类群取样与系统发育分析精确度之探索

Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phylogenetic analyses is improved significantly by thorough taxon sampling efforts. Many recent efforts to improve phylogenetic estimates have focused instead on increasing sequence length or the number of overall characters in the analysis, and this often does have a beneficial effect on the accuracy of phylogenetic analyses. However, phylogenetic analyses of few taxa (but each represented by many characters) can be subject to strong systematic biases, which in turn produce high measures of repeatability (such as bootstrap proportions) in support of incorrect or misleading phylogenetic results. Thus, it is important for phylogeneticists to consider both the sampling of taxa, as well as the sampling of characters, in designing phylogenetic studies. Taxon sampling also improves estimates of evolutionary parameters derived from phylogenetic trees, and is thus important for improved applications of phylogenetic analyses. Analysis of sensitivity to taxon inclusion, the possible effects of long-branch attraction, and sensitivity of parameter estimation for model-based methods should be a part of any careful and thorough phylogenetic analysis. Furthermore, recent improvements in phylogenetic algorithms and in computational power have removed many constraints on analyzing large, thoroughly sampled data sets. Thorough taxon sampling is thus one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracy of biological inferences that are based on these phylogenetic trees.     

The quality of the fossil record of Mesozoic birds

The Mesozoic fossil record has proved critical for understanding the early evolution and subsequent radiation of birds. Little is known, however, about its relative completeness: just how 'good' is the fossil record of birds from the Mesozoic? This question has come to prominence recently in the debate over differences in estimated dates of origin of major clades of birds from molecular and palaeontological data. Using a dataset comprising all known fossil taxa, we present analyses that go some way towards answering this question. Whereas avian diversity remains poorly represented in the Mesozoic, many relatively complete bird specimens have been discovered. New taxa have been added to the phylogenetic tree of basal birds, but its overall shape remains constant, suggesting that the broad outlines of early avian evolution are consistently represented: no stage in the Mesozoic is characterized by an overabundance of scrappy fossils compared with more complete specimens. Examples of Neornithes (modern orders) are known from later stages in the Cretaceous, but their fossils are rarer and scrappier than those of basal bird groups, which we suggest is a biological, rather than a geological, signal.     

The fossil record of ichthyosaurs,completeness metrics and sampling biases

Ichthyosaurs were highly successful marine reptiles with an abundant and well‐studied fossil record. However, their occurrences through geological time and space are sporadic, and it is important to understand whether times of apparent species richness and rarity are real or the result of sampling bias. Here, we explore the skeletal completeness of 351 dated and identified ichthyosaur specimens, belonging to all 102 species, the first time that such a study has been carried out on vertebrates from the marine realm. No correlations were found between time series of different skeletal metrics and ichthyosaur diversity. There is a significant geographical variation in completeness, with the well‐studied northern hemisphere producing fossils of much higher quality than the southern hemisphere. Medium‐sized ichthyosaurs are significantly more complete than small or large taxa: the incompleteness of small specimens was expected, but it was a surprise that larger specimens were also relatively incomplete. Completeness varies greatly between facies, with fine‐grained, siliciclastic sediments preserving the most complete specimens. These findings may explain why the ichthyosaur diversity record is low at times, corresponding to facies of poor preservation potential, such as in the Early Cretaceous. Unexpectedly, we find a strong negative correlation between skeletal completeness and sea level, meaning the most complete specimens occurred at times of global low sea level, and vice versa. Completeness metrics, however, do not replicate the sampling signal and have limited use as a global‐scale sampling proxy.     

Myxomycete diversity and distribution from the fossil record to the present

The myxomycetes (plasmodial slime molds or myxogastrids) are a group of eukaryotic microorganisms usually present and sometimes abundant in terrestrial ecosystems. Evidence from molecular studies suggests that the myxomycetes have a significant evolutionary history. However, due to the fragile nature of the fruiting body, fossil records of the group are exceedingly rare. Although most myxomycetes are thought to have very large distributional ranges and many species appear to be cosmopolitan or nearly so, results from recent studies have provided evidence that spatial distribution patterns of these organisms can be successfully related to (1) differences in climate and/or vegetation on a global scale and (2) the ecological differences that exist for particular habitats on a local scale. A detailed examination of the global distribution of four examples (Barbeyella minutissima, Ceratiomyxa morchella, Leocarpus fragilis and Protophysarum phloiogenum) demonstrates that these species have recognizable distribution patterns in spite of the theoretical ability of their spores to bridge continents. Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner.     

