The influence of spatial scale on the genetic structure of a widespread tropical wetland tree, Pterocarpus officinalis (Fabaceae)

Identifying factors that cause genetic differentiation in plant populations and the spatial scale at which genetic structuring can be detected will help to understand plant population dynamics and identify conservation units. In this study, we determined the genetic structure and diversity of Pterocarpus officinalis, a widespread tropical wetland tree, at three spatial scales: (1) drainage basin “watershed” (<10 km), (2) within Puerto Rico (<100 km), and (3) Caribbean-wide (>1000 km) using AFLP. At all three spatial scales, most of the genetic variation occurred within populations, but as the spatial scale increased from the watershed to the Caribbean region, there was an increase in the among population variation (Φ_ST=0.19 to Φ_ST=0.53). At the watershed scale, there was no significant differentiation (P=0.77) among populations in the different watersheds, although there was some evidence that montane and coastal populations differed (P<0.01). At the island scale, there was significant differentiation (P<0.001) among four populations in Puerto Rico. At the regional scale (>1000 km), we found significant differentiation (P<0.001) between island and continental populations in the Caribbean region, which we attributed to factors associated with the colonization history of P. officinalis in the Neotropics. Given that genetic structure can occur from local to regional spatial scales, it is critical that conservation recommendations be based on genetic information collected at the appropriate spatial scale.     

Colonization processes and the maintenance of genetic diversity: insights from a pioneer rainforest tree, Aucoumea klaineana

Despite recurrent episodes of range expansion and contraction, forest trees often harbour high genetic diversity. Studies of temperate forest trees suggest that prolonged juvenile phase and high pollen flow are the main factors limiting founder effects. Here, we studied the local colonization process of a pioneer rainforest tree in central Africa, Aucoumea klaineana. We identified 87% of parents among trees up to 20-25 years old and could thus compare direct parentage structure data with classical population genetics estimators. In this species, genetic diversity was maintained during colonization. The absence of founder effects was explained by (i) local random mating and (ii) local recruitment, as we showed that 75% of the trees in the close neighbourhood participated in the recruitment of new saplings. Long-distance pollen flow contributed little to genetic diversity: pollen and seed dispersal was mainly within stand (128 and 118 m, respectively). Spatial genetic structure was explained by aggregated seed dispersal rather than by mother-offspring proximity as assumed in classical isolation-by-distance models. Hence, A. klaineana presents a genetic diversity pattern typical of forest trees but does not follow the classical rules by which this diversity is generally achieved. We suggest that while high local genetic variability is of general importance to forest tree survival, the proximate mechanisms by which it is achieved may follow very different scenarios.     

Regional genetic diversity patterns in Antarctic hairgrass (Deschampsia antarctica Desv.)

Aim  To determine patterns in diversity of a major Antarctic plant species, including relationships of Antarctic populations with those outside the Antarctic zone.
Location  Antarctic Peninsula, Maritime Antarctica, sub-Antarctic islands, Falkland Islands and South America.
Methods  Amplified fragment length polymorphisms (AFLPs) and chloroplast sequences were used to study patterns of genetic diversity in Antarctic hairgrass ( Deschampsia antarctica Desv.) and the genetic relationships between populations over its distribution range. Thirty-eight populations were sampled from a large part of the distribution of D. antarctica , and additionally, herbarium specimens were included for areas from which we could not obtain fresh samples.
Results  A gradient in AFLP diversity was observed going from the Falklands southwards into the Antarctic. This gradient in diversity was also observed within the Antarctic Peninsula: diversity was lower further south. Diversity in the chloroplast genome of D. antarctica was low. Only three chloroplast haplotypes were found, each with a strong regional distribution.
Main conclusions  The phylogenetic construction of AFLP marker frequencies in meta-populations of D. antarctica supports a stepping-stone model of colonization, whereby gene flow mainly occurs between neighbouring populations. It is concluded that long-distance gene flow is very limited in D. antarctica . A very low diversity was found in the sub-Antarctic islands in the Indian Ocean, indicating that these populations have experienced a recent evolutionary bottleneck.     

Isolation and characterization of microsatellite markers in Pterocarpus officinalis Jacq.

