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Accounting for female reproductive cycles in a superpopulation capture-recapture framework.
Ecol Appl. 2013 Oct;23(7):1677-90
Authors: Carroll EL, Childerhouse SJ, Fewster RM, Patenaude NJ, Steel D, Dunshea G, Boren L, Baker CS
Abstract Superpopulation capture-recapture models are useful for estimating the abundance of long-lived, migratory species because they are able to account for the fluid nature of annual residency at migratory destinations. Here we extend the superpopulation POPAN model to explicitly account for heterogeneity in capture probability linked to reproductive cycles (POPAN-tau). This extension has potential application to a range of species that have temporally variable life stages (e.g., non-annual breeders such as albatrosses and baleen whales) and results in a significant reduction in bias over the standard POPAN model. We demonstrate the utility of this model in simultaneously estimating abundance and annual population growth rate (lamda) in the New Zealand (NZ) southern right whale (Eubalaena australis) from 1995 to 2009. DNA profiles were constructed for the individual identification of more than 700 whales, sampled during two sets of winter expeditions in 1995-1998 and 2006-2009. Due to differences in recapture rates between sexes, only sex-specific models were considered. The POPAN-tau models, which explicitly account for a decrease in capture probability in non-calving years, fit the female data set significantly better than do standard superpopulation models (deltaAIC > 25). The best POPAN-tau model (AIC) gave a super-population estimate of 1162 females for 1995-2009 (95% CL 921, 1467) and an estimated annual increase of 5% (95% CL--2%, 13%). The best model (AIC) gave a superpopulation estimate of 1007 males (95% CL 794, 1276) and an estimated annual increase of 7% (95% CL 5%, 9%) for 1995-2009. Combined, the total superpopulation estimate for 1995-2009 was 2169 whales (95% CL 1836, 2563). Simulations suggest that failure to account for the effect of reproductive status on the capture probability would result in a substantial positive bias (+19%) in female abundance estimates.
PMID: 24261048 [PubMed - in process]
For those titillated by Strangelovian fantasies of nuclear apocalypse, the early 1980s were a golden age. That was the height of the Cold War, when nuclear arms and rhetoric escalated, and President Ronald Reagan envisioned a space-based anti-missile “shield”–promptly dubbed “Star Wars” by skeptics–that could thwart attacks by the “Evil Empire,” also known as the Soviet Union.
Late last week Texas public health officials confirmed a new wave of dengue fever has cropped up in the southernmost tip of Texas, marking the first outbreak the state has seen since 2005. The news came on the heels of reporting in Scientific American about how scientists are trying to uncover why the mosquito-borne infection is cropping up in Florida but not in other regions of the nation that host the same Aedes aegypti species of dengue-carrying mosquitoes.
GENETIC AND MORPHOLOGICAL APPROACHES DISTINGUISH THE THREE SIBLING SPECIES OF THE ANISAKIS SIMPLEX SPECIES COMPLEX, WITH A SPECIES DESIGNATION AS ANISAKIS BERLANDI N. SP. FOR A. SIMPLEX SP. C (NEMATODA: ANISAKIDAE).
