Inbreeding depression in the partially self-incompatible endemic plant species <Emphasis Type="Italic">Scalesia affinis</Emphasis> (Asteraceae) from Galápagos islands

A previous study showed that some individuals of the tetraploid Galápagos endemic Scalesia affinis were able to produce offspring after selfing. The present study compares the fitness of self-pollinated offspring with the fitness of cross-pollinated offspring. Germination success, seedling survival, and four different growth parameters was measured. In most of the studied characters selfed offspring were significantly inferior to outcrossed progeny. The effect was very clear in germination and survival. Outcrossed embryos were 3.4 times more likely to germinate than those that were selfed-fertilized, and the mortality was 84% higher among selfed individuals. Also, there was no genetic variation in inbreeding depression. The present study is based on material from a large population on Isabela Island, Galápagos. At other localities in the archipelago, populations have been through recent dramatic bottlenecks due to the grazing of introduced mammals. Considering the significant inbreeding depression found in the large population and the presence of a partial self-incompatibility system, these small populations are likely to be highly vulnerable and their future survival critically threatened.     

Cape buffalo mitogenomics reveals a Holocene shift in the African human-megafauna dynamics

Africa is unique among the continents in having maintained an extraordinarily diverse and prolific megafauna spanning the Pleistocene-Holocene epochs. Little is known about the historical dynamics of this community and even less about the reasons for its unique persistence to modern times. We sequenced complete mitochondrial genomes from 43 Cape buffalo (Syncerus caffer caffer) to infer the demographic history of this large mammal. A combination of Bayesian skyline plots, simulations and Approximate Bayesian Computation (ABC) were used to distinguish population size dynamics from the confounding effect of population structure and identify the most probable demographic scenario. Our analyses revealed a late Pleistocene expansion phase concurrent with the human expansion between 80 000 and 10 000 years ago, refuting an adverse ecological effect of Palaeolithic humans on this quarry species, but also showed that the buffalo subsequently declined during the Holocene. The distinct two-phased dynamic inferred here suggests that a major ecological transition occurred in the Holocene. The timing of this transition coincides with the onset of drier conditions throughout tropical Africa following the Holocene Optimum (～9000-5000 years ago), but also with the explosive growth in human population size associated with the transition from the Palaeolithic to the Neolithic cultural stage. We evaluate each of these possible causal factors and their potential impact on the African megafauna, providing the first systematic assessment of megafauna dynamics on the only continent where large mammals remain abundant.     

Population genetics of the native caribou (Rangifer tarandus groenlandicus) and the semi-domestic reindeer (Rangifer tarandus tarandus) in Southwestern Greenland: Evidence of introgression

Over the past centuries the native caribou ofWest Greenland has gone through extensive population size fluctuations, with reductionsas great as 90% in less than 20 years.Norwegian semi-domestic reindeer wereintroduced to the Nuuk area in 1952 because ofthe small number of caribou in Greenland.Although the reindeer and caribou wereinitially kept separated, mixing has occurredsince the 1970's. We investigated the genotypicstructure of caribou and reindeer in South-westGreenland, using five polymorphicmicrosatellite markers isolated from cattle,sheep, goat and red deer. A total of ninetysamples were collected, which included samplesfrom caribou of four different regions andsamples from two different reindeer herds.Based on the genetic variation of the fivemarkers, our results shows that the caribou andthe reindeer populations in the six regionssampled are genetically differentiated withineach group and the two subspecies aredifferentiated from each other. A likelyexplanation for the genetic isolation of thepopulations investigated is that naturalbarriers (glaciers and wide fjords) exists inthe area. Furthermore we found that introducedNorwegian domestic reindeer hybridized with thenative Greenlandic caribou in two areasneighbouring Nuuk.     

Local differentiation and gene dispersal distances in a Danish population of Armaria maritima

In a continuously distributed population of the self-incompatible species Armeria maritima , nine artificially delimited subpopulations were sampled in a transect with a length of 1300 m. Genetic variation was quantified with enzyme electrophoresis, which revealed five polymorphic loci. The genotypic distribution within subpopulations accorded to Hardy-Weinberg proportions, but revealed a Wahlund effect at one of the loci when the total population was considered. The Wahlund effect was supported by significant differences in allele frequencies among the nine subpopulations. The differentiation was low with a F_ST value of 0.028, which is much smaller than the previously reported value of 0.18 for 17 geographically separated Danish populations of this species. The low differentiation of the subpopulations was also revealed by an assignment test. In this test, the multilocus genotype of an individual is used to assign it to the subpopulation it has the highest likelihood to appear in. With this test, a lower percentage of individuals were assigned to the subpopulation of origin (24) than was seen with assignment of individuals to populations in Denmark (34). No abrupt changes in allele frequencies were observed. A spatial autocorrelation analysis suggested a breeding patch size of 500–700 m in diameter along the transect.     