The leguminous Pterocarpus officinalis Jacq. is one of the dominant freshwater wetland tree species in the Caribbean basin. Anthromorphic factors threaten to reduce its population. In order to investigate the genetic diversity and structure of this species, we developed eight pairs of primers for nuclear microsatellites. One hundred ninety‐one individuals were analysed within nine Caribbean and continental populations. These loci were polymorphic in all the populations, with four to 20 alleles per locus. Significant Hardy–Weinberg deviation was detected and was interpreted as a result of Wahlund effect. These loci constitute a powerful tool to investigate the genetic patterns within populations of the swamp species P. officinalis.     

The role of disjunction and postglacial population expansion on phylogeographical history and genetic diversity of the circumboreal plant Chamaedaphne calyculata

In the last decade a number of studies has illustrated quite different phylogeographical patterns amongst plants with a northern present‐day geographical distribution, spanning the entire circumboreal region and/or circumarctic region and southern mountains. These works, employing several marker systems, have brought to light the complex evolutionary histories of this group. Here I focus on one circumboreal plant species, Chamaedaphne calyculata (leatherleaf), to unravel its phylogeographical history and patterns of genetic diversity across its geographical range. A survey of 29 populations with combined analyses of chloroplast DNA (cpDNA), internal transcribed spacer (ITS) and AFLP markers revealed structuring into two groups: Eurasian/north‐western North American, and north‐eastern North American. The present geographical distribution of C. calyculata has resulted from colonization from two putative refugial areas: east Beringia and south‐eastern North America. The variation of chloroplast DNA (cpDNA) and ITS sequences strongly indicated that the evolutionary histories of the Eurasian/north‐western North American and the north‐eastern North American populations were independent of each other because of a geographical disjunction in the distribution area and ice‐sheet history between north‐eastern and north‐western North America. Mismatch analysis using ITS confirmed that the present‐day population structure is the result of rapid expansion, probably since the last glacial maximum. The AFLP data revealed low genetic diversity of C. calyculata (P = 19.5%, H = 0.085) over the whole geographical range, and there was no evidence of loss of genetic diversity within populations in the continuous range, either at the margins or in formerly glaciated and nonglaciated regions. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 761–775.     

Patterns of litter production across a salinity gradient in a Pterocarpus officinalis tropical wetland

Historically, Pterocarpus officinalisJacq. (Leguminoseae) dominated freshwater wetlands in the coastal plains of Puerto Rico, but deforestation has reduced its distribution to small patches adjacent to mangrove forests in areas of higher salinity. The objective of this study was to determine how a gradient in soil salinity affected litter, flower, and fruit production in a Pterocarpus officinalis.Three 100 m² plots were established in each of three sites along a salinity gradient: pasture/Pterocarpus edge (low salinity, mean salinity at 60 cm–9.7 g Kg^–1), Pterocarpus forest (intermediate salinity, 11.5 g Kg^–1) and a Pterocarpus/mangrove ecotone (high salinity, 15.0 g Kg^–1). Across this gradient, P. officinalis accounted for 100% of the relative basal area in the low and intermediate sites and 43% in the high salinity site which was domimated by Laguncularia racemosa. The basal area of P. officinalis decreased along the gradient from 73.5 m² ha^–1 in the low salinity site to 42.0 m² ha^–1 in the high salinity site. Litterfall was sampled on average every 23 days in 45 0.25 m² traps (5 traps per plot) for two years. Annual litterfall for the forest was 11.9 Mg ha^–1 yr^–1. Peaks in litterfall were associated with high precipitation in May 1995 and tropical storms in September 1995. Leaf fall of P. officinalis was significantly higher in the low salinity site (4.8 Mg ha^–1 yr^–1) than the high salinity site (1.8 Mg ha^–1 yr^–1), but total stand litterfall was greatest in the area of high salinity due to the greater contribution of L. racemosa. Pterocarpus flower and fruit production was approximately 10 times greater in low and intermediate salinity sites in comparison with the high salinity site. An increase in global temperature, will lead to higher sea level and higher soil salinity in costal wetlands. To conserve this wetland forest type it is critical to expand the distribution into areas of lower salinity where this species occurred historically.     

Evolutionary history of almond tree domestication in the Mediterranean basin

Genetic diversity of contemporary domesticated species is shaped by both natural and human‐driven processes. However, until now, little is known about how domestication has imprinted the variation of fruit tree species. In this study, we reconstruct the recent evolutionary history of the domesticated almond tree, Prunus dulcis, around the Mediterranean basin, using a combination of nuclear and chloroplast microsatellites [i.e. simple sequence repeat (SSRs)] to investigate patterns of genetic diversity. Whereas conservative chloroplast SSRs show a widespread haplotype and rare locally distributed variants, nuclear SSRs show a pattern of isolation by distance with clines of diversity from the East to the West of the Mediterranean basin, while Bayesian genetic clustering reveals a substantial longitudinal genetic structure. Both kinds of markers thus support a single domestication event, in the eastern side of the Mediterranean basin. In addition, model‐based estimation of the timing of genetic divergence among those clusters is estimated sometime during the Holocene, a result that is compatible with human‐mediated dispersal of almond tree out of its centre of origin. Still, the detection of region‐specific alleles suggests that gene flow from relictual wild preglacial populations (in North Africa) or from wild counterparts (in the Near East) could account for a fraction of the diversity observed.     

History vs. habitat type: explaining the genetic structure of European nine‐spined stickleback (Pungitius pungitius) populations

The genetic structure of contemporary populations can be shaped by both their history and current ecological conditions. We assessed the relative importance of postglacial colonization history and habitat type in the patterns and degree of genetic diversity and differentiation in northern European nine‐spined sticklebacks (Pungitius pungitius), using mitochondrial DNA (mtDNA) sequences and 12 nuclear microsatellite and insertion/deletion loci. The mtDNA analyses identified – and microsatellite analyses supported – the existence of two historically distinct lineages (eastern and western). The analyses of nuclear loci among 51 European sites revealed clear historically influenced and to minor degree habitat dependent, patterns of genetic diversity and differentiation. While the effect of habitat type on the levels of genetic variation (coastal > freshwater) and differentiation (freshwater > coastal) was clear, the levels of genetic variability and differentiation in the freshwater sites were independent of habitat type (viz. river, lake and pond). However, levels of genetic variability, together with estimates of historical effective population sizes, decreased dramatically and linearly with increasing latitude. These geographical patterns of genetic variability and differentiation suggest that the contemporary genetic structure of freshwater nine‐spined sticklebacks has been strongly impacted by the founder events associated with postglacial colonization and less by current ecological conditions (cf. habitat type). In general, the results highlight the strong and persistent effects of postglacial colonization history on genetic structuring of northern European fauna and provide an unparalleled example of latitudinal trends in levels of genetic diversity.     

Genetic Diversity Patterns and Functional Traits of Bradyrhizobium Strains Associated with Pterocarpus officinalis Jacq. in Caribbean Islands and Amazonian Forest (French Guiana)

Pterocarpus officinalis Jacq. is a legume tree native to the Caribbean islands and South America growing as a dominant species in swamp forests. To analyze (i) the genetic diversity and (ii) the symbiotic properties of its associated nitrogen-fixing soil bacteria, root nodules were collected from P. officinalis distributed in 16 forest sites of the Caribbean islands and French Guiana. The sequencing of the 16S-23S ribosomal RNA intergenic spacer region (ITS) showed that all bacteria belonged to the Bradyrhizobium genus. Bacteria isolated from insular zones showed very close sequence homologies with Bradyrhizobium genospecies V belonging to the Bradyrhizobium japonicum super-clade. By contrast, bacteria isolated from continental region displayed a larger genetic diversity and belonged to B. elkanii super-clade. Two strains from Puerto Rico and one from French Guiana were not related to any known sequence and could be defined as a new genospecies. Inoculation experiments did not show any host specificity of the Bradyrhizobium strains tested in terms of infectivity. However, homologous Bradyrhizobium sp. strain-P. officinalis provenance associations were more efficient in terms of nodule production, N acquisition, and growth than heterologous ones. The dominant status of P. officinalis in the islands may explain the lower bacterial diversity compared to that found in the continent where P. officinalis is associated with other leguminous tree species. The specificity in efficiency found between Bradyrhizobium strains and host tree provenances could be due to a coevolution process between both partners and needs to be taken in consideration in the framework of rehabilitation plantation programs.     

