We review the widespread notion that the inclusion of taxa scored for relatively few characters is problematic in phylogenetic analyses. Taxa scored for few characters may lead to lack of resolution, but need not. Lack of resolution may be unrelated to missing data when characters conflict. Missing data cannot produce groupings for which there is no evidence. A common approach to avoid the “missing data problem” is to exclude incomplete taxa, but excluding such taxa is inadvisable because the information content of taxa is not necessarily correlated with degree of completeness. Another prevalent strategy—excluding characters with a high proportion of missing data—may actually contribute to the low resolution problem rather than ameliorate it because removing any character data removes potentially informative synapomorphies. Other approaches, including the use of less-than-strict consensus techniques, have the potential to obscure evidence for alternative relationships or, at best, provide incomplete summaries of the primary trees. Missing data simply represent the unknown and should not be viewed as an impediment to considering all available evidence in phylogenetic analyses, nor used as justification for excluding specific taxa or characters.

Almost all phylogenetic studies utilizing fossils are faced with the problem of missing data. With the development of methods allowing total evidence phylogenies where fossils are combined with extant taxa, and molecular evidence is available, this problem is compounded. Standard methods ignore missing data and often result in poorly resolved trees, and procedures such as culling of taxa or partitioning data have been proposed to improve resolution. Here, we take a different tack, one grounded in the fact that because we do not know what the behavior of missing data would be, it is worthwhile to examine the universe of possible outcomes. The MERDA value is the frequency with which a particular clade is recovered in replicated analyses where missing observations are replaced randomly with observable states. A technique to de-resolve missing data-dependent clades is also proposed. We also show that, in published data sets, there is little obvious relationship between MERDA performance and standard measures of clade support such as Bremer and Jacknife indices.

Vertebrate skeletons, particularly fossils, commonly have damaged, distorted, or missing structures. Because multivariate morphometric methods require complete data matrices, there are two possible solutions: to omit the specimens or characters having missing values, or to estimate missing values from the remainder of the data. Omission of specimens or characters reduces the data available for analysis, and thus the power to detect patterns or differences. Univariate and bivariate-regression methods are known to reduce the total variance of the data, and thus are not considered here. We compared the two most common multivariate methods: expectation-maximization (EM), which uses the covariance matrix directly, and principal-component (PC) estimation, based on regression of characters on principal components. Performance was evaluated by computer simulation of randomly introduced missing data in constructed data sets of known structure, and in several complete fossil (Pterodactylus skeleton) and recent (Alligator skeleton, Canis skull) data sets. The EM and PC methods displayed consistent and similar patterns of behavior for varying combinations of specimens and characters and across a broad range of amounts of missing data. Reliability was greatest for moderate numbers of characters (6–12) and larger sample sizes. For fewer characters the maximum amount of missing data that can be predicted increases substantially, but with a decrease in reliability. Both methods produce accurate estimates of missing values, but EM estimates are more precise. EM also outperforms the PC method in the maximum proportion of missing values that can be reliably estimated (almost 50% for small numbers of characters).

The problem of missing data is often considered to be the most significant obstacle in reconstructing the phylogeny of fossil taxa and their relationships to extant taxa. In this paper, I review the results of recent simulation studies and present new results that explore how missing data affect phylogenetic accuracy, which is defined here as the success of a method at reconstructing the true phylogeny. Missing data cells are typically added to a phylogenetic analysis in the form of incomplete taxa (e.g., highly fragmentary fossil taxa) or incomplete characters (e.g., a set of DNA sequence or soft anatomical characters in an analysis including living and fossil taxa). These two types of incomplete data affect phylogenetic analyses in two very different ways, suggesting that there is not a single “missing data problem.” Recent simulation results show that including incomplete taxa is a problem of including too few characters rather than too many missing data cells—if enough characters are scored in these taxa, even the relationships of highly incomplete taxa (e.g., 95% missing data) can be accurately reconstructed. Including incomplete characters is largely a problem of taxon sampling. Adding incomplete characters can improve accuracy under many conditions, but inadequate taxon sampling in these characters can lead to problems of long branch attraction (which causes methods to reconstruct an incorrect tree). New simulation results show that highly incomplete taxa may have little impact on the relationships estimated for the complete taxa. Thus, adding highly incomplete taxa may not adversely affect relationships among the complete taxa. However, these added taxa may be unable to improve accuracy for the complete taxa if they are too incomplete. These results suggest that analyses which combine data from fossils and molecular data sets can be successful, despite large amounts of missing data. The accuracy of these analyses will depend on adequate sampling of characters for fossil taxa and adequate sampling of taxa for molecular data sets.

It is widely recognized that missing entries can render some taxa unstable in phylogenetic parsimony analyses, leading to multiple most parsimonious trees and poorly resolved consensus trees that fail to reveal strictly supported relationships (relationships that are common to all the most parsimonious trees). An illustrated and non-technical review of strategies for ameliorating this problem, including safe taxonomic reduction and the strict reduced consensus method, is presented. Importantly, taxon instability is not necessarily a problem of missing entries per se, but it may be exacerbated by missing entries. A less widely recognized, but nonetheless important potential impact of missing entries and instability is obfuscation of the levels of the support provided by the data for particular relationships. Low bootstrap proportions and/or decay indices may reflect the instability of a subset of the taxa rather than more systemic deficiencies of the data. Even when there is no gross instability, relative instability can negatively impact upon measures of support. Rather than eschewing measures of support because of such problems, phylogeneticists should use methods of evaluating support that are not unduly affected by relatively unstable taxa. The majority-rule reduced consensus method provides one method that can be used to enhance bootstrap and jackknife analyses so as to reveal ‘hidden support’. Double decay analysis provides an analogous extension to traditional decay analysis. Non-technical summaries of these methods are presented and their potential benefits and limitations are discussed and illustrated.

Recognition of avascular necrosis through propodial head subsidence in fossils indicates that plesiosaurs were susceptible to decompression syndrome and implies deep, prolonged or repetitive diving behavior for these animals. Contrary to the situation in mosasaurs, plesiosaur vertebrae were not targets of avascular necrosis. This suggests that the anastomosing internal vascularization of plesiosaur vertebral centra was functionally adaptive. No phyletic trend is evident in the susceptibility of plesiosaurs to the pathology, although stem group sauropterygians were almost never affected (not surprising for near-shore, shallow water animals). Cryptoclididae were the only plesiosaur family not regularly afflicted with decompression syndrome. The difference between this and other groups is most likely to have been behavioral and/or ecological.

A new taxon of sphenosuchian crocodylomorph, Dromicosuchus grallator, is described on the basis of a well-preserved, largely articulated partial skeleton from Late Triassic strata in the Durham sub-basin of the Deep River basin (Newark Supergroup) of Durham County, North Carolina. The holotype was preserved directly beneath the skeleton of a rauisuchian archosaur; this association, along with apparent bite marks to the head and neck of the crocodylomorph, suggests that the two animals died and were buried together during the act of predation. Dromicosuchus grallator is most closely related to Hesperosuchus agilis from the Petrified Forest Member of the Chinle Formation (late Carnian or early Norian) of Arizona and New Mexico and Saltoposuchus connectens from the Middle Stubensandstein (Löwenstein Formation; middle Norian) of Württemberg, Germany. The monophyly of Sphenosuchia is only weakly supported at present.

The vertebrae of sauropod dinosaurs are characterized by complex architecture involving laminae, fossae, and internal chambers of various shapes and sizes. These structures are interpreted as osteological correlates of an intricate system of air sacs and pneumatic diverticula similar to that of birds. In basal sauropods pneumatic features are limited to fossae. Camerae and camellae are internalized pneumatic chambers independently acquired in neosauropods and some Chinese forms. The polycamerate and camellate vertebrae of higher neosauropods are characterized by internal pneumatic chambers of considerable complexity. The independent acquisition of these derived morphologies in Mamenchisaurus, derived diplodocids, and most titanosauriforms is correlated with increasing size and neck length.

The presacral vertebrae of basal sauropods were probably pneumatized by diverticula of cervical air sacs similar to those of birds. Although pneumatic characters in sauropods are most extensive and complex in presacral vertebrae, the sacrum was also pneumatized in most neosauropods. Pneumatization of the proximal caudal vertebrae was achieved independently in diplodocids and titanosaurids. In birds, the synsacrum is pneumatized via abdominal air sacs which function primarily in lung ventilation. The presence of pneumatized sacral and caudal vertebrae in neosauropods indicates that abdominal air sacs were probably present in at least some sauropods.

A partial sauropod skeleton from the Middle Jurassic (Callovian) Balabansai Formation in Kirghizia, comprising two dorsal and 16 caudal vertebrae, pelvis and limb bones is described and referred to Ferganasaurus verzilini, gen. et sp. nov. The manus is known only from drawings as original material has been lost; foot bones, except the astragalus, are unknown. Ferganasaurus forms an unresolved polytomy with neosauropods Jobaria, Diplodocoidea (Nemegtosauridae, Rebbachisauridae, Diplodocidae, and Dicraeosauridae), and Macronaria (Camarasaurus, Haplocanthosaurus and Titanosauriformes). The neosauropod characters of Ferganasaurus include five coossified sacral vertebra, metacarpal proximal ends subtriangular, composite proximal articular surface of metacarpus U-shaped, tibia with subcircular proximal end, astragalar ascending process extends to the posterior margin of the astragalus, and astragalus wedge-shaped in anterior view. Ferganasaurus is one of the oldest known neosauropods, and possesses two primitive characters unusual for a neosauropod (femur shaft with sigmoid curve, and fourth trochanter of the femur blade-like with acuminate apex).

An analysis of 80 thin-sections of the long bones of a relatively large and presumably adult specimen of Confuciusornis sanctus, a basal bird from the Early Cretaceous of China, reveals osteohistological patterns similar in some ways to those of extant birds of approximate size, but different in other ways. The fibrolamellar tissue typical of its cortex is commonly laid down by adult birds at standard estimates of 10 μm or more radial growth per day. If this rate were characteristic of its ontogeny, Confuciusornis could have reached maturity in 20 weeks or less. These tissue patterns, read straight, suggest lower growth rates than in the larger immediate relatives of Confuciusornis, the coelurosaurian dinosaurs, as well as in large extant birds, taxa that reached their large adult size relatively quickly. However, tissues of the inner cortex, as well as new analyses of rates in living variants of the fibro-lamellar tissue complex, suggest far faster growth and an estimated time to maturation as short as 8–13 weeks, longer than in most small living birds but commensurate with larger birds or relatively slowly growing birds such as tinami.

Described here is a new fossil species of crane (Aves: Gruidae), Palaeogrus mainburgensis, sp. nov., from the early middle Miocene fossil site of Sandelzhausen in Bavaria, southern Germany. The study includes morphological and metric comparisons with all known Tertiary gruids from Eurasia, along with a discussion of the taxonomic distribution of morphological characters in fossil gruids. The new species is represented by a distal tibiotarsus, a proximal tarsometatarsus, and a distal radius. It is the smallest species within the genus Palaeogrus that is known from the middle Eocene through the early Miocene. Palaeogrus mainburgensis, sp. nov. is the only known gruid taxon from Sandelzhausen.

Sineoamphisbaena hexatabularis, a fossil squamate recovered from Upper Cretaceous deposits in Inner Mongolia, China, was reported to be the oldest known amphisbaenian and the sister group to all other amphisbaenians. However, the conclusion of amphisbaenian affinities was based on a partitioned analysis that excluded relevant data and included reconstructed characters. When characters for analysis are limited to those that are observable on the fossils and all evidence is included and analyzed simultaneously, results do not support S. hexatabularis as an amphisbaenian, but instead suggest that S. hexatabularis may be related to macrocephalosaurids. Several potential synapomorphies of S. hexatabularis and macrocephalosaurids are provided, including: presence of lateral process of palatal ramus of pterygoid; postorbital large, extending posteriorly beyond supratemporal fenestra, and approaching posterior edge of cranial roof; and tall, narrow, dorsal process of maxilla. S. hexatabularis is tentatively reassigned to the Macrocephalosauridae. The origin of amphisbaenians remains obscure.

Kulbeckia, a placental mammal from the late Turonian–Coniacian (Late Cretaceous) of Uzbekistan, was originally placed in the monotypic Kulbeckiidae. Important new material indicates that Kulbeckia is the basal most member of “Zalambdalestidae”, which also includes Zalambdalestes, Barunlestes, and the poorly known Alymlestes, all from the Late Cretaceous of Asia. Kulbeckia shares with other zalambdalestids: a narrow, somewhat elongated snout; procumbent, enlarged, and open-rooted medial lower incisor with enamel restricted to the more ventrolabial surface; and anteroposteriorly compressed and centrally pinched molar trigonids. Commensurate with its 10-million-year earlier age relative to other zalambdalestids, it is notable in its smaller size, probable retention of four lower incisors, bifurcated or two-rooted lower canine, relatively smaller or absent diastemata between anterior teeth, more lingually placed cristid obliqua, less reduced M3 and m3, and more dorsal and posterior placement of the angular process in adults. Kulbeckia kansaica (Tadjikistan) and Kulbeckia rara (Uzbekistan) are regarded as synonyms of Kulbeckia kulbecke, the only recognized species of Kulbeckia.

The rodents (Baluchimyinae and Fallomus) from the Bugti, Sulaiman, and Ladakh deposits (Indian subcontinent) were originally considered a distinct early Miocene group that arose via local evolution from the Eocene Chapattimyidae in the Indo-Pakistan province. The Bugti Member, the lowermost continental beds of the previously ascribed Miocene Chitarwata Formation, is now considered to be Oligocene. A new continental vertebrate locality from the basal part of the Bugti Member (Paali nala C2) has yielded an important early Oligocene small mammal fauna including a well-diversified rodent assemblage that allows revision of the age attributed to the classic Bugti rodent fauna. Additional specimens (mainly isolated teeth) allow a systematic review of Fallomus (Diatomyidae) and Hodsahibia (“Baluchimyinae”), and two new species are described for each genus (F. ginsburgi, sp. nov.; F. quraishyi, sp. nov.; H. gracilis, sp. nov.; and H. beamshaiensis, sp. nov.). The presence of several higher rodent taxa at Paali nala C2 suggest that there was not an extended period of mid-Tertiary faunal isolation on the Indian subcontinent, nor an abrupt turnover between Chitarwata and Lower Siwalik rodent faunas. “Baluchimyines,” here considered Hystricognathi incertae sedis, are part of a diverse assemblage of hystricognathous rodents in South Asia at the end of the Paleogene. A close phylogenetic relationship between “baluchimyines” and earliest Asian hystricid rodents is plausible.

Three acaremyid rodents from the Miocene of Patagonia are described. Galileomys antelucanus, gen. et sp. nov. (Colhuehuapian SALMA, early Miocene) is the most plesiomorphic genus within the Acaremyidae. Galileomys? colloncurensis, sp. nov. is the first acaremyid recorded from the Colloncuran SALMA (middle Miocene). The generic referral is tentative because the known material does not display enough characters. Acaremys cf. murinus Ameghino, 1887 represents a second Colhuehuapian acaremyid. Cladistic analyses of dental and mandibular characters do not support previous hypotheses that Sciamys and Acaremys are the ancestors of the Octodontidae. On the contrary, these two genera and Galileomys constitute a monophyletic group united by the presence of a hypoflexus in P4, a well defined anterodorsal limit of mandibular masseteric fossa, and a figure-eight-shaped molar pattern. The inclusion of other genera in the Acaremyidae is not supported by cladistic analysis. A shared figure-eight-shaped dental pattern was the primary basis for a presumed close relationship between the Acaremyidae and Octodontidae, but this state evolved independently in the two taxa. The Acaremyidae is an extinct, early radiation of the Octodontoidea that persisted at least until the middle Miocene. The Octodontidae probably originated from an ancestor closer to the “echimyids” than to the Acaremyidae, with neither normal dental replacement nor mental foramen.

A new species of the notoungulate Eopachyrucos is described on the basis of mandibles and lower cheek teeth from the upper Oligocene Fray Bentos Formation of Uruguay. Eopachyrucos ranchoverdensis, sp. nov., is most similar to the pre-Deseadan/post-Mustersan (late Eocene) Eopachyrucos pliciferus from Patagonia, but is much larger and less hypsodont. The new species has a well-developed postmetacristid on p3 similar to that of Notopithecinae but with higher crowned teeth. The Oligocene record of Eopachyrucos greatly extends its chronologic range. A cladistic analysis of Eopachyrucos and other interatheriids supports the hypothesis that Eopachyrucos is the most primitive interatheriine, retaining a number of primitive features also found in advanced Notopithecinae. The Fray Bentos Fauna shares a few typical elements with Deseadan faunas from Patagonia, but an important distinction between the two faunas is the persistence of some archaic taxa in the Fray Bentos Fauna. The overall composition of the Fray Bentos Fauna is more similar to late Oligocene Deseadan faunas of Bolivia, and this may be attributed to temporal (younger than the Deseadan of Patagonia) or ecological factors.