BackgroundThe antisense insertion of a canine short interspersed element (SINEC_Cf) in the pigmentation gene PMEL (or SILV) causes a coat pattern phenotype in dogs termed merle. Merle is a semi-dominant trait characterized by patches of full pigmentation on a diluted background. The oligo(dT) tract of the Merle retrotransposon is long and uninterrupted and is prone to dramatic truncation. Phenotypically wild-type individuals carrying shorter oligo(dT) lengths of the Merle allele have been previously described and termed cryptic merles. Two additional coat patterns, dilute merle (uniform, steely-grey coat) and harlequin merle (white background with black patches), also appear in breeds segregating the Merle allele.ResultsSequencing of all PMEL exons in a dilute and a harlequin merle reveals that variation exists solely within the oligo(dT) tract of the SINEC_Cf insertion. In fragment analyses from 259 dogs heterozygous for Merle, we observed a spectrum of oligo(dT) lengths spanning 25 to 105 base pairs (bp), with ranges that correspond to the four varieties of the merle phenotype: cryptic (25–55 bp), dilute (66–74 bp), standard (78–86 bp), and harlequin (81–105 bp). Somatic contractions of the oligo(dT) were observed in 43% of standard and 51% of harlequin merle dogs. A small proportion (4.6%) of the study cohort inherited de novo contractions or expansions of the Merle allele that resulted in dilute or harlequin coat patterns, respectively.ConclusionsThe phenotypic consequence of the Merle SINE insertion directly depends upon oligo(dT) length. In transcription, we propose that the use of an alternative splice site increases with oligo(dT) length, resulting in insufficient PMEL and a pigment dilution spectrum, from dark grey to complete hypopigmentation. We further propose that during replication, contractions and expansions increase in frequency with oligo(dT) length, causing coat variegation (somatic events in melanocytes) and the spontaneous appearance of varieties of the merle phenotype (germline events).Electronic supplementary materialThe online version of this article (10.1186/s13100-018-0131-6) contains supplementary material, which is available to authorized users.

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The U.S. East Coast has 1.7 million acres of federal bottom under lease for the development of wind energy installations, with plans for more than 1,500 foundations to be placed. The scale of these wind farms has the potential to alter the unique and delicate oceanographic conditions along the expansive Atlantic continental shelf, a region characterized by a strong seasonal thermocline that overlies cold bottom water, known as the “Cold Pool.” Strong seasonal stratification traps cold (typically less than 10°C) water above the ocean bottom sustaining a boreal fauna that represents vast fisheries, including the most lucrative shellfish fisheries in the United States. This paper reviews the existing literature and research pertaining to the ways in which offshore wind farms may alter processes that establish, maintain, and degrade stratification associated with the Cold Pool through vertical mixing in this seasonally dynamic system. Changes in stratification could have important consequences in Cold Pool setup and degradation, processes fundamental to high fishery productivity of the region. The potential for these multiple wind energy arrays to alter oceanographic processes and the biological systems that rely on them is possible; however, a great deal of uncertainty remains about the nature and scale of these interactions. Research should be prioritized that identifies stratification thresholds of influence, below which turbines and wind farm arrays may alter oceanographic processes. These should be examined within context of spatial and seasonal dynamics of the Cold Pool and offshore wind lease areas to identify potential areas of further study.