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Figure 4 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069

Figure 4 Unrooted minimum spanning tree showing the genetic relationships among the Cytb haplotypes of P. minor. Circle sizes are proportional to haplotype frequency. Perpendicular tick marks on the lines joining the haplotypes represent the number of nucleotide substitutions.

Figure 1 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069

Figure 1 Sampling locations of P. minor. Populations are marked by abbreviations that correspond to Table 1.

Figure 2 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069

Figure 2 Composition and distribution of 22 Cytb haplotypes in the Chinese and Malaysian populations.

Figure 3 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069

Figure 3 NJ tree and distribution of Cytb haplotypes among populations for P. minor. Bootstrap supports of > 50 in 1000 replicates are shown.

opencc-zeroAug 2020View details →

Environmental filtering and spatial processes shape the beta diversity of liana communities in a valley savanna in Southwest China

Questions: Lianas contribute substantially to diversity and function of ecosystems. What is the relative importance of environmental filtering and spatial processes on structuring liana beta diversity at taxonomic, functional and phylogenetic levels? Is there any synergy between these drivers (environmental factors and spatial distance) on shaping three dimensions of beta diversity in a savanna liana community? Location: A dry-hot valley savanna in Yunnan Province, southwest China. Methods: We established 30 20×20 m plots in the savanna to collect data on the distribution of 22 liana species, 19 functional traits, and plot-level soil nutrients, elevation, and slope. The relative contributions of these environmental factors and spatial distance to liana taxonomic, functional and phylogenetic dissimilarity were analyzed using multiple regression on distance matrices. We also tested which environmental factors influence the beta diversity of liana community using permutational multivariate analysis of variance. Results: Both environmental and spatial distances were significantly correlated with taxonomic, functional and phylogenetic dissimilarity. Spatial distance explained more variation in taxonomic beta diversity than environmental factors. But for both nearest neighbor functional and phylogenetic distance Dnn', environment explained a relatively higher variation than space did. Moreover, the proportion explained by environmental variables was ranked in decreasing order as follows: functional Dnn', phylogenetic Dnn', and taxonomic beta diversity. We found soil pH had the highest contribution to taxonomic and functional beta diversity, while soil total nitrogen contributed most to phylogenetic beta diversity. Conclusions: This study revealed that liana taxonomic, functional and phylogenetic beta diversity in the study hot-dry savanna ecosystem are affected and maintained by both environmental filtering and spatial processes. Moreover, the functional and phylogenetic diversities were more strongly subject to environmental filtering. Our study provides the information on mechanisms underlying liana diversity maintenance in savanna, which are necessary to inform conservation management in this vulnerable ecosystem.

openbsd-3-clauseFeb 2019View details →

Enhanced proximity effect in zigzag-shaped Majorana Josephson junctions

Dataset and source code for the paper "Enhanced proximity effect in zigzag-shaped Majorana Josephson junctions".

opencc-zeroDec 2019View details →

Interspecific competition slows range expansion and shapes range boundaries

Species expanding into new habitats as a result of climate change or human introductions will frequently encounter resident competitors. Theoretical models suggest that such interspecific competition can alter the speed of expansion and the shape of expanding range boundaries. However, competitive interactions are rarely considered when forecasting the success or speed of expansion, in part because there has been no direct experimental evidence that competition affects either expansion speed or boundary shape. Here we demonstrate that interspecific competition alters both expansion speed and range boundary shape. Using a two-species experimental system of the flour beetles Tribolium castaneum and Tribolium confusum, we show that interspecific competition dramatically slows expansion across a landscape over multiple generations. Using a parameterized stochastic model of expansion, we find that this slowdown can persist over the long-term. We also find that the shape of the moving range boundary changes continuously over many generations of expansion, first steepening and then becoming shallower, due to the competitive effect of the resident and density-dependent dispersal of the invader. This dynamic boundary shape suggests that current forecasting approaches assuming a constant shape could be misleading. More broadly, our results demonstrate that interactions between competing species can play a large role during range expansions and thus should be included in models and studies that monitor, forecast, or manage expansions in natural systems.

opencc-zeroOct 2020View details →

Social status, forest disturbance, and Barred Owls shape long-term trends in breeding dispersal distance of Northern Spotted Owls

