Biases with the Generalized Euclidean Distance measure in disparity analyses with high levels of missing data

The Generalized Euclidean Distance (GED) measure has been extensively used to conduct morphological disparity analyses based on palaeontological matrices of discrete characters. This is in part because some implementations allow the use of morphological matrices with high percentages of missing data without needing to prune taxa for a subsequent ordination of the data set. Previous studies have suggested that this way of using the GED may generate a bias in the resulting morphospace, but a detailed study of this possible effect has been lacking. Here, we test whether the percentage of missing data for a taxon artificially influences its position in the morphospace, and if missing data affects pre‐ and post‐ordination disparity measures. We find that this use of the GED creates a systematic bias, whereby taxa with higher percentages of missing data are placed closer to the centre of the morphospace than those with more complete scorings. This bias extends into pre‐ and post‐ordination calculations of disparity measures and can lead to erroneous interpretations of disparity patterns, especially if specimens present in a particular time interval or clade have distinct proportions of missing information. We suggest that this implementation of the GED should be used with caution, especially in cases with high percentages of missing data. Results recovered using an alternative distance measure, Maximum Observed Rescaled Distance (MORD), are more robust to missing data. As a consequence, we suggest that MORD is a more appropriate distance measure than GED when analysing data sets with high amounts of missing data.     

Phylogeny of snout butterflies (Lepidoptera: Nymphalidae: Libytheinae): combining evidence from the morphology of extant, fossil, and recently extinct taxa

Snout butterflies (Nymphalidae: Libytheinae) are morphologically one of the most unusual groups of Lepidoptera. Relationships among libytheines remain uncertain, especially in the placement of the recently extinct Libythea cinyras and two fossils, L. florissanti , and L. vagabunda . The aim of this study is to present the first phylogenetic hypothesis of Libytheinae utilizing all available morphological data from extant and extinct species. Forty-three parsimony-informative characters were coded, and the all-taxa analysis resulted in six most parsimonious trees (length 92 steps, CI = 0.66, RI = 0.82). The subfamily was resolved as monophyletic and was split into Old World and New World clades. Inclusion of extinct species with considerable missing data had little effect on relationships of extant taxa, although Bremer support values and jackknife frequencies generally decreased if extinct species were included. In order to preserve the monophyly of extant genera, two fossils are assigned to Libytheana for the first time ( L. florissanti comb. n. and L. vagabunda comb. n.). This study demonstrates the value of morphological data in phylogenetic analysis, and highlights the contribution that can be made by scoring extinct taxa and including them directly into the analysis.     

The disparity of priapulid, archaeopriapulid and palaeoscolecid worms in the light of new data

Priapulids and their extinct relatives, the archaeopriapulids and palaeoscolecids, are vermiform, carnivorous ecdysozoans with an armoured, extensible proboscis. These worms were an important component of marine communities during the Palaeozoic, but were especially abundant and diverse in the Cambrian. Today, they comprise just seven genera in four families. Priapulids were among the first groups used to test hypotheses concerning the morphological disparity of Cambrian fossils relative to the extant fauna. A previous study sampled at the generic level, concluding that Cambrian genera embodied marginally less morphological diversity than their extant counterparts. Here, we sample predominantly at the species level and include numerous fossils and some extant forms described in the last fifteen years. Empirical morphospaces for priapulids, archaeopriapulids and palaeoscolecids are relatively insensitive to changes in the taxon or character sample: their overall form has altered little, despite the markedly improved sampling. Cambrian and post-Cambrian genera occupy adjacent rather than broadly overlapping regions of these spaces, and Cambrian species still show lower morphological disparity than their post-Cambrian counterparts. Crucially, the significance of this difference has increased with improved taxon sampling over research time. In contrast with empirical morphospaces, the phylogeny of priapulids, archaeopriapulids and palaeoscolecids derived from morphological characters is extremely sensitive to details of taxon sampling and the manner in which characters are weighted. However, the extant Priapulidae and Halicryptidae invariably resolve as sister families, with this entire clade subsequently being sister group to the Maccabeidae. In our most inclusive trees, the extant Tubiluchidae are separated from these other living taxa by a number of small, intervening fossil clades.     

