Effective population sizes and adaptive genetic variation in a captive bird population
Captive populations are considered a key component of ex situ conservation programs. Research on multiple taxa has shown the differential success of maintaining demographic versus genetic stability and viability in captive populations. In typical captive populations, usually founded by few or related individuals, genetic diversity can be lost and inbreeding can accumulate rapidly, calling into question their ultimate utility for release into the wild. Furthermore, domestication selection for survival in captive conditions is another concern. Therefore, it is crucial to understand the dynamics of population sizes, particularly the effective population size, and genetic diversity at non-neutral and adaptive loci in captive populations. In this study, we assessed effective population sizes and genetic variation at both neutral microsatellite markers, as well as SNP variants from the MHC-B locus of a captive Red Junglefowl population. This population represents a rare instance of a population with a well-documented history in captivity, following a realistic scenario of chain-of-custody, unlike many captive lab populations. Our analyses, which included 27 individuals comprising the entirety of one captive population show very low neutral and adaptive genetic variation, as well as low effective sizes, which correspond with the known demographic history. Finally, our study also shows the divergent impacts of small effective size and inbreeding in captive populations on microsatellite versus adaptive genetic variation in the MHC-B locus. Our study provides insights into the difficulties of maintaining adaptive genetic variation in small captive populations.
Athrey et al. (2018) Effective population sizes and adaptive genetic variation in a captive bird population. PeerJ 6:e5803 https://doi.org/10.7717/peerj.5803
What is an archaeon and are the Archaea really unique?
The recognition of the group Archaea as a major branch of the tree of life (ToL) prompted a new view of the evolution of biodiversity. The genomic representation of archaeal biodiversity has since significantly increased. In addition, advances in phylogenetic modeling of multi-locus datasets have resolved many recalcitrant branches of the ToL. Despite the technical advances and an expanded taxonomic representation, two important aspects of the origins and evolution of the Archaea remain controversial, even as we celebrate the 40th anniversary of the monumental discovery. These issues concern (i) the uniqueness (monophyly) of the Archaea, and (ii) the evolutionary relationships of the Archaea to the Bacteria and the Eukarya; both of these are relevant to the deep structure of the ToL. To explore the causes for this persistent ambiguity, I examine multiple datasets and different phylogenetic approaches that support contradicting conclusions. I find that the uncertainty is primarily due to a scarcity of information in standard datasets—universal core-genes datasets—to reliably resolve the conflicts. These conflicts can be resolved efficiently by comparing patterns of variation in the distribution of functional genomic signatures, which are less diffused unlike patterns of primary sequence variation. Relatively lower heterogeneity in distribution patterns minimizes uncertainties and supports statistically robust phylogenetic inferences, especially of the earliest divergences of life. This case study further highlights the limitations of primary sequence data in resolving difficult phylogenetic problems, and raises questions about evolutionary inferences drawn from the analyses of sequence alignments of a small set of core genes. In particular, the findings of this study corroborate the growing consensus that reversible substitution mutations may not be optimal phylogenetic markers for resolving early divergences in the ToL, nor for determining the polarity of evolutionary transitions across the ToL.
Harish (2018) What is an archaeon and are the Archaea really unique?. PeerJ 6:e5770 https://doi.org/10.7717/peerj.5770
Thumbs up: movements made by the thumb are smoother and larger than fingers in finger-thumb opposition tasks
Background In humans, the thumb plays a crucial role in producing finger opposition movements. These movements form the basis of several activities of the hand. Hence these movements have been used to study phenomena like prehension, motor control, motor learning, etc. Although such tasks have been studied extensively, the relative contribution of the thumb vis-à-vis the fingers in finger opposition tasks is not well understood. In this study, we investigated the kinematics of thumb and fingers in a simple finger opposition task. Further, we quantified the relative contribution and the movement smoothness aspects and compared these between fingers and thumb. Methods Eight, young healthy participants (four males and four females) were asked to perform a full finger to thumb opposition movement, where they were required to reach for different phalanges of the fingers. Position (X, Y and Z) of individual segments of the four fingers and the thumb were measured with reference to the wrist by a 16-sensor kinematics measurement system. Displacements and velocities were computed. An index, displacement ratio, that quantifies the relative contribution of thumb and fingers was computed from displacement data. Velocity data was used to quantify the smoothness of movement of thumb and fingers. Results The Displacement Ratio showed that contribution of the thumb is higher than contribution of any other target finger or target phalanges, except for the distal phalanx of the index and middle fingers. Smoothness of movement of the thumb was higher than all the finger phalanges in all cases. Conclusion We conclude that in the task considered (thumb opposition movements to different targets within the hand & fingers), the thumb made a greater relative contribution in terms of displacement ratio and also produced smoother movements. However, smoothness of thumb did not vary depending on the target. This suggests that the traditional notion of the thumb being a special digit when compared to other fingers is true at least for the opposition movements considered in this study.
