Diversity and Genetic Structure of Dioon holmgrenii (Cycadales: Zamiaceae) in the Mexican Pacific Coast Biogeographic Province: Implications for Conservation.
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ABSTRACT:
SUBMITTER: Velasco-Garcia MV
PROVIDER: S-EPMC8623071 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Raw sequence reads from multiple individuals from all species in the genus Dioon Lindl.
| PRJNA454905 | ENA
Project description: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. 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. 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.
| S-EPMC4760746 | biostudies-literature
Project description:Background and Aims:Biogeographic transition zones are promising areas to study processes of biogeographic evolution and its influence on biological groups. The Mexican transition zone originated due to the overlap of Nearctic and Neotropical biota, which promoted great biological diversification. However, since most previous studies in this area were focused on revealing the phylogeography of Nearctic plants, how historical biogeographic configuration influenced the expansion and diversification of the Neotropical flora remains almost unknown. Using the cycad genus Dioon (Zamiaceae), this study aimed to test whether the biogeographic provinciality of the Mexican transition zone reflects the history of diversification of Neotropical plants. Methods:Two chloroplast DNA (cpDNA) regions were analysed from 101 specimens of 15 Dioon species to reveal the distribution of haplogroups. In addition, genome-wide single nucleotide polymorphisms (SNPs) from 84 specimens were used to test the concordance between phylogenetic clusters and the biogeographic provinces. An ultrametric tree was constructed from the sequences containing SNPs to reconstruct the biogeographic events of vicariance and dispersal of Dioon across the Neotropical biogeographic provinces. Key Results:Four Dioon lineages with strong phylogeographic structures were recognized using both cpDNA and SNP data. The lineages correspond to two clades that originated from a common ancestor in Eastern Mexico. One clade expanded and diversified in South-east Mexico and Central America. Another clade diversified into three lineages that dispersed to North-east, South and North-west Mexico. Each lineage was biogeographically delimitated. Biogeographic provinces might have provided disparate ecological conditions that facilitated speciation in Dioon since the Miocene. Conclusions:The current genetic structure and species diversity of Dioon depict the history of expansion and diversification of the northernmost Neotropical provinces. Past biogeographic connectivities were favoured by elevated topographies, since mountain systems served as corridors for the migration of Dioon and as refugia of tropical communities that diversified during the formation of modern Neotropical forests.
| S-EPMC5838841 | biostudies-literature
Project description:Cycadales is an extant group of seed plants occurring in subtropical and tropical regions comprising putatively three families and 10 genera. At least one complete plastid genome sequence has been reported for all of the 10 genera except Microcycas, making it an ideal plant group to conduct comprehensive plastome comparisons at the genus level. This article reports for the first time the plastid genome of Microcycas calocoma. The plastid genome has a length of 165,688 bp with 134 annotated genes including 86 protein-coding genes, 47 non-coding RNA genes (39 tRNA and eight rRNA) and one pseudogene. Using global sequence variation analysis, the results showed that all cycad genomes share highly similar genomic profiles indicating significant slow evolution and little variation. However, identity matrices coinciding with the inverted repeat regions showed fewer similarities indicating that higher polymorphic events occur at those sites. Conserved non-coding regions also appear to be more divergent whereas variations in the exons were less discernible indicating that the latter comprises more conserved sequences. Phylogenetic analysis using 81 concatenated protein-coding genes of chloroplast (cp) genomes, obtained using maximum likelihood and Bayesian inference with high support values (>70% ML and = 1.0 BPP), confirms that Microcycas is closest to Zamia and forms a monophyletic clade with Ceratozamia and Stangeria. While Stangeria joined the Neotropical cycads Ceratozamia, Zamia and Microcyas, Bowenia grouped with the Southern Hemisphere cycads Encephalartos, Lepidozamia and Macrozamia. All Cycas species formed a distinct clade separated from the other genera. Dioon, on the other hand, was outlying from the rest of Zamiaceae encompassing two major clades-the Southern Hemisphere cycads and the Neotropical cycads. Analysis of the whole cp genomes in phylogeny also supports that the previously recognized family-Stangeriaceae-which contained Bowenia and Stangeria, is not monophyletic. Thus, the cp genome topology obtained in our study is congruent with other molecular phylogenies recognizing only a two-family classification (Cycadaceae and Zamiaceae) within extant Cycadales.
