Transcriptome Profiles: Diagnostic Signature of Dolphin Populations

Abstract

Peripheral blood leukocyte samples were collected from 151 common bottlenose dolphins (Tursiops truncatus) in the course of capture/release health evaluation studies at four different sites: Charleston Harbor, SC; Indian River Lagoon, FL; Sarasota Bay, FL; and St. Joseph Bay, FL. RNA was extracted and hybridized to a first-generation dolphin microarray. We tested the hypothesis that individual dolphins could be assigned to their home regions (by machine learning methods) using only their transcriptomic signatures as classifiers. The machine learning approaches used in this study were artificial neural networks (ANNs) which were able to identify gene expression differences in males and females in some geographical locations. As the sex ratios sampled in each location were not the same and could influence the classification of individuals to locations, males and females at each location were considered separately. ANNs were able to correctly classify dolphins according to their site of sampling with a high degree of confidence. The basis for this result may lie in genetic differences between populations, or in environmental factors (including for example diet, infection, contaminant load, or exposure to biotoxins) or in combinations of these factors. These results suggest that a combination of microarrays and machine learning analytical approaches will be a powerful approach to understanding the interaction of dolphins with the marine environment

Seasonal Variation in the Skin Transcriptome of Common Bottlenose Dolphins (Tursiops truncatus) from the Northern Gulf of Mexico

“…In all further analyses we used a set of 21,978 probes consisting of only probes present in both males and females, minus 4 probes that were more than two-fold different in expression between the two sexes. Sex-specific gene expression patterns, previously reported in the blood of bottlenose dolphins [ 12 ], were shown to have an impact on the ability to use transcriptome profiles for classification.…”

“…Since genes function in networks of coordinated pathways, the measurement of global gene expression has the potential to more precisely define the health and physiological status of cetaceans from integument biopsies. Microarray analysis of blood in bottlenose dolphins demonstrated global gene expression patterns that differed between populations from different estuaries in the southeast US and Gulf of Mexico [ 12 ]. Yet, blood transcriptomes were predictive of PCB contaminant concentrations in blubber, independent of sampling location [ 13 ].…”

Health status, infection and disease in California sea lions (Zalophus californianus) studied using a canine microarray platform and machine-learning approaches

“…Raw intensity microarray data for the 73 animal samples hybridized were variance stabilized normalization (VSN) transformed (Huber et al, 2002) and 500 genes showing the greatest statistical significance (lowest p-value) in pair wise comparisons of each group were selected using t-tests (Table S3). These genes were then used in artificial neural network (ANN) modeling following established protocols (Chapman et al, 2009;Mancia et al, 2010). The comparisons were balanced by randomly selecting roughly 70% of the individuals from the smaller of the groups compared and randomly selecting an equal number of individuals from the larger group.…”

“…Third, wild populations are often heterogeneous in their genetic structure, habitats and life style. Despite these limitations, studies utilizing large data sets (especially transcriptomic information) have been attempted, with some success, in the context of both the ecology and the health status of wild populations (Mancia et al, 2010(Mancia et al, , 2008.…”

New Technologies for Monitoring Marine Mammal Health

“…It was a species-specific cDNA microarray containing 1395 unigenes selected from targeted cloning and T and B cells cDNA libraries features (Mancia et al, 2007). The first microarray was useful for stress response and immune function studies in wild dolphins (Mancia et al, 2008(Mancia et al, , 2010. The blood transcriptome reveled that (1) the dolphin immune system mechanisms have high similarity to those of humans and other terrestrial mammals; (2) the immune system of the dolphins, resident inhabitants of coastal locations of temperate waters worldwide, reflects the environmental condition in which they live; and (3) the sampling method impact on downstream analysis underlines the need for species-specific baseline data.…”