Colonization history and genetic diversity: adaptive potential in early stage invasions

The introduction of Anolis cristatellus from the multiple species anole community of Puerto Rico in the Greater Antilles to the island of Dominica in the Lesser Antilles, with its solitary endemic anole, provides an example of a very recent, timed, single colonization. We investigate the geographic origin and adaptive potential of the Dominican population using a range of methods including mtDNA phylogeography, nuclear microsatellite variation and multiple paternity studies, as well as heritability estimates, common garden experiments and comparative geographic studies of quantitative scalation traits. Phylogeographic analysis of NADH2 and microsatellite studies suggests that the Dominican population arose from a set of individuals from the central west area of Puerto Rico within their endemic range. The multiple‐individual inoculation, together with sperm storage and evidence of multiple paternity indicate genetic variability and suggest the potential for adaptation by natural selection. Estimates of heritability, common garden experiments and broad sense Q_ST/F_ST ratios, linked to replicated comparisons along elevational transects go some way to suggesting that the invasive populations may be adapting by natural selection, in parallel with the endemic anole, in the brief period since their introduction.     

Cumulative effects of founding events during colonisation on genetic diversity and differentiation in an island and stepping-stone model

This paper investigates the cumulative effect of founding events on the genetic differentiation and the within-population heterozygosity in a metapopulation increasing its size by colonisation. Two contrasting models are considered: first, an island model, where migrants and colonists are taken at random from the entire metapopulation, and second, a linear stepping-stone model, where migrants and colonists are sampled from a limited neighbourhood. The genetic consequences of a range expansion depend on the relative magnitudes of the number of colonists and migrants, in a way similar to extinction and colonisation processes (Wade and McCauley, 1988). The cumulative effect of founding events, resulting most often in a transient increase in genetic differentiation and a gradual loss of within-population heterozygosity, also depends on the age-structure that is established during colonisation. It is the highest when colonists are sampled from recently founded populations and migrants are exchanged among populations of similar ages. The genetic consequences of a range expansion are therefore far more pronounced and lasting in the linear stepping-stone model than in the island model. These two models, however, represent the two extremes between which real populations will fall.     

Inferring recruitment history from spatial genetic structure within populations of the colonizing tree Albizia julibrissin (Fabaceae)

Comparative analyses of spatial genetic structure (SGS) among species, populations, or cohorts give insight into the genetic consequences of seed dispersal in plants. We analysed SGS of a weedy tree in populations with known and unknown recruitment histories to first establish patterns in populations with single vs. multiple founders, and then to infer possible recruitment scenarios in populations with unknown histories. We analysed SGS in six populations of the colonizing tree Albizia julibrissin Durazz. (Fabaceae) in Athens, Georgia. Study sites included two large populations with multiple, known founders, two small populations with a single, known founder, and two large populations with unknown recruitment histories. Eleven allozyme loci were used to genotype 1385 individuals. Insights about the effects of colonization history from the SGS analyses were obtained from correlograms and Sp statistics. Distinct differences in patterns of SGS were identified between populations with multiple founders vs. a single founder. We observed significant, positive SGS, which decayed with increasing distance in the populations with multiple colonists, but little to no SGS in populations founded by one colonist. Because relatedness among individuals is estimated relative to a local reference population, which usually consists of those individuals sampled in the study population, SGS in populations with high background relatedness, such as those with a single founder, may be obscured. We performed additional analyses using a regional reference population and, in populations with a single founder, detected significant, positive SGS at all distances, indicating that these populations consist of highly related descendants and receive little seed immigration. Subsequent analyses of SGS in size cohorts in the four large study populations showed significant SGS in both juveniles and adults, probably because of a relative lack of intraspecific demographic thinning. SGS in populations of this colonizing tree is pronounced and persistent and is determined by the number and relatedness of founding individuals and adjacent seed sources. Patterns of SGS in populations with known histories may be used to indirectly infer possible colonization scenarios for populations where it is unknown.     

