The Basal Penguin (Aves: Sphenisciformes) Perudyptes devriesi and a Phylogenetic Evaluation of the Penguin Fossil Record
08 Jun 2010-Bulletin of the American Museum of Natural History (American Museum of Natural History, Library‐Scientific Publications Central Park West at 79th St., New York, NY 10024)-Vol. 2010, Iss: 337, pp 1-77
TL;DR: These two species, known from relatively complete partial skeletons, are the oldest crown clade penguin fossils and represent well-corroborated temporal calibration points for the Spheniscus-Eudyptula divergence and Megadyptes-EUDyptes divergence, respectively.
Abstract: We present the first detailed description of Perudyptes devriesi, a basal penguin from the middle Eocene (~42 Ma) Paracas Formation of Peru, and a new analysis of all published extinct penguin species as well as controversial fragmentary specimens. The Perudyptes devriesi holotype includes key regions of the skull and significant postcranial material, thus helping to fill a major phylogenetic and stratigraphic (~20 million year) gap between the earliest fossil penguins (Waimanu manneringi and Waimanu tuatahi, ~58–61.6 Ma) and the next oldest partial skeletons. Perudyptes devriesi is diagnosable by five autapomorphies: (1) an anteroventrally directed postorbital process, (2) marked anterior expansion of the parasphenoid rostrum, (3) posterior trochlear ridge of the humerus projecting distal to the middle trochlear ridge and conformed as a large, broadly curved surface, (4) convex articular surface for the antitrochanter of the femur, and (5) extremely weak anterior projection of the lateral condyl...
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TL;DR: The FBD model and a model of morphological trait evolution are incorporated into a Bayesian total‐evidence approach to dating species phylogenies and it is shown that including stem‐fossil diversity can greatly improve the estimates of the divergence times of crown taxa.
Abstract: The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples, that is, ancestors of fossil or extant species or of clades. The fossilized birth–death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at ∼12.7 ∼12.7 Ma and most splits leading to extant species occurring in the last 2 myr. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (version 2.4) software www.beast2.org with packages SA (version at least 1.1.4) and morph-models (version at least 1.0.4) installed.
256 citations
Cites methods or result from "The Basal Penguin (Aves: Spheniscif..."
...We updated the fossil stratigraphic ages—previously summarized in Ksepka and Clarke (2010)—to introduce time intervals for fossil samples as presented in online Supplementary Material (SM), Table 1 available on dryad at http://dx.doi.org/10.5061/dryad.44pf8)....
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...2014), and so had been recommended as a calibration point for the Eudyptes– Megadyptes divergence (Ksepka and Clarke 2010) and used as such (Subramanian et al....
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...This fossil taxon was inferred as the sister taxon to Eudyptes by several previous studies (Hospitaleche et al. 2007; Ksepka and Clarke 2010; Ksepka et al. 2012); though see (Chávez Hoffmeister et al. 2014), and so had been recommended as a calibration point for the Eudyptes– Megadyptes divergence…...
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...by several previous studies (Hospitaleche et al. 2007; Ksepka and Clarke 2010; Ksepka et al. 2012); though see (Chávez Hoffmeister et al....
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...…previous studies (Hospitaleche et al. 2007; Ksepka and Clarke 2010; Ksepka et al. 2012); though see (Chávez Hoffmeister et al. 2014), and so had been recommended as a calibration point for the Eudyptes– Megadyptes divergence (Ksepka and Clarke 2010) and used as such (Subramanian et al. 2013)....
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TL;DR: The fossil reveals that key feathering features, including undifferentiated primary wing feathers and broad body contour feather shafts, evolved early in the penguin lineage, and analyses of fossilized color-imparting melanosomes reveal that their dimensions were similar to those of non-penguin avian taxa and that the feathering may have been predominantly gray-brown.
Abstract: Penguin feathers are highly modified in form and function, but there have been no fossils to inform their evolution. A giant penguin with feathers was recovered from the late Eocene (~36 million years ago) of Peru. The fossil reveals that key feathering features, including undifferentiated primary wing feathers and broad body contour feather shafts, evolved early in the penguin lineage. Analyses of fossilized color-imparting melanosomes reveal that their dimensions were similar to those of non-penguin avian taxa and that the feathering may have been predominantly gray and reddish-brown. In contrast, the dark black-brown color of extant penguin feathers is generated by large, ellipsoidal melanosomes previously unknown for birds. The nanostructure of penguin feathers was thus modified after earlier macrostructural modifications of feather shape linked to aquatic flight.
156 citations
TL;DR: The literature on marine vertebrate groups over time is reviewed and the innovations that facilitated the evolution of these marine forms, the environmental conditions that selected for such convergence of form, and the threats they face from future environment change are described.
