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High Genetic Diversity in a Potentially Vulnerable Tropical Tree Species Despite Extreme Habitat Loss

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PLOS ONE
Authors:
Annika M E Noreen
Annika M E Noreen
Edward L. Webb at University of Helsinki
Edward L. Webb
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Abstract and Figures

Over the last 150 years, Singapore's primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter), 193 saplings (>1 yr), and 1,822 seedlings (<1 yr) of the canopy tree Koompassia malaccensis (Fabaceae). We tested hypotheses relevant to the genetic consequences of habitat loss: (1) that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2) K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843-0.854), high allelic richness (R = 16.7-19.5), low inbreeding co-efficients (FIS = 0.013-0.076), and a large proportion (30.1%) of rare alleles (i.e. frequency <1%). However, spatial genetic structure (SGS) analyses showed significant differences between the adults and the recruits. We detected significantly greater SGS intensity, as well as higher relatedness in the 0-10 m distance class, for seedlings and saplings compared to the adults. Demographic factors for this population (i.e. <200 adult trees) are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961), calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss.
Map of Singapore’s remaining primary forest fragments within a secondary forest and urban matrix. Dark green – primary forest; Light green – secondary forest; red dots – adult K. malaccensis individuals. doi:10.1371/journal.pone.0082632.g001
Map of Singapore’s remaining primary forest fragments within a secondary forest and urban matrix. Dark green – primary forest; Light green – secondary forest; red dots – adult K. malaccensis individuals. doi:10.1371/journal.pone.0082632.g001
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Sample size (N) per locus, size range of alleles, total number of alleles detected, observed (Ho) and expected (He) heterozygosity, genotyping error rate, percent missing data, percent null alleles, and inbreeding co-efficient values (FIS).
Sample size (N) per locus, size range of alleles, total number of alleles detected, observed (Ho) and expected (He) heterozygosity, genotyping error rate, percent missing data, percent null alleles, and inbreeding co-efficient values (FIS).
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Map of Singapore’s remaining primary forest fragments within a secondary forest and urban matrix. Dark green – primary forest; Light green – secondary forest; red dots – adult K. malaccensis individuals.
Map of Singapore’s remaining primary forest fragments within a secondary forest and urban matrix. Dark green – primary forest; Light green – secondary forest; red dots – adult K. malaccensis individuals.
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Allele frequencies for each locus. Alleles present in very low numbers have the frequency presented above the allele if the bar too small to be easily visualized. All potential allele sizes within the captured range (assuming normal dinucleotide repeat units) are included in the x-axis; blanks indicate that this allele size was not captured. A dot below the allele indicates an unusual size (1 bp difference from nearest allele). ‘a’ indicates a private allele in the adult age class, ‘s’ indicates a private allele in the seedling cohort. doi:10.1371/journal.pone.0082632.g002
Allele frequencies for each locus. Alleles present in very low numbers have the frequency presented above the allele if the bar too small to be easily visualized. All potential allele sizes within the captured range (assuming normal dinucleotide repeat units) are included in the x-axis; blanks indicate that this allele size was not captured. A dot below the allele indicates an unusual size (1 bp difference from nearest allele). ‘a’ indicates a private allele in the adult age class, ‘s’ indicates a private allele in the seedling cohort. doi:10.1371/journal.pone.0082632.g002
… 
Allele frequencies for each locus. Alleles present in very low numbers have the frequency presented above the allele if the bar too small to be easily visualized. All potential allele sizes within the captured range (assuming normal dinucleotide repeat units) are included in the x-axis; blanks indicate that this allele size was not captured. A dot below the allele indicates an unusual size (1 bp difference from nearest allele). ‘a’ indicates a private allele in the adult age class, ‘s’ indicates a private allele in the seedling cohort.
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Allele frequencies for each locus. Alleles present in very low numbers have the frequency presented above the allele if the bar too small to be easily visualized. All potential allele sizes within the captured range (assuming normal dinucleotide repeat units) are included in the x-axis; blanks indicate that this allele size was not captured. A dot below the allele indicates an unusual size (1 bp difference from nearest allele). ‘a’ indicates a private allele in the adult age class, ‘s’ indicates a private allele in the seedling cohort.
