Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters?

The conservation of humpback dolphins, distributed in coastal waters of the Indo‐West Pacific and eastern Atlantic Oceans, has been hindered by a lack of understanding about the number of species in the genus (Sousa) and their population structure. To address this issue, we present a combined analysis of genetic and morphologic data collected from beach‐cast, remote‐biopsied and museum specimens from throughout the known Sousa range. We extracted genetic sequence data from 235 samples from extant populations and explored the mitochondrial control region and four nuclear introns through phylogenetic, population‐level and population aggregation frameworks. In addition, 180 cranial specimens from the same geographical regions allowed comparisons of 24 morphological characters through multivariate analyses. The genetic and morphological data showed significant and concordant patterns of geographical segregation, which are typical for the kind of demographic isolation displayed by species units, across the Sousa genus distribution range. Based on our combined genetic and morphological analyses, there is convincing evidence for at least four species within the genus (S. teuszii in the Atlantic off West Africa, S. plumbea in the central and western Indian Ocean, S. chinensis in the eastern Indian and West Pacific Oceans, and a new as‐yet‐unnamed species off northern Australia).     

Pooled sample-based GWAS: a cost-effective alternative for identifying colorectal and prostate cancer risk variants in the Polish population

Background

Prostate cancer (PCa) and colorectal cancer (CRC) are the most commonly diagnosed cancers and cancer-related causes of death in Poland. To date, numerous single nucleotide polymorphisms (SNPs) associated with susceptibility to both cancer types have been identified, but their effect on disease risk may differ among populations.

Methods

To identify new SNPs associated with PCa and CRC in the Polish population, a genome-wide association study (GWAS) was performed using DNA sample pools on Affymetrix Genome-Wide Human SNP 6.0 arrays. A total of 135 PCa patients and 270 healthy men (PCa sub-study) and 525 patients with adenoma (AD), 630 patients with CRC and 690 controls (AD/CRC sub-study) were included in the analysis. Allele frequency distributions were compared with t-tests and χ²-tests. Only those significantly associated SNPs with a proxy SNP (p<0.001; distance of 100 kb; r²>0.7) were selected. GWAS marker selection was conducted using PLINK. The study was replicated using extended cohorts of patients and controls. The association with previously reported PCa and CRC susceptibility variants was also examined. Individual patients were genotyped using TaqMan SNP Genotyping Assays.

Results

The GWAS selected six and 24 new candidate SNPs associated with PCa and CRC susceptibility, respectively. In the replication study, 17 of these associations were confirmed as significant in additive model of inheritance. Seven of them remained significant after correction for multiple hypothesis testing. Additionally, 17 previously reported risk variants have been identified, five of which remained significant after correction.

Conclusion

Pooled-DNA GWAS enabled the identification of new susceptibility loci for CRC in the Polish population. Previously reported CRC and PCa predisposition variants were also identified, validating the global nature of their associations. Further independent replication studies are required to confirm significance of the newly uncovered candidate susceptibility loci.     

Histone H3 lysine 27 acetylation is altered in colon cancer

Background

Histone post-translational modifications (PTMs) play an important role in the regulation of the expression of genes, including those involved in cancer development and progression. However, our knowledge of PTM patterns in human tumours is limited.

Methods

MS-based analyses were used to quantify global alterations of histone PTMs in colorectal cancer (CRC) samples. Histones isolated from 12 CRCs and their corresponding normal mucosa by acidic extraction were separated by SDS-PAGE and analysed by liquid chromatography-mass spectrometry.

Results

Among 96 modified peptides, 41 distinct PTM sites were identified, of which 7, 13, 11, and 10 were located within the H2A, H2B, H3, and H4 sequences, respectively, and distributed among the amino-terminal tails and the globular domain of the four histones. Modification intensities were quantified for 33 sites, of which 4 showed significant (p-value ≤ 0.05) differences between CRC tissues and healthy mucosa samples. We identified histone H3 lysine 27 acetylation (H3K27Ac) as a modification upregulated in CRC, which had not been shown previously.