Initial genetic diversity enhances population establishment and alters genetic structuring of a newly established Daphnia metapopulation

When newly created habitats are initially colonized by genotypes with rapid population growth rates, later arriving colonists may be prevented from establishing. Although these priority effects have been documented in multiple systems, their duration may be influenced by the diversity of the founding population. We conducted a large‐scale field manipulation to investigate how initial clonal diversity influences temporal and landscape patterns of genetic structure in a developing metapopulation. Six genotypes of obligately asexual Daphnia pulex were stocked alone (no clonal diversity) or in combination (‘high’ clonal diversity) into newly created experimental woodland ponds. We also measured the population growth rate of all clones in the laboratory when raised on higher‐quality and lower‐quality resources. Our predictions were that in the 3 years following stocking, clonally diverse populations would be more likely to persist than nonclonally diverse populations and exhibit evidence for persistent founder effects. We expected that faster growing clones would be found in more pools and comprise a greater proportion of individuals genotyped from the landscape. Genetic composition, both locally and regionally, changed significantly following stocking. Six of 27 populations exhibited evidence for persistent founder effects, and populations stocked with ‘high’ clonal diversity were more likely to exhibit these effects than nonclonally diverse populations. Performance in the laboratory was not predictive of clonal persistence or overall dominance in the field. Hence, we conclude that although laboratory estimates of fitness did not fully explain metapopulation genetic structure, initial clonal diversity did enhance D. pulex population establishment and persistence in this system.     

A strong genetic footprint of the re‐introduction history of Alpine ibex (Capra ibex ibex)

A population’s neutral genetic variation is a composite of its size, degree of isolation and demographic history. Bottlenecks and founder events increase genetic drift, leading to the loss of genetic variation and increased genetic differentiation among populations. Gene flow has the opposite effects. Thus, gene flow can override the genetic patterns caused by founder events. Using 37 microsatellite loci, we investigated the effects of serial bottlenecks on genetic variation and differentiation among 42 Alpine ibex populations in Switzerland with known re‐introduction histories. We detected a strong footprint of re‐introduction events on contemporary genetic structure, with re‐introduction history explaining a substantial part of the genetic differentiation among populations. As a result of the translocation of a considerable number of individuals from the sole formerly surviving population in northern Italy, most of the genetic variation of the ancestral population is now present in the combined re‐introduced Swiss populations. However, re‐introductions split up the genetic variation among populations, such that each contemporary Swiss population showed lower genetic variation than the ancestral population. As expected, serial bottlenecks had different effects on the expected heterozygosity (He) and standardized number of alleles (sNa). While loss of sNa was higher in the first bottlenecks than in subsequent ones, He declined to a similar degree with each bottleneck. Thus, genetic drift was detected with each bottleneck, even when no loss of sNa was observed. Overall, more than a hundred years after the beginning of this successful re‐introduction programme, re‐introduction history was the main determinant of today’s genetic structure.     

Species distribution modeling and molecular markers suggest longitudinal range shifts and cryptic northern refugia of the typical calcareous grassland species Hippocrepis comosa (horseshoe vetch)

Calcareous grasslands belong to the most diverse, endangered habitats in Europe, but there is still insufficient information about the origin of the plant species related to these grasslands. In order to illuminate this question, we chose for our study the representative grassland species Hippocrepis comosa (Horseshoe vetch). Based on species distribution modeling and molecular markers, we identified the glacial refugia and the postglacial migration routes of the species to Central Europe. We clearly demonstrate that H. comosa followed a latitudinal and due to its oceanity also a longitudinal gradient during the last glacial maximum (LGM), restricting the species to southern refugia situated on the Peninsulas of Iberia, the Balkans, and Italy during the last glaciation. However, we also found evidence for cryptic northern refugia in the UK, the Alps, and Central Germany. Both species distribution modeling and molecular markers underline that refugia of temperate, oceanic species such as H. comosa must not be exclusively located in southern but also in western of parts of Europe. The analysis showed a distinct separation of the southern refugia into a western cluster embracing Iberia and an eastern group including the Balkans and Italy, which determined the postglacial recolonization of Central Europe. At the end of the LGM, H. comosa seems to have expanded from the Iberian refugium, to Central and Northern Europe, including the UK, Belgium, and Germany.     

