Genetic Variation in Fragmented Forest Stands of the Andean Oak Quercus humboldtii Bonpl. (Fagaceae)1

Quercus humboldtii is a montane forest dominant species in Colombia, which has experienced significant habitat loss. Using three microsatellite loci, we compared the genetic diversity of adults and seedlings in fragments of small and large size. Results show high genetic diversity, comparable to other temperate oak species (H_o= 0.813, H_e= 0.780, and f=?0.044). However, allelic richness reduction in seedlings of the most fragmented part of the landscape, suggested restricted gene flow and risk of future genetic bottlenecks, if larger tracts of forest disappear.     

Heterozygote excess through life history stages in Cestrum miradorense Francey (Solanaceae), an endemic shrub in a fragmented cloud forest habitat

Comparisons of genetic diversity and population genetic structure among different life history stages provide important information on the effect of the different forces and micro‐evolutionary processes that mould diversity and genetic structure after fragmentation. Here we assessed genetic diversity and population genetic structure using 32 allozymic loci in adults, seeds, seedlings and juveniles of eight populations of the micro‐endemic shrub Cestrum miradorense in a highly fragmented cloud forest in central–eastern Mexico. We expected that due to its long history or rarity, this species may have endured the negative effects of fragmentation and would show moderate to high levels of genetic diversity. High genetic diversity (H_e = 0.445 ± 0.03), heterozygote excess (F_IT = ?0.478 ± 0.034, F_IS = ?0.578 ± 0.023) and low population differentiation (F_ST = 0.064 ± 0.011) were found. Seeds had higher genetic diversity (H_e = 0.467 ± 0.05) than the later stages (overall mean for adults, seedlings and juveniles H_e = 0.438 ± 0.08). High gene flow was observed despite the fact that the fragmentation process began more than 100 years ago. We conclude that the high genetic diversity was the result of natural selection, which favours heterozygote excess in all stages, coupled with a combination of a reproductive system and seed/pollen dispersal mechanisms that favour gene flow.     

Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rain forest skink, Gnypetoscincus queenslandiae

To examine the effects of recent habitat fragmentation, we assayed genetic diversity in a rain forest endemic lizard, the prickly forest skink (Gnypetoscincus queenslandiae), from seven forest fragments and five sites in continuous forest on the Atherton tableland of northeastern Queensland, Australia. The rain forest in this region was fragmented by logging and clearing for dairy farms in the early 1900s and most forest fragments studied have been isolated for 50-80 years or nine to 12 skink generations. We genotyped 411 individuals at nine microsatellite DNA loci and found fewer alleles per locus in prickly forest skinks from small rain forest fragments and a lower ratio of allele number to allele size range in forest fragments than in continuous forest, indicative of a decrease in effective population size. In contrast, and as expected for populations with small neighbourhood sizes, neither heterozygosity nor variance in allele size differed between fragments and sites in continuous forests. Considering measures of among population differentiation, there was no increase in FST among fragments and a significant isolation by distance pattern was identified across all 12 sites. However, the relationship between genetic (FST) and geographical distance was significantly stronger for continuous forest sites than for fragments, consistent with disruption of gene flow among the latter. The observed changes in genetic diversity within and among populations are small, but in the direction predicted by the theory of genetic erosion in recently fragmented populations. The results also illustrate the inherent difficulty in detecting genetic consequences of recent habitat fragmentation, even in genetically variable species, and especially when effective population size and dispersal rates are low.     

Genetic variation within a fragmented population of swietenia humilis zucc

With large tracts of once continuous forest now modified by human use to leave reduced and highly fragmented stands of trees, the determination of the genetic consequences of forest fragmentation is a priority for ascertaining the conservation value of resultant stands, and in formulating sustainable management strategies. The levels and distribution of genetic diversity over 10 microsatellite loci were investigated within a fragmented population of the neotropical tree Swietenia humilis Zucc. High levels of genetic variation, typical of a highly outcrossing species, were found in all fragments at all loci (mean HE = 0.548). The majority of the variation was within rather than between fragments (RST = 0.032), giving high indirect estimates of gene flow (Nm = 8.9), probably reflecting the genetic structure of the trees present under more continuous forest. A high proportion of loci also showed significant departures from Hardy-Weinberg equilibrium with associated significant levels of FIS. The initial effects of fragmentation were, however, seen in the fragments through the loss of low-frequency alleles present in the continuous 'control' stand. The percentage of this allelic loss increased with a decrease in fragment size.     