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High Genetic Diversity in a Potentially Vulnerable Tropical Tree Species Despite Extreme Habitat Lo
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... By examining genetic changes over time through temporal sampling (where material from individuals that pre-date the impact of interest should be sampled, as well as populations that established after the impact has had the opportunity to affect diversity; Leigh et al. 2021), researchers may gain valuable insights into the adaptive potential of populations, the impact of environmental factors on genetic diversity, and the efficacy of conservation interventions (Díez-del-Molino et al. 2018). While microsatellite markers have traditionally been used to survey genetic variation across age classes (Kettle et al. 2007;Noreen and Webb 2013), the advent of next-generation sequencing (NGS) data offers several advantages to study the conservation genomics of non-model organisms. NGS methods such as genotyping by sequencing (GBS; Hall et al. 2020) or double-digest restriction-site associated DNA (ddRAD) sequencing (Peterson et al. 2012), can provide useful snapshots of genomic variation across the entire genome, allowing for the assessment of genetic variation across a wide range of loci, and fine-scale resolution of genetic diversity and population structure (Hauser et al. 2011;Niissalo et al. 2018;Yang et al. 2022). ...
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... In the only other study investigating possible genetic erosion of a forest tree species in Singapore, Noreen and Webb (2013) found high genetic diversity in Koompassia malaccensis, with connectivity between BTNR, CCNR and the Singapore Botanic Gardens facilitated by a mobile pollinator, the giant honeybee Apis dorsata (Noreen et al. 2016). However, there were already signs of increased relatedness between individuals at short distances. ...
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The diversity of genetic resources is essential to cope with environmental changes. However, despite forests play a crucial role in mitigating changes, genetic knowledge has scarcely been used for forest conservation. In this study, we used nuclear microsatellites to understand the patterns of genetic diversity and population genetic structure in Ocotea rotundata van der Werff (Lauraceae), an endemic Ecuadorian tree, highly affected by habitat changes and fragmentation. Our results show high levels of genetic diversity, except in one population. The level of genetic differentiation between populations was low and genetic clusters showed no apparent spatial pattern. In fact, a high degree of genetic admixture was found between most populations. Migration rates were asymmetric but overall high, except in one population, where outgoing gene dispersal was limited. Nevertheless, allelic fixation values suggested a general deficit in heterozygotes, probably due to an increase in the levels of mating between close relatives. Although long-lived organisms, such as trees, can often accumulate a surprising amount of genetic diversity, the results found here could be an early sign of a decline in the diversity of O. rotundata. These findings provide baseline information on genetic resources to support future restoration programs to mitigate the impacts of changes in O. rotundata populations.
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... However, these directional trends of influence on tropical trees' genetic variation are not entirely always constant (Minn et al., 2014;Akinnagbe et al., 2019). For instance, Noreen & Webb (2013) found high genetic diversity in Koompassia malaccensis populations across Singapore despite the high habitat loss. Silvestrini et al. (2015) reported similar levels of genetic diversity of Croton floribundus within some Brazilian primary and successional forests. ...
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The global efforts to restore tropical forests and their productive and ecological functions through plantation forestry largely depend on the available genetic variation in the tree species used to establish the plantations. However, there is limited information on the levels and trends of the genetic variation and variability of different plantation tree species in the tropics. Therefore, this study reviews several marker-based studies that have investigated genetic variation. Most of the top economic species like Eucalyptus tereticornis and Mansonia altissima are attributed to low levels of genetic diversity, while others like Pinus caribaea and Swietenia macrophylla still exhibit high expected heterozygosity across different populations. However, the levels of genetic diversity assessed may depend on the markers used. Microsatellites, i.e., simple sequence repeats (SSRs), mostly give higher estimates when compared to other polymerase chain reaction-based markers. Other factors that typically contribute to the directional pattern of genetic variation in tropical tree species and populations include their distribution, density, seed dispersal, succession, and reproduction. Also, anthropogenic impacts like logging and fragmentation have contributed to the vast genetic base reduction of many tropical species and populations. Having adequate genetic variation within the plantation populations is significant in improving their fitness, resilience, fecundity, productivity, and other ecological functions. It also provides a basis for tree improvement and breeding in plantation forests. Although clonal forestry is becoming widespread and considered highly productive, it is attributed to specific economic, technical, and ecological risks, such as the increased spread of pests and diseases. Therefore, further discussions and recommendations to maximise genetic diversity in tropical (clonal) plantations are provided.
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... This hybrid individual was observed to have been pollinated by the giant honey bee (Apis dorsata). These bees are known to be able to transfer pollen over sizeable distances, and have also been inferred to facilitate pollen dispersal of another leguminous tree species, Koompassia malaccensis, between rainforest patches across a distance of more than 2.5 km within the urban landscape of Singapore (Noreen and Webb 2013;Noreen et al. 2016). Given that these bees are likely to be pollinators of other Sindora species, it is therefore possible that this hybrid could have come about by the transfer of pollen between S. coriacea and S. echinocalyx trees at Changi in the past. ...
