Using ghost lineages to identify diversification events in the fossil record

Observed rises in taxic diversity could reflect bias of the fossil record or a genuine diversification. Here we outline a new method that attempts to differentiate between these two possible explanations. The method is based on the calculations of average ghost lineage duration through successive intervals of time. Biases due to variation in preservational conditions affect taxa independently from their position in the tree of life. A genuine radiation event will affect some parts of the tree of life more than others. During periods of rapid diversification, there will be a high proportion of new taxa showing short ghost lineages and therefore the average ghost lineage duration will drop as diversity rises, allowing us to distinguish such events from preservational bias during which ghost lineage duration remains unchanged. We test the method on Aptian-Maastrichtian (Cretaceous) ray-finned fish diversity. The result shows that a peak of diversity in the Cenomanian is associated with a drop in average ghost lineage duration, indicating that a genuine biological radiation occurred at that time.     

Clinical and Environmental Isolates of Legionella pneumophila Serogroup 1 Cannot Be Distinguished by Sequence Analysis of Two Surface Protein Genes and Three Housekeeping Genes

We used gene sequencing to determine whether clinical (sporadic, epidemic, and endemic) and environmental isolates of Legionella pneumophila serogroup (sg) 1 belong to specific lineages. A total of 178 clinical and environmental L. pneumophila sg 1 isolates, defined by pulsed-field gel electrophoresis and epidemiological data as sporadic, epidemic, or endemic, were analyzed for polymorphisms in five gene fragments. The fragments belonged to three housekeeping genes (coding for aconitase [acn], aspartate-β-semialdehyde dehydrogenase [asd], and RNA polymerase β subunit [rpoB]) and two surface protein genes (coding for the macrophage infectivity potentiator [mip] and the major outer membrane protein [mompS]). The phylogenetic tree inferred from sequence polymorphisms of the five genes identified two large clusters, one consisting of 133 poorly differentiated strains and containing two smaller clusters (10 and 2 strains) unrelated to each other and the other consisting of 42 strains. Clinical and environmental isolates could not be distinguished on this basis, and no link between genetic background and epidemiological type was found, suggesting that other factors are responsible for differences in pathogenicity.     

Latimeria chalumnae and its pedigree

Synopsis Latimeria is the product of a long coelacanth lineage, usually viewed as having changed very little. In this paper a classification of better known coelacanth genera is proposed based on a cladistic computer analysis of 56 morphological characters. Biometrical data are then matched with the classification to explore the possibility of identifying subtle change. It is concluded that throughout coelacanth history there have been changes in the structure of the vertebral column involving an overall increase in the number of vertebral elements, and a consequent crowding of these elements within the abdominal region. These changes may be associated with increasing lobation of the second dorsal and anal fins. In the skull, parameters involving the intracranial joint have also changed in such a way that the anterior part of the skull has lengthened in relation to the posterior part and this may be associated with an increase in length of the basicranial muscle.Abbreviations in text figures Ang angular - a.o.r anterior opening of th rostral organ - Art articular - ba.cr.m basicranial muscle - Basi basisphenoid - Boc basioccipital - bpt.pr basipterygoid process - c.p.l cheek pit line - De dentary - Esc extrascapular - eth.sp etmosphenoid - f.e frontoethmoid - Fr frontal - Fr.d descending process of frontal - intr. j intracranial joint - io.s interorbital septum - sc jugal sensory canal - L.e lateral ethmoid - m.Cor modified coronoid - Mm memtomeckelian - m.ot.sc medial branch of otic canal - Op operculum - o.p.l oral pit line - ot,occ otico-occipital - Pa parietal - Pa.d descending process of parietal - Par parasphenoid - pa.s parietal shield - p.Cor principal coronoid - Po postorbital - Pop preoperculum - p.o.r posterior openings of the rostral organ - Pmx premaxilla, Pre-preorbital - Pro prootic - Pro.p posterior process of prootic - Rart retroarticular - Sc.o sclerotic ossicle - So supraorbital - Soc supraoccipital - Sop suboperculum - Sp spiracular - spl splenial - Sq squamosal - Stt supratemporal - Stt.com supratemporal commissure - Stt.d descending process of supratemporal - Par.a.w ascending wing of parasphenoid - Te tectal - X level of vagus exit     

Clinical and environmental isolates of Legionella pneumophila serogroup 1 cannot be distinguished by sequence analysis of two surface protein genes and three housekeeping genes

We used gene sequencing to determine whether clinical (sporadic, epidemic, and endemic) and environmental isolates of Legionella pneumophila serogroup (sg) 1 belong to specific lineages. A total of 178 clinical and environmental L. pneumophila sg 1 isolates, defined by pulsed-field gel electrophoresis and epidemiological data as sporadic, epidemic, or endemic, were analyzed for polymorphisms in five gene fragments. The fragments belonged to three housekeeping genes (coding for aconitase [acn], aspartate-beta-semialdehyde dehydrogenase [asd], and RNA polymerase beta subunit [rpoB]) and two surface protein genes (coding for the macrophage infectivity potentiator [mip] and the major outer membrane protein [mompS]). The phylogenetic tree inferred from sequence polymorphisms of the five genes identified two large clusters, one consisting of 133 poorly differentiated strains and containing two smaller clusters (10 and 2 strains) unrelated to each other and the other consisting of 42 strains. Clinical and environmental isolates could not be distinguished on this basis, and no link between genetic background and epidemiological type was found, suggesting that other factors are responsible for differences in pathogenicity.     

