Utility of Mitochondrial DNA Barcodes in Species Conservation

Abstract:  Molecular tools are a standard part of many conservation studies and can be informative at many different levels of analysis, although there are inherent limitations and strengths of different genes or parts of genes to inform specific questions. Animal DNA barcodes, 600- to 800-base-pair segments of the mitochondrial gene cytochrome oxidase I, have been proposed as a means to quantify global biodiversity. Although mitochondrial (mt) DNA has a long history of use at the species level, recent analyses suggest that the use of a single gene, particularly mitochondrial, is unlikely to yield data that are balanced, universally acceptable, or sufficient in taxonomic scope to recognize many species lineages. Mitochondrial and nuclear genomes have different patterns of evolution and modes of inheritance, which can result in very different assessments of biodiversity. The ramifications of choosing a particular definition of species (species concept) need to be carefully considered because current efforts have designated DNA barcodes as the universal species concept without demonstrating its superiority over preexisting concepts. The results of such a barcoding paradigm may include a failure to recognize significant portions of biodiversity or nuclear/mitochondrial mixed lineages and could spuriously focus conservation resources on populations with relatively minor mtDNA divergence. DNA barcodes are most likely to provide potentially useful information for groups that are already well studied, and such taxa do not constitute the majority of biodiversity or those in most need of research attention. DNA barcode-length sequences are an important source of data but, when used alone or out of context, may offer only a fraction of the information needed to characterize species while taking resources from broader studies that could produce information essential to robust and informed conservation decisions.     

A Contemporary,Sex‐Limited Change in Body Size of an Estuarine Turtle in Response to Commercial Fishing

Abstract: Juvenile growth rate and adult body size are important components of life‐history strategies because of their direct impact on fitness. The diamondback terrapin (Malaclemys terrapin) is a sexually dimorphic, long‐lived turtle inhabiting brackish waters throughout the Atlantic and Gulf coasts of the United States. In parts of its range, terrapins face anthropogenically imposed mortality: juveniles of both sexes inadvertently enter commercial crab traps and drown. For adult females, the carapace eventually grows large enough that they cannot enter traps, whereas males almost never reach that critical size. We compared age structure, carapace dimensions, growth curves, and indices of sexual dimorphism for a Chesapeake Bay population of terrapins (where mortality of turtles is high due to crab traps) with contemporary terrapins from Long Island Sound and museum specimens from Chesapeake Bay (neither group subject to commercial crab traps). We also calculated the allochronic and synchronic rates of evolutionary change (haldanes) for males and females to measure the rate of trait change in a population or between populations, respectively. We found a dramatic shift to a younger male age structure, a decrease in the length of time to terminal female carapace size, a 15% increase in female carapace width, and an increase in sexual dimorphism in Chesapeake Bay. In a new twist, our results implicate a fishery in the selective increase in size of a reptilian bycatch species. These sex‐specific changes in life history and demography have implications for population viability that need to be considered when addressing conservation of this threatened turtle.     

Globalization of the Amazon Soy and Beef Industries: Opportunities for Conservation

Abstract:  Amazon beef and soybean industries, the primary drivers of Amazon deforestation, are increasingly responsive to economic signals emanating from around the world, such as those associated with bovine spongiform encephalopathy (BSE, "mad cow disease") outbreaks and China's economic growth. The expanding role of these economic "teleconnections" (coupled phenomena that take place in distant places on the planet) led to a 3-year period (2002–2004) of historically high deforestation rates. But it also increases the potential for large-scale conservation in the region as markets and finance institutions demand better environmental and social performance of beef and soy producers. Cattle ranchers and soy farmers who have generally opposed ambitious government regulations that require forest reserves on private property are realizing that good land stewardship—including compliance with legislation—may increase their access to expanding domestic and international markets and to credit and lower the risk of "losing" their land to agrarian reform. The realization of this potential depends on the successful negotiation of social and environmental performance criteria and an associated system of certification that are acceptable to both the industries and civil society. The foot-and-mouth eradication system, in which geographic zones win permission to export beef, may provide an important model for the design of a low-cost, peer-enforced, socioenvironmental certification system that becomes the mechanism by which beef and soy industries gain access to markets outside the Amazon.     

Cost‐Effectiveness of Translocation Options for a Threatened Waterbird

Abstract: Reintroduction of captive‐reared animals has become increasingly popular in recent decades as a conservation technique, but little is known of how demographic factors affect the success of reintroductions. We believe whether the increase in population persistence associated with reintroduction is sufficient to warrant the cost of rearing and relocating individuals should be considered as well. We examined the trade‐off between population persistence and financial cost of a reintroduction program for Crested Coots (Fulica cristata). This species was nearly extirpated from southern Europe due to unsustainable levels of hunting and reduction in amount and quality of habitat. We used a stochastic, stage‐based, single‐sex, metapopulation model with site‐specific parameters to examine the demographic effects of releasing juveniles or adults in each population for a range of durations. We parameterized the model with data from an unsuccessful reintroduction program in which juvenile captive‐bred Crested Coots were released between 2000 and 2009. Using economic data from the captive‐breeding program, we also determined whether the strategy that maximized abundance coincided with the least expensive strategy. Releasing adults resulted in slightly larger final abundance than the release of nonreproductive juveniles. Both strategies were equally poor in achieving a viable metapopulation, but releasing adults was 2–4 times more expensive than releasing juveniles. To obtain a metapopulation that would be viable for 30 years, fecundity in the wild would need to increase to the values observed in captivity and juvenile survival would need to increase to almost unity. We suggest that the most likely way to increase these vital rates is by increasing habitat quality at release sites.     

Biofuel Plantations on Forested Lands: Double Jeopardy for Biodiversity and Climate

Abstract: The growing demand for biofuels is promoting the expansion of a number of agricultural commodities, including oil palm (Elaeis guineensis). Oil‐palm plantations cover over 13 million ha, primarily in Southeast Asia, where they have directly or indirectly replaced tropical rainforest. We explored the impact of the spread of oil‐palm plantations on greenhouse gas emission and biodiversity. We assessed changes in carbon stocks with changing land use and compared this with the amount of fossil‐fuel carbon emission avoided through its replacement by biofuel carbon. We estimated it would take between 75 and 93 years for the carbon emissions saved through use of biofuel to compensate for the carbon lost through forest conversion, depending on how the forest was cleared. If the original habitat was peatland, carbon balance would take more than 600 years. Conversely, planting oil palms on degraded grassland would lead to a net removal of carbon within 10 years. These estimates have associated uncertainty, but their magnitude and relative proportions seem credible. We carried out a meta‐analysis of published faunal studies that compared forest with oil palm. We found that plantations supported species‐poor communities containing few forest species. Because no published data on flora were available, we present results from our sampling of plants in oil palm and forest plots in Indonesia. Although the species richness of pteridophytes was higher in plantations, they held few forest species. Trees, lianas, epiphytic orchids, and indigenous palms were wholly absent from oil‐palm plantations. The majority of individual plants and animals in oil‐palm plantations belonged to a small number of generalist species of low conservation concern. As countries strive to meet obligations to reduce carbon emissions under one international agreement (Kyoto Protocol), they may not only fail to meet their obligations under another (Convention on Biological Diversity) but may actually hasten global climate change. Reducing deforestation is likely to represent a more effective climate‐change mitigation strategy than converting forest for biofuel production, and it may help nations meet their international commitments to reduce biodiversity loss.     

Integrating Nonindigenous Aquatic Plant Control with Protection of Snail Kite Nests in Florida

The endangered snail kite (Rostrhamus sociabilis) feeds primarily on the freshwater apple snail (Pomacea paludosa) in Florida. The nonindigenous, floating water hyacinth (Eichhornia crassipes) and water lettuce (Pistia stratiotes) impede kites from finding snails. Effective control of these aquatic plants in the littoral zone of central and south Florida lakes benefits kites by maintaining open foraging habitat. However, incidental herbicide spraying of nesting substrates result in nest collapse when kites breed in nonwoody, emergent plants [cattail (Typha spp.) and giant bulrush (Scirpus validus)] in the outer littoral zone during lower lake levels. Many endangered species recovery plans and their implementation have experienced problems due to inaction and/or noncooperation by various governmental agencies and their personnel. Herein, we describe the development and implementation of a buffer zone strategy to prevent secondary impacts from an aquatic plant control program to snail kites nesting on lakes in central and south Florida. A strategy was jointly developed by personnel of five state and federal agencies to control herbicide application near kite nesting areas during the normal breeding season. Although requiring various modifications during its implementation, this cooperative effort successfully integrated aquatic plant control objectives with snail kite conservation on Lake Okeechobee during 1988. The program was expanded the following year to lakes Kissimmee and Tohopekaliga. Since the implementation of the snail kite impact preclusion program, no nest loss was attributed to incidental herbicide applications on lakes Okeechobee, Kissimmee, and Tohopekaliga.