Temporal information,fossil record and phylogeny

Fossils, i.e. remains of living organisms, provide critical data to reconstruct the history of life on Earth because they are the source of unique information concerning the past. Fossils allow statements to be made about morphological features that would otherwise remain unknown, that also help clarifying the phylogenetic relationships of organisms, which results in a better knowledge of the fossil record and, partly, of the stratigraphic record. The latter constitutes the basic source for palaeontologists in order to reconstruct the History of Life. Some palaeontologists consider that the stratigraphical record provides us with essential information necessary to propose phylogenetic hypotheses and to build evolutionary scenarios. However, this point of view is not generally accepted, some authors putting forward that the fossil record is too fragmentary to be accurate (see, e.g.: G.J. Nelson, N.I. Platnick, Systematics and Biogeography: Cladistics and Vicariance, Columbia University Press, New York, 1981; K.J. Peterson, A phylogenetic test of the calcichordate scenario, Lethaia 28 (1995) 25–38). We critically analyze the indices used to estimate the quality of the fossil record and the fit of phylogenetic hypotheses to stratigraphy. We use the concept of temporal paralogy to explain why all these measurements are biased.     

The occurrence of 2-methylhopanoids in modern bacteria and the geological record

The 2-methylhopanes (2-MeHops) are molecular fossils of 2-methylbacteriohopanepolyols (2-MeBHPs) and among the oldest biomarkers on Earth. However, these biomarkers’ specific sources are currently unexplained, including whether they reflect an expansion of marine cyanobacteria. Here, we study the occurrence of 2-MeBHPs and the genes involved in their synthesis in modern bacteria and explore the occurrence of 2-MeHops in the geological record. We find that the gene responsible for 2-MeBHP synthesis (hpnP) is widespread in cyano- and ?-proteobacteria, but absent or very limited in other classes/phyla of bacteria. This result is consistent with the dominance of 2-MeBHP in cyano- and ?-proteobacterial cultures. The review of their geological occurrence indicates that 2-MeHops are found from the Paleoproterozoic onwards, although some Precambrian samples might be biased by drilling contamination. During the Phanerozoic, high 2-MeHops’ relative abundances (index >15%) are associated with climatic and biogeochemical perturbations such as the Permo/Triassic boundary and the Oceanic Anoxic Events. We analyzed the modern habitat of all hpnP-containing bacteria and find that the only one species coming from an undisputed open marine habitat is an ?-proteobacterium acting upon the marine nitrogen cycle. Although organisms can change their habitat in response to environmental stress and evolutionary pressure, we speculate that the high sedimentary 2-MeHops’ occurrence observed during the Phanerozoic reflect ?-proteobacteria expansion and marine N-cycle perturbations in response to climatic and environmental change.     

Preface: The phylogeny, fossil record and ecological diversity of ostracod crustaceans

After more than two centuries of research, more than 65,000 living and fossil ostracod species have been described and studied, yet much remains to be learned about this ancient, widespread and diverse group of bivalved arthropods. Their higher classification and phylogeny are subjects of vigorous debate, as is their position in the broader picture of crustacean phylogeny. At the same time, major advances in our understanding of ostracod lineages and their relationships are resulting from the application of innovative approaches and techniques. This preface provides a contextual overview of the 15 contributions to this volume, which resulted from the 14th International Symposium on Ostracoda (ISO2001) held in 2001at Shizuoka, Japan. As such it provides a cross-section of topics at the forefront of research on the evolution and diversity of Ostracoda, and indicates directions for future work.     

The geological record of a mid-Holocene marine storm in southwestern Spain

Integrated analysis of a 50-m long sedimentary core collected in the central part of the Odiel estuary (SW Atlantic coast of Spain) allows delineation of the main paleoenvironmental changes that occurred in this area during the Holocene. Eight sedimentary facies were deposited in the last ca. 9000 years BP, confirming a transgressive-regressive cycle that involves the transition from fluvial to salt marsh deposits with intermediate marine tidal deposits. A storm event is detected at ca. 5705 ¹⁴C years BP (mean calibrated age) with distinct lithostratigraphical, textural, geochemical, and palaeontological features.     

Basic features of gymnosperm systematics and phylogeny as evidenced by the fossil record