J Parasitol. 2013 Nov 13;
Authors: Mattiucci S, Cipriani P, Webb SC, Paoletti M, Marcer F, Bellisario B, Gibson DI, Nascetti G
Abstract Abstract Numerous specimens of the three sibling species of the Anisakis simplex species complex (A. pegreffii, A. simplex (sensu stricto) and A. simplex sp. C), recovered from cetacean species stranded within the known geographical ranges of these nematodes, were studied morphologically and genetically. The genetic characterization was performed on diagnostic allozymes and sequences analysis of nuclear (ITS of rDNA) and mitochondrial (mtDNA cox2 and rrnS) genes. These markers showed: (i) the occurrence of sympatry of the two sibling species A. pegreffii and A. simplex sp. C in the same individual host, the pilot whale Globicephala melas, from New Zealand waters; (ii) the identification of specimens of A. pegreffii in the striped dolphin Stenella coeruleoalba from the Mediterranean Sea; (iii) the presence of A. simplex (s. s.) in the pilot whale G. melas and the minke whale Balaenoptera acutorostrata from the NE Atlantic waters. No F1 hybrids were detected among the three species using the nuclear markers. The phylogenetic inference, obtained by Maximum Parsimony (MP) analysis of separate nuclear (ITS rDNA region), combined mitochondrial (mtDNA cox2 and rrnS) sequences datasets, and by concatenated analysis obtained at both Maximum Parsimony (MP) and Bayesian (BI) phylogenetic inference of the sequences datasets at the three studied genes, resulted in a similar topology. They were congruent in depicting the existence of the three species as distinct phylogenetic lineages, and the tree topologies support the finding that A. simplex (s. s.), A. pegreffii and A. berlandi n. sp. (= A. simplex sp. C) represent a monophyletic group. The morphological and morphometric analyses revealed the presence of morphological features that differed between the three biological species. Morphological analysis using Principle Component Analysis, and Procrustes Analysis, combining morphological and genetic datasets, showed the specimens clustering into three well-defined groups. Nomenclatural designation and formal description are given for A. simplex species C: the name Anisakis berlandi n. sp. is proposed. Key morphological diagnostic traits are: between A. berlandi n. sp. and A. simplex (s. s.): ventriculus length, tail shape, tail length/total body length ratio and left spicule length/total body length ratio; between A. berlandi n. sp. and A. pegreffii: ventriculus length and plectane 1 width/plectane 3 width ratio; and between A. simplex (s. s.) and A. pegreffii: ventriculus length, left and right spicule length/total body length ratios and tail lengthy/total body length ratio. Ecological data pertaining to the geographical ranges and host distribution of the three species are updated.
PMID: 24224764 [PubMed - as supplied by publisher]
Highlighting pros and cons of abundance estimation using passive acoustic data: monitoring fin whales (Balaenoptera physalus) off the southern Portuguese coast using seismometers.
J Acoust Soc Am. 2013 Nov;134(5):3971
Authors: Harris D, Marques T, Matias L, Mellinger DK, Küsel ET, Thomas L
Abstract Monitoring marine mammals using passive acoustic sensors is increasingly popular. Generating abundance estimates from acoustic data would be extremely useful for marine environment stakeholders. To achieve accurate abundance estimates, there are three broad areas to consider: (1) survey design, (2) data collection and processing, and (3) data analysis. Here, we use an analysis of fin whale (Balaenoptera physalus) calls recorded on ocean bottom seismometers (OBSs) to discuss the main advantages, disadvantages and considerations of abundance estimation using acoustic data. The OBS array was deployed for one year (2007-2008) and demonstrates how an opportunistic dataset can meet survey design requirements. Ranges to detected calls (detected with a matched filter) were estimated using the seismological three-component method. Point transect sampling, an abundance estimation method, was then used to estimate average call density. Animal density or abundance could not be estimated because the appropriate average calling rate was unknown. Finally, spatiotemporal patterns of call density were modeled. This dataset has also allowed new methods development-a method that estimates abundance as a function of total energy in a species' frequency band has been developed. In summary, abundance estimation using acoustic data is possible but challenging, and improved knowledge of vocal behavior is essential.
PMID: 24180873 [PubMed - as supplied by publisher]
Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations.
Nat Commun. 2013 Oct 29;4:2708
Authors: Zhou X, Sun F, Xu S, Fan G, Zhu K, Liu X, Chen Y, Shi C, Yang Y, Huang Z, Chen J, Hou H, Guo X, Chen W, Chen Y, Wang X, Lv T, Yang D, Zhou J, Huang B, Wang Z, Zhao W, Tian R, Xiong Z, Xu J, Liang X, Chen B, Liu W, Wang J, Pan S, Fang X, Li M, Wei F, Xu X, Zhou K, Wang J, Yang G
Abstract The baiji, or Yangtze River dolphin (Lipotes vexillifer), is a flagship species for the conservation of aquatic animals and ecosystems in the Yangtze River of China; however, this species has now been recognized as functionally extinct. Here we report a high-quality draft genome and three re-sequenced genomes of L. vexillifer using Illumina short-read sequencing technology. Comparative genomic analyses reveal that cetaceans have a slow molecular clock and molecular adaptations to their aquatic lifestyle. We also find a significantly lower number of heterozygous single nucleotide polymorphisms in the baiji compared to all other mammalian genomes reported thus far. A reconstruction of the demographic history of the baiji indicates that a bottleneck occurred near the end of the last deglaciation, a time coinciding with a rapid decrease in temperature and the rise of eustatic sea level.
