, especially because published examples likely represent the tip of the iceberg in terms of the total extent of ancient hybridization. However, future research should increasingly explore the macroevolutionary significance of this process, in terms of its impact on evolutionary trajectories (e.g. how does hybridization influence trait evolution or the generation of biodiversity over long time scales?), as well as how life history and ecological factors shape, or have shaped, the frequency of hybridization across geologic time and plant phylogeny. Finally, we consider the implications of ubiquitous ancient hybridization for how we conceptualize, analyze, and classify plant phylogeny. Networks, as opposed to bifurcating trees, represent more accurate representations of evolutionary history in many cases, although our ability to infer, visualize, and use networks for comparative analyses is highly limited. Developing improved methods for the generation, visualization, and use of networks represents a critical future direction for plant biology. Current classification systems also do not generally allow for the recognition of reticulate lineages, and our classifications themselves are largely based on evidence from the chloroplast genome. Updating plant classification to better reflect nuclear phylogenies, as well as considering whether and how to recognize hybridization in classification systems, will represent an important challenge for the plant systematics community.
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Abstract Order Diplobathrida is a major clade of camerate crinoids spanning the Ordovician–Mississippian, yet phylogenetic relationships have only been inferred for Ordovician taxa. This has hampered efforts to construct a comprehensive tree of life for crinoids and develop a classification scheme that adequately reflects diplobathrid evolutionary history. Here, I apply maximum parsimony and Bayesian phylogenetic approaches to the fossil record of diplobathrids to infer the largest tree of fossil crinoids to date, with over 100 genera included. Recovered trees provide a framework for evaluating the current classification of diplobathrids. Notably, previous suborder divisions are not supported, and superfamily divisions will require significant modification. Although numerous revisions are required for families, most can be retained through reassignment of genera. In addition, recovered trees were used to produce phylogeny‐based estimates of diplobathrid lineage diversity. By accounting for ghost lineages, phylogeny‐based richness estimates offer greater insight into diversification and extinction dynamics than traditional taxonomy‐based approaches alone and provide a detailed summary of the ~150 million‐year evolutionary history of Diplobathrida. This study constitutes a major step toward producing a phylogeny of the Crinoidea and documenting crinoid diversity dynamics. In addition, it will serve as a framework for subsequent phylogeny‐based investigations of macroevolutionary questions.
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Abstract A fuller understanding of the role of developmental bias in shaping large‐scale evolutionary patterns requires integrating bias (the probability distribution of variation accessible to an ancestral phenotype) with clade dynamics (the differential survival and production of species and evolutionary lineages). This synthesis could proceed as a two‐way exchange between the developmental data available to neontologists and the strictly phenotypic but richly historical and dynamic data available to paleontologists. Analyses starting in extant populations could aim to predict macroevolution in the fossil record from observed developmental bias, while analyses starting in the fossil record, particularly the record of extant species and lineages, could aim to predict developmental bias from macroevolutionary patterns, including the broad range of extinct phenotypes. Analyses in multivariate morphospaces are especially effective when coupled with phylogeny, theoretical and developmental models, and diversity–disparity plots. This research program will also require assessing the “heritability” of an ancestral bias across phylogeny, and the tendency for bias change in strength and orientation over evolutionary time. Such analyses will help find a set of general rules for the macroevolutionary effects of developmental bias, including its impact on and interactions with the other intrinsic and extrinsic factors governing the movement, expansion, and contraction of clades in morphospace.
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Summary Lycopodiaceae are one of three surviving families of lycopsids, a lineage of vascular plants with a fossil history dating to at least the Early Devonian or perhaps the Late Silurian (
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1098/rspb.2021.2178