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... Furthermore, there is a lack of studies on the minimum viable size of tree populations in the conserved areas. Molecular marker studies of genetic diversity, intrapopulation spatial genetic structure (SGS), mating system and pollen/seed dispersal of remaining adult trees of species from before fragmentation and juveniles established after fragmentation help us to determine the evolutionary viability of populations over generations, as well as to estimate the minimum viable area ( MVA ) for in situ conservation (Saccheri and Hanski 2006;Noreen and Webb 2013). ...
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... There have been few genetic studies on the impacts of isolation on plants and animals at Bukit Timah, and possible genetic erosion of their populations. In one of the few population genetic studies of a tree species found at Bukit Timah, Noreen and Webb (2013) looked at genetic diversity and structure in the forest giant Koompassia malaccensis. They found no evidence of a genetic bottleneck nor a reduction in effective population size. ...
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THE SIGNIFICANCE OF GENETIC EROSION IN THE PROCESS OF EXTINCTION. IV. INBREEDING LOAD AND HETEROSIS IN RELATION TO POPULATION SIZE IN THE MINT SALVIA PRATENSIS
Article
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If, because of genetic erosion, the level of homozygosity in small populations is high, additional selfing will result in small reductions of fitness. In addition, in small populations with a long inbreeding history selection may have purged the population of its genetic load. Therefore, a positive relationship between population size (or level of genetic variation) and level of additional inbreeding depression, here referred to as inbreeding load, may be expected. In a previous study on the rare and threatened perennial Salvia pratensis, a positive correlation between population size and level of allozyme variation has been demonstrated. In the present study, the inbreeding load in six populations of varying size and allozyme variation was investigated. In the greenhouse, significant inbreeding load in mean seed weight, proportion of germination, plant size, regenerative capacity, and survival was demonstrated. In a field experiment with the two largest and the two smallest populations, survival of selfed progeny was 16% to 63% lower than survival of outcrossed progeny. In addition, survival of outcrossed progeny was, with the exception of the largest population, lower (16% to 37%) than of hybrid progeny, resulting from crosses between populations. Effects on plant size were qualitatively similar to the effects on survival, but these effects were variable in time because of differential survival of larger individuals. In all populations the total inbreeding load, that is, the effects on size and survival multiplicated, increased in time. It was demonstrated that inbreeding load in different characters may be independent. At no time and for no character was inbreeding load or the heterosis effect correlated to the mean number of alleles per locus, indicating that allozyme variation is not representative for variation at fitness loci in these populations. Combined with results of previous investigations, these results suggest that the small populations are in an early phase of the genetic erosion process. In this phase, allozyme variation, which is supposed to be (nearly) neutral, has been affected by genetic erosion but the selectively nonneutral variation is only slightly affected. These results stress the need for detailed information about the inbreeding history of small populations. The relative performance of selfed progeny was lowest in all populations, in the greenhouse as well as in the field, and inbreeding depression could still influence the extinction probabilities of the small populations.
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New insights from fine-scale spatial genetic structure analysis in plant population
Article
  • Jan 2004
Many empirical studies have assessed fine-scale spatial genetic structure (SGS), i.e. the nonrandom spatial distribution of genotypes, within plant populations using genetic markers and spatial autocorrelation techniques. These studies mostly provided qualitative descriptions of SGS, rendering quantitative comparisons among studies difficult. The theory of isolation by distance can predict the pattern of SGS under limited gene dispersal, suggesting new approaches, based on the relationship between pairwise relatedness coefficients and the spatial distance between individuals, to quantify SGS and infer gene dispersal parameters. Here we review the theory underlying such methods and discuss issues about their application to plant populations, such as the choice of the relatedness statistics, the sampling scheme to adopt, the procedure to test SGS, and the interpretation of spatial autocorrelograms. We propose to quantify SGS by an ' Sp ' statistic primarily dependent upon the rate of decrease of pairwise kinship coefficients between individuals with the logarithm of the distance in two dimensions. Under certain conditions, this statistic estimates the reciprocal of the neighbourhood size. Reanalysing data from, mostly, published studies, the Sp statistic was assessed for 47 plant species. It was found to be significantly related to the mating system (higher in selfing species) and to the life form (higher in herbs than trees), as well as to the population density (higher under low density). We discuss the necessity for comparing SGS with direct estimates of gene dispersal distances, and show how the approach presented can be extended to assess (i) the level of biparental inbreeding, and (ii) the kurtosis of the gene dispersal distribution.
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