A Test of Computer-assisted Matching Using the North Pacific Humpback Whale, Megaptera novaeangliae, Tail Flukes Photograph Collection

Testing was conducted of a computer-assisted system for matching humpback whale tail flukes photographs. Trials with a 12,000-photographs database found no differences in match success between matching by computer and matching by comparing smaller catalogs ranging in size from 200 to 400 photographs. Tests with a 24,000-photographs database showed that, on average, the first match was found after examining about 130 photographs whether the photograph quality was excellent, good, or poor. Match success did not appear to be strongly related to whether the tail flukes had especially distinctive markings or pigment patterns (recognition quality). An advantage of computer-assisted matching is the ability to compare new photographs to the entire North Pacific collection, where no bias is introduced based on expectation of resightings within or between specific areas, or based on expectation of behavioral role (e.g. matching “known” females to “known” females).

Agassiz, Garman, Albatross, and the Collection of Deep-sea Fishes

The first of Alexander Agassiz’ voyages on the U.S. Fish Commission steamer Albatross in 1891 yielded significant scientific results. This paper reviews the background of the voyage, including the career path that led Agassiz to the back deck of the Albatross. We also give a brief account of the life and work of Samuel Garman. Garman wrote up the ichthyological material from this Albatross voyage in a magnificent book on deep-sea fishes published in 1899. This book was exceptional in its coverage, anatomical detail, and recognition of phylogenetically important morphology.

Reserved parking : marine reserves and small-scale fishing communities: a collection of articles from SAMUDRA report

As the earth’s resources continue to face increasing pressure from a variety of human and natural causes, protection of the environment and biodiversity is a matter of contemporary concern, The conservation of coastal and marine resources, in particular, has become a priority for countries around the world. In this context, marine protected areas (MPAs) are being widely promoted as one of the most effective tools for the conservation of coastal and marine resources. Most MPAs are located in coastal areas of great biodiversity, and hence their development has direct impacts on the lives and livelihoods of coastal communities, especially small-scale and traditional fishing communities. Typically, they are the ones who have to bear the costs of conservation practices–lost livelihood options, expulsion from traditional fishing grounds and living spaces, and violation of human/community rights, to name a few. The articles in this dossier, drawn chronologically from the pages of Samudra Report, the triannual publication of ICSF, draw attention to these issues. They show that conservation and livelihoods are closely intertwined, and that top-down, non-participatory models of conservation can be counter-productive. Despite being poor and powerless, fishing and coastal communities can be powerful allies in conservation efforts, given their longstanding dependence on natural resources and their traditional ecological knowledge systems. As the examples in this dossier reveal, it is possible for fishing communities to protect and conserve the environment, while continuing with sustainable fishing operations. Clearly, only an integrated approach to fisheries management and conservation will prove successful. This dossier will be useful for policymakers, social scientists, non-governmental organizations and others interested in fisheries, conservation, communities and livelihoods.

Saline-saturated DMSO-EDTA as a storage medium for microbial DNA analysis from coral mucus swab samples

The mucus surface layer of corals plays a number of integral roles in their overall health and fitness. This mucopolysaccharide coating serves as vehicle to capture food, a protective barrier against physical invasions and trauma, and serves as a medium to host a community of microorganisms distinct from the surrounding seawater. In healthy corals the associated microbial communities are known to provide antibiotics that contribute to the coral’s innate immunity and function metabolic activities such as biogeochemical cycling. Culture-dependent (Ducklow and Mitchell, 1979; Ritchie, 2006) and culture-independent methods (Rohwer, et al., 2001; Rohwer et al., 2002; Sekar et al., 2006; Hansson et al., 2009; Kellogg et al., 2009) have shown that coral mucus-associated microbial communities can change with changes in the environment and health condition of the coral. These changes may suggest that changes in the microbial associates not only reflect health status but also may assist corals in acclimating to changing environmental conditions. With the increasing availability of molecular biology tools, culture-independent methods are being used more frequently for evaluating the health of the animal host. Although culture-independent methods are able to provide more in-depth insights into the constituents of the coral surface mucus layer’s microbial community, their reliability and reproducibility rely on the initial sample collection maintaining sample integrity. In general, a sample of mucus is collected from a coral colony, either by sterile syringe or swab method (Woodley, et al., 2008), and immediately placed in a cryovial. In the case of a syringe sample, the mucus is decanted into the cryovial and the sealed tube is immediately flash-frozen in a liquid nitrogen vapor shipper (a.k.a., dry shipper). Swabs with mucus are placed in a cryovial, and the end of the swab is broken off before sealing and placing the vial in the dry shipper. The samples are then sent to a laboratory for analysis. After the initial collection and preservation of the sample, the duration of the sample voyage to a recipient laboratory is often another critical part of the sampling process, as unanticipated delays may exceed the length of time a dry shipper can remain cold, or mishandling of the shipper can cause it to exhaust prematurely. In remote areas, service by international shipping companies may be non-existent, which requires the use of an alternative preservation medium. Other methods for preserving environmental samples for microbial DNA analysis include drying on various matrices (DNA cards, swabs), or placing samples in liquid preservatives (e.g., chloroform/phenol/isoamyl alcohol, TRIzol reagent, ethanol). These methodologies eliminate the need for cold storage, however, they add expense and permitting requirements for hazardous liquid components, and the retrieval of intact microbial DNA often can be inconsistent (Dawson, et al., 1998; Rissanen et al., 2010). A method to preserve coral mucus samples without cold storage or use of hazardous solvents, while maintaining microbial DNA integrity, would be an invaluable tool for coral biologists, especially those in remote areas. Saline-saturated dimethylsulfoxide-ethylenediaminetetraacetic acid (20% DMSO-0.25M EDTA, pH 8.0), or SSDE, is a solution that has been reported to be a means of storing tissue of marine invertebrates at ambient temperatures without significant loss of nucleic acid integrity (Dawson et al., 1998, Concepcion et al., 2007). While this methodology would be a facile and inexpensive way to transport coral tissue samples, it is unclear whether the coral microbiota DNA would be adversely affected by this storage medium either by degradation of the DNA, or a bias in the DNA recovered during the extraction process created by variations in extraction efficiencies among the various community members. Tests to determine the efficacy of SSDE as an ambient temperature storage medium for coral mucus samples are presented here.

A study on damage caused to crustacean and finfish larvae during collection of Penaeus monodon (Fab.) postlarvae in the estuaries of Barguna, Bangladesh

A year round investigation in the estuaries of Barguna district revealed that for each Penaeus monodon postlarvae (PL), about 37 larvae of other shrimp species, 12 finfishes and 10 macrozooplankters are destroyed during the process of shrimp seed collection. Although abundance of P. monodon PL was not recorded throughout the year, a significant number of other shrimp spp., fin fishes including macrozooplankters are being damaged by the shrimp seed collectors. This indiscriminate destruction of aquatic organisms during P. monodon PL collection is serious threat to aquatic biodiversity.