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Allele frequencies, numbers of heterozygotes and homozygotes, observed and expected heterozygosities at eight microsatellite loci in 83 adults and 91 saplings of Magnolia obovata
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We analysed the regeneration process of Magnolia obovata using polymorphic microsatellite markers. Eighty-three adult trees standing in a watershed covering an area of 69 ha, and saplings collected from a smaller research plot (6 ha) located at the centre of the watershed were genotyped using microsatellite markers. Among 91 saplings analysed, 24 (...
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... This method made it possible to use noninvasively collected urine, feces, and hair samples from free-ranging animals and led to an increase in laboratory-based primatologists' efforts to study wild animals. Other studies examined the dynamics of hormonal levels in relation to sexual behavior (Fujita et al., 2001), feeding habits, seed-dispersal behaviors (Isagi et al., 2000;Terakawa et al., 2009), and so on. Field primatology began to attract researchers from the laboratory for collaborations, and fieldworkers began to implement these techniques themselves, leading to further insights for primates and other mammals, and even for insects (Shotake & Wada, 1996;Takenaka et al., 2006). ...
... CC is a subtropical evergreen broadleaved tree species [43]. YD is a deciduous tree species [44]. The three tree species are common street trees along all urban streets in Hangzhou. ...
In this paper, a method for extracting the height of urban forest trees based on a smartphone was proposed to efficiently and accurately determine tree heights. First, a smartphone was used to obtain person–tree images, LabelImg was used to label the images, and a dataset was constructed. Secondly, based on a deep learning method called You Only Look Once v5 (YOLOv5) and the small-hole imaging and scale principles, a person–tree scale height measurement model was constructed. This approach supports recognition and mark functions based on the characteristics of a person and a tree in a single image. Finally, tree height measurements were obtained. By using this method, the heights of three species in the validation set were extracted; the range of the absolute error was 0.02 m–0.98 m, and the range of the relative error was 0.20–10.33%, with the RMSE below 0.43 m, the rRMSE below 4.96%, and the R2 above 0.93. The person–tree scale height measurement model proposed in this paper greatly improves the efficiency of tree height measurement while ensuring sufficient accuracy and provides a new method for the dynamic monitoring and investigation of urban forest resources.
... 69 A pairwise comparison of SNP profiles of 40 trees generated a kinship pattern where the 70 within population relatedness exceeded that of between population (Fig. S4). Further, a 71 Kendall's rank correlation of association on kinship coefficients had positive values for 72 within population comparisons reflecting local founder effect (Fig. S4, Table S1). In 73 both populations, there are few distantly related individuals that stand out with 74 negative correlations (Fig. S4). ...
... The nature of the retained diversity ie. whether it is 304 based on gene flow, emergence of novel variants through mutation and recombination as 305 well as plasticity contribute to this picture [3,64,[67][68][69][70][71][72][73][74][75][76][77]. Our kinship analysis has shown 306 that SERC and HARV populations were genetically distinct and at the same time 307 harbored some degree of background relatedness characteristic of second-growth forests 308 (Fig. S4). ...
Transcriptomics, the quantification of gene expression, provides a versatile tool for ecological monitoring. Here, we show that through genome-guided profiling of transcripts mapping to 33,042 loci, gene expression differences can be discerned among multi-year and seasonal leaf samples collected from American beech trees at two latitudinally separated sites. Despite a bottleneck imposed due to large-scale post-Columbian deforestation, the SNP-based population genetic background analysis has yielded sufficient variation to account for differences between populations and among individuals. Our time series of expression analyses during spring-summer and summer-fall transitions for two consecutive years involved 4197 differentially expressed protein coding genes. A global comparison of 12 seasons has revealed that spring gene expression sets the pace for the rest of the growing season. Using \textit{Populus} orthologs of the differentially expressed genes, we reconstructed a protein-protein interactome as a representation of the leaf physiological states of trees during the seasonal transitions. Gene set enrichment analysis revealed GO terms that highlight molecular functions and biological processes possibly influenced by abiotic forcings such as recovery from drought and response to excess precipitation. Further, based on 324 co-regulated transcripts, we focused on a subset of terms that could be putatively attributed to phenological shifts due to late spring. Our conservative results indicate that extended transcriptome-based monitoring of forests can capture ranges of responses arising from other factors including air quality, chronic disease as well as herbivore outbreaks that require activation and/or downregulation of genes collectively tuning reaction norms needed for the survival of long living trees such as the American beech.
... Beyond the specific case of measuring dispersal along such idealised geometric features, the problem of estimating the distance between parents and saplings (accounting for seed dispersal from maternal or paternal parents plus pollen movement) is explicitly addressed in Isagi et al. (2000) via microsatellite analysis. Other plant based dispersal issues such as seed versus pollen dispersal from spatial genetic structure are discussed in Heuertz et al. (2003), see also Lavorel et al. (1995) and the references therein. ...
We consider a space structured population model generated by two point clouds: a homogeneous Poisson process $M=\sum_{j}\delta_{X_{j}}$ with intensity of order $n\to\infty$ as a model for a parent generation together with a Cox point process $N=\sum_{j}\delta_{Y_{j}}$ as offspring generation, with conditional intensity of order $M\ast(\sigma^{-1}f(\cdot/\sigma))$, where $\ast$ denotes convolution, $f$ is the so-called dispersal density, the unknown parameter of interest, and $\sigma>0$ is a physical scale parameter. Based on a realisation of $M$ and $N$, we study the nonparametric estimation of $f$, for several regimes $\sigma=\sigma_{n}$. We establish that the optimal rates of convergence do not depend monotonously on the scale $\sigma$ and construct minimax estimators accordingly. Depending on $\sigma$, the reconstruction problem exhibits a competition between a direct and a deconvolution problem. Our study reveals in particular the existence of a least favourable intermediate inference scale.
... It is becoming increasingly important to understand the mating patterns, the composition of parents contributing to the next generation and their effect on the maintenance of genetic diversity in natural populations of A. firma, to conserve the species against fluctuating environmental conditions (see Introduction). The total parentage exclusion probability values of the seven SSR loci were not so high, which may result in the candidate parents of some seeds not being fully excluded, consequently resulting in the underestimation of immigrant gene flow ("cryptic gene flow": e.g., Dow and Ashley 1996;Isagi et al. 2000) when many seeds are being analyzed in future studies. However, the construction of a marker set selected from both previously developed markers (including those of other related Abies species) and our newly developed ones should achieve higher discriminatory power for accurate biparentage identification. ...
The momi fir (Abies firma) has been targeted as a species for genetic resource conservation because of the recent decline in its natural populations. Additional molecular marker resources are needed to examine gene flow to understand the genetic dynamics of each population. We developed 15 genomic microsatellite (SSR) markers for A. firma and applied them to separate biparentage assignments of dispersed seeds in a natural population by assaying embryos and megagametophytes. The 15 markers were polymorphic, with the expected heterozygosity averaging greater than 0.74. Separate biparentage analysis, using the seven selected effective markers, was successful to assign paternal and maternal trees separately and thus estimate the paternal and maternal immigrant gene flow from nearby populations. The newly developed genomic SSR markers in the present study, by constructing a marker set together with previously developed markers, will provide higher discriminatory power for parentage analysis and should be useful for estimating gene flow for ongoing conservation genetics studies of A. firma.
... In forest tree species as well as other plant species, pollen dispersal may thus be the most important component of the gene flow that maintains genetic diversity within their populations. Gene movement via seeds and pollen in forest tree species has been directly studied by parentage analysis using microsatellite markers, which are suited to such studies as they have very high levels of polymorphism and codominant expression (Chase et al. 1996;Ashley 1996, 1998;Streiff et al. 1999;Isagi et al. 2000;Bacles et al. 2006). ...
... Forest tree species that naturally occur in low densities are also suitable for parentage analysis because all of the potential parents in populations of such species can be relatively easily found and genotyped (Hardy 2009;Kamm et al. 2009). Consequently, most studies that have used parentage analysis have focused on low-density species (Chase et al. 1996;Isagi et al. 2000Isagi et al. , 2007Sezen et al. 2005;Kamm et al. 2009). In contrast, there has been very little Journal of Heredity 2012: 103(4) parentage analysis of species with high-density populations, except for a few investigations of wind-pollinated species (see Streiff et al. 1999;Bittencourt and Sebben 2007). ...