Rachaveti et al. (2018) Thumbs up: movements made by the thumb are smoother and larger than fingers in finger-thumb opposition tasks. PeerJ 6:e5763 https://doi.org/10.7717/peerj.5763
Metabolic, inflammatory, and oxidative stress markers in women exposed to secondhand smoke
Background Secondhand smoke (SHS) exposure has adverse effects on the cardiovascular system. This study aimed to determine the effects of SHS on the cardiovascular disease biomarkers, namely the metabolic, inflammatory, and oxidative stress markers in healthy adult women. Methods This comparative cross-sectional study was conducted among healthy women. The cases included those women exposed to SHS, and the controls included those women not exposed to SHS. SHS exposure was defined as being exposed to SHS for at least 15 min for 2 days per week. Venous blood was taken to measure the metabolic markers (high molecular weight adiponectin, insulin level, insulin resistance, and nonesterified fatty acids), oxidative stress markers (oxidized low density lipoprotein cholesterol and 8-isoprostane), and inflammatory markers (high-sensitivity C-reactive protein and interleukin-6). A hair nicotine analysis was also performed. An analysis of covariance and a simple linear regression analysis were conducted. Results There were 101 women in the SHS exposure group and 91 women in the non-SHS exposure group. The mean (with standard deviation) of the hair nicotine levels was significantly higher in the SHS exposure group when compared to the non-SHS exposure group [0.22 (0.62) vs. 0.04 (0.11) ng/mg; P = 0.009]. No significant differences were observed in the high molecular weight adiponectin, insulin and insulin resistance, nonesterified fatty acids, 8-isoprostane, oxidized low density lipoprotein cholesterol, interleukin-6, and high-sensitivity C-reactive protein between the two groups. The serum high molecular weight adiponectin was negatively associated with the insulin level and insulin resistance in the women exposed to SHS. However, no significant relationships were seen between the high molecular weight adiponectin and nonesterified fatty acids, 8-isoprostane, oxidized low density lipoprotein cholesterol, high-sensitivity C-reactive protein in the SHS group. Discussion There were no significant differences in the metabolic, oxidative stress, and inflammatory markers between the SHS exposure and non-SHS exposure healthy women. A low serum level of high molecular weight adiponectin was associated with an increased insulin level and resistance in the women exposed to SHS.
Siti Hajar et al. (2018) Metabolic, inflammatory, and oxidative stress markers in women exposed to secondhand smoke. PeerJ 6:e5758 https://doi.org/10.7717/peerj.5758
Genome-wide identification and analysis of the CNGC gene family in maize
As one of the non-selective cation channel gene families, the cyclic nucleotide-gated channel (CNGC) gene family plays a vital role in plant physiological processes that are related to signal pathways, plant development, and environmental stresses. However, genome-wide identification and analysis of the CNGC gene family in maize has not yet been undertaken. In the present study, twelve ZmCNGC genes were identified in the maize genome, which were unevenly distributed on chromosomes 1, 2, 4, 5, 6, 7, and 8. They were classified into five major groups: Groups I, II, III, IVa, and IVb. Phylogenetic analysis showed that gramineous plant CNGC genes expanded unequally during evolution. Group IV CNGC genes emerged first, whereas Groups I and II appeared later. Prediction analysis of cis-acting regulatory elements showed that 137 putative cis-elements were related to hormone-response, abiotic stress, and organ development. Furthermore, 120 protein pairs were predicted to interact with the 12 ZmCNGC proteins and other maize proteins. The expression profiles of the ZmCNGC genes were expressed in tissue-specific patterns. These results provide important information that will increase our understanding of the CNGC gene family in maize and other plants.
