Clustering of fMRI data: the elusive optimal number of clusters
Model-free methods are widely used for the processing of brain fMRI data collected under natural stimulations, sleep, or rest. Among them is the popular fuzzy c-mean algorithm, commonly combined with cluster validity (CV) indices to identify the ‘true’ number of clusters (components), in an unsupervised way. CV indices may however reveal different optimal c-partitions for the same fMRI data, and their effectiveness can be hindered by the high data dimensionality, the limited signal-to-noise ratio, the small proportion of relevant voxels, and the presence of artefacts or outliers. Here, the author investigated the behaviour of seven robust CV indices. A new CV index that incorporates both compactness and separation measures is also introduced. Using both artificial and real fMRI data, the findings highlight the importance of looking at the behavior of different compactness and separation measures, defined here as building blocks of CV indices, to depict a full description of the data structure, in particular when no agreement is found between CV indices. Overall, for fMRI, it makes sense to relax the assumption that only one unique c-partition exists, and appreciate that different c-partitions (with different optimal numbers of clusters) can be useful explanations of the data, given the hierarchical organization of many brain networks.
Seghier (2018) Clustering of fMRI data: the elusive optimal number of clusters. PeerJ 6:e5416 https://doi.org/10.7717/peerj.5416
Seeing spots: quantifying mother-offspring similarity and assessing fitness consequences of coat pattern traits in a wild population of giraffes (Giraffa camelopardalis)
Polymorphic phenotypes of mammalian coat coloration have been important to the study of genetics and evolution, but less is known about the inheritance and fitness consequences of individual variation in complex coat pattern traits such as spots and stripes. Giraffe coat markings are highly complex and variable and it has been hypothesized that variation in coat patterns most likely affects fitness by camouflaging neonates against visually hunting predators. We quantified complex coat pattern traits of wild Masai giraffes using image analysis software, determined the similarity of spot pattern traits between mother and offspring, and assessed whether variation in spot pattern traits was related to fitness as measured by juvenile survival. The methods we described could comprise a framework for objective quantification of complex mammal coat pattern traits based on photographic coat pattern data. We demonstrated that some characteristics of giraffe coat spot shape were likely to be heritable, as measured by mother-offspring regression. We found significant variation in juvenile survival among phenotypic groups of neonates defined by multivariate clustering based on spot trait measurement variables. We also found significant variation in neonatal survival associated with spot size and shape covariates. Larger spots (smaller number of spots) and irregularly shaped or rounder spots (smaller aspect ratio) were correlated with increased survival. These findings will inform investigations into developmental and genetic architecture of complex mammal coat patterns and their adaptive value.
Lee et al. (2018) Seeing spots: quantifying mother-offspring similarity and assessing fitness consequences of coat pattern traits in a wild population of giraffes (Giraffa camelopardalis). PeerJ 6:e5690 https://doi.org/10.7717/peerj.5690
Effects of knee extension with different speeds of movement on muscle and cerebral oxygenation