Extinction,diversity and survivorship of taxa in the fossil record

Using data drawn from large-scale databases, a number of interesting trends in the fossil record have been observed in recent years. These include the average decline in extinction rates throughout the Phanerozoic, the average increase in standing diversity, correlations between rates of origination and extinction, and simple laws governing the form of survivorship curves and the distribution of the lifetimes of taxa. In this paper we derive a number of mathematical relationships between these quantities and show how these different trends are interrelated. We also derive a variety of constraints on the possible forms of these trends, such as limits on the rate at which extinction may decline and limits on the allowed difference between extinction and origination rates at any given time.     

Field sampling bias, museum collections and completeness of the fossil record

Museum specimens, particularly old collections, typically lack comprehensive field data and determination of substrate, sampling biases, etc., is problematic. Diversity at the generic level of all identifiable latest Cretaceous (Campanian–Maastrichtian) echinoderm remains in major museum collections from the Mons (southern Belgium) and Danish (Jylland (Jutland) and Sjælland (Zealand)) basins were compared to those of the Liège-Limburg Basin. The last-named has been studied in detail, including microscopical analysis of ossicles picked from bulk samples. Echinoids of the Mons Basin show similarities to those of the Liège-Limburg Basin, but crinoids, asteroids and ophiuroids remain poorly known from the former. Echinoderms of the Danish Basin resemble those of similar chalk lithofacies in the Liège-Limburg Basin, despite significant geographical separation. These disparities can be explained, at least in part, by collector bias in sampling methodology, although differences in substrate presumably also had an influence.     

Taxonomic structure of the fossil record is shaped by sampling bias

Understanding biases that affect how species are partitioned into higher taxa is critical for much of paleobiology, as higher taxa are commonly used to estimate species diversity through time. We test the validity of using higher taxa as a proxy for species diversity for the first time by examining one of the best fossil records we have, that of deep-sea microfossils. Using a new, taxonomically standardized, data set of coccolithophorid species and genera recorded from 143 deep-sea drilling sites in the North Atlantic, Caribbean, and Mediterranean, we show that there is a two-stepped change in the ratio of species to genera over the last 150 myr. This change is highly unexpected and correlates strongly with changes in both the number of deep-sea sites yielding coccolithophorids that have been studied and with the number of taxonomists who have published on those sections. The same pattern is present in both structurally complex heterococcoliths and the simpler nannoliths, suggesting that increasing complexity is not the driving factor. As a stepped species-to-genus ratio exists even after subsampling to standardize either the numbers of sites or numbers of papers, both factors must be contributing substantially to the observed pattern. Although some limited biological signature from major extinction events can be recognized from changes in the species-to-genus ratio, the numbers of sites and the numbers of taxonomists combined explain some 82% of the observed variation over long periods of geological time. Such a strong correlation argues against using raw species-to-genus ratios to infer biological processes without taking sampling into account and suggests that higher taxa cannot be taken as unbiased proxies for species diversity.     

The Leinster and Cobbold indices improve inferences about microbial diversity

An increasing number of ecological studies compare the diversity of microbial taxa along environmental gradients or between imposed treatments. Estimates are often based on analysis-of-variance of taxon-richness inferred from pyrosequencing data. We conducted a reanalysis of three 454-pyrosequencing studies on arbuscular-mycorrhizal-fungal diversity to evaluate the suitability of using the Leinster and Cobbold diversity-indices (LCdis) to assess diversity. We expected that the potential of LCdis to consider phylogenic relationships could resolve problems arising from ambiguous species-delineation in microbial-systems. Our reanalysis showed that comparisons between studies differing considerably in sequencing depth may be risky. Moreover, we show that LCdis not only reproduce the results of analyses of variance but can also resolve issues connected to variation in sequence read number, while additionally representing a less conservative metric of diversity than analysis-of-variance of taxa-richness. Based on these results we advocate the use of inclusive diversity indices in ecological studies targeting microbial communities.     

