Paleontological Data Sets Research Articles

Paleotree: an R package for paleontological and phylogenetic analyses of evolution

Summary1. paleotree is a library of functions for the R statistical computing environment dedicated to analyses that combine paleontological and phylogenetic data sets, particularly the time‐scaling of phylogenetic trees, which include extinct fossil lineages.2. The functions included in this library focus on simulating paleontological data sets, measuring sampling rates, time‐scaling cladograms of fossil taxa and plotting historical diversity curves.3. I describe the capabilities and analytical basis of the functions in paleotree by presenting two examples. The first example showcases the simulation capabilities and plotting the output as diversity curves. The second example demonstrates time‐scaling a cladogram of fossil taxa and estimating sampling rates and completeness from temporal ranges.

Nemesis reconsidered

Abstract The hypothesis of a companion object (Nemesis) orbiting the Sun was motivated by the claim of a terrestrial extinction periodicity, thought to be mediated by comet showers. The orbit of a distant companion to the Sun is expected to be perturbed by the Galactic tidal field and encounters with passing stars, which will induce variation in the period. We examine the evidence for the previously proposed periodicity, using two modern, greatly improved paleontological data sets of fossil biodiversity. We find that there is a narrow peak at 27 Myr in the cross-spectrum of extinction intensity time series between these independent data sets. This periodicity extends over a time period nearly twice that for which it was originally noted. An excess of extinction events is associated with this periodicity at 99 per cent confidence. In this sense we confirm the originally noted feature in the time series for extinction. However, we find that it displays extremely regular timing for about 0.5 Gyr. The regularity of the timing compared with earlier calculations of orbital perturbation would seem to exclude the Nemesis hypothesis as a causal factor.

Neoproterozoic chemostratigraphy

Chemostratigraphy has diverse applications to investigating the rock record, such as reconstructing paleoenvironments, determining the tectonic setting of sedimentary basins, indirect dating, and establishing regional or global correlations. Chemostratigraphy is thus an integral component of many investigations of the ancient sedimentary record. In this contribution, we review the principle inorganic geochemical methods that have been applied to the Neoproterozoic sedimentary record. Analysis of the traditional stable and radiogenic isotope systems, such as δ 13C, δ 18O, δ 34S, and 87Sr/ 86Sr, is routine, particularly in successions rich in carbonate. These mainstay applications have yielded invaluable data and information bearing on the chronology and evolution of this eventful era in Earth history. Alongside the growing database of traditional data, a series of novel geochemical techniques have given rise to important new models and constraints on Neoproterozoic biogeochemical change. In particular, a range of proxies for water column redox, mainly obtained from black shales, have shed light on the pace and tempo of Neoproterozoic oxygenation and its link to the appearance of early animal evolution. Increased integration of diverse geochemical, sedimentological, and paleontological datasets, and the gradual radiometric calibration of the stratigraphic record promise to bring the details of the evolution of the Neoproterozoic Earth system into ever greater focus.

Evidence for a western extension of the Angaran phytogeographic province in the Early Permian

Abstract A newly described Early Permian fossil plant assemblage in the Mt. Dall conglomerate in the Farewell terrane (Alaska Range, USA) is analyzed from a paleobiogeographic perspective. These data constitute the youngest paleontological dataset yet discovered in this terrane, represent the terrane's only predominantly terrestrial fossil assemblage, and are the only plant macrofossil remains of Early Permian age within a > 1500 km radius today. A suite of multivariate statistical analyses comparing the Mt. Dall paleoflora to similar age (Asselian–Artinskian) collections from the Angaran, Euramerican, and Cathaysian Permian phytogeographic provinces reveals that the Mt. Dall paleoflora has a paleobiogeographic affinity with Sub-Angaran plant fossil assemblages collected from Mongolia and the Primorye region of southeastern Russia. The paleoflora has dual importance in the construction and testing of hypotheses for which there are geographically and temporally few controls. First, these data may be used in association with other faunal and floral remains to test models of the assembly of Alaska, which seek, in part, an understanding of the paleogeographic and lithological origins of accreted terranes. That the Mt. Dall paleoflora indicates mixed Eurasia–North America paleobiogeographic affinity among individual taxa and plots in multivariate space with mid-latitude assemblages on northern Pangea may suggest deposition in that latitudinal belt. Second, contrary to the well-sampled fossil plant-bearing Permo-Carboniferous of the paleotropics and the northeastern temperate Pangean regions (Angaraland), terrestrial biome structure and vegetation type of northwestern Pangea are poorly known. This lack of understanding is due to the paucity of paleofloral collections from this region in this time period and the paleogeographic uncertainty of their position along the ancient active margin of Laurentia. The Mt. Dall paleoflora's phytogeographic affinity to paleobotanical collections from the northeastern Pangea therefore suggests that the Angaran province extended meridionally westward in the Early Permian into what is now northern North America.

