CT scan reconstruction of the palate region of Latimeria chalumnae

Synopsis The palate of Latimeria chalumnae is described based mainly on three-dimensional CT scan reconstruction. It is compared with that of other osteichthyans. The palate of L. chalumnae compares best with that of rhipidistians; it is more advanced than that of actinopterygians in having fewer bones. This tendency toward bone reduction in the palate is even more pronounced in dipnoans. The interpretation of features of the Early Devonian genus Diabolepis determines if authors consider dipnoans or actinistians more closely related to tetrapods. Both groups are only distant relatives of tetrapods.     

Evolutionary patterns in early tetrapods. I. Rapid initial diversification followed by decrease in rates of character change

Although numerous studies have examined morphological diversification during major radiations of marine taxa, much less attention has been paid to terrestrial radiations. Here, we examine rates of character change over phylogeny and over time for Palaeozoic limbed tetrapods. Palaeozoic tetrapods show significant decreases in rates of character change whether the rate is measured per sampled cladistic branch or per million years along phylogeny. Given changes per branch, rates decrease significantly from the Devonian through the Pennsylvanian, but not from the Pennsylvanian through the Permian. Given changes per million years, rates decrease significantly over each boundary, although the decrease is least significant over the Pennsylvanian-Permian boundary. Decreasing rates per million years through the Permian might be an artefact of the method being able to ascribe longer durations to Permian branches than to Carboniferous ones; however, it is difficult to ascribe the general pattern of decreasing rates of change over time to sampling biases or methodological biases. Thus, the results implicate biological explanations for this pattern.     

Physicochemical properties of the hemoglobin of the coelocanth Latimeria chalumnae

The hemoglobin of Latimeria chalumnae, the only known extant representative of the coelocanth fishes from the Devonian period, the closest fish relative of land vertebrates, is characterized physicochemically, in view of its evolutionary significance, and in order to provide a molecular basis for functional characteristics earlier reported.On the basis of ultracentrifugational experiments the hemoglobin appears tetrameric with a sedimentation constant,S_{20 °,W} of 4.46 and a molecular weighf of 68,500, and SDS gel electrophoresis reveal a heterogeneity in monomer composition. Further characteristic features include the absence of marked diversification into component hemoglobins on the basis of isoelectric point, the apparent ease of dimerization, and some distinctive features of amino acid composition. The results are discussed comparatively and in the evolutionary context.     

Interspecies Insertion Polymorphism Analysis Reveals Recent Activity of Transposable Elements in Extant Coelacanths

Coelacanths are lobe-finned fish represented by two extant species, Latimeria chalumnae in South Africa and Comoros and L. menadoensis in Indonesia. Due to their intermediate phylogenetic position between ray-finned fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the L. chalumnae genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both Latimeria species. Comparison of 5.7 Mb (0.2%) of the L. chalumnae genome with orthologous Bacterial Artificial Chromosome clones from L. menadoensis allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both Latimeria species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in Latimeria.     

Molecules,fossils, and the origin of tetrapods

Summary Since the discovery of the coelacanth, Latimeria chalumnae, more than 50 years ago, paleontologists and comparative morphologists have debated whether coelacanths or lungfishes, two groups of lobe-finned fishes, are the closest living relatives of land vertebrates (Tetrapoda). Previously, Meyer and Wilson (1990) determined partial DNA sequences from two conservative mitochondrial genes and found support for a close relationship of lungfishes to tetrapods. We present additional DNA sequences from the 12S rRNA mitochondria gene for three species of the two lineages of lungfishes that were not represented in the first study: Protopterus annectens and Protopterus aethiopicus from Africa and Neoceratodus forsteri (kindly provided by B. Hedges and L. Maxson) from Australia. This extended data set tends to group the two lepidosirenid lungfish lineages (Lepidosiren and Protopterus) with Neoceratodus as their sister group. All lungfishes seem to be more closely related to tetrapods than the coelacanth is. This result appears to rule out the possibility that the coelacanth lineage gave rise to land vertebrates. The common ancestor of lungfishes and tetrapods might have possessed multiple morphological traits that are shared by lungfishes and tetrapods [Meyer and Wilson (1990) listed 14 such traits]. Those traits that seem to link Latimeria and tetrapods are arguably due to convergent evolution or reversals and not to common descent. In this way, the molecular tree facilitates an evolutionary interpretation of the morphological differences among the living forms. We recommended that the extinct groups of lobe-finned fishes be placed onto the molecular tree that has lungfishes and not the coelacanth more closely related to tetrapods. The placement of fossils would help to further interpret the sequence of morphological events and innovations associated with the origin of tetrapods but appears to be problematic because the quality of fossils is not always high enough, and differences among paleontologists in the interpretation of the fossils have stood in the way of a consensus opinion for the branching order among lobefinned fishes. Marshall and Schultze (1992) criticized the morphological analysis presented by Meyer and Wilson (1990) and suggest that 13 of the 14 morphological traits that support the sister group relationship of lungfishes and tetrapods are not shared derived characters. Here we present further alternative viewpoints to the ones of Marshall and Schultze (1992) from the paleontological literature. We argue that all available information (paleontological, neontological, and molecular data) and rigorous cladistic methodology should be used when relating fossils and extant taxa in a phylogenetic framework. Offprint requests to: Axel Meyer     

