Projected development in Borneo and Sumatra will greatly reduce connectivity for an apex carnivore.

The islands of Borneo and Sumatra are strongholds for biodiversity and home for many endemic species. They also have experienced amongst the highest deforestation rates globally. Both islands are undergoing massive, rapid infrastructure development, leading to further deforestation and habitat fragmentation. Here, we identify priority areas for continued functional forest connectivity across Borneo and Sumatra, using spatial models of clouded leopard (Neofelis diardi, a forest indicator species) movement, and impacts thereto from existing and future infrastructure development. We specifically measure and map the anticipated impacts on forest functional connectivity of three major infrastructure development projects (Pan Borneo Highway, Trans-Sumatran Toll Road, and the new Indonesian capital city of Nusantara). We found that core clouded leopard habitats are already highly fragmented in Sumatra, constituting only ∼13 % of the island, with potential dispersal corridors still linking some habitat fragments. In Borneo, clouded leopard core habitats cover 34 % of the island, with one large central core area and several much smaller satellite cores, which are largely unprotected (15 % protected, compared to 42 % in Sumatra). The largest negative effect on habitat connectivity was predicted for Nusantara (66 % of the total connectivity loss predicted for all three infrastructure projects), reverberating across the entirety of Borneo with the strongest effects in East Kalimantan. The Pan Borneo Highway accounted for 28 % of the total connectivity loss, affecting every province in Borneo and Brunei, with 6 % of this decrease located within protected areas. The Trans-Sumatran Toll Road had the smallest negative effect on connectivity (6 %) but only when excluding the already built segments, which, when included, produce a total negative impact similar to that of the Pan Borneo Highway.

A new mechanism of flowering regulation by the competition of isoforms in Osmanthus fragrans.

The regulation of flowering time is typically governed by transcription factors or epigenetic modifications. Transcript isoforms can play important roles in flowering regulation. Recently, transcript isoforms were discovered in the key genes, OfAP1 and OfTFL1, of the flowering regulatory network in Osmanthus fragrans. OfAP1-b generates a full-length isoform of OfAP1-b1 as well as an isoform of OfAP1-b2 that lacks the C-terminal domain. Although OfAP1-b2 does not possess an activation domain, it has a complete K domain that allows it to form heterodimers. OfAP1-b2 competes with OfAP1-b1 by binding with OfAGL24 to create non-functional and functional heterodimers. As a result, OfAP1-b1 promotes flowering while OfAP1-b2 delays flowering. OfTFL1 produces two isoforms located in different areas: OfTFL1-1 in the cytoplasm and OfTFL1-2 in the nucleus. When combined with OfFD, OfTFL1-1 does not enter the nucleus to repress AP1 expression, leading to early flowering. Conversely, when combined with OfFD, OfTFL1-2 enters the nucleus to repress AP1 expression, resulting in later flowering. Tissue-specific expression and functional conservation testing of OfAP1 and OfTFL1 support the new model's effectiveness in regulating flowering. Overall, this study provides new insights into regulating flowering time by the competition of isoforms.

Expression dosage effects of a small number of genes after the artificial doubling of weeping forsythia.

Whole genome doubling (WGD) plays a critical role in plant evolution, yet the mechanisms underlying the maintenance of overall equilibrium following an artificial doubling event, as well as its impact on phenotype and adaptability, remain unclear. By comparing the gene expression of naturally occurring weeping forsythia diploids and colchicine-induced autotetraploids under normal growth conditions and cold stress, we identified gene expression dosage responses resulting from ploidy change. Only a small proportion of effectively expressed genes showed dosage effect, and most genes did not exhibit significant expression differences. However, the genes that showed expression dosage effect were largely random. The autotetraploids had slower overall growth rates, possibly resulting from negative gene dosage effects on zeatin synthesis and multiple metabolic delays caused by other negative dosage genes. Our comparative analysis of cold response genes in diploids and autotetraploids revealed that genes related to "response to abscisic acid" and "cold acclimation" were key factors contributing to greater cold tolerance in the autotetraploids. In particular, gene expression related to "cold acclimation" might mitigate the effects of cold stress. Taken together, our findings suggested that overall gene expression equilibrium following WGD of weeping forsythia autotetraploids was achieved through the inactivation of the majority of duplicated genes. Our research provides new insights into the mechanisms regulating expression dosage balance following polyploidization events.

