Stephan M. Funk

Ecological factors influence population genetic structure of European grey wolves

Although the mechanisms controlling gene flow among populations are particularly important for evolutionary processes, they are still poorly understood, especially in the case of large carnivoran mammals with extensive continuous distributions. We studied the question of factors affecting population genetic structure in the grey wolf, Canis lupus, one of the most mobile terrestrial carnivores. We analysed variability in mitochondrial DNA and 14 microsatellite loci for a sample of 643 individuals from 59 localities representing most of the continuous wolf range in Eastern Europe. We tested an array of geographical, historical and ecological factors to check whether they may explain genetic differentiation among local wolf populations. We showed that wolf populations in Eastern Europe displayed nonrandom spatial genetic structure in the absence of obvious physical barriers to movement. Neither topographic barriers nor past fragmentation could explain spatial genetic structure. However, we found that the genetic differentiation among local populations was correlated with climate, habitat types, and wolf diet composition. This result shows that ecological processes may strongly influence the amount of gene flow among populations. We suggest natal‐habitat‐biased dispersal as an underlying mechanism linking population ecology with population genetic structure.

Flexible spatial organization of urban foxes, Vulpes vulpes, before and during an outbreak of sarcoptic mange

The social and spatial organization of urban fox groups prior to and during an outbreak of sarcoptic mange was compared with predictions derived from the resource dispersion hypothesis (RDH). We investigated the availability of three key resources. Neither daytime rest sites nor breeding sites appeared to be limited in availability. The availability of food deliberately supplied by local householders was examined by questionnaire surveys. The daily and weekly amount of food supplied was greatly in excess of the minimum requirements of a pair of foxes, but was consistent between territories. The availability of this food source increased markedly as a result of more people feeding the foxes. In agreement with the RDH, group size prior to the outbreak of mange increased from 2.25 animals (N=4) to 6.57 animals (N=7). Before the outbreak of mange, two territories were divided. Increased scavenge availability on smaller territories may have promoted these changes. Excluding these spatial changes, territories were very stable between years. After the outbreak of mange, group size declined as a direct result of mange-induced mortality. Surviving animals increased their ranges only after neighbouring groups had died out. Ranges did not increase in size in response to a decline in food availability. Nor were the increases in range size associated with the relinquishment of parts of the existing territory. These postmange changes are contrary to the RDH. Three factors may have promoted these changes: the elimination of interstitial space, the forced dispersal of young or future division of the territory. Copyright 2000 The Association for the Study of Animal Behaviour.

The city-fox phenomenon: genetic consequences of a recent colonization of urban habitat

The red fox (Vulpes vulpes) is one of the best‐documented examples of a species that has successfully occupied cities and their suburbs during the last century. The city of Zurich (Switzerland) was colonized by red foxes 15 years ago and the number of recorded individuals has increased steadily since then. Here, we assessed the hypothesis that the fox population within the city of Zurich is isolated from adjacent rural fox populations against the alternative hypothesis that urban habitat acts as a constant sink for rural dispersers. We examined 11 microsatellite loci in 128 foxes from two urban areas, separated by the main river crossing the city, and three adjacent rural areas from the region of Zurich. Mean observed heterozygosity across individuals and the number of detected alleles were lower for foxes collected within the city as compared with their rural conspecifics. Genetic differentiation was significantly lower between rural than between rural and urban populations, and highest value of pairwise FST was recorded between the two urban areas. Our results indicate that the two urban areas were independently founded by a small number of individuals from adjacent rural areas resulting in genetic drift and genetic differentiation between rural and urban fox populations. Population admixture and immigration analysis revealed that urban–rural gene flow was higher than expected from FST statistics. In the five to seven generations since colonization, fox density has dramatically increased. Currently observed levels of migration between urban and rural populations will probably erode genetic differentiation over time.

Patterns of nuclear DNA degeneration over time — a case study in historic teeth samples

The amount of nuclear DNA extracted from teeth of 279 individual red fox Vulpes vulpes collected over a period spanning the last three decades was determined by quantitative polymerase chain reaction (PCR). Although teeth were autoclaved during initial collection, 73.8% of extracts contained sufficient DNA concentration (> 5 pg/µL) suitable for reliable microsatellite genotyping but the quantity of nuclear DNA decayed significantly over time in a nonlinear pattern. The success of PCR amplification across four examined canine microsatellites over time was dependent on fragment size. By including data from two different tests for human contamination and from frequencies of allelic dropout and false alleles, the methodological constraints of population genetic studies using microsatellite loci amplified from historic DNA are discussed.

Behavioural structuring of relatedness in the spotted hyena ( Crocuta crocuta ) suggests direct fitness benefits of clan-level cooperation

Spotted hyenas (Crocuta crocuta) are gregarious carnivores that live in multigenerational social groups, called clans, containing one to several matrilines. Members of multiple matrilines within a clan cooperate during dangerous interactions with inter‐ and intraspecific competitors. The evolution of cooperation may be influenced by relatedness between individuals, which in turn is influenced by reproductive skew and mate choice, dispersal and territorial behaviours. Behavioural data exist for spotted hyenas, but corresponding data on patterns of relatedness are unavailable; this lack of data makes it difficult to assess the relative importance of selection pressures favouring cooperative behaviour within and among groups. Therefore we conducted a longitudinal analysis of relatedness within a single large clan of spotted hyenas, as well as a cross‐sectional analysis of relatedness among hyenas from multiple clans. Within a clan, patterns of relatedness reflected known pedigree relationships, and relatedness was higher within than among matrilines, even across generations. Although mean within‐matriline relatedness varied among matrilines, it did not decline with matriline rank. On average, clan members were not related closely, due to high levels of male‐mediated gene flow among clans, and relatedness declined very slightly across clan borders. Low mean relatedness within clans suggests that spotted hyenas cooperate with unrelated clan‐mates against close paternal kin in other clans. Our data also suggest that spotted hyenas must derive large net direct fitness benefits from group living and cooperation.

