New protocol for successful isolation and amplification of DNA from exiguous fractions of specimens: a tool to overcome the basic obstacle in molecular analyses of myxomycetes
Herbarium collections provide an essential basis for a wide array of biological research and, with development of DNA-based methods, they have become an invaluable material for genetic analyses. Yet, the use of such material is hindered by technical limitations related to DNA degradation and to quantity of biological material. The latter is inherent for some biological groups, as best exemplified by myxomycetes which form minute sporophores. It is estimated that ca. two-thirds of myxomycete taxa are represented by extremely scanty material. As DNA isolation methods applied so far in myxomycete studies require destructive sampling of many sporophores, a large part of described diversity of the group remains unavailable for phylogenetic studies or barcoding. Here, we tested several procedures of DNA isolation and amplification to seek for an efficient and possibly non-destructive method of sampling. Tests were based on herbarium specimens of 19 species representing different taxonomic orders. We assayed several variants of isolation based on silica gel membrane columns, and a newly designed procedure using highly reduced amount of biological material (small portion of spores), based on fine disruption of spores and direct PCR. While the most frequently used column-based method led to PCR success in 89.5% of samples when a large amount of material was used, its performance dropped to 52% when based on single sporophores. Single sporophores provided amplicons in 89.5% of samples when using a kit dedicated to low-amount DNA samples. Our new procedure appeared the most effective (94.7%) while it used only a small fraction of spores, being nearly non-destructive; it was also the most cost-effective. We thus demonstrate that combination of adequate handling of spore micro-disruption coupled with application of direct PCR can be an efficient way to circumvent technical limitations for genetic studies in myxomycetes and thus can substantially improve taxon sampling for phylogeny and barcoding. Additionally, this approach gives a unique possibility to apply both molecular and morphological assays to the same structure (sporophore), which then can be further stored as documentation.
Janik et al. (2020) New protocol for successful isolation and amplification of DNA from exiguous fractions of specimens: a tool to overcome the basic obstacle in molecular analyses of myxomycetes. PeerJ 8:e8406 https://doi.org/10.7717/peerj.8406
Characterization of the complete mitochondrial genome sequences of three Merulinidae corals and novel insights into the phylogenetics
Over the past few decades, modern coral taxonomy, combining morphology and molecular sequence data, has resolved many long-standing questions about scleractinian corals. In this study, we sequenced the complete mitochondrial genomes of three Merulinidae corals (Dipsastraea rotumana, Favites pentagona, and Hydnophora exesa) for the first time using next-generation sequencing. The obtained mitogenome sequences ranged from 16,466 bp (D. rotumana) to 18,006 bp (F. pentagona) in length, and included 13 unique protein-coding genes (PCGs), two transfer RNA genes, and two ribosomal RNA genes . Gene arrangement, nucleotide composition, and nucleotide bias of the three Merulinidae corals were canonically identical to each other and consistent with other scleractinian corals. We performed a Bayesian phylogenetic reconstruction based on 13 protein-coding sequences of 86 Scleractinia species. The results showed that the family Merulinidae was conventionally nested within the robust branch, with H. exesa clustered closely with F. pentagona and D. rotumana clustered closely with Favites abdita. This study provides novel insight into the phylogenetics of species within the family Merulinidae and the evolutionary relationships among different Scleractinia genera.
Niu et al. (2020) Characterization of the complete mitochondrial genome sequences of three Merulinidae corals and novel insights into the phylogenetics. PeerJ 8:e8455 https://doi.org/10.7717/peerj.8455
Developing and assessing a density surface model in a Bayesian hierarchical framework with a focus on uncertainty: insights from simulations and an application to fin whales (Balaenoptera physalus)
Density surface models (DSMs) are an important tool in the conservation and management of cetaceans. Most previous applications of DSMs have adopted a two-step approach to model fitting (hereafter referred to as the Two-Stage Method), whereby detection probabilities are first estimated using distance sampling detection functions and subsequently used as an offset when fitting a density-habitat model. Although variance propagation techniques have recently become available for the Two-Stage Method, most previous applications have not propagated detection probability uncertainty into final density estimates. In this paper, we describe an alternative approach for fitting DSMs based on Bayesian hierarchical inference (hereafter referred to as the Bayesian Method), which is a natural framework for simultaneously propagating multiple sources of uncertainty into final estimates. Our framework includes (1) a mark-recapture distance sampling observation model that can accommodate two team line transect data, (2) an informed prior for the probability a group of animals is at the surface and available for detection (i.e. surface availability) (3) a density-habitat model incorporating spatial smoothers and (4) a flexible compound Poisson-gamma model for count data that incorporates overdispersion and zero-inflation. We evaluate our method and compare its performance to the Two-Stage Method with simulations and an application to line transect data of fin whales (Balaenoptera physalus) off the east coast of the USA. Simulations showed that both methods had low bias (<1.5%) and confidence interval coverage close to the nominal 95% rate when variance was propagated from the first step. Results from the fin whale analysis showed that density estimates and predicted distribution patterns were largely similar among methods; however, the coefficient of variation of the final abundance estimate more than doubled (0.14 vs 0.31) when detection variance was correctly propagated into final estimates. An analysis of the variance components demonstrated that overall detectability as well as surface availability contributed substantial amounts of variance in the final abundance estimates whereas uncertainty in mean group size contributed a negligible amount. Our method provides a Bayesian alternative to DSMs that incorporates much of the flexibility available in the Two-Stage Method. In addition, these results demonstrate the degree to which uncertainty can be underestimated if certain components of a DSM are assumed fixed.
