The chromosomes of afrotheria and their bearing on Mammalian genome evolution

Afrotheria is the clade of placental mammals that, together with Xenarthra, Euarchontoglires and Laurasiatheria, represents 1 of the 4 main recognized supraordinal eutherian clades. It reunites 6 orders of African origin: Proboscidea, Sirenia, Hyracoidea, Macroscelidea, Afrosoricida and Tubulidentata. The apparently unlikely relationship among such disparate morphological taxa and their possible basal position at the base of the eutherian phylogenetic tree led to a great deal of attention and research on the group. The use of biomolecular data was pivotal in Afrotheria studies, as they were the basis for the recognition of this clade. Although morphological evidence is still scarce, a plethora of molecular data firmly attests to the phylogenetic relationship among these mammals of African origin. Modern cytogenetic techniques also gave a significant contribution to the study of Afrotheria, revealing chromosome signatures for the group as a whole, as well as for some of its internal relationships. The associations of human chromosomes HSA1/19 and 5/21 were found to be chromosome signatures for the group and provided further support for Afrotheria. Additional chromosome synapomorphies were also identified linking elephants and manatees in Tethytheria (the associations HSA2/3, 3/13, 8/22, 18/19 and the lack of HSA4/8) and elephant shrews with the aardvark (HSA2/8, 3/20 and 10/17). Herein, we review the current knowledge on Afrotheria chromosomes and genome evolution. The already available data on the group suggests that further work on this apparently bizarre assemblage of mammals will provide important data to a better understanding on mammalian genome evolution.     

A new estimate of afrotherian phylogeny based on simultaneous analysis of genomic,morphological, and fossil evidence

Background  

The placental mammalian clade Afrotheria is now supported by diverse forms of genomic data, but interordinal relationships within, and morphological support for, the group remains elusive. As a means for addressing these outstanding problems, competing hypotheses of afrotherian interordinal relationships were tested through simultaneous parsimony analysis of a large data set (> 4,590 parsimony informative characters) containing genomic data (> 17 kb of nucleotide data, chromosomal associations, and retroposons) and 400 morphological characters scored across 16 extant and 35 extinct afrotherians.     

Gonadal Maturity in Wild Sturgeons, Huso dauricus, Acipenser mikadoi and A. schrenckii Caught near Hokkaido, Japan

We investigated the occurrence and gonadal maturity of wild sturgeons, which are rarely caught off Hokkaido island in Japan. Based on their morphological features, combined with the data on their cell DNA content, 48 sturgeons were classified into three species and one hybrid. These were the kaluga, Huso dauricus; the Japanese (Sakhalin) sturgeon, Acipenser mikadoi (historically, this species has been considered conspecific with the American green sturgeon, A. medirostris); the Amur sturgeon, A. schrenckii; and the kaluga–Amur sturgeon hybrid; with a ratio of 36:10:1:1. All of them were caught in saline waters, rather than in the fresh-water of the river, although some of them were in saline waters in the mouth of the river. Most of them were smaller than adult size; however, early juvenile fish were not detected. Histological analysis of gonadal development revealed early stages of gametogenesis in the majority of the fish of both genders. These results indicate that several sturgeon species are still occurring in the coastal waters of northern Japan, at different stages of gonadal maturity. In contrast, the lack of reports of both mature and early juvenile sturgeon capture in the Hokkaido rivers may suggest that native spawning populations of Japanese sturgeon have become extinct in Japan.     

Morphology of freeze-etchedTreponema refringens (Nichols)

The freeze-etch technique was used to study the morphology ofTreponema refringens (Nichols). There is a single band of cytoplasmic fibrils which follows a path in the form of a right-handed helix with a periodicity of 1500 nm around the body of the treponeme just below the cytoplasmic membrane. There are two major fracture planes, one located in the interior of the outer envelope and the second in the interior of the cytoplasmic membrane. The blebs or surface protuberances, which are quite prominent in negativestained preparations, were not evident with freeze-etch preparation, indicating they are not a part of the normal structure of this organism. The outer envelope in untreated cells was observed to closely fit the body of the treponeme, whereas the outer envelope of glutaraldehyde-treated cells had a loose, wrinkled appearance. Thus the loose-fitting outer envelope generally described for treponemes is most likely an artifact of preparation for negative-staining and thinsectioning.     