Hao et al. (2018) Genome-wide identification and analysis of the CNGC gene family in maize. PeerJ 6:e5816 https://doi.org/10.7717/peerj.5816
C9orf72, a protein associated with amyotrophic lateral sclerosis (ALS) is a guanine nucleotide exchange factor
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), two late onset neurodegenerative diseases, have been shown to share overlapping cellular pathologies and genetic origins. Studies suggest that a hexanucleotide repeat expansion in the first intron of the C9orf72 gene is the most common cause of familial FTD and ALS pathology. The C9orf72 protein is predicted to be a differentially expressed in normal and neoplastic cells domain protein implying that C9orf72 functions as a guanine nucleotide exchange factor (GEF) to regulate specific Rab GTPases. Reported studies thus far point to a putative role for C9orf72 in lysosome biogenesis, vesicular trafficking, autophagy and mechanistic target of rapamycin complex1 (mTORC1) signaling. Here we report the expression, purification and biochemical characterization of C9orf72 protein. We conclusively show that C9orf72 is a GEF. The distinctive presence of both Rab- and Rho-GTPase GEF activities suggests that C9orf72 may function as a dual exchange factor coupling physiological functions such as cytoskeleton modulation and autophagy with endocytosis.
Iyer et al. (2018) C9orf72, a protein associated with amyotrophic lateral sclerosis (ALS) is a guanine nucleotide exchange factor. PeerJ 6:e5815 https://doi.org/10.7717/peerj.5815
Sclerostin promotes human dental pulp cells senescence
Background Senescence-related impairment of proliferation and differentiation limits the use of dental pulp cells for tissue regeneration. Deletion of sclerostin improves the dentinogenesis regeneration, while its role in dental pulp senescence is unclear. We investigated the role of sclerostin in subculture-induced senescence of human dental pulp cells (HDPCs) and in the senescence-related decline of proliferation and odontoblastic differentiation. Methods Immunohistochemical staining and qRT-PCR analyses were performed to examine the expression pattern of sclerostin in young (20–30-year-old) and senescent (45–80-year-old) dental pulps. HDPCs were serially subcultured until senescence, and the expression of sclerostin was examined by qRT-PCR analysis. HDPCs with sclerostin overexpression and knockdown were constructed to investigate the role of sclerostin in HDPCs senescence and senescence-related impairment of odontoblastic differentiation potential. Results By immunohistochemistry and qRT-PCR, we found a significantly increased expression level of sclerostin in senescent human dental pulp compared with that of young human dental pulp. Additionally, elevated sclerostin expression was found in subculture-induced senescent HDPCs in vitro. By sclerostin overexpression and knockdown, we found that sclerostin promoted HDPCs senescence-related decline of proliferation and odontoblastic differentiation potential with increased expression of p16, p53 and p21 and downregulation of the Wnt signaling pathway. Discussion The increased expression of sclerostin is responsible for the decline of proliferation and odontoblastic differentiation potential of HDPCs during cellular senescence. Anti-sclerostin treatment may be beneficial for the maintenance of the proliferation and odontoblastic differentiation potentials of HDPCs.
Ou et al. (2018) Sclerostin promotes human dental pulp cells senescence. PeerJ 6:e5808 https://doi.org/10.7717/peerj.5808
Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation
Oaks (Quercus) comprise more than 400 species worldwide and centres of diversity for most sections lie in the Americas and East/Southeast Asia. The only exception is the Eurasian sect. Cerris that comprises about 15 species, most of which are confined to western Eurasia. This section has not been comprehensively studied using molecular tools. Here, we assess species diversity and provide a first comprehensive taxonomic and phylogeographic scheme of western Eurasian members of sect. Cerris using plastid (trnH-psbA) and nuclear (5S-IGS) DNA variation with a dense intra-specific and geographic sampling. Chloroplast haplotypes primarily reflected phylogeographic patterns originating from interspecific cytoplasmic gene flow within sect. Cerris and its sister section Ilex. We identified two widespread and ancestral haplotypes, and locally restricted derived variants. Signatures shared with Mediterranean species of sect. Ilex, but not with the East Asian Cerris oaks, suggest that the western Eurasian lineage came into contact with Ilex only after the first (early Oligocene) members of sect. Cerris in Northeast Asia had begun to radiate and move westwards. Nuclear 5S-IGS diversification patterns were more useful for establishing a molecular-taxonomic framework and to reveal hybridization and reticulation. Four main evolutionary lineages were identified. The first lineage is comprised of Q. libani, Q. trojana and Q. afares and appears to be closest to the root of sect. Cerris. These taxa are morphologically most similar to the East Asian species of Cerris, and to both Oligocene and Miocene fossils of East Asia and Miocene fossils of western Eurasia. The second lineage is mainly composed of the widespread Q. cerris and the narrow endemic species Q. castaneifolia, Q. look, and Q. euboica. The third lineage comprises three Near East species (Q. brantii, Q. ithaburensis and Q. macrolepis), well adapted to continental climates with cold winters. The forth lineage appears to be the most derived and comprises Q. suber and Q. crenata. Q. cerris and Q. trojana displayed high levels of variation; Q. macrolepis and Q. euboica, previously treated as subspecies of Q. ithaburensis and Q. trojana, likely deserve independent species status. A trend towards inter-specific crosses was detected in several taxa; however, we found no clear evidence of a hybrid origin of Q. afares and Q. crenata, as currently assumed.
