Traditionally, deep time was the domain of paleontology. Origination time could be assessed only through reference to first appearance data in the rock record. This changed almost from the beginnings of modern molecular biology, when it was realized that molecules could be used to calculate divergence times between living species. Early studies relied on immunological distance information, and the underlying rationale was simple: because evolution involves changes to the genetic code, and because these changes accumulate over time, we should expect the number of accumulated changes (the molecular distance) between living taxa to increase as their time of divergence becomes older (Zuckerkandl and Pauling, 1962). By inferring a rate of evolution of the genetic code, we can place absolute time estimates on divergence points.

Because more than one calibration is used, quartet dating (a molecular dating method) is thought to reduce error that might arise from a single calibration point. Within crocodylians, there is a strong correlation between calibration age and divergence estimate for five mitochondrial genes and one nuclear gene—estimates based on two Neogene calibrations are all younger than those based on two Paleogene calibrations, and estimates based on one Neogene and one Paleogene calibration are of intermediate age. Confidence limits on the youngest estimates exclude the oldest estimates, and in several cases they exclude known minimum divergences from fossil occurrences. Addition of time to the calibrations improves among-quartet and stratigraphic consistency, but not all kinds of modifications have the same impact; addition of uniform blocks of time to all calibrations efficiently increases among-quartet consistency, but with range extensions that more than double some of the Neogene calibrations. Modest increases in calibration age disproportionately impact divergence estimates based on later calibrations. Some among-quartet disparity might reflect calibration error, especially among caimans, but some range extensions necessary to improve consistency are unreasonably long. Quartet dating appears to systematically undercompensate branch length error with late calibrations and overcompensate it with early calibrations, but in all cases very reasonable results—alligatorid-crocodylid divergence in the Late Cretaceous and Alligator-caiman divergence at or near the Cretaceous-Tertiary boundary—are obtained when both a Neogene and a Paleogene calibration is used. This suggests that, given current likelihood models, the use of calibrations sampling different parts of a clade's history is the best strategy when using quartet dating.

A molecular survey of animal phylogeny (Wray et al., 1996) recovered the presumed correct temporal order of the phylogenetic splits Protostomata-Deuterostomata, Echinodermata-Chordata, and Agnatha-Gnathostomata in studies of six of seven gene sequences. This result raised the question of how this order could be recovered if all of the phyla had appeared in a Cambrian “explosion” of less than 10 m.y., given the expected erratic nature of the molecular “clock.” We simulated trees, and molecular sequence evolution along the trees, under different evolutionary radiation scenarios, with different periods of radiation, relative to times of subsequent evolution. Simulations and phylogenetic analyses of sequences derived from a simulated “Cambrian explosion” of 10–35 million years did not allow the successful recovery of the correct tree, using neighbor-joining, maximum likelihood, or parsimony methods. Success in recovering phylogenies under a Cambrian divergence scenario (520 million years ago) did not exceed 80 percent without an extended divergence time interval of at least 100 m.y. An increased substitution rate during the initial radiation improved the ability to recover correct phylogenies, especially when the rate was 8–10 times the rate following the radiation. Our results militate against the likelihood of an Early Cambrian or slightly longer explosion of the animal phyla, as apparently supported by the fossil record. Some limitations to these conclusions are discussed.