Relationship among coelacanths,lungfishes, and tetrapods: A phylogenetic analysis based on mitochondrial cytochrome oxidase I gene sequences

To clarify the relationship among coelacanths, lungfishes, and tetrapods, the amino acid sequences deduced from the nucleotide sequences of mitochondrial cytochrome oxidase subunit I (COI) genes were compared. The phylogenetic tree of these animals, including the coelacanth Latimeria chalumnae and the lungfish Lepidosiren paradoxa, was inferred by several methods. These analyses consistently indicate a coelacanth/lungfish clade, to which little attention has been paid by previous authors with the exception of some morphologists. Overall evidence of other mitochondrial genes reported previously and the results of this study equally support the coelacanth/lungfish and lungfish/tetrapod clades, ruling out the coelacanth/tetrapod clade.Correspondence to: K. Watanabe 0592     

Morphology and angiosperm systematics in the molecular era

Several ways in which morphology is used in systematic and evolutionary research in angiosperms are shown and illustrated with examples: 1) searches for special structural similarities, which can be used to find hints for hitherto unrecognized relationships in groups with unresolved phylogenetic position; 2) cladistic studies based on morphology and combined morphological and molecular analyses; 3) comparative morphological studies in new, morphologically puzzling clades derived from molecular studies; 4) studies of morphological character evolution, unusual evolutionary directions, and evolutionary lability based on molecular studies; and 5) studies of organ evolution. Conclusions: Goals of comparative morphology have shifted in the present molecular era. Morphology no longer plays the primary role in phylogenetic studies. However, new opportunities for morphology are opening up that were not present in the premolecular era: 1) phylogenetic studies with combined molecular and morphological analyses; 2) reconstruction of the evolution of morphological features based on molecularly derived cladograms; 3) refined analysis of morphological features induced by inconsistencies of previous molecular and molecular phylogenetic analyses; 4) better understanding of morphological features by judgment in a wider biological context; 5) increased potential for including fossils in morphological analyses; and 6) exploration of the evolution of morphological traits by integration of comparative structural and molecular developmental genetic aspects (Evo-Devo); this field is still in its infancy in botany; its advancement is one of the major goals of evolutionary botany.     

The series,the network,and the tree: changing metaphors of order in nature

The history of biological systematics documents a continuing tension between classifications in terms of nested hierarchies congruent with branching diagrams (the ‘Tree of Life’) versus reticulated relations. The recognition of conflicting character distribution led to the dissolution of the scala naturae into reticulated systems, which were then transformed into phylogenetic trees by the addition of a vertical axis. The cladistic revolution in systematics resulted in a representation of phylogeny as a strictly bifurcating pattern (cladogram). Due to the ubiquity of character conflict—at the genetic or morphological level, or at any level in between—some characters will necessarily have to be discarded (qua noise) in favor of others in support of a strictly bifurcating phylogenetic tree. Pattern analysts will seek maximal congruence in the distribution of characters (ultimately of any kind) relative to a branching tree-topology; process explainers will call such tree-topologies into question by reference to incompatible evolutionary processes. Pattern analysts will argue that process explanations must not be brought to bear on pattern reconstruction; process explainers will insist that the reconstructed pattern requires a process explanation to become scientifically relevant, i.e., relevant to evolutionary theory. The core question driving the current debate about the adequacy of the ‘Tree of Life’ metaphor seems to be whether the systematic dichotomization of the living world is an adequate representation of the complex evolutionary history of global biodiversity. In ‘Questioning the Tree of Life’, it seems beneficial to draw at least four conceptual distinctions: pattern reconstruction versus process explanation as different epistemological approaches to the study of phylogeny; open versus closed systems as expressions of different kinds of population (species) structures; phylogenetic trees versus cladograms as representations of evolutionary processes versus patterns of relationships; and genes versus species as expressions of different levels of causal integration and evolutionary transformation.     

