Population genetic structure and the effect of founder events on the genetic variability of moose, Alces alces, in Canada

Moose, Alces alces, occur naturally throughout most of Canada but successful introductions of known numbers of animals have been made to the islands of Newfoundland and Cape Breton. Five microsatellite loci were used to investigate the population genetic structure and any change in genetic variability due to founder events of moose in Canada. Comparisons of allele frequencies for moose from 11 regions of the country suggested that there are at least seven genetically distinct populations (P < 0.05) in North America, namely Alberta, eastern Ontario, New Brunswick, Cape Breton, Labrador, western Newfoundland, and the Avalon Peninsula of Newfoundland. The average population heterozygosity was approximately 33% (range from 22 to 41%). UPGMA analysis of Nei's genetic distances produced phenograms similar to what would be expected when geographical location and population history are considered. The loss of heterozygosity due to a single founder event (n = 3; two introductions and a natural colonization) ranged from 14 to 30%, and the cumulative loss of heterozygosity due to two successive founder events (an introduction followed by a natural colonization) was 46%. In these examples loss of genetic variability has not been associated with any known phenotypic deviances, suggesting that populations may be established from a small number of founders. However, the viability of these founded populations over evolutionary timescales cannot be determined and is highly dependent upon chance.     

Genetic variation in rural and urban populations of Epipactis helleborine (L.) Crantz. (Orchidaceae) in Britain

Genetic variation in Epipactis helleborine in the British Isles was assessed using starch gel electrophoresis of isozymes; 273 individuals were sampled from 13 populations and examined for genetic variation using eight enzyme systems encoded for by 13 loci. Overall, 46% of the loci examined were polymorphic, with an average of 1.69 alleles per locus. Within populations, a mean of 33% of the loci were polymorphic, with a mean number of 1.46 alleles per locus. Levels of genetic variation were compared between urban and well established rural populations to assess the genetic consequences of colonization of the urban sites. The average levels of genetic variation detected in urban populations were lower than that found in rural populations, although there was a much greater range of variation among the urban populations. Large urban populations actually have patterns of variation similar to rural populations and show evidence of multiple founders. This indicates that the high dispersibility of Epipactis seeds can in some cases overcome the predicted loss of genetic variation associated with founder effects during colonization. Small urban populations, however, show significantly lower levels of genetic variation compared with these large urban populations and the rural populations, and it seems likely that this is attributable to single founding events and/or genetic drift.     

swinger: a user‐friendly computer program to establish captive breeding groups that minimize relatedness without pedigree information

Captive breeding programmes are often a necessity for the continued persistence of a population or species. They typically have the goal of maintaining genetic diversity and minimizing inbreeding. However, most captive breeding programmes have been based on the assumption that the founding breeders are unrelated and outbred, even though in situ anthropogenic impacts often mean these founders may have high relatedness and substantial inbreeding. In addition, polygamous group‐breeding species in captivity often have uncertain pedigrees, making it difficult to select the group composition for subsequent breeding. Molecular‐based estimates of relatedness and inbreeding may instead be used to select breeding groups (≥two individuals) that minimize relatedness and filter out inbred individuals. swinger constructs breeding groups based on molecular estimates of relatedness and inbreeding. The number of possible combinations of breeding groups quickly becomes intractable by hand. swinger was designed to overcome this major issue in ex situ conservation biology. The user can specify parameters within swinger to reach breeding solutions that suit the mating system of the target species and available resources. We provide evidence of the efficiency of the software with an empirical example and using simulations. The only data required are a typical molecular marker data set, such as a microsatellite or SNP data set, from which estimates of inbreeding and pairwise relatedness may be obtained. Such molecular data sets are becoming easier to gather from non‐model organisms with next‐generation sequencing technology. swinger is an open‐source software with a user‐friendly interface and is available at http://www.molecularecology.flinders.edu.au/molecular-ecology-lab/software/swinger/swinger/ and https://github.com/Yuma248/Swinger .     

