Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
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Item Unintended Maladaptation: How Agritourism Development Policies in Iran Have Increased Vulnerability to Climate Change(MDPI (Basel, Switzerland), 2023-08-29) Torabi Z-A; Khavarian-Garmsir AR; Hall CM; Khatibi NB; Borghi ADImplementing appropriate policies is crucial for adapting the agricultural sector to climate change. However, adopting incorrect policies can exacerbate unsustainable development. Hence, this study investigated the unintended consequences of agritourism development policies as a climate change adaptation strategy in the villages of Shahrud, Iran. It demonstrated how such policies have inadvertently heightened farmers’ vulnerability to climate change impacts. Data were collected through 44 semi-structured interviews, which underwent thematic analysis to identify emerging patterns. The study’s findings indicate that the rapid expansion of Agritourism in Iran, aimed at addressing climate change, has failed to achieve its intended goals. Inadequate government support, increased supply, legal gaps, and lack of empowerment were identified as contributing factors leading to unsustainable development and financial losses. Consequently, smallholder farmers were found to harbor negative perceptions of agritourism and expressed dissatisfaction with existing policies. These findings underscore the necessity of comprehensive policies and support systems to facilitate the effective implementation of sustainable agritourism by stakeholders in Iran.Item Editorial: Mobile DNA element-driven evolution of bacterial pathogens(Frontiers Media S A, 2025-03-19) Cloeckaert A; Zygmunt MS; Vale FF; Altermann E; Li TItem Phenotypic and genetic divergence in a cold-adapted grasshopper may lead to lineage-specific responses to rapid climate change(John Wiley and Sons Ltd, 2024-04-12) Meza-Joya FL; Morgan-Richards M; Trewick SA; Briski EAim: Species responses to global warming will depend on intraspecific diversity, yet studies of factors governing biogeographic patterns of variability are scarce. Here, we investigate the evolutionary processes underlying genetic and phenotypic diversity in the flightless and cold-adapted grasshopper Sigaus piliferus, and project its suitable space in time. Location: Te Ika-a-Māui Aotearoa—North Island of New Zealand. Methods: We used mitochondrial sequences to investigate population connectivity and demographic trends using phylogeographic tools and neutrality statistics. Metric data were used to document phenotypic variation using naïve clustering. We used niche metrics to assess intraspecific niche variation, and niche modelling to investigate suitability under past and future scenarios. Multiple matrix regressions with randomization explored the processes contributing to phenotypic differentiation among grasshopper populations. Results: Niche models and demographic analyses suggest suitable space for this grasshopper was more restricted during glacial than interglacial stages. Genealogical relationships among ND2 haplotypes revealed a deep north–south split partly concordant with phenotypic and niche variation, suggesting two ecotypes that have mixed during recolonisation of the central volcanic region. Multiple matrix regressions with randomization indicate a link between climate and phenotypic differentiation inferred from leg and pronotum dimensions but not pronotum shape. Niche projections predict severe habitat reduction due to climate warming. Main conclusions: The current distribution and intraspecific diversity of S. piliferus reflect complex biogeographical scenarios consistent with Quaternary climates and volcanism. Phenotypic divergence appears adaptive. Current levels of genetic and phenotypic variation suggest adaptive potential, yet the pace of anthropogenic warming over the next 50 years could result in small populations that may collapse before adapting. Differences in niche features between diverging intraspecific lineages suggest distinct responses to climate change, and this has implications for prioritising conservation actions and management strategies.Item Seed Morphology of Three Neotropical Orchid Species of the Lycaste Genus(MDPI (Basel, Switzerland), 2023-09) Alfaro Pinto A; McGill C; Nadarajan J; Archila Morales F; Clavijo McCormick AC; Cortés JAH; Lombraña ACNeotropical orchids are vulnerable to extinction due to overharvesting, habitat destruction and climate change. However, a basic understanding of orchid seed biology to support conservation efforts is still lacking for most species. Seed morphology is linked to plant adaptation and evolution, influencing seed dispersal, dormancy, longevity, and germination, which are valuable traits for conservation. In this study, we characterized and compared the morphological traits of seed capsules (size, shape, and colour) and seeds (seed and embryo shape and size and internal airspace volume) for three epiphytic Neotropical orchid species of the genus Lycaste native to Guatemala: L. cochleata, L. lasioglossa, and L. virginalis. The three species show qualitative similarities in seed capsule colour and appearance and in seed morphology (i.e., scobiform oval-shaped seeds and prolate-spheroid embryos). All species have small-sized seeds (length of L. cochleata: 210 µm, L. lasioglossa: 230 µm, and L. virginalis: 260 µm), with proportionally large embryos (length of L. cochleata: 140 µm, L. lasioglossa: 120 µm, and L. virginalis: 150 µm) and an internal air-space volume that occupies less than half of the seed (L. cochleata: 17%, L. lasioglossa: 42%, and L. virginalis: 30%). This finding is consistent with previous reports for other epiphytic orchid species, which typically have lower air volumes than terrestrial orchids. These differences are likely a result of evolutionary changes associated with different habits and may influence seed dispersal. We also found some significant differences in seed morphology between the studied species, but their taxonomic, biological, and ecological relevance remain to be elucidated. More comparative studies, including on other Lycaste species with different habits, are needed to explore relationships between seed morphology, taxonomy, biology, and ecology in this genus to support its conservation.Item Fitness of evolving bacterial populations is contingent on deep and shallow history but only shallow history creates predictable patterns(The Royal Society, 2022-09-14) Smith CE; Smith ANH; Cooper TF; Moore FB-GLong-term evolution experiments have tested the importance of genetic and environmental factors in influencing evolutionary outcomes. Differences in phylogenetic history, recent adaptation to distinct environments and chance events, all influence the fitness of a population. However, the interplay of these factors on a population's evolutionary potential remains relatively unexplored. We tracked the outcome of 2000 generations of evolution of four natural isolates of Escherichia coli bacteria that were engineered to also create differences in shallow history by adding previously identified mutations selected in a separate long-term experiment. Replicate populations started from each progenitor evolved in four environments. We found that deep and shallow phylogenetic histories both contributed significantly to differences in evolved fitness, though by different amounts in different selection environments. With one exception, chance effects were not significant. Whereas the effect of deep history did not follow any detectable pattern, effects of shallow history followed a pattern of diminishing returns whereby fitter ancestors had smaller fitness increases. These results are consistent with adaptive evolution being contingent on the interaction of several evolutionary forces but demonstrate that the nature of these interactions is not fixed and may not be predictable even when the role of chance is small.Item The cost of evolved constitutive lac gene expression is usually, but not always, maintained during evolution of generalist populations(John Wiley and Sons Ltd, 2021-09-24) Phillips KN; Cooper TFBeneficial mutations can become costly following an environmental change. Compensatory mutations can relieve these costs, while not affecting the selected function, so that the benefits are retained if the environment shifts back to be similar to the one in which the beneficial mutation was originally selected. Compensatory mutations have been extensively studied in the context of antibiotic resistance, responses to specific genetic perturbations, and in the determination of interacting gene network components. Few studies have focused on the role of compensatory mutations during more general adaptation, especially as the result of selection in fluctuating environments where adaptations to different environment components may often involve trade-offs. We examine whether costs of a mutation in lacI, which deregulated the expression of the lac operon in evolving populations of Escherichia coli bacteria, were compensated. This mutation occurred in multiple replicate populations selected in environments that fluctuated between growth on lactose, where the mutation was beneficial, and on glucose, where it was deleterious. We found that compensation for the cost of the lacI mutation was rare, but, when it did occur, it did not negatively affect the selected benefit. Compensation was not more likely to occur in a particular evolution environment. Compensation has the potential to remove pleiotropic costs of adaptation, but its rarity indicates that the circumstances to bring about the phenomenon may be peculiar to each individual or impeded by other selected mutations.Item Historical Contingency Causes Divergence in Adaptive Expression of the lac Operon(Oxford University Press on behalf of The Society for Molecular Biology and Evolution (SMBE), 2021-07) Karkare K; Lai H-Y; Azevedo RBR; Cooper TF; Wittkopp PPopulations of Escherichia coli selected in constant and fluctuating environments containing lactose often adapt by substituting mutations in the lacI repressor that cause constitutive expression of the lac operon. These mutations occur at a high rate and provide a significant benefit. Despite this, eight of 24 populations evolved for 8,000 generations in environments containing lactose contained no detectable repressor mutations. We report here on the basis of this observation. We find that, given relevant mutation rates, repressor mutations are expected to have fixed in all evolved populations if they had maintained the same fitness effect they confer when introduced to the ancestor. In fact, reconstruction experiments demonstrate that repressor mutations have become neutral or deleterious in those populations in which they were not detectable. Populations not fixing repressor mutations nevertheless reached the same fitness as those that did fix them, indicating that they followed an alternative evolutionary path that made redundant the potential benefit of the repressor mutation, but involved unique mutations of equivalent benefit. We identify a mutation occurring in the promoter region of the uspB gene as a candidate for influencing the selective choice between these paths. Our results detail an example of historical contingency leading to divergent evolutionary outcomes.Item Dynamics of bacterial adaptation(Portland Press Limited on behalf of the Biochemical Society, 2021-04-12) Lai H-Y; Cooper TFDetermining pattern in the dynamics of population evolution is a long-standing focus of evolutionary biology. Complementing the study of natural populations, microbial laboratory evolution experiments have become an important tool for addressing these dynamics because they allow detailed and replicated analysis of evolution in response to controlled environmental and genetic conditions. Key findings include a tendency for smoothly declining rates of adaptation during selection in constant environments, at least in part a reflection of antagonism between accumulating beneficial mutations, and a large number of beneficial mutations available to replicate populations leading to significant, but relatively low genetic parallelism, even as phenotypic characteristics show high similarity. Together, there is a picture of adaptation as a process with a varied and largely unpredictable genetic basis leading to much more similar phenotypic outcomes. Increasing sophistication of sequencing and genetic tools will allow insight into mechanisms behind these and other patterns.Item Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies.(2016-12) Riginos C; Crandall ED; Liggins L; Bongaerts P; Treml EAPopulation genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region (e.g., geographical distance, average sea surface temperature, average salinity). We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water (experienced by most marine taxa at some point in their life cycle), require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for landscape genomics with an emphasis on marine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated selection and that seascape genomic approaches are especially useful for identifying robust locus-by-environment associations.