Assessing reliability of microsatellite genotypes from kit fox faecal samples using genetic and GIS analyses.

Noninvasive faecal DNA sampling has the potential to provide a wealth of information necessary for monitoring and managing endangered species while eliminating the need to capture, handle or observe rare individuals. However, scoring problems, and subsequent genotyping errors, associated with this monitoring method remain a great concern as they can lead to misidentification of individuals and biased estimates. We examined a kit fox scat data set (353 scats; 80 genotypes) for genotyping errors using both genetic and GIS analyses, and evaluated the feasibility of combining both approaches to assess reliability of the faecal DNA results. We further checked the appropriateness of using faecal genotypes to study kit fox populations by describing information about foxes that we could deduce from the 'acceptable' scat genotypes, and comparing it to information gathered with traditional field techniques. Overall, genetic tests indicated that our data set had a low rate of genotyping error. Furthermore, examination of distributions of scat locations confirmed our data set was relatively error free. We found that analysing information on sex primer consistency and scat locations provided a useful assessment of scat genotype error, and greatly limited the amount of additional laboratory work that was needed to identify potentially 'false' scores. 'Acceptable' scat genotypes revealed information on sex ratio, relatedness, fox movement patterns, latrine use, and size of home range. Results from genetic and field data were consistent, supporting the conclusion that our data set had a very low rate of genotyping error and that this noninvasive method is a reliable approach for monitoring kit foxes.

A noninvasive method for distinguishing among canid species: amplification and enzyme restriction of DNA from dung.

Endangered San Joaquin kit foxes Vulpes macrotis mutica can be sympatrically distributed with as many as four other canids: red fox, gray fox, coyote and domestic dog. Canid scats are often found during routine fieldwork, but cannot be reliably identified to species. To detect and study the endangered kit fox, we developed mitochondrial DNA markers that can be amplified from small amounts of DNA extracted from scats. We amplified a 412-bp fragment of the mitochondrial cytochrome-b gene from scat samples and digested it with three restriction enzymes. The resulting restriction profiles discriminated among all five canid species and correctly identified 10 'unknown' fox scats to species in blind tests. We have applied our technique to identify canids species for an environmental management study and a conservation study. We envision that our protocol, and similar ones developed for other endangered species will be greatly used for conservation management in the future.

Elephant seal genetic variation and the use of simulation models to investigate historical population bottlenecks.

Because the northern elephant seal (Mirounga angustirostrus) was heavily exploited during the 19th century, it experienced an extreme population bottleneck. Since then, under legislative protection in the United States and Mexico, northern elephant seals have recovered dramatically in number, although their genomic diversity was greatly reduced, apparently as a consequence of the bottleneck. In this study we investigated DNA sequence diversity in two mtDNA regions (the control region and 16S RNA) and found low genetic variation in the northern elephant seal: there were only two control region haplotypes (sequence difference = 1%), which was consistent with an extreme founder event in the recent history of the northern species. We also reaffirmed the lack of allozyme diversity in this species. In contrast, the southern elephant seal (M. leonina), which though similarly exploited never fell below 1,000 animals, had 23 control region mtDNA haplotypes (average sequence difference = 2.3%). To investigate the extent of the founder event in the northern elephant seal we devised a simulation model based on extensive demographic data. This allowed a statistical analysis of the likely outcome of bottlenecks of different size and duration. Given these historical data, our results indicate (within 95% confidence) a bottleneck of less than 30 seals and 20-year duration, or, if hunting was the primary pressure on the population, a single-year bottleneck of less than 20 seals.

Captive breeding programs for populations with a small number of founders.

Small captive populations are likely to become extinct. Detailed breeding plans based on the principles of population genetics and demography can greatly increase their chances of long-term survival. Zoos have now begun to implement such plans but lack the resources to extend them to the many species that are likely to become extinct in the wild in the near future.

Effect of inbreeding on juvenile mortality in some small mammal species.