Sigourney et al. (2020) Developing and assessing a density surface model in a Bayesian hierarchical framework with a focus on uncertainty: insights from simulations and an application to fin whales (Balaenoptera physalus). PeerJ 8:e8226 https://doi.org/10.7717/peerj.8226
Life history traits and reproductive performance of the caridean shrimp Lysmata boggessi, a heavily traded invertebrate in the marine aquarium industry
The most intense commercial harvest of marine aquarium species in North America occurs in the coastal waters surrounding Florida, yet very often little information exists on the life histories, population dynamics, or reproductive characteristics of these organisms. The peppermint shrimp Lysmata boggessi is one such species and is heavily targeted along the west coast of Florida. It is known primarily among aquarists for its ability to control pest anemones and in the scientific community for its unique sexual system, protandric simultaneous hermaphroditism. However, no study has addressed fishery interactions or long-term population dynamics for L. boggessi. We used monthly fisheries-dependent sampling, with a trained observer present, for a full year to assess seasonality in sex phase ratio (males to males + hermaphrodites), size at sex change, fecundity, embryo volume and reproductive output of an exploited L. boggessi population. L. boggessi exhibited distinct seasonality in size distribution, sex phase ratio, size at sex phase change and reproductive activity. The peak reproductive season was in spring, when the population was dominated by small but fecund hermaphrodites. Reproduction decreased during fall and winter and sex phase ratios favored male phase shrimp that exhibited delayed sex change. This population and individual level information is the first of its kind for L. boggessi and fills a much needed data gap for the informed management of this fishery.
Dickson et al. (2020) Life history traits and reproductive performance of the caridean shrimp Lysmata boggessi, a heavily traded invertebrate in the marine aquarium industry. PeerJ 8:e8231 https://doi.org/10.7717/peerj.8231
Analysis and prediction of vegetation dynamics under the background of climate change in Xinjiang, China
Background Vegetation dynamics is defined as a significant indictor in regulating terrestrial carbon balance and climate change, and this issue is important for the evaluation of climate change. Though much work has been done concerning the correlations among vegetation dynamics, precipitation and temperature, the related questions about relationships between vegetation dynamics and other climatic factors (e.g., specific humidity, net radiation, soil moisture) have not been thoroughly considered. Understanding these questions is of primary importance in developing policies to address climate change. Methods In this study, the least squares regression analysis method was used to simulate the trend of vegetation dynamics based on the normalized difference vegetation index (NDVI) from 1981 to 2018. A partial correlation analysis method was used to explore the relationship between vegetation dynamics and climate change; and further,the revised greyscale model was applied to predict the future growth trend of natural vegetation. Results The Mann-Kendall test results showed that th e air temperature rose sharply in 1997 and had been in a state of high fluctuations since then. Strong changes in hydrothermal conditions had major impact on vegetation dynamics in the area. Specifically, the NDVI value of natural vegetation showed an increasing trend from 1981 to 2018, and the same changes occurred in the precipitation. From 1981 to 1997, the values of natural vegetation increased at a rate of 0.0016 per year. From 1999 to 2009, the NDVI value decreased by an average rate of 0.0025 per year. From 2010 to 2018, the values began an increasing trend and reached a peak in 2017, with an average annual rate of 0.0033. The high vegetation dynamics areas were mainly concentrated in the north and south slopes of the Tianshan Mountains, the Ili River Valley and the Altay area. The greyscale prediction results showed that the annual average NDVI values of natural vegetation may present a fluctuating increasing trend. The NDVI value in 2030 is 0.0196 higher than that in 2018, with an increase of 6.18%. Conclusions Our results indicate that: (i) the variations of climatic factors have caused a huge change in the hydrothermal conditions in Xinjiang; (ii) the vegetation dynamics in Xinjiang showed obvious volatility, and then in the end stage of the study were higher than the initial stage the vegetation dynamics in Xinjiang showed a staged increasing trend; (iii) the vegetation dynamics were affected by many factors,of which precipitation was the main reason; (iv) in the next decade, the vegetation dynamics in Xinjiang will show an increasing trend.
