Relationships between the diet and dentition of Asian leaf monkeys

Colobines have been generally described as primates that use the anterior teeth minimally, but the posterior teeth extensively, to process leaves and related food items. However, variation among leaf monkeys in both anterior and posterior dental morphology has been recognized for decades. In this study, we turn to Hylander's (Science 189 (1975) 1095-1098) analysis of anterior incisor row length and Kay's (Adaptations for foraging in nonhuman primates, 1984) examination of relative molar crest length to test hypotheses proposed by them for Asian colobines. We present findings based on data from the largest Asian colobine sample measured to date. Our findings for incisor row length and molar cresting are not amenable to broad generalizations. In those instances when our morphological findings concur with those of Hylander (Science 189 (1975) 1095-1098) and Kay and Hylander (The ecology of arboreal folivores, 1978), the ecological evidence seldom supports the morphological predictions. The disassociation between diet and dental patterns may be a consequence of differential selection by fallback foods, anthropogenic disturbance or climatic shifts limiting preferred diets, or the use of food types as opposed to food mechanical properties for dietary categorization. We also found that in the case of both incisor row length and molar crest length, the patterns for males and females differed markedly. The reasons for these differences may in part be ascribed to the metabolic challenges faced by females and subsequent niche partitioning. We propose integrated analyses of the ingestive and digestive systems of our study taxa to clarify relationships among behavior, dental morphology, and diet in extant and extinct colobines.     

Relationships between the fossil colobine Mesopithecus pentelicus and extant cercopithecoids, based on dental metrics

Maxillary dental measurements from six specimens of Mesopithecus pentelicus, 64 cercopithecines, 59 African colobines, and 64 Asian colobines were analyzed by means of a "nested research design" that was specifically designed to explore the affiliation between fossils and extant cercopithecoids at different systematic levels. The results showed that the variation among taxonomic groups was mainly associated with size; however, in addition, interesting shape differences emerