Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces

BACKGROUND: Poorly preserved biological tissues have become an important source of DNA for a wide range of zoological studies. Measuring the quality of DNA obtained from these samples is often desired; however, there are no widely used techniques available for quantifying damage in highly degraded DNA samples. We present a general method that can be used to determine the frequency of polymerase blocking DNA damage in specific gene-regions in such samples. The approach uses quantitative PCR to measure the amount of DNA present at several fragment sizes within a sample. According to a model of random degradation the amount of available template will decline exponentially with increasing fragment size in damaged samples, and the frequency of DNA damage (λ) can be estimated by determining the rate of decline. RESULTS: The method is illustrated through the analysis of DNA extracted from sea lion faecal samples. Faeces contain a complex mixture of DNA from several sources and different components are expected to be differentially degraded. We estimated the frequency of DNA damage in both predator and prey DNA within individual faecal samples. The distribution of fragment lengths for each target fit well with the assumption of a random degradation process and, in keeping with our expectations, the estimated frequency of damage was always less in predator DNA than in prey DNA within the same sample (mean λ(predator )= 0.0106 per nucleotide; mean λ(prey )= 0.0176 per nucleotide). This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first to quantify the amount of predator and prey DNA present within individual faecal samples. CONCLUSION: We present an approach for characterizing mixed, highly degraded PCR templates such as those often encountered in ecological studies using non-invasive samples as a source of DNA, wildlife forensics investigations and ancient DNA research. This method will allow researchers to measure template quality in order to evaluate alternate sources of DNA, different methods of sample preservation and different DNA extraction protocols. The technique could also be applied to study the process of DNA decay

Fluctuating Environments, Sexual Selection and the Evolution of Flexible Mate Choice in Birds

Environmentally-induced fluctuation in the form and strength of natural selection can drive the evolution of morphology, physiology, and behavior. Here we test the idea that fluctuating climatic conditions may also influence the process of sexual selection by inducing unexpected reversals in the relative quality or sexual attractiveness of potential breeding partners. Although this phenomenon, known as ‘ecological cross-over’, has been documented in a variety of species, it remains unclear the extent to which it has driven the evolution of major interspecific differences in reproductive behavior. We show that after controlling for potentially influential life history and demographic variables, there are significant positive associations between the variability and predictability of annual climatic cycles and the prevalence of infidelity and divorce within populations of a taxonomically diverse array of socially monogamous birds. Our results are consistent with the hypothesis that environmental factors have shaped the evolution of reproductive flexibility and suggest that in the absence of severe time constraints, secondary mate choice behaviors can help prevent, correct, or minimize the negative consequences of ecological cross-overs. Our findings also illustrate how a basic evolutionary process like sexual selection is susceptible to the increasing variability and unpredictability of climatic conditions that is resulting from climate change

Consumption of crustaceans by megaherbivorous dinosaurs: dietary flexibility and dinosaur life history strategies

Abstract Large plant-eating dinosaurs are usually presumed to have been strictly herbivorous, because their derived teeth and jaws were capable of processing fibrous plant foods. This inferred feeding behavior offers a generalized view of dinosaur food habits, but rare direct fossil evidence of diet provides more nuanced insights into feeding behavior. Here we describe fossilized feces (coprolites) that demonstrate recurring consumption of crustaceans and rotted wood by large Late Cretaceous dinosaurs. These multi-liter coprolites from the Kaiparowits Formation are primarily composed of comminuted conifer wood tissues that were fungally degraded before ingestion. Thick fragments of laminar crustacean cuticle are scattered within the coprolite contents and suggest that the dinosaurian defecators consumed sizeable crustaceans that sheltered in rotting logs. The diet of decayed wood and crustaceans offered a substantial supply of plant polysaccharides, with added dividends of animal protein and calcium. Nevertheless, it is unlikely that the fossilized fecal residues depict year-round feeding habits. It is more reasonable to infer that these coprolites reflected seasonal dietary shifts—possibly related to the dinosaurs’ oviparous breeding activities. This surprising fossil evidence challenges conventional notions of herbivorous dinosaur diets and reveals a degree of dietary flexibility that is consistent with that of extant herbivorous birds

Variation in the fatty acid composition of the blubber in Cape fur seals (Arctocephalus pusillus pusillus) and the implications for dietary interpretation

Analysis of the fatty acid (FA) composition of blubber is a valuable tool in interpreting the diet of marine mammals. This technique is based on the principle that particular FA present in prey can be incorporated largely untransformed into predator adipose tissue stores, thereby providing biochemical signatures with which to identify prey species. Several studies of phocid seals and cetaceans have documented vertical stratification in the FA composition of blubber such that inferences about diet may vary greatly depending on the layer of the blubber that is analysed. It is not known whether blubber in otariid seals (fur seals and sea lions) also displays vertical stratification in FA composition. Furthermore, it is not known whether the FA composition of blubber is uniform in these species. In the present study, the vertical and regional variation in FA composition of blubber was investigated in seven adult female Cape fur seals (Arctocephalus pusillus pusillus). The proportion of monounsaturated fatty acids (MUFA) was greater in the outer (43.6&plusmn;1.3%) than inner portion (40.9&plusmn;1.2%; t20=5.59, P&lt;0.001) whereas the proportions were greater in the inner than outer portions for saturated fatty acids (23.6&plusmn;0.5% and 21.9&plusmn;0.6%, respectively, t20 = 5.31, P&lt;0.001) and polyunsaturated fatty acids (PUFA, 35.5&plusmn;0.7% and 34.5&plusmn;0.7%, respectively, t20 = 3.81, P &lt; 0.001). There was an inverse relationship between MUFA and PUFA in the blubber, independent of sampling location. In addition, with the exception of the inner portion from non-lactating females, blubber from the mammary area had the highest proportions of 18:1&omega;9c and total MUFA, followed by blubber from the rump and neck, suggesting that the deposition and mobilisation of blubber lipids may not be uniform around the body in otariid seals. These results support the need for blubber tissue to be sampled from the same site on animals, and to the full depth of the blubber layer, to minimise variation in FA profiles that could occur if different sites and depths were sampled. Such standardisation of sampling will further aid in interpreting diet in otariid seals using the FA Signature Analysis approach.<br /

Spatial avoidance of invading pastoral cattle by wild ungulates: insights from using point process statistics

Traditional rangelands in many developing countries are currently being encroached by cultivation, driving some herders to illegally use protected areas for grazing their cattle. Since cattle are an exotic species in these ecosystems, they might have an impact on the local wild herbivore communities, notably through competition. We used point pattern statistics to characterise the spatial relationships between wild ungulate species and cattle herds within a protected area in west Africa undergoing seasonal intrusions by cattle. We predicted that the wild ungulate species that are ecologically and morphologically similar to cattle, in terms of body mass and diet, would be more sensitive to grass depletion by cattle and would be separated from cattle to a larger extent. The spatial distribution of browsing and mixed-feeding antelopes did not seem to be affected much by cattle presence, whereas most grazing species showed spatial separation from cattle. Interestingly, elephants also showed significant separation from cattle herds. We discuss the likely processes that may have contributed to the observed spatial patterns. Thespatial displacement of certain wild species, including megaherbivores, affects the whole community structure and, thus, other components of the ecosystem