Genetic structure and temporal environmental niche dynamics of sideoats grama [Bouteloua curtipendula (Michx.) Torr.] populations in Mexico.
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SUBMITTER: Alvarez-Holguin A
PROVIDER: S-EPMC8282060 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Understanding how species respond to the environment is essential in ecology, evolution, and conservation. Abiotic factors can influence species responses and the multi-dimensional space of abiotic factors that allows a species to grow represents the environmental niche. While niches are often assumed to be constant and robust, they are most likely changing over time and estimation can be influenced by population biology, sampling intensity, and computation methodology. Here, we used a 12-year time series of survey data to fit annual ecological niche models (ENMs) for 10 marine fish species by using two regression and two machine learning algorithms to evaluate the variation and differentiation of environmental niches. Fitted ENMs were used to develop multi-dimensional annual and pooled hypervolumes that were evaluated over time and across ENM algorithms, species, and years by computing volume, distance, and dissimilarity metrics for each annual estimated niche. We then investigated potential drivers of estimated hypervolume dynamics including species abundance, species occurrence, sampling effort, salinity, red tides severity, and algorithm. Overall, our results revealed that estimated niches varied over time and across ENM, species, and algorithms. Niche estimation was influenced over time by multiple factors suggesting high complexity on niche dynamics interpretation. Species with high occurrence tended to have a closer representation of the pooled niche and years with higher abundance tended to produce niche expansion. ENM algorithm, sampling effort, seawater salinity, and red tides explained the deviations from the pooled niche. Greater sampling effort led to more comprehensive and complete estimates of species niches. High red tides severity triggered niche contraction. Our results emphasize the predictable effects of population, sampling, and environment on species niche estimation and interpretation, and that each should be considered when performing and interpreting ecological niche analyses. Our niche analysis approach may contribute to effectively quantifying and assessing niche dynamics.
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Project description:Variation within the Type and Sidney 81 strains of wheat streak mosaic virus was assessed by single-strand conformation polymorphism (SSCP) analysis and confirmed by nucleotide sequencing. Limiting-dilution subisolates (LDSIs) of each strain were evaluated for polymorphism in the P1, P3, NIa, and CP cistrons. Different SSCP patterns among LDSIs of a strain were associated with single-nucleotide substitutions. Sidney 81 LDSI-S10 was used as founding inoculum to establish three lineages each in wheat, corn, and barley. The P1, HC-Pro, P3, CI, NIa, NIb, and CP cistrons of LDSI-S10 and each lineage at passages 1, 3, 6, and 9 were evaluated for polymorphism. By passage 9, each lineage differed in consensus sequence from LDSI-S10. The majority of substitutions occurred within NIa and CP, although at least one change occurred in each cistron except HC-Pro and P3. Most consensus sequence changes among lineages were independent, with substitutions accumulating over time. However, LDSI-S10 bore a variant nucleotide (G(6016)) in NIa that was restored to A(6016) in eight of nine lineages by passage 6. This near-global reversion is most easily explained by selection. Examination of nonconsensus variation revealed a pool of unique substitutions (singletons) that remained constant in frequency during passage, regardless of the host species examined. These results suggest that mutations arising by viral polymerase error are generated at a constant rate but that most newly generated mutants are sequestered in virions and do not serve as replication templates. Thus, a substantial fraction of variation generated is static and has yet to be tested for relative fitness. In contrast, nonsingleton variation increased upon passage, suggesting that some mutants do serve as replication templates and may become established in a population. Replicated mutants may or may not rise to prominence to become the consensus sequence in a lineage, with the fate of any particular mutant subject to selection and stochastic processes such as genetic drift and population growth factors.
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Project description:AimTo infer the geological and climatic factors that have shaped the genetic diversity and structure of a willow species (Salix humboldtiana) in three basins of Central Mexico.LocationCentral Mexico.MethodsWe collected samples from 11 populations across two hydrological basins (Balsas and Lerma) and one population from another basin (Ameca) within the Mexican Central Plateau (MCP). Individuals were analyzed using sequences of two chloroplast DNA (cpDNA) regions and eight nuclear simple sequence repeats (nSSR). Population genetic diversity and structure were determined from these data. To evaluate whether genetic structure was associated with ecological niche differentiation, we determined whether there is niche equivalence, overlap, or divergence between the Balsas and Lerma basins. Also, we evaluated the relative contributions of geographic distribution and climatic variation on population genetic structuring through redundancy analysis (RDA) and partial RDA.ResultsBoth cpDNA and nSSRs data indicated the presence of three highly differentiated genetic groups, mostly geographically congruent with the three main hydrological basins. According to nSSRs, the three genetic groups can be further subdivided into eight subgroups corresponding to different rivers within the main basins. The niche equivalency test showed that the niches of the species in the Balsas and Lerma basins are significantly nonequivalent. The RDA indicated a significant association of genetic variation among populations with climate variables (particularly those related to the precipitation regime), while controlling for geographic distribution.Main conclusionsThe genetic structure of S. humboldtiana is strongly associated with the historical and current geological configuration of the basins and the rivers within basins. The observed hierarchical genetic differentiation can be due to gene flow limitation resulting from physical barriers to the dispersal of S. humboldtiana, but also to some degree of isolation by environment, as suggested by the significant association between genetic variation among populations and precipitation regime.
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Project description:Government based Payments for Ecosystem Services (PES) have been criticized for not maximizing environmental effectiveness through appropriate targeting, while instead prioritizing social side-objectives. In Mexico, existing literature on how the Payments for Ecosystem Services-Hydrological program (PSA-H) has targeted deforestation and forest degradation shows that both the process of identifying the eligible areas and the choice of the selection criteria for enrolling forest parcels have been under the influence of competing agendas. In the present paper we study the influence of the PSA-H multi-level governance on the environmental effectiveness of the program-the degree to which forest at high risk of deforestation is enrolled- building from a "policyscape" framework. In particular, we combine governance analysis with two distinct applications of the policyscape framework: First, at national level we assess the functional overlap between the PSA-H and other environmental and rural programs with regard to the risk of deforestation. Second, at regional level in the states of Chiapas and Yucatan, we describe the changing policy agenda and the role of technical intermediaries in defining the temporal spatialization of the PSA-H eligible and enrolled areas with regard to key socio-economic criteria. We find that, although at national level the PSA-H program has been described as coping with both social and environmental indicators thanks to successful adaptive management, our analysis show that PSA-H is mainly found in communities where deforestation risk is low and in combination with other environmental programs (protected areas and forest management programs). Such inertia is reinforced at regional level as a result of the eligible areas' characteristics and the behaviour of technical intermediaries, which seek to minimise transaction costs and sources of uncertainty. Our project-specific analysis shows the importance of integrating the governance of a program in the policyscape framework as a way to better systematize complex interactions at different spatial and institutional scales between policies and landscape characteristics.
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Project description:With the increasing frequency of large-scale restoration efforts, the need to understand the adaptive genetic structure of natural plant populations and their relation to heavily utilized cultivars is critical. Bouteloua gracilis (blue grama) is a wind-dispersed, perennial grass consisting of several cytotypes (2n = 2×-6×) with a widespread distribution in western North America. The species is locally dominant and used regularly in restoration treatments. Using amplified fragment length polymorphism (AFLP) and cpDNA analyses, we assessed the genetic variability and adaptive genetic structure of blue grama within and among 44 sampling sites that are representative of the species' environmental and habitat diversity in the southwestern United States. Five cultivars were also included to investigate genetic diversity and differentiation in natural versus cultivated populations. Three main findings resulted from this study: (a) Ninety-four polymorphic AFLP markers distinguished two population clusters defined largely by samples on and off the Colorado Plateau; (b) substructure of samples on the Colorado Plateau was indicated by genetic divergence between boundary and interior regions, and was supported by cytotype distribution and cpDNA analysis; and (c) six AFLP markers were identified as "outliers," consistent with being under selection. These loci were significantly correlated to mean annual temperature, mean annual precipitation, precipitation of driest quarter, and precipitation of wettest quarter in natural populations, but not in cultivated samples. Marker × environment relationships were found to be largely influenced by cytotype and cultivar development. Our results demonstrate that blue grama is genetically variable, and exhibits genetic structure, which is shaped, in part, by environmental variability across the Colorado Plateau. Information from our study can be used to guide the selection of seed source populations for commercial development and long-term conservation management of B. gracilis, which could include genetic assessments of diversity and the adaptive potential of both natural and cultivated populations for wildland restoration.
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Project description:BackgroundAs resistance to insecticides increases in disease vectors, it has become exceedingly important to monitor populations for susceptibility. Most studies of field populations of Aedes aegypti have largely characterized resistance patterns at the spatial scale of the city or country, which may not be completely informative given that insecticide application occurs at the scale of the house or city block. Phenotypic resistance to pyrethroids dominates in Ae. aegypti, and it has been partially explained by mutations in the voltage-gated sodium channel gene. Here, we assess community-level patterns of four knockdown resistance (kdr) haplotypes (C1534/I1016, F1534/I1016, C1534/V1016 and F1534/V1016) in Ae. aegypti in 24 randomly chosen city blocks from a city in Yucatán State, Mexico, during both the dry and wet season and over two years.ResultsThree of the four haplotypes, C1534/I1016, C1534/V1016 and F1534/V1016 were heterogeneous between city blocks at all four sampling time points, and the double mutant haplotype, C1534/I1016, showed a significant increase following the wet season. The F1534/I1016 haplotype was rarely detected, similar to other studies. However, when haplotype frequencies were aggregated to a coarser spatial scale, the differences in space and time were obscured.ConclusionsOur results provide empirical evidence that the selection of kdr alleles is occurring at fine spatial scales, indicating that future studies should include this scale to better understand evolutionary processes of resistance in natural populations.
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Project description:The seasonal timing of recurring biological processes is essential for organisms living in temperate regions. While ample knowledge of these processes exists for terrestrial environments, seasonal timing in the marine environment is relatively understudied. Here, we characterized the annual rhythm of habitat use in six fish species belonging to the Sparidae family, highlighting the main environmental variables that correlate to such rhythms. The study was conducted at a coastal artificial reef through a cabled observatory system, which allowed gathering underwater time-lapse images every 30?minutes consecutively over 3 years. Rhythms of fish counts had a significant annual periodicity in four out of the six studied species. Species-specific temporal patterns were found, demonstrating a clear annual temporal niche partitioning within the studied family. Temperature was the most important environmental variable correlated with fish counts in the proximity of the artificial reef, while daily photoperiod and salinity were not important. In a scenario of human-induced rapid environmental change, tracking phenological shifts may provide key indications about the effects of climate change at both species and ecosystem level. Our study reinforces the efficacy of underwater cabled video-observatories as a reliable tool for long-term monitoring of phenological events.
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