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

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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.
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... Consequently, high genetic diversity has been reported in many trees, such as Koompassia malaccensis Maingay ex Benth. [9], Cercis canadensis L. [10], and Shorea leprosula Miq. [11]. ...
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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.
... 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.
... 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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Sindora × changiensis L.M.Choo, Loo, W.F.Ang & K.Er is a new hybrid from the subfamily Detarioideae in Fabaceae. This is the first reported instance of natural hybridisation in Sindora. Based on population genetics analyses using ddRAD and morphological observations, this taxon represents a fertile hybrid between Sindora coriacea and Sindora echinocalyx. This new hybrid is so far only known to occur naturally from Changi at the northeastern coast of Singapore. It has pods that are sparsely spiny. This is intermediate between the smooth, non-spiny pods of S. coriacea, and the densely spiny pods of S. echinocalyx. The calyx is smooth and unarmed, resembling S. coriacea. Last but not least, the ovary is entirely pubescent, different from S. coriacea and S. echinocalyx. The ovary of S. coriacea has a glabrous patch in the middle , while that of S. echinocalyx has minute spines protruding from the dense pubescence. A taxonomic description and an updated key to the Sindora of Singapore and Peninsular Malaysia are also provided.
... 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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Key message Although all populations show extensive pollen immigration, the occurrence of spatial genetic structure and biparental inbreeding decreased genetic diversity and effective population size. Abstract The Brazilian savanna is the second largest Neotropical biome, and a globally important biodiversity hotspot. Basic knowledge of the ecology and genetics of its species can help conserve this important biome. We investigated genetic diversity, spatial genetic structure (SGS), pollen dispersal, and mating system in three Hymenaea stigonocarpa populations (AS, PE, IT) in the Brazilian savanna, using microsatellite loci and samples of adult trees from all populations and seeds from the IT population. As a result of the long geographic distance between populations, the genetic differentiation among them was high (0.397). Individuals of the IT population presented a grouped distribution due to root propagation, resulting in low genotypic richness (GR\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\mathrm{GR}$$\end{document} = 0.194) and allelic richness (R\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$R$$\end{document} = 4), and high SGS (Sp\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\mathrm{Sp}$$\end{document} = 0.064) compared to AS and PE (GR\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\mathrm{GR}$$\end{document} > 0.98, R > 5, Sp\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\mathrm{Sp}$$\end{document} < 0.026) populations. The IT population showed high pollen immigration (46.4%), pollen dispersal distance (up to 3.57 km), and outcrossing rate (0.934–1.0), but matings were correlated (0.01–1), and some occurred among relatives (up to 0.098), resulting in some inbred seeds (0.140), a lower variance effective population size (Ne\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${N}_{e}$$\end{document} = 3.02) than expected with random mating, and an estimate of 50 seed-trees required to retain an Ne\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${N}_{e}$$\end{document} of 150 in samples of maternal progeny. The estimated minimum viable area to retain a reference (Ner\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${N}_{\mathrm{er}}$$\end{document}) of 1000 indicates that the current AS and IT population areas are insufficient to maintain viable populations in the long-term, demonstrating the importance of maintaining surrounding areas for conservation of these H. stigonocarpa populations.
... 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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Forest fragments are increasingly common in the tropics as pristine forests are cleared. Fragments stranded within cities are especially stress-prone due to their greatly altered environment and high human impacts. We review biodiversity and ecological studies from Bukit Timah, a tropical forest fragment in Singapore, to ask how this forest has contributed to our understanding of tropical ecology and fragmentation effects, and list the conservation values of this forest. Evidence from Amazonian fragments predicts that losses in diversity and forest function follow fragmentation, and although Bukit Timah has adhered to some of those predictions, other aspects of the forest appeared remarkably resilient. As might be expected, declines in plant, invertebrate, bird, and mammal diversity occurred not only historically but also across two surveys made about 20 years apart. In other ways Bukit Timah proved surprising. Aboveground biomass fluctuated but did not plummet drastically, and was comparable to levels found in primary forests in the region. The extirpation of large fauna did not appear to reduce the dispersal of large seeded plant species, likely due to continued dispersal by small-mammals and birds. Exotic tree species are confined to recovering secondary forest fringes and do not threaten the primary forest, except for perhaps shade tolerant Pará rubber and a handful of cultivated fruit trees. Studies of birds and plants found that life history differences could account for differences in genetic connectivity or isolation for different species, with population genetic implications for other taxa. Despite being a small fragment, new species of plants and animals continue to be discovered or rediscovered. Clearly, there are reasons to celebrate Bukit Timah as a forest fragment that withstood two centuries of human impacts. Nonetheless, many measures can be implemented to better secure its future.