Simeone et al. (2018) Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation. PeerJ 6:e5793 https://doi.org/10.7717/peerj.5793
Intraspecific phenotypic variation in life history traits of Daphnia galeata populations in response to fish kairomones
Phenotypic plasticity is the ability of a genotype to produce different phenotypes depending on the environment. It has an influence on the adaptive potential to environmental change and the capability to adapt locally. Adaptation to environmental change happens at the population level, thereby contributing to genotypic and phenotypic variation within a species. Predation is an important ecological factor structuring communities and maintaining species diversity. Prey developed different strategies to reduce their vulnerability to predators by changing their behaviour, their morphology or their life history. Predator-induced life history responses in Daphnia have been investigated for decades, but intra-and inter-population variability was rarely addressed explicitly. We addressed this issue by conducting a common garden experiment with 24 clonal lines of European Daphnia galeata originating from four populations, each represented by six clonal lines. We recorded life history traits in the absence and presence of fish kairomones. Additionally, we looked at the shape of experimental individuals by conducting a geometric morphometric analysis, thus assessing predator-induced morphometric changes. Our data revealed high intraspecific phenotypic variation within and between four D. galeata populations, the potential to locally adapt to a vertebrate predator regime as well as an effect of the fish kairomones on morphology of D. galeata.
Tams et al. (2018) Intraspecific phenotypic variation in life history traits of Daphnia galeata populations in response to fish kairomones. PeerJ 6:e5746 https://doi.org/10.7717/peerj.5746
Machine-learning-based quantitative estimation of soil organic carbon content by VIS/NIR spectroscopy
Soil organic carbon (SOC) is an important soil property that has profound impact on soil quality and plant growth. With 140 soil samples collected from Ebinur Lake Wetland National Nature Reserve, Xinjiang Uyghur Autonomous Region of China, this research evaluated the feasibility of visible/near infrared (VIS/NIR) spectroscopy data (350–2,500 nm) and simulated EO-1 Hyperion data to estimate SOC in arid wetland regions. Three machine learning algorithms including Ant Colony Optimization-interval Partial Least Squares (ACO-iPLS), Recursive Feature Elimination-Support Vector Machine (RF-SVM), and Random Forest (RF) were employed to select spectral features and further estimate SOC. Results indicated that the feature wavelengths pertaining to SOC were mainly within the ranges of 745–910 nm and 1,911–2,254 nm. The combination of RF-SVM and first derivative pre-processing produced the highest estimation accuracy with the optimal values of Rt (correlation coefficient of testing set), RMSEt and RPD of 0.91, 0.27% and 2.41, respectively. The simulated EO-1 Hyperion data combined with Support Vector Machine (SVM) based recursive feature elimination algorithm produced the most accurate estimate of SOC content. For the testing set, Rt was 0.79, RMSEt was 0.19%, and RPD was 1.61. This practice provides an efficient, low-cost approach with potentially high accuracy to estimate SOC contents and hence supports better management and protection strategies for desert wetland ecosystems.
Spatial and Geographic Information Science
Ding et al. (2018) Machine-learning-based quantitative estimation of soil organic carbon content by VIS/NIR spectroscopy. PeerJ 6:e5714 https://doi.org/10.7717/peerj.5714