Age- and tactic-related paternity success in male African elephants

Information on age- and tactic-related paternity success isessential for understanding the lifetime reproductive strategyof males and constitutes an important component of the fitnesstrade-offs that shape the life-history traits of a species.The degree of reproductive skew impacts the genetic structureof a population and should be considered when developing conservationstrategies for threatened species. The behavior and geneticstructure of species with large reproductive skew may be disproportionatelyimpacted by anthropogenic actions affecting reproductively dominantindividuals. Our results on age- and tactic-specific paternitysuccess in male African elephants are the first from a free-rangingpopulation and demonstrate that paternity success increasesdramatically with age, with the small number of older bullsin the competitive state of musth being the most successfulsires. However, nonmusth males sired 20% of genotyped calves,and 60% of mature bulls (>20 years old) were estimated tohave sired offspring during the 5-year study period. The 3 mostsuccessful males sired less than 20% of the genotyped offspring.Hence, contrary to prediction from behavior and life-historytraits, reproduction was not heavily skewed compared with manyother mammalian systems with a similar breeding system. Nevertheless,these results indicate that trophy hunting and ivory poaching,both of which target older bulls, may have substantial behavioraland genetic effects on elephant populations. In addition, theseresults are critical to the current debate on methods for managingand controlling increasing populations of this species.     

High variation and very low differentiation in wide ranging plains zebra (Equus quagga): insights from mtDNA and microsatellites

Patterns of genetic differentiation in the plains zebra ( Equus quagga ) were analysed using mitochondrial DNA control region variation and seven microsatellites. The six morphologically defined subspecies of plains zebra lacked the population genetic structure indicative of distinct evolutionary units. Both marker sets showed high levels of genetic variation and very low levels of differentiation. There was no geographical structuring of mitochondrial DNA haplotypes in the phylogenetic tree, and the plains zebra showed the lowest overall differentiation recorded in any African ungulate studied so far. Arid-adapted African ungulates have shown significant regional genetic structuring in support of the Pleistocene refuge theory. This was not the case in the zebra, and the data are discussed in relation to the impact of Pleistocene climate change on a nonbovid member of the savannah ungulate community. The only other species showing a similar absence of genetic structuring is the African buffalo ( Syncerus caffer ), but this taxon lacks the high levels of morphological variation present in the plains zebra.     

Genetic subspecies diversity of the chimpanzee CD4 virus-receptor gene

Chimpanzees are naturally and asymptomatically infected by simian immunodeficiency virus (SIV). Pathogenic properties of SIV/HIV vary and differences in susceptibility and pathogenicity of SIV/HIV depend in part on host-specific factors such as virus-receptor/co-receptor interactions. Since CD4 plays a primary role in virus binding and since SIVcpz have been found only in two African chimpanzee subspecies, we characterized the genetic diversity of CD4 receptors in all four recognized subspecies of chimpanzees. We found noticeable variation in the first variable region V1 of CD4 and in intron six among the subspecies of chimpanzees. We found the CD4 receptor to be conserved in individuals belonging to the P. t. verus subspecies and divergent from the other three subspecies, which harbored highly variable CD4 receptors. The CD4 receptor of chimpanzees differed from that of humans. We question whether the observed diversity can explain the species-specific differences in susceptibility to and pathogenicity of SIV/HIV.     

Where sociality and relatedness diverge: the genetic basis for hierarchical social organization in African elephants

Hierarchical properties characterize elephant fission–fusion social organization whereby stable groups of individuals coalesce into higher order groups or split in a predictable manner. This hierarchical complexity is rare among animals and, as such, an examination of the factors driving its emergence offers unique insight into the evolution of social behaviour. Investigation of the genetic basis for such social affiliation demonstrates that while the majority of core social groups (second-tier affiliates) are significantly related, this is not exclusively the case. As such, direct benefits received through membership of these groups appear to be salient to their formation and maintenance. Further analysis revealed that the majority of groups in the two higher social echelons (third and fourth tiers) are typically not significantly related. The majority of third-tier members are matrilocal, carrying the same mtDNA control region haplotype, while matrilocality among fourth-tier groups was slightly less than expected at random. Comparison of results to those from a less disturbed population suggests that human depredation, leading to social disruption, altered the genetic underpinning of social relations in the study population. These results suggest that inclusive fitness benefits may crystallize elephant hierarchical social structuring along genetic lines when populations are undisturbed. However, indirect benefits are not critical to the formation and maintenance of second-, third- or fourth-tier level bonds, indicating the importance of direct benefits in the emergence of complex, hierarchical social relations among elephants. Future directions and conservation implications are discussed.     

Contrasting demographic histories of the neighboring bonobo and chimpanzee

The Pleistocene epoch was a period of dramatic climate change that had profound impacts on the population sizes of many animal species. How these species were shaped by past events is often unclear, hindering our understanding of the population dynamics resulting in present day populations. We analyzed complete mitochondrial genomes representing all four recognized chimpanzee subspecies and the bonobo to infer the recent demographic history and used simulations to exclude a confounding effect of population structure. Our genus-wide Bayesian coalescent-based analysis revealed surprisingly dissimilar demographic histories of the chimpanzee subspecies and the bonobo, despite their overlapping habitat requirements. Whereas the central and eastern chimpanzee subspecies were inferred to have expanded tenfold between around 50,000 and 80,000 years ago and today, the population size of the neighboring bonobo remained constant. The changes in population size are likely linked to changes in habitat area due to climate oscillations during the late Pleistocene. Furthermore, the timing of population expansion for the rainforest-adapted chimpanzee is concurrent with the expansion of the savanna-adapted human, which could suggest a common response to changed climate conditions around 50,000–80,000 years ago.