Colonization genetics of an animal-dispersed plant (Vaccinium membranaceum) at Mount St Helens, Washington

Population founding and spatial spread may profoundly influence later population genetic structure, but their effects are difficult to quantify when population history is unknown. We examined the genetic effects of founder group formation in a recently founded population of the animal-dispersed Vaccinium membranaceum (black huckleberry) on new volcanic deposits at Mount St Helens (Washington, USA) 24 years post-eruption. Using amplified fragment length polymorphisms and assignment tests, we determined sources of the newly founded population and characterized genetic variation within new and source populations. Our analyses indicate that while founders were derived from many sources, about half originated from a small number of plants that survived the 1980 eruption in pockets of remnant soil embedded within primary successional areas. We found no evidence of a strong founder effect in the new population; indeed genetic diversity in the newly founded population tended to be higher than in some of the source regions. Similarly, formation of the new population did not increase among-population genetic variance, and there was no evidence of kin-structured dispersal in the new population. These results indicate that high gene flow among sources and long-distance dispersal were important processes shaping the genetic diversity in this young V. membranaceum population. Other species with similar dispersal abilities may also be able to colonize new habitats without significant reduction in genetic diversity or increase in differentiation among populations.     

Extreme homogeneity and low genetic diversity in Kryptolebias ocellatus from south-eastern Brazil suggest a recent foundation for this androdioecious fish population

This study documents unexpectedly low levels of intra and interpopulation genetic diversity in Kryptolebias ocellatus, an androdioecious and predominantly self-fertilizing killifish from south-eastern Brazil. This finding generally is inconsistent with the established opinion that the K. ocellatus and K. marmoratus clade originated in this geographic region and later dispersed northward into the Caribbean.     

Arabidopsis poly(A) polymerase PAPS1 limits founder‐cell recruitment to organ primordia and suppresses the salicylic acid‐independent immune response downstream of EDS1/PAD4

Polyadenylation of pre‐mRNAs by poly(A) polymerase (PAPS) is a critical process in eukaryotic gene expression. As found in vertebrates, plant genomes encode several isoforms of canonical nuclear PAPS enzymes. In Arabidopsis thaliana these isoforms are functionally specialized, with PAPS1 affecting both organ growth and immune response, at least in part by the preferential polyadenylation of subsets of pre‐mRNAs. Here, we demonstrate that the opposite effects of PAPS1 on leaf and flower growth reflect the different identities of these organs, and identify a role for PAPS1 in the elusive connection between organ identity and growth patterns. The overgrowth of paps1 mutant petals is due to increased recruitment of founder cells into early organ primordia, and suggests that PAPS1 activity plays unique roles in influencing organ growth. By contrast, the leaf phenotype of paps1 mutants is dominated by a constitutive immune response that leads to increased resistance to the biotrophic oomycete Hyaloperonospora arabidopsidis and reflects activation of the salicylic acid‐independent signalling pathway downstream of ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1)/PHYTOALEXIN DEFICIENT4 (PAD4). These findings provide an insight into the developmental and physiological basis of the functional specialization amongst plant PAPS isoforms.     

Local and regional founder effects in lake zooplankton persist after thousands of years despite high dispersal potential

We reconstructed the genetic structure of a planktonic crustacean Daphnia longispina living in high mountain lakes and ponds in the Pyrenees to investigate whether it was shaped by persistent founder effects originating shortly after the last glacial maximum or by ongoing dispersal and effective migration (gene flow). We found that the genetic structure can largely be explained by a single colonization event following gradual deglaciation of the Pyrenees ~10 000–15 000 years ago. Nuclear genetic diversity declined steeply from southeast to northwest, suggestive of serial colonization of available habitats with advancing deglaciation. The spatial genetic structure suggests that founder effects were major determinants of the present‐day diversity, both at the catchment level and at the level of individual water bodies, further supporting extremely low effective migration rates. This study reveals a prime example of a founder effect that is both long lasting and maintained at small spatial scales. Our data suggest a process of isolation by colonization as a result of strong priority effects and monopolization. We found evidence for the spread of haplotypes with Pyrenean ancestry across the Palaearctic over distances up to 5500 km, although the local genetic structure after colonization was hardly influenced by contemporary dispersal. Finally, our data also suggest that mitochondrial mutation rates in the studied populations were seven times higher than typically assumed. Overall, we show that founder effects can persist for centuries even at small spatial scales at which the potential for dispersal is high.     

