Oldest coelacanth, from the Early Devonian of Australia

Coelacanths are well-known sarcopterygian (lobe-finned) fishes, which together with lungfishes are the closest extant relatives of land vertebrates (tetrapods). Coelacanths have both living representatives and a rich fossil record, but lack fossils older than the late Middle Devonian (385-390 Myr ago), conflicting with current phylogenies implying coelacanths diverged from other sarcopterygians in the earliest Devonian (410-415 Myr ago). Here, we report the discovery of a new coelacanth from the Early Devonian of Australia (407-409 Myr ago), which fills in the approximately 20 Myr 'ghost range' between previous coelacanth records and the predicted origin of the group. This taxon is based on a single lower jaw bone, the dentary, which is deep and short in form and possesses a dentary sensory pore, otherwise seen in Carboniferous and younger taxa.     

Latest European coelacanth shows Gondwanan affinities

The last European fossil occurrence of a coelacanth is from the Mid-Cretaceous of the English Chalk (Turonian, 90 million years ago). Here, we report the discovery of a coelacanth from Late Cretaceous non-marine rocks in southern France. It consists of a left angular bone showing structures that imply close phylogenetic affinities with some extinct Mawsoniidae. The closest relatives are otherwise known from Cretaceous continental deposits of southern continents and suggest that the dispersal of freshwater organisms from Africa to Europe occurred in the Late Cretaceous.     

Extremely slow rate of evolution in the HOX cluster revealed by comparison between Tanzanian and Indonesian coelacanths

Coelacanths are known as "living fossils" because their morphology has changed very little from that in the fossil record. To elucidate why coelacanths have evolved so slowly is thus of primary importance in evolutionary biology. In the present study, we determined the entire sequence of the HOX cluster of the Tanzanian coelacanth (Latimeria chalumnae) and compared it with that of the Indonesian coelacanth (L. menadoensis), which was available in the literature. The most intriguing result was the extremely small genetic divergence between the two coelacanths. The synonymous divergence of the HOX coding region between the two coelacanths was estimated to be 0.07%, which is ~11-fold smaller than that of human-chimp. When we applied the estimated divergence time of the two coelacanths of 6 million years ago (MYA) and 30 MYA, which were proposed in independent mitochondrial DNA analyses, the synonymous substitution rate of the coelacanth HOX cluster was estimated to be ~11-fold and 56-fold smaller than that of human-chimp, respectively. Thus, the present study implies that the reduction of the nucleotide substitution rate in coelacanth HOX genes may account for the conservation of coelacanth morphology during evolution.     

Early Growth Stages in Coelacanth Fishes

ALL known specimens of the Recent coelacanth fish, Latimeria, are large specimens (mostly more than 100 cm total length) and only one female with eggs has been recorded^1,2. Consequently, the ontogeny and the early growth stages of the Recent coelacanth are unknown. In the fossil record, one specimen of Holophagus (= Undina) from the Upper Jurassic of Solnhofen, southern Germany, has been recorded with two young coelacanths inside³. Watson has argued from this finding that the coelacanths are viviparous but it seems more reasonable to interpret this fossil specimen as a cannibal that had just swallowed two young of its own kind. This interpretation is favoured by the position of the two specimens and by the discovery of other fossil coelacanths containing large specimens of other kinds of fishes in their stomachs⁴.     

An Endogenous Foamy-like Viral Element in the Coelacanth Genome

Little is known about the origin and long-term evolutionary mode of retroviruses. Retroviruses can integrate into their hosts'' genomes, providing a molecular fossil record for studying their deep history. Here we report the discovery of an endogenous foamy virus-like element, which we designate ‘coelacanth endogenous foamy-like virus’ (CoeEFV), within the genome of the coelacanth (Latimeria chalumnae). Phylogenetic analyses place CoeEFV basal to all known foamy viruses, strongly suggesting an ancient ocean origin of this major retroviral lineage, which had previously been known to infect only land mammals. The discovery of CoeEFV reveals the presence of foamy-like viruses in species outside the Mammalia. We show that foamy-like viruses have likely codiverged with their vertebrate hosts for more than 407 million years and underwent an evolutionary transition from water to land with their vertebrate hosts. These findings suggest an ancient marine origin of retroviruses and have important implications in understanding foamy virus biology.     

