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Unweighted pair group method with arithmetic mean phenogram based on Nei's (1972) genetic distances among 11 populations of two species of Dioon, estimated from 13 loci (Table 5)
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Allozyme diversity and population genetic structure studies were conducted in populations of two Mexican cycad species occurring in adjacent and closely related biogeographic regions. We evaluated if rarity traits in Dioon caputoi, a micro-endemic species, and Dioon merolae, a regional endemic with a wider distribution, influence levels of genetic...
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... AMOVA test (Table 3) Table 4), indicating a global (F IT ) and local (F IS ) heterozygote excess for each species. These excesses were higher for D. merolae (p \ 0.001 in Mann-Whitney test). Finally, the UPGMA tree based on Nei's (1972) genetic distances revealed two major groups (i.e., D. caputoi and D. merolae; Fig. 2; Table ...
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The effect of host cacti on the breeding structure of an isolated population of cactophilic Drosophila gouveai was studied. A comparison was made, using F statistics, of the allozyme frequencies at 11 loci among temporal samples of the adult population and six samples of progeny obtained from individual rotting cactus cladodes. The population appea...
Population structure, diversity and gene flow in four populations of Aciphylla glaucescens were studied using allozymes. Six of the seven putative loci were polymorphic in at least one population. Within populations the mean percentage of polymorphic loci was 68%. Gene diversity for Aciphylla glaucescens (H(e)=0.258) was greater at the species leve...
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Premise of the study:
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Citations
... These particular species manifest heightened levels of genetic diversity, as evidenced by elevated genetic diversity values (He) and an overabundance of heterozygotes (FIT and FIS) [51,53]. Another investigation conducted by Cabrera-Toledo et al. discovered an excess of heterozygotes in all four populations of Dioon caputoi, which implies a significant degree of genetic diversity [54][55][56]. Likewise, Reyes-Zepeda et al. observed a surplus of heterozygotes in all life stages of the shrub Cestrum miradorense, indicating that natural selection and gene flow contribute to this phenomenon [52]. ...
The Hardy-Weinberg Equilibrium (HWE) is a fundamental principle employed in the analysis of genetic data,
encompassing studies of meta-analysis and genomic sequencing. It has been demonstrated that HWE possesses the
property of transitivity, wherein a multi-allelic polymorphism in equilibrium will persist in its equilibrium state even
when alleles are deleted or combined. Nonetheless, the practice of filtering loci that do not adhere to HWE has been
observed to impact the inference of population genetics within RADseq datasets. In response to this concern, the
Robust Unified Test for HWE (RUTH) has been devised to consider population structure and genotype uncertainty,
thereby offering a more precise evaluation of the quality of genotype data. Furthermore, deviations from HWE, such
as extreme heterozygote excess, can be effectively utilized to identify genotyping errors or to pinpoint the presence
of rare recessive disease-causing variants. In summary, it is evident that HWE holds immense significance in the field
of genetic analysis, and its application in meta-analysis studies and genomic sequencing can yield invaluable insights
into the intricacies of population structure and the genetics of diseases.
... The ornamental appeal of cycads has generated a great demand on the world market, which has led to over-collection and illegal removal from the wild (Pérez-Farrera et al. 2006;Torgersen 2017). Many cycad populations have declined in size (González-Astorga et al. 2008;Shuguang et al. 2006;Octavio-Aguilar et al. 2009;Da Silva et al. 2012;Cabrera-Toledo et al. 2012), with many species surviving in small and fragmented populations with low genetic diversity (Long-Qian et al. 2004;Meerow et al. 2012), especially in Africa (Ekué et al. 2008;Da Silva et al. 2012) and North America (Cabrera-Toledo et al. 2010). However, genetic diversity in cycads is not always correlated with population size; for example, small and isolated populations of Cycas multipinnata C.J.Chen & S.Y.Yang were found to have high levels of genetic diversity (Gong et al. 2015). ...