A Paleozoological Perspective on White-Tailed Deer (Odocoileus virginianus texana) Population Density and Body Size in Central Texas

Archaeological and paleontological datasets are used in conservation to add time-depth to ecology. In central Texas, several top carnivores including prehistoric Native American hunters have been extirpated or have had their historic ranges restricted, which has resulted in pest-level white-tailed deer (Odocoileus virginianus texana) populations in some areas. Differences in body size of deer between prehistory and modernity are expected, given that a lack of predation likely has increased intraspecific competition for forage among deer, resulting in smaller body size today. In fact, modern deer from settings without harvest pressure are significantly smaller than those from harvested areas and from prehistoric deer. From a natural history perspective, this research highlights potential evolutionary causes and effects of top-predator removal on deer populations and related components of biological communities in central Texas.

Is the greenhouse theory a fallacy? A paleontological paradox

Over a hundred years ago, Svante Arrhenius (1896), building on earlier work of the French physicist Joseph Fourier, Tyndall (1861), Langley (1884), and others, was the first to model quantitatively the effects of changes in the concentration of atmospheric carbon dioxide on climate (Uppenbrink, 1996; Fleming, 1998). A “greenhouse theory”, or “hothouse theory” as it was then called (Arrhenius, 1908), thus was born and has stood the test of time pretty well since its 19th-century origins, despite falling out of favor for a brief period between 1900 and 1940 (Fleming, 1998). Quaternary ice-core records, now spanning four complete glacial-interglacial cycles (Petit et al., 1997), have provided the strongest support, to date, for the role of greenhouse gasses as primary drivers of global climate change rather than as mere feedback effects (Shackleton, 2000). A number of recent publications based on paleontological and geochemical proxy data sets, however, have challenged the notion that climate and atmospheric CO2 have been coupled throughout pre-Quaternary time (Pagani et al., 1999; Pearson and Palmer, 2000; Viezer et al., 2000; Royer et al., 2001). Intervals of extreme global warmth, such as the late Paleocene and early Eocene, appear to be associated with relatively low ambient CO2 concentrations (Royer et al., 2001), invoking alternative or additional mechanisms, such as altered ocean circulation, for high-latitude warmth during this interval. Similarly, the mid-Miocene climatic optimum (∼ 17 to ∼15 Ma), according to some proxy CO2 records, was not associated with high concentrations of greenhouse gasses (Pagani et al., 1999; Pearson and Palmer, 2000), but rather with concentrations lower than today. An apparent paradox has emerged—the pre-Quaternary history of CO2 and climate interaction, which once appeared to be relatively well coupled based on temporal correlation of …

Random sampling of carbonate mounds: an example from the Upper Ordovician of Alabama

Paleontological and lithological studies of a carbonate mound provide the necessary data from which characterizations for that mound or locality can be constructed. These data-based characterizations are a convenient mechanism for making qualitative comparisons with other mounds, as has been done in some previous studies that discussed Middle Ordovician (now considered Upper Ordovician) mounds of the Appalachian Basin. Each of these studies had a different focus, including the paleoecology of individual mound localities, issues of ecological zonation, and regional stratigraphical investigation. Quantitative comparisons are precluded among these studies because each mound was sampled using different procedures, resulting in paleontological data sets of dissimilar density and depth. Two mound localities from carbonates of the Upper Ordovician Chickamauga Group (Stones River equivalent) of Jefferson and Blount counties, AL, were chosen for study to investigate the application of random sampling techniques to mound populations in outcrop. One mound from each locality was completely censused to generate population compositional and structural data. The location and higher-level identification of each macrofossil on the surface of these mounds were recorded. These bryozoan-dominated data sets represent the best estimates available concerning the underlying population of mound constructors, dwellers, and occasional “visitors.” Rarefaction analysis was used to predict the number of randomly chosen fossils needed to detect the major taxonomic groups from each of these populations. A computer program (TARGET) was written to validate rarefaction predictions by conducting random sampling experiments using the census data sets. The program prompts for input of three user-defined variables that set the parameters of a sampling experiment and then throws randomly located sampling boxes at the mound data set, recording the results. Statistical analysis of results from these sampling experiments validated the predictions of rarefaction analysis and led us to employ a conservative approach for sampling additional mounds at these localities.