Ciliated Sensory Cells in the Rostral Organ of the Coelacanth Latimeria chalumnae (Smith 1939)

The rostral organ of the coelacanth Latimeria chalumnae contains a sensory epithelium with luminated ciliated sensory cells, which very much resemble electroreceptors from other non-teleost fish. This, as well as the innervation and a dorsal nucleus, indicate that this interesting species is electroreceptive.     

Phylogenetic implications of corolla morphology in subfamily Barnadesioideae (Asteraceae)

The previously insignificant and small South American subtribe Barnadesiinae of tribe Mutisieae has been shown recently to be ancient within Asteraceae. Due to absence of a 22 kb diagnostic chloroplast inversion, plus other features, this subtribe has been elevated to subfamilial status as Barnadesioideae, now containing 90 species in nine genera. Recent cladistic analyses at the generic and specific levels based on morphology and DNA sequences (ITS and trnL intron) have revealed different relationships among taxa of the subfamily. To better understand these conflicts, we analyze specific morphological features of corollas (shape and vascularization) to develop trends (trees) in these features based on minimal structural change (i.e., morphological parsimony), and to compare these with relationships among genera derived from the two recent cladistic analyses. We define six principal types of corollas in Barnadesioideae (tubular, split, double split, ligulate, subbilabiate and bilabiate) and six principal types of corolla vascularization patterns (combinations of presence or absence of central bundles, fusion of adjacent bundles and fusion of bundles at the apex of corolla lobes). In all features we assume character states in Calyceraceae to be ancestral. In corolla shape, from tubular ancestry, we hypothesize two general evolutionary trends within the subfamily: (1) splitting of the tube, and (2) flattening of the tube. In vascularization of corollas, from an ancestral condition of one central and one lateral bundle in each corolla lobe and all traces fused at the apex, we hypothesize four basic trends: (1) gain or (2) loss of lateral vascular traces in each lobe, (3) loss of the central vein, and (4) loss of fusion of traces in lobe apices. These morphological trends allow tests of the two previous phylogenetic hypotheses by (1) counting step changes (following steps in the morphological network) in the two characters on the two competing phylogenetic trees and (2) constructing an index of morphological advancement for each genus (based on morphological trees of the two characters) and correlating these with cladistic distances within the two phylogenies. Results of both tests reveal the molecular phylogeny to be more compatible with evolutionary inferences from the two morphological features. With Fulcaldea excluded, a highly significant correlation is seen between morphological advancement and cladistic distance in the molecular phylogeny.     

Phylogeny reconstruction in the neogene bryozoan metrarabdotos: A paleontologic evaluation of methodology

An adequate stratigraphic record can not only aid in both cladistic and stratophenetic reconstruction of phytogenies, but can also serve in estimating the temporal consistency of the resulting phylogenetic trees. For hypothetical data sets, cladistically constructed trees can be as consistent with the temporal distribution of sampled populations or species as those constructed stratophenetically. Empirical testing in taxonomic groups with sufficiently dense fossil records is needed to show whether, and under what conditions, this potential can be realized. A stratophenetic tree and cladistic trees based on several approaches to character weighting were constructed for Caribbean Neogene species of the bryozoan Metrarabdotos with multiple‐character data from closely spaced sequential populations. The modular morphology and highly punctuated evolutionary pattern of these species blur the distinction between continuous and discrete characters, so that all available characters are potentially of equal significance in establishing phytogenies, rather than just those with discrete states conventionally used in cladistic analysis. However, only the cladistic trees generated with all characters weighted to emphasize contribution to species discrimination have temporal consistencies that are clearly significant statistically and approach that of the stratophenetic tree in magnitude. These results provide a start toward establishing general guidelines for cladistic analysis of taxa with stratigraphie records too sparse for stratophenetic reconstruction.     