Abstract: Many top consumers in today's oceans are marine tetrapods, a collection of lineages independently derived from terrestrial ancestors. The fossil record illuminates their transitions from land to sea, yet these initial invasions account for a small proportion of their evolutionary history. We review the history of marine invasions that drove major changes in anatomy, physiology, and ecology over more than 250 million years. Many innovations evolved convergently in multiple clades, whereas others are unique to individual lineages. The evolutionary arcs of these ecologically important clades are framed against the backdrop of mass extinctions and regime shifts in ocean ecosystems. Past and present human disruptions to marine tetrapods, with cascading impacts on marine ecosystems, underscore the need to link macroecology with evolutionary change.
123 citations
Cites background from "The Basal Penguin (Aves: Spheniscif..."
...After the K-Pg mass extinction, Early Cenozoic diversification of cetaceans (3), sirenians (96), and penguins (24, 97) brought Paleogene marine tetrapod richness back to peak Mesozoic levels....
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TL;DR: This time-calibrated supertree supports radiation of all three major avian clades near the Cretaceous-Paleogene boundary and will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.
Abstract: This research was funded by the US National Science Foundation, grant numbers DEB-1655683, DEB-1655624, DEB-1655559, DEB-1655736.
86 citations
TL;DR: New materials described here, along with re-study of previously described specimens, resolve several long-standing phylogenetic, biogeographic, and taxonomic issues stemming from the inadequate comparative material of several of the first-named fossil penguin species.
Abstract: Three skeletons collected from the late Oligocene Kokoamu Greensand of New Zealand are among the most complete Paleogene penguins known. These specimens, described here as Kairuku waitaki, gen. et sp. nov., and Kairuku grebneffi, sp. nov., reveal new details of key elements of the stem penguin skeleton associated with underwater flight, including the sternum, flipper, and pygostyle. Relative proportions of the trunk, flippers, and hind limbs can now be determined from a single individual for the first time, offering insight into the body plan of stem penguins and improved constraints on size estimates for ‘giant’ taxa. Kairuku is characterized by an elongate, narrow sternum, a short and flared coracoid, an elongate narrow flipper, and a robust hind limb. The pygostyle of Kairuku lacks the derived triangular cross-section seen in extant penguins, suggesting that the rectrices attached in a more typical avian pattern and the tail may have lacked the propping function utilized by living penguins. Ne...
74 citations
Cites background or result from "The Basal Penguin (Aves: Spheniscif..."
...This implies a lower number of synsacral vertebrae is plesiomorphic in penguins (Ksepka and Clarke, 2010)....
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...Kaiika maxwelli, a new Early Eocene archaic penguin (Sphenisciformes, Aves) from Waihao Valley, South Canterbury, New Zealand....
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...…tibiotarsus from the late Eocene of Australia as Palaeeudyptes cf. antarcticus, but the humerus appears to represent a more crownward species than P. antarcticus, whereas the tibiotarsus is phylogenetically uninformative beyond placing the fossil within Sphenisciformes (Ksepka and Clarke, 2010)....
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...Simpson (1957) described a humerus and tibiotarsus from the late Eocene of Australia as Palaeeudyptes cf. antarcticus, but the humerus appears to represent a more crownward species than P. antarcticus, whereas the tibiotarsus is phylogenetically uninformative beyond placing the fossil within Sphenisciformes (Ksepka and Clarke, 2010)....
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...Outgroup representation includes 13 species from the extant sister taxon of Sphenisciformes, Procellariiformes (e.g., Hackett et al., 2008)....
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References
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TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
Abstract: CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.
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"The Basal Penguin (Aves: Spheniscif..." refers methods in this paper
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TL;DR: This study examined ∼32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods.
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Book•
01 Nov 1992
TL;DR: Part I Introducing MacClade: introduction - a tutorial overview of MacClades and an introduction to phylogeny reconstructing character evolution using parsimony stratigraphic parsimony.
Abstract: Part I Introducing MacClade: introduction - a tutorial overview of MacClade. Part II Phylogenetic theory: a phylogenetic perspective an introduction to phylogeny reconstructing character evolution using parsimony stratigraphic parsimony Part III Using MacClade: using MacClade on your Macintosh managing data files importing and exporting text files the data editor assumptions about characters trees and tree manipulation tracing character evolution basic tree and character statistics charting tree and character statistics continuous characters patterns of correlated character evolution generating random data and random trees using MacClade with molecular data recording your work. Appendix: file format.
1,472 citations
"The Basal Penguin (Aves: Spheniscif..." refers methods in this paper
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