Conclusions

The present results indicate the usefulness of a bottom-up proteomic approach for the detection of histone modifications at a global scale. The differential abundance of H3K27Ac mark in CRC, a PTM associated with active enhancers, suggests its role in regulating genes whose expression changes in CRC.     

HABITAT USE AND PREFERENCES OF INDO-PACIFIC HUMPBACK DOLPHINS SOUSA CHINENSIS IN ALGOA BAY, SOUTH AFRICA

This paper examines environmental and behavioral determinants of the habitat use and preferences of Indo-Pacific humpback dolphins inhabiting the Algoa Bay region on the south Eastern Cape coast of South Africa. In order to quantify the habitat use and preference, two indices were used, the Coefficient of Area Use (AU) and the Activity Index (AI). The dolphins inhabit a narrow strip of shallow, inshore waters of Algoa Bay and remain mostly within 400 m of the shore, in water less than 15 m deep, with no apparent preference for clear or turbid water. Water depth is probably the main factor limiting their inshore distribution, and the 25-m isobath seems to represent the critical depth. Within this confined, inshore distribution, dolphin activities concentrate in the vicinity of rocky reefs-their primary feeding grounds. Dolphin dependence on these shallow-water habitats is evident throughout the year and, consequently, the inshore shallow reefs are identified as the "key habitat" which is of primary importance for humpback dolphins in Eastern Cape waters. The dolphins' dependence on this restricted type of habitat within an already restricted inshore distribution makes them particularly vulnerable to alteration or loss of this habitat.     

Spinner dolphins in a remote Hawaiian atoll: social grouping and population structure

Spinner dolphins (Stenella longirostris) commonly use inshoreisland and atoll habitats for daytime rest and social interactionsand forage over deep waters at night. In Hawaii, they occurthroughout the archipelago. We applied photoidentification mark-recapturetechniques to study the population structure of spinner dolphinsassociated with remote Midway Atoll, far-western Hawaii. AtMidway, spinner dolphins live in stable bisexually bonded societiesof long-term associates, with strong geographic fidelity, noobvious fission-fusion, and limited contacts with other populations.Their large cohesive groups change little over time and arebehaviorally/socially discrete from other spinner dolphin groups.This social pattern differs considerably from the fluid fission-fusionmodel proposed previously for spinner dolphins associated witha large island habitat in the main Hawaiian Archipelago. Thesedifferences correspond to geographic separation and habitatvariation. While in the main islands there are several daytimeresting places available at each island habitat; in far-westernHawaii, areas of suitable habitat are limited and separatedby large stretches of open pelagic waters with potentially highrisk of shark predation. We hypothesize that with deepwaterfood resources in close proximity and other atolls relativelyfar away for easy (day-to-day) access, it is energetically morebeneficial in the remote Hawaiian atolls to remain "at home"than to travel to other atolls, so there is stability insteadof variability; there is no fission-fusion effect. Thus, thegeographic isolation and small size of remote atolls triggera process in which the fluidity of the fission-fusion spinnerdolphin society is replaced with long-term group fidelity andsocial stability.     

The evolving male: spinner dolphin (Stenella longirostris) ecotypes are divergent at Y chromosome but not mtDNA or autosomal markers