Gene Structure and Amino Acid Sequence of Latimeria chalumnae (Coelacanth) Myelin DM20: Phylogenetic Relation of the Fish

The structure of Latimeria chalumnae (coelacanth) proteolipid protein/DM20 gene excluding exon 1 was determined, and the amino acid sequence of Latimeria DM20 corresponding to exons 2–7 was deduced. The nucleotide sequence of exon 3 suggests that only DM20 isoform is expressed in Latimeria. The structure of proteolipid protein/DM20 gene is well preserved among human, dog, mouse, and Latimeria. Southern blot analysis indicates that Latimeria DM20 gene is a single-copy gene. When the amino acid sequences of DM20 were compared among various species, Latimeria was more similar to tetrapods than other fishes including lungfish, confirming the previous finding by immunoreactivity (Waehneldt and Malotka 1989 J. Neurochem. 52:1941–1943). However, when phylogenetic trees were constructed from the DM20 sequences, lungfish was clearly the closest to tetrapods. Latimeria was situated outside of lungfish by the maximum likelihood method. The apparent similarity of Latimeria DM20 to tetrapod proteolipid protein/DM20 is explained by the slow amino acid substitution rate of Latimeria DM20.     

Observations on locomotion and feeding of released coelacanths,Latimeria chalumnae

Synopsis Two line-caught coelacanths, Latimeria chalumnae, were released for observation of their free-swimming movements in the open sea at a depth of about 50 m. Observations were made of their movement and use of the fins, interaction with humans (scuba diver), and colouration (white patches on dark background) as a possible means of camouflage. A new nomenclature is proposed for the caudal fin region and finnage.     

Structure of the kidney in the coelacanth Latimeria chalumnae with reference to osmoregulation

The morphology of the nephrons of the coelacanth Latimeria chalumnae was investigated by light microscopy. Each nephron is composed of a large renal corpuscle with well‐vascularized glomerulus, non‐ciliated neck segment, proximal convoluted tubule divided into distinct first and second segments, non‐ciliated intermediate segment, distal tubule, collecting tubule and collecting duct. The parietal layer of the Bowman's capsule of the renal corpuscle is composed of low cuboidal cells. The short non‐ciliated neck segment is lined by cuboidal epithelium. The first and second proximal segments display a prominent brush border and contain amorphous material in their lumen. The second proximal segment differs from the first segment in having taller columnar epithelium and a relatively narrow lumen. The intermediate segment is lined by non‐ciliated columnar epithelium and its lumen appears empty. The distal tubule is narrow in diameter and its cuboidal epithelium is devoid of intercalated cells. A unique feature of L. chalumnae is having binucleate cells in the tubule and collecting duct epithelium. The renal arteries have poorly developed tunica media and its cells contain granular material. The structure of L. chalumnae nephrons correlates well with their osmoregulatory function and resembles those of euryhaline teleosts.     

Über die Epidermis von Latimeria chalumnae J. L. B. Smith 1939 (Crossopterygii,Pisces)

The skin of Latimeria chalumnae J. L. B. Smith 1939 (Crossopterygii, Pisces) was studied by light microscopy. The epidermis contains only epithelium cells, mucus cells, and pigment cells. It differs from the epidermis of the Actinopterygii, Brachiopterygii, and Dipnoi.

---

---

Mit dankenswerter Unterstützung durch die Deutsche Forschungsgemeinschaft.     

CoelacanthLatimeria chalumnae aggregates in caves: first observations on their resting habitat and social behavior

Synopsis We report first observations on social behavior ofLatimeria chalumnae in its natural environment at around 200 m depth in the Comoro Archipelago, Western Indian Ocean. Coelacanths aggregate in small nonaggressive groups in sheltered lava-caves. They live in open site-attached social systems with individuals occupying large overlapping home ranges of more than 8 km coastline, some for a period of at least 2 years.     