Northern spotted owl nesting habitat under high potential wildfire threats along the California Coastal Redwood Forest.

Large and severe wildfires, exacerbated by climate change and human behavior, are occurring more frequently in many forests across the western United States. While wildfire is a natural part of most terrestrial ecosystems, rapidly changing fire regimes have the potential to alter habitat beyond the adaptive capabilities of species. Spatial assessments of wildfire risks to species habitat may allow managers to pinpoint locations for management activities. To illustrate this, we spatially assessed wildfire risk within habitat that supports the nesting activity of the federally threatened northern spotted owl (Strix occidentalis caurina) in the California redwood coast ecoregion. To accomplish this, we built a scale-optimized ensemble nesting habitat suitability model and identified habitat with the highest wildfire hazard potential. Percent canopy cover at 100-m scale, slope at 400-m scale, and January precipitation at 800-m scale were the most influential environmental covariates for predicting northern spotted owl nesting habitat. Nearly 60% of nesting habitat was predicted to be at high or very high (>1986 index value) wildfire risks. We identified three areas in the Maple Creek Area of Humboldt County, Jackson State Demonstration Forest in Mendocino County, and Point Reyes National Seashore in Marin County, California with a high concentration of nesting habitat that are at a very high risk of experiencing high severity wildfires. We recommend these areas be targeted for future research to understand the impact of wildfire on northern spotted owl as well as management attention.

Entropy, Ecology and Evolution: Toward a Unified Philosophy of Biology.

Darwin proposed that the capacity of organisms to produce more offspring that can be supported by the environment would lead to a struggle for existence, and individuals that are most fit for survival and reproduction would be selected through natural selection. Ecology is the science that studies the interaction between organisms and their environment within the context of Darwinian evolution, and an ecosystem is defined as a community of living organisms in conjunction with the nonliving components of their environment, interacting as a system. One topic that has been very much understudied and largely ignored in evolutionary biology is the overarching context of thermodynamics in controlling all biological processes and the evolution of life. Most fundamentally, organisms are self-replicating dissipative structures. Evolution is the process whereby variation in the structure of organisms have differential fitness in terms of their effectiveness at building and maintaining their structure, efficiently consuming free energy, and effectively reproducing and passing on those heritable variations, leading to change in the frequency of genetic variation and associated change in the characteristics in the population. The central process is dissipation of free energy according to the second law of thermodynamics, and evolution therefore is better conceptualized as the emergence of self-replicating dissipative structures that through natural selection become increasingly more efficient at degrading free energy. Ecosystems are linked series of dissipative structures with heat engine dynamics driven by random dissipation of energy and increasing entropy. The structure and composition of ecosystems across scales are emergent dissipative structures driven by the flow of energy and the increase in entropy. Communities and ecosystems are emergent properties of a system that has evolved to most efficiently dissipate energy and increase entropy. By focusing on the fundamental entity (energy), and the fundamental process (dissipation and disordering of energy and increasing of entropy), we are able to have a much clearer and powerful understanding of what life is, from the level of biochemistry, to evolution, to the nature of the organism itself, and to the emergent structures of ecosystems, food webs and communities.

Genome-wide investigation of the WRKY transcription factor gene family in weeping forsythia: expression profile and cold and drought stress responses.