Spatial and Geographic Information Science
Zhuang et al. (2020) Analysis and prediction of vegetation dynamics under the background of climate change in Xinjiang, China. PeerJ 8:e8282 https://doi.org/10.7717/peerj.8282
Occurrence, ecological function and medical importance of dermestid beetle hastisetae
Hastisetae are a specific group of detachable setae characterizing the larvae of Megatominae (Coleoptera: Dermestidae), commonly known as carpet and khapra beetles. These setae are located on both thoracic and abdominal tergites and they are the primary defense of the larva against invertebrate predators. According to previous studies, the main purpose of hastisetae is to work as a mechanical obstacle, but they are also capable to block and kill a predator. Hastisetae, single or aggregate, function as an extremely efficient mechanical trap, based on an entangling mechanism of cuticular structures (spines and hairs) and body appendages (antennae, legs and mouthparts). It is believed that this defensive system evolved primarily to contrast predation by invertebrates, however it has been observed that hastisetae may affect vertebrates as well. Although information on the impacts of vertebrate predators of the beetles is lacking, hastisetae have been shown to be a possible threat for human health as an important contaminant of stored products (food and fabric), work and living environment. Review of past and recent literature on dermestid larvae has revealed that despite these structures indicated as one of the distinctive characters in species identification, very little is known about their ultrastructure, evolution and mechanism of action. In the present work, we will provide the state of knowledge on hastisetae in Dermestidae and we will present and discuss future research perspectives intended to bridge the existing knowledge gaps.
Ruzzier et al. (2020) Occurrence, ecological function and medical importance of dermestid beetle hastisetae. PeerJ 8:e8340 https://doi.org/10.7717/peerj.8340
Growth rate and locomotor performance tradeoff is not universal in birds
Though a tradeoff between growth rate and locomotor performance has been proposed, empirical data on this relationship are still limited. Here we statistically analyze the associations of growth rate and flight ability in birds by assessing how growth rate is correlated with three wing parameters of birds: flight muscle ratio, wing aspect ratio, and wing loading. We find that fast-growing birds tended to have higher flight muscle ratios and higher wing loadings than slow-growing birds, which suggests that fast-growing birds may have better takeoff performance, but lower efficiency in maneuvering flight. Accordingly, our findings suggest that the relationship between growth rate and flight ability is more complex than a simple tradeoff. Since the hindlimbs also contribute greatly to the locomotion of birds, future investigations on the relationship between growth rate and hindlimb performance will provide more insights into the evolution of birds.
Zhao et al. (2020) Growth rate and locomotor performance tradeoff is not universal in birds. PeerJ 8:e8423 https://doi.org/10.7717/peerj.8423
Permutation-based methods for mediation analysis in studies with small sample sizes
Background Mediation analysis can be used to evaluate the effect of an exposure on an outcome acting through an intermediate variable or mediator. For studies with small sample sizes, permutation testing may be useful in evaluating the indirect effect (i.e., the effect of exposure on the outcome through the mediator) while maintaining the appropriate type I error rate. For mediation analysis in studies with small sample sizes, existing permutation testing methods permute the residuals under the full or alternative model, but have not been evaluated under situations where covariates are included. In this article, we consider and evaluate two additional permutation approaches for testing the indirect effect in mediation analysis based on permutating the residuals under the reduced or null model which allows for the inclusion of covariates. Methods Simulation studies were used to empirically evaluate the behavior of these two additional approaches: (1) the permutation test of the Indirect Effect under Reduced Models (IERM) and (2) the Permutation Supremum test under Reduced Models (PSRM). The performance of these methods was compared to the standard permutation approach for mediation analysis, the permutation test of the Indirect Effect under Full Models (IEFM). We evaluated the type 1 error rates and power of these methods in the presence of covariates since mediation analysis assumes no unmeasured confounders of the exposure–mediator–outcome relationships. Results The proposed PSRM approach maintained type I error rates below nominal levels under all conditions, while the proposed IERM approach exhibited grossly inflated type I rates in many conditions and the standard IEFM exhibited inflated type I error rates under a small number of conditions. Power did not differ substantially between the proposed PSRM approach and the standard IEFM approach. Conclusions The proposed PSRM approach is recommended over the existing IEFM approach for mediation analysis in studies with small sample sizes.
