An important step in species conservation is to identify populations that significantly contribute to it. Considering both in situ and ex situ populations provides an integrated approach to the ...preservation of a species' evolutionary potential. The joint use of molecular and environmental analyses allows conservation schemes to be implemented when reintroducing captive populations, and wild populations to be prioritized for conservation purposes. We used genetic data and environmental analyses to select candidate areas for the reintroduction of a captive population of the Mexican prairie dog, Cynomys mexicanus, and prioritize wild populations for the conservation of this endangered endemic species. We estimated the levels of genetic diversity and differentiation of the captive population and compared them with those of six wild populations. We used species distribution modeling (SDM) to perform forecasts under future climate change scenarios and identify areas with suitable environmental conditions for the populations to persist in the medium to long term. The captive population showed high levels of genetic diversity (Hd=0.692, HE=0.52), but was genetically differentiated from the wild populations. The genetic structure of wild populations should therefore be considered when reintroducing captive Mexican prairie dogs. In the wild populations, we found a correlation between colony area and nuclear genetic diversity, suggesting that genetic drift and/or inbreeding have been stronger in smaller colonies. The occupied climate space was well differentiated among wild colonies. The impact of agriculture and roads was stronger in the northeastern area of the species range, where SDM forecasts suggest that environmental conditions may remain suitable in the future. Finally, we identified three colonies as conservation priorities based on both genetic and ecological criteria.
•Genetic and environmental analyses allowed to assess reintroduction potential.•Reintroduction plans should consider genetic and environmental differentiation.•We propose a prioritization index based on both genetic and ecological criteria.•Climate change scenarios were also used to prioritize populations for conservation.•This approach can be applied to a wide set of endangered taxa.
Across North America, anthropogenically induced habitat fragmentation has led to a severe decline in populations of black-tailed prairie dogs (Cynomys ludovicianus). Although the area occupied by ...black-tailed prairie dogs in Chihuahua, northwestern Mexico, also has recently declined, this site remains comparatively unaffected by human disturbance. Cytochrome-b sequences and 10 nuclear microsatellite loci were analyzed across 13 colonies to test if due to large size, absence of plague, and protected status, the black-tailed prairie dogs from Janos possess relatively high levels of genetic variation and low genetic structure; or if recent population decline and peripheral effects result in relatively low genetic variation and high genetic structure. Analysis suggests moderate mitochondrial genetic variation relative to other sciurids, and not significantly different nuclear genetic variation relative to other populations of prairie dogs. Furthermore, in accordance to black-tailed prairie dog social organization, genetic structure among local populations was significant, and within-colony variation was higher than among-colony variation for both markers. FST was higher for mitochondrial than for nuclear DNA related to female philopatry and male-biased gene flow. Finally, a negative correlation between genetic differentiation as a function of colony area and population size found for nuclear microsatellite loci suggests an increased effect of genetic drift in smaller and less-dense colonies because of recent habitat fragmentation. In conclusion, despite being a peripheral and declining population, Janos black-tailed prairie dogs retained genetic variation that has been maintained by their social structure and dispersal pattern. En Norte América, la fragmentación del hábitat inducida por el hombre ha provocado una reducción considerable de las poblaciones de perros llaneros de cola negra (Cynomys ludovicianus). Aunque el área ocupada por las colonias de perros llaneros en Chihuahua, al noroeste de México, también se ha reducido recientemente, esta población ha sido menos afectada por la perturbación humana. Se analizaron secuencias del citocromo b (Cytb) y 10 microsatélites nucleares en 13 colonias para poner a prueba si la población de perros llaneros de cola negra de Janos posee niveles de variación genética relativamente altos y baja estructura genética debido a su gran tamaño, ausencia de peste y estatus de protección; o si la disminución poblacional reciente y los efectos periféricos han resultado en la presencia de baja variación y alta estructura genética. Los análisis sugieren que la variación genética mitocondrial es moderada con relación a otros sciúridos y que la variación genética nuclear no es significativamente distinta en relación a otras poblaciones de perros llaneros. Además, de acuerdo con la organización social de los perros llaneros de cola negra, la estructura genética entre poblaciones locales fue significativa y la variación hacia el interior de las colonias fue mayor que entre las colonias para ambos marcadores. Con relación a la filopatría de las hembras y la dispersión sesgada hacia los machos, la FST fue mayor para el ADN mitocondrial que para el ADN nuclear. Finalmente, para los marcadores nucleares se encontró una correlación negativa entre la diferenciación genética y el área de la colonia y el tamaño poblacional, lo que sugiere un incremento en el efecto de la deriva génica en las colonias más pequeñas y menos densas como resultado de la fragmentación del hábitat reciente. En conclusión, la estructura social y el patrón de dispersión ha mantenido la variación genética de los perros llaneros de cola negra de Janos a pesar de considerarse una población periférica y en declive.
Cucurbita pepo is an economically important crop, which consists of cultivated C. pepo ssp. pepo, and two wild taxa (C. pepo ssp. fraterna and C. pepo ssp. ovifera). We aimed at understanding the ...domestication and the diversity of C. pepo in Mexico. We used two chloroplast regions and nine nuclear microsatellite loci to assess the levels of genetic variation and structure for C. pepo ssp. pepo’s landraces sampled in 13 locations in Mexico, five improved varieties, one C. pepo ssp. fraterna population and ornamental C. pepo ssp. ovifera. We tested four hypotheses regarding the origin of C. pepo ssp. pepo’s ancestor through approximate Bayesian computation: C. pepo ssp. ovifera as the ancestor; C. pepo ssp. fraterna as the ancestor; an unknown extinct lineage as the ancestor; and C. pepo ssp. pepo as hybrid from C. pepo ssp. ovifera and C. pepo ssp. fraterna ancestors. Cucurbita pepo ssp. pepo showed high genetic variation and low genetic differentiation. Cucurbita pepo ssp. fraterna and C. pepo ssp. pepo shared two chloroplast haplotypes. The three subspecies were well differentiated for microsatellite loci. Cucurbita pepo ssp. fraterna was probably C. pepo ssp. pepo’s wild ancestor, but subsequent hybridization between taxa complicate defining C. pepo ssp. pepo’s ancestor.
Societal Impact Statement
Crop wild relatives (CWR) are plant taxa closely related to crops and are a source of high genetic diversity that can help adapt crops to the impacts of global change, ...particularly to meet increasing consumer demand in the face of the climate crisis. CWR provide vital ecosystem services and are increasingly important for food and nutrition security and sustainable and resilient agriculture. They therefore are of major biological, social, cultural and economic importance. Assessing the extinction risk of CWR is essential to prioritise in situ and ex situ conservation strategies in Mesoamerica to guarantee the long‐term survival and availability of these resources for present and future generations worldwide.
Summary
Ensuring food security is one of the world's most critical issues as agricultural systems are already being impacted by global change. Crop wild relatives (CWR)—wild plants related to crops—possess genetic variability that can help adapt agriculture to a changing environment and sustainably increase crop yields to meet the food security challenge.
Here we report the results of an extinction risk assessment of 224 wild relatives of some of the world's most important crops (i.e. chilli pepper, maize, common bean, avocado, cotton, potato, squash, vanilla and husk tomato) in Mesoamerica—an area of global significance as a centre of crop origin, domestication and of high CWR diversity.
We show that 35% of the selected CWR taxa are threatened with extinction according to The International Union for Conservation of Nature (IUCN) Red List demonstrates that these valuable genetic resources are under high anthropogenic threat. The dominant threat processes are land use change for agriculture and farming, invasive and other problematic species (e.g. pests, genetically modified organisms) and use of biological resources, including overcollection and logging. The most significant drivers of extinction relate to smallholder agriculture—given its high incidence and ongoing shifts from traditional agriculture to modern practices (e.g. use of herbicides)—smallholder ranching and housing and urban development and introduced genetic material.
There is an urgent need to increase knowledge and research around different aspects of CWR. Policies that support in situ and ex situ conservation of CWR and promote sustainable agriculture are pivotal to secure these resources for the benefit of current and future generations.
Crop wild relatives (CWR) are plant taxa closely related to crops and are a source of high genetic diversity that can help adapt crops to the impacts of global change, particularly to meet increasing consumer demand in the face of the climate crisis. CWR provide vital ecosystem services and are increasingly important for food and nutrition security, and sustainable and resilient agriculture. They therefore are of major biological, social, cultural and economic importance. Assessing the extinction risk of CWR is essential to prioritise in situ and ex situ conservation strategies in Mesoamerica to guarantee the long‐term survival and availability of these resources for present and future generations worldwide.
Across North America, anthropogenically induced habitat fragmentation has led to a severe decline in populations of black-tailed prairie dogs (Cynomys ludovicianus). Although the area occupied by ...black-tailed prairie dogs in Chihuahua, northwestern Mexico, also has recently declined, this site remains comparatively unaffected by human disturbance. Cytochrome-b sequences and 10 nuclear microsatellite loci were analyzed across 13 colonies to test if due to large size, absence of plague, and protected status, the black-tailed prairie dogs from Janos possess relatively high levels of genetic variation and low genetic structure; or if recent population decline and peripheral effects result in relatively low genetic variation and high genetic structure. Analysis suggests moderate mitochondrial genetic variation relative to other sciurids, and not significantly different nuclear genetic variation relative to other populations of prairie dogs. Furthermore, in accordance to black-tailed prairie dog social organization, genetic structure among local populations was significant, and within-colony variation was higher than among-colony variation for both markers. FST was higher for mitochondrial than for nuclear DNA related to female philopatry and male-biased gene flow. Finally, a negative correlation between genetic differentiation as a function of colony area and population size found for nuclear microsatellite loci suggests an increased effect of genetic driftin smaller and less-dense colonies because of recent habitat fragmentation. In conclusion, despite being a peripheral and declining population, Janos black-tailed prairie dogs retained genetic variation that has been maintained by their social structure and dispersal pattern.
Twenty-nine DNA regions of plastid origin have been previously identified in the mitochondrial genome of
Cucurbita pepo
(pumpkin; Cucurbitaceae). Four of these regions harbor homolog sequences of
...rbcL
,
matK
,
rpl20–rps12
and
trnL–trnF
, which are widely used as molecular markers for phylogenetic and phylogeographic studies. We extracted the mitochondrial copies of these regions based on the mitochondrial genome of
C. pepo
and, along with published sequences for these plastome markers from 13
Cucurbita
taxa, we performed phylogenetic molecular analyses to identify inter-organellar transfer events in the
Cucurbita
phylogeny and changes in their nucleotide substitution rates. Phylogenetic reconstruction and tree selection tests suggest that
rpl20
and
rbcL
mitochondrial paralogs arose before
Cucurbita
diversification whereas the mitochondrial
matK
and
trnL–trnF
paralogs emerged most probably later, in the mesophytic
Cucurbita
clade. Nucleotide substitution rates increased one order of magnitude in all the mitochondrial paralogs compared to their original plastid sequences. Additionally, mitochondrial
trnL–trnF
sequences obtained by PCR from nine
Cucurbita
taxa revealed higher nucleotide diversity in the mitochondrial than in the plastid copies, likely related to the higher nucleotide substitution rates in the mitochondrial region and loss of functional constraints in its tRNA genes.
Cucurbita ficifolia is a squash grown from Mexico to Bolivia. Its ancestor is unknown, but it has limited compatibility with wild xerophytic Cucurbita from Mexico’s highlands. We assembled the ...reference genome of C. ficifolia and assessed the genetic diversity and historical demography of the crop in Mexico with 2524 nuclear single nucleotide polymorphisms (SNPs). We also evaluated the gene flow between C. ficifolia and xerophytic taxa with 6292 nuclear and 440 plastome SNPs from 142 individuals sampled in 58 sites across their area of sympatry. Demographic modelling of C. ficifolia supports an eight-fold decrease in effective population size at about 2409 generations ago (95% CI = 464–12,393), whereas plastome SNPs support the expansion of maternal lineages ca. 1906–3635 years ago. Our results suggest a recent spread of C. ficifolia in Mexico, with high genetic diversity (π = 0.225, FST = 0.074) and inbreeding (FIS = 0.233). Coalescent models suggest low rates of gene flow with C. radicans and C. pedatifolia, whereas ABBA-BABA tests did not detect significant gene flow with wild taxa. Despite the ecogeographic proximity of C. ficifolia and its relatives, this crop persists as a highly isolated lineage of puzzling origin.
Studies in evolutionary biology have commonly been focused on insular systems because of their natural geographic isolation and relatively simpler biotas. Using mitochondrial DNA sequences of 4 ...passerine bird species distributed in the Tres Marías Archipelago (TMA) and the nearby mainland of western Mexico—Cardinalis cardinalis, Turdus rufopalliatus, Vireo hypochryseus, and Icterus pustulatus—we determined interspecific and intraspecific phylogenetic relationships between insular and mainland populations, conducted insular age-based time calibration for the estimation of divergence times, and used Bayesian analyses to examine the colonization history of islands. Specifically, we tested whether the study species from the TMA share the same colonization history since the emergence of the islands ∼120 kya, taking advantage of the reduced isolation due to sea-level fluctuations during the Pleistocene, or whether there were independent colonization events. We also looked for evidence in the genetic structure of the island populations that would support the idea of colonization by a small number of individuals. Phylogenetic relationships consistently recovered lineage divergence between the TMA and mainland populations, with strong support in 3 of the 4 species. Our estimates for the sea level and coastline of the west coast of Mexico during the Pleistocene showed that the distance between the TMA and the mainland was ∼25 km. We tested several island colonization scenarios according to the phylogenetic relationships, haplotype networks, divergence time estimates, historical demography, and different glaciation dates. The most supported scenario of colonization of the TMA suggests that a single event occurred ∼120 kya when the islands emerged, which is highly concordant with geological evidence, and simultaneously affected the 4 species.
Species of restricted distribution are considered more vulnerable to extinction because of low levels of genetic variation relative to widespread taxa. Species of the subgenus Cynomys are an ...excellent system to compare genetic variation and degree of genetic structure in contrasting geographic distributions. We assessed levels of genetic variation, genetic structure, and genetic differentiation in widespread Cynomys ludovicianus and restricted C. mexicanus using 1997bp from the cytochrome b and control region (n = 223 C. ludovicianus; 77 C. mexicanus), and 10 nuclear microsatellite loci (n = 207 and 78, respectively). Genetic variation for both species was high, and genetic structure in the widespread species was higher than in the restricted species. C. mexicanus showed values of genetic variation, genetic structure, and genetic differentiation similar to C. ludovicianus at smaller geographic scales. Results suggest the presence of at least 2 historical refuges for C. ludovicianus and that the Sierra Madre Occidental represents a barrier to gene flow. Chihuahua and New Mexico possess high levels of genetic diversity and should be protected, while Sonora should be treated as an independent management unit. For C. mexicanus, connectivity among colonies is very important and habitat fragmentation and habitat loss should be mitigated to maintain gene flow.
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