Bird evolution: testing the Metaves clade with six new mitochondrial genomes

Background Evolutionary biologists are often misled by convergence of morphology and this has been common in the study of bird evolution. However, the use of molecular data sets have their own problems and phylogenies based on short DNA sequences have the potential to mislead us too. The relationships among clades and timing of the evolution of modern birds (Neoaves) has not yet been well resolved. Evidence of convergence of morphology remain controversial. With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe) we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade. Results Our mitochondrial trees did not return the Metaves clade that had been proposed based on one nuclear intron sequence. We suggest that the high number of indels within the seventh intron of the β-fibrinogen gene at this phylogenetic level, which left a dataset with not a single site across the alignment shared by all taxa, resulted in artifacts during analysis. With respect to the overall avian tree, we find the flamingo and grebe are sister taxa and basal to the shorebirds (Charadriiformes). Using a novel site-stripping technique for noise-reduction we found this relationship to be stable. The hummingbird/swift clade is outside the large and very diverse group of raptors, shore and sea birds. Unexpectedly the kagu is not closely related to the rail in our analysis, but because neither the kagu nor the rail have close affinity to any taxa within this dataset of 41 birds, their placement is not yet resolved. Conclusion Our phylogenetic hypothesis based on 41 avian mitochondrial genomes (13,229 bp) rejects monophyly of seven Metaves species and we therefore conclude that the members of Metaves do not share a common evolutionary history within the Neoaves

Evidence That Replication-Associated Mutation Alone Does Not Explain Between-Chromosome Differences In Substitution Rates

Since Haldane first noticed an excess of paternally derived mutations, it has been considered that most mutations derive from errors during germ line replication. Miyata et al. (1987) proposed that differences in the rate of neutral evolution on X, Y, and autosome can be employed to measure the extent of this male bias. This commonly applied method assumes replication to be the sole source of between-chromosome variation in substitution rates. We propose a simple test of this assumption: If true, estimates of the male bias should be independent of which two chromosomal classes are compared. Prior evidence from rodents suggested that this might not be true, but conclusions were limited by a lack of rat Y-linked sequence. We therefore sequenced two rat Y-linked bacterial artificial chromosomes and determined evolutionary rate by comparison with mouse. For estimation of rates we consider both introns and synonymous rates. Surprisingly, for both data sets the prediction of congruent estimates of α is strongly rejected. Indeed, some comparisons suggest a female bias with autosomes evolving faster than Y-linked sequence. We conclude that the method of Miyata et al. (1987) has the potential to provide incorrect estimates. Correcting the method requires understanding of the other causes of substitution that might differ between chromosomal classes. One possible cause is recombination-associated substitution bias for which we find some evidence. We note that if, as some suggest, this association is dominantly owing to male recombination, the high estimates of α seen in birds is to be expected as Z chromosomes recombine in males

A new perspective on avian phylogeny - a study based on mitochondrial genomes

The Class Aves (birds) is generally divided into two main groups - the Palaeognathae and the Neognathae. Paleognathous birds are the flightless ratites and the tinamous, while Neognathae include all other extant birds (more than 9,000 species). This opinion has prevailed for more than a century and is primarily based on morphological studies of the avian bony palate. In this study, the relationships between Palaeognathae and Neognathae along with other avian divergences have been investigated in phylogenetic analyses of complete mitochondrial (mt) genomes as well as in analyses of the mt cytochrome b gene. The complete mt genomes of the ostrich (Struthioniformes; Struthio camelus), the greater rhea (Struthioniformes; Rhea americana) and the rook (Passeriformes; Corvus frugilegus) were sequenced. At the time when this study was initiated and conducted, only one complete avian mt genome had been presented, that of the chicken (Galliformes; Gallus gallus), but this year four other complete avian mt genomes (representing the orders Anseriformes, Falconiformes and Passeriformes) were released. The phylogenetic analyses were carried out on the concatenated nucleotide and amino acid sequences (9,597 and 3,199 characters respectively) of twelve mt protein-coding genes from avian, mammalian, reptilian and piscine taxa. The results of the phylogenetic analyses did not support the most commonly accepted view of a basal divergence between paleognaths and neognaths. Instead, the earliest divergence among the taxa included was between the Passeriformes and all other birds including the ratites which were reconstructed at a more apical position in the tree as a sister group of galliforms and anseriforms. The origin of the Passeriformes was estimated to the early Cretaceous, about 120 MYBP (million years before present). A basal position of the ratites has in fact been questioned before, suggesting that ratites are not "primitive" birds but that ratite morphology includes a number of juvenile or neotenous traits (for example the downy plumage and the paleognathous palate) which have been maintained in adulthood. Because of the lack of pre-Tertiary passerine fossils (> 65MYBP) the order Passeriformes is generally regarded as one of the most recent avian lineages. It has been proposed, however, that the order Passeriformes originated already in the Cretaceous and that a recent origin of passerines is due to a misinterpretation of the fossil record. It is probable that the discrepancies between this study and the previous ones are attributable to the considerable length of the present dataset. Most importantly, however, the inclusion of a non-avian outgroup permits a different rooting strategy than used in most studies of avian relationships to date

Diabetes Mellitus in Pancreatic Cancer and the Need for Diagnosis of Asymptomatic Disease.