This paper introduces an integrated system of morphological concepts for gymnosperm fructifications, which does not lean upon any system existing for other higher plants. Comparative analytical treatment of all available characters of the most thoroughly studied fossil genera provided the foundation for an ordered ranking of congregations, each unit being assigned to the status of families, orders and classes. The transformation of the generative and vegetative organs has been traced along various phylogenetic branches. A new large phylogenetic branch (class Ginkgoopsida), beginning with the Lower Carboniferous Calamopityales, has been established. The lineage evolved from this order to Callistophytales and further to Peltaspermales. The family Peltaspermaceae encompasses, among others, plant types formerly regarded as ginkgoaleans. The orders Ginkgoales, Leptostrobales (Czekanowskiales) and Caytoniales evolved from the Peltaspermales. The order Arberiales (glossopterids) evidently evolved from the Calamopityales. In the lineage from Calamopityales to Ginkgoales a common seed type is conserved (platyspermic, non-cupular with two vascular bundles in the integument). Radiospermic seeds are conserved in the class Cycadopsida. In the lineage from Lagenostomales to Trigonocarpales the radially symmetrical cupule underwent modification into an integument of the same type of symmetry. The earliest Lagenostomales with the bilaterally symmetrical cupule evolved into the Cordaitanthales, where the cupule, also undergoing modification, was transformed into a bilaterally-symmetrical integument. In Cordaitanthales and their descendents the Pinales the seeds became secondarily platyspermic (in contrast to the primary non-cupular and primary platyspermic seeds in Ginkgoopsida); their vascularization was progressively reduced. These two orders are grouped into the class Pinopsida. It is believed that angiosperm seeds are in effect radiospermic with a radial cupule, their vascularization also being progressively reduced. If this holds true, the angiosperm ancestry should be sought in the class Cycadopsida. The Caytoniales, Arberiales, Peltaspermales, Leptostrobales and other orders of the class Ginkgoopsida should be excluded from the stock of probable angiosperm ancestors. A new gymnosperm phylogeny has been proposed and the evolution of the phylogenetic branches outlined in terms of the phytochoria system of the geological past. The basic evolutionary innovations took place within the Equatorial Belt and adjacent ecotone areas. Three types of processes, often underrated, have a paramount role in gymnosperm phylogeny. They are defined as follows: (1) homoeotic transformations of organs; corresponding to them are heterotopies, in the morphological aspect, and saltations, in the evolutionary sense; (2) dedifferentiation of the organs (the shift of one ontogenetic program onto various organs); (3) transitive polymorphism (conservation in diversity of a certain organ during phylogeny). These processes probably serve to indicate that rearrangement in the functions of the regulatory genes played an important role in the evolution of gymnosperms.     

Internal phylogeny of the Chilopoda (Myriapoda, Arthropoda) using complete 18S rDNA and partial 28S rDNA sequences

The internal phylogeny of the 'myriapod' class Chilopoda is evaluated for 12 species belonging to the five extant centipede orders, using 18S rDNA complete gene sequence and 28S rDNA partial gene sequence data. Equally and differentially weighted parsimony, neighbour-joining and maximum-likelihood were used for phylogenetic reconstruction, and bootstrapping and branch support analyses were performed to evaluate tree topology stability. The results show that the Chilopoda constitute a monophyletic group that is divided into two lines, Notostigmophora (= Scutigeromorpha) and Pleurostigmophora, as found in previous morphological analyses. The Notostigmophora are markedly modified for their epigenic mode of life. The first offshoot of the Pleurostigmophora are the Lithobiomorpha, followed by the Craterostigmomorpha and by the Epimorpha s. str. (= Scolopendromorpha + Geophilomorpha), although strong support for the monophyly of the Epimorpha s. lat. (= Craterostigmomorpha + Epimorpha s. str.) is only found in the differentially weighted parsimony analysis.     

Aspects of the fossil record and phylogeny of the familyRutaceae (Zanthoxyleae,Toddalioideae)

A comparative analysis of the seed morphology and anatomy of fossil and extantRutaceae (mainlyZanthoxyleae andToddalioideae) is presented. This allows to place the most important fossil taxa in a time-table and on paleogeographical maps. A phylogenetic scheme demonstrates the postulated historical relationships ofEvodia, Zanthoxylum, Fagara, Rutaspermum, Acronychia, Toddalia, Fagaropsis, andPhellodendron.     

Revival of forgotten characters and modern imaging techniques help to produce a robust phylogeny of the Diplopoda (Arthropoda,Myriapoda)

The external and internal anatomy of millipedes (Diplopoda) is poorly known compared to some of the other myriapod and arthropod groups. Due to both language barriers, which hindered the assessment of the character-rich older literature, and non-phylogenetic thinking, our knowledge of morphological characters useful for phylogenetic work diminished over the last decades. Here, a new character matrix with 64 characters, mainly derived from old literature data, is used to reconstruct a phylogeny of Diplopoda. As a tool to further our knowledge about the morphology of the different millipede orders, we show how micro-computer tomography (μCT) can be used to assess and illustrate specific parts of the Platydesmida. With the advent of μCT it is now possible to analyse many taxa and characters in a comparatively short time. A focus is put on potential phylogenetically useful characters. Our results support a Verhoeffian classification of the Diplopoda: Polyxenida + Chilognatha. Pentazonia are the sistergroup to the Helminthomorpha. Colobognatha form the sistergroup to Eugnatha, the latter split into monophyletic Juliformia and Polydesmida + Nematophora.     