The susceptibility of the Y chromosome to sexual selection may make this chromosome an important player in the formation of reproductive isolating barriers, and ultimately speciation. Here, we investigate the role of the Y chromosome in phenotypic divergence and reproductive isolation of spinner dolphin (Stenella longirostris) ecotypes. This species contains six known ecotypes (grouped into four subspecies) that exhibit striking differences in morphology, habitat and mating system, despite having adjacent or overlapping ranges and little genetic divergence at previously studied mtDNA and autosomal markers. We examined the phylogeographic structure for all six ecotypes across the species range (n = 261, 17 geographic locations) using DNA sequences from three Y chromosome markers, two maternally inherited mitochondrial (mtDNA) markers, and a biparentally inherited autosomal intron. mtDNA and autosomal analyses revealed low divergence (most Φ_ST values <0.1) between ecotypes and geographic regions, concordant with previous studies. In contrast, Y intron analyses revealed fixed differences amongst the three most phenotypically divergent groups: S. l. longirostris vs. S. l. roseiventris vs. combined S. l. orientalis/S. l. centroamericana/Tres Marias ecotypes). Another ecotype (whitebelly), previously postulated to be a hybrid between the two phenotypically most divergent ecotypes, had Y haplotypes from both putative parent ecotypes, supporting a hybrid designation. Reduced introgression of the Y chromosome has previously been observed in other organisms ranging from insects to terrestrial mammals, and here we demonstrate this phenomenon in a marine mammal with high dispersal capabilities. These results indicate that reduced introgression of the Y chromosome occurs in a wide taxonomic range of organisms and support the growing body of evidence that rapid evolution of the Y chromosome is important in evolutionary diversification.     

Landscape of the hnRNP K protein-protein interactome

The heterogeneous nuclear ribonucleoprotein K is an ancient RNA/DNA-binding protein that is involved in multiple processes that compose gene expression. The pleiotropic action of K protein reflects its ability to interact with different classes of factors, interactions that are regulated by extracellular signals. We used affinity purification and MS to better define the repertoire of K protein partners. We identified a large number of new K protein partners, some typically found in subcellular compartments, such as plasma membrane, where K protein has not previously been seen. Electron microscopy showed K protein in the nucleus, cytoplasm, mitochondria, and in vicinity of plasma membrane. These observations greatly expanded the view of the landscape of K protein-protein interaction and provide new opportunities to explore signal transduction and gene expression in several subcellular compartments.     

Area utilization patterns of humpback dolphins (Sousa plumbea) in Richards Bay, KwaZulu-Natal, South Africa

Geographically referenced data on humpback dolphin (Sousa plumbea) distribution and behaviour were collected in Richards Bay, South Africa, between 1998 and 2006. Utilization distributions presented a clear pattern in the distribution of dolphin activities and use of various locations within the study area. The 50 % kernel density estimate (core area) for foraging/feeding (2.1 km²) was clustered around the harbour mouth (including the shark net installation). The core areas for resting, socialising and travelling were more widespread (>2.95 km²). A mixed effects model indicated that location (longitude and latitude), distance from shore, year and group size are important variables in predicting foraging/feeding behaviour as opposed to other behaviours. The resting core was found in the southern part of study area and socialising was less clustered. This indicates preferential use of certain areas for specific behaviours. The overlap of foraging/feeding areas with stationary fishing gear (shark nets) and boat traffic are a major concern due to the risk of human-induced incidental mortalities. Any future alteration of the coastal area of Richards Bay, particularly development in the harbour, should be considered carefully, as further intrusion into areas critical to humpback dolphins, such as their foraging grounds, will inevitably carry negative implications for this already severely impacted population.     

Daylight occurrence of humpback dolphins Sousa chinensis in Algoa Bay, South Africa

This paper describes the pattern of daylight occurrence of humpback dolphins Sousa chinensis in Algoa Bay, the Eastern Cape, South Africa, between May 1991 and May 1994. Two indices, the Sighting Index (SI) and the Total Recorded Dolphin Presence (TRDP), were used to quantify the dolphins' daylight occurrence. Humpback dolphins display a clear pattern of daylight occurrence in Algoa Bay and can be seen mostly in the morning, and, to a lesser extent, in the evening. This pattern varies little between seasons (with possible exception for the evening hours), follows the time of the solar day, is not related to the tidal cycle and is probably governed by the diurnal cycles of dolphins' prey.