Kroehl et al. (2020) Permutation-based methods for mediation analysis in studies with small sample sizes. PeerJ 8:e8246 https://doi.org/10.7717/peerj.8246
Rapid digitization to reclaim thematic maps of white-tailed deer density from 1982 and 2003 in the conterminous US
Background Despite availability of valuable ecological data in published thematic maps, manual methods to transfer published maps to a more accessible digital format are time-intensive. Application of object-based image analysis makes digitization faster. Methods Using object-based image analysis followed by random forests classification, we rapidly digitized choropleth maps of white-tailed deer (Odocoileus virginianus) densities in the conterminous US during 1982 and 2001 to 2005 (hereafter, 2003), allowing access to deer density information stored in images. Results The digitization process took about one day each per deer density map, of which about two hours was computer processing time, which will differ due to factors such as resolution and number of objects. Deer were present in 4.75 million km2 (60% of the area) and 5.56 million km2 (70%) during 1982 and 2003, respectively. Population and density in areas with deer presence were 17.15 million and 3.6 deer/km2 during 1982 and 29.93 million and 5.4 deer/km2 during 2003. Greatest densities were 7.2 deer/km2 in Georgia during 1982 and 14.6 deer/km2 in Wisconsin during 2003. Six states had deer densities ≥9.8 deer/km2 during 2003. Colorado, Idaho, and Oregon had greatest increases in population and area of deer presence, and deer expansion is likely to continue into western states. Error in these estimates may be similar to error resulting from differential reporting by state agencies. Deer densities likely are within historical levels in most of the US. Discussion This method rapidly reclaimed informational value of deer density maps, enabling greater analysis, and similarly may be applied to digitize a variety of published maps to geographic information system layers, which permit greater analysis.
Hanberry et al. (2020) Rapid digitization to reclaim thematic maps of white-tailed deer density from 1982 and 2003 in the conterminous US. PeerJ 8:e8262 https://doi.org/10.7717/peerj.8262
Social rank overrides environmental and community fluctuations in determining meat access by female chimpanzees in the Taï National Park, Côte d’Ivoire
Meat, long hypothesized as an important food source in human evolution, is still a substantial component of the modern human diet, with some humans relying entirely on meat during certain times of the year. Understanding the socio-ecological context leading to the successful acquisition and consumption of meat by chimpanzees (Pan troglodytes), our closest living relative, can provide insight into the emergence of this trait because humans and chimpanzees are unusual among primates in that they both (i) hunt mammalian prey, (ii) share meat with community members, and (iii) form long-term relationships and complex social hierarchies within their communities. However, females in both human hunter-gatherer societies as well as chimpanzee groups rarely hunt, instead typically accessing meat via males that share meat with group members. In general, female chimpanzee dominance rank affects feeding competition, but so far, the effect of female dominance rank on meat access found different results within and across studied chimpanzee groups. Here we contribute to the debate on how female rank influences meat access while controlling for several socio-ecological variables. Multivariate analyses of 773 separate meat-eating events collected over more than 25 years from two chimpanzee communities located in the Taï National Park, Côte d’Ivoire, were used to test the importance of female dominance rank for being present at, and for acquiring meat, during meat-eating events. We found that high-ranking females were more likely to be present during a meat-eating event and, in addition, were more likely to eat meat compared to the subordinates. These findings were robust to both large demographic changes (decrease of community size) and seasonal ecological changes (fruit abundance dynamics). In addition to social rank, we found that other female properties had a positive influence on presence to meat-eating events and access to meat given presence, including oestrus status, nursing of a small infant, and age. Similar to findings in other chimpanzee populations, our results suggest that females reliably acquire meat over their lifetime despite rarely being active hunters. The implication of this study supports the hypothesis that dominance rank is an important female chimpanzee property conferring benefits for the high-ranking females.
Riedel et al. (2020) Social rank overrides environmental and community fluctuations in determining meat access by female chimpanzees in the Taï National Park, Côte d’Ivoire. PeerJ 8:e8283 https://doi.org/10.7717/peerj.8283