Weeping forsythia is a wide-spread shrub in China with important ornamental, medicinal and ecological values. It is widely distributed in China's warm temperate zone. In plants, WRKY transcription factors play important regulatory roles in seed germination, flower development, fruit ripening and coloring, and biotic and abiotic stress response. To date, WRKY transcription factors have not been systematically studied in weeping forsythia. In this study, we identified 79 WRKY genes in weeping forsythia and classified them according to their naming rules in Arabidopsis thaliana. Phylogenetic tree analysis showed that, except for IIe subfamily, whose clustering was inconsistent with A. thaliana clustering, other subfamily clustering groups were consistent. Cis-element analysis showed that WRKY genes related to pathogen resistance in weeping forsythia might be related to methyl jasmonate and salicylic acid-mediated signaling pathways. Combining cis-element and expression pattern analyses of WRKY genes showed that more than half of WRKY genes were involved in light-dependent development and morphogenesis in different tissues. The gene expression results showed that 13 WRKY genes were involved in drought response, most of which might be related to the abscisic acid signaling pathway, and a few of which might be regulated by MYB transcription factors. The gene expression results under cold stress showed that 17 WRKY genes were involved in low temperature response, and 9 of them had low temperature responsiveness cis-elements. Our study of WRKY family in weeping forsythia provided useful resources for molecular breeding and important clues for their functional verification.

Enhanced regional connectivity between western North American national parks will increase persistence of mammal species diversity.

Many protected areas worldwide increasingly resemble habitat isolates embedded in human-modified landscapes. However, establishing linkages among protected areas could significantly reduce species-loss rates. Here we present a novel method having broad applicability for assessing enhanced regional connectivity on persistence of mammal diversity. We combine theoretically-derived species relaxation rates for mammal communities with empirically-derived pathways. We assess the value of enhanced regional connectivity for two hypothetical networks of national parks in western North America: the Yellowstone-Glacier network and the Mount Rainier-North Cascades network. Linking the Yellowstone and Glacier park assemblages by eliminating barriers to movement in identified mammal dispersal pathways and by incorporating adjacent wilderness areas and known ungulate migratory routes into a protected area network would greatly enlarge available habitat. This would enhance medium to large mammal species persistence time by factor of 4.3, on average, or ~ 682 generations relative to individual parks. Similarly, linking Mount Rainier and North Cascades park assemblages would enhance mammal species persistence time by a factor of 4.3, on average, or ~305 generations relative to individual parks. Enhancing regional connectivity among western North America parks could serve as an important template for landscape-scale conservation in the 21st century.

Connectivity modelling in conservation science: a comparative evaluation.

Landscape connectivity, the extent to which a landscape facilitates the flow of ecological processes such as organism movement, has grown to become a central focus of applied ecology and conservation science. Several computational algorithms have been developed to understand and map connectivity, and many studies have validated their predictions using empirical data. Yet at present, there is no published comparative analysis which uses a comprehensive simulation framework to measure the accuracy and performance of the dominant methods in connectivity modelling. Given the widespread usage of such models in spatial ecology and conservation science, a thorough evaluation of their predictive abilities using simulation techniques is essential for guiding their appropriate and effective application across different contexts. In this paper, we address this by using the individual-based movement model Pathwalker to simulate different connectivity scenarios generated from a wide range of possible movement behaviours and spatial complexities. With this simulated data, we test the predictive abilities of three major connectivity models: factorial least-cost paths, resistant kernels, and Circuitscape. Our study shows the latter two of these three models to consistently perform most accurately in nearly all cases, with their abilities varying substantially in different contexts. For the majority of conservation applications, we infer resistant kernels to be the most appropriate model, except for when the movement is strongly directed towards a known location. We conclude this paper with a review and interdisciplinary discussion of the current limitations and possible future developments of connectivity modelling.

Contrasting effects of human settlement on the interaction among sympatric apex carnivores.

In the face of a growing human footprint, understanding interactions among threatened large carnivores is fundamental to effectively mitigating anthropogenic threats and managing species. Using data from a large-scale camera trap survey, we investigated the effects of environmental and anthropogenic variables on the interspecific interaction of a carnivore guild comprising of tiger, leopard and dhole in Bhutan. We demonstrate the complex effects of human settlement density on large carnivore interactions. Specifically, we demonstrate that leopard-dhole co-occupancy probability was higher in areas with higher human settlement density. The opposite was true for tiger-leopard co-occupancy probability, but it was positively affected by large prey (gaur) abundance. These findings suggest that multi-carnivore communities across land-use gradients are spatially structured and mediated also by human presence and/or the availability of natural prey. Our findings show that space-use patterns are driven by a combination of the behavioural mechanism of each species and its interactions with competing species. The duality of the effect of settlement density on species interactions suggests that the benefits of exploiting anthropogenic environments are a trade-off between ecological opportunity (food subsidies or easy prey) and the risk of escalating conflict with humans.

Synthesizing habitat connectivity analyses of a globally important human-dominated tiger-conservation landscape.

As ecological data and associated analyses become more widely available, synthesizing results for effective communication with stakeholders is essential. In the case of wildlife corridors, managers in human-dominated landscapes need to identify both the locations of corridors and multiple stakeholders for effective oversight. We synthesized 5 independent studies of tiger (Panthera tigris) connectivity in central India, a global priority landscape for tiger conservation, to quantify agreement on landscape permeability for tiger movement and potential movement pathways. We used the latter analysis to identify connectivity areas on which studies agreed and stakeholders associated with these areas to determine relevant participants in corridor management. Three or more of the 5 studies' resistance layers agreed in 63% of the study area. Areas in which all studies agree on resistance were of primarily low (66%, e.g., forest) and high (24%, e.g., urban) resistance. Agreement was lower in intermediate resistance areas (e.g., agriculture). Despite these differences, the studies largely agreed on areas with high levels of potential movement: >40% of high average (top 20%) current-flow pixels were also in the top 20% of current-flow agreement pixels (measured by low variation), indicating consensus connectivity areas (CCAs) as conservation priorities. Roughly 70% of the CCAs fell within village administrative boundaries, and 100% overlapped forest department management boundaries, suggesting that people live and use forests within these priority areas. Over 16% of total CCAs' area was within 1 km of linear infrastructure (437 road, 170 railway, 179 transmission line, and 339 canal crossings; 105 mines within 1 km of CCAs). In 2019, 78% of forest land diversions for infrastructure and mining in Madhya Pradesh (which comprises most of the study region) took place in districts with CCAs. Acute competition for land in this landscape with globally important wildlife corridors calls for an effective comanagement strategy involving local communities, forest departments, Appendix 1 and infrastructure planners. This article is protected by copyright. All rights reserved.

Generalizing Boltzmann Configurational Entropy to Surfaces, Point Patterns and Landscape Mosaics.

Several methods have been recently proposed to calculate configurational entropy, based on Boltzmann entropy. Some of these methods appear to be fully thermodynamically consistent in their application to landscape patch mosaics, but none have been shown to be fully generalizable to all kinds of landscape patterns, such as point patterns, surfaces, and patch mosaics. The goal of this paper is to evaluate if the direct application of the Boltzmann relation is fully generalizable to surfaces, point patterns, and landscape mosaics. I simulated surfaces and point patterns with a fractal neutral model to control their degree of aggregation. I used spatial permutation analysis to produce distributions of microstates and fit functions to predict the distributions of microstates and the shape of the entropy function. The results confirmed that the direct application of the Boltzmann relation is generalizable across surfaces, point patterns, and landscape mosaics, providing a useful general approach to calculating landscape entropy.

Thermodynamic Consistency of the Cushman Method of Computing the Configurational Entropy of a Landscape Lattice.

There has been a recent surge of interest in theory and methods for calculating the entropy of landscape patterns, but relatively little is known about the thermodynamic consistency of these approaches. I posit that for any of these methods to be fully thermodynamically consistent, they must meet three conditions. First, the computed entropies must lie along the theoretical distribution of entropies as a function of total edge length, which Cushman showed was a parabolic function following from the fact that there is a normal distribution of permuted edge lengths, the entropy is the logarithm of the number of microstates in a macrostate, and the logarithm of a normal distribution is a parabolic function. Second, the entropy must increase over time through the period of the random mixing simulation, following the expectation that entropy increases in a closed system. Third, at full mixing, the entropy will fluctuate randomly around the maximum theoretical value, associated with a perfectly random arrangement of the lattice. I evaluated these criteria in a test condition involving a binary, two-class landscape using the Cushman method of directly applying the Boltzmann relation (s = klogW) to permuted landscape configurations and measuring the distribution of total edge length. The results show that the Cushman method directly applying the classical Boltzmann relation is fully consistent with these criteria and therefore fully thermodynamically consistent. I suggest that this method, which is a direct application of the classical and iconic formulation of Boltzmann, has advantages given its direct interpretability, theoretical elegance, and thermodynamic consistency.