Large extinctions of articulate brachiopods in the paleozoic and their ecological and evolutionary consequences

The largest Paleozoic extinctions of articulate brachiopods occurred at the Frasnian—Famennian boundary in the Late Devonian and at the Permian—Triassic boundary. Both extinctions affected taxa of all levels, including orders, but differed in scale, course, and ecological and evolutionary consequences. The Frasnian—Famennian extinction event was selective and evolutionary activity after the crisis varied in different orders. However, in the Early Carboniferous, the brachiopod diversity was mostly restored in comparison with the Devonian maximum. In particular groups, preadaptation played a role in changes in diversity and reconstruction of communities. The brachiopod composition at this boundary changed sharply. The extinction event at the end of Permian was global and accompanied by changes in the biota. Later, in the Meso-Cenozoic, the brachiopod diversity was not restored, and bivalves acquired primary importance in various bottom communities of different sea zones where Paleozoic brachiopods previously dominated. Extinction of brachiopods at this boundary was long and gradual. The symptoms of the ecological crisis in the development of Permian brachiopods are recognized beginning from the Roadian Age, which was probably the onset of this crisis.     

An investigation into the cladistic relationships and monophyly of therocephalian therapsids (Amniota: Synapsida)

A comprehensive phylogenetic investigation was performed to elucidate the cladistic relationships and possible monophyly of therocephalian therapsids (Amniota: Synapsida). The phylogenetic positions of 30 therapsid taxa were examined under maximum parsimony, including 23 therocephalian genera. The analysis incorporated 110 cranial and postcranial characters in order to assess the interrelationships of basal therocephalians and eutherocephalians and their relationships to Cynodontia, representing the most complete review of therocephalian phylogeny to date. The analysis supports the hypothesis that Therocephalia represents the monophyletic sister taxon to Cynodontia, with as many as 15 morphological synapomorphies, in contrast with other recent analyses of lesser taxon sampling. The results also support the hypothesis that Scylacosauridae is more closely related to Eutherocephalia than to the basal therocephalian family Lycosuchidae, supporting a ‘Scylacosauria’ clade. The taxa suggested here to be neotenic forms (e.g. Ictidosuchoides and Ictidosuchops) are positioned near the base of a monophyletic Baurioidea. Neotenic development of the therocephalian feeding apparatus and evolutionary parallelism with cynodonts are suggested to have been important trends in the early evolution of baurioid therocephalians into the Late Permian and Early Triassic.     

The first record of a nyctiphruretid parareptile from the Early Permian of North America,with a discussion of parareptilian temporal fenestration

The Richards Spur Locality of Oklahoma, USA, long known for its highly diverse Early Permian terrestrial tetrapod assemblage, is particularly interesting for the presence of many endemic taxa. The parareptilian component of the assemblage, rare members of other Early Permian communities, is especially diverse at Richards Spur, consisting of six species. The newest parareptile, A byssomedon williamsi gen. et sp. nov. , consists of an articulated left jaw and various disarticulated cranial and postcranial elements. A new phylogenetic analysis of parareptiles, based on an updated modified data matrix revealed that Ab . williamsi is a member of the small clade Nyctiphruretidae. This makes Ab . williamsi the first and oldest nyctiphruretid, a clade of parareptiles otherwise known from the Middle and Late Permian of Russia, extending the age of the clade back into the Early Permian. This discovery also raises the possibility that nyctiphruretids may have dispersed from western Laurasia to eastern Laurasia. The characteristic jugal morphology of Ab . williamsi shows that it would have possessed a slender, deep, temporal emargination. The current topology of Parareptilia indicates that there was considerable variability in the patterns of lateral temporal openings amongst the various members of this clade, suggesting that there may have been multiple, independent modifications of this region of the skull. © 2014 The Linnean Society of London     

Parallel evolution of jugal structures in Devonian athyridide brachiopods

Here, we describe Sinathyris crassa gen. et sp. nov., a new early Emsian (Early Devonian) athyridide brachiopod with a double spiralium from the Guangxi Province of southern China. Unlike the majority of genera of the subfamily Helenathyridinae, which possess accessory spiral lamellae developed directly from the jugal branches, the form described here shows these lamellae arising from a distally bifurcating jugal stem. These differences suggest that the double spiralium in S. crassa might have appeared independently from the double spiralium of the helenathyridins. To test the subfamily assignment of Sinathyris gen. nov., we carried out phylogenetic analyses, which indicate that the new genus is more appropriately referred to the Didymothyridinae. The cladistic analyses of the athyridides indicate that double spiralia have developed independently among these brachiopods at least five times during their evolutionary history.