Phylogeny and habitat adaptations within a monophyletic group of wetland moss genera (Amblystegiaceae)

Genus level phylogenetic patterns within a monophyletic group of wetland mosses consisting ofTomentypnum, Hamatocaulis, Scorpidium, Conardia, Calliergon, Warnstorfia, Straminergon, andLoeskypnum (Amblystegiaceae) are cladistically analysed, usingPalustriella and partlyCratoneuron as outgroups. The ingroup consists of two clades, one withTomentypnum, Hamatocaulis andScorpidium, the other with the other ingroup genera. The second clade gets completely resolved only with the inclusion of habitat data. The adaptation to relatively dry wetland habitats probably evolved in the ancestor ofStraminergon andLoeskypnum, the species ofCalliergon andWarnstorfia, which are more ancestral, growing in wetter habitats. The more primitive taxa of the ingroup, as well asPalustriella species, occur in relatively mineral-rich habitats and adaptations to poorer habitats occurred several times in the two clades.     

Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting

Extant xenarthrans (armadillos, anteaters and sloths) are among the most derived placental mammals ever evolved. South America was the cradle of their evolutionary history. During the Tertiary, xenarthrans experienced an extraordinary radiation, whereas South America remained isolated from other continents. The 13 living genera are relics of this earlier diversification and represent one of the four major clades of placental mammals. Sequences of the three independent protein-coding nuclear markers alpha2B adrenergic receptor (ADRA2B), breast cancer susceptibility (BRCA1), and von Willebrand Factor (VWF) were determined for 12 of the 13 living xenarthran genera. Comparative evolutionary dynamics of these nuclear exons using a likelihood framework revealed contrasting patterns of molecular evolution. All codon positions of BRCA1 were shown to evolve in a strikingly similar manner, and third codon positions appeared less saturated within placentals than those of ADRA2B and VWF. Maximum likelihood and Bayesian phylogenetic analyses of a 47 placental taxa data set rooted by three marsupial outgroups resolved the phylogeny of Xenarthra with some evidence for two radiation events in armadillos and provided a strongly supported picture of placental interordinal relationships. This topology was fully compatible with recent studies, dividing placentals into the Southern Hemisphere clades Afrotheria and Xenarthra and a monophyletic Northern Hemisphere clade (Boreoeutheria) composed of Laurasiatheria and Euarchontoglires. Partitioned likelihood statistical tests of the position of the root, under different character partition schemes, identified three almost equally likely hypotheses for early placental divergences: a basal Afrotheria, an Afrotheria + Xenarthra clade, or a basal Xenarthra (Epitheria hypothesis). We took advantage of the extensive sampling realized within Xenarthra to assess its impact on the location of the root on the placental tree. By resampling taxa within Xenarthra, the conservative Shimodaira-Hasegawa likelihood-based test of alternative topologies was shown to be sensitive to both character and taxon sampling.     

Extrinsic Snout Musculature in Afrotheria and Lipotyphla

As currently recognized, the mammalian order Lipotyphla contains six extant families: Chrysochloridae, Erinaceidae, Solenodontidae, Soricidae, Talpidae, and Tenrecidae. Although most mammalogists have accepted this taxon, the morphological support for Lipotyphla is relatively weak, and recent phylogenetic studies using molecular data have concluded that it is not monophyletic. Instead, these molecular studies place chrysochlorids and tenrecids in the proposed clade Afrotheria, together with aardvarks, elephants, elephant shrews, hyraxes, and sirenians. Despite strong molecular support, Afrotheria has received little or no morphological support. It was recently suggested that a mobile snout might be a morphological feature uniting afrotherians. To test this proposal, I dissected the extrinsic snout musculature in an assortment of lipotyphlan and afrotherian mammals. These muscles provide support for Lipotyphla but not for Afrotheria. The snout is moved by different muscles in different afrotherian taxa, suggesting that the mobile snout is not homologous across different afrotherian lineages. In contrast, lipotyphlans have a distinctive set of five snout muscles moving the snout tip that appears to be unique to these six families. In addition, in soricids and talpids, four of the five snout muscles originate posterior to the zygomatic arch, supporting sister-taxon status for these two lineages. Although the extrinsic snout musculature does not support Afrotheria as presently proposed, it is consistent with an Afrotheria that does not include chrysochlorids and tenrecids.     

Morphological patterns in Petunia hybrida plants regenerated from tissue cultures and differing by their ploidy

Summary Quantitative variation in seven morphological characteristics (leaf length and width, leaf length/ width ratio, flower, petal and stomata length, and number of chloroplasts in guard cells) were studied in Petunia hybrida plants regenerated from anther tissue culture and belonging to four different classes of ploidy (2n, 2n–3n, 3n–2n, 4n–8n). Results showed that leaf size is not a good characteristic for discriminating between plants of different ploidy — flower and stomata characteristics being more adequate for this purpose. After applying stepwise discriminant analysis the association chloroplast number — leaf length/width ratio — petal length was verified to be more appropriate for the discrimination of ploidy classes.     

