Molecular identification of evolutionarily significant units in the Amazon River dolphin Inia sp. (Cetacea: Iniidae).
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The Amazon river dolphin, genus Inia, is endemic to the major river basins of northern South America. No previous studies have focused on the genetic structure of this genus. In this work, 96 DNA samples from specimens of this genus were collected in the Orinoco basin (four rivers), the Putumayo River, a tributary of the Colombian Amazon and the Mamore, and the Tijamuchi and Ipurupuru rivers in theBolivian Amazon. These samples were used to amplify a fragment of 400 bp of the mitochondrial DNA (mtDNA) control region. In addition, 38 of these samples were also used to sequence 600 bp of the mitochondrial cytochrome b gene. The analysis of the population structure subdivision with an analysis of molecular variance (AMOVA) revealed important aspects about the genetic structure of Inia groups fromthese three geographically separate regions. By comparing the control region DNA and cytochrome b sequences, distinct types of nonshared haplotypes were observed. The net genetic divergence of control region sequences was 6.53% between the Orinoco and Bolivian rivers, 5.32% between the Putumayo and Bolivian rivers, and 2.50% between the Orinoco and Putumayo rivers. For the cytochrome b gene, these values were 2.48%, 2.98%, and 0.06%, respectively. The nucleotide sequences were analyzed phylogenetically using several genetic distance matrices and applying neighbor-joining, maximum likelihood, and maximum parsimony procedures. The results support the proposal to subdivide the Inia genus into at least two evolutionarily significant units: one confined to the Bolivian river basin and the other widely distributed across the Amazon and Orinoco basins. (+info)
Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10p.
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Contiguous finished sequence from highly duplicated pericentromeric regions of human chromosomes is needed if we are to understand the role of pericentromeric instability in disease, and in gene and karyotype evolution. Here, we have constructed a BAC contig spanning the transition from pericentromeric satellites to genes on the short arm of human chromosome 10, and used this to generate 1.4 Mb of finished genomic sequence. Combining RT-PCR, in silico gene prediction, and paralogy analysis, we can identify two domains within the sequence. The proximal 600 kb consists of satellite-rich pericentromerically duplicated DNA which is transcript poor, containing only three unspliced transcripts. In contrast, the distal 850 kb contains four known genes (ZNF248, ZNF25, ZNF33A, and ZNF37A) and up to 32 additional transcripts of unknown function. This distal region also contains seven out of the eight intrachromosomal duplications within the sequence, including the p arm copy of the approximately 250-kb duplication which gave rise to ZNF33A and ZNF33B. By sequencing orthologs of the duplicated ZNF33 genes we have established that ZNF33A has diverged significantly at residues critical for DNA binding but ZNF33B has not, indicating that ZNF33B has remained constrained by selection for ancestral gene function. These results provide further evidence of gene formation within intrachromosomal duplications, but indicate that recent interchromosomal duplications at this centromere have involved transcriptionally inert, satellite rich DNA, which is likely to be heterochromatic. This suggests that any novel gene structures formed by these interchromosomal events would require relocation to a more open chromatin environment to be expressed. (+info)
Contrasting relatedness patterns in bottlenose dolphins (Tursiops sp.) with different alliance strategies.
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Male bottlenose dolphins (Tursiops sp.) in Shark Bay have one of the most complex male societies outside humans. Two broad mating strategies have been identified in males. In the first strategy, there are two types of alliances: stable 'first-order' pairs and trios that herd individual females in reproductive condition, and 'second-order' teams of two first-order alliances (five or six individuals) that join forces against rivals in contests for females. In the alternative strategy, a 'super-alliance' of ca. 14 individuals, males form pairs or trios to herd females, but in contrast to the stable alliances, these pairs and trios are highly labile. Here, we show that males in stable first-order alliances and the derived second-order alliances are often strongly related, so that they may gain inclusive fitness benefits from alliance membership. By contrast, members of the super-alliance are no more closely related than expected by chance. Further, the strength of the association of alliance partners within the super-alliance, as measured by an index of joint participation in consorting a female, was not correlated with their genetic relatedness. Thus, within one population and one sex, it appears that there may be simultaneous operation of more than one mode of group formation. (+info)
A poorly differentiated pulmonary squamous cell carcinoma in a free-ranging Atlantic bottlenose dolphin (Tursiops truncatus).
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A free-ranging, adult, female offshore bottlenose dolphin (Tursiops truncatus) was found freshly dead in 1999 on Ocean Park Beach in San Juan, Puerto Rico. The left-lung and right-lung pleura had multiple white, firm-to-hard nodules with coagulative necrosis. Histologically, the neoplasms were characterized by multiple well-circumscribed, nonencapsulated expansile masses consisting mostly of polygonal cells with fewer circumferential flattened basaloid cells that compressed alveoli, bronchioles, and bronchi. Neoplastic cells stained positive for cytokeratin, with sporadic vimentin staining, and were negative for epithelial membrane antigen, thyroid transcription factor-1, calretinin, and human mesothelial cell antigen. A diagnosis of poorly differentiated pulmonary squamous cell carcinoma with lymph node and renal metastases was made on the basis of histomorphology and immunohistochemical staining. This is the first documentation of pulmonary squamous cell carcinoma in a dolphin. (+info)
DNA surveillance: web-based molecular identification of whales, dolphins, and porpoises.
