Richard S. Dodd

Intra-clonal variation and a similarity threshold for identification of clones: application to Salix exigua using AFLP molecular markers.

Abstract Although molecular methods are a major advance over phenological or root connectivity studies in the identification of clonal plants, there is still a level of ambiguity associated with two types of error: misidentification of genetically similar seedlings as clones and misidentification of dissimilar fingerprints from clones as genetically distinct individuals. We have addressed the second of these error types by determining the level of variation for AFLP fingerprints in Salix exigua, and then by developing a threshold value of Jaccards similarity index for assigning individuals to clones or to siblings. Variation in AFLP banding patterns among clones was partitioned into three potential sources; clones, stems within-clones and foliage within-stems. Most of the variation was attributable to clones and then to stems within-clones. To provide an objective means of identifying clones, we developed a method for establishing a threshold similarity index to assign individuals to the same clone. Our method yielded a Jaccard similarity threshold of 0.983 that resulted in a potential pairwise error rate of 8.1% putative clone assigned to siblings and 1.5% sibling assigned to clones. The method was tested on independent clonal and sibling individuals resulting in the same threshold value and similar error rates. We applied our method to assign individuals to clones in a population of S. exigua along the Cosumnes River, California. A total of 11 clones were identified, with one clone including 43% of the individuals sampled. Our results show that this approach can be useful in the accurate identification of clones.

SELECTION AND DISPERSAL IN A MULTISPECIES OAK HYBRID ZONE

Abstract The four western North American red oak species (Quercus wislizeni, Q. parvula, Q. agrifolia, and Q. kelloggii) are known to produce hybrid products in all interspecific combinations. However, it is unknown whether hybrids are transitory resulting from interspecific gene flow or whether they are maintained through extrinsic selection. Here, we examine cryptic hybrid structure in Q. wislizeni through a broad region including contact and isolation from three other western North American red oaks using amplified fragment length polymorphism molecular markers. All four species were simultaneously detected in the genetic background of individuals morphologically assigned to Q. wislizeni, although the contribution of Q. kelloggii was minor. In some cases, introgression was detected well outside the region of sympatry with one of the parental species. Molecular structure at the individual level indicated this was due to long‐distance pollen dispersal and not to local extinction of parental species. Species admixture proportions were correlated with climatic variables and greater proportions of Q. agrifolia and Q. parvula were present in the genetic background of Q. wislizeni in sites with cooler and more humid summers, corresponding with habitat preferences of the parental species. Partial Mantel tests indicated that climate was more important than distance from pollen source in this association. Despite high levels of introgression, species integrity was maintained in some populations in close proximity to the other species, providing further support to environmental selection in determining population genetic structure. Thus, the contribution of species mixtures to population genetic structure varies across the landscape according to availability of pollen, but more importantly to varying environmental selection pressures that produce a complex pattern of hybrid and pure gene pools.

Chloroplast DNA supports a hypothesis of glacial refugia over postglacial recolonization in disjunct populations of black pine (Pinus nigra) in western Europe

European black pine (Pinus nigra Arn.) is a widely distributed Mediterranean conifer. To test the hypothesis that fragmented populations in western Europe survived in situ during the last glacial rather than having been re‐colonized in the postglacial period, genetic variation was assessed using a suite of 10 chloroplast DNA microsatellites. Among 311 individuals analysed, 235 haplotypes were detected revealing high levels of chloroplast haplotype diversity in most populations. Bayesian analysis using a model of linked loci, with no prior assumption of population structure, assigned individuals to 10 clusters that corresponded well with the six predefined sampling regions, while an analysis carried out at the population level and assuming unlinked loci, recovered the original six sampling regions. This regional structure was supported by a biogeographical analysis that detected five barriers, with the two most significant separating Alps from Corsica and southern Italy, and southern Spain from the Pyrenees. No signals of demographic expansion were detected, and comparisons of RST with pRST suggested that a stepwise mutational model was important in regional differentiation, but not in population‐within‐region differentiation. These tests support long‐term persistence of the species within the six regions. The temporal depth estimate, assuming a high mutation rate in coalescent modelling, placed the deepest split between the Alps and the other regions at about 150 000 years ago, and the most recent split of Pyrenees from southern France at about 30 000 years ago. Taken together, the data suggest that chloroplast DNA is structured in black pine and disjunct populations in western Europe are likely to have been present during the Last Glacial Maximum.

Land barriers and open oceans: effects on gene diversity and population structure in Avicennia germinans L. (Avicenniaceae).

Avicennia germinans L. is a widespread mangrove species occupying the west coast of Africa and the Atlantic and Pacific coasts of the Americas from the Bahamas to Brazil and Baja California to Peru. An amplified fragment length polymorphism (AFLP) molecular analysis was carried out to assess genetic architecture within this species and to evaluate the effects of the Atlantic Ocean and the Central American Isthmus (CAI) on population and regional genetic diversity and differentiation. In total, 349 polymorphic AFLP fragments were identified among 144 individuals from 14 populations from the east Atlantic, west Atlantic and east Pacific. Levels of genetic diversity varied considerably among populations, but were generally higher in populations from the east Atlantic. Regional differentiation between the Pacific coast and Atlantic populations was greater than between east and west Atlantic populations, suggesting that the CAI has had an important influence on population genetic structure in this species. The lower level of divergence of east Atlantic from west Atlantic populations suggests some dispersal across the Atlantic Ocean, although migration rates are probably low; Nm from GST equal to 0.41 and accumulation of private and rare alleles in the east Atlantic. Population differentiation did not appear to follow an isolation by distance model and has probably resulted from complex patterns of population bottlenecks, and founder events due to landscape changes during the Pleistocene, particularly in the west Atlantic. The molecular data provide no support for the treatment of east Atlantic populations as a separate species A. africana.

DRIFTING PROPAGULES AND RECEDING SWAMPS: GENETIC FOOTPRINTS OF MANGROVE RECOLONIZATION AND DISPERSAL ALONG TROPICAL COASTS

Abstract Two issues that have captured the attention of tropical plant evolutionary biologists in recent years are the relative role of long distance dispersal (LDD) over vicariance in determining plant distributions and debate about the extent that Quaternary climatic changes affected tropical species. Propagules of some mangrove species are assumed to be capable of LDD due to their ability to float and survive for long periods of time in salt water. Mangrove species responded to glaciations with a contraction of their range. Thus, widespread mangrove species are an ideal system to study LDD and recolonization in the tropics. We present phylogenetic and phylogeographic analyses based on internal transcribed spacers region (ITS) sequences, chloroplast DNA (cpDNA), and amplified fragment length polymorphisms (AFLPs) of genomic DNA that demonstrate recent LDD across the Atlantic, rejecting the hypothesis of vicariance for the widespread distribution of the black mangrove (Avicennia germinans). Northern latitude populations likely became extinct during the late Quaternary due to frosts and aridification; these locations were recolonized afterward from southern populations. In some low latitude regions populations went extinct or were drastically reduced during the Quaternary because of lack of suitable habitat as sea levels changed. Our analyses show that low latitude Pacific populations of A. germinans harbor more diversity and reveal deeper divergence than Atlantic populations. Implications for our understanding of phylogeography of tropical species are discussed.

SALIX EXIGUA CLONAL GROWTH AND POPULATION DYNAMICS IN RELATION TO DISTURBANCE REGIME VARIATION

Willows are important riparian colonizers. However, the predominant models of early riparian colonization, which emphasize seedling recruitment, are inadequate to explain the success of these species in light of the extremely low rates of seedling survival observed. We used molecular fingerprinting markers (AFLPs) to identify and characterize Salix exigua clones on six sites, ranging in size from 850 to 1150 m(2), located on two rivers. Clones as large as 325 m(2) were detected, and an average of six clones per site occupied 75% of the vegetated area. Building on Mahoney and Roods recruitment box model, we propose a model whereby prolific clonal growth allows for long-term colonization of riparian zones, and the balance between the relative importance of seedling regeneration and clonal growth varies based upon disturbance regime. A reduction in disturbance regime resulted in greater clonal growth and reduced genotypic variation. It is probable that, with an extended reduction in disturbance, the Salix exigua component would be represented by fewer, larger clones and would eventually decline significantly when these clones are replaced by taller and more shade tolerant species.