Utilization of dimeric lignin model compounds by mixed bacterial cultures

Summary The degradation of dimeric phenylpropanoid lignin model compounds using mixed bacterial cultures was studied. The six model compounds contained the most common linkages of lignin: -O-4, -, -5, and -1. The results indicate that it is possible to enrich bacteria which are able to degrade all these compounds. Bacteria were also able to use these dimers as the sole source of carbon for growth. In view of these results it seems probable that bacterial inability to degrade polymeric lignin is due to the physical properties such as the molecular size of lignin.     

Levels of Homoplasy in the Evolution of the Mammalian Skeleton

It is commonly believed that there are differences in the evolutionary lability of the crania, dentition, and postcrania of mammals, the latter two being more prone to homoplasy because of strong selective pressures for feeding and locomotion, respectively. Further, because of the fragmentary nature of fossils, phylogenetic analyses of extinct taxa often must utilize characters based on only one of these systems. In this paper the levels of homoplasy (as measured by the consistency index; CI) were compared in characters based on these three anatomical systems in therian mammals. No statistically significant differences were found in the overall CIs of 41 data sets based on dental, cranial, or postcranial characters. Differences in homoplasy within data sets with two or three kinds of data were not statistically significant. These findings suggest that dental, cranial, and postcranial characters can be equally prone to homoplasy and none should be automatically dismissed, disregarded, or systematically weighted in phylogenetic analyses. The level of homoplasy in characters derived from a given region of the skeleton may differ depending on the taxonomic level of the taxa considered. Dental, cranial, and postcranial characters may not constitute natural classes, yet examination of the phylogenetic signal of these subsets of data previous to a simultaneous analysis can shed light on significant aspects of the evolutionary process.     

Early Tertiary mammals from North Africa reinforce the molecular Afrotheria clade

The phylogenetic pattern and timing of the radiation of mammals, especially the geographical origins of major crown clades, are areas of controversy among molecular biologists, morphologists and palaeontologists. Molecular phylogeneticists have identified an Afrotheria clade, which includes several taxa as different as tenrecs (Tenrecidae), golden moles (Chrysochloridae), elephant-shrews (Macroscelididae), aardvarks (Tubulidentata) and paenungulates (elephants, sea cows and hyracoids). Molecular data also suggest a Cretaceous African origin for Afrotheria within Placentalia followed by a long period of endemic evolution on the Afro-Arabian continent after the mid-Cretaceous Gondwanan breakup (approx. 105-25 Myr ago). However, there was no morphological support for such a natural grouping so far. Here, we report new dental and postcranial evidence of Eocene stem hyrax and macroscelidid from North Africa that, for the first time, provides a congruent phylogenetic view with the molecular Afrotheria clade. These new fossils imply, however, substantial changes regarding the historical biogeography of afrotheres. Their long period of isolation in Africa, as assumed by molecular inferences, is now to be reconsidered inasmuch as Eocene paenungulates and elephant-shrews are here found to be related to some Early Tertiary Euramerican 'hyopsodontid condylarths' (archaic hoofed mammals). As a result, stem members of afrotherian clades are not strictly African but also include some Early Paleogene Holarctic mammals.     

Mutationsuntersuchungen am Tabakmosaikvirusin vitro

Summary Tobacco mosaic virus nucleoprotein was irradiated with UVin vitro and tested on Java tobacco plants for virus mutations. Both the mutation rate of systemicvulgare-TMV to local-necrotic mutants as well as the rate of the local-nercotic strainsdahlemense andnecans to systemic wild type mutants remained unaffected. The results are, therefore, independent of the direction of mutation. They confirm the earlier claim that UV has no mutagenic effect on TMVin vitro.     

Recapitulating the evolution of Afrotheria: 57 genes and rare genomic changes (RGCs) consolidate their history

The decipherment of higher level relationships among the orders of Afrotheria – an extraordinary assumption in mammalian evolution – constitutes one of the major disputes in the evolutionary history of mammals. Recent comprehensive studies of various genomic data, including mitochondrial and nuclear DNA sequences, chromosomal syntenic associations and retroposon insertions support strongly the monophyly of Afrotheria. However, the relationships within Afrotheria have remained ambiguous and there is a necessity for a more sophisticated analysis (i.e. combination of gene phylogeny and Rare Genomic Changes (RGCs)), which could aid in the comprehension of the evolutionary history of this old group of mammals. The present study investigated the phylogenetic relationships within Afrotheria by analysing a data set of coding and non-coding sequences (～32 000 bp) comprising 57 orthologous genes and 31 RGCs, such as chromosomal associations and retroposon insertions, and re-evaluated a molecular timescale for afrotherian mammals using a Bayesian relaxed clock approach. The interordinal afrotherians phylogeny presented here contributed to the elucidation of the evolutionary history of this ancient clade of mammals, which is one of the most unorthodox proposals in mammalian biology. This is critical not only for understanding how Afrotheria evolved in Africa, but also to comprehend the early biogeographical history of placental mammals.     

Combined use of radioimagers and radioactive 3′OH DNA nick end labelling to quantify apoptosis in cell lines and tissue sections: applications to virus-induced apoptosis

DNA fragmentation is a key feature of the degradation phase of apoptosis. In this work we have developed an assay, based on radioimager (-IMAGER and -IMAGER) quantification of radioactive nick end labelling (RANEL), which is quantitative, rapid and sensitive to study in vitro and in vivo induced apoptosis. To establish the technique, in vitro apoptosis of T cell lines was induced by stimulation of the Fas receptor; cells were labelled using TdT-mediated [-³³P] dCTP nick end labelling, after which then radioactivity was quantified using a -IMAGER. We have also shown that the RANEL method can be applied to the quantification and visualisation, by -IMAGER analysis, of liver tissue sections from mouse Fas-induced fulminant hepatitis or from Dengue-1 virus infected individuals. Finally, this system has also been used to detect apoptosis induced by rabies virus in Jurkat T cells. These data have established a large field of application for the RANEL assay.     

Removal of uranium by an exopolysaccharide from Pseudomonas sp.

Summary Accumulation of uranium (U) is reported for isolated exopolysaccharide produced by Pseudomonas sp. EPS-5028. A maximum uptake of 96 g U/mg polymer was observed. In contrast, the maximum accumulation of uranium by deacylated polysaccharide was 46 g/mg. This metal-complexing capacity observed suggests that the anionic reactive sites on the structure could be responsible for this activity. Metal uptake was affected by pH and was not affected by temperature. Expolysaccharide from Pseudomonas sp. EPS-5028 obeyed the Freundlich isotherm indicating single layer adsorption. Offprint requests to: F. Congregado     

Phylogenetic relationships among the ciliate arthrodontous mosses: Evidence from chloroplast and nuclear DNA sequences

Parsimony and maximum likelihood analyses of combinedtrnL (UAA) 5 exon —trnF (GAA) andrps4 exon cpDNA, and 18S nrDNA sequences of 60 arthrodontous moss taxa indicate strong support for the monophyly of a clade containing theSplachnineae, Orthotrichineae, and diplolepideous alternate sub-orders. A clade including theSplachnineae, Meesiaceae andLeptobryum (Bryaceae) is similarly well supported and forms the sister group to a clade comprising theOrthotrichineae and the other diplolepideous alternate mosses. Within this latter clade a number of well supported lineages are identified, but relationships among these remain poorly resolved. These analyses indicate that the Splachnaceous and Orthotrichaceous peristomes have been independently derived from an ancestral perfect bryoid peristome.     

Studies in Festuca. II. Fertility relationships between species of sections bovinae and scariosae,and their affinities with Lolium

Crossability anf F₁ hybrid fertility were studied using chromosome races (species or infra-specific taxa) representative of broad-leaved fescues in sections bovinae and scariosae. Hybrids were also obtained with Lolium multiflorum. The hybridization results, when considered in relation to morphology, cytology, and geographical distribution, support the idea that the Moroccan fescues studied here are more closely related amongst themselves, than to taxa from outside this region. These findings are discussed in relation to the evolution of the polyploids.     

Morphological and molecular comparisons ofCampsis grandiflora andC. radicans (Bignoniaceae), an eastern Asian and eastern North American vicariad species pair

Morphological and molecular comparisons were made forCampsis grandiflora (Thunb.)K. Schumann (Bignoniaceae) from eastern Asia andC. radicans (L.)Seemann from eastern North America. Chloroplast DNA (cpDNA) variation was surveyed with 20 restriction endonucleases. The cpDNA divergence between the two vicariad species was 2.44%, which is the highest reported among North Temperate disjunct taxa and one of the highest reported for infrageneric taxa. Detailed morphological comparisons also suggest a high level of divergence. Cluster analyses based on 22 morphological characters and 39 OTUs revealed two distinct groups corresponding with the two species. The average taxonomic distance between the two species was 1.806. Analyses of variance (ANOVA) revealed that 12 of the 18 quantitative characters differed significantly ( 0.01) betweenC. grandiflora andC. radicans. Divergence time based on cpDNA data was estimated as 24.4 million years. The Bering land bridge hypothesis was favored over the North Atlantic land bridge hypothesis based on the estimated divergence time and the geological history of the North Temperate region. The high levels of morphological and cpDNA divergence are not consistent with morphological stasis, which has been proposed as a common mode of evolution for North Temperate disjunct taxa.     

Ozone detoxification in the apoplasm and symplasm of spinach,broad bean and beech leaves at ambient and elevated concentrations of ozone in air

Spinach (Spinacia oleracea L.), broad bean (Vicia faba L.) and beech (Fagus sylvatica L.) plants were exposed to ozone at concentrations often measured in air during the summer months (120–300 g·m^–3) and antioxidants were determined in the leaf tissue and in the aqueous phase of the cell wall, the apoplasm. Concentrations of both reduced ascorbate (AA) and its oxidized form, dehydroascorbate (DHA), showed the tendency to increase transiently in the apoplasm of spinach leaves 6–24 h after starting fumigation with ozone. In beech leaves, apoplasmic AA and DHA increased 3–7 d after beginning of treatment. At the very high concentration of 1600 g O₃·m^–3, an increase of apoplasmic AA was already measured after 1 d in beech leaves. Apparently, spinach and beech leaves respond to oxidative stress by increasing AA transport into the apoplasm and by accelerating DHA export. In contrast to these observations, DHA accumulated during 3 d of fumigation with only 120 g O₃·m^–3 in the apoplasm of broad bean leaves, while AA contents did not increase. After termination of fumigation, the extracellular redox state of ascorbate normalized within 1 d. Glutathione could not be detected in the apoplasm of any of the three leaf species. Intracellular AA changed its redox state in response to exposure to elevated concentrations of ozone. After 4–6 weeks of fumigation with 200–300 g O₃·m^–3 an increase of intracellular DHA was measured in beech leaves. At the same time, chlorophyll contents decreased and characteristic symptoms of ozone damage could be observed. However, no significant change in the redox state of apoplasmic ascorbate could be detected in beech leaves. Evidently, detoxification of ozone by apoplasmic AA was insufficient to protect the leaf tissue. Fumigation with a high ozone concentration (1600 g·m^–3) caused an appreciable increase in the cellular contents of the oxidized forms of ascorbate and glutathione in beech leaves. Whereas in spinach leaves intracellular antioxidant contents and redox states were not altered during fumigation with 120–240 g O₃·m^–3, in broad bean leaves the intracellular DHA concentration increased and intracellular ascorbate became more oxidized after fumigation of the plants with 120 g O₃·m^–3. Apparently, broad bean leaves are more sensitive to ozone than beech and spinach leaves.Abbreviations AA ascorbate, reduced form - DHA ascorbate, oxidized form (dehydroascorbate) - FW fresh weight - GSH glutathione, reduced form - GSSG glutathione, oxidized form - IWF intercellular washing fluid - V_air intercellular air space volume of leaves - V_apo apoplasmic water volume of leaves This work was supported within the Sonderforschungsbereich 251 of the University of Würzburg.     

Fossils and living taxa agree on patterns of body mass evolution: a case study with Afrotheria

Most of life is extinct, so incorporating some fossil evidence into analyses of macroevolution is typically seen as necessary to understand the diversification of life and patterns of morphological evolution. Here we test the effects of inclusion of fossils in a study of the body size evolution of afrotherian mammals, a clade that includes the elephants, sea cows and elephant shrews. We find that the inclusion of fossil tips has little impact on analyses of body mass evolution; from a small ancestral size (approx. 100 g), there is a shift in rate and an increase in mass leading to the larger-bodied Paenungulata and Tubulidentata, regardless of whether fossils are included or excluded from analyses. For Afrotheria, the inclusion of fossils and morphological character data affect phylogenetic topology, but these differences have little impact upon patterns of body mass evolution and these body mass evolutionary patterns are consistent with the fossil record. The largest differences between our analyses result from the evolutionary model, not the addition of fossils. For some clades, extant-only analyses may be reliable to reconstruct body mass evolution, but the addition of fossils and careful model selection is likely to increase confidence and accuracy of reconstructed macroevolutionary patterns.