Background One of the mechanisms responsible for enhancing muscular hypertrophy is the high metabolic stress associated with a reduced muscular oxygenation occurring during exercise, which can be achieved by reducing the speed of movement. Studies have tested that lowered muscle oxygenation artificially induced by an inflatable cuff, could provoke changes in prefrontal cortex oxygenation, hence, to central fatigue. It was hypothesized that (1) exercising with a slow speed of movement would result in greater increase in cerebral and greater decrease in muscle oxygenation compared with exercises of faster speed and (2) the amount of oxygenation increase in the ipsilateral prefrontal cortex would be lower than the contralateral one. Methods An ISS Imagent frequency domain near infrared spectroscopy (NIRS) system was used to quantify oxygenation changes in the vastus lateralis muscle and prefrontal cortex (contra- and ipsilateral) during unilateral resistance exercises with different speeds of movement to voluntary fatigue. After one maximal repetition (1RM) test, eight subjects performed three sets of unilateral knee extensions (∼50% of 1RM), separated by 2 min rest periods, following the pace of 1 s, 3 s and 5 s for both concentric and eccentric phases, in a random order, during separate sessions. The amount of change for NIRS parameters for muscle (ΔHb: deoxyhemoglobin, ΔHbO: oxyhemoglobin, ΔHbT: total hemoglobin, ΔStO2: oxygen saturation) were quantified and compared between conditions and sets by two-way ANOVA RM. Differences in NIRS parameters between contra- and ipsilateral (lobe) prefrontal cortex and conditions were tested. Results Exercising with slow speed of movement was associated to larger muscle deoxygenation than normal speed of movement, as revealed by significant interaction (set × condition) for ΔHb (p = 0.01), and by significant main effects of condition for ΔHbO (p = 0.007) and ΔStO2 (p = 0.016). With regards to the prefrontal cortex, contralateral lobe showed larger oxygenation increase than the ipsilateral one for ΔHb, ΔHbO, ΔHbT, ΔStO2 in each set (main effect of lobe: p < 0.05). Main effects of condition were significant only in set1 for all the parameters, and significant interaction lobe × condition was found only for ΔHb in set1 (p < 0.05). Discussion These findings provided evidence that speed of movement influences the amount of muscle oxygenation. Since the lack of oxygen in muscle is associated to increased metabolic stress, manipulating the speed of movement may be useful in planning resistance-training programs. Moreover, consistent oxygenation increases in both right and left prefrontal lobes were found, suggesting a complementary interaction between the ipsi- and contralateral prefrontal cortex, which also seems related to fatigue.
Formenti et al. (2018) Effects of knee extension with different speeds of movement on muscle and cerebral oxygenation. PeerJ 6:e5704 https://doi.org/10.7717/peerj.5704
The potential contribution of miRNA-200-3p to the fatty acid metabolism by regulating AjEHHADH during aestivation in sea cucumber
The sea cucumber (Apostichopus japonicus) has become a good model organism for studying environmentally-induced aestivation by a marine invertebrate more recently. In the present study, we hypothesized that miRNA-200-3p may contribute to establish rapid biological control to regulate fatty acid metabolism during a estivation. The peroxisomal bi-functional enzyme (EHHADH) is a crucial participant of the classical peroxisomal fatty acid β-oxidation pathway, the relative mRNA transcripts and protein expressions of EHHADH were analyzed in intestine from sea cucumbers experienced long-term aestivation. Both mRNA transcripts and protein expressions of EHHADH in intestine decreased significantly during deep-aestivation as compared with non-aestivation controls. Analysis of the 3′ UTR of AjEHHADH showed the presence of a conserved binding site for miR-200-3p. Level of miR-200-3p showed an inverse correlation with EHHADH mRNA transcripts and protein levels in intestine, implicating miR-200-3p may directly targeted AjEHHADH by inducing the degradation of AjEHHADH mRNA in the aestivating sea cucumber, further dual-luciferase reporter assay validated the predicted role of miRNA-200-3p in regulating AjEHHADH. In order to further understand their regulatory mechanism, we conducted the functional experiment in vivo. The overexpression of miR-200-3p in sea cucumber significantly decreased mRNA and protein expression levels of AjEHHADH. Taken together, these findings suggested the potential contribution of miRNA-200-3p to the fatty acid metabolism by regulating AjEHHADH during aestivation in sea cucumber.