Spatiotemporal sampling patterns in the 230 million year fossil record of terrestrial crocodylomorphs and their impact on diversity

The 24 extant crocodylian species are the remnants of a once much more diverse and widespread clade. Crocodylomorpha has an approximately 230 million year evolutionary history, punctuated by a series of radiations and extinctions. However, the group's fossil record is biased. Previous studies have reconstructed temporal patterns in subsampled crocodylomorph palaeobiodiversity, but have not explicitly examined variation in spatial sampling, nor the quality of this record. We compiled a dataset of all taxonomically diagnosable non‐marine crocodylomorph species (393). Based on the number of phylogenetic characters that can be scored for all published fossils of each species, we calculated a completeness value for each taxon. Mean average species completeness (56%) is largely consistent within subgroups and for different body size classes, suggesting no significant biases across the crocodylomorph tree. In general, average completeness values are highest in the Mesozoic, with an overall trend of decreasing completeness through time. Many extant taxa are identified in the fossil record from very incomplete remains, but this might be because their provenance closely matches the species’ present‐day distribution, rather than through autapomorphies. Our understanding of nearly all crocodylomorph macroevolutionary ‘events’ is essentially driven by regional patterns, with no global sampling signal. Palaeotropical sampling is especially poor for most of the group's history. Spatiotemporal sampling bias impedes our understanding of several Mesozoic radiations, whereas molecular divergence times for Crocodylia are generally in close agreement with the fossil record. However, the latter might merely be fortuitous, i.e. divergences happened to occur during our ephemeral spatiotemporal sampling windows.     

Preface: The phylogeny, fossil record and ecological diversity of ostracod crustaceans

After more than two centuries of research, more than 65,000 living and fossil ostracod species have been described and studied, yet much remains to be learned about this ancient, widespread and diverse group of bivalved arthropods. Their higher classification and phylogeny are subjects of vigorous debate, as is their position in the broader picture of crustacean phylogeny. At the same time, major advances in our understanding of ostracod lineages and their relationships are resulting from the application of innovative approaches and techniques. This preface provides a contextual overview of the 15 contributions to this volume, which resulted from the 14th International Symposium on Ostracoda (ISO2001) held in 2001at Shizuoka, Japan. As such it provides a cross-section of topics at the forefront of research on the evolution and diversity of Ostracoda, and indicates directions for future work.     

Mass extinctions among tetrapods and the quality of the fossil record

The fossil record of tetrapods is very patchy because of the problems of preservation, in terrestrial sediments in particular, and because vertebrates are rarely very abundant. However, the fossil record of tetrapods has the advantages that it is easier to establish a phylogenetic taxonomy than for many invertebrate groups, and there is the potential for more detailed ecological analyses. The relative incompleteness of a fossil record may be assessed readily, and this can be used to test whether drops in overall diversity are related to mass extinctions or to gaps in our knowledge. Absolute incompleteness cannot be assessed directly, but a historical approach may offer clues to future improvements in our knowledge. One of the key problems facing palaeobiologists is paraphyly, the fact that many higher taxa in common use do not contain all of the descendants of the common ancestor. This may be overcome by cladistic analysis and the identification of monophyletic groups. The diversity of tetrapods increased from the Devonian to the Permian, remained roughly constant during the Mesozoic, and then began to increase in the late Cretaceous, and continued to do so during the Tertiary. The rapid radiation of 'modern' tetrapod groups--frogs, salamanders, lizards, snakes, turtles, crocodilians, birds and mammals--was hardly affected by the celebrated end-Cretaceous extinction event. Major mass extinctions among tetrapods took place in the early Permian, late Permian, early Triassic, late Triassic, late Cretaceous, early Oligocene and late Miocene. Many of these events appear to coincide with the major mass extinctions among marine invertebrates, but the tetrapod record is largely equivocal with regard to the theory of periodicity of mass extinctions.     

Completeness of the fossil record and the validity of sampling proxies at outcrop level

Abstract: Most studies of the adequacy of the fossil record have been carried out at a global or continental scale, and they have used sampling proxies that generally do not incorporate all aspects of sampling (i.e. rock volume, accessibility, effort). Nonetheless, such studies have identified positive correlations between apparent diversity and various sampling proxies. The covariation of fossil and rock record signals has been interpreted as evidence for bias or for a common cause, such as sea level change, or as evidence that the signals are in some ways redundant with each other. Here, we compare a number of proxies representing the three main aspects of sampling, (1) sedimentary rock volume, (2) rock accessibility and (3) worker effort, with palaeodiversity in a geographically and stratigraphically constrained data set, the marine Lower Jurassic outcrop of the Dorset and East Devon Coast. We find that the proxies for rock volume and accessibility do not correlate well with the other sampling proxies, nor with apparent diversity, suggesting that the total amount of sedimentary rock preserved does not influence apparent diversity at a local scale, that is, the rock record at outcrop has been sampled efficiently. However, we do find some correlations between apparent diversity and proxies for worker effort. The fact that the proxies do not correlate significantly with each other suggests that none can be regarded as an all‐encompassing sampling proxy that covers all aspects of bias. Further, the presence of some correlations between sampling proxies and diversity most probably indicates the bonanza effect, as palaeontologists have preferentially sampled the richest rock units.     

The mosasaur fossil record through the lens of fossil completeness

The quality of the fossil record affects our understanding of macroevolutionary patterns. Palaeodiversity is filtered through geological and human processes; efforts to correct for these biases are part of a debate concerning the role of sampling proxies and standardization in biodiversity models. We analyse the fossil record of mosasaurs in terms of fossil completeness as a measure of fossil quality, using three novel, correlating metrics of fossil completeness and 4083 specimens. A new qualitative measure of character completeness (QCM) correlates with the phylogenetic character completeness metric. Mean completeness by species decreases with specimen count; average completeness by substage varies significantly. Mean specimen completeness is higher for species‐named fossils than those identified to genus and family. We consider the effect of tooth‐only specimens. Importantly, we find that completeness of species does not correlate with completeness of specimens. Completeness varies by palaeogeography: North American specimens show higher completeness than those from Eurasia and Gondwana. These metrics can be used to identify exceptional preservation; specimen completeness varies significantly by both formation and lithology. The Belgian Ciply Formation displays the highest completeness; clay lithologies show higher completeness values. Neither species diversity nor sea level correlates significantly with fossil completeness. A generalized least squares (GLS) analysis using multiple variables agrees with this result, but reveals two variables with significant predictive value for modelling averaged diversity: sea level, and mosasaur and plesiosaur‐bearing formations (the latter is redundant with diversity). Mosasaur completeness is not driven by sea level, nor does completeness limit the mosasaur diversity signal.     

The fossil record of the sixth extinction

Comparing the magnitude of the current biodiversity crisis with those in the fossil record is difficult without an understanding of differential preservation. Integrating data from palaeontological databases with information on IUCN status, ecology and life history characteristics of contemporary mammals, we demonstrate that only a small and biased fraction of threatened species (< 9%) have a fossil record, compared with 20% of non‐threatened species. We find strong taphonomic biases related to body size and geographic range. Modern species with a fossil record tend to be large and widespread and were described in the 19^th century. The expected magnitude of the current extinction based only on species with a fossil record is about half of that of one based on all modern species; values for genera are similar. The record of ancient extinctions may be similarly biased, with many species having originated and gone extinct without leaving a tangible record.     

1 Taxon sampling and inferences about diatom phylogeny

Proper taxon sampling is one of the greatest challenges to understanding phylogenetic relationships, perhaps as important as choice of optimality criterion or data type. This has been demonstrated in diatoms where centric diatoms may either be strongly supported as monophyletic or paraphyletic when analyzing SSU rDNA sequences using the same optimality criterion. The effect of ingroup and outgroup taxon sampling on relationships of diatoms is explored for diatoms as a whole and for the order Thalassiosirales. In the latter case, SSU rDNA and rbcL sequence data result in phylogenetic relationships that appear to be strongly incongruent with morphology and broadly incongruent with the fossil record. For example, Cyclotella stelligera Cleve & Grunow behaves like a rogue taxon, jumping from place to place throughout the tree. Morphological data place C. stelligera near the base of the freshwater group as sister to the extinct genus Mesodictyon Theriot and Bradbury, suggesting that it is an old, long branch that might be expected to “misbehave” in poorly sampled trees. Cyclotella stelligera and C. bodanica Grunow delimit the diameter of morphological diversity in Cyclotella, so increased sampling of intermediate taxa will be critical to resolving this part of the tree. Morphology is sampled for a much greater number of taxa and many transitional states of putative synapomorphies seem to suggest a robust morphological hypothesis. The Thalassiosirales are unstable with regards to taxon sampling in the genetic data, suggesting that perhaps the morphological hypothesis is (for now) preferable.