Understanding the genetic diversity of wild populations is fundamental to conserving species in-situ and ex-situ. To aid conservation plans and to inform ex-situ conservation, we examined the genetic diversity of the cycad Cycas calcicola (Cycadaceae). Samples were collected from wild populations in the Litchfield National Park and Katherine regions in the Northern Territory, Australia. Additional samples were obtained from botanic garden plants that were originally collected in the Katherine region, Daly River and Spirit Hills in the Northern Territory, Australia. Using RADseq we recovered 2271 informative genome-wide SNPs, revealing low to moderate levels of gene diversity (uHe = 0.037 to 0.135), very low levels of gene flow, and significant levels of inbreeding (mean FIS = 0.491). Population structure and multivariate analysis showed that populations fall into two genetic groups (Katherine vs Litchfield + Daly River + Spirit Hills). Genetic differentiation was twice as high between populations of the Katherine and Litchfield regions (FST ~ 0.1) compared to within these two regions (FST ~ 0.05). Increasing population fragmentation together with high levels of inbreeding and very little gene flow are concerning for the future adaptability of this species. The results indicated that the ex-situ collections (1) had significantly lower genetic diversity than the wild populations, and (2) only partly capture the genetic diversity present, particularly because the Litchfield National Park populations are not represented. We recommend that ex-situ collections be expanded to incorporate the genetic diversity found in Litchfield National Park and to increase the number of representatives from Daly River/Spirit Hills, and that in-situ populations from the Katherine and Greater Litchfield regions be conserved as separate management units.
... This conclusion was reached based on general observations and unpublished vegetative morphological analyses. More recent studies (e.g., Cabrera-Toledo et al. 2010, Dorsey et al. 2018, Gutiérrez-Ortega et al. 2018c) considered that other Dioon populations from the Valles Centrales region of Oaxaca also belonged to D. merolae. Gutiérrez-Ortega et al. (2020) showed evidence that morphological and genetic variation exists among populations of D. merolae in Chiapas and Oaxaca. ...
Dioon oaxacensis sp. nov. (Zamiaceae), a new cycad species from Oaxaca, Mexico, is described. The morphological traits of the new taxon are compared with its sister species, D. merolae. The species delimitation between the two species is consistent with previously published genetic evidence. Dioon oaxacensis can be easily identified by its flat, stiff, straight leaflets obliquely inserted to rachis, and by its large reproductive structures. Populations of D. oaxacensis usually occur in dry habitats, growing on rocky hillsides, and co-habiting with plants well recognized to be adapted to aridity.
... Isolation-by-distance has been detected in other studies on Dioon (e.g. Cabrera-Toledo et al., 2010;Guti errez-Ortega et al., 2018c), suggesting that gene flow among Dioon populations might be restricted. This can be attributed to the low seed and pollen dispersal capabilities of cycads. ...
Niche conservatism is the tendency of lineages to retain the same niche as their ancestors. It constrains biological groups and prevents ecological divergence. However, theory predicts that niche conservatism can hinder gene flow, strengthen drift and increase local adaptation: does it mean that it also can facilitate speciation? Why does this happen? We aim to answer these questions.
We examined the variation of chloroplast DNA, genome‐wide single nucleotide polymorphisms, morphological traits and environmental variables across the Dioon merolae cycad populations. We tested geographical structure, scenarios of demographic history, and niche conservatism between population groups.
Lineage divergence is associated with the presence of a geographical barrier consisting of unsuitable habitats for cycads. There is a clear genetic and morphological distinction between the geographical groups, suggesting allopatric divergence. However, even in contrasting available environmental conditions, groups retain their ancestral niche, supporting niche conservatism.
Niche conservatism is a process that can promote speciation. In D. merolae, lineage divergence occurred because unsuitable habitats represented a barrier against gene flow, incurring populations to experience isolated demographic histories and disparate environmental conditions. This study explains why cycads, despite their ancient lineage origin and biological stasis, have been able to diversify into modern ecosystems worldwide.
... JAM, however, also had the highest degree of among-population genetic variation (31%). High in- trapopulation genetic diversity has also been reported in Dioon with allozyme markers (Cabrera-Toledo et al. 2010) and in En- cephalartos Lehm. with amplified fragment length polymor- phisms (Da Silva et al. 2012) but is very typical of microsatellite data sets (Heller and Siegismund 2009). ...
Premise of research. After Cuba, the three largest islands of the Greater Antilles are Hispaniola, Jamaica (JAM), and Puerto Rico (PR), all of which are inhabited by the Zamia pumila complex, a monophyletic group of dioecious gymnosperms treated as a single polymorphic or as many as nine species. We sought to test the following hypotheses for Zamia: (i) Dominican Republic (DR) and JAM fit evolutionary models of panmixis and isolation, respectively; (ii) historical gene flow has occurred between PR and DR, and admixture has occurred between the Caymans (CAY) and JAM; and (iii) vegetative morphological characters in common with populations on different islands do not conform to genetic relationships. Methodology. We genotyped a total of 30 populations from CAY, DR, JAM, and PR with 21–28 microsatellite (simple sequence repeat [SSR]) loci and haplotypes from 10 single-copy nuclear genes (SCNGs) and analyzed the data with permuted analysis of molecular variance, Bayesian clustering, approximate Bayesian computation coalescent modeling, and network and gene flow analyses. By using two different sets of molecular markers with very different mutation rates (SSRs and SCNGs), we sought to capture two distinct time slices of evolutionary history in the populations of each island. Pivotal results. Diversification of Caribbean Zamia follows a different path on each island after migration or vicariance from ancestors putatively originating in Cuba. DR and PR evolved from a common ancestral gene pool. DR fits a model of panmixis, while PR fits a vicariance model of semispeciation. Northern and western populations in JAM represent separate introductions to the island. Overall, JAM shows minimal levels of gene flow among populations and apparent admixture with CAY. Conclusions. We conclude that niche adaptation and associated vegetative morphological character states evolve convergently among different islands in response to environmental and other stochastic variables. We present a model of how these dioecious gymnosperms diversified in the Greater Antilles.