Of teeth and trees: A fossil tip‐dating approach to infer divergence times of extinct and extant squaliform sharks

Fossil tip‐dating allows for the inclusion of morphological data in divergence time estimates based on both extant and extinct taxa. Neoselachii have a cartilaginous skeleton, which is less prone to fossilization compared to skeletons of Osteichthyans. Therefore, the majority of the neoselachian fossil record is comprised of single teeth, which fossilize more easily. Neoselachian teeth can be found in large numbers as they are continuously replaced. Tooth morphologies are of major importance on multiple taxonomic levels for identification of shark and ray taxa. Here, we review dental morphological characters of squalomorph sharks and test these for their phylogenetic signal. Subsequently, we combine DNA sequence data (concatenated exon sequences) with dental morphological characters from 85 fossil and extant taxa to simultaneously infer the phylogeny and re‐estimate divergence times using information of 61 fossil tip‐dates as well as eight node age calibrations of squalomorph sharks. Our findings show that the phylogenetic placement of fossil taxa is mostly in accordance with their previous taxonomic allocation. An exception is the phylogenetic placement of the extinct genus ?Protospinax , which remains unclear. We conclude that the high number of fossil taxa as well as the comprehensive DNA sequence data for extant taxa may compensate for the limited number of morphological characters identifiable on teeth, serving as a backbone for reliably estimating the phylogeny of both extinct and extant taxa. In general, tip‐dating mostly estimates older node ages compared to previous studies based on calibrated molecular clocks.     

The position of Cetacea within mammalia: phylogenetic analysis of morphological data from extinct and extant taxa

Knowledge of the phylogenetic position of the order Cetacea (whales, dolphins, and porpoises) within Mammalia is of central importance to evolutionary biologists studying the transformations of biological form and function that accompanied the shift from fully terrestrial to fully aquatic life in this clade. Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids. We tested morphological evidence for several hypotheses concerning the sister taxon relationships of Cetacea in a maximum parsimony analysis of 123 morphological characters from 10 extant and 30 extinct taxa. We advocate treating certain multistate characters as ordered because such a procedure incorporates information about hierarchical morphological transformation. In all most-parsimonious trees, whether multistate characters are ordered or unordered, Artiodactyla is the extant sister taxon of Cetacea. With certain multistate characters ordered, the extinct clade Mesonychia (Mesonychidae + Hapalodectidae) is the sister taxon of Cetacea, and Artiodactyla is monophyletic. When all fossils are removed from the analysis, Artiodactyla is paraphyletic with Cetacea nested inside, indicating that inclusion of mesonychians and other extinct stem taxa in a phylogenetic analysis of the ungulate clade is integral to the recovery of artiodactyl monophyly. Phylogenies derived from molecular data alone may risk recovering inconsistent branches because of an inability to sample extinct clades, which by a conservative estimate, amount to 89% of the ingroup. Addition of data from recently described astragali attributed to cetaceans does not overturn artiodactyl monophyly.     

Morphological Evidence for the Phylogeny of Cetacea

A cladistic analysis of 54 extant and extinct cetacean taxa scored for 304 morphological characters supports a monophyletic Odontoceti, Mysticeti, Autoceta, and Cetacea. Forcing a sister-group relationship between Mysticeti and Physeteridae, as suggested by some, but not all, molecular studies, requires an additional 72 steps. In agreement with recent molecular studies, morphological data divide extant mysticetes into two clades: Balaenopteroidea (Eschrichtiidae + Balaenopteridae) and Balaenoidea (Balaenidae + Neobalaenidae). Cetotheriopsinae is removed from Cetotheriidae, elevated to Family Cetotheriopsidae, and placed within the Superfamily Eomysticetoidea. All extant mysticetes and all cetotheriids are placed in a new Parvorder Balaenomorpha, which is diagnosed by many morphological characters, including fusion of the anterior and posterior processes of petrosal to ectotympanic bulla, pronounced median keel on palate, and absence of ventral margin of sigmoid process of bulla. Many of the clades within Odontoceti in the most parsimonious trees of this study are at odds with recent phylogenetic analyses. For example, Platanistidae is not closely related to the extinct odontocete families Squalodontidae and Squalodelphinidae. Instead, it is more closely related to extant river-dwelling odontocetes (i.e., Lipotes, Inia), suggesting a single dispersal of odontocetes into freshwater habitats. We found several characters to support Physeteroidea (Physeteridae + Ziphiidae), a taxon considered paraphyletic by several molecular and some morphological analyses. Lack of agreement on the phylogeny within Odontoceti indicates that additional analyses, which include molecular and anatomical data as well as extant and extinct taxa, are needed.     

Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets

It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character evolution. The importance of this process has been further magnified because of the crucial role of fossils in dating divergence times. Outstanding issues remain, including appropriate methods to place fossils in phylogenetic trees, the importance of molecules versus morphology in these analyses, as well as the impact of potentially large amounts of missing data for fossil taxa. In this study we used the angiosperm clade Juglandaceae as a model for investigating methods of integrating fossils into a phylogenetic framework of extant taxa. The clade has a rich fossil record relative to low extant diversity, as well as a robust molecular phylogeny and morphological database for extant taxa. After combining fossil organ genera into composite and terminal taxa, our objectives were to (1) compare multiple methods for the integration of the fossils and extant taxa (including total evidence, molecular scaffolds, and molecular matrix representation with parsimony [MRP]); (2) explore the impact of missing data (incomplete taxa and characters) and the evidence for placing fossils on the topology; (3) simulate the phylogenetic effect of missing data by creating "artificial fossils"; and (4) place fossils and compare the impact of single and multiple fossil constraints in estimating the age of clades. Despite large and variable amounts of missing data, each of the methods provided reasonable placement of both fossils and simulated "artificial fossils" in the phylogeny previously inferred only from extant taxa. Our results clearly show that the amount of missing data in any given taxon is not by itself an operational guideline for excluding fossils from analysis. Three fossil taxa (Cruciptera simsonii, Paleoplatycarya wingii, and Platycarya americana) were placed within crown clades containing living taxa for which relationships previously had been suggested based on morphology, whereas Polyptera manningii, a mosaic taxon with equivocal affinities, was placed firmly as sister to two modern crown clades. The position of Paleooreomunnea stoneana was ambiguous with total evidence but conclusive with DNA scaffolds and MRP. There was less disturbance of relationships among extant taxa using a total evidence approach, and the DNA scaffold approach did not provide improved resolution or internal support for clades compared to total evidence, whereas weighted MRP retained comparable levels of support but lost crown clade resolution. Multiple internal minimum age constraints generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages.     

Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record

A recent molecular phylogeny of the mammalian order Carnivora implied large body size as the ancestral condition for the caniform subclade Arctoidea using the distribution of species mean body sizes among living taxa. "Extant taxa-only" approaches such as these discount character state observations for fossil members of living clades and completely ignore data from extinct lineages. To more rigorously reconstruct body sizes of ancestral forms within the Caniformia, body size and first appearance data were collected for 149 extant and 367 extinct taxa. Body sizes were reconstructed for four ancestral nodes using weighted squared-change parsimony on log-transformed body mass data. Reconstructions based on extant taxa alone favored large body sizes (on the order of 10 to 50 kg) for the last common ancestors of both the Caniformia and Arctoidea. In contrast, reconstructions incorporating fossil data support small body sizes (< 5 kg) for the ancestors of those clades. When the temporal information associated with fossil data was discarded, body size reconstructions became ambiguous, demonstrating that incorporating both character state and temporal information from fossil taxa unambiguously supports a small ancestral body size, thereby falsifying hypotheses derived from extant taxa alone. Body size reconstructions for Caniformia, Arctoidea, and Musteloidea were not sensitive to potential errors introduced by uncertainty in the position of extinct lineages relative to the molecular topology, or to missing body size data for extinct members of an entire major clade (the aquatic Pinnipedia). Incorporating character state observations and temporal information from the fossil record into hypothesis testing has a significant impact on the ability to reconstruct ancestral characters and constrains the range of potential hypotheses of character evolution. Fossil data here provide the evidence to reliably document trends of both increasing and decreasing body size in several caniform clades. More generally, including fossils in such analyses incorporates evidence of directional trends, thereby yielding more reliable ancestral character state reconstructions.     

ESTIMATING SPECIATION AND EXTINCTION RATES FROM DIVERSITY DATA AND THE FOSSIL RECORD

Understanding the processes that underlie biodiversity requires insight into the evolutionary history of the taxa involved. Accurate estimation of speciation, extinction, and diversification rates is a prerequisite for gaining this insight. Here, we develop a stochastic birth–death model of speciation and extinction that predicts the probability distribution of both extinct and extant numbers of species in a clade. We present two estimation methods based on this model given data on the number of extinct species (from the fossil record) and extant species (from diversity assessments): a multivariate method of moments approach and a maximum-likelihood approach. We show that, except for some special cases, the two estimation methods produce very similar estimates. This is convenient, because the usually preferred maximum-likelihood approach is much more computationally demanding, so the method of moments can serve as a proxy. Furthermore, we introduce a correction for possible bias that can arise by the mere fact that we will normally only consider extant clades. We find that in some cases the bias correction affects the estimates profoundly. Finally, we show how our model can be extended to incorporate incomplete preservation. Preservation rates can, however, not be reliably estimated on the basis of numbers of extant and extinct species alone.     