... ⎯ D.J. Mabberley (1992: 265) Another area which we know very little about is the population genetics of rainforest plants. Some investigations are throwing light on genetic processes, including how pollen flow (Ng et al., 2006) and seed dispersal (Foster & Sork, 1997) affect genetic differentiation, and the possible influences of life history and ecological traits on levels of genetic diversity (Hamrick et al., 1992;Noreen & Webb, 2013). Whereas selective logging may not significantly reduce the genetic diversity of some canopy tree species (Ang et al., 2017), it appears to do so in a number of cases, where inbreeding with a reduced number of individuals may be a potential outcome (Shorea megistophylla P.S. Ashton: Murawski et al., 1994; Dryobalanops aromatica C.F.Gaertn.: Lee, 2000). ...
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Contemporary studies into the spectrum of plant life assembled on the island of Borneo continue to demonstrate an astonishing richness for some groups. Not all lineages are equivalent in their richness, and both biogeographic and ecological factors are the principal correlates of species richness and lineage diversification. The ways in which population genetic factors may influence the generation and persistence of variation, and their interaction with environmental change, could have fundamental importance in how diversity is maintained. Central Sarawak in the northwest Borneo hotspot is a premier ecological theatre where the interplay of such factors operates: its plant species richness is astounding, floristic documentation continues perhaps too slowly, and research and conservation priorities continue to loom large. Unfortunately, this resource has been severely modified in the several decades spanning the turn of the 21st century. The importance of increasing public perception, especially with well-illustrated accounts of this biological richness and its significance through a natural history perspective, will be as critical as the slowly advancing frontiers of the scientific platform on which our understanding depends.
... Other studies in endangered tree species have found high levels of genetic diversity in small fragmented populations, such as for the critically endangered Rhododendron protistum var. giganteum (Forrest ex Tagg) D.F. Chamb. in China (Wu et al. 2015), the locally endangered Koompassia malaccensis Maing. in Singapore (Noreen and Webb 2013), or the locally rare Guaiacum sanctum L. in Costa Rica (Fuchs and Hamrick 2010), which were explained by high levels of historical gene flow. In contrast, low genetic diversity has been found in other endangered species, which was revealed when seedlings and adults were contrasted, such as for the tropical tree Prunus africana (Hook. ...
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Magnolias are characteristic tree species of the Tropical Montane Cloud Forest (TMCF) in Mexico, an ecosystem that is highly threatened by habitat fragmentation and climate change. In this study, based on DNA sequences from five regions (chloroplast: trnT-trnL, trnK5-matK, trnS-trnG, rpl32-trnL, nuclear: ITS) and seven nuclear microsatellite markers, we aimed to delineate species boundaries between two-endemic species of the TMCF, Magnolia pedrazae and Magnolia schiedeana, and to estimate levels of genetic structure and diversity among populations. Phylogenetic and haplotype network analyses for the chloroplast and ITS regions did not support genetic differentiation as two distinctive species. Results from Bayesian and multivariate cluster analyses based on microsatellite loci showed high genetic differentiation across most populations, which was consistent with a strong and significant pattern of isolation by geographical distance. We found moderate to high levels of population genetic diversity, but it was lower in small populations relative to large populations. Our results suggest a contemporary decrease of genetic connectivity among populations, likely as a consequence of the current decline of suit-able TMCF habitat. Managing landscape connectivity among remnant Magnolia populations within protected natural parks and surroundings, and with emphasis of small populations, would be key for the species conservation. Link to read the pdf: https://rdcu.be/bh0qY
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Forests play an essential role in protecting natural resources such as soil, water and environmental services. The aims of the current study are to analyze definitions involving issues such as forest cover and its vulnerability, as well as to present arguments to help reducing deforestation. Solutions focused on mitigating tree vulnerability are herein presented, namely: genetic conservation and local creation of genetic databases on natural forests; pursuit of maximum genetic diversity to maintain reproduction index and avoid cloning effects; scientifically investigating how to help trees to adapt to environmental changes; use of genetic improvement and programs such as Payment for Environmental Services, Bolsa Floresta Program, Crop-Livestock-Forest Integration and ABC Program to reduce deforestation in tropical forests.
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