... They can live up to 2000 yr and have slow growth rates with long reproductive cycles (Vovides, 1990). Despite legal protection in the Norma Oficial Mexicana of the Secretaría de Allozyme variation in D. edule has shown that there is unusually high genetic diversity in this genus (González-Astorga et al., 2003; Cabrera-Toledo et al., 2010, 2012 ), but these markers are limited in their scale of analysis and in their use for conservation, as they lack individual-level resolution and are dominant markers. Independent laboratories (J. ...
Premise of the study:
Dioon (Zamiaceae) is an endangered North American cycad genus of evolutionary and ornamental value. We designed and validated a set of microsatellite markers from D. edule that can be used for population-level and conservation studies, and that transferred successfully to D. angustifolium, D. spinulosum, and D. holmgrenii.
Methods and results:
We tested 50 primers from 80 microsatellite candidate loci in the OneKP D. edule transcriptome. Genotypes from 21 loci in 20 D. edule individuals revealed up to 14 alleles per locus and observed heterozygosity from 0.15 to 0.92; one locus was monomorphic. Seven of those 21 loci were polymorphic in D. angustifolium, D. spinulosum, and D. holmgrenii, with up to seven alleles, and an observed heterozygosity up to 0.89.
Conclusions:
The transcriptome-derived microsatellites generated here will serve as tools to advance population genetic studies and inform conservation strategies of Dioon, including the identification and origin of illegal plants in the cycad trade.
... One other example that can be used as a reference to guide the plant conservation efforts in the Tehuacán-Cuicatlán valley is the wellknown endangered rare cycad, Dioon caputoi. For this species population genetic diversity has been evaluated (Cabrera-Toledo et al., 2008;, the pollen and seed dispersion was documented (Cabrera-Toledo et al., 2012), as well as its biogeographic and the evolutionary history (Cabrera-Toledo et al., 2010). These studies demonstrated that illegal harvesting has severe effects on the reproductive adults, which may need between 100 and 300 years to recover their abundance. ...
Nearly 168 species of Mammillaria are endangered at the global level; most of these cactus species exhibit a narrow distribution range and/or small population size. Recently, the first population genetics studies showed low to moderate levels of heterozygosity in this genus. This study examines Mammillaria huitzilopochtli and M. supertexta, 2 threatened species endemic to the central semiarid region of Mexico, to propose conservation actions, as well as to identify the underlying processes that determine the levels of population genetic diversity in these species. A total of 106 and 148 individuals from 5 populations were sampled for M. huitzilopochtli and M. supertexta, respectively. Each individual was genotyped at 8 microsatellite loci. The levels of heterozygosity were high in the 2 species, but differences in allelic richness were detected. Genetic differentiation between populations was significant in both species, with evidence for isolation by distance in M. supertexta but not in M. huitzilopochtli. We postulated that genetic drift; geographic isolation and inbreeding are the most important processes shaping the populations' genetic variability and differentiation. We identified 3 and 4 genetic groups for M. huitzilopochtli and M. supertexta, respectively. In the Tehuacan-Cuicatlan valley these groups may be used as references to guide plant conservation efforts under ecosystem-based approach.
... Z. tenuis is another species reported for the Bahamas but it is only known from a single specimen collected in the early 19th century from a plant cultivated at Berlin Botanical Garden. Z. tenuis was formerly considered a synonym of Z. angustifolia by Britton & Millspaugh (1920) and is currently treated as a synonym of Z. integrifolia (Osborne et al., 2012). ...