... In contrast, there has been very little Journal of Heredity 2012: 103(4) parentage analysis of species with high-density populations, except for a few investigations of wind-pollinated species (see Streiff et al. 1999;Bittencourt and Sebben 2007). Most parentage analyses of pollen flow in low-density species that rely on insect pollination to date have detected a high proportion of long-distance pollen flow (Chase et al. 1996;Isagi et al. 2000;Sezen et al. 2005;Isagi et al. 2007). However, measures of pollen dispersal obtained for lowdensity species may not necessarily be representative of high-density species, because density can affect effective gene dispersal in two ways (Hardy 2009). ...
Insect pollinations of tree species with high-density populations have rarely been studied. Since the density of adults can affect effective pollen dispersal, short-distance pollination, even by insects, may frequently occur in high-density populations. To test this prediction, we investigated pollination patterns in a high-density population of the insect-pollinated canopy tree species Castanopsis sieboldii by paternity analysis using genotypes at 8 microsatellite loci of 145 adult trees and 439 seeds from 11 seed parents in a 4-ha plot. We then explored their genetic effects on the population by calculating other population genetics parameters. Although C. sieboldii has high potential for long-distance dispersal of pollen (as indicated by a fat-tailed dispersal kernel), the cumulative pollination at the local scale was spatially limited and strongly dependent on the distance between parents due to the high density of adults. Genetic diversity estimates for pollen pools accepted by each seed parent converged on a maximum as the effective number of pollen parents increased. The genetic diversity of pollen pool bulked over all the seed parents from inside the plot did not differ from that of the total pollen pools. Therefore, although pollen flow from distant pollen parents may help to maintain the genetic diversity of offspring, pollen parents neighboring seed parents may be the main contributors to the genetic diversity of the offspring at the seed stage.
... In the present study, moderate genetic variation was found in M. maudiae, an average of 8 alleles per locus and a mean observed heterozygosity of 0.475 were revealed in nuclear microsatellites, and eight haplotypes were observed in chloroplast DNA. The genetic variation of M. maudiae was similar to that reported in other close related species such as Magnolia obovata (Isagi et al. 2000), Magnolia sieboldii (Kikuchi and Isagi 2002), Magnolia stellata (Ueno et al. 2005), and Michelia coriacea (Zhao et al. 2009). Populations of Xiaodanjiang, Tianjingshan, Laopengding, Xiangzhou, and Minjiangyuan had significant positive values of F IS across ten nuclear loci, however, these values were not significant after excluding the six loci deviated from Hardy-Weinberg equilibrium. ...
Michelia maudiae Dunn. is a Magnoliaceae species threatened by habitat destruction and over-exploitation. Genetic diversity and differentiation, population contribution to total diversity and allelic/haplotypic richness, and the relative importance of pollen- and seed-mediated gene flow were investigated in nine populations (192 individuals) of M. maudiae using nuclear and chloroplast microsatellites to further our understanding of the genetic structure and evolutionary history of this tree species and to provide a genetic perspective for its conservation. The species had strong pollen mediated gene flow in the past. The ratio of pollen to seed gene flow was 25.4. Three clusters from the western, central, and eastern China were identified by both chloroplast and nuclear microsatellites. Western populations at Xiaodanjiang and Daoxian were phylogenetically divergent from the remaining populations and might be particularly important for the conservation of this species. The populations of Xiaodanjiang, Daoxian, and Minjiangyuan made positive contribution to the total diversity and allelic/haplotypic richness, and were worthy of being conserved with priority. In the central cluster, population at Laopengding should be protected since it harbored the greatest genetic diversity.
... Hence, inbred offspring of M. stellata are likely to be eliminated from the population. In M. obovata, it is reported that no saplings more than 1 year old originated from selfing (Isagi et al. 2000), while 70.8% of current-year seedlings originated from selfing (Isagi et al. 2004). These facts suggest that selfed offspring are also eliminated from the population. ...
Plant size and light availability may affect male and (or) female reproductive success and their relative contribution (functional gender). To test this hypothesis, we identified parents of 184 seedlings in a local population within a metapopulation of a hermaphroditic, insect-pollinated tree species, Magnolia stellata (Siebold & Zucc.) Maxim., using 14 nuclear and 3 chloroplast microsatellite markers. Parent pairs of all the seedlings were determined, and both seed and pollen parents could be distinguished for 49.5% of the seedlings. We also measured the parents' plant size (diameter at breast height of the thickest ramet within each genet; DBH(t)) and the relative photosynthetic photon flux density (rPPFD) they received. The proportion of seedlings that originated from selfing was 20.7%. The number of seedlings parental trees produced as seed parents (S) was positively affected by DBH(t) and rPPFD. DBH(t) (but not rPPFD) also positively affected the number of seedlings sired as pollen parents (P). The femaleness of the parental trees (S/(S + P)) was positively affected by DBH(t), probably because DBH(t) had a stronger effect on the trees' reproductive success as seed parents than on their success as pollen parents. These results suggest that plant size affects not only reproductive success (male and female), but also functional gender.
... They found an average pollination distance of 334 m, more than six-fold greater than the mean distances between nearest male-female pairs (54 m). Notable mean pollination distances of hundreds of meters have been reported for both temperate (Hoebee et al., 2007;Isagi et al., 2000;Isagi et al., 2007) and tropical insect-pollinated trees (Chase et al., 1996;Hanson et al., 2008;Hardesty et al., 2006). Dinizia excelsa briefly held the record for the most distant documented insect pollination event, 3.2 km (Dick, 2001), until 4.5 km was reported for Swietenia humilis study the following year (White et al., 2002). ...
DNA microsatellites provide plant ecologists with molecular markers precise enough to assign parentage to seeds and seedlings. This allows the exact distance and trajectory of successful pollen to be traced to characterize pollination patterns. Parentage assignment of established seedlings also allows researchers to accurately determine how far new recruits have traveled from their seed parent. This paper reviews the history and development of molecular parentage assignment in studies of native plants, as well as the limitations and constraints to this approach. This paper also reviews 53 articles published in the past 15 years that use parentage assignment to study pollination and seed dispersal in native plants. These parentage studies have overturned many common assumptions regarding pollen and seed dispersal patterns. They show that long-distance dispersal of pollen is common in both wind and animal dispersed systems, with average pollination distances commonly being hundreds of meters. The pollination neighborhood is often extremely large, and simple dispersal functions based on distance alone fail to make accurate predictions of pollination. Rather than hindering gene flow, fragmentation and isolation sometimes, and perhaps even commonly, results in increased pollination distances. Studies of seed dispersal using parentage assignment have also yielded some surprises. We now know that it may be erroneous to assume that seeds growing under the crown of a conspecific adult are growing beneath their mother, or that seed dispersal distances are more limited than pollen dispersal distances. Taken together, the studies to date demonstrate that both seed and pollen dispersal are quite complex phenomena influenced by many ecological processes.
... Immigrant gene flow has previously been evaluated in theoretical studies of interpopulation genetic structure (e.g., Slatkin 1985;Petit et al. 1993;Ennos 1994;reviewed in McCauley 1995), mainly in terms of the average number of immigrants exchanged per generation among a set of populations (island model; e.g., Wright 1943), that is, indirect estimates from the larger scale of genetic dynamics. More recently, progress in the use of molecular markers has enhanced genetic resolutions, facilitating a number of studies that directly measure gene-flow patterns in woody species (e.g., Chase et al. 1996;Dow and Ashley 1996;Streiff et al. 1999;Isagi et al. 2000) and then evaluate the withinpopulation genetic variation based on a smaller scale of genetic dynamics (e.g., Nakanishi et al. 2005;Sato et al. 2006). The above studies have accumulated information with regard to gene-flow distances, proportions of immigrant or long-distance gene flow, and individual-level mating patterns or reproductive successes. ...
... However, very few studies have examined both pollen flow and seed dispersal simultaneously and with high accuracy. Previous studies of gene flow have used ordinary parentage analysis, which assumes that the nearer parent is the maternal parent (e.g., Dow and Ashley 1996;Isagi et al. 2000;Sato et al. 2006;Nakanishi et al. 2008), and in some studies, more accurate analyses using seed coats (e.g., Godoy and Jordano 2001) or nuclear and organellar genomes (e.g., Lian et al. 2008; see also Discussion). ...
