Contemporary Taxa Research Articles

Stable carbon and oxygen isotopic evidence for Late Cenozoic environmental change in Northern China

Stable carbon and oxygen isotope ratios of 311 enamel samples from a diverse group of herbivorous mammals including Equidae, Rhinocerotidae, Bovidae, Rodentia and Ochotonidaewere were analyzed in order to reconstruct the Late Cenozoic history of vegetation and environmental change in the Yushe Basin in North China. The δ13C values of bulk and serial enamel samples from large mammals show a wide range of variation from −13.3‰ to 1.4‰, with a mean of −7.4‰±3.5‰ (n=294). This indicates that large herbivorous mammals in the area had a variety of diets since 6.5Ma, ranging from pure C3 to mixed C3–C4 and pure C4 diets. In contrast, the δ13C values of small mammals vary from −11.9‰ to −7.6‰, with a mean of −9.7±1.1‰ (n=17), indicating that rodents and ochotonids were feeding mostly on C3 plants. Variations in δ13C values within and between species reflect the variations in the habitat and the vegetation consumed by the animals. In general, horses had higher amounts of C4 grasses in their diets than other contemporary taxa such as bovids, rhinos, rodents and deer, suggesting that horses exploited more open habitats such as grasslands while deer, rhinos and rodents may have preferred more C3 vegetation, which is more indicative of forested environments. The carbon isotope data show that C4 grasses have been an important component of horses' diets and of local ecosystems since ~6.5Ma, confirming that the “late Miocene C4 expansion” occurred in North China as it did in Africa, Indian subcontinent and the Americas. This supports a global factor as a main driver of the late Miocene C4 expansion. The combined carbon and oxygen isotope data reveal major shifts in climate to drier and/or warmer conditions after ~5.8, ~4.1, ~3.3, and ~2.5Ma, and significant shifts to relatively wetter and/or cooler conditions after ~6.4, ~5, ~3.5Ma. The shifts to drier and/or warmer climate after ~5.8Ma and ~2.5Ma coincide with two major fauna turnover events. Intra-tooth δ13C and δ18O values are negatively correlated within individual modern teeth and some fossil teeth, displaying the characteristic pattern of the summer monsoon regime and confirming a strong monsoon influence in the area since at least the early Pliocene. The data also suggest that the C4 abundance in the area has fluctuated over the past 6.5Ma in response to changes in climate, with more C4 grasses during warmer and/or drier periods and a reduced C4 component at cooler and/or wetter times.

Stomatal density and index data of Platanus neptuni leaf fossils and their evaluation as a CO2 proxy for the Oligocene

Platanus neptuni (Ettingshausen) Bůžek, Holý and Kvaček is a deciduous and preferentially azonal taxon of temperate to warm-temperate vegetation in Europe from the Late Eocene to the Late Miocene. The high fossilization potential of its leaves and easily identifiable stomata and epidermal cells make P. neptuni an excellent source of stomatal data that can be utilized as a CO2 proxy. Moreover, it was found in former studies that CO2 data based on stomatal frequency data of P. neptuni overlapped to a high degree with CO2 results which are provided by other, contemporaneous taxa. In this study, the stomatal CO2 signal of P. neptuni is expanded to include the early Oligocene and is analyzed in more detail with three aims: 1) to evaluate the CO2 signal of P. neptuni stomatal data, 2) to check SI and SD data of P. neptuni for consistency, and 3) to contribute additional terrestrial CO2 data to the Oligocene record. During the Oligocene, full scale Antarctic glaciation occurred, punctuated by various distinct glaciation events. There is evidence that Oligocene glaciation was coupled to atmospheric CO2 level. Presently, the main proxy sources for Oligocene CO2 levels are alkenones and boron-isotope data, both obtained from marine sediments.Since P. neptuni is an extinct taxon, CO2 was reconstructed by using an ecophysiological modeling approach to plant gas exchange which utilizes various other data in addition to stomatal density. Material was considered from sites which are dated to the following time intervals: early Oligocene — 33.9 to 32Ma, late Oligocene — 27 to 26.2Ma and 25.3 to 23Ma, and latest Oligocene — around 24Ma. Comparison of raw SI and SD data of P. neptuni revealed partially conflicting results, with the SD data indicating a decrease in CO2 from the early to the late Oligocene whereas SI data indicate an increase. In contrast, CO2 results calculated with the gas exchange model indicate relatively stable CO2 for the considered time intervals, with levels of about 400ppm. The reconstructed CO2 data points are similar to other proxy data and are consistent with the general climate development during the Oligocene.

Younger Dryas – early Holocene transition in the south‐eastern Iberian Peninsula: insights from land snail shell middens

ABSTRACTThe land snail Sphincterochila candidissima from archeological records in Villena (SE Spain) was studied isotopically to estimate the Younger Dryas (YD)–early Holocene transition in the western Mediterranean. Live‐collected individuals exhibited body (−21.8 ± 1.6‰) and shell (−5.8 ± 1.4‰) δ13C values typical of a C3 plant diet, probably combined with carbonate ingestion. Calculations of a carbon flux balance‐mixing model suggest that living specimens experienced similar metabolic rates, with comparable ratio of input and output fluxes of bicarbonate from the snail hemolymph. All fossil shells showed comparable δ13C values among each other, but values were ∼2‰ higher than living specimens. This may be explained by higher water stress at the YD–Holocene transition or by the Suess effect. Shell δ18O values averaged +1.3 ± 0.8‰ for living individuals, −0.5 ± 0.8‰ for Holocene (8.4–10.2 cal ka BP) specimens and +0.4 ± 0.6‰ for YD (12.0–12.4 cal ka BP) snails. An oxygen flux balance‐mixing model suggests that YD shells precipitated during relative humidity (RH) values of ∼79–82%, after which RH increased gradually reaching maximum values of ∼87–88% at ∼8.4–8.6 cal ka BP and, from there, RH eventually declined to present values of ∼82%. Comparisons with other snail data suggest that the xerophilous Sphincterochila records different environmental signatures fro other contemporaneous taxa.

New Palaeogene cingulates (Mammalia, Xenarthra) from Santa Rosa, Perú and their importance in the context of South American faunas

The record of Palaeogene cingulate xenarthrans in low latitudes is very poor. The cingulate fauna from the Yurúa River near Santa Rosa in eastern Perú is important because it is one of the oldest known from the Palaeogene of Perú and because of its tropical latitudinal position. Although remains are scarce, we recognize three new taxa: two species of Astegotheriini (Dasypodidae); Parastegosimpsonia peruana gen. et sp. nov., of small size, related to Eocene species from Patagonia; and another new species, ?Parastegosimpsonia sp. nov., which consists of an incomplete osteoderm representing the largest species of this tribe. A third species, Yuruatherium tropicalis gen. et sp. nov., of indeterminate suprageneric rank, shares features with Machlydotherium Ameghino (Casamayoran-Tinguirirican SALMA – middle Eocene-early Oligocene of Patagonia) and is similar to Eocoleophorus Oliveira et al. (Deseadan SALMA – late Oligocene of Brazil). We assign ?Machlydotherium intortum Ameghino (from the late Eocene of Patagonia) to Yuruatherium. Sediments bearing these cingulates also yielded rodents, marsupials and notoungulates, among the most frequent mammals. The absolute age of the sediments is unknown but an estimated age is inferred from studies of the mammalian assemblages. The age of the Santa Rosa local fauna is still controversial and given the groups taken into account, could be from Early Eocene to Late Oligocene. According to sequences of southern cingulate faunas (especially those of Dasypodidae), the cingulates from Santa Rosa also suggest an age between the Late Eocene and Early Oligocene. Nevertheless, the very low latitude of the Santa Rosa local fauna should be taken into account because in lower latitudes it is not uncommon to find taxa with a more generalized set of characters than those present in contemporary taxa from higher latitudes. http://zoobank.org/urn:lsid:zoobank.org:pub:37CAEF7C-3CCC-4C3C-9869-D584FD73323C

The oldest known metriorhynchid super-predator: a new genus and species from the Middle Jurassic of England, with implications for serration and mandibular evolution in predacious clades

The Oxford Clay Formation of England has yielded numerous sympatric species of metriorhynchid crocodylomorphs, although disagreement has persisted regarding the number of valid species. For over 140 years teeth reminiscent of the genus Dakosaurus have been known from the Oxford Clay Formation but these have never been properly described and their taxonomy and systematic affinity remain contentious. Furthermore, an enigmatic mandible and associated postcranial skeleton discovered by Alfred Leeds in the Fletton brick pits near Peterborough also remains undescribed. We show that this specimen, and several isolated teeth, represents the oldest known remains of a large-bodied predatory metriorhynchid. This material is described herein and referred to Tyrannoneustes lythrodectikos gen. et sp. nov. This species has a unique occlusal pattern: the dentition was arranged so that the posterior maxillodentary teeth interlock in the same plane and occlude mesiodistally. It is the first described crocodylomorph with microscopic denticles that are not contiguous along the carinae (forming short series of up to 10 denticles) and do not noticeably alter the height of the keel. Additionally, the dorsally expanded and curved posterior region of the mandible ventrally displaced the dentary tooth row relative to the jaw joint facilitating the enlargement of the dentition and increasing optimum gape. Therefore, Tyrannoneustes would have been a large-bodied marine predator that was well-suited to feed on larger prey than other contemporaneous metriorhynchids. A new phylogenetic analysis finds Tyrannoneustes to be the sister taxon to the subclade Geosaurini. An isolated tooth, humerus, and well-preserved mandible suggest a second species of metriorhynchid super-predator may also have lived in the Oxford Clay sea. Finally, we revise the diagnoses and descriptions of the other Oxford Clay metriorhynchid species, providing a guide for differentiating the many contemporaneous taxa from this exceptional fossil assemblage. http://zoobank.org/urn:lsid:zoobank.org:pub:C6222858-EC36-430D-8E28-1F636A6697CA

Taxonomic affinity of halictid bee fossils (Hymenoptera: Anthophila) based on geometric morphometrics analyses of wing shape

Taxonomic assignment of fossils can be difficult because descriptions and phylogenetic analyses are often based on a limited number of discrete visible morphological characters. Quantitative, morphometric analyses can help to assign fossil specimens to modern groups, especially when two-dimensional features, such as insect wings, provide easily identifiable landmarks that are not likely to be deformed in the fossil specimens. Here we study taxonomic attribution of bee fossils by analysing wing shape of fossil and contemporary taxa. Our study focuses on the bee family Halictidae (Hymenoptera: Halictidae: Halictinae). Halictinae is a well-known cosmopolitan group including more than 2500 species in five tribes described from robust molecular and morphological analyses. We analysed 202 specimens of 48 species of Halictinae and Nomiinae. To analyse wing shape, we performed a Geometric Morphometrics analysis by using 19 2D-landmarks. Ordination methods, such as canonical variates analysis (CVA) and linear discriminant analysis (LDA), were used to discriminate tribes based on wing shape. CVA and LDA were both powerful enough to recover tribes previously delimited by adult morphology and DNA sequences. We then assigned fossils in CVA and LDA groups based on Mahalanobis distances. The ‘morphometric affinity’ of the two fossil taxa did not confirm their previous taxonomic attribution. By re-examining the fossil description we propose a new taxonomic attribution for Electrolictus antiquus.

A taxonomic revision of orthosternous scorpions from the English Coal-measures aided by X-ray Micro-Tomography (XMT)

Fossil scorpion systematics – particularly that of the diverse assemblage found in Carboniferous Coal Measure deposits – are problematic, being characterised by a large number of frequently monotypic taxa, based on a limited set of characters. These Palaeozoic scorpions have the potential to elucidate the nature of the scorpion stemgroup and hence to inform long running debates regarding the origin of the crown group and relationships between extant lineages. Carboniferous taxa are often found in siderite concretions and can be preserved in three dimensions. This study investigates two such fossils of the species Compsoscorpius buthiformis (Pocock, 1911) with the aid of X-ray Micro-Tomography (XMT) and computer reconstruction. These scans reveal important new details of the anatomy, such as the walking legs, that allow more detailed comparison with coeval taxa. Many of these taxa are revealed here to be junior synonyms of C. buthiformis and previous taxonomic practice, as it relates to Coal Measures scorpions, is criticised. The ecology of C. buthiformis is also reviewed in light of the new evidence from XMT. In particular, aspects of its walking leg and metastomal anatomy are analogous to that of extant lithophilic and ‘errant’ leaf-litter scorpions.

