Aim: The history of Agave lechuguilla, a characteristic and dominant plant of the Chihuahuan Desert, was reconstructed in order to determine the importance of the Neogene orogenic uplift and the ...Quaternary glacial-interglacial climatic changes on the genetic patterns of a native Chihuahuan Desert species. Location: Chihuahuan Desert, Mexico and United States. Methods: Chloroplast DNA data from A. lechuguilla were analysed to describe levels of genetic diversity and structure and to infer the species' demographic history, using traditional methods and approximate Bayesian computation (ABC). The time of divergence of the different haplogroups was estimated with a Bayesian approach. In addition, ecological niche modelling was used to identify possible refugia. Results: Molecular dating analyses showed that A. lechuguilla originated 4.46 Ma and later differentiated into four haplogroups. The average chloroplast genetic diversity was low (Hd, 0.24), with high levels of genetic differentiation (GST, 0.780). Demographic analysis, niche modelling and ABC indicated a recent expansion from at least five glacial refugia located south of the species' current distribution. Main conclusion: Agave lechuguilla originated in the Neogene, and the glacial-interglacial events of the Pleistocene resulted in the expansion and contraction of its range, playing an important role in its intraspecific diversification. These contraction-expansion events are consistent with biogeographical regions previously identified in the Chihuahuan Desert.
With more than 200 species, the genus Agave is one of the most interesting and complex groups of plants in the world, considering for instance its great diversity and adaptations. The adaptations ...include the production of a single, massive inflorescence (the largest among plants) where after growing for many years, sometimes more than 30, the rosette dies shortly afterward, and the remarkable coevolution with their main pollinators, nectarivorous bats, in particular of the genus Leptonycteris. The physiological adaptations of Agave species include a photosynthetic metabolism that allows efficient use of water and a large degree of succulence, helping to store water and resources for their massive flowering event. Ecologically, the agaves are keystone species on which numerous animal species depend for their subsistence due to the large amounts of pollen and nectar they produce, that support many pollinators, including bats, perching birds, hummingbirds, moths, and bees. Moreover, in many regions of Mexico and in the southwestern United States, agaves are dominant species. We describe the contributions of H. S. Gentry to the understanding of agaves and review recent advances on the study of the ecology and evolution of the genus. We analyze the present and inferred past distribution patterns of different species in the genus, describing differences in their climatic niche and adaptations to dry conditions. We interpret these patterns using molecular clock data and phylogenetic analyses and information of their coevolving pollinators and from phylogeographic, morphological, and ecological studies and discuss the prospects for their future conservation and management.
Despite multiple conservation efforts of the Mexican government, the leatherback turtle is at serious risk of extinction. In this study, we investigated the possible presence of a genetic bottleneck ...that could prevent the recovery of this species and compared these findings with those of the olive ridley turtle, which is in true recovery. Our results confirmed that a demographic change occurred in the past and the presence of two different leatherback turtle lineages that diverged approximately 13.5 million years ago. Local ecological knowledge (LEK) also described the presence of these two lineages and warned that one is at higher risk of extinction than the other. Genetic analysis confirmed 124 mutations between the two lineages, and much lower genetic diversity in one lineage than the other. Our study highlights and substantiates the power of mixing LEK, environmental history, and genetics to better understand conservation challenges of highly threatened species such as the leatherback turtle. Moreover, we report a new lineage of the leatherback turtle which may represent a distinct species. Future studies should focus on morphological, ecological, biogeographical, evolutionary and conservation perspectives for the analysis of the new lineage.
Social Impact Statement
The genetic variation of crop wild relatives will be key for our survival, as environmental change represents an increasing global threat for agriculture and food security. ...Cucurbita lundelliana and Cucurbita okeechobeensis subsp. martinezii are wild relatives of cultivated squashes and pumpkins that could be used for crop improvement. A genomic approach was used to characterize genetic resources in these taxa, that is, to identify candidate sites in the genome involved in responses to abiotic stress, and to understand the roles of gene flow and environmental differentiation in their divergence. This study highlights the importance of conserving these two species as phytogenetic resources for crop improvement.
Summary
Crop wild relatives (CWR) are reservoirs of genetic diversity and they are important for the maintenance of crop evolutionary potential. Mexico is the centre of domestication and diversity for many CWR. The genus Cucurbita originated in America, where at least six independent domestication events took place. Nonetheless, Cucurbita CWR have been seldom studied. In the present study, we test the role of incomplete lineage sorting (ILS) and secondary contact in the divergence of C. okeechobeensis subsp. martinezii and C. lundelliana. Additionally, we seek to understand the role of environmental differentiation in their divergence.
We obtained 1,638 single nucleotide polymorphisms (SNPs) for 107 individuals from the most recently diverged wild species in this genus, encompassing 25 localities of C. lundelliana and nine localities of C. okeechobeensis subsp. martinezii in Mexico.
We found higher genetic variation in C. lundelliana (HE = 0.227) than in C. okeechobeensis subsp. martinezii (HE = 0.187). Each taxon constitutes a well‐differentiated genetic group, with an area of introgression in Pantanos de Centla. We found candidate loci associated to hydric and thermal stress, which could be valuable for crop improvement. Our study supported a scenario of ILS followed by secondary contact, where divergence was probably driven by Pleistocene climate change.
These CWR represent important phytogenetic resources for crop improvement given their high levels of genetic variation and differentiation and their SNPs associated to different climatic variables.
La variación genética de los parientes silvestres de los cultivos será clave para nuestra sobrevivencia, dado que el cambio ambiental representa una amenaza global creciente tanto para la agricultura como para la seguridad alimentaria. Cucurbita lundelliana y Cucurbita okeechobeensis subsp. martinezii son parientes silvestres de las calabazas cultivadas que pueden ser utilizadas para el mejoramiento de los cultivos. Una aproximación genómica fue utilizada para caracterizar los recursos genéticos de estos taxa, es decir, para identificar sitios candidatos en el genoma que pueden estar involucrados en la respuesta al estrés abiótico, y para comprender el papel de flujo génico y de la diferenciación ambiental en su divergencia. Este estudio resalta la importancia de conservar estas especies como recursos fitogenéticos para el mejoramiento de los cultivos.
The genetic variation of crop wild relatives will be key for our survival, as environmental change represents an increasing global threat for agriculture and food security. Cucurbita lundelliana and Cucurbita okeechobeensis subsp. martinezii are wild relatives of cultivated squashes and pumpkins that could be used for crop improvement. A genomic approach was used to characterize genetic resources in these taxa, that is, to identify candidate sites in the genome involved in responses to abiotic stress, and to understand the roles of gene flow and environmental differentiation in their divergence. This study highlights the importance of conserving these two species as phytogenetic resources for crop improvement.
Premise
Domestication usually involves local adaptation to environmental conditions. Cucurbita species are a promising model for studying these processes. Cucurbita moschata is the third major crop ...in the genus because of its economic value and because it displays high landrace diversity, but research about its genetic diversity, population structure, and phylogeography is limited. We aimed at understanding how geography and elevation shape the distribution of genetic diversity in C. moschata landraces in Mexico.
Methods
We sampled fruits from 24 localities throughout Mexico. We assessed 11 nuclear microsatellite loci, one mtDNA region, and three cpDNA regions but found no variation in cpDNA. We explored genetic structure with cluster analysis, and phylogeographic relationships with haplotype network analysis.
Results
Mitochondrial genetic diversity was high, and nuclear genetic differentiation among localities was intermediate compared to other domesticated Cucurbita. We found high levels of inbreeding. We recovered two mitochondrial lineages: highland (associated with the Trans‐Mexican Volcanic Belt) and lowland. Nuclear microsatellites show that localities from the Yucatan Peninsula constitute a well‐differentiated group.
Conclusions
Mexico is an area of high diversity for C. moschata, and these landraces represent important plant genetic resources. In Mexico this species is characterized by divergence processes linked to an elevational gradient, which could be related to adaptation and may be of value for applications in agriculture. The Isthmus of Tehuantepec may be a partial barrier to gene flow. Morphological variation, agricultural management, and cultural differences may be related to this pattern of genetic structure, but further studies are needed.
The most recent glacial cycles of the Pleistocene affected the distribution, population sizes, and levels of genetic structure of temperate-forest species in the main Mexican mountain systems. Our ...objective was to investigate the effects these cycles had on the genetic structure and distribution of a dominant species of the "mexical" vegetation across North and Central America. We studied the genetic diversity of
, a conifer distributed from the Southwestern United States to the highlands of Central America. We combined information of one plastid marker and two nuclear markers to infer phylogeographic structure, genetic diversity and demographic changes. We also characterized the climatic niche for each variety to infer the plausible area of suitability during past climatic conditions and to evaluate climatic niche discontinuities along with the species distribution. We found a marked phylogeographic structure separating the populations North and South of the Isthmus of Tehuantepec, with populations to the South of this barrier forming a distinct genetic cluster corresponding to
var.
. We also found signals of population expansion in the Northern genetic cluster. Ecological niche modeling results confirmed climatic niche differences and discontinuities among
varieties and heterogeneous responses to climatic oscillations. Overall,
's genetic diversity has been marked by distribution shifts, population growth and secondary contact the North, and
permanence in the South since the last interglacial to the present. High genetic variation suggests a wide and climatically diverse distribution during climatic oscillations. We detected the existence of two main genetic clusters, supporting previous proposals that
and
may be considered two separate species.
The recent emergence of the pathogen
(
) is associated with rapid population declines of salamanders in Europe and its arrival to new areas could cause dramatic negative effects on other amphibian ...populations and species. Amphibian species, present in areas with high amphibian diversity such as Mexico, could be highly threatened due to the arrival of
, particularly salamander species which are more vulnerable to chytridiomycosis caused by this pathogen. Thus, immediate surveillance is needed as a strategy to efficiently contend with this emerging infectious disease. In this study, we analyzed 490 wild and captive amphibians from 48 species across 76 sites in the North, Central, and South of Mexico to evaluate the presence of
. Amphibians were sampled in sites with variable degrees of amphibian richness and suitability for
according to previous studies. From the 76 sampling sites, 10 of them were located in areas with high amphibian richness and potential moderate to high
habitat suitability. We did not detect
in any of the samples, and no signs of the disease were observed in any individual at the time of sampling. Our results suggest that
has not yet arrived at the sampled sites or could be at low prevalence within populations with low occurrence probability. This is the first study that evaluates the presence of
in different regions and amphibian species in Mexico, which is the second most diverse country in salamander species in the world. We highlight the risk and the importance of continuing surveillance of
in Mexico and discuss control strategies to avoid the introduction and spread of
in the country.
, the lesser long-nosed bat is an abundant migratory nectar-feeding bat found in most of Mexico, and in some areas of northern Central America and small sections of southwestern USA. We analyzed the ...distribution of the maternal and paternal lineages of this species with phylogeographic methods based on two mitochondrial markers,
and
, and a marker located in the Y chromosome,
. We obtained tissue samples from 220 individuals from 23 localities. Levels of genetic diversity (haplotype diversity,
) were high (
= 0.757;
= 0.8082;
= 0.9137). No clear patterns of population genetic structure were found for mitochondrial markers, while male genetic differentiation suggested the presence of two lineages: one from Mexican Pacific coast states and another from central-southern Mexico; in accordance to strong male philopatry and higher female migration. We used genealogical reconstructions based on Bayesian tools to calculate divergence times, and to test coalescent models to explain changes in
.
historical demography. Our results show that recent demographic changes were consistent with global climatic changes (∼130,000 kyr ago for
and ∼160,000 kyr for
) and divergence times dated from molecular genealogies exhibited older divergence times,
(4.03 mya),
(10.26 mya) and
(12.23 mya). Accordingly, the female lineage underwent demographic expansion associated to Pleistocene climate change, whereas the male lineage remained constant.
Abstract
Despite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in
...Cucurbita
species (pumpkins and squashes) is currently lacking.
Cucurbita argyrosperma
, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study
Cucurbita
domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of
C. argyrosperma
across Mexico. We also assembled the first high-quality wild
Cucurbita
genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species
Cucurbita moschata
suggests domestication-related introgression between both taxa.
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