Morphological disparity in theropod jaws: comparing discrete characters and geometric morphometrics

Disparity, the diversity of form and function of organisms, can be assessed from cladistic or phenetic characters, and from discrete characters or continuous characters such as landmarks, outlines, or ratios. But do these different methods of assessing disparity provide comparable results? Here we provide evidence that all metrics correlate significantly with each other and capture similar patterns of morphological variation. We compare three methods of capturing morphological disparity (discrete characters, geometric morphometric outlines and geometric morphometric landmarks) in coelurosaurian dinosaurs. We standardize our study by focusing all our metrics on the mandible, so avoiding the risk of confounding disparity methods with anatomical coverage of the taxa. The correlation is strongest between the two geometric morphometric methods, and weaker between the morphometric methods and the discrete characters. By using phylogenetic simulations of discrete character and geometric morphometric data sets, we show that the strength of these correlations is significantly greater than expected from the evolution of random data under Brownian motion. All disparity metrics confirm that Maniraptoriformes had the highest disparity of all coelurosaurians, and omnivores and herbivores had higher disparity than carnivores.     

Histological variability in fossil and recent alligatoroid osteoderms: Systematic and functional implications

Statements about morphological variation in extinct taxa often suffer from insufficient sampling that can be remedied by taking advantage of larger sample sizes provided by related, extant taxa. This analysis quantitatively and qualitatively examines histological and morphological variation of osteoderms from extant and extinct alligatoroid specimens. Statistically significant differences were correlated with changes in osteoderm size and shape. These differences are independent of position on the body, taxonomy, or evolution. Histological variation in alligatoroid osteoderms is due to morphological constraints on the elements themselves, and not taxonomic differences. This has implications for the recognition of histological characters in the osteoderms of extinct archosaur groups that lack extant representatives. J. Morphol., 2013. © 2013 Wiley Periodicals, Inc.     

Evolution of fossil and living spider flies based on morphological and molecular data (Diptera,Acroceridae)

The phylogeny of spider flies is presented based on an analysis of DNA sequence data combined with morphological characters for both living and fossil species. We sampled 40 extant and extinct genera across all major lineages of Acroceridae, which were compared with outgroup taxa from various lower brachyceran families. In all, 81 morphological characters of 60 extant and 10 extinct ingroup species were combined with 7.1 kb of DNA sequences of two nuclear (CAD and 28S rDNA) and two mitochondrial genes (COI and 16S rDNA). Results strongly support the monophyly of Acroceridae, with major clades contained within classified here in five extant subfamilies (Acrocerinae, Cyrtinae stat. rev. , Ogcodinae stat. rev. , Panopinae and Philopotinae) and one extinct subfamily, Archocyrtinae. The evolution of important spider fly traits is discussed, including genitalia and wing venation. The status of the enigmatic Psilodera Gray and Pterodontia Gray as members of the Panopinae is confirmed based on both molecular and morphological data.     

Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia

Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological data sets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and some studies have merged morphological and molecular data to estimate combined evidence phylogenies containing both extinct and extant taxa. However, few, if any, studies have attempted to estimate divergence times using phylogenies containing both fossil and living taxa sampled for both molecular and morphological data. Here, I infer both the phylogeny and the time of origin for Lissamphibia and a number of stem tetrapods using Bayesian methods based on a data set containing morphological data for extinct taxa, molecular data for extant taxa, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post hoc age constraints on internal nodes and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined evidence analyses whenever possible.     

HOMOPLASY AS PATTERN: MULTIVARIATE ANALYSIS OF MORPHOLOGICAL CONVERGENCE IN ANSERIFORMES

Abstract— A multivariatc model for taxa and characters is presented that represents taxa as points in an ordination space such that shared derived character states define groups of taxa or regions in this space. This model is compared, in terms of concepts of information content and explanatory power, to the eladistie model that relates characters and taxa to a hierarchical pattern. While a cladogram may be identified with a phylogenetic hypothesis, the ordination pattern may be equated with hypotheses about similarities among the taxa in habitat, feeding mode, or other ecological factors.
This basic data-pattern model is appropriate for the explanation of the character convergences implied by a particular phylogenetic hypothesis. Under the assumptions of the model, the underlying ordination pattern may be inferred from the observed character data using robust ordination procedures recently developed in community ecology.
As an illustration of the method, the morphological convergences derived from a recent phylogenetic hypothesis for genera of Anseriformes are analysed. In the resulting two-dimensional ordination, the genera are arranged such that the convergenlly derived states form regions in the space. While this pattern implies that some of the taxa that are close together in the space are phylogcnetically dissimilar , taxa that are close together in the space are found to be similar in their mode of feeding. Thus, the ordination demonstrates that taxa sharing these morphological convergences tend to utilize habitat in the same way in terms of mode of feeding.
The explanatory power of the pattern and the degree of recovery of habitat information are tested against null hypotheses using Monte Carlo simulations.
Extensions of the method are discussed, including applications to studies of parasite—host relationships and to biogeography.     

Morphological and molecular phylogenetic context of the angiosperms: contrasting the 'top-down' and 'bottom-up' approaches used to infer the likely characteristics of the first flowers

Recent attempts to address the long-debated 'origin' of the angiosperms depend on a phylogenetic framework derived from a matrix of taxa versus characters; most assume that empirical rigour is proportional to the size of the matrix. Sequence-based genotypic approaches increase the number of characters (nucleotides and indels) in the matrix but are confined to the highly restricted spectrum of extant species, whereas morphology-based approaches increase the number of phylogenetically informative taxa (including fossils) at the expense of accessing only a restricted spectrum of phenotypic characters. The two approaches are currently delivering strongly contrasting hypotheses of relationship. Most molecular studies indicate that all extant gymnosperms form a natural group, suggesting surprisingly early divergence of the lineage that led to angiosperms, whereas morphology-only phylogenies indicate that a succession of (mostly extinct) gymnosperms preceded a later angiosperm origin. Causes of this conflict include: (i) the vast phenotypic and genotypic lacuna, largely reflecting pre-Cenozoic extinctions, that separates early-divergent living angiosperms from their closest relatives among the living gymnosperms; (ii) profound uncertainty regarding which (a) extant and (b) extinct angiosperms are most closely related to gymnosperms; and (iii) profound uncertainty regarding which (a) extant and (b) extinct gymnosperms are most closely related to angiosperms, and thus best serve as 'outgroups' dictating the perceived evolutionary polarity of character transitions among the early-divergent angiosperms. These factors still permit a remarkable range of contrasting, yet credible, hypotheses regarding the order of acquisition of the many phenotypic characters, reproductive and vegetative, that distinguish 'classic' angiospermy from 'classic' gymnospermy. The flower remains ill-defined and its mode (or modes) of origin remains hotly disputed; some definitions and hypotheses of evolutionary relationships preclude a role for the flower in delimiting the angiosperms. We advocate maintenance of parallel, reciprocally illuminating programmes of morphological and molecular phylogeny reconstruction, respectively supported by homology testing through additional taxa (especially fossils) and evolutionary-developmental genetic studies that explore genes potentially responsible for major phenotypic transitions.     

THE PHYLOGENETIC RELATIONSHIPS AND BIOGEOGRAPHY OF TRUE PORPOISES (MAMMALIA: PHOCOENIDAE) BASED ON MORPHOLOGICAL DATA

Prior studies of phylogenetic relationships among phocoenids based on morphology and molecular sequence data conflict and yield unresolved relationships among species. This study evaluates a comprehensive set of cranial, postcranial, and soft anatomical characters to infer interrelationships among extant species and several well-known fossil phocoenids, using two different methods to analyze polymorphic data: polymorphic coding and frequency step matrix. Our phylogenetic results confirmed phocoenid monophyly. The division of Phocoenidae into two subfamilies previously proposed was rejected, as well as the alliance of the two extinct genera Salumiphocaena and Piscolithax with Phocoena dioptrica and Phocoenoides dalli . Extinct phocoenids are basal to all extant species. We also examined the origin and distribution of porpoises within the context of this phylogenetic framework. Phocoenid phylogeny together with available geologic evidence suggests that the early history of phocoenids was centered in the North Pacific during the middle Miocene, with subsequent dispersal into the southern hemisphere in the middle Pliocene. A cooling period in the Pleistocene allowed dispersal of the southern ancestor of Phocoena sinus into the North Pacific (Gulf of California).