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DNA Surveillance is a Web-based application that assists in the identification of the species and population of unknown specimens by aligning user-submitted DNA sequences with a validated and curated data set of reference sequences. Phylogenetic analyses are performed and results are returned in tree and table format summarizing the evolutionary distances between the query and reference sequences. DNA Surveillance is implemented with mitochondrial DNA (mtDNA) control region sequences representing the majority of recognized cetacean species. Extensions of the system to include other gene loci and taxa are planned. The service, including instructions and sample data, is available at http://www.dna-surveillance.auckland.ac.nz. (+info)
The locus coeruleus complex of the bottlenose dolphin (Tursiops truncatus) as revealed by tyrosine hydroxylase immunohistochemistry.
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Using tyrosine hydroxylase immunohistochemistry we examined the structure of the pontine, or rostral rhombencephalic, catecholaminergic cells groups, which may be collectively termed the locus coeruleus complex (LC), in the bottlenose dolphin. The present study is the first to describe the LC in a cetacean species and, at 1.3 kg, represents the largest non-human brain to date in which the LC has been investigated. We identified four catecholaminergic cell groups in the dorsal pontine tegementum and peri-aqueductal gray matter: A6 dorsal (locus coeruleus), A6 ventral (locus coeruleus alpha), A7 (subcoeruleus), and A5 (fifth arcuate nucleus). No patterns of cellular distribution, nuclear subdivision, or cellular morphology indicate specialization of the LC, which might have been anticipated because of the large absolute brain size and unihemispheric sleep phenomenology of cetaceans. (+info)
Distribution of MHC II (+) cells in skin of the Atlantic bottlenose dolphin (Tursiops truncatus): an initial investigation of dolphin dendritic cells.
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The skin is an important tissue of the immune system; however, little is known about immune cells in dolphin skin, and very few cetacean-specific immunoreagents are available for investigative purposes. Therefore, in this study immunohistochemistry techniques were used with species-specific and non-species-specific antibodies to characterize immune cells, primarily focusing on Langerhans cells, in skin from the Atlantic bottlenose dolphin (Tursiops truncatus). An antibody to human major histocompatibility complex (MHC) class II molecules labeled cells with a dendritic-like morphology. The immunophenotype, morphology, and distribution of some of these cells are consistent with those of Langerhans cells. The cells were predominantly found in dermal papillae, primarily along the epidermal-dermal junction. Thus, the location of these cells was somewhat different from that in terrestrial mammals. Other MHC II (+) cells of varying morphology were observed deeper in the dermis, with a perivascular concentration, and had characteristics of macrophages and dermal dendritic cells. There was no immunostaining with cetacean-specific CD2 or CD21. In diseased skin, a subjective increase of MHC II (+) cells, most notably in the superficial skin layers, was associated with an ulcerative dermatitis. A few CD2 (+) cells were also present. Differences between dolphins and terrestrial mammals in terms of morphology, mechanisms of response to insult and repair, and environmental challenges may explain the modified distribution of MHC II (+) cells in dolphin skin. An elucidation of the immune cells in cetacean skin will contribute to our understanding of the evolution of functional adaptations to various environments, facilitate diagnosis of skin diseases, and define the potential for intradermal administration of vaccines and other immunotherapeutics. (+info)
Comparison of diagnostic techniques for Helicobacter cetorum infection in wild Atlantic bottlenose dolphins (Tursiops truncatus).
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Helicobacter cetorum sp. nov. has been cultured from the stomach of Atlantic white-sided dolphins (Lagenorhynchus acutus) and the feces of Pacific white-sided (L. obliquidens) and Atlantic bottlenose (Tursiops truncatus) dolphins and a beluga whale (Delphinapterus leucas). H. cetorum has high homology to Helicobacter pylori as shown by 16S rRNA sequencing, and H. cetorum infection has been associated with gastritis and clinical signs in cetaceans. Because the prevalence of H. cetorum in wild populations is unknown, minimally invasive techniques for detecting H. cetorum were compared for 20 wild bottlenose dolphins sampled as part of a long-term health study. Fecal samples were tested for helicobacter by culture, Southern blotting, and PCR using genus-specific and H. cetorum-specific primers. An enzyme-linked immunosorbent assay (ELISA) was developed to measure H. cetorum immunoglobulin G (IgG). H. cetorum was cultured from 4 of 20 fecal samples, 7 samples were positive using Helicobacter sp. PCR, and 8 samples were positive for H. cetorum using species-specific primers. Two additional fecal samples were positive by Helicobacter sp. Southern blotting, suggesting infection with another helicobacter. All 20 sera contained high levels of IgG antibodies to H. cetorum that were significantly lowered by preabsorption of the sera with whole-cell suspensions of H. cetorum (P < 0.02). Until the specificity of the serum ELISA can be determined by testing sera from dolphins confirmed to be uninfected, PCR and Southern blot screenings of feces are the most sensitive techniques for detection of H. cetorum, and results indicate there is at least a 50% prevalence of H. cetorum infection in these dolphins. (+info)