Molecular clock estimates of divergence times for artiodactyls and whales vary widely in their agreement with the fossil record. Recent estimates indicate that the divergence of whales from artiodactyls occurred 60 Ma, a date which compares well with the first appearances of fossil whales around 53.5 Ma, and artiodactyls at 55 Ma. Other estimates imply significant gaps in the fossil record. A date of 65 Ma for the divergence of Suidae and Ruminantia predates the appearance of Ruminantia by over 10 million years, and an estimate of 58 Ma for the divergence of Suidae from Cetacea implies a gap of over 20 million years. Further, although a molecular clock estimate has not been reported, the hypothesis that hippos are the closest living relatives of the whales implies a potential ghost lineage for hippos of over 40 million years. There are only two living species of hippos, and their fossil record is sparse, while cetaceans and other artiodactyls are speciose and have rich fossil records. A 40-million-year gap in the fossil record of hippos could be explained by several possibilities: inadequate biogeographic sampling, taphonomic biases, or undifferentiated primitive morphology. Similarly, a number of possible problems may exist in the molecular data: rate variation in the genes sampled, the low numbers of genes examined, and insufficient age calibrations. In addition, there are potential problems in molecular phylogeny estimation, such as long branch attraction and inappropriate taxonomic sampling. Additional estimates of divergence times among living taxa should provide a broader framework for comparison with the fossil record and provide information to help identify which of these factors are causing conflict.

Molecular clocks can provide insights into the evolutionary timescale of groups with unusually biased or fragmentary fossil records, such as birds. In those cases, it is advantageous to establish internal anchor points—molecular time estimates—using the best external fossil calibrations. In turn, those anchor points can be used as calibrations for more detailed time estimation within the group under study. This method also avoids the inherent problems in drawing conclusions about the evolution of a group based on data tied to the poor fossil record of that same group. The galliform-anseriform divergence (∼90 million years ago) is an example of such an ideal anchor point for molecular clock analyses in birds.

Many of the late Neoproterozoic “Ediacaran fossils” have been referred to the Cnidaria, often on the basis of vague or poorly known features. However, representatives of the living Chondrophorina (=Porpitidae, Hydrozoa), Pennatulacea (Anthozoa), and Coronatae and/or Stauromedusae (Scyphozoa) have all been identified in Ediacaran biotas, based on specific morphological features preserved in a number of specimens. These three cnidarian groups have plausible Paleozoic representatives as well, but many of their Paleozoic fossils are also somewhat problematic. We test these systematic hypotheses by using them to calibrate divergence dates across the Cnidaria, based on an extensive molecular phylogeny of extant cnidarians. In this reductio ad absurdum approach, if a calibration based on one interpretation of a problematic fossil yields a glaringly inconsistent age for a better-known clade, that interpretation is likely to be mistaken. We find that assuming the existence of Pennatulacea and Scyphozoa in the “Ediacara biota” places the root of the Cnidaria between 800 and 1,000 Ma, a figure which is, at least, not out of line with other molecular clock estimates. However, assuming the existence of the Chondrophorina in the Neoproterozoic, or anywhere in the Paleozoic, pushes the root of the Cnidaria back to between 1,500 and 2,000 Ga, which is considerably older than the oldest previous estimates for the origin of the Cnidaria. We suggest that the likeliest explanation is that chondrophorines were not present in the late Precambrian or Paleozoic. The Ediacaran and Paleozoic fossils previously interpreted as chondrophorines probably represent other taxa.

A limestone block in the Shirokawa-Nomura area of western Shikoku (Japan) is interpreted to have been originated as a Panthalassan seamount, and is assigned to the northern part of the Southern Chichibu Terrane. The Late Permian foraminiferal fauna from this block is composed of 33 species, and is characterized by Nanlingella? sp., three unidentified species of Staffellidae, Paraglobivalvulina mira, Dagmarita chanakchiensis, Paradagmarita sp., and Partisania sp. Among them, four unidentified species are systematically described and discussed. Although this fauna is indeterminately either Wuchiapingian or Changhsingian, it is clearly Late Permian in age by comparison with Late Permian faunas in the Tethyan regions, and by the complete absence of neoschwagerinids, verbeekinids, and schwagerinids, which became extinct by the end of Middle Permian time. The limestone block in the Shirokawa-Nomura area is clearly distinguished from Upper Permian shelf limestones from the Kurosegawa, Southern Kitakami, and Maizuru terranes by its lithology and by the complete absence of the foraminifer Colaniella, one of the most important index genera in Upper Permian strata throughout the Tethyan and peri-Gondwana regions.

A new small twiglike anthaspidellid sponge, Virgaspongiella ramosa new genus and species, and an incrusting lithistid sponge have been recovered from silicified residues of etched limestone blocks from the Middle Permian Franson Member of the Park City Formation in western Wyoming. Virgaspongiella n. gen. has a skeleton of upwardly and outwardly divergent trabs formed of merged tips of runglike dendroclone spicules in ladderlike series. One to a few oxeas function as coring spicules in the trabs and project as fine spines from the dermal surface, and other monaxial spicules project from pores of the canals.

The incrusting sponge, Incrustatospongia superficiala new genus and species, forms a distinct, thin, uniform lithistid skeletal layer, composed largely of X-shaped dendroclones, incrusted on both the inner and outer surfaces of productoid brachiopod valves. Separated monaxial spicules locally protrude from the sponge's dermal surface apparently as spinose defensive elements.

Based on 137 specimens examined, the new species Commutia exoleta is characterized by a small, slightly scolecoid shape with 21 septa at a mean maximum corallite diameter of 6 mm (range 3 to 10.5 mm); a persistent inner wall, which encloses an aulos with a mean maximum diameter of 1.2 mm, formed during an early ontogenetic stage when the axial ends of the cardinal, alar and counter-lateral septa fused; short counter septa are lacking in the earliest stage of development.

Corallites are highly variable. Characters exhibiting a wide range of variation are: size and shape of corallites, number of septa, diameter of aulos and the timing of its appearance, number of septa connected to the inner wall, and the septal arrangement in each growth quadrant. Combinations of these variable characters result in corallites that are each uniquely different. Variations of those characters are partly due to stressed environments, such as unstable, muddy substrates resulting in corallite rejuvenescence and redirection.

Numidiaphyllum is one of the Paleozoic scleractiniamorphs. The genus is characterized by a poorly integrated, uniserial fasciculate form with an epithecate wall and simple morphological traits. Parent corallites are divided into several daughter corallites using one mode of division among several theoretically possible alternatives. Bipartite increase is most common, followed by hexapartite and then tripartite increase. Daughter corallites possess relatively large diameters from the beginning, along with a robust colonial pattern. This parricidal increase caused the morphologies of both parent and daughter corallites to be greatly altered and to show high morphological variability. For ecological and structural reasons, co-occurring daughter corallites generally are equal or subequal in size. Daughter corallites initially show a bilateral symmetry in both outline and septal arrangement during the course of hystero-ontogeny. However, this symmetry results only from structural necessity and is transitory. It is not homologous with the bilaterality of body plans characteristic of anthozoan groups. The morphological simplicity, related parricidal reproduction, and resulting poorly integrated growth form as seen in Numidiaphyllum, all suggest conservative features that could have resulted from phylogenetic antiquity within the scleractiniamorph body plan. Those generalized features are not themselves related to immediate phylogenetic relationships with any simply constructed rugosan group, nor would they have been due to surrounding, stressful ecologic conditions. They may have been phylogenetic-specific.

Paleontological study of 16 samples from four sections through the Silurian-Devonian marine deposits of the Hodh region establishes the development of the Middle Devonìan and adds to our knowledge of the Paleozoic sequence in the West African platform. Above Silurian deposits locally dated by graptolites from the Llandovery, Devonian shales yield an abundant although low diversity benthic fauna, which is assigned to a Givetian age. The brachiopod fauna shows strong affinity with the NE Americas Realm. Two new species are described, Arcuaminetes deynouxi and Eleutherokomma monodi. The revision of the Devonian fauna of the Hodh area supports: 1) the apparent lack of Lower Devonian deposits; 2) the Givetian age of the Devonian succession; and 3) the strong eastern Americas Realm affinity of the fauna, as previously established for the Mauritanian Adrar area.