Fine-scale spatial genetic structure and gene flow in a small, fragmented population of Sinojackia rehderiana (Styracaceae), an endangered tree species endemic to China

Populations of Sinojackia rehderiana are highly threatened and have small and scattered distribution due to habitat fragmentation and human activities. Understanding changes in genetic diversity, the fine-scale spatial genetic structure (SGS) at different life stages and gene flow of S. rehderiana is critical for developing successful conservation strategies for fragmented populations of this endangered species. In this study, 208 adults, 114 juveniles and 136 seedlings in a 50 × 100-m transect within an old-growth forest were mapped and genotyped using eight microsatellite makers to investigate the genetic diversity and SGS of this species. No significant differences in genetic diversity among different life-history stages were found. However, a significant heterozygote deficiency in adults and seedlings may result from substantial biparental inbreeding. Significant fine-scale spatial structure was found in different life-history stages within 19 m, suggesting that seed dispersal mainly occurred near a mother tree. Both historical and contemporary estimates of gene flow (13.06 and 16.77 m) indicated short-distance gene dispersal in isolated populations of S. rehderiana. The consistent spatial structure revealed in different life stages is most likely the result of limited gene flow. Our results have important implications for conservation of extant populations of S. rehderiana. Measures for promoting pollen flow should be taken for in situ conservation. The presence of a SGS in fragmented populations implies that seeds for ex situ conservation should be collected from trees at least 19-m apart to reduce genetic similarity between neighbouring individuals.     

GENETIC COMPARISONS OF SEED BANK AND SEEDLING POPULATIONS OF A PERENNIAL DESERT MUSTARD,LESQUERELLA FENDLERI

Soil seed banks may accumulate and store seed genotypes produced over many seasons. If germination and establishment of these soil seeds are influenced by seed genotypes, then seed bank and seedling populations may differ genetically. I compared the genetic structure of dormant but viable soil seeds of the desert mustard Lesquerella fendleri with the genetic structure of Lesquerella seedlings at the Sevilleta Long-Term Ecological Research Site. In 1991 and 1992, soil seeds and seedlings were mapped and genetically analyzed using starch gel electrophoresis. When data from all loci were lumped, there were highly significant differences in allele frequencies between soil seeds and seedlings at the population level (all plots) in both years, in all subpopulation (adjacent plots) comparisons in 1991, and three of five subpopulations in 1992. Differences at some individual loci were also detected in one or both years. Analysis of data pooled across both years revealed highly significant differences in the distribution of multilocus soil seed and seedling heterozygosity, but no significant differences in mean heterozygosity. F_st values showed small but statistically significant genetic differentiation within soil seeds and seedlings in both years. F_st values also showed significant genetic differentiation between these two groups at three of seven loci in 1991, and at one locus in 1992. Soil seeds and seedlings showed a general pattern of decreasing genetic relationship with distance, as estimated by the coefficient of coancestry analyses. In 1991, seedlings were roughly twice as genetically related to each other than were soil seeds at fine spatial scales (0–0.25 and 0.25–0.50 m). This study suggests that Lesquerella seedlings in this system represent a nonrandom genetic subset of the underlying Lesquerella seed bank. Such temporal genetic change may be an important yet frequently overlooked mechanism for generating population genetic structure.     

Pollen dispersal and genetic structure of the tropical tree Dipteryx panamensis in a fragmented Costa Rican landscape

In the face of widespread deforestation, the conservation of rainforest trees relies increasingly on their ability to maintain reproductive processes in fragmented landscapes. Here, we analysed nine microsatellite loci for 218 adults and 325 progeny of the tree Dipteryx panamensis in Costa Rica. Pollen dispersal distances, genetic diversity, genetic structure and spatial autocorrelation were determined for populations in four habitats: continuous forest, forest fragments, pastures adjacent to fragments and isolated pastures. We predicted longer but less frequent pollen movements among increasingly isolated trees. This pattern would lead to lower outcrossing rates for pasture trees, as well as lower genetic diversity and increased structure and spatial autocorrelation among their progeny. Results generally followed these expectations, with the shortest pollen dispersal among continuous forest trees (240 m), moderate distances for fragment (343 m) and adjacent pasture (317 m) populations, and distances of up to 2.3 km in isolated pastures (mean: 557 m). Variance around pollen dispersal estimates also increased with fragmentation, suggesting altered pollination conditions. Outcrossing rates were lower for pasture trees and we found greater spatial autocorrelation and genetic structure among their progeny, as well as a trend towards lower heterozygosity. Paternal reproductive dominance, the pollen contributions from individual fathers, did not vary among habitats, but we did document asymmetric pollen flow between pasture and adjacent fragment populations. We conclude that long-distance pollen dispersal helps maintain gene flow for D. panamensis in this fragmented landscape, but pasture and isolated pasture populations are still at risk of long-term genetic erosion.     