PMID: 24169659 [PubMed - in process]
For years, biologists have argued over the number of species of humpback dolphins. Recent research somewhat settles the debate, as a team of biologists have discovered at least four distinct species – one of which had previously gone unnoticed.
Evaluation of Potential Protective Factors Against Metabolic Syndrome in Bottlenose Dolphins: Feeding and Activity Patterns of Dolphins in Sarasota Bay, Florida.
Front Endocrinol (Lausanne). 2013;4:139
Authors: Wells RS, McHugh KA, Douglas DC, Shippee S, McCabe EB, Barros NB, Phillips GT
Abstract Free-ranging bottlenose dolphins (Tursiops truncatus) living in Sarasota Bay, Florida appear to have a lower risk of developing insulin resistance and metabolic syndrome compared to a group of dolphins managed under human care. Similar to humans, differences in diet and activity cycles between these groups may explain why Sarasota dolphins have lower insulin, glucose, and lipids. To identify potential protective factors against metabolic syndrome, existing and new data were incorporated to describe feeding and activity patterns of the Sarasota Bay wild dolphin community. Sarasota dolphins eat a wide variety of live fish and spend 10-20% of daylight hours foraging and feeding. Feeding occurs throughout the day, with the dolphins eating small proportions of their total daily intake in brief bouts. The natural pattern of wild dolphins is to feed as necessary and possible at any time of the day or night. Wild dolphins rarely eat dead fish or consume large amounts of prey in concentrated time periods. Wild dolphins are active throughout the day and night; they may engage in bouts of each key activity category at any time during daytime. Dive patterns of radio-tagged dolphins varied only slightly with time of day. Travel rates may be slightly lower at night, suggesting a diurnal rhythm, albeit not one involving complete, extended rest. In comparison, the managed dolphins are older; often fed a smaller variety of frozen-thawed fish types; fed fish species not in their natural diet; feedings and engaged activities are often during the day; and they are fed larger but fewer meals. In summary, potential protective factors against metabolic syndrome in dolphins may include young age, activity, and small meals fed throughout the day and night, and specific fish nutrients. These protective factors against insulin resistance and type 2 diabetes are similar to those reported in humans. Further studies may benefit humans and dolphins.
PMID: 24133483 [PubMed - as supplied by publisher]
Read more of this story at Slashdot.
Allie and Bailey knew each other when they both lived in Florida. More than 20 years later, Allie lives near Chicago and Bailey lives in Bermuda, but Allie’s name still rings a bell for Bailey. That would not be breaking news, except that Allie and Bailey are not people: they are dolphins.
Identification of Lactobacillus Strains with Probiotic Features from the Bottlenose Dolphin (Tursiops truncatus).
J Appl Microbiol. 2013 Jul 15;
Authors: Diaz MA, Bik EM, Carlin KP, Venn-Watson SK, Jensen ED, Jones SE, Gaston EP, Relman DA, Versalovic J
Abstract AIMS: In order to develop complementary health management strategies for marine mammals, we used culture-based and culture-independent approaches to identify gastrointestinal lactobacilli of the common bottlenose dolphin, Tursiops truncatus. METHODS AND RESULTS: We screened 307 bacterial isolates from oral and rectal swabs, milk, and gastric fluid, collected from 38 dolphins in the U.S. Navy Marine Mammal Program, for potentially beneficial features. We focused our search on lactobacilli and evaluated their ability to modulate TNF secretion by host cells and inhibit growth of pathogens. We recovered Lactobacillus salivarius strains which secreted factors that stimulated TNF production by human monocytoid cells. These L. salivarius isolates inhibited growth of selected marine mammal and human bacterial pathogens. In addition, we identified a novel Lactobacillus species by culture and direct sequencing with 96.3% 16S rDNA sequence similarity to Lactobacillus ceti. CONCLUSIONS: Dolphin-derived L. salivarius isolates possess features making them candidate probiotics for clinical studies in marine mammals. SIGNIFICANCE AND IMPACT OF STUDY: This is the first study to isolate lactobacilli from dolphins, including a new strain of L. salivarius, with potential for veterinary probiotic applications. The isolation and identification of novel Lactobacillus spp. and other indigenous microbes from bottlenose dolphins will enable the study of the biology of symbiotic members of the dolphin microbiota and facilitate the understanding of the microbiomes of these unique animals. This article is protected by copyright. All rights reserved.
PMID: 23855505 [PubMed - as supplied by publisher]