Entropy in Landscape Ecology: A Quantitative Textual Multivariate Review.

This paper presents a multivariate textual analysis of more than 1300 papers on entropy in ecology. There are six main insights that emerged. First, there is a large body of literature that has addressed some aspect of entropy in ecology, most of which has been published in the last 5-10 years. Second, the vast majority of these papers focus on species distribution, species richness, relative abundance or trophic structure and not landscape-scale patterns or processes, pe se. Third, there have been few papers addressing landscape-level questions related to entropy. Fourth, the quantitative analysis with hierarchical clustering identified a strongly nested structure among papers that addressed entropy in ecology. Fifth, there is clear differentiation of papers focused on landscape-level applications of entropy from other papers, with landscape focused papers clustered together at each level of the hierarchy in a relatively small and closely associated group. Sixth, this group of landscape-focused papers was substructured between papers that explicitly adopted entropy measures to quantify the spatial pattern of landscape mosaics, often using variations on Boltzmann entropy, versus those that utilize Shannon entropy measures from information theory, which are not generally explicit in their assessment of spatial configuration. This review provides a comprehensive, quantitative assessment of the scope, trends and relationships among a large body of literature related to entropy in ecology and for the first time puts landscape ecological research on entropy into that context.

Evidence of spatial genetic structure in a snow leopard population from Gansu, China.

Understanding the spatial structure of genetic diversity provides insights into a populations' genetic status and enables assessment of its capacity to counteract the effects of genetic drift. Such knowledge is particularly scarce for the snow leopard, a conservation flagship species of Central Asia mountains. Focusing on a snow leopard population in the Qilian mountains of Gansu Province, China, we characterised the spatial genetic patterns by incorporating spatially explicit indices of diversity and multivariate analyses, based on different inertia levels of Principal Component Analysis (PCA). We compared two datasets differing in the number of loci and individuals. We found that genetic patterns were significantly spatially structured and were characterised by a broad geographical division coupled with a fine-scale cline of differentiation. Genetic admixture was detected in two adjoining core areas characterised by higher effective population size and allelic diversity, compared to peripheral localities. The power to detect significant spatial relationships depended primarily on the number of loci, and secondarily on the number of PCA axes. Spatial patterns and indices of diversity highlighted the cryptic structure of snow leopard genetic diversity, likely driven by its ability to disperse over large distances. In combination, the species' low allelic richness and large dispersal ability result in weak genetic differentiation related to major geographical features and isolation by distance. This study illustrates how cryptic genetic patterns can be investigated and analysed at a fine spatial scale, providing insights into the spatially variable isolation effects of both geographic distance and landscape resistance.

Genetic connectivity of two marine gastropods in the Mediterranean Sea: seascape genetics reveals species-specific oceanographic drivers of gene flow.

Oceanographic features such as currents, waves, temperature and salinity, together with life history traits, control patterns and rates of gene flow and contribute to shaping the population genetic structure of marine organisms. Seascape genetics is an emerging discipline that adopts a spatially explicit approach to examine biotic and abiotic factors that drive gene flow in marine environments. In this study, we examined factors that contribute to genetic differentiation in two coastal Mediterranean gastropods whose geographical ranges overlap but which inhabit different environments. The two species differ in several life history traits and in their dispersal capabilities. Genetic differentiation was relatively low for the trochid species Gibbula divaricata (FST  =0.059), and high for the vermetid species Dendropoma lebeche (FST  =0.410). Salinity emerged as the most important variable explaining the genetic structure of both species; sea surface temperature was also important for G. divaricata. For the more sessile D. lebeche, the coastline was predicted to provide important pathways for stepping-stone connectivity and gene flow. Our results provide a greater understanding of the factors influencing marine population connectivity, which may be useful to guide marine conservation and management in the Mediterranean.

Integrating spatial analysis and questionnaire survey to better understand human-onager conflict in Southern Iran.

Southern Iran is a conservation priority area for the endangered Persian onager (Equus hemionus onager), which is threatened by habitat fragmentation and conflict with local communities. To better understand factors that influence onager conservation, we administered a questionnaire in local communities to survey their ecological knowledge, personal experience related to onager, and attitudes toward traditional solutions for reducing crop damage by onager. In addition, we used resistant kernel and factorial least-cost path analyses to identify core areas and corridors for onager movement, and spatial randomization of vehicle collisions and crossing locations to test the predictive ability of resistant kernel and factorial least-cost path predictions of movement. We found that local communities that were knowledgeable about onagers experienced less crop damage from onager compared with those who used traditional methods. Habitat connectivity models revealed that core areas of movement are highly concentrated at the center of protected areas. Some sections of core areas have been cut off by roads where most vehicle collisions with onagers occurred. We propose that effective onager conservation will require integrated landscape-level management to reduce mortality risk, protection of core areas and corridors, development of mitigation strategies to reduce vehicle collisions, and conflict mediation between local communities and onagers.

Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia.

BACKGROUND: Understanding the genetic mechanisms of local adaptation is an important emerging topic in molecular ecology and evolutionary biology. RESULTS: Here, we identify the physiological changes and differential expression of genes among different weeping forsythia populations under drought stress in common garden experiments. Physiological results showed that HBWZ might have higher drought tolerance among four populations. RNA-seq results showed that significant differential expression in the genes responding to the synthesis of flavonoids, aromatic substances, aromatic amino acids, oxidation-reduction process, and transmembrane transport occured among four populations. By further reanalysis of results of previous studies, sequence differentiation was found in the genes related to the synthesis of aromatic substances among different weeping forsythia populations. CONCLUSIONS: Overall, our study supports the hypothesis that the dual differentiation in gene efficiency and expression increases among populations in response to heterogeneous environments and is an important evolutionary process of local adaptation. Here, we proposed a new working model of local adaptation of weeping forsythia populations under different intensities of drought stress, which provides new insights for understanding the genetic mechanisms of local adaptation for non-model species.

Transcriptomic responses and physiological changes to cold stress among natural populations provide insights into local adaptation of weeping forsythia.

Genetic mechanisms of species local adaptation are an emerging topic of great interest in evolutionary biology and molecular ecology. In this study, we compared the changes of physiological and phenotypic indexes and gene expression of four weeping forsythia populations under cold stress through a common garden experiment. Physiological and phenotypic results showed that there were differences in cold tolerance among populations. cold tolerance of high the latitude population (HBWZ) was the strongest, followed by the middle latitude population (SXWL), while the low latitude populations (SXHM) and (SXLJ) expressed the weakest cold tolerance. We identified significant differences in gene expression of cold tolerance related pathways and ontologies, including genes of oxylipin and isoquinoline alkaloid biosynthetic process, galactose, tyrosine and unsaturated fatty acids metabolism, among these populations under the same experimental temperature treatments. Even under the same degree of stress, there were notable differences in gene expression among natural populations. In this study, we present a working model of weeping forsythia populations which evolved in the context of different intensities of cold stress. Our study provides new insights for comprehending the genetic mechanisms of local adaptation for non-model species.

Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants.

Extant conifer species may be susceptible to rapid environmental change owing to their long generation times, but could also be resilient due to high levels of standing genetic diversity. Hybridisation between closely related species can increase genetic diversity and generate novel allelic combinations capable of fuelling adaptive evolution. Our study unravelled the genetic architecture of adaptive evolution in a conifer hybrid zone formed between Pinus strobiformis and P. flexilis. Using a multifaceted approach emphasising the spatial and environmental patterns of linkage disequilibrium and ancestry enrichment, we identified recently introgressed and background genetic variants to be driving adaptive evolution along different environmental gradients. Specifically, recently introgressed variants from P. flexilis were favoured along freeze-related environmental gradients, while background variants were favoured along water availability-related gradients. We posit that such mosaics of allelic variants within conifer hybrid zones will confer upon them greater resilience to ongoing and future environmental change and can be a key resource for conservation efforts.