Colonization history and population genetics of the color-polymorphic hawaiian happy-face spider theridion grallator (araneae, theridiidae)

Past geological and climatological processes shape extant biodiversity. In the Hawaiian Islands, these processes have provided the physical environment for a number of extensive adaptive radiations. Yet, single species that occur throughout the islands provide some of the best cases for understanding how species respond to the shifting dynamics of the islands in the context of colonization history and associated demographic and adaptive shifts. Here, we focus on the Hawaiian happy-face spider, a single color-polymorphic species, and use mitochondrial and nuclear allozyme markers to examine (1) how the mosaic formation of the landscape has dictated population structure, and (2) how cycles of expansion and contraction of the habitat matrix have been associated with demographic shifts, including a "quantum shift" in the genetic basis of the color polymorphism. The results show a marked structure among populations consistent with the age progression of the islands. The finding of low genetic diversity at the youngest site coupled with the very high diversity of haplotypes on the slightly older substrates that are highly dissected by recent volcanism suggests that the mosaic structure of the landscape may play an important role in allowing differentiation of the adaptive color polymorphism.     

Spatial structure and genetic diversity of two tropical tree species with contrasting breeding systems and different ploidy levels

Analyses of the spatial distribution pattern, spatial genetic structure and of genetic diversity were carried out in two tropical tree species with contrasting breeding systems and different ploidy levels using a 50-ha demographic plot in a lowland dipterocarp forest in Peninsular Malaysia. Shorea leprosula is a diploid and predominantly outcrossed species, whereas S. ovalis ssp. sericea is an autotetraploid species with apomictic mode of reproduction. Genetic diversity parameters estimated for S. leprosula using microsatellite were consistently higher than using allozyme. In comparisons with S. leprosula and other tropical tree species, S. ovalis ssp. sericea also displayed relatively high levels of genetic diversity. This might be explained by the lower pressure of genetic drift due to tetrasomic inheritance, and for autotetraploids each locus can accommodate up to four different alleles and this allows maintenance of more alleles at individual loci. The observed high levels of genetic diversity in S. ovalis ssp. sericea can also be due to a random retention of more heterogeneous individuals in the past, and the apomictic mode of reproduction might be an evolutionary strategy, which allows the species to maintain high levels of genetic diversity. The spatial distribution pattern analyses of both species showed significant levels of aggregation at small and medium but random distribution at the big diameter-class. The decrease in magnitude of spatial aggregation from small- to large-diameter classes might be due to compensatory mortality during recruitment and survival under competitive thinning process. Spatial genetic structure analyses for both species revealed significant spatial genetic structure for short distances in all the three diameter-classes. The magnitude of spatial genetic structure in both species was observed to be decreasing from smaller- to larger-diameter classes. The high spatial genetic structuring observed in S. ovalis ssp. sericea at the small-diameter class is due primarily to limited seed dispersal and apomictic mode of reproduction. The similar observation in S. leprosula, however, can be explained by limited seed and pollen dispersal, which supports further the fact that the species is pollinated by weak fliers, mainly of Thrips and Megalurothrips in the lowland dipterocarp forest.     

Patterns of genetic diversity reveal multiple introductions and recurrent founder effects during range expansion in invasive populations of Geranium carolinianum (Geraniaceae)

Genetic diversity, and thus the adaptive potential of invasive populations, is largely based on three factors: patterns of genetic diversity in the species'' native range, the number and location of introductions and the number of founding individuals per introduction. Specifically, reductions in genetic diversity (‘founder effects'') should be stronger for species with low within-population diversity in their native range and few introductions of few individuals to the invasive range. We test these predictions with Geranium carolinianum, a winter annual herb native to North America and invasive in China. We measure the extent of founder effects using allozymes and microsatellites, and ask whether this is consistent with its colonization history and patterns of diversity in the native range. In the native range, genetic diversity is higher and structure is lower than expected based on life history traits. In China, our results provide evidence for multiple introductions near Nanjing, Jiangsu province, with subsequent range expansion to the west and south. Patterns of genetic diversity across China reveal weak founder effects that are driven largely by low-diversity populations at the expansion front, away from the introduction location. This suggests that reduced diversity in China has resulted from successive founder events during range expansion, and that the loss of genetic diversity in the Nanjing area was mitigated by multiple introductions from diverse source populations. This has implications for the future of G. carolinianum in China, as continued gene flow among populations should eventually increase genetic diversity within the more recently founded populations.