Chen et al. (2018) The potential contribution of miRNA-200-3p to the fatty acid metabolism by regulating AjEHHADH during aestivation in sea cucumber. PeerJ 6:e5703 https://doi.org/10.7717/peerj.5703
What’s for dinner? Diet and potential trophic impact of an invasive anuran Hoplobatrachus tigerinus on the Andaman archipelago
Amphibian invasions have considerable detrimental impacts on recipient ecosystems. However, reliable risk analysis of invasive amphibians still requires research on more non-native amphibian species. An invasive population of the Indian bullfrog, Hoplobatrachus tigerinus, is currently spreading on the Andaman archipelago and may have significant trophic impacts on native anurans through competition and predation. We carried out diet analyses of the invasive H. tigerinus and native anurans, across four habitat types and two seasons; we hypothesized that (i) small vertebrates constitute a majority of the H. tigerinus diet, particularly by volume and (ii) the diet of H. tigerinus significantly overlaps with the diet of native anurans, thereby, leading to potential competition. We assessed the diet of the invasive H. tigerinus (n = 358), and individuals of the genera Limnonectes (n = 375) and Fejervarya (n = 65) and found a significant dietary overlap of H. tigerinus with only Limnonectes. Small vertebrates, including several endemic species, constituted the majority of H. tigerinus, diet by volume, suggesting potential impact by predation. Prey consumption and electivity of the three anurans indicated a positive relationship between predator-prey body sizes. Individuals of H. tigerinus and Fejervarya chose evasive prey, suggesting that these two taxa are mostly ambush predators; individuals of Limnonectes chose a mixture of sedentary and evasive prey indicating that the species employs a combination of ‘active search’ and ‘sit and wait’ foraging strategies. All three species of anurans mostly consumed terrestrial prey. This intensive study on a genus of newly invasive amphibian contributes to knowledge of the impact of amphibian invasions, and elucidates the feeding ecology of H. tigerinus, and species of the genera Limnonectes and Fejervarya. We also stress the necessity to evaluate prey availability and volume in future studies for meaningful insights into diet of amphibians.
Mohanty et al. (2018) What’s for dinner? Diet and potential trophic impact of an invasive anuran Hoplobatrachus tigerinus on the Andaman archipelago. PeerJ 6:e5698 https://doi.org/10.7717/peerj.5698
Osteology of a forelimb of an aetosaur Stagonolepis olenkae (Archosauria: Pseudosuchia: Aetosauria) from the Krasiejów locality in Poland and its probable adaptations for a scratch-digging behavior
Aetosaurs are armored basal archosaurs that played a significant role in land ecosystems during the Late Triassic (237–201 Ma). The polish species Stagonolepis olenkae Sulej, 2010 described from the Krasiejów locality (southern Poland) is one of the oldest known representatives of the group. Abundant and well-preserved material, including partially articulated specimens, allows a detailed description of the forelimbs in this species. The forelimbs of S. olenkae are the most similar to that of large aetosaurs like Desmatosuchus smalli, Desmatosuchus spurensis, Longosuchus meadei, Typothorax coccinarum or Stagonolepis robertsoni. Several characters recognized in the forelimbs of S. olenkae suggest its adaptation for scratch-digging. The most salient of these features are: short forearm, carpus, and hands, with the radius shorter than the humerus, carpus and manus shorter than the radius (excluding terminal phalanges); a prominent deltopectoral crest that extends distally on the humerus and a wide prominent entepicondyle, a long olecranon process with well-marked attachment of triceps muscle; hooked, laterally compressed, claw-like terminal phalanges with ornamentation of small pits (indicative of well-developed keratin sheaths). S. olenkae might have used its robust forelimbs to break through the compacted soil with its claws and proceed to dig in search of food in softened substrate with the shovel-like expansion at the tip of its snout. The entire forelimb of S. olenkae is covered by osteoderms, including the dorsal surface of the hand, which is unusual among aetosaurs and have not been noted for any species up to date.