| S-EPMC6964695 | biostudies-literature
Project description:Ceratozamia is a genus of cycads occurring in eastern Mexico and Central America. In this study, we describe a new species from the Pacific region of Mexico in Guerrero state. This locality represents the most northwestern Mexico distribution for the genus. We focus the comparison of this species with the most geographically proximate and phenotypically relevant lineages for this taxon. We followed an integrative taxonomy approach to evaluate the classification of these species, including geographic location, morphology, DNA barcoding and phenology as primary sources of systematic data. Within the morphological dataset, reproductive structures are described in detail and new characters are proposed for microsporophylls. The comparative morphology of these structures facilitated the elucidation of differences in forms and species for identification. The two chosen DNA barcoding markers - namely, the chloroplast genome coding region matK and the nuclear ribosomal internal transcribed spacer (ITS) region - had low divergence, allowing only 61% of species identification, suggesting slow molecular evolutionary rates. Besides employing these three basic sources of evidence, we introduced phenology as additional information for species circumscription. In addition, this work includes a brief review of the genus at the species-level. This is therefore the most recent review for Ceratozamia across its full geographic range (latitudinal and elevational). Overall, this work further contributes to a comprehensive framework for systematic studies in Mexican cycads.
| S-EPMC7471474 | biostudies-literature
Project description:Globally, instrumentally based assessments of tsunamigenic potential of subduction zones have underestimated the magnitude and frequency of great events because of their short time record. Historical and sediment records of large earthquakes and tsunamis have expanded the temporal data and estimated size of these events. Instrumental records suggests that the Mexican Subduction earthquakes produce relatively small tsunamis, however historical records and now geologic evidence suggest that great earthquakes and tsunamis have whipped the Pacific coast of Mexico in the past. The sediment marks of centuries old-tsunamis validate historical records and indicate that large tsunamigenic earthquakes have shaken the Guerrero-Oaxaca region in southern Mexico and had an impact on a bigger stretch of the coast than previously suspected. We present the first geologic evidence of great tsunamis near the trench of a subduction zone previously underestimated as potential source for great earthquakes and tsunamis. Two sandy tsunami deposits extend over 1.5 km inland of the coast. The youngest tsunami deposit is associated with the 1787 great earthquake, M 8.6, producing a giant tsunami that poured over the coast flooding 500 km alongshore the Mexican Pacific coast and up to 6 km inland. The oldest event from a less historically documented event occurred in 1537. The 1787 earthquake, and tsunami and a probable predecessor in 1537, suggest a plausible recurrence interval of 250 years. We prove that the common believe that great tsunamis do not occur on the Mexican Pacific coast cannot be sustained.
| S-EPMC7351727 | biostudies-literature
Project description:Background and Aims:Aridification is considered a selective pressure that might have influenced plant diversification. It is suggested that plants adapted to aridity diversified during the Miocene, an epoch of global aridification (?15 million years ago). However, evidence supporting diversification being a direct response to aridity is scarce, and multidisciplinary evidence, besides just phylogenetic estimations, is necessary to support the idea that aridification has driven diversification. The cycad genus Dioon (Zamiaceae), a tropical group including species occurring from humid forests to arid zones, was investigated as a promising study system to understand the associations among habitat shifts, diversification times, the evolution of leaf epidermal adaptations, and aridification of Mexico. Methods:A phylogenetic tree was constructed from seven chloroplast DNA sequences and the ITS2 spacer to reveal the relationships among 14 Dioon species from habitats ranging from humid forests to deserts. Divergence times were estimated and the habitat shifts throughout Dioon phylogeny were detected. The epidermal anatomy among Dioon species was compared and correlation tests were performed to associate the epidermal variations with habitat parameters. Key Results:Events of habitat shifts towards arid zones happened exclusively in one of the two main clades of Dioon. Such habitat shifts happened during the species diversification of Dioon, mainly during the Miocene. Comparative anatomy showed epidermal differences between species from arid and mesic habitats. The variation of epidermal structures was found to be correlated with habitat parameters. Also, most of the analysed epidermal traits showed significant phylogenetic signals. Conclusions:The diversification of Dioon has been driven by the aridification of Mexico. The Miocene timing corresponds to the expansion of arid zones that embedded the ancestral Dioon populations. As response, species in arid zones evolved epidermal traits to counteract aridity stress. This case study provides a robust body of evidence supporting the idea that aridification is an important driver of biodiversity.
| S-EPMC5786249 | biostudies-literature
Project description:Rockfish (Sebastes spp.) are a common marine fish in nearshore and continental shelf environments in the North Pacific Ocean. They are frequently identified in coastal archaeological sites in western North America; however, the morphological similarity of rockfish species limits conventional zooarchaeological identifications to the genus level. This study applies ancient DNA analysis to 96 archaeological rockfish specimens from four sites on separate islands in an archipelago on western Vancouver Island, British Columbia, Canada. Two of the archaeological sites are located within a marine protected area specifically designed to facilitate the recovery of inshore rockfish populations; two sites are located outside this boundary and remain subject to considerable fishing pressure. Using mitochondrial 16S and control region DNA sequences, we identify at least twelve different rockfish species utilized during the past 2,500 years. Identification of rockfish at closely spaced and contemporaneously occupied sites confirms that a variety of Sebastes species were consistently exploited at each site, with more exposed areas having a higher number of species present. Identification results indicate that four of the twelve species did not occur within the conservation area boundary and, instead, were found in sites where commercial and recreational fishing continues to be permitted. This study demonstrates that ancient DNA identifications of archaeological assemblages can complement and expand perspective on modern day fisheries conservation and management in this National Park Reserve and First Nations ancestral territory.
| S-EPMC5811035 | biostudies-literature
Project description:The new genus Mexicaphorura, and its type species Mexicaphorura guerrerensis sp. n. are described from marine littoral sand. The new genus is similar to Sensilatullbergia Thibaud & Ndiaye, 2006 in having very big sensilla on sensorial organ of antennal segment III, but of different shape, the kind of postantennal organ, with simple vesicles in Mexicaphorura versus composed vesicles in Sensilatullbergia and formulae of the pseudocelli.
| S-EPMC3764539 | biostudies-literature
Project description:BackgroundThis study documents cycad-human relationships in Mexico, Belize, Guatemala, El Salvador, and Honduras over the last 6000 years. The impetus was acute need for a better understanding of previously undocumented uses of cycads in this region, and the need to improve cycad conservation strategies using ethnobotanical data. We hypothesized that cycads are significant dietary items with no long-term neurological effects, are important to religious practice, and contribute to cultural identity and sense of place, but that traditional knowledge and uses are rapidly eroding. Guiding questions focused on nomenclature, food and toxicity, relationships to palms and maize, land management issues, roles in religious ceremony, and medicinal uses, among others, and contributions of these to preservation of cycads.MethodsFrom 2000 to 2017, the authors conducted 411 semi-structured ethnographic interviews, engaged in participant-observation in Mexican and Honduran communities, and carried out archival research and literature surveys.ResultsWe documented 235 terms and associated uses that 28 ethnic groups have for 57 species in 19 languages across 21 Mexican states and 4 Central American nations. Carbohydrate-rich cycads have been both famine foods and staples for at least six millennia across the region and are still consumed in Mexico and Honduras. Certain parts are eaten without removing toxins, while seed and stem starches are detoxified via several complex processes. Leaves are incorporated into syncretic Roman Catholic-Mesoamerican religious ceremonies such as pilgrimages, Easter Week, and Day of the Dead. Cycads are often perceived as ancestors and protectors of maize, revealing a close relationship between both groups. Certain beliefs and practices give cycads prominent roles in conceptions of sense of place and cultural heritage.ConclusionsCycads are still used as foods in many places. Though they do not appear to cause long-term neurological damage, their health effects are not fully understood. They are often important to religion and contribute to cultural identity and sense of place. However, because most traditional knowledge and uses are rapidly eroding, new community-based biocultural conservation efforts are needed. These should incorporate tradition where possible and seek inspiration from existing successful cases in Honduras and Mexico.
| S-EPMC6339304 | biostudies-literature