Comparative pollen morphology and ultrastructure of Platanus: Implications for phylogeny and evaluation of the fossil record

Pollen of Platanus was studied using light (LM) and electron microscopy (SEM and TEM). Overall, pollen is uniform in modern Platanus (small, tricolpate, prolate to spheroidal, reticulate, semitectate). A number of characters, however, display remarkable variability within a taxon and even a single anther (size; foveo‐reticulate, fine to coarse reticulate ornamentation). Platanus kerrii (subgenus Castaneophyllum) differs from the remaining species by its high and “folded” reticulum and possibly the smooth colpus membrane. Moreover, to our knowledge, pollen of the P. kerrii – type is not known from the fossil record. The exine in modern and fossil Platanaceae shows great structural similarity, but the thickness of the foot layer within the ectexine is less variable and normally smaller in modern taxa. Furthermore, in Early Cretaceous to Early Cainozoic Platanaceae a number of distinct pollen types occurred that are not known within the modern Platanus. Considering pollen of Platanaceae from the Early Cretaceous to today, a dynamic picture of the evolution of the family emerges. In the first phase (Early Cretaceous) pollen of extinct genera such as Aquia differed considerably from modern Platanus and shows strong similarity to basal eudicot taxa such as Ranunculales (e.g. Lardizabalaceae). The Late Cretaceous Platananthus hueberi displays a distinct coarse reticulum that is unknown from modern Platanus but similar to some taxa of Hamamelidaceae (e.g. Exbucklandia). After the first phase of eudicot radiation that appears to have been characterized by strongly reticulate evolution, platanaceous diversity decreased in the course of the Cainozoic. Despite this, the pollen type of the modern subgenus Castaneophyllum (P. kerrii type) seems to be an innovation that originated after the initial radiation of the family.     

Arthropod phylogeny: An overview from the perspectives of morphology,molecular data and the fossil record

Monophyly of Arthropoda is emphatically supported from both morphological and molecular perspectives. Recent work finds Onychophora rather than Tardigrada to be the closest relatives of arthropods. The status of tardigrades as panarthropods (rather than cycloneuralians) is contentious from the perspective of phylogenomic data. A grade of Cambrian taxa in the arthropod stem group includes gilled lobopodians, dinocaridids (e.g., anomalocaridids), fuxianhuiids and canadaspidids that inform on character acquisition between Onychophora and the arthropod crown group. A sister group relationship between Crustacea (itself likely paraphyletic) and Hexapoda is retrieved by diverse kinds of molecular data and is well supported by neuroanatomy. This clade, Tetraconata, can be dated to the early Cambrian by crown group-type mandibles. The rival Atelocerata hypothesis (Myriapoda + Hexapoda) has no molecular support. The basal node in the arthropod crown group is embroiled in a controversy over whether myriapods unite with chelicerates (Paradoxopoda or Myriochelata) or with crustaceans and hexapods (Mandibulata). Both groups find some molecular and morphological support, though Mandibulata is presently the stronger morphological hypothesis. Either hypothesis forces an unsampled ghost lineage for Myriapoda from the Cambrian to the mid Silurian.     

Diplopod hemocyanin sequence and the phylogenetic position of the Myriapoda

Hemocyanins are copper-containing respiratory proteins of the Arthropoda that have so far been thoroughly investigated only in the Chelicerata and the Crustacea but have remained unstudied until now in the Myriapoda. Here we report the first sequence of a myriapod hemocyanin. The hemocyanin of Spirostreptus sp. (Diplopoda: Spirostreptidae) is composed of two distinct subunits that are arranged in a 6 x 6 native molecule. The cloned hemocyanin subunit cDNA codes of for a polypeptide of 653 amino acids (75.5 kDa) that includes a signal peptide of 18 amino acids. The sequence closely resembles that of the chelicerate hemocyanins. Molecular phylogenetic analyses reject with high statistical confidence the integrity of the Tracheata (i.e., Myriapoda + Insecta) but give conflicting results on the position of the myriapod hemocyanin. While distance matrix and maximum-likelihood methods support a basal position of the Spirostreptus hemocyanin with respect to the other hemocyanins, parsimony analysis suggests a sister group relationship with the chelicerate hemocyanins. The latter topology is also supported by a unique shared deletion of an alpha-helix. A common ancestry of Myriapoda and Chelicerata should be seriously considered.     

The phylogeny of the Rosaceae

KALKMAN, C., 1988. The phylogemy of the Rosaceae. A phylogenetic (cladistic) analysis of Rosaceae (excluding Chrysobalanaceae and Neuradaceae) is presented, based on the postulated direction of evolution in 14 morphological characters. Tribes or smaller groups, considered to be holophyletic, are taken as operational units. Three possible cladograms, made by hand, are presented and discussed. One of them is, within the limits of the method, selected as the most plausible image of real history, but this cladogram is not fully resolved and contains much homoplasy. Also presented is a fourth cladogram, produced by computer (CAFCA program); it is of about the same quality.
It is not justified to base drastic alterations in current classification on the weak phylogenetic hypothesis. For the time being it seems better not to recognize any subfamilies, but only a number of tribes.
It is hypothesized that the family originated in West Gondwana. A diagram is presented in which the most plausible cladogram is combined with the present distribution, clarifying the postulated routes of migration.
The sistergroup of Rosaceae is far from evident. The Cunoniaceae are considered to be the most plausible choice.     

The phylogeny of the felidae

Ohne Zusammenfassung

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The phylogeny of the felidae