Fishes from the Akkuyu Formation (Tithonian),Western Taurus,Turkey

Two fragmentary fishes are described from theUpper Jurassic (Tithonian) Akkuyu Formation of the Akseki region in the western Taurus (Turkey). Both are determinable, one as a caudal fin of an ichthyodectiform teleost, either Thrissops or Allothrissops, the other as a coelacanthid coelacanth, cf. Undina. This discovery extends the geographic range of these taxa and draw attention to the possibility of collecting a more extensive fish fauna from the region.     

Avian exposure and bronchogenic carcinoma.

OBJECTIVE--To investigate the association between bird keeping and risk of lung cancer. DESIGN--Case-control study asking detailed questions on exposure to domestic birds and other pets, smoking, and various demographic and potentially confounding variables. SETTING--District general hospital; current admissions interviewed in hospital or recent admissions interviewed at home. PATIENTS--143 patients with lung cancer, 143 controls with heart disease, and 143 controls with orthopaedic conditions individually matched for age, sex, date of admission, and current or past admission. MAIN OUTCOME MEASURES--Odds ratios for lung cancer in relation to various aspects of bird keeping, after adjustment for smoking and other relevant confounding variables. RESULTS--Risk of lung cancer was not significantly associated with household exposure to pet birds at any time or at various specific periods in life, or to keeping large numbers of birds. For specific types of birds no association was seen for living in households with budgerigars or canaries but risk was significantly associated with keeping pigeons (odds ratio 3.53, 95% confidence interval 1.56 to 7.98). This remained significant after regression analysis to account for confounding variables (3.9, 1.2 to 12.62) in both sexes and all age groups. CONCLUSION--Bird keeping may confer some risk of lung cancer but the relation is not as strong as previously reported.     

Spatial patterns of association at local and regional scales in coastal sand dune communities

Questions: Are positive understorey‐dominant associations important in physically severe dune communities and does the strength of positive associations vary with disturbance at the local scale and with stress at the regional scale? Do associational patterns observed at the neighbourhood scale predict diversity at higher scales? Location: Coastal sand dunes, Aquitaine (France). Methods: Associational patterns with five dominant species were recorded along a local gradient of disturbance and a 240‐km long regional gradient. Density, richness, cover and variance ratio of understorey species were recorded in quadrats located in dominant and in open areas. Spatial pattern of dominant plant species was recorded using a distance‐based method. Results: Positive understorey‐dominant associations were most frequent at both regional and local scale, although negative associations with understorey species were observed for one of the five dominants. At the regional scale, there was a shift in the magnitude of spatial associations, with higher positive associations in the most stressful sites, whereas spatial associations where not affected by the local disturbance gradient. Positive associations were not related to the size of the dominants but rather influenced by the identity of the dominant species. Conclusions: Our study highlights the potential crucial role of facilitation together with the importance of turnover of the dominants in explaining large‐scale variation in diversity. However, because positive associations may also be attributed to environmental heterogeneity or co‐occurrence of microhabitat preferences of species, experiments are needed to fully assess the relative importance of facilitation versus other drivers of community diversity.     

Characterization of the Legionella anisa population structure by pulsed-field gel electrophoresis

We analysed 38 French isolates of Legionella anisa by means of pulsed-field gel electrophoresis (PFGE) with single or double digestion. Double digestion was more discriminatory than single digestion, and can thus be useful for epidemiological studies of L. anisa. Several isolates from different parts of France clustered together on the basis of their PFGE patterns (similarity cutoff of 80%), suggesting that the L. anisa population structure is homogenous or that a few clones of L. anisa strains have spread widely in France.     

Conodont affinity and chordate phylogeny

Current information on the conodonts Clydagnathus windsorensis (Globensky) and Promissum pulchrum Kovács‐ Endrödy, together with the latest interpretations of conodont hard tissues, are reviewed and it is concluded that sufficient evidence exists to justify interpretation of the conodonts on a chordate model. A new phylogenetic analysis is undertaken, consisting of 17 chordate taxa and 103 morphological, physiological and biochemical characters; conodonts are included as a primary taxon. Various experiments with character coding, taxon deletion and the use of constraint trees are carried out. We conclude that conodonts are cladistically more derived than either hagfishes or lampreys because they possess a mineralised dermal skeleton and that they are the most plesiomorphic member of the total group Gnathostomata. We discuss the evolution of the nervous and sensory systems and the skeleton in the context of our optimal phylogenetic tree. There appears to be no simple evolution of free to canal‐enclosed neuromasts; organised neuromasts within canals appear to have arisen at least three times from free neuromasts or neuromasts arranged within grooves. The mineralised vertebrate skeleton first appeared as odontodes of dentine or dentine plus enamel in the paraconodont/euconodont feeding apparatus. Bone appeared later, co‐ordinate with the development of a dermal skeleton, and it appears to have been primitively acellular. Atubular dentine is more primitive than tubular dentine. However, the subsequent distribution of the different types of dentine (e.g. mesodentine, orthodentine), suggests that these tissue types are homoplastic. The topology of relationships and known stratigraphic ranges of taxa in our phylogeny predict the existence of myxinoids and petromyzontids in the Cambrian.