Phylogeography of the jumping spider Habronattus pugillis (araneae: salticidae): recent vicariance of sky island populations?

In island systems with diverging populations, the history of island formation and genealogical estimates of divergence dates can be mutually informative. In the "sky islands" of southeastern Arizona, climate-induced contraction of woodlands appears to have fragmented populations of woodland-dwelling species onto disjunct mountain ranges. Montane populations of the jumping spider, Habronattus pugillis, display striking amounts of phenotypic divergence among ranges. Paleoclimatic estimates date woodland fragmentation at approximately 10,000 years ago, suggesting that phenotypic divergence has been extraordinarily rapid in these spiders. This phylogeographic study of populations of H. pugillis attempts to clarify the species' history of isolation and divergence and to address the suitability of available paleoclimatic data for dating divergences among populations of the region's woodland-dwelling organisms. Mitochondrial sequence data of spiders from 13 mountain ranges was used to reconstruct genealogical relationships. Gene trees show that small mountain ranges tend to have populations whose sequences form monophyletic groups, whereas larger ranges do not. Paraphyly among genes from larger ranges could result from either recent migration or incomplete lineage sorting. I use phylogenetic and geographic information to test these alternatives, and conclude that incomplete lineage sorting best explains the observed paraphyly. Gene trees are concordant with some of the predictions of vegetation history generated by examination of topography. Dates estimated for divergence of populations vary from 30,000 years to more than 2 million years ago, suggesting multiple vicariance events that are older than would be inferred from paleoclimatic studies. These findings illustrate that use of any single paleontological dataset to calibrate molecular clocks can potentially greatly underestimate actual divergence times.

PHYLOGEOGRAPHY OF THE JUMPING SPIDER HABRONATTUS PUGILLIS (ARANEAE: SALTICIDAE): RECENT VICARIANCE OF SKY ISLAND POPULATIONS?

In island systems with diverging populations, the history of island formation and genealogical estimates of divergence dates can be mutually informative. In the “sky islands” of southeastern Arizona, climate-induced contraction of woodlands appears to have fragmented populations of woodland-dwelling species onto disjunct mountain ranges. Montane populations of the jumping spider, Habronattus pugillis, display striking amounts of phenotypic divergence among ranges. Paleoclimatic estimates date woodland fragmentation at approximately 10,000 years ago, suggesting that phenotypic divergence has been extraordinarily rapid in these spiders. This phylogeographic study of populations of H. pugillis attempts to clarify the species' history of isolation and divergence and to address the suitability of available paleoclimatic data for dating divergences among populations of the region's woodland-dwelling organisms. Mitochondrial sequence data of spiders from 13 mountain ranges was used to reconstruct genealogical relationships. Gene trees show that small mountain ranges tend to have populations whose sequences form monophyletic groups, whereas larger ranges do not. Paraphyly among genes from larger ranges could result from either recent migration or incomplete lineage sorting. I use phylogenetic and geographic information to test these alternatives, and conclude that incomplete lineage sorting best explains the observed paraphyly. Gene trees are concordant with some of the predictions of vegetation history generated by examination of topography. Dates estimated for divergence of populations vary from 30,000 years to more than 2 million years ago, suggesting multiple vicariance events that are older than would be inferred from paleoclimatic studies. These findings illustrate that use of any single paleontological dataset to calibrate molecular clocks can potentially greatly underestimate actual divergence times.Corresponding Editor: S. Edwards