Can balancing selection on MHC loci counteract genetic drift in small fragmented populations of black grouse?

The ability of natural populations to adapt to new environmental conditions is crucial for their survival and partly determined by the standing genetic variation in each population. Populations with higher genetic diversity are more likely to contain individuals that are better adapted to new circumstances than populations with lower genetic diversity. Here, we use both neutral and major histocompatibility complex (MHC) markers to test whether small and highly fragmented populations hold lower genetic diversity than large ones. We use black grouse as it is distributed across Europe and found in populations with varying degrees of isolation and size. We sampled 11 different populations; five continuous, three isolated, and three small and isolated. We tested patterns of genetic variation in these populations using three different types of genetic markers: nine microsatellites and 21 single nucleotide polymorphisms (SNPs) which both were found to be neutral, and two functional MHC genes that are presumably under selection. The small isolated populations displayed significantly lower neutral genetic diversity compared to continuous populations. A similar trend, but not as pronounced, was found for genotypes at MHC class II loci. Populations were less divergent at MHC genes compared to neutral markers. Measures of genetic diversity and population genetic structure were positively correlated among microsatellites and SNPs, but none of them were correlated to MHC when comparing all populations. Our results suggest that balancing selection at MHC loci does not counteract the power of genetic drift when populations get small and fragmented.     

Proximity is not a proxy for parentage in an animal-dispersed Neotropical canopy palm

We used parentage analysis to estimate seedling recruitment distances and genetic composition of seedling patches centred around reproductive trees of the animal-dispersed Neotropical canopy palm Iriartea deltoidea in two 0.5 ha plots within second-growth forest and one 0.5 ha plot in adjacent old-growth forest at La Selva Biological Field Station in north-eastern Costa Rica. Seedlings were significantly spatially aggregated in all plots, but this pattern was not due to dispersal limitation. More than 70 per cent of seedlings were dispersed at least 50 m from parent trees. Few seedlings were offspring of the closest reproductive trees. Seedling patches observed beneath reproductive trees originate from dozens of parental trees. Observed patterns of seedling distribution and spatial genetic structure are largely determined by the behaviour of vertebrate seed dispersers rather than by spatial proximity to parental trees.     

Gone with the wind: Negative genetic and progeny fitness consequences of habitat fragmentation in the wind pollinated dioecious tree Brosimum alicastrum

Premise

Habitat fragmentation negatively affects population size and mating patterns that directly affect progeny fitness and genetic diversity; however, little is known about the effects of habitat fragmentation on dioecious, wind pollinated trees. We assessed the effects of habitat fragmentation on population sex ratios, genetic diversity, gene flow, mating patterns, and early progeny vigor in the tropical dioecious tree, Brosimum alicastrum.

Methods

We conducted our study in three continuous and three fragmented forest sites in a Mexican tropical dry forest. We used eight microsatellite loci to characterize the genetic diversity, gene flow via pollen distances, and mean relatedness of progeny. We compared early progeny vigor parameters of seedlings growing under greenhouse conditions.

Results

Sex ratios did not deviate from 1:1 between habitat conditions except for one population in a fragmented habitat, which was female biased. The genetic diversity of adult trees and their offspring was similar in both habitat conditions. Pollen gene flow distances were similar across habitat types; however, paternity correlations were greater in fragmented than in continuous habitats. Germination rates did not differ between habitat conditions; however, progeny from fragmented habitats produced fewer leaves and had a lower foliar area, total height, and total dry biomass than progeny from continuous habitats.

Conclusions

Changes in mating patterns because of habitat fragmentation have negative effects on early progeny vigor. We conclude that negative habitat fragmentation effects on mating patterns and early progeny vigor may be a serious threat to the long-term persistence of tropical dioecious trees.