Environmental gradients and population divergence contribute to variation in cuticular wax composition in Juniperus communis

The alkane fraction of cuticular lipids was analyzed in populations of Juniperus communis var. saxitilis and var. montana from the Pyrenees, the Alps, Corsica and California. The New World and Old World populations showed highly divergent alkane chain length distributions that were not correlated with climatic variables, suggesting a strong phylogeographic pattern to this holarctic species. Within Europe, the Corsican populations formed a distinct clade, but there was no consistent separation of populations from the Alps and from the Pyrenees. An elevational transect within the Pyrenees revealed a complex pattern for weighted mean alkane chain length (N) which was greatest at both low and at high elevations. Dispersion about this mean (d) showed a linear increase with elevation. A matrix of distances based on alkane composition for the Pyrenees populations was correlated with a distance matrix of temperature and an aridity index. Greater weighted mean alkane chain length at low and at high elevations was possibly a result of adaptation to minimize cuticular permeability due to high summer temperatures at low elevation and freezing causing physiological drought at high elevations. It seems probable that environment interactions determining selection forces, together with direct environmental effects may lead to the complex patterns of N and d observed over this elevational transect.

Incidence, size and spatial structure of clones in second-growth stands of coast redwood, Sequoia sempervirens (Cupressaceae).

The ecology and evolutionary potential of coast redwood (Sequoia sempervirens) is significantly influenced by the important role clonal spread plays in its reproduction and site persistence. In nine second-growth stands, amplified fragment length polymorphisms (AFLPs) were used to identify redwood clonal architecture. Clones (multistem genets) dominated sites by representing an average of 70% of stems measured, ranging in size from two to 20 stems. As a result, a relatively small number of genets can monopolize a disproportionate amount of site resources, are more likely to persist over time, and have greater on-site genetic representation. Clones were not limited to fairy-ring structures, but consisted of a wide range of shapes including concentric rings, ring chains, disjunct, and linear structures. Between-ramet distances of up to 40 m were measured, indicating that clonal reproduction is not limited to basal stump resprouting. Clonal structure in second-growth stands was similar to earlier reports from old growth, emphasizing the importance of site persistence and long-term, gradual site development. Smaller ramet numbers per genet in old growth is probably due to local within-genet self thinning. Management and conservation of redwoods will benefit from a better understanding of the dynamics and structure of clonal spread in these forests.

Evolutionary genetics of mangroves: continental drift to recent climate change

Abstract. Recent advances in our knowledge of the genetic architecture of mangrove species are reviewed and the consequences of this genetic architecture for species response to environmental change are inferred. The origins of mangrove taxa have been discussed many times, particularly in the context of centers of origin and continental drift. While global patterns of mangrove species diversity have been interpreted in the context of tectonic events and opening and closing of seawater passages, species evolution on a finer scale depends on more recent processes of population extinction and advances in response to spatio-temporal climatic and environmental flux. Understanding the likely effects of global climate change on mangrove distributions requires a focus on these more recent intraspecific evolutionary processes. Many mangrove taxa have wide geographic ranges that have been attributed to efficient propagule dispersal. Such gene flow should provide a genetic cohesiveness among populations. However, as with many wide-ranging marine organisms, we are finding important population genetic structure in widespread mangrove species, suggesting that gene flow is less effective than previously thought. Are these widespread taxa more recent and undergoing speciation? Spatial patterns in genetically adaptive traits indicate that some populations may survive more successfully under changing environmental conditions. However, is the present-day genetic architecture best poised to respond to predictions of climate change? These questions are addressed in the light of our increasing knowledge of genetic diversity in mangrove species.

Evolutionary diversity among Atlantic coast mangroves

Current knowledge of intraspecific variation of mangrove species is limited in terms of rangewide distributions and is mostly restricted to morphological analyses, which have indicated a high degree of homogeneity. However, our analyses of the aliphatic hydrocarbon and triterpenoid fraction of foliar waxes (by gas chromatography and mass spectroscopy) of mangrove species (Rhizophora mangle, Avicennia germinans and Laguncularia racemosa) from Gabon in West Africa and French Guiana in South America show significant genetic differentiation between eastern and western Atlantic provenances. The greater diversity in lipid composition, and the tendency for longer carbon chain lengths in all taxa from Africa, may suggest that American mangroves exhibit derived characteristics. A consequence of this hypothesis would be that Atlantic mangroves are unlikely to have dispersed from the Tethys via the Pacific, as has been proposed by some authors. More widespread sampling within the Atlantic and east Pacific region is needed to support and confirm these results.