Isolation of Microsatellite Markers in Animals

Microsatellites, or simple sequences, consist of tandemly repeated units of DNA, each between one and ten base-pairs in length, such as (TG)n or (AAT)n (1). Their characteristics and their amplification for genotyping are discussed in Box 11.1 and Chapter 11.1, respectively. Because of their high variability and rapid evolution, microsatellites are becoming increasingly important in gene mapping and population studies.

Association patterns among male and female spotted hyenas (Crocuta crocuta) reflect male mate choice

Abstract. Although female animals tend to be choosier than males in selecting mates, sexual selection theory predicts that males should also be choosy when female fecundity varies. Reproductive success among female spotted hyenas varies greatly with social rank. Our goals were therefore to determine whether male hyenas preferentially associate with high-ranking females, and whether male preferences are affected by female reproductive state. Interactions between adult males and females were observed intensively, and association indices calculated for all male-female pairs, over a 7-year period in one population of free-living hyenas. Males initiated most affiliative interactions with females, and males associated most closely with females that were likeliest to be fertile. High- and middle-ranking males associated most closely with high-ranking females, but low-ranking males associated equally closely with females in all rank categories. We used molecular markers to determine the paternity of cubs born during the study period, and found that sires associated more closely with the mothers of those cubs than did non-sires, particularly during the last months before conception. These association data indicate that male spotted hyenas do indeed exhibit selective mate choice, and that they prefer females likeliest to maximize male reproductive success.

The effect of the last glacial age on speciation and population genetic structure of the endangered Ethiopian wolf ( Canis simensis )

During the last glacial age, Afro‐alpine habitats were widespread across the highlands of Ethiopia. A wolf‐like canid ancestor is thought to have colonized this expanding habitat and given rise to a new species that was remarkably well adapted to the high altitude environment: the Ethiopian wolf Canis simensis. Here, we address the timing of genetic divergence and examine population genetic history and structure by investigating the distribution of mitochondrial DNA (mtDNA) sequence variation. The pattern of mtDNA variation and geographical distribution indicate an initial population expansion, probably immediately after divergence from the wolf‐like ancestor, around 100 000 years ago. The partition of mtDNA haplotypes that followed was most likely the result of habitat reduction and fragmentation at the onset of deglaciation ~ 15 000 years ago. Phylogenetic and geographical associations suggest that the most likely genetic partitioning corresponds to three mountain areas, Arsi/Bale, Wollo/Shoa and Simien/Mt. Guna. Although there is a degree of clustering of haplotypes from both sides of the Rift Valley, the lack of reciprocal monophyly does not support the taxonomic classification of two subspecies. This study highlights the importance of populations north of the Rift Valley for the maintenance of genetic variability within the species and has consequent implications for conservation.

Philopatry and reproductive success in Bornean orang-utans ( Pongo pygmaeus )

Behavioural observations suggest that orang‐utans are semi‐solitary animals with females being philopatric and males roaming more widely in search of receptive partners, leading to the prediction that females are more closely related than males at any given site. In contrast, our study presents evidence for male and female philopatry in the orang‐utan. We examined patterns of relatedness and parentage in a wild orang‐utan population in Borneo using noninvasively collected DNA samples from animals observed to defecate, and microsatellite markers to assess dispersal and mating strategies. Surprisingly, resident females were equally as related to other resident females (mean rxy = 0.303) as resident males were to other resident males (mean rxy = 0.305). Moreover, resident females were more related to each other and to the resident males than they were to nonresident females, and resident males were more related to each other (and resident females) than they were to nonresident males. We assigned genetic mothers to 12 individuals in the population, while sires could be identified for eight. Both flanged males and unflanged males achieved paternity, similar to findings reported for Sumatran orang‐utans.

Measuring genetic diversity in translocation programmes: principles and application to a chimpanzee release project

Logging and poaching have dramatically reduced chimpanzee density and distribution in the Republic of Congo. Most chimpanzee translocations attempted in the past failed because a number of biological and non-biological factors can influence success. Biological considerations include knowledge of behaviour, disease, habitat requirements and genetics. We critically review genetic considerations in pre- and post-release phases of translocations and apply them to a welfare-based chimpanzee release project in the Republic of Congo which aimed to re-establish orphan chimpanzees in the wild with a native chimpanzee population. We analyze genetic diversity and relatedness in released animals and devise a genotyping strategy for monitoring of released individuals and their future offspring. Fifty-nine confiscated chimpanzees from different areas of the Republic of Congo were typed for 20 microsatellites using plucked hair as the DNA source. Genetic diversity was high, with an average expected heterozygosity of 81%, and three to 18 alleles per locus. Between 1996 and 1998, 19 individuals were released, and genetic analysis showed that these are unrelated (mean r± jack-knifed SD =−0.014 ± 0.001). Using FST and population admixture analysis, we identified population structure in wild chimpanzees. For long-term genetic monitoring of released and native chimpanzees, we identified a set of six informative markers, which are easy to score using basic techniques.