Population structure of the invasive forest pathogen Hymenoscyphus pseudoalbidus

Understanding the genetic diversity and structure of invasive pathogens in source and in introduced areas is crucial to the revelation of hidden biological features of an organism, to the reconstruction of the course of invasions and to the establishment of effective control measures. Hymenoscyphus pseudoalbidus (anamorph: Chalara fraxinea) is an invasive and highly destructive fungal pathogen found on common ash Fraxinus excelsior in Europe and is native to East Asia. To gain insights into its dispersal mechanisms and history of invasion, we used microsatellite markers and characterized the genetic structure and diversity of H. pseudoalbidus populations at three spatial levels: (i) between Europe and Japan, (ii) in Europe and (iii) at the epidemic's front in Switzerland. Phylogenetic and network analysis demonstrated that individuals from both regions are conspecific. However, populations from Japan harboured a higher genetic diversity and were genetically differentiated from European ones. No evident population structure was found among the 1208 European strains using Bayesian and multivariate clustering analysis. Only the distribution of genetic diversity in space, pairwise population differentiation (G_ST) and the spatial analysis of principal components revealed a faint geographical pattern around Europe. A significant allele deficiency in most European populations pointed to a recent genetic bottleneck, whereas no pattern of isolation by distance was found. Our data suggest that H. pseudoalbidus was introduced just once by at least two individuals. The potential source region of H. pseudoalbidus is vast, and further investigations are required for a more accurate localization of the source population.     

Rapid increase in southern elephant seal genetic diversity after a founder event

Genetic diversity provides the raw material for populations to respond to changing environmental conditions. The evolution of diversity within populations is based on the accumulation of mutations and their retention or loss through selection and genetic drift, while migration can also introduce new variation. However, the extent to which population growth and sustained large population size can lead to rapid and significant increases in diversity has not been widely investigated. Here, we assess this empirically by applying approximate Bayesian computation to a novel ancient DNA dataset that spans the life of a southern elephant seal (Mirounga leonina) population, from initial founding approximately 7000 years ago to eventual extinction within the past millennium. We find that rapid population growth and sustained large population size can explain substantial increases in population genetic diversity over a period of several hundred generations, subsequently lost when the population went to extinction. Results suggest that the impact of diversity introduced through migration was relatively minor. We thus demonstrate, by examining genetic diversity across the life of a population, that environmental change could generate the raw material for adaptive evolution over a very short evolutionary time scale through rapid establishment of a large, stable population.     

Effect of founding events on coat colour polymorphism of Apodemus speciosus (Rodentia: Muridae) on the Izu Islands

To infer the evolutionary mechanism of phenotypic variation among isolated island populations, we investigated coat colour and genetic variation in the large Japanese field mouse (Apodemus speciosus) on the Izu Islands (Ohshima, Niijima, Kouzushima, and Miyakejima). Coat colour in the most remote population (Miyakejima) was unique and significantly darker than that in the other populations. Ohshima that is closest to the source population showed variation in coat colour within its population. Phylogeographical analyses using mitochondrial and microsatellite markers suggested that the island populations (except Kouzushima) were founded sequentially from the closest Ohshima to remote Niijima and Miyakejima during or before the penultimate interglacial period. Secondary gene flow from the source population was rare and occurred only for the closest (Ohshima) population. In addition, we found that an amino acid mutation in the Agouti signalling protein gene (Asip) was associated with coat colour variation among the island populations. The mutation was rare in the source population but completely fixed in the Miyakejima population. The phenotypic and genetic variation suggested that severe reduction of genetic variation and changes in allele frequency as a result of sequential colonization (i.e. the founder effect) had significant effects on colour polymorphism. The findings of the present study suggest that the founder effect, in addition to natural selection, facilitated the morphological changes below the species level over a relatively long time scale. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 522–535.