Dróżdż (2018) Osteology of a forelimb of an aetosaur Stagonolepis olenkae (Archosauria: Pseudosuchia: Aetosauria) from the Krasiejów locality in Poland and its probable adaptations for a scratch-digging behavior. PeerJ 6:e5595 https://doi.org/10.7717/peerj.5595
Targeting restoration sites to improve connectivity in a tiger conservation landscape in India
Background Maintaining and restoring connectivity between source populations is essential for the long term viability of wide-ranging species, many of which occur in landscapes that are under pressure to meet increasing infrastructure needs. Identifying barriers in corridors can help inform conservation and infrastructure development agencies so that development objectives can be achieved without compromising conservation goals. Here, we use the tiger landscape in central India as a case study to identify barriers, associate them with existing infrastructure, and quantify the potential improvement by restoring or mitigating barriers. Additionally, we propose an approach to categorize linkages based on their current status within and between Protected Areas (PAs). Methods We generated a hybrid landuse-landcover map of our study area by merging datasets. We used least-cost methods and circuit theory to map corridors and generate linkage metrics. We mapped barriers and used the improvement score (IS) metric to quantify potential improvement by restoring or mitigating them. Based on criteria that represent the status of corridors between-PAs and populations within-PAs, we ranked linkages into one of four categories: Cat1—linkages that currently have high quality and potential for tiger connectivity and should be maintained, Cat2W—linkages where focus on habitat and tiger populations may improve connectivity, Cat2B—linkages where focus on reducing barriers between PAs may improve connectivity, and Cat3—linkages where effort is needed to both reduce barriers between PAs and improve tiger populations and habitat within PAs. We associated barriers with infrastructure and present maps to show where restoration or mitigation measures can be targeted to have the highest potential impact. Results We mapped 567 barriers within 30 linkages in this landscape, of which 265 barriers intersect with infrastructure (694 km of roads, 150 km of railway, 48 reservoirs, 10 mines) and 302 barriers are due to land-use or gaps in forest cover. Eighty-six barriers have both roads and railways. We identified 7 Cat1, 4 Cat2w, 9 Cat2b, and 10 Cat3 linkages. Eighty surface mines and thermal power plants are within 10 km of the least-cost paths, and more coal mines are closer to connectivity areas where linkages are narrow and rank poorly on both axes. Discussion We present spatial and quantitative results that can help conservation practitioners target mitigation and restoration efforts. India is on the path to rapid economic growth, with infrastructure development planned in biodiversity-rich areas. The mitigation hierarchy of avoiding, minimizing, and offsetting impacts due to proposed development projects can be applied to corridors in this landscape. Cross-sectoral cooperation at early stages of project life-cycles to site, design, and implement solutions can maintain connectivity while meeting infrastructure needs in this rapidly changing landscape.
Spatial and Geographic Information Science
Dutta et al. (2018) Targeting restoration sites to improve connectivity in a tiger conservation landscape in India. PeerJ 6:e5587 https://doi.org/10.7717/peerj.5587
Conserved microbiota among young Heliconius butterfly species
Background Insects are the most diverse group of animals which have established intricate evolutionary interactions with bacteria. However, the importance of these interactions is still poorly understood. Few studies have focused on a closely related group of insect species, to test the similarities and differences between their microbiota. Heliconius butterflies are a charismatic recent insect radiation that evolved the unique ability to use pollen as a protein source, which affected life history traits and resulted in an elevated speciation rates. We hypothesize that different Heliconius butterflies sharing a similar trophic pollen niche, harbor a similar gut flora within species, population and sexes. Methods To test our hypothesis, we characterized the microbiota of 38 adult male and female butterflies representing six species of Heliconius butterflies and 2 populations of the same species. We sequenced the V4 region of the 16S rRNA gene with the Roche 454 system and analyzed the data with standard tools for microbiome analysis. Results Overall, we found a low microbial diversity with only 10 OTUs dominating across all individuals, mostly Proteobacteria and Firmicutes, which accounted for 99.5% of the bacterial reads. When rare reads were considered, we identified a total of 406 OTUs across our samples. We identified reads within Phyla Chlamydiae, found in 5 butterflies of four species. Interestingly, only three OTUs were shared among all 38 individuals (Bacillus, Enterococcus and Enterobacteriaceae). Altogether, the high individual variation overshadowed species and sex differences. Thus, bacterial communities were not structured randomly with 13% of beta-diversity explained by species, and 40 rare OTUs being significantly different across species. Finally, 13 OTUs, including the intercellular symbiont Spiroplasma, varied significantly in relative abundance between males and females. Discussion The Heliconius microbial communities in these 38 individuals show a low diversity with few differences in the rare microbes between females, males, species or populations. Indeed, Heliconius butterflies, similarly to other insects, are dominated by few OTUs, mainly from Proteobacteria and Firmicutes. The overall low microbial diversity observed contrasts with the high intra-species variation in microbiome composition. This could indicate that much of the microbiome maybe acquired from their surroundings. The significant differences between species and sexes were restricted to rare taxa, which could be important for microbial community stability under changing conditions as seen in other host-microbiome systems. The presence of symbionts like Spiroplasma or Chlamydiae, identified in this study for the first time in Heliconius, could play a vital role in their behavior and evolution by vertical transmission. Altogether, our study represents a step forward into the description of the microbial diversity in a charismatic group of closely related butterflies.
