The Effect of Inappropriate Calibration: Three Case Studies in Molecular Ecology

Time-scales estimated from sequence data play an important role in molecular ecology. They can be used to draw correlations between evolutionary and palaeoclimatic events, to measure the tempo of speciation, and to study the demographic history of an endangered species. In all of these studies, it is paramount to have accurate estimates of time-scales and substitution rates. Molecular ecological studies typically focus on intraspecific data that have evolved on genealogical scales, but often these studies inappropriately employ deep fossil calibrations or canonical substitution rates (e.g., 1% per million years for birds and mammals) for calibrating estimates of divergence times. These approaches can yield misleading estimates of molecular time-scales, with significant impacts on subsequent evolutionary and ecological inferences. We illustrate this calibration problem using three case studies: avian speciation in the late Pleistocene, the demographic history of bowhead whales, and the Pleistocene biogeography of brown bears. For each data set, we compare the date estimates that are obtained using internal and external calibration points. In all three cases, the conclusions are significantly altered by the application of revised, internally-calibrated substitution rates. Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events

Biogeographic problem-solving reveals the Late Pleistocene translocation of a short-faced bear to the California Channel Islands

An accurate understanding of biodiversity of the past is critical for contextualizing biodiversity patterns and trends in the present. Emerging techniques are refining our ability to decipher otherwise cryptic human-mediated species translocations across the Quaternary, yet these techniques are often used in isolation, rather than part of an interdisciplinary hypothesis-testing toolkit, limiting their scope and application. Here we illustrate the use of such an integrative approach and report the occurrence of North America’s largest terrestrial mammalian carnivore, the short-faced bear, Arctodus simus, from Daisy Cave (CA-SMI-261), an important early human occupation site on the California Channel Islands. We identified the specimen by corroborating morphological, protein, and mitogenomic lines of evidence, and evaluated the potential natural and anthropogenic mechanisms of its transport and deposition. While representing just a single specimen, our combination of techniques opened a window into the behavior of an enigmatic species, suggesting that A. simus was a wide-ranging scavenger utilizing terrestrial and marine carcasses. This discovery highlights the utility of bridging archaeological and paleontological datasets to disentangle complex biogeographic scenarios and reveal unexpected biodiversity for island systems worldwide.Open Access fees paid for in whole or in part by the University of Oklahoma Libraries Radiocarbon and isotope laboratory work was supported in part by the NSF Archaeometry Program BCS-1460369 (to D.J.K. and B.J.C). M.B was supported by a Royal Society fellowship. Additional funding was provided by the University of Oklahoma, the University of Oregon, and the Smithsonian Institution.Ye

Sentinel lymph node biopsy in penile cancer: a comparative study using modified inguinal dissection

INTRODUCTION: In the case of clinically negative inguinal regions in penile cancer, the treatments proposed might vary from careful observation to radical dissection for all patients. We evaluated the effectiveness of the sentinel lymph node biopsy using lymphoscintigraphy in patients with penile cancer and at least one negative inguinal region. MATERIALS AND METHODS: In 18 patients, biopsy of the sentinel lymph node from the 32 negative inguinal regions and modified radical lymphadenectomy in these regions regardless of the biopsy results was performed. Clinical staging, pathological results of the sentinel and the other lymph nodes removed during lymphadenectomy, tumor behavior, local and inguinal recurrence and specific disease mortality were accessed. RESULTS: The mean age of the study sample was 57.7 years (44 - 81 years) and the sentinel lymph node presented 0% false negative 66% sensitivity, and 79.3% specificity when compared with the modified inguinal lymphadenectomy as the gold standard treatment. CONCLUSION: Sentinel lymph node biopsy is a feasible method of assessing the presence of regional metastasis in patients with penile cancer and clinically negative inguinal regions. However, the optimal lymphoscintigraphy technique is still in evolution and requires further optimization at high volume centers