Joint estimation of contemporary seed and pollen dispersal rates among plant populations

Measuring recent effective gene flow among large populations in Pinus sylvestris: Local pollen shedding does not preclude substantial long-distance pollen immigration

The estimation of recent gene flow rates among vast and often weakly genetically differentiated tree populations remains a great challenge. Yet, empirical information would help understanding the interaction between gene flow and local adaptation in present-day non-equilibrium forests. We investigate here recent gene flow rates between two large native Scots pine (Pinus sylvestris L.) populations in central Iberian Peninsula (Spain), which grow on contrasting edaphic conditions six kilometers apart from each other and show substantial quantitative trait divergence in common garden experiments. Using a sample of 1,200 adult and offspring chloroplast-microsatellite haplotypes and a Bayesian inference model, we estimated substantial male gametic gene flow rates (8 and 21%) between the two natural populations, and even greater estimated immigration rates (42 and 64%) from nearby plantations into the two natural populations. Our results suggest that local pollen shedding within large tree populations does not preclude long-distance pollen immigration from large external sources, supporting the role of gene flow as a homogenizing evolutionary force contributing to low molecular genetic differentiation among populations of widely distributed wind-pollinated species. Our results also indicate the high potential for reproductive connectivity in large fragmented populations of wind-pollinated trees, and draw attention to a potential scenario of adaptive genetic divergence in quantitative traits under high gene flow.

The future of parentage analysis: From microsatellites to SNPs and beyond

Parentage analysis is a cornerstone of molecular ecology that has delivered fundamental insights into behaviour, ecology and evolution. Microsatellite markers have long been the king of parentage, their hypervariable nature conferring sufficient power to correctly assign offspring to parents. However, microsatellite markers have seen a sharp decline in use with the rise of next-generation sequencing technologies, especially in the study of population genetics and local adaptation. The time is ripe to review the current state of parentage analysis and see how it stands to be affected by the emergence of next-generation sequencing approaches. We find that single nucleotide polymorphisms (SNPs), the typical next-generation sequencing marker, remain underutilized in parentage analysis but are gaining momentum, with 58 SNP-based parentage analyses published thus far. Many of these papers, particularly the earlier ones, compare the power of SNPs and microsatellites in a parentage context. In virtually every case, SNPs are at least as powerful as microsatellite markers. As few as 100-500 SNPs are sufficient to resolve parentage completely in most situations. We also provide an overview of the analytical programs that are commonly used and compatible with SNP data. As the next-generation parentage enterprise grows, a reliance on likelihood and Bayesian approaches, as opposed to strict exclusion, will become increasingly important. We discuss some of the caveats surrounding the use of next-generation sequencing data for parentage analysis and conclude that the future is bright for this important realm of molecular ecology.

Assessing early fitness consequences of exotic gene flow in the wild: a field study with Iberian pine relicts

Gene flow from plantations of nonlocal (genetically exotic) tree provenances into natural stands of the same species is probably a widespread phenomenon, but its effects remain largely unexamined. We investigated early fitness consequences of intraspecific exotic gene flow in the wild by assessing differences in survival among native, nonlocal, and F1 intraspecific hybrid seedlings naturally established within two native pine relicts (one of Pinus pinaster and the other of P. sylvestris) surrounded by nonlocal plantations. We obtained broad‐scale temporally sequential genotypic samples of a cohort of recruits in each pine relict, from seeds before dispersal to established seedlings months after emergence, tracking temporal changes in the estimated proportion of each parental cross‐type. Results show significant proportions of exotic male gametes before seed dispersal in the two pine relicts. Subsequently to seedling establishment, the frequency of exotic male gametes became nonsignificant in P. pinaster, and dropped by half in P. sylvestris. Exotic zygotic gene flow was significantly different from zero among early recruits for P. sylvestris, decreasing throughout seedling establishment. Seedling mortality resulted in small late sample sizes, and temporal differences in exotic gene flow estimates were not significant, so we could not reject the null hypothesis of invariant early viability across parental cross types in the wild.

Space, time and complexity in plant dispersal ecology

Dispersal of pollen and seeds are essential functions of plant species, with far-reaching demographic, ecological and evolutionary consequences. Interest in plant dispersal has increased with concerns about the persistence of populations and species under global change. We argue here that advances in plant dispersal ecology research will be determined by our ability to surmount challenges of spatiotemporal scales and heterogeneities and ecosystem complexity. Based on this framework, we propose a selected set of research questions, for which we suggest some specific objectives and methodological approaches. Reviewed topics include multiple vector contributions to plant dispersal, landscape-dependent dispersal patterns, long-distance dispersal events, spatiotemporal variation in dispersal, and the consequences of dispersal for plant communities, populations under climate change, and anthropogenic landscapes.

Ecological genomics of local adaptation

It is increasingly important to improve our understanding of the genetic basis of local adaptation because of its relevance to climate change, crop and animal production, and conservation of genetic resources. Phenotypic patterns that are generated by spatially varying selection have long been observed, and both genetic mapping and field experiments provided initial insights into the genetic architecture of adaptive traits. Genomic tools are now allowing genome-wide studies, and recent theoretical advances can help to design research strategies that combine genomics and field experiments to examine the genetics of local adaptation. These advances are also allowing research in non-model species, the adaptation patterns of which may differ from those of traditional model species.

Evolution of a hotspot genus: geographic variation in speciation and extinction rates in Banksia (Proteaceae)

BACKGROUND

Hotspots of angiosperm species richness and endemism in Mediterranean-climate regions are among the most striking, but least well-understood, geographic patterns of biodiversity. Recent studies have emphasized the importance of rapid diversification within hotspots, compared to non-hotspot regions, as a major contributor to these patterns. We constructed the first near-complete phylogeny of Banksia (Proteaceae) to test whether diversification rates have differed between lineages confined to the southwest Australian hotspot and those found throughout southern, eastern and northern Australia. We then tested for variation in diversification rates among the bioclimatic zones within the southwest hotspot itself.

RESULTS

Although Banksia species richness in the southwest is ten times that of the rest of the continent, we find little evidence for more rapid diversification in the southwest, although this result is inconclusive. However, we find firmer support for substantial rate variation within the southwest hotspot, with more rapid diversification in the semi-arid heaths and shrublands, compared to the high-rainfall forests. Most of the Banksia diversity of the southwest appears to be generated in the heaths and shrublands, with a high migration rate out of this zone boosting diversity of the adjacent forest zone.

CONCLUSIONS

The geographic pattern of diversification in Banksia appears more complex than can be characterized by a simple hotspot vs. non-hotspot comparison, but in general, these findings contrast with the view that the high diversity of Mediterranean hotspots is underpinned by rapid radiations. Steady accumulation of species at unexceptional rates, but over long periods of time, may also have contributed substantially to the great botanical richness of these regions.

Low rate of between-population seed dispersal restricts genetic connectivity and metapopulation dynamics in a clonal shrub

Clonal species normally have low seed production, low recruitment rates and long lifespans, and it is expected that the rates of long-distance dispersal (LDD) of seeds will be low as well. Banksia candolleana is a clonal shrub in Mediterranean-type, fire-prone sclerophyll shrublands of southwestern Australia, whose reproductive biology and population dynamics contrast with those of co-occurring nonclonal congeneric species, all of which are restricted to a mosaic of sand dunes set within a matrix of inhospitable swales. Using microsatellite markers, we genotyped 499 plants in all 15 populations of B. candolleana within a 12-km(2) area, assessed population genetic differentiation, and quantified the effective rate of interpopulation seed dispersal through genetic assignment of individuals to populations. We measured life history, reproductive and demographic attributes, and compared these with two co-occurring Banksia species, a non-clonal resprouter and a nonsprouter. B. candolleana has much higher levels of population genetic differentiation, and one-third the rate of interpopulation seed migration, as the other two species (2.2% vs 5.5-6.8% of genotyped plants inferred to be immigrants), though distances reached by LDD are comparable (0.3-2.3 km). The low rate of interpopulation dispersal was supported by an analysis of the age structure of three populations that suggests a mean interdune migration rate of <800 m in 200 years, and 60% of suitable dunes remain uninhabited. Thus, B. candolleana has poor properties for promoting long-distance dispersal. It is unclear if these are idiosyncratic to this species or whether such properties are to be expected of clonal species in general where LDD is less critical for species survival.