Pancreatic cancer is strongly associated with the development of hyperglycemia, peripheral insulin resistance and diabetes mellitus, especially when presented as new-onset diabetes mellitus. Peripheral insulin resistance and hyperinsulinemia have been suggested to promote growth of pancreatic cancer cells, and therefore a relation between long-standing diabetes mellitus type 2 and pancreatic cancer has been implied. Epidemiological studies, though, give incongruent results to this problem. There are data supporting a tumor-derived influence on glucose metabolism, insulin secretion and eventually the development of diabetes mellitus in early stages of pancreatic cancer. The only possibility for curative intent in pancreatic cancer is to diagnose the disease before symptoms occur. Patients with newly diagnosed diabetes mellitus type 2 or hyperglycemia as a risk group have been recommended for primary screening for pancreatic cancer. To date, there is no specific biomarker to identify patients with an asymptomatic pancreatic cancer. The review discuss the relationship between pancreatic cancer and diabetes mellitus and the possibility of secondary screening of patients with newly diagnosed diabetes mellitus type 2 or hyperglycemia in an artificial neural network. PubMed was searched for articles using the Mesh term 'pancreatic neoplasms' combined with 'insulin resistance' and 'glucose metabolism disorders'. Additional articles were retrieved through hyperlinks and by manually searching reference lists in original published articles. In total 36 articles were systematically reviewed. and IAP

Cystic pancreatic lesions : current evidence for diagnosis and treatment

Pancreatic cystic neoplasms are detected at an increasing frequency due to an increased use and quality of abdominal imaging. There are well known differential diagnostic difficulties concerning these lesions. The aim is to review current literature on the diagnostic options and the following treatment for cystic lesions in the pancreas focusing on serous cystadenomas, primary mucinous neoplasm of the pancreas and mucinous cystadenocarcinomas, as well as intraductal papillary mucinous neoplasms, starting with excluding pseudocysts. A conservative approach is feasible in patients with a clinical presentation suggestive of an asymptomatic serous cystadenoma. Surgical management, as well as follow-up, is discussed for each of the types of neoplastic lesions, including an uncharacterized cyst, based on patient data, symptoms, serum analysis, cyst fluid analysis and morphological features. Aspects for future diagnostics and management of these neoplasia are commented upon

The impact of fossil calibrations, codon positions and relaxed clocks on the divergence time estimates of the native Australian rodents (Conilurini).

The native rodents are the most species-rich placental mammal group on the Australian continent. Fossils of native Australian rodents belonging to the group Conilurini are known from Northern Australia at 4.5Ma. These fossil assemblages already display a rich diversity of rodents, but the exact timing of their arrival on the Australian continent is not yet established. The complete mitochondrial genomes of two native Australian rodents, Leggadina lakedownensis (Lakeland Downs mouse) and Pseudomys chapmani (Western Pebble-mound mouse) were sequenced for investigating their evolutionary history. The molecular data were used for studying the phylogenetic position and divergence times of the Australian rodents, using 12 calibration points and various methods. Phylogenetic analyses place the native Australian rodents as the sister-group to the genus Mus. The Mus-Conilurini calibration point (7.3-11.0Ma) is highly critical for estimating rodent divergence times, while the influence of the different algorithms on estimating divergence times is negligible. The influence of the data type was investigated, indicating that amino acid data are more likely to reflect the correct divergence times than nucleotide sequences. The study on the problems related to estimating divergence times in fast-evolving lineages such as rodents, emphasize the choice of data and calibration points as being critical. Furthermore, it is essential to include accurate calibration points for fast-evolving groups, because the divergence times can otherwise be estimated to be significantly older. The divergence times of the Australian rodents are highly congruent and are estimated to 6.5-7.2Ma, a date that is compatible with their fossil record

Artificial neural networks in pancreatic disease.

BACKGROUND: An artificial neural network (ANNs) is a non-linear pattern recognition technique that is rapidly gaining in popularity in medical decision-making. This study investigated the use of ANNs for diagnostic and prognostic purposes in pancreatic disease, especially acute pancreatitis and pancreatic cancer. METHODS: PubMed was searched for articles on the use of ANNs in pancreatic diseases using the MeSH terms 'neural networks (computer)', 'pancreatic neoplasms', 'pancreatitis' and 'pancreatic diseases'. A systematic review of the articles was performed. RESULTS: Eleven articles were identified, published between 1993 and 2007. The situations that lend themselves best to analysis by ANNs are complex multifactorial relationships, medical decisions when a second opinion is needed and when automated interpretation is required, for example in a situation of an inadequate number of experts. CONCLUSION: Conventional linear models have limitations in terms of diagnosis and prediction of outcome in acute pancreatitis and pancreatic cancer. Management of these disorders can be improved by applying ANNs to existing clinical parameters and newly established gene expression profiles

Artificiella neurala nätverk underlättar svåra medicinska beslut. Exempel från pankreatologin.

Artificial neural networks (ANNs) is a nonlinear pattern recognition technique inspired by the function of the human brain. ANNs have been used successfully in analysis of complex medical relationships, for example prognostic predictions of various forms of cancer. Acute pancreatitis and pancreatic cancer are commonly recognized to be extremely difficult conditions in making diagnostic and prognostic predictions with traditional methods. The two pancreatic disorders thus represent suitable candidates for analysis by ANNs. We hereby present a systematic review of the applications of ANNs in the treatment of acute pancreatitis and pancreatic cancer