A significant number of small-sized gastropods are described from Emsian (late Early Devonian) strata on the south flank of Limestone Mountain, Medfra B-4 quadrangle, west-central Alaska, providing the first detailed taxonomic inventory of Emsian gastropods from the Farewell terrane of southwestern and west-central Alaska. The fauna is distinctly of Old World Realm character, and contains not a single species in common with Emsian faunas of nearby nonaccreted rocks of western Canada and east-central Alaska (“Western Canada Province” of Blodgett et al., 2001a). The genera Balbinipleura Bandel and Frýda, 1996 and Nanochilina Frýda, 1998, as well as the subgenus Palaeozygopleura (Rhenozyga) Frýda, 2000, are reported for the first time in the Devonian of the Western Hemisphere. The gastropod fauna includes members of three (i.e., Archaeogastropoda, Caenogastropoda, and Heterobranchia) of the five modern gastropod subclasses, illustrating that these gastropod lineages were separated from each other since the Early Devonian. New taxa include the new genera Arctozone, Farewellia, and Medfrazyga, represented by the new species Arctozone cooki, Farewellia heidelbergerae, and Medfrazyga clauticae. Further new species include Quadricarina (Quadricarina?) noklebergi, Balbinipleura krawczynskii, Decorospira lepaini, Decorospira? minutula, Palaeozygopleura (Rhenozyga) reifenstuhli, and Nanochilina gubanovi. In addition, the following previously described gastropods are also discussed and illustrated: Alaskiella medfraensis Frýda and Blodgett, 1998; Alaskacirrus bandeli Frýda and Blodgett, 1998; and Kuskokwimia moorei Frýda and Blodgett, 2001a.

New material collected from Cretaceous and Tertiary rocks of the Pacific Northwest of North America has prompted a reevaluation of the fossil record of the Homolidae de Haan, 1839 and the Homolodromiidae Alcock, 1900. The fossil records of the homolid genera Homola Leach, 1815; Homolopsis Bell, 1863; and Hoplitocarcinus Beurlen, 1928 are restricted, and Latheticocarcinus Bishop, 1988, which is synonymous with Eohomola Collins and Rasmussen, 1992 and Metahomola Collins and Rasmussen, 1992, is reinstated as a distinctive genus. Thirteen new combinations resulted from reinstatement of Latheticocarcinus: L. adelphinus (Collins and Rasmussen, 1992), L. affinis (Jakobsen and Collins, 1997), L. atlanticus (Roberts, 1962), L. brevis (Collins, Kanie, and Karasawa, 1992), L brightoni (Wright and Collins, 1972), L. centurialis (Bishop, 1992), L. declinata (Collins, Fraaye, and Jagt, 1995), L. dispar (Roberts, 1962), L. pikeae (Bishop and Brannen, 1992), L. punctatus (Rathbun, 1917), L. schlueteri (Beurlen, 1928), L. shapiroi Bishop, 1988, L. spiniga (Jakobsen and Collins, 1997), and L. transiens (Segerberg, 1900). A new species, Latheticocarcinus ludvigseni, is described from Cretaceous rocks of British Columbia. The first fossil occurrence of the extant homolid genus Paromolopsis, P. piersoni new species, is recorded from Miocene rocks of Oregon. Paromola pritchardi Jenkins, 1977 is formally transferred to Dagnaudus Guinot and Richer de Forges (1995) as suggested by Guinot and Richer de Forges (1995). The extinct family Prosopidae von Meyer, 1860 is referred to the Homolodromioidea Alcock, 1900, following previous work. Palehomola gorrelli Rathbun, 1926 is transferred from the Homolidae to the Homolodromiidae, and the new genus Rhinodromia is erected to contain Homolopsis richardsoni Woodward, 1896, from Cretaceous rocks of British Columbia. A new terminology is suggested for describing the rostral area in homolodromiids, in an attempt to alleviate considerable confusion over that issue. The morphologic similarity of fossil and extant members in both the Homolidae and the Homolodromiidae suggest that these two brachyuran families are evolutionarily conservative, much as the lobsters are. In addition, the similar paleobiogeographic and evolutionary patterns seen in the two families suggests that either they are closely related or that brachyuran families exhibited similar evolutionary and dispersal trends early in their history.

Chimaerastacus pacifluvialis, new genus and species, is established on the basis of fossils from the Middle Triassic Liard Formation of northeastern British Columbia. It has well-defined cervical, postcervical, and branchiocardiac grooves; three longitudinal ridges on the cephalic region; and true chelae on the first through third pereiopods. The morphological features of the carapace are a combination of traits used to define both the erymids and the glypheids. A cladistic analysis of 31 decapod genera defines the Astacidea as a monophyletic group, supports the inclusion of the Glypheoidea within the infraorder Astacidea, illustrates the relationships of the Glypheoidea with other astacid groups, and suggests erection of a new family, the Chimaerastacidae, for our new genus and species of decapod. Specimens of C. pacifluvialis are preserved in a sandy bioclastic floatstone that was deposited near the Peace River Embayment in the Middle Triassic. The host lithology suggests that the decapods inhabited a transitional environment between low relief biostromes and the shoreface. This environment provided a unique set of conditions that allowed exceptional preservation of the decapod material.

New millipede specimens from the Paleozoic of Scotland are described, including Archidesmus macnicoli Peach, 1882, from the Lower Devonian (Lochkovian) Tillywhandland Quarry SSSI and three new taxa—Albadesmus almondi, Pneumodesmus newmani, and Cowiedesmus eroticopodus—from the mid Silurian (late Wenlock—early Ludlow) Cowie Formation at Cowie Harbour. Cowiedesmus eroticopodus new species is placed within the new Cowiedesmidae within the new order Cowiedesmida. Kampecaris tuberculata Brade-Birks from the Lower Devonian (Siegenian) of the Lanark Basin near Dunure is shown not to be a kampecarid myriapod, redescribed as Palaeodesmus tuberculata and placed order incertae sedis within Archipolypoda. Anthracodesmus macconochiei Peach is also redescribed and tentatively placed order incertae sedis within Archipolypoda. Archidesmus macnicoli, Albadesmus almondi, and Palaeodesmus tuberculata are each demonstrated to have broad sternites with laterally placed coxal sockets and paramedian pores containing paired valves. These pores are interpreted as having housed eversible vesicles. Some specimens of Archidesmus macnicoli and Cowiedesmus eroticopodus are male and have a pair of modified legs on trunk segment 8, identified as leg pairs 10 and 11, respectively. The presence of modified anterior legs restricted to segment 8 increases the range of variability known in modified appendage location in male millipedes and compounds existing uncertainty about using the presence of gonopods on trunk segment 7 as a synapomorphy of Helminthomorpha. An affinity between Archidesmida and Cowiedesmida is suggested based on possession of modified legs on segment 8 and Archidesmida + Cowiedesmida is placed along with Euphoberiida in Archipolypoda based on possession of free, broad sternites with bivalved paramedian pores and fused pleurotergites. The oldest known evidence of spiracles is demonstrated in Pneumodesmus newmani, proving that the oldest known millipedes were fully terrestrial.

A Lower Pennsylvanian (Morrowan) silicified ostracode fauna occurs just above the conformable Mississippian-Pennsylvanian boundary within the Barnett Formation in Texas. The fauna contains several taxa that were previously restricted to the Upper Mississippian and numerous taxa only known from the Lower Pennsylvanian. New taxa proposed include Amphissites (Amphissites) morrowanensis n. sp., Polytylites subrectus n. sp., Kirkbyella (Berdanella) delicata n. sp., Kindlella proscillata n. sp., Libumella walkerorum n. sp., Moorites tumidus n. sp., Leptoderos arytaina n. gen. and sp., and Cribroconcha prolixa n. sp.

Protostegids are Cretaceous marine turtles. Fossil materials assignable to the family Protostegidae range from early Albian to Late Campanian in age and have been described from all continents except Antarctica (Hirayama, 1995). The group includes two gigantic forms, Archelon Wieland and Protostega Cope, that reached maximum carapace lengths in excess of 2 m and rank among the largest turtles that ever lived.

In this paper, we describe two specimens of Protostega gigas Cope housed in the Field Museum of Natural History (FMNH), Chicago, Illinois: FMNH P27452 and FMNH PR58. Both are from the Mooreville Chalk (Upper Santonian to Lower Campanian: Mancini et al., 1995) in Greene County, Alabama, and are noteworthy because they show tooth marks from at least one large shark. One of the specimens also exhibits five embedded teeth of the Late Cretaceous cretoxyrhinid shark Cretoxyrhina mantelli (Agassiz). This note constitutes the first report of protostegid turtles bitten by C. mantelli.

The Matoniaceae is one of the most ancient lineages of extant ferns, with a fossil record that extends from the early Mesozoic. Currently they are considered to be a systematically isolated group that occupies a basal position in the phylogeny of leptosporangiate ferns. Although the extant taxa of Matoniaceae are today restricted to the Malaysian archipelago, a diverse assemblage of matoniaceous ferns occurred on every continent, including Antarctica, during the Mesozoic. Here we describe anatomically preserved, detached fern sori and sporangia from the Fremouw Formation with a combination of characters that affiliates them with the Matoniaceae. Sori are peltate with more than 25 crowded sporangia that display simple maturation. The indusium is multiseriate and centrally attached to a massive, vascularized receptacle. Sporangia are globose to ovoid with vertical, meandering, incomplete annuli, and are helically attached to the receptacle in three to four gyres. This report places this fern as the earliest known occurrence of the Matoniaceae in the fossil record. Characters observed in the sori offer insights regarding organizational patterns of reproductive structures in the family. Additionally, the presence of a peltate indusium in the earliest known representative of the family contradicts the hypothesized evolutionary sequence in development of this structure in the family.

Ceratopea Ulrich, 1911, from the Lower Ordovician of North America, Greenland, and Scotland, is one of a few gastropod genera that was established on the calcareous operculum and not the shell. The operculum is commonly found disassociated, and for many years the nature of the shell itself was unknown (Yochelson, 1975). Yochelson and Bridge (1957, pl. 38, figs. 8–9) illustrated an artificial association of C. unguis with its presumed shell made years earlier by Ulrich and Bridge (Yochelson, written commun.). However, the basal part of the shell is not present. Only one life association of the shell and operculum has been previously documented (Yochelson and Wise, 1972), and that shell is incompletely preserved.

Spinous oniscomorph millipedes are rare faunal components of the upper Palaeozoic (Shear, 1997). Amynilyspes (type species A. wortheni Scudder, 1882; OD) is an Upper Carboniferous spinous oniscomorph (pill millipede) which was first described from the Middle Pennsylvanian (Westphalian D equivalent) Fossil-Lagerstätte of Mazon Creek. Later Fritsch (1899) described two species (A. typicus and A. crescens) from the Wesphalian D Gaskohle of Nýřany in Bohemia. More recently A. typicus was recorded from the Stephanian B of the Saarland (Förster, 1973), then from the Stephanian B of the Blanzy-Montceau-les-Mines Basin (Langiaux and Sotty, 1977; Poplin, 1994). Although myriapods were already known to occur in the Montceau-les-Mines Lagerstätte (Langiaux and Sotty, 1976; Rolfe et al., 1982; Poplin and Heyler, 1994) the presence of Amynilyspes at Montceau-les-Mines was first published in a regional publication (“La Physiophile” Langiaux and Sotty, 1976, 1977), and it has passed almost unnoticed.