In breeding records for 12 species of small mammals from 9 families in 3 orders, individuals with an inbreeding coefficient of 0 were classified as non-inbred, those with inbreeding coefficients greater than 0 as inbred. Juvenile mortality was defined as all deaths prior to 1/2 of the age of sexual maturity for each species. It was significantly higher for inbred than for noninbred animals in 11 of the 12 species using a 1-tailed sign test, and by Fisher's exact test in 3 species. Monodelphis domestica, Wiedomys pyrrhorhinos and and Dolichotis salinicola. The higher mortality of inbred young of the species with the largest sample size, Elephantulus rufescens, was irrespective of litter size and of the parity of the dam.

Inbreeding and juvenile mortality in small populations of ungulates.

Juvenile mortality of inbred young was higher than that of noninbred young in 15 of 16 species of captive ungulates. In 19 of 25 individual females, belonging to ten species, a larger percentage of young died when the female was mated to a related male than when she was mated to an unrelated male.

Mammals in which females are larger than males.

Females are larger than males in more species of mammals than is generally supposed. A provisional list of the mammalian cases is provided. The phenomenon is not correlated with an unusually large degree of male parental investment, polyandry, greater aggressiveness in females than in males, greater development of weapons in females, female dominance, or matriarchy. The phenomenon may have evolved in a variety of ways, but it is rarely, if ever, the result of sexual selection acting upon the female sex. The most common selective pressures favoring large size in female mammals are probably those associated with the fact that a big mother is often a better mother and those resulting from more intense competintion among females for some resource than among males. It appears that, in general, more than one such pressure must affect the females of a species, and that their combined effects must not be countered by even stronger selective pressures favoring large size in males, before the result is that of larger size in the female sex. Sexual selection may often be operating upon the male sux in mammals even when it is smaller. Present knowledge about the species of mammals in which females are lager than males is quite rudimentary. Much more information is needed before we will be able to speak of the selective pressures accounting for the phenomenon with any reasomable degree of certainty. Perhaps the most fruitful approach would be a series of field studies of groups of related species in which females are larger in some species and males are larger in others.

Behavior of captive mouse deer, Tragulus napu.

1. The behavior of a breeding colony of larger Malayan mouse deer was observed for seven months. 2. Mouse deer produce a noise by stamping with one or both hind feet when slightly alarmed. Other individuals may or may not stamp in response. 3. Both males and females mark objects with the inter-mandibular gland. Males mark much more frequently than females. 4. Males often lick the urine of females; less frequently, females lick the urine of males. Mouse deer do not "flehmen" in response to urine. 5. Males court both receptive and unreceptive females. Courting males mark the female on the back or rump with the inter-mandibular gland and emit a series of squeaks. The behavior of both unreceptive and receptive females and copulation are described. 6. Females have a post-partum estrus and return to estrus at approximately 14 day intervals unless they become pregnant. 7. Mothers spend little time with infants. Mothers emit a vocalization which sounds like the squeak of courting males. Both mothers and infants emit a higher pitched vocalization. If her infant emitted this vocalization the mother answered and approached and stood by it. The mother nurses in a standing position and raises the hind leg on the side towards the infant. 8. Intense agonistic behavior was seen only when strange individuals were introduced into established groups. Males fight by facing each other and biting each other on the ears, neck, and shoulders with their large upper canines. Fighting males usually hold the tail in a vertical position, exposing the white ventral surface, and may emit loud growls. If one male flees, the other pursues and attempts to bite him on the neck and body. 9. Mouse deer are morphologically primitive and many of their motor patterns are also thought to be primitive. 10. The behavior of all four living tragulid species appears to be quite similar, both with respect to motor patterns and social behavior.

Mammalian scent marking.

Mammals mark frequently in any situation where they are both intolerant of and dominant to other members of the same species. In other words, they mark when they are likely to attack another member of the same species, and are likely to win if they do attack. Such a situation occurs, as Hediger (13) pointed out, in connection with territoriality but it also occurs in other kinds of social systems. Frequent, vigorous marking occurs at times when there is reason to infer that the animal is motivated to aggression. The effects of marks and marking upon other individuals are poorly understood. Many species mark with more than one source of scent in response to one stimulus or set of stimuli.