Molecular Clock Calibrations and Metazoan Divergence Dates

It has recently been argued that living metazoans diverged over 800 million years ago, based on evidence from 22 nuclear genes for such a deep divergence between vertebrates and arthropods (Gu 1998). Two ``internal' calibration points were used. However, only one fossil divergence date (the mammal–bird split) was directly used to calibrate the molecular clock. The second calibration point (the primate–rodent split) was based on molecular estimates that were ultimately also calibrated by the same mammal–bird split. However, the first tetrapods that can be assigned with confidence to either the mammal (synapsid) lineage or the bird (diapsid) lineage are approximately 288 million years old, while the first mammals that can be assigned with confidence to either the primate or the rodent lineages are 65 million years old, or 85 million years old if ferungulates are part of the primate lineage and zhelestids are accepted as ferungulate relatives. Recalibration of the protein data using these fossil dates indicates that metazoans diverged between 791 and 528 million years ago, a result broadly consistent with the palaeontological documentation of the ``Cambrian explosion.' The third, ``external' calibration point (the metazoan–fungal divergence) was similarly problematic, since it was based on a controversial molecular study (which in turn used fossil dates including the mammal–bird split); direct use of fossils for this calibration point gives the absurd dating of 455 million years for metazoan divergences. Similar calibration problems affect another recent study (Wang et al. 1999), which proposes divergences for metazoans of 1000 million years or more: recalibrations of their clock again yields much more recent dates, some consistent with a ``Cambrian explosion' scenario. Molecular clock studies have persuasively argued for the imperfection of the fossil record but have rarely acknowledged that their inferences are also directly based on this same record. Received: 26 January 1999 / Accepted: 14 April 1999     

First discovery of a primitive coelacanth fin fills a major gap in the evolution of lobed fins and limbs

The fossil record provides unique clues about the primitive pattern of lobed fins, the precursors of digit-bearing limbs. Such information is vital for understanding the evolutionary transition from fish fins to tetrapod limbs, and it guides the choice of model systems for investigating the developmental changes underpinning this event. However, the evolutionary preconditions for tetrapod limbs remain unclear. This uncertainty arises from an outstanding gap in our knowledge of early lobed fins: there are no fossil data that record primitive pectoral fin conditions in coelacanths, one of the three major groups of sarcopterygian (lobe-finned) fishes. A new fossil from the Middle-Late Devonian of Wyoming preserves the first and only example of a primitive coelacanth pectoral fin endoskeleton. The strongly asymmetrical skeleton of this fin corroborates the hypothesis that this is the primitive sarcopterygian pattern, and that this pattern persisted in the closest fish-like relatives of land vertebrates. The new material reveals the specializations of paired fins in the modern coelacanth, as well as in living lungfishes. Consequently, the context in which these might be used to investigate evolutionary and developmental relationships between vertebrate fins and limbs is changed. Our data suggest that primitive actinopterygians, rather than living sarcopterygian fishes and their derived appendages, are the most informative comparators for developmental studies seeking to understand the origin of tetrapod limbs.     

Fossil Araceae from a Paleocene neotropical rainforest in Colombia

Both the fossil record and molecular data support a long evolutionary history for the Araceae. Although the family is diverse in tropical America today, most araceous fossils, however, have been recorded from middle and high latitudes. Here, we report fossil leaves of Araceae from the middle-late Paleocene of northern Colombia, and review fossil araceous pollen grains from the same interval. Two of the fossil leaf species are placed in the new fossil morphogenus Petrocardium Herrera, Jaramillo, Dilcher, Wing et Gomez-N gen. nov.; these fossils are very similar in leaf morphology to extant Anthurium; however, their relationship to the genus is still unresolved. A third fossil leaf type from Cerrejón is recognized as a species of the extant genus Montrichardia, the first fossil record for this genus. These fossils inhabited a coastal rainforest ～60-58 million years ago with broadly similar habitat preferences to modern Araceae.     

Enzymes of the coelacanth Latimeria chalumnae evidenced by starch gel electrophoresis

Synopsis The coelacanth, Latimeria chalumnae, is often referred to as a living relic. The opportunity to examine its biochemical molecular structure was sought in an effort to define the degree of its genetic variability. The coelacanth is thought to live only in a small area around the Comoro Islands in the Western Indian Ocean. The scenario presented suggests that the coelacanth may have lost genetic variability as a result of genetic drift within a small population. The narrow geographic range of the coelacanth suggests adjustment to a relatively limited environment. The loss of specific alleles through genetic drift can reduce the ability of a fish population to adapt to changes in environmental conditions. The coelacanth needs strong conservation measures to be taken to curtail the capture of specimens and for the protection of its limited natural habitat.     

Evaluation of the fossil fish‐specific diversity in a chadian continental assemblage: Exploration of morphological continuous variation in Synodontis (Ostariophysi,Siluriformes)

In the fossil record, the quantification of continuous morphological variation has become a central issue when dealing with species identification and speciation. In this context, fossil taxa with living representatives hold great promise, because of the potential to characterise patterns of intraspecific morphological variation in extant species prior to any interpretation in the fossil record. The vast majority of catfish families fulfil this prerequisite, as most of them are represented by extant genera. However, although they constitute a major fish group in terms of distribution, and ecological and taxonomic diversity, the quantitative study of their past morphological variation has been neglected, as fossil specimens are generally identified based on the scarcest remains, that is, complete neurocrania that bear discrete characters. Consequently, a part of freshwater catfish history is unprospected and unknown. In this study, we explored the morphological continuous variation of the humeral plate shape in Synodontis catfishes using Elliptic Fourier Analysis (EFA), and compared extant members and fossil counterparts. We analysed 153 extant specimens of 11 Synodontis species present in the Chad basin, in addition to 23 fossil specimens from the Chadian fossiliferous area of Toros Menalla which is dated around 7 Ma. This highly speciose genus, which is one of the most diversified in Africa, exhibits a rich fossil record with several hundred remains mostly identified as Synodontis sp. The analysis of the outline of the humeral plate reveals that some living morphological types were already represented in the Chad Basin 7 My ago, and allows for the discovery of extinct species. Beside illuminating the complex Neogene evolutionary history of Synodontis, these results underline the interest in the ability of isolated remains to reconstruct a past dynamic history and to validate the relevance of EFA as a tool to explore specific diversity through time. J. Morphol. 277:1486–1496, 2016. © 2016 Wiley Periodicals, Inc.     

A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data

We present a complete phylogeny of macroperforate planktonic foraminifer species of the Cenozoic Era (∼65 million years ago to present). The phylogeny is developed from a large body of palaeontological work that details the evolutionary relationships and stratigraphic (time) distributions of species‐level taxa identified from morphology (‘morphospecies’). Morphospecies are assigned to morphogroups and ecogroups depending on test morphology and inferred habitat, respectively. Because gradual evolution is well documented in this clade, we have identified many instances of morphospecies intergrading over time, allowing us to eliminate ‘pseudospeciation’ and ‘pseudoextinction’ from the record and thereby permit the construction of a more natural phylogeny based on inferred biological lineages. Each cladogenetic event is determined as either budding or bifurcating depending on the pattern of morphological change at the time of branching. This lineage phylogeny provides palaeontologically calibrated ages for each divergence that are entirely independent of molecular data. The tree provides a model system for macroevolutionary studies in the fossil record addressing questions of speciation, extinction, and rates and patterns of evolution.     

Hominid and gelada baboon evolution: Agreement between molecular and fossil time scales

The time of origin of the hominid lineage has long been debated. Macromolecular studies have consistently shown genetic distances between living humans and African apes to be quite small. The molecular clock hypothesis proposes that the time of separation of these lineages is relatively recent (in the range of 4–8 million years ago) and not 15 million years or more ago as usually suggested. Three independent molecular comparisons yield a mean estimate of 4.6 million years for the hominid-African pongid divergence. The relationship of Theropithecusand Papiois a parallel case within Primates of two taxa which are quite similar at the molecular level, but which are usually thought to have separated relatively long ago. The two cases of seeming discordance between different lines of evidence are analogous. Each involves a speciation event which eventually resulted in one substantially derived lineage and one or more relatively unchanged lineages. In each case, claims of the antiquity of the divergence event extend to at least twice the age of the first certain appearance of the more derived lineage in the fossil record. Finally, in each case, the molecular clock model suggests a range of possible divergence times that overlaps with the first appearances of undoubted hominids and Theropithecusin the fossil record. This test involving paleontological evidence supports the molecular clock hypothesis.     

The evolution of the mechanical properties of amniote bone

162 specimens from 19 species of amniote were tested for various mechanical and physical properties to ascertain whether there were characteristic differences between different groups. All mechanical properties showed very great variation. In general the reptiles were not inferior to the mammals and birds. The histology of living forms was compared to that of fossil forms, to see whether 'weak' histology was more characteristic of primitive amniotes. The earliest reptiles probably had rather complaint bone, but it was probably tough. Modern types of bone appeared over two hundred million years ago. Very specialised bone, like that of the bullae of whales and antlers, may have evolved only in the mammals, but the fossil record is not complete enough to assert this confidently.     

An Account of the First Living Coelacanth known to Scientists from Indonesian Waters

A brief narrative is presented of the events surrounding the initial discovery of a coelacanth in an Indonesian fish market in Manado, Sulawesi, on 18 September 1997. Although the specimen was not purchased and preserved, photographs were taken and enough information gathered about the fish to warrant an official entry in the Coelacanth Conservation Council (CCC) inventory of known specimens of the living coelacanth Latimeria chalumnae. All known information about this first Indonesian specimen is summarized in the official CCC inventory format, and the specimen is herein numbered CCC no. 174.     

A molecular-clock date for the origin of the animal phyla

Although the reliability of the molecular clock for determining divergence times that are not visible in the fossil record has been questioned, the amino-acid sequence differences in the α and β haemoglobins of a variety of living vertebrates do not support this view. While the molecular clock is clearly probabilistic rather than metronomic, it can be shown that the α and β haemoglobins have been evolving at a statistically equal rate since they first appeared some 450–500 million years ago. If this rate has always been constant for all globins, then the percentage sequence differences between several invertebrate and some vertebrate globins can be used to indicate that the initial radiation of the animal phyla occurred at least 900–1000 million years ago. ?Molecular evolution, Metazoa, haemoglobin.     

Evolutionary explosions and the phylogenetic fuse

A literal reading of the fossil record indicates that the early Cambrian (c. 545 million years ago) and early Tertiary (c. 65 million years ago) were characterized by enormously accelerated periods of morphological evolution marking the appearance of the animal phyla, and modern bird and placental mammal orders, respectively. Recently, the evidence for these evolutionary `explosions' has been questioned by cladistic and biogeographic studies which reveal that periods of diversification before these events are missing from the fossil record. Furthermore, molecular evidence indicates that prolonged periods of evolutionary innovation and cladogenesis lit the fuse long before the `explosions' apparent in the fossil record.     

The ecology and conservation of the coelacanth Latimeria chalumnae

Synopsis Studies on the ecology of the living coelacanth, Latimeria chalumnae, are reviewed and assessed. Early predictions on the life history of the coelacanth have proved to be accurate but recent findings have improved our understanding of its habitat and feeding preferences, diel activity patterns and social behaviour. A history of coelacanth conservation reveals that there has been a sustained concern for the survival of this species which has eventually culminated in several effective conservation actions in recent years. The coelacanth is threatened by a number of socio-economic and biological factors, but international action directed at managing the fishery in the Comoros should ensure that the species survives. Recent observations on living coelacanths in their natural environment have greatly improved our knowledge of the behaviour and relative abundance of adults. Important priorities for future research include studies on the distribution and abundance of juveniles and breeding adults, both off the Comoros and elsewhere. The coelacanth is a highly specialised, precocial fish which occupies a unique place in biology. Co-ordinated international efforts should continue to be made to understand and conserve this remarkable fish.     