A conservation assessment for the three cycad species native to the Bahamas Islands is presented. Results are based on field surveys on all islands where these species occur. Zamia angustifolia is native to Eleuthera, Zamia integrifolia is native to Abaco, Andros, Eleuthera, Grand Bahama and New Providence, and Zamia lucayana is endemic to Long Island. Z. angustifolia is of the highest conservation concern because of the small number of adult plants, its restricted distribution and the extensive development occurring within its habitat. Z. integrifolia also has a restricted distribution on Eleuthera and Grand Bahama and, although threatened by urban development in New Providence, it is relatively common on Abaco and Andros. Z. lucayana comprises three populations within a narrow strip of land of c. 1 km2; we propose a reassignment of its current conservation status from Endangered to Critically Endangered. We assessed the genetic structure of Z. lucayana based on 15 polymorphic microsatellite DNA loci; this indicated that the three known populations should be considered a single management unit. However, the high number of private alleles suggests that genetic drift, indicative of recent fragmentation, is progressing. We propose in situ conservation strategies, and we also collected germplasm from a total of 24 populations of these three cycad species, for ex situ conservation.
... — It has long been thought that species with limited geographic distribution would show lower genetic diversity than congeneric, widespread species ( Loveless and Hamrick, 1984 ; Karron, 1987 ; Hamrick et al., 1991 ), but the phylogenetic relationships of the taxa in question have not always been factored into comparison ( Gitzendanner and Soltis, 2000 ; Cole, 2003 ; Leimu et al., 2006 ; Cabrera-Toledo et al., 2010 ). Where these have been considered, some studies have found that congeneric species with differing geographic ranges can share similar genetic structure and diversity ( Morjan and Rieseberg, 2004 ; Duminil et al., 2007 ). ...
... Where these have been considered, some studies have found that congeneric species with differing geographic ranges can share similar genetic structure and diversity ( Morjan and Rieseberg, 2004 ; Duminil et al., 2007 ). Toledo et al. (2010) compared allozyme diversity patterns across two Dioon Lindl. (Zamiaceae) species, D. caputoi De Luca, Sabato & Vázq. ...
... We found 87–96% of the total genetic variation partitioned within the individual populations of Puerto Rican Zamia , and, consequently, much lower levels among populations. High infrapopulation genetic diversity has also been reported in Dioon with allozyme markers ( Toledo et al., 2010 ), and in Encephalartos Lehm. with AFLPs ( Da Silva et al., 2012 ), but is very typical of microsatellite data sets ( Heller and Siegismund, 2009 ). ...
... Rico? -It has long been thought that species with limited geographic distribution would show lower genetic diversity than congeneric, widespread species ( Loveless and Hamrick, 1984 ;Karron, 1987 ;Hamrick et al., 1991 ), but the phylogenetic relationships of the taxa in question have not always been factored into comparison ( Gitzendanner and Soltis, 2000 ;Cole, 2003 ;Leimu et al., 2006 ;Cabrera-Toledo et al., 2010 ). Where these have been considered, some studies have found that congeneric species with differing geographic ranges can share similar genetic structure and diversity ( Morjan and Rieseberg, 2004 ;Duminil et al., 2007 ) Torres, which are closely related phylogenetically but differ markedly in their geographic range and relative abundance. ...
... We found 87-96% of the total genetic variation partitioned within the individual populations of Puerto Rican Zamia , and, consequently, much lower levels among populations. High infrapopulation genetic diversity has also been reported in Dioon with allozyme markers ( Cabrera-Toledo et al., 2010 ), and in Encephalartos Lehm. with AFLPs ( Da Silva et al., 2012 ), but is very typical of microsatellite data sets ( Heller and Siegismund, 2009 ). ...
Premise of the study:
This study of Zamia in Puerto Rico is the most intensive population genetics investigation of a cycad to date in terms of number of markers, and one of few microsatellite DNA studies of plants from the highly critical Caribbean biodiversity hotspot. Three distinctive Zamia taxa occur on the island: Z. erosa on the north coast, and Z. portoricensis and Z. pumila, both in the south. Their relationships are largely unknown. We tested three hypotheses about their genetic diversity, including the possibility of multiple introductions.
Methods:
We used 31 microsatellite loci across 10 populations and analyzed the data with AMOVA, Bayesian clustering, and ABC coalescent modeling.
Key results:
Puerto Rican zamias exhibit an amalgam of patterns of genetic differentiation that have been reported for cycads. Overall, the taxa are slightly inbred, with high infra-populational variation and little evidence of recent bottlenecks. Zamia erosa exhibits a more than threefold greater degree of population differentiation than the other two taxa. Admixture is evident only between Z. portoricensis and Z. pumila. Zamia portoricensis is inferred to be the youngest taxon on the island, on the basis of estimates of coalescence time and effective population size. A selective sweep may be underway in a small population of Z. erosa in a saline environment.
Conclusions:
Zamia erosa may represent an independent introduction into Puerto Rico; Z. portoricensis and Z. pumila fit a scenario of allopatric speciation. This will be explored further in the context of genetic analysis across the entire Caribbean region.
