Dataset Information

Phylogeography and Genetic Diversity in a Southern North American Desert: Agave kerchovei From the Tehuacan-Cuicatlan Valley, Mexico.

ABSTRACT: The Tehuacán-Cuicatlán Valley, located at the southeast of the state of Puebla and the northeast of the state of Oaxaca in Central Mexico, south of the Trans-Mexican Volcanic Belt (TMVB), is of particular interest for understanding the evolutionary dynamics of arid and semi-arid environments, being one of the main reservoirs of biological diversity for the arid zones of North America, including the highest diversity of Agavaceae worldwide and high levels of endemism. Studying in detail the phylogeography, environmental history and population genetics of representative species will hopefully shed light on the evolutionary and ecological dynamics that generated the tremendous biodiversity and endemism of this important region in Mexico. We sequenced three non-coding regions of chloroplast genome of Agave kerchovei, a representative species of the Tehuacán Valley, generating 2,188 bp from 128 individuals sampled from eight populations throughout the species range. We used this data set to (i) characterize the levels of genetic diversity and genetic structure in A. kerchovei; (ii) predict the distribution of A. kerchovei for the present day, and to reconstruct the past geographical history of the species by constructing ecological niche models (ENM); and (iii) compare the levels of diversity in this species with those estimated for the widely distributed Agave lechuguilla. Agave kerchovei has high levels of total chloroplast genetic variation (Hd = 0.718), especially considering that it is a species with a very restricted distribution. However, intrapopulation diversity is low (zero in some populations), and genetic structure is high (F ST = 0.928, G ST = 0.824), which can be expected for endemic species with isolated populations. Our data suggest that Pleistocene glacial cycles have played an important role in the distribution of A. kerchovei, where the climatic variability of the region - likely associated with its topographic complexity - had a significant effect on the levels of genetic diversity and population dynamics, while the potential distribution of the species seems to be stable since the middle Holocene (6 kya). We conclude that in A. kerchovei there is a core group of populations in the Tehuacán Valley, and peripheric populations that appear to be evolving independently and thus the species is fundamentally an endemic species from the Tehuacán Valley while the populations outside the Valley appear to be in the process of incipient speciation.

SUBMITTER: Aguirre-Planter E

PROVIDER: S-EPMC7358651 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Phylogeography and Genetic Diversity in a Southern North American Desert: <i>Agave kerchovei</i> From the Tehuacán-Cuicatlán Valley, Mexico.

Aguirre-Planter Erika E Parra-Leyva J Gilberto JG Ramírez-Barahona Santiago S Scheinvar Enrique E Lira-Saade Rafael R Eguiarte Luis E LE

Frontiers in plant science 20200623

The Tehuacán-Cuicatlán Valley, located at the southeast of the state of Puebla and the northeast of the state of Oaxaca in Central Mexico, south of the Trans-Mexican Volcanic Belt (TMVB), is of particular interest for understanding the evolutionary dynamics of arid and semi-arid environments, being one of the main reservoirs of biological diversity for the arid zones of North America, including the highest diversity of Agavaceae worldwide and high levels of endemism. Studying in detail the phylo ...[more]

PMID: 32733498

Similar Datasets

Project description:BackgroundInteractions between humans and fauna lay in the heart of the history of human subsistence. In Mesoamerica, the Tehuacán-Cuicatlán Valley (TCV) harbours a high biodiversity with archaeological and ethnoecological evidence of its use by people inhabiting the area since at least 12,000 B.P. It is recognized as one of the most ancient areas of agriculture in the Americas, and a broad spectrum of management practices aimed to ensure the availability of desirable plants has been documented, but it has not been analysed for animals. This study aimed to investigate the use and management practices directed to wild animals along current settlements within the TCV and neighbouring areas.MethodsWe conducted an extensive search, review and analysis of documental sources for the period between 1967 and 2018. We found 38 documents providing information about the presence of animal species and 15 describing their use and/or management. We included our own observations from four case studies among the Ixcatec, Cuicatec, Nahua and Mestizo people, as well as from regional studies of biodiversity. We used unconstrained multivariate data analysis to describe the management typology of the animals in the region.ResultsHitherto, 652 vertebrate species and 765 species of insects have been recorded in this area; and until present, 107 wild animal species have been reported to be used in 11 use-type categories, mostly for food (65.42%), ornamental (27.52%) and medicinal (21.10%) purposes by the Nahua, Cuicatec, Popolocan, Ixcatec, Mazatec and Mestizo people. Their extraction entails manual capture and gathering as well as hunting and trapping strategies, some of them involving planning in time or space and communitarian regulations; in addition, relocation actions and care in captivity were recorded. Nearly 178 of the species distributed in the region with no reports of local use are used in other localities of Mesoamerica. Ethnozoological information is still lacking for the Mixtec, Chinantec and Chocholtec people in the area.ConclusionsWild fauna is still a valuable resource for the inhabitants of the TCV. Animals are obtained through extractive practices, which vary from one another in their qualitative attributes. With this work, we provide a context for further research priorities on fauna management in a region of high biocultural significance.

Project description:BackgroundThe primary objective of this study is to reconstruct the phylogeny of the hentzi species group and sister species in the North American tarantula genus, Aphonopelma, using a set of mitochondrial DNA markers that include the animal "barcoding gene". An mtDNA genealogy is used to consider questions regarding species boundary delimitation and to evaluate timing of divergence to infer historical biogeographic events that played a role in shaping the present-day diversity and distribution. We aimed to identify potential refugial locations, directionality of range expansion, and test whether A. hentzi post-glacial expansion fit a predicted time frame.Methods and findingsA Bayesian phylogenetic approach was used to analyze a 2051 base pair (bp) mtDNA data matrix comprising aligned fragments of the gene regions CO1 (1165 bp) and ND1-16S (886 bp). Multiple species delimitation techniques (DNA tree-based methods, a "barcode gap" using percent of pairwise sequence divergence (uncorrected p-distances), and the GMYC method) consistently recognized a number of divergent and genealogically exclusive groups.ConclusionsThe use of numerous species delimitation methods, in concert, provide an effective approach to dissecting species boundaries in this spider group; as well they seem to provide strong evidence for a number of nominal, previously undiscovered, and cryptic species. Our data also indicate that Pleistocene habitat fragmentation and subsequent range expansion events may have shaped contemporary phylogeographic patterns of Aphonopelma diversity in the southwestern United States, particularly for the A. hentzi species group. These findings indicate that future species delimitation approaches need to be analyzed in context of a number of factors, such as the sampling distribution, loci used, biogeographic history, breadth of morphological variation, ecological factors, and behavioral data, to make truly integrative decisions about what constitutes an evolutionary lineage recognized as a "species".

Project description:The agaves are plants of cultural importance which have been used by humans for about 10,000 years and about 40 specific uses. The most culturally and economically important of those uses are for the production of fermented (pulque) and distilled beverages (mescal). Pulque continues to be produced in nearly all of Mexico, and the agaves used for this purpose have shown domestication syndrome. We carry out an ethnobotanical, morphological, and genetic analysis of the traditional varieties of pulque agave used in the production of aguamiel (agave sap) and pulque in the state of Hidalgo. We did semi-structured interviews, free listings, and tours with 11 agave managers. We analyzed morphology and studied genetic diversity and structure using nuclear microsatellites. We found wild-collected, tolerated, transplanted, and cultivated varieties of agave. This comprised 19 traditional varieties of pulque agave, 12 of them in production during the study, which corresponded to the species Agave americana, A. salmiana y A. mapisaga and five intraspecific entities. The varieties were grouped morphologically according to a management gradient; the wild-collected varieties were the smallest, with more lateral teeth and a larger terminal spine. The cultivated varieties clearly exhibited domestication syndrome, with larger plants and smaller dentition. The expected heterozygosity (He) of the varieties ranged from 0.204 to 0.721. Bayesian clustering suggested the existence of three genetic groups, both at the level of traditional varieties of pulque agaves and for management categories, a result that matches multivariate clustering. Pulque producers in the studied localities maintain high agrobiodiversity. The cultivated varieties exhibit domestication syndrome, as has been reported for other species of the genus with the same selection purposes. Our results support the hypothesis of a decrease in genetic diversity in crops compared to wild-growing agaves, which seems to be due to vegetative propagation, among other factors.

Project description:BackgroundThe Tehuacán Valley, Mexico is a region with exceptionally high biocultural richness. Traditional knowledge in this region comprises information on nearly 1,600 plant species used by local peoples to satisfy their subsistence needs. Plant resources with higher cultural value are interchanged in traditional markets. We inventoried the edible plant species interchanged in regional markets documenting economic, cultural and ecological data and about their extraction and management in order to: (1) assess how commercialization and ecological aspects influence plant management, (2) identify which species are more vulnerable, and (3) analyze how local management contributes to decrease their risk. We hypothesized that scarcer plant species with higher economic value would be under higher pressure motivating more management actions than on more abundant plants with lower economic value. However, construction of management techniques is also influenced by the time-span the management responses have taken as well as biological and ecological aspects of the plant species that limit the implementation of management practices. Plant management mitigates risk, but its absence on plant species under high risk may favor local extinction.MethodsSix traditional markets were studied through 332 semi-structured interviews to local vendors about barter, commercialization, and management types of local edible plant species. We retrieved ethnobotanical information on plant management from ten communities in a workshop and sampled regional vegetation in a total of 98 sites to estimate distribution and abundance of plant species commercialized. Through Canonical Correspondence Analysis (CCA) we analyzed the amount of variation of management types that can be explained from socioeconomic and ecological information. A risk index was calculated relating distribution, abundance, economic value and management of plant resources to identify the most vulnerable species.ResultsWe recorded 122 edible plant species interchanged in the main regional markets. CCA explained significantly 24% of management variation, spatial distribution and plant parts used being particularly important in management decisions. The indeterminate 76% of variation suggests that management decisions depend on particular variables that are not explained by the ecological and socioeconomic factors studied and/or their high variation in the context at the regional scale. The risk index indicated that management was the factor that mostly influences decreasing of risk of interchanged plant species. We identified Clinopodium mexicanum, Pachycereus weberi, Dasylirion serratifolium, Disocorea sp., Ceiba aesculifolia, Neobuxbamia tetetzo, Lippia graveolens, Litsea glaucescens, L. neesiana, Jatropha neopauciflora, Agave potatorum and other agave species used for producing mescal among the more endangered plant species due to human pressure, their relative scarcity and limited or inexistent management.ConclusionSpatial distribution and plant parts used are particularly meaningful factors determining risk and influencing management actions on edible plant species interchanged in the region. Limited or inexistent management may favor extinction of local populations under risk. Local management techniques synthesize knowledge and experiences crucial for designing sustainable management programs. Traditional management techniques supported by ecological information and environmental management approaches could make valuable contributions for sustainable use of plant species, particularly those becoming economically important more recently.

Project description:BackgroundSurvival in microrefugia represents an important paradigm in phylogeography for explaining rapid postglacial re-colonization by species in temperate regions. Microrefugia may allow populations to persist in areas where the climatic conditions on the surface have become unfavourable. Caves generally contain stable microclimates and may represent microrefugia for species capable of exploiting both cave and surface habitats (troglophiles). We examine the phylogeography of the troglophilic North American vaejovid scorpion Pseudouroctonus reddelli using 1,993 base pairs of mitochondrial and nuclear DNA sequence data generated from 12 populations. We use (i) descriptive measures of genetic diversity and population genetics statistics, (ii) reconstructions of phylogeographical structure, spatial diffusion during diversification, and population sizes through time, and (iii) species distribution modelling to test predictions of the hypothesis that caves serve as microrefugia. We compare phylogeographical patterns in P. reddelli with other troglophilic species across the Edwards Plateau karst region of Texas.ResultsResults revealed high haplotype and nucleotide diversity and substantial phylogeographical structure, probably generated during the Pleistocene. Spatial diffusion occurred along the southern edge of the Edwards Plateau from multiple refugia along the Balcones Escarpment. There was little evidence for population and geographical expansion. Species distribution models predicted substantial reductions in suitable epigean habitat for P. reddelli at the Last Glacial Maximum (LGM).ConclusionsHigh genetic diversity, strong phylogeographical structure, diffusion from multiple refugia, and unfavourable climatic conditions at the LGM collectively support the hypothesis that caves served as microrefugia for P. reddelli. Similar patterns of genetic structure in P. reddelli and other troglophilic species across the Edwards Plateau karst region of Texas suggest that caves serving as microrefugia are important for the formation, maintenance, and future survival of troglophilic species in temperate karst regions.

Project description:Genetic variation in Arctic species is often influenced by vicariance during the Pleistocene, as ice sheets fragmented the landscape and displaced populations to low- and high-latitude refugia. The formation of secondary contact or suture zones during periods of ice sheet retraction has important consequences on genetic diversity by facilitating genetic connectivity between formerly isolated populations. Brant geese (Branta bernicla) are a maritime migratory waterfowl (Anseriformes) species that almost exclusively uses coastal habitats. Within North America, brant geese are characterized by two phenotypically distinct subspecies that utilize disjunct breeding and wintering areas in the northern Pacific and Atlantic. In the Western High Arctic of Canada, brant geese consist of individuals with an intermediate phenotype that are rarely observed nesting outside this region. We examined the genetic structure of brant geese populations from each subspecies and areas consisting of intermediate phenotypes using mitochondrial DNA (mtDNA) control region sequence data and microsatellite loci. We found a strong east-west partition in both marker types consistent with refugial populations. Within subspecies, structure was also observed at mtDNA while microsatellite data suggested the presence of only two distinct genetic clusters. The Western High Arctic (WHA) appears to be a secondary contact zone for both Atlantic and Pacific lineages as mtDNA and nuclear genotypes were assigned to both subspecies, and admixed individuals were observed in this region. The mtDNA sequence data outside WHA suggests no or very restricted intermixing between Atlantic and Pacific wintering populations which is consistent with published banding and telemetry data. Our study indicates that, although brant geese in the WHA are not a genetically distinct lineage, this region may act as a reservoir of genetic diversity and may be an area of high conservation value given the potential of low reproductive output in this species.

Project description:BackgroundCuatrociénegas, part of the Chihuahuan Desert, is a region of unique biological, geological, geographical, and evolutionary importance. Its current population is mestizo; nevertheless, it has high national historical, cultural, and touristic relevance in Mexico. It has been cataloged as nationally significant for its flora and fauna by Mexican law, as well as being designated a High Protection site by the World Wildlife Fund and UNESCO. Because of its diverse and complex biological and sociocultural characteristics, we considered it important to determine, identify, and analyze various aspects of the traditional ethnobotanical knowledge and practices in this region.MethodsBetween 2016 and 2019, seven field trips were made to document the knowledge and use of flora. Cuatrociénegas is a protected area, collecting botanical material is regulated, so specimens were photographed and collected in neighboring communities, and in public and private gardens. Later permission was obtained to complete the collection of specimens (2019-2020). The plants were identified and entered into the flora database of the state of Coahuila, and deposited in the Herbarium of the Faculty of Forest Sciences, Autonomous University of Nuevo León, Mexico. One hundred ten local residents (50 men and 60 women), aged between 27 and 91 years, were interviewed (semi-structured interviews). The cultural importance of ethnobotanical resources (cultural significance index) and its significance with respect to ethnobotanical richness in other Biosphere Reserves in Mexico (Mann-Whitney test), and similarities in the diversity of exotic species (Sørensen index) were studied.Results and discussionThe ethnobotanical information registers 158 species and 132 genera in 57 vascular and non-vascular families, documenting a greater knowledge and use of cultivated species (84) with respect to wild species (74). The diversity of plants reported is compared to other ethnobotanical studies carried out in Mexican Biosphere Reserves. These results are highly relevant, in spite of unique exotic species. The people local pay special attention to medicinal and ornamental plants. The species that presented the highest use values are Larrea tridentata, Jatropha dioica, and Machaeranthera pinnatifida, three species characteristic of the desert region.ConclusionsThe particular diversity of wild flora in Cuatrociénegas Valley, combined with the varied introduced flora, is an important multifunctional resource. Special attention to introduced species is associated with harvesting use restrictions in the protected area as well as the high value of ornamental species that are difficult to maintain in desert areas. The extensive use of ethnobotanical knowledge is an example that biocultural diversity (at the conceptual level) is also strongly associated with socio-ecological systems incorporating mestizo groups and semi-urban rural landscapes, thus ceasing to be an exclusive focus of indigenous communities and regions.

Dataset Information

Phylogeography and Genetic Diversity in a Southern North American Desert: Agave kerchovei From the Tehuacan-Cuicatlan Valley, Mexico.

Publications

Phylogeography and Genetic Diversity in a Southern North American Desert: <i>Agave kerchovei</i> From the Tehuacán-Cuicatlán Valley, Mexico.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets