Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo).

BACKGROUND: Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting. RESULTS: In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail. CONCLUSIONS: The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity.

Genetic diversity of lion populations in Kenya: Evaluating past management practices and recommendations for future conservation actions.

The decline of lions (Panthera leo) in Kenya has raised conservation concerns about their overall population health and long-term survival. This study aimed to assess the genetic structure, differentiation and diversity of lion populations in the country, while considering the influence of past management practices. Using a lion-specific Single Nucleotide Polymorphism (SNP) panel, we genotyped 171 individuals from 12 populations representative of areas with permanent lion presence. Our results revealed a distinct genetic pattern with pronounced population structure, confirmed a north-south split and found no indication of inbreeding in any of the tested populations. Differentiation seems to be primarily driven by geographical barriers, human presence and climatic factors, but management practices may have also affected the observed patterns. Notably, the Tsavo population displayed evidence of admixture, perhaps attributable to its geographic location as a suture zone, vast size or past translocations, while the fenced populations of Lake Nakuru National Park and Solio Ranch exhibited reduced genetic diversity due to restricted natural dispersal. The Amboseli population had a high number of monomorphic loci likely reflecting a historical population decline. This illustrates that patterns of genetic diversity should be seen in the context of population histories and that future management decisions should take these insights into account. To address the conservation implications of our findings, we recommend prioritizing the maintenance of suitable habitats to facilitate population connectivity. Initiation of genetic restoration efforts and separately managing populations with unique evolutionary histories is crucial for preserving genetic diversity and promoting long-term population viability.

Phylogeographic Patterns in Africa and High Resolution Delineation of Genetic Clades in the Lion (Panthera leo).

Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.

Direct and indirect estimates of the selfing rate in small and large individuals of the bumblebee pollinated Cynoglossum officinale L (Boraginaceae).

We measured the relationship between selfing rates and flower number in an experimental population of bumblebee pollinated Cynoglossum officinale, with plants differing in flower number. Results were compared with the prediction of a model based on pollen dynamics and pollinator behaviour. The selfing rate, as measured by multilocus oligonucleotide DNA fingerprinting, increased with flower number and ranged from 0% to 70%. Flowers on large plants received an equal number of visits from bumblebees as flowers on small plants. On large plants more flowers in a row were visited, inducing geitonogamy. The overall relationship between selfing rate and number of flowers can be explained by pollen dynamics and pollinator behaviour without invoking postpollination processes such as differential pollen tube growth and abortion.

Cost assessment of the production of pyrrolizidine alkaloids in ragwort (Senecio jacobaea L.).

Costs of pyrrolizidine alkaloid (Pa) production in vegetative ragwort (Senecio jacobaea) were examined under conditions in which plant growth was limited by light, nitrogen and phosphorus. Measurable costs of Pa production were demonstrated under light-limiting conditions. Plants with higher Pa concentrations grew more slowly than those with lower Pa concentration. Under nitrogen- and phosphorus-limited conditions no trade-off between Pa production and growth was observed.

Bryophyte DNA sequences from faeces of an arctic herbivore, barnacle goose (Branta leucopsis).

We tested DNA extraction methods and PCR conditions for the amplification of bryophyte DNA from barnacle goose (Branta leucopsis) faeces collected from Spitsbergen (Svalbard). Both the Qiagen stool kit and a silica-based extraction method received sufficient DNA from fresh and older droppings, as indicated by successful amplification of the plastid psbA-trnH spacer. Standard Taq polymerase outperformed two hot start polymerases. Sequencing of cloned PCR products revealed at least ten moss and two angiosperm sequences. This first example of identifying bryophyte DNA from faeces will allow analysing moss diets of arctic herbivores with a DNA barcoding approach.

Palatability to a generalist herbivore, defence and growth of invasive and native Senecio species: testing the evolution of increased competitive ability hypothesis.

This paper tests the prediction that introduced plants may become successful invaders because they experience evolutionary changes in growth and defence in their new range [evolution of increased competitive ability hypothesis (EICA)]. Interspecific and intraspecific binary feeding choices were offered to the snail Helix aspersa. The choices were between: (1) plants of the invasive Senecio inaequidens and Senecio pterophorus derived from populations in the introduced range (Europe) and plants of three indigenous species (Senecio jacobea, Senecio vulgaris and Senecio malacitanus) from populations in Europe; (2) plants of the invasive S. inaequidens and S. pterophorus from populations in the introduced range (Europe) and from populations in the native range (South Africa). We did not find a clear pattern of preference for indigenous or alien species of Senecio. However, we found that European invasive populations of S. inaequidens and S. pterophorus were less palatable than South African native populations. Moreover, in contrast to the predictions of the EICA hypothesis, the invasive genotypes of both species also showed a higher total concentration of pyrrolizidine alkaloids, and in the case of S. inaequidens we also found higher growth than in native genotypes. Our results are discussed with respect to the refinement of the EICA hypothesis that takes into account the difference between specialist and generalist herbivores and between qualitative and quantitative defences. We conclude that invasive populations of S. inaequidens and S. pterophorus are less palatable than native populations, suggesting that genetic differentiation associated with founding may occur and contribute to the plants' invasion success by selecting the best-defended genotypes in the introduced range.

Heritability of nectar production in Echium vulgare.

Heritabilities of nectar production in the wild species Echium vulgare were estimated as realised heritability under controlled and field conditions. The nectar production of offspring from high- and low-nectar-producing parents was significantly different in both controlled and field conditions, indicating that nectar production is in part genetically determined. The present study is the first one to report a genetic component of variation of nectar production in a wild plant species in the field. Heritability estimated under controlled conditions was 0.13 and therewith less than the heritability estimated under field conditions, which amounted to 0.26. Offspring of high-nectar-producing plants produced comparable amounts of nectar in the growth chamber (1.28 microl) and in the field (1.22 microl). In contrast, the nectar production of offspring of low-nectar-producing plants was significantly higher in the growth chamber (0.95 microl) than in the field (0.55 microl), indicating a genotype by environment interaction. The level of heritability of nectar production was dependent on the environment. Under less favourable conditions, like those in the field, heritability of nectar production increased. Nectar production was not correlated with any of the vegetative or reproductive traits measured, and hence no costs of nectar production could be detected. Results obtained stress the importance of field measurements in determining heritabilities.