Dispersal among breeding sites in territorial animals (i.e. breeding dispersal) is driven by numerous selection pressures, including competition and spatiotemporal variation in habitat quality. The scale and trend of dispersal movements over time may signal changing conditions within the population or on the landscape. We examined 2,158 breeding dispersal events from 694 male and 608 female individually-marked Northern Spotted Owls (Strix occidentalis caurina) monitored over 28 years on seven study areas to assess the relative importance of individual (sex, experience), reproductive (annual productivity, mate availability), and environmental (forest alteration, presence of competitor) sources of variation in breeding dispersal distance. Median breeding dispersal distance was 3.17 km, with 99% of all breeding dispersal events less than 37 km. Mean annual dispersal distances increased by 2.43 km in Oregon and 9.40 km in Washington between 1990 and 2017, which coincided with increases in annual detections of non-native Barred Owl (S. varia). Frequency of breeding dispersal events, both among and within individuals, also increased over time. Female owls moved farther than males (median of 3.26 km and 3.10 km respectively), and birds with less experience (territory tenure) moved farther than those with more experience. Owls that were single in the year prior to dispersal moved 13–31% farther than those paired prior to dispersal. The greatest environmental change occurring over the course of our study was the expansion of Barred Owl populations. Breeding dispersal distance was positively related to Barred Owls in the study area and disturbance within the originating territory. While it appears that social factors continue to be important drivers of breeding dispersal distance in Spotted Owls, increased competition from Barred Owls and habitat alteration have a contributing effect. Increased breeding dispersal distances should be of concern for conservation efforts and considered in population monitoring because changing dispersal behavior may lead to higher rates of mortality and/or emigration from historic study areas.

opencc-zeroNov 2020View details →

Data from: Altitude shapes the environmental drivers of large-scale variation in abundance of a widespread mammal species

Habitat quality and heterogeneity directly influence the distribution and abundance of organisms at different spatial scales. Determining the main environmental factors driving the variation in species abundance is crucial to understand the underlying ecological processes and this is especially important for widely distributed species living in contrasting environments. However, the responses to environmental variation are usually described at relatively small spatial scales. Here, we studied the variation in abundance of a widely distributed mustelid, the European badger (Meles meles), across France. We used (1) direct detections of 9,439 dead and living badgers, from 2006 to 2009, to estimate badger relative abundance in 703 small agricultural regions of metropolitan France and (2) a Bayesian modelling approach to identify the main environmental determinants influencing badger abundance. Despite a continuous distribution of badger in France, we found large variation in badger abundance between regions, explained by environmental factors. Among a set of 13 environmental variables, we demonstrated that badger abundance in lowlands (< 400 m a.s.l.) was mostly driven by biotic factors such as potential food resources (earthworm abundance and fruits crops) and forest fragmentation. Conversely, in mountainous areas, abiotic factors (i.e. soil texture and climate) drove the variation in badger relative abundance. These results underline the importance of mapping the abundance of wildlife species based on environmental suitability, and highlight the complexity of drivers influencing species abundance at such large spatial scales. Altitude shaped the environmental drivers (biotic vs. abiotic) that most influenced relative abundance of a widespread species. In the case of badger, such abundance maps are crucial to identify critical areas for species management as this mustelid is a main wild vector of bovine tuberculosis in several countries.

opencc-by-4.0Nov 2020View details →

Species-specific but not phylosymbiotic gut microbiomes of New Guinean Passerines are shaped by diet and flight-associated gut modifications

The folder includes the r script and main data files used to conduct main analyses

opencc-zeroNov 2020View details →

How does prescribed fire shape bird and plant communities in a temperate dry forest ecosystem?

To mitigate the impact of severe wildfire on human society and the environment, prescribed fire is widely used in forest ecosystems to reduce fuel loads and limit fire spread. To avoid detrimental effects on conservation values, it is imperative to understand how prescribed fire affects taxa having a range of different adaptations to disturbance. Such studies will have greatest benefit if they extend beyond short-term impacts of burning. We used a field study to examine the effects of prescribed fire on birds and plants across a 36-year post-fire chronosequence in a temperate dry forest ecosystem in south-eastern Australia, and by making comparison with long-unburnt reference sites (79 years since wildfire). We modelled changes in the relative abundance of 22 bird species and the cover of 39 plant species, and examined how individual species, functional groups, species richness and community composition differed between sites with different fire history. For most individual bird and plant species modelled, relative abundance or cover at sites subject to prescribed fire did not change significantly with time since fire or differ from that of long-unburnt vegetation. When bird species were pooled into functional groups, time since prescribed fire had strong effects on birds that forage in the lower-midstorey, facultative-resprouting shrubs and obligate-seeding shrubs. Species richness for both taxa did not differ between sites subject to prescribed fire and those in long-unburnt vegetation. Bird communities varied significantly between the youngest (0-3 years) and oldest (79 years) post-fire age-classes, driven by species associated with understorey vegetation. Plant community composition showed little evidence of a post-fire successional trajectory. The prevalence of bird species with broad habitat and dietary niches and plant regeneration through resprouting, make bird and plant communities in these forests relatively resilient to small and patchy prescribed fires they have experienced to date. Application of prescribed fire will be most compatible with maintaining biodiversity by taking a landscape approach that: 1) plans for a geographic spread of stands with a range of between-prescribed-fire intervals to ensure provision of suitable habitat for all taxa, and 2) avoids burning in moist gullies to maintain their value as fire refuges.

opencc-zeroDec 2020View details →

Evolutionary and morphological patterns underlying carnivoran body shape diversity

The diversity of body shapes is one of the most prominent features of phenotypic variation in vertebrates. Biologists, however, still lack a full understanding of the underlying morphological components that contribute to its diversity, particularly in endothermic vertebrates such as mammals. In this study, I tested hypotheses pertaining to the evolution of the cranial and axial components that contribute to the diversity of carnivoran body shapes. I found three trends in the evolution of carnivoran body shapes: 1) carnivorans exhibit diverse body shapes with intrafamilial variation predicted best by family clade age, 2) body shape is driven by strong allometric effects of body size where species become more elongate with decreasing size, and 3) the thoracic and lumbar regions and rib length contribute the most to body shape variation, albeit pathways differ between different families. These results reveal the morphological patterns that led to increased diversity in carnivoran body shapes and provide elucidate the similarities and dissimilarities that govern body shape diversity across vertebrates.

opencc-zeroDec 2019View details →

Habitat fragmentation shapes natal dispersal and sociality in an Afrotropical cooperative breeder

It remains poorly understood how effects of anthropogenic activity, such as large-scale habitat fragmentation, impact sociality in animals. In cooperatively breeding species, groups are mostly formed through delayed offspring dispersal, and habitat fragmentation can affect this process in two opposite directions. Increased habitat isolation may increase dispersal costs, promoting delayed dispersal. Alternatively, reduced patch size and quality may decrease benefits of philopatry, promoting dispersal. Here, we test both predictions in a cooperatively breeding bird (placid greenbul, Phyllastrephus placidus) from an Afrotropical cloud forest archipelago. Males born in fragmented forest dispersed about one year earlier than those born in continuous forest. Contrary to females, males also started to reproduce earlier and mostly settled within their natal patch. Females only rarely delayed their dispersal for more than one year, both in fragmented and continuous forests. Our results suggest that early male dispersal and reproduction is jointly driven by a decrease in the value of the natal territory and an increase in local breeding opportunities in fragmented forest. While plasticity in dispersal strategies of cooperative breeders in response to anthropogenic change is believed to optimize reproduction-survival trade-offs, to what extent it shapes the ability of species to respond to rapid environmental change remains to be studied.

opencc-zeroDec 2020View details →

Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot

As human-induced change eliminates natural habitats, it impacts genetic diversity and population connectivity for local biodiversity. The South African Cape Floristic Region (CFR) is the most diverse extratropical area for plant biodiversity, and much of its habitat is protected as a UNESCO World Heritage site. There has long been great interest in explaining the underlying factors driving this unique diversity, especially as much of the CFR is endangered by urbanization and other anthropogenic activity. Here, we use a population and landscape genetic analysis of SNP data from the CFR endemic plant Leucadendron salignum or "common sunshine conebush" as a model to address the evolutionary and environmental factors shaping the vast CFR diversity. We found that high population structure, along with relatively deeper and older genealogies, are characteristic of the southwestern CFR, whereas, low population structure and more recent lineage coalescence depicts the eastern CFR. Population network analyses show genetic connectivity is facilitated in areas of lower elevation and higher seasonal precipitation. These population genetic signatures corroborate CFR species-level patterns consistent with high Pleistocene biome stability and landscape heterogeneity in the southwest, but with coincident instability in the east. Finally, we also find evidence of human land-usage as a significant gene flow barrier, especially in severely-threatened lowlands where genetic connectivity has been historically the highest. These results help identify areas where conservation plans can prioritize protecting high genetic diversity threatened by contemporary human activities within this unique cultural UNESCO site.

opencc-zeroJan 2021View details →

Reconstructing dietary ecology of extinct strepsirrhines (Primates, Mammalia) with new approaches for characterizing and analyzing tooth shape

The morphological and ecological diversity of lemurs and lorisiformes once rivalled the rest of the primate order. Here, we assemble a dataset of 3D models representing the second mandibular molars of a wide range of extant and fossil strepsirrhines encompassing this diversity. We use these models to distill quantitative descriptors of tooth form and then analyze these data using new analytical methods. We employ a recently developed dental topography metric (ariaDNE), which is less sensitive to details of random error in 3D model quality than previously used metrics (e.g., DNE); Bayesian multinomial modelling with metrics designed to measure overfitting risk; and a tooth segmentation algorithm that allows the shapes of disaggregated tooth surface features to be quantified using dental topography metrics. This approach is successful at reclassifying extant strepsirrhine primates to known dietary ecology and indicates that the averaging of morphological information across the tooth surface does not interfere with the ability of dental topography metrics to predict dietary adaptation. When applied to extinct species, many subfossil lemurs and the most basal fossil strepsirrhines are predicted to have been primarily frugivorous or gummivorous. This supports an ecological contraction among the extant lemurs and the importance of frugivory in the origins of crown Strepsirrhini, potentially to avoid competition with more insectivorous and folivorous members of Paleogene Afro-Arabian primate faunas.

opencc-zeroJan 2021View details →

Similarity between agricultural and natural land covers shapes how biodiversity responds to agricultural expansion at landscape scales

The impact of agriculture on biodiversity depends on the extent and types of agriculture and the degree to which agricultural land contrasts with the natural ecosystem. Most research on the latter comes from studies on the influence of different agricultural types within a single ecosystem with far less study on how the natural ecosystem context shapes the response of biodiversity to agricultural production. We used citizen science data from agricultural areas in Canada's Eastern Hardwood-Boreal (forest ecosystem, n=108 landscapes) and Prairie Pothole (prairie ecosystem, n=99) regions to examine how ecosystem context shapes the response of avian species diversity, functional diversity and abundance to the amount of arable crop and pastoral agriculture at landscape scales. Avian surveys were conducted along 8km transects of Breeding Bird Survey routes with land cover assembled within a 20km2 landscape around each transect. The amount of agriculture at which species diversity peaked differed between the forest (15%) and prairie (51%) ecosystems, indicating that fewer species tolerated the expansion of agriculture in the former. In both ecosystems, functional diversity initially increased with agriculture and peaked at higher amounts (forest: 42%, prairie: 77 %) than species diversity suggesting that functional redundancy was lost first as agriculture increased. Species turnover with increasing agriculture was primarily among functional groups in forest where a shift from a low to a high agriculture landscape led to a decline in the percent of the community represented by Neotropical migrants, insectivores, upper foliage gleaners and bark foragers, and an increase in the percent of the community represented by short-distance migrants, granivores, omnivores and ground gleaners. There were few distinct shifts in the percent of the community represented by different functional groups in the prairie ecosystem. Total abundance was the least sensitive measure examined in both ecosystems and indicated that species losses with agriculture are likely followed by numerical compensation from agriculture tolerant species. Our results highlight the importance of ecosystem context for understanding how biodiversity is affected by agricultural production with declines in diversity occurring at lower agricultural extents in ecosystems with lower similarity between natural and agricultural land covers. These findings allow for more specific conservation recommendations including managing for species intolerant to agriculture in prairie ecosystems and limiting the expansion of high contrast agriculture and the loss of semi-natural habitat, such as hedge rows, in historically forested ecosystems.