The Proboscidea (Mammalia) from the Miocene of Sandelzhausen (southern Germany)

Presented here is the complete proboscidean assemblage from the vertebrate locality of Sandelzhausen (southern Germany), dated to the Early/Middle Miocene boundary, early middle MN5. The material is preserved as mostly isolated and disarticulated remains and is composed of about 200 dental remains (cheek teeth and tusks), cranial fragments, and postcrania. The main part of this assemblage is identified as belonging to Gomphotherium subtapiroideum (Schlesinger, 1917), and a few specimens are attributed to Zygolophodon turicensis (Schinz, 1824). Remarkable is the high percentage of remains of young individuals in this proboscidean assemblage and the lack of Prodeinotherium Ehik, 1930. The rich material of G. subtapiroideum enables the description of some tooth positions not known before for this taxon. Furthermore, morphological and metrical comparisons with material of more or less contemporaneous taxa from other European localities are provided, especially G. angustidens (Cuvier, 1817), G. sylvaticum Tassy, 1985, and “Trilophodon” ratisbonensis Rinnert, 1956.

The application of intertidal foraminifera to reconstruct coastal subsidence during the giant Cascadia earthquake of AD 1700 in Oregon, USA

Changes in species assemblages of intertidal foraminifera can be used to estimate the amount of earthquake-related subsidence during plate-boundary earthquakes at the Cascadia subduction zone. The accuracy and precision of foraminiferal methods in paleoenvironmental reconstruction is underpinned by the relations between contemporary taxa and their environment, which are used to calibrate fossil foraminiferal assemblages in sediment sequences. A contemporary training set of surface sediment samples from five intertidal marshes along the Oregon coast was used to determine foraminiferal distributions and prevailing environmental control(s) along elevational transects. Dominant taxa include Balticammina pseudomacrescens, Trochamminita irregularis, Haplophragmoides wilberti, Trochammina inflata, Jadammina macrescens and Miliammina fusca. Unconstrained cluster analysis and detrended correspondence analysis was used to identify two elevation-dependent faunal zones: Faunal Zone I (upland, high marsh, middle marsh) dominated by Balticammina pseudomacrescens, Haplophragmoides wilberti and Trochammina inflata, and Faunal Zone II (low marsh and tidal flat) dominated by Miliammina fusca. Site-specific differences in assemblages at three marshes enabled further subdivision of Faunal Zone I. Zone Ia is based on one or more of Balticammina pseudomacrescens, Trochammina inflata, Trochamminita irregularis and Haplophragmoides sp., and Zone Ib on Jadammina macrescens, Haplophragmoides sp., Trochammina inflata and Miliammina fusca. Canonical correspondence analysis (CCA) and partial CCA of the training set from the Nehalem River marsh transect was used to infer that the zonation of foraminifera is elevation-dependent (39% of explained variance). A transfer function was developed to reconstruct sudden changes in relative sea-level during plate-boundary earthquakes in Oregon. The results indicate a robust performance of the transfer function ( r jack 2 = 0.82) with the error estimate (RMSEP jack = 0.20 m) comparable to local and regional transfer functions from other temperate marshes. To illustrate the potential of the technique, the transfer function was applied to reconstruct subsidence during the AD 1700 earthquake using at Alsea Bay, Oregon. The reconstruction (0.18 ± 0.20 m) is less than half the subsidence estimate of Nelson et al. [2008. Great-earthquake palogeoesy and tsunamis of the past 2000 years at Alsea Bay, central Oregon coast, USA. Quaternary Science Reviews, 27, 747–768] using their foraminiferal transfer function, perhaps because of differences in taxonomy and the species relationship to elevation.

A revision of the western North Pacific swellsharks, genus Cephaloscyllium Gill 1862 (Chondrichthyes: Carcharhiniformes: Scyliorhinidae), including descriptions of two new species

The genus Cephaloscyllium Gill 1862 (Chondrichthyes, Carcharhiniformes, Scyliorhinidae) until recently had only two species recognized, C. isabellum [= C. umbratile (Jordan & Fowler 1903)] and C. fasciatum Chan 1966, from the western North Pacific (WNP), with one dubious species, C. formosanum, having been described by Teng in 1962. Recently, three additional species were described, C. circulopullum Yano et al. 2005, C. sarawakensis Yano et al. 2005, and C. parvum Inoue & Nakaya 2006 from this region. Here we present a revision of this genus for the WNP, including redescriptions of C. fasciatum and C. umbratile based on the holotypes, a re-examination of the recently described species, and descriptions of two new species from Taiwan. Cephaloscyllium umbratile can be distinguished from its congeners based on maximum size, length of first dorsal-fin base, anal–caudal space, and dorsal–caudal space. We conclude, based on a comparison of C. parvum and C. sarawakensis, that the former is a junior synonym of the latter species. The two new Taiwanese species can be separated from other WNP species by color pattern, shape of the anterior nasal flap, anal and dorsal-fin size, internarial width, and mouth size. Finally, we present a revised dichotomous key to the WNP Cephaloscyllium recognizing six contemporary taxa: C. circulopullum, C. fasciatum, C. sarawakensis, C. umbratile, C. pardelotum sp. nov. and C. maculatum sp. nov.

Late Devonian – Early Carboniferous vertebrate microremains from the Carnic Alps, northern Italy

Vertebrate microremains from the Late Devonian–Early Carboniferous of the Carnic Alps are predominantly chondrichthyan, with minor placoderm and actinopterygian remains. The faunas are sparse and, with very few exceptions, occur only in conodont-rich pelagic limestones (Pramosio Limestone) representative of the palmatolepid-bispathodid conodont biofacies. Phoebodont and jalodont chondrichthyans, also reflecting open-ocean environments, predominated during the Famennian, and eventually symmoriids seem to predominate during the Early Carboniferous. The presence of Siamodus in this assemblage gives a new locality for this genus known from few regions in the world and allows confirming its stratigraphical range ( limpidus Zone) and its relation to deep-water environments. The Late Devonian vertebrate faunas are tropical and cosmopolitan, having much in common with coeval taxa from the North-Gondwanan margins and Asian terranes. Composition of the vertebrate faunas is consistent with the Carnic Alps terrane having occupied a position intermediate between Gondwana and Laurussia, as hypothesized by various authors, but because of sparsity of the taxa represented and the pronounced cosmopolitan nature of both the conodont and vertebrate faunas, the data are not compelling.

Sliding MinPD: building evolutionary networks of serial samples via an automated recombination detection approach

Traditional phylogenetic methods assume tree-like evolutionary models and are likely to perform poorly when provided with sequence data from fast-evolving, recombining viruses. Furthermore, these methods assume that all the sequence data are from contemporaneous taxa, which is not valid for serially-sampled data. A more general approach is proposed here, referred to as the Sliding MinPD method, that reconstructs evolutionary networks for serially-sampled sequences in the presence of recombination. Sliding MinPD combines distance-based phylogenetic methods with automated recombination detection based on the best-known sliding window approaches to reconstruct serial evolutionary networks. Its performance was evaluated through comprehensive simulation studies and was also applied to a set of serially-sampled HIV sequences from a single patient. The resulting network organizations reveal unique patterns of viral evolution and may help explain the emergence of disease-associated mutants and drug-resistant strains with implications for patient prognosis and treatment strategies.

A taxonomic revision of the catshark genus Haploblepharus Garman 1913 (Chondrichthyes: Carcharhiniformes: Scyliorhinidae)

This paper examines the alpha level taxonomy of the genus Haploblepharus Garman, 1913 (Chondrichthyes; Scyliorhinidae). Three species are endemic to South Africa, with one species occurring in Namibia and South Africa. Haploblepharus pictus exhibits considerable colour variation which has led to some confusion between that species and H. edwardsii, resulting in a significant range extension for H. pictus. A neotype is designated for H. edwardsii, and problematic Haploblepharus juveniles are tentatively assigned to H. kistnasamyi. A novel species identification key is presented for Haploblepharus, and a comprehensive review of the taxonomy (including type material and synonyms) and distribution of all taxa is presented. The genus Haploblepharus contains four contemporary taxa: H. edwardsii (Schinz, 1822), H. pictus (Müller & Henle, 1838), H. fuscus Smith, 1950, and H. kistnasamyi Human & Compagno, 2006.

A taxonomic revision of the catshark genus Holohalaelurus Fowler 1934 (Chondrichthyes: Carcharhiniformes: Scyliorhinidae), with descriptions of two new species

This paper examines the alpha level taxonomy of the genus Holohalaelurus Fowler 1934 (Chondrichthyes: Carcharhiniformes: Scyliorhinidae), which is endemic to southern and east Africa. A novel species identification key is presented for Holohalaelurus, and a comprehensive review of the taxonomy (including type material and synonyms) and distribution of all taxa is presented. Holohalaelurus regani (Gilchrist 1922) is restricted to southern Africa and the taxa that occur in tropical east Africa are discrete taxonomic units, resulting in the resurrection of H. melanostigma Norman 1939, and two new species, which are described here. Holohalaelurus polystigma (Regan 1921) is shown to be a junior synonym of H. punctatus (Gilchrist 1914), the validity of the type series for H. regani is discussed, and neotypes are designated for H. regani and H. punctatus. The genus Holohalaelurus contains the contemporary taxa H. punctatus (Gilchrist 1914), H. regani (Gilchrist 1922), H. melanostigma Norman 1939, H. favus sp. nov., and H. grennian sp. nov.

A taxonomic revision of the catshark genus Poroderma Smith, 1837 (Chondrichthyes: Carcharhiniformes: Scyliorhinidae)

This paper examines the alpha level taxonomy of the genus Poroderma Smith, 1837 (Chondrichthyes: Scyliorhinidae), which is endemic to South Africa. A novel species identification key is presented for Poroderma, and a comprehensive review of the taxonomy (including type material and synonyms) and distribution of all taxa is presented. Conoporoderma Fowler, 1934 is shown to be a junior synonym of Poroderma Smith, 1837, P. marleyi Fowler, 1934 is shown to be a junior synonym of P. pantherinum, and a new colour form of P. pantherinum is described. This review is the first to offer a comprehensive description of the colour variation exhibited by P. pantherinum. The genus Poroderma contains the contemporary taxa P. africanum (Gmelin, 1789) and P. pantherinum (Smith in Müller and Henle, 1838).

A new pipoid anuran from the Late Cretaceous of South Africa

ABSTRACT Numerous fossil pipoid frogs recovered from Late Cretaceous deposits of a closed crater-lake of Late Cretaceous age in the Marydale District of South Africa are described and referred to a new genus and species of pipoid anuran. The fossils include larvae and adult frogs that are thought to have been killed en masse following breakdown of the thermal stratification or possibly by CO2 degassing from the underlying magma. A cladistic analysis of fossil and extant pipoid frogs based on 49 osteological characters reveals the new taxon to be a member of the pipinomorph clade, which includes the Late Cretaceous Eoxenopoides reuningi also from South Africa, fossil and Recent hymenochirines from Africa, and living Pipa from South America. The new taxon is distinctly larger than Eoxenopoides and further differs from this contemporaneous taxon in having an antorbital process on the maxilla and seven presacral vertebrae, with the first presacral being formed by fusion of Presacrals I and II. The curved shape of the ventral part of the braincase distinguishes this frog from hymenochirines, Palaeobatrachus, and Eoxenopoides. The new anuran is distinguished from the Israeli fossil Thoraciliacus of about the same age by the possession of a conch-shaped tympanosquamosal bone, a short jaw, and fusion of the sacrum and urostyle.

Functional and phylogenetic implications of molar flare variation in Miocene hominoids.

Comparative analyses of molar shape figure prominently in Miocene hominoid evolutionary studies, and incomplete understanding of functional and phylogenetic influences on molar shape variation can have direct consequences for the interpretation of fossil taxa. Molar flare is a shape trait whose polarity, phylogenetic distribution, and functional significance have been sources of contention. To clarify the determinants of molar flare variation in the hominoid radiation, a combination of statistical methods was employed to investigate the effects of diet, phylogeny, and geologic age upon several measures of molar shape, to identify interactions among these factors, and to estimate their relative influence. Classic indices of molar crown shape and cusp relief are highly significantly associated with diet and show no clear phylogenetic or temporal patterning. Correlations with diet are insignificant when phylogenetic effects are controlled, a result which is interpreted as an artifact of the distribution of folivory in the Miocene hominoid radiation. Possession of pronounced molar flare was found to be the primitive condition for Miocene hominoids, but molar flare reduction cannot be considered a crown hominoid synapomorphy. Molar flare is strongly correlated with geologic age but differs significantly among dietary categories when the effects of time are controlled. Among contemporaneous taxa, hard-object feeders consistently show the highest levels of flare. Molar flare reduction is hypothesized to arise from realignment of cusp positions to maximize molar shearing and increase working occlusal surface area, while variation in flare among contemporaneous taxa may be due, at least in part, to enamel thickness variation. The pronounced molar flare of Otavipithecus is interpreted as a primitive retention, although alternative dietary and phylogenetic interpretations cannot be excluded. A dramatic reversal of molar flare reduction in Mio-Pliocene hominins is interpreted as a synapomorphy of the crown hominin clade, thus supporting the hominin status of the Lukeino hominine. The last common ancestor of the Pan-Homo clade is predicted to have possessed relatively non-flaring molars, and implications of this hypothesis for early hominin recognition are discussed.

Clarifying Aetosaur Phylogeny Requires More Fossils, Not More Trees—Reply to Intraorganismal Homology, Character Construction, and the Phylogeny of Aetosaurian Archosaurs (Reptilia, Diapsida)

Harris et al. (2003) presented a lengthy discussion of problems of character construction in phylogenetic analysis, in part based on our (Heckert et al., 1996; Heckert and Lucas, 1999, 2000) cladistic analyses of aetosaur phylogeny. Their principal point with regard to character construction in aetosaurs is that certain characters of separate osteoderm regions (cervical paramedian, dorsal paramedian, lateral, and ventral osteoderms) should not be treated as independent characters because they covary. In terminology we prefer, they thus argue that these characters are redundant. Harris et al. preferred to call them intraorganismal homologues, making an unverifiable assumption about underlying genetic control of osteoderm morphology. When these redundancies are eliminated by combining various sets of the covarying osteoderm characters into one character, the tree obtained is still the same as that published by us (compare Harris et al., 2003: fig. 2a with Heckert and Lucas, 1999: fig. 9). Harris et al. then argued that their newly constructed “composite coding” tree (their fig. 2a), topologically similar trees (e.g., their fig. 2b), and our topologically similar tree (Heckert and Lucas, 1999; fig. 9) are weakly supported, based on various algorithms by which they estimated support. Not surprisingly, when they used fewer characters to describe some of the key morphological changes, the support declined for the nodes that these characters diagnose. We do not argue against the conclusion that aetosaur phylogeny is weakly supported, because we believe that aetosaurs are in general poorly understood. This poor understanding has little to do with analytical tools and much to do with the especially fragmentary nature of the aetosaurian fossil record. This problem was obvious to us even before we published an analysis with approximately 23% missing (unknown) data (Heckert and Lucas, 1999). We, our coworkers, and a growing number of fellow field researchers are attempting to rectify this problem by searching for new aetosaur fossils and redescribing the known specimens, many of which are fragmentary but diagnostic (e.g., Hunt and Lucas, 1990, 1991, 1992; Hunt et al., 1993; Heckert et al., 1996, 1999; Heckert and Lucas, 1998, 1999, 2000, 2002a, 2002b; Lucas and Heckert, 1996, 2001; Lucas, 1998; Lucas et al., 1998, 1999, 2002; Small, 1998, 2002; Zeigler et al., 2002). Not cited but also underway are specimen-based theses and dissertations in North and South America by Parker, Martz, and Desojo, preliminary results of which have been published in recent Society of Vertebrate Paleontology abstracts. It is abundantly obvious from these studies of new and existing collections that aetosaur skulls are, for example, much rarer than those of many contemporaneous taxa, including phytosaurs, rhynchosaurs, and dinosaurs. Aetosaurs apparently lived in environments that were not particularly favorable for preservation, resulting in an exceptionally fragmentary fossil record in desperate need of improvement. Furthermore, many of the studies cited above described fossils discovered, excavated, and collected by us, our coworkers, and volunteers as we try to improve this record. Our perspective, from the plaster-spattered highwall of one of our many excavations, is that we are far from the “upper bound” of better fossils, additional characters, and more character systems alluded to by Harris et al. (2003). Of the problems with aetosaur phylogeny that are related to analytical method, some of those Harris et al. (2003) pointed out are inherent to cladistic methodology, not just to our analysis. For example, there is actually a wide range of structures emanating from the dorsal (or lateral) surface of paramedian (or lateral) scutes, but in our analyses, we lumped them into apparently primitive keels (0) and presumably derived knobs (1). Consequently, our data matrix appears to have a bimodal distribution of many character states, when in fact the actual morphology is more variable. This problem is inherent to any attempt in cladistic analyses to quantify discretely the variation of essentially continuous characters. Now that we have examined many more aetosaurs and have collected new fossils of still others, we will address this variation in future analyses.

Oxymonads Are Closely Related to the Excavate Taxon Trimastix

Despite intensive study in recent years, large-scale eukaryote phylogeny remains poorly resolved. This is particularly problematic among the groups considered to be potential early branches. In many recent systematic schemes for early eukaryotic evolution, the amitochondriate protists oxymonads and Trimastix have figured prominently, having been suggested as members of many of the putative deep-branching higher taxa. However, they have never before been proposed as close relatives of each other. We amplified, cloned, and sequenced small-subunit ribosomal RNA genes from the oxymonad Pyrsonympha and from several Trimastix isolates. Rigorous phylogenetic analyses indicate that these two protist groups are sister taxa and are not clearly related to any currently established eukaryotic lineages. This surprising result has important implications for our understanding of cellular evolution and high-level eukaryotic phylogeny. Given that Trimastix contains small, electron-dense bodies strongly suspected to be derived mitochondria, this study constitutes the best evidence to date that oxymonads are not primitively amitochondriate. Instead, Trimastix and oxymonads may be useful organisms for investigations into the evolution of the secondary amitochondriate condition. All higher taxa involving either oxymonads or Trimastix may require modification or abandonment. Affected groups include four contemporary taxa given the rank of phylum (Metamonada, Loukozoa, Trichozoa, Percolozoa), and the informal excavate taxa. A new "phylum-level" taxon may be warranted for oxymonads and Trimastix.

Computational advances in maximum likelihood methods for molecular phylogeny.

We have developed a generalization of Kimura's Markov chain model for base substitution at a single nucleotide site. This generalized model incorporates more flexible transition rates and consequently allows irreversible as well as reversible chains. Because the model embodies just the right amount of symmetry, it permits explicit calculation of finite-time transition probabilities and equilibrium distributions. The model also meshes well with maximum likelihood methods for phylogenetic analysis. Quick calculation of likelihoods and their derivatives can be carried out by adapting Baum's forward and backward algorithms from the theory of hidden Markov chains. Analysis of HIV sequence data illustrates the speed of the algorithms on trees with many contemporary taxa. Analysis of some of Lake's data on the origin of the eukaryotic nucleus contrasts the reversible and irreversible versions of the model.