Coping with Abundant Missing Entries in Phylogenetic Inference Using Parsimony

?When cladistic data sets include taxa with abundant missing entries, parsimony anal? ysis may yield multiple equally optimal trees and necessitate the use of consensus methods,to summarize relationships that are common to the multiple trees. Determination of those relation? ships that are common to the equally parsimonious trees and are thus unambiguously supported by the parsimonious interpretation of the data may not be possible using consensus methods that are widely employed by systematists. Thus, missing data may have an obfuscatory effect upon phylogenetic relationships. This problem can be ameliorated or overcome by adopting a strategy of safe taxonomic reduction. In this approach, taxa that can have no effect upon the relationships inferred for other taxa but that may increase the numbers of equally most-parsimonious trees are identified. Eliminating such taxa through the application of a series of safe deletion rules may reduce the number of equally most-parsimonious trees and thereby facilitate the consensus rep? resentation of unambiguous relationships supported by the data. The methods are illustrated by reanalysis of cladistic data for the Saurischia. [Phylogeny; parsimony; underdetermination; equiv? alence; safe taxonomic reduction; consensus; Saurischia.] Missing entries are a common feature of cladistic data sets. Characters commonly need to be coded as missing for some taxa because the relevant parts are not pre? served or have not been examined. In ad? dition, some characters may be inapplica? ble in some taxa (e.g., tooth characters in birds and turtles, limb characters in snakes and caecilians) and must also be coded as missing for these taxa (Platnick et al., 1991). In both cases, the coding reflects ig? norance about the relationships of a char? acter state (known or unknown) to other character states (Wilkinson, 1992a). Amounts of missing data vary greatly from study to study. Although missing en? tries are not rare in neontological cladistic data, the greatest abundance of missing entries are encountered in paleontological data sets that include poorly preserved fos? sils as terminal taxa. In a survey of 30 pa? leontological and 51 neontological data sets drawn from the literature on tetrapod phylogeny, the average level of missing data, expressed as a percentage of the total number of data points, is 12.6% for the pa? leontological data (rang?, 0-52%) and 2.29% (0-12.25%) for the neontological data. 1 E-mail: mark.wilkinson@bris.ac.uk. When analyzed using parsimony, miss? ing entries contribute nothing positive to the analysis. According to Swofford (1990: 17), only those characters that have nonmissing values will affect the location of any taxon on the tree. In turn, the place? ment of taxa on the tree, as determined by informative characters, can lead to parsi? monious reconstructions of the values of missing entries. The principles of parsi? monious reconstruction of missing entries underpin the approach to the reconstruc? tion of unpreserved fossil morphology re? cently advocated by Bryant and Russell (1992). However, missing entries are not always innocuous to phylogenetic inference using parsimony analysis. It has been widely recognized that including poorly known taxa (with much missing data) in comput? erized parsimony analyses may lead to a dramatic increase in the numbers of equal? ly most-parsimonious trees (MPTs) and an accompanying loss of resolution in consen? sus trees that are used to summarize com? mon elements of the MPTs (Gauthier, 1986; Nixon and Wheeler, 1992; Novacek, 1992a, 1992b; Wilkinson, 1992a; Wilkinson and Benton, 1995). Several authors have there? fore excluded poorly known taxa from parsimony analyses to minimize the num-

Monte Carlo simulation of selected binomial similarity coefficients; II, Effect of sparse data

Binary similarity coefficients are applied widely to many types of paleontological data. Unfortunately, many of these paleontological data sets are (i. e., contain substantially more than 50% zeros, or absences, in the data matrix). We have run a series of Monte Carlo simulations with sparse data (10% or p = 0.10) on a series of selected coefficients that have been tested previously using 50% 1 s, or p = 0.50 (Archer and Maples, in press). In decreasing order of ability to approximate the mean of the sparse-data binomial (0.10) and general utility, we rank the coefficients tested as Dice, Braun-Blanquet, Simpson, Jaccard, Baroni-Urbani and Buser, Simple Matching, and Hamann. This ranking is generally the opposite of thatfor Monte Carlo simulations using 50% 1s or p = 0.50 (Archer and Maples, in press). Because the mean has such a low value, Dice, Braun-Blanquet, Simpson, Jaccard, and Baroni-Urbani and Buser all truncate the lower zones of significance. Therefore, statistically meaningful comparisons of the differences between any two samples cannot be made using these coefficients. This does not render these particular coefficients as useless, as long as it is realized that significantly similar linkages will occur at what would normally be interpreted as abnormally low values, especially in comparison with data in which a greater percentage of 1 s is present. In contrast, the Simple Matching and Hamann coefficients greatly overestimate the mean because the mutual absence of a character or taxon is considered to be a trait in common between any two samples. Because of the shifted mean, lower zones of significance are present; however, all linkages are high-even those that are significantly dissimilar. The mutual absence of one or more characters between any two samples is usually meaningless for most paleontological problems; coefficients should therefore be selected with this in mind.