opencc-zeroJan 2021View details →

How adaptive capacity shapes the Adapt, React, Cope Response to climate impacts: insights from small-scale fisheries

As the impacts of climate change on human society accelerate, coastal communities are vulnerable to changing environmental conditions. The capacity of communities and households to respond to these changes (i.e., their adaptive capacity) will determine the impacts of climate and co-occurring stressors. To date, empirical evidence linking theoretical measures of adaptive capacity to community and household responses remains limited. Here we conduct a global meta-analysis examining how metrics of adaptive capacity translate to human responses to change (Adapt, React, Cope Response) in 22 small-scale fishing case studies from 20 countries (n=191 responses). Using both thematic and Qualitative Comparative Analysis, we evaluate how responses to climate, environmental, and social change were influenced by domains of adaptive capacity. Our findings show that adaptive responses at the community level only occurred in situations where the community had Access to Assets, in combination with other domains including Diversity and Flexibility, Learning and Knowledge, and Natural Capital. In contrast, Access to Assets was nonessential for adaptive responses at the household level. Adaptive households demonstrated Diversity and Flexibility when supported by strong Governance or Institutions and were able often able to substitute Learning and Knowledge and Natural Capital with one another. Standardized metrics of adaptive capacity are essential to designing effective policies promoting resilience in natural resource-dependent communities and understanding how social and ecological aspects of communities interact to influence responses. Our framework describes how small-scale fishing communities and households respond to environmental changes and can inform policies that support vulnerable populations.

opencc-zeroJul 2019View details →

Data from: Head-turning morphologies: evolution of shape diversity in the mammalian atlas-axis complex

Mammals flex, extend, and rotate their spines as they perform behaviors critical for survival, such as foraging, consuming prey, locomoting, and interacting with conspecifics or predators. The atlas-axis complex is a mammalian innovation that allows precise head movements during these behaviors. While morphological variation in other vertebral regions has been linked to ecological differences in mammals, less is known about morphological specialization in the cervical vertebrae, which are developmentally constrained in number but highly variable in size and shape. Here, we present the first phylogenetic comparative study of the atlas-axis complex across mammals. We used spherical harmonics to quantify 3D shape variation of the atlas and axis across a diverse sample of species, and performed phylogenetic analyses to investigate if vertebral shape is associated with body size, locomotion, and diet. We found that differences in atlas and axis shape are partly explained by phylogeny, and that mammalian subclades differ in morphological disparity. Atlas and axis shape diversity is associated with differences in body size and locomotion; large terrestrial mammals have craniocaudally elongated vertebrae, while smaller mammals and aquatic mammals have more compressed vertebrae. These results provide a foundation for investigating functional hypotheses underlying the evolution of neck morphologies across mammals.

opencc-zeroDec 2016View details →

Data from: Scale dependencies and generalism in host use shape virus prevalence

Processes that generate the distribution of pathogens and their interactions with hosts are not insensitive to changes in spatial scale. Spatial scales and species traits are often selected intentionally, based on practical considerations, ignoring biases that the scale and type of observation may introduce. Specifically, these biases might change the interpretation of disease-diversity relationships that are reported as either 'dilution' or 'amplification' effects. Here, we combine field data of a host-pathogen community with empirical models to test the effects that i) spatial scale and ii) host range have on the relationship between plant-virus infection prevalence and diversity. We show that prevalence-diversity relationships are scale dependent, and can produce opposite effects associated with different habitats at sub-ecosystem scales. The total number of host species of each virus reflected generalism at the ecosystem scale. However, plasticity in host-range resembled habitat-specific specialisation and also changed model predictions. We show that habitat heterogeneity, ignored at larger (ecosystem) spatial scales, influences pathogen distributions. Hence, understanding disease distributions and the evolution of pathogens requires reconciling specific hypotheses of the study with an appropriate spatial scale, or scales, and consideration of traits, such as host range, that might strongly contribute to biotic interactions.