van Schooten et al. (2018) Conserved microbiota among young Heliconius butterfly species. PeerJ 6:e5502 https://doi.org/10.7717/peerj.5502
Resource availability and adjustment of social behaviour influence patterns of inequality and productivity across societies
Animal societies vary widely in the diversity of social behaviour and the distribution of reproductive shares among their group members. It has been shown that individual condition can lead to divergent social roles and that social specialisation can cause an exacerbation or a mitigation of the inequality among group members within a society. This work, however, has not investigated cases in which resource availability varies between different societies, a factor that is thought to explain variation in the level of cooperation and the disparities in reproductive shares within each social group. In this study, I focus on how resource availability mediates the expression of social behaviour and how this, in turn, mediates inequality both within and between groups. I find that when differences in resource availability between societies persist over time, resource-rich societies become more egalitarian. Because lower inequality improves the productivity of a society, the inequality between resource-rich and resource-poor societies rises. When resource availability fluctuates over time, resource-rich societies tend to become more unequal. Because inequality hinders the productivity of a society, the inequality between resource-rich and resource-poor societies falls. From the evolutionary standpoint, my results show that spatial and temporal variation in resource availability may exert a strong influence on the level of inequality both within and between societies.
Rodrigues (2018) Resource availability and adjustment of social behaviour influence patterns of inequality and productivity across societies. PeerJ 6:e5488 https://doi.org/10.7717/peerj.5488
Periwinkle climbing response to water- and airbone predator chemical cues may depend on home-marsh geography
The salt marsh periwinkle, Littorina irrorata, exhibits a spatial refuge from predation by climbing the stems of Spartina alterniflora in order to avoid benthic predators. Salt marsh periwinkles have a broad geographic distribution, and for many species, responses to predators also varies with biogeography. This study sought to determine if the geographical location of the home marsh influenced the response of periwinkles (climbing height) to blue crab predator cues both via air and water. Snails from Louisiana (LA) climbed higher in general than those from North Carolina (NC), regardless of chemical cue. However, LA snails climbed 11 cm higher in the presence of waterborne predators than control snails with no cue, while NC snails only climbed five cm higher in the same comparisons. Airborne chemical cue tended to have snails climbing at intermediate heights. These responses were significantly enhanced when both populations of snails were housed together. Periwinkle response to predator cues was stronger in LA than NC, and so it is possible that the behavioral response of these snails to predators varies with biogeography of the home marsh. Also interestingly, the results of this study also suggest that cue delivery is probably occurring via mechanisms other than water, and potentially via airborne cues. Therefore, salt marsh periwinkles likely respond to numerous cues that initiate behavioral responses, including airborne cues, and these responses may vary by home-marsh geography.
Carroll et al. (2018) Periwinkle climbing response to water- and airbone predator chemical cues may depend on home-marsh geography. PeerJ 6:e5744 https://doi.org/10.7717/peerj.5744