Extinction and biogeography in the Caribbean: new evidence from a fossil riodinid butterfly in Dominican amber

We describe a new species of extinct riodinid butterfly, Voltinia dramba, from Oligo-Miocene Dominican amber (15-25 Myr ago). This appears to be the first butterfly to be taxonomically described from amber, and the first adult riodinid fossil. The series of five specimens represents probably the best-preserved fossil record for any lepidopteran. The phenomenon of extant Voltinia females ovipositing on arboreal epiphytes probably explains the discovery of multiple female V. dramba specimens in amber. Voltinia dramba appears to be one of many extinct butterfly species on Hispaniola. The northwestern Mexican distribution of the explicitly hypothesized sister species, the extant V. danforthi, supports the hypothesis that V. dramba reached Hispaniola by the 'proto-Greater Antillean arc', dating the divergence of V. dramba and V. danforthi to 40-50 Myr ago. This date is contemporaneous with the oldest known butterfly fossils, and implies a more ancient date of origin for many of the higher-level butterfly taxa than is often conceded.     

Human and ape molecular clocks and constraints on paleontological hypotheses

Although the relationships of the living hominoid primates (humans and apes) are well known, the relationships of the fossil species, times of divergence of both living and fossil species, and the biogeographic history of hominoids are not well established. Divergence times of living species, estimated from molecular clocks, have the potential to constrain hypotheses of the relationships of fossil species. In this study, new DNA sequences from nine protein-coding nuclear genes in great apes are added to existing datasets to increase the precision of molecular time estimates bearing on the evolutionary history of apes and humans. The divergence of Old World monkeys and hominoids at the Oligocene-Miocene boundary (approximately 23 million years ago) provides the best primate calibration point and yields a time and 95% confidence interval of 5.4 +/- 1.1 million years ago (36 nuclear genes) for the human-chimpanzee divergence. Older splitting events are estimated as 6.4 +/- 1.5 million years ago (gorilla, 31 genes), 11.3 +/- 1.3 million years ago (orangutan, 33 genes), and 14.9 +/- 2.0 million years ago (gibbon, 27 genes). Based on these molecular constraints, we find that several proposed phylogenies of fossil hominoid taxa are unlikely to be correct.     

The fossil record and limb disparity of enantiornithines, the dominant flying birds of the Cretaceous

Morphometric and stratigraphic analyses that encompass the known fossil record of enantiornithine birds (Enantiornithes) are presented. These predominantly flighted taxa were the dominant birds of the second half of the Mesozoic; the enantiornithine lineage is known to have lasted for at least 60 million years (Ma), up until the end of the Cretaceous. Analyses of fossil record dynamics show that enantiornithine 'collectorship' since the 1980s approaches an exponential distribution, indicating that an asymptote in proportion of specimens has yet to be achieved. Data demonstrate that the fossil record of enantiornithines is complete enough for the extraction of biological patterns. Comparison of the available fossil specimens with a large data set of modern bird (Neornithes) limb proportions also illustrates that the known forelimb proportions of enantiornithines fall within the range of extant taxa; thus these birds likely encompassed the range of flight styles of extant birds. In contrast, most enantiornithines had hindlimb proportions that differ from any extant taxa. To explore this, ternary diagrams are used to graph enantiornithine limb variation and to identify some morphological oddities ( Otogornis , Gobipteryx ); taxa not directly comparable to modern birds. These exceptions are interesting – although anatomically uniform, and similar to extant avians in their wing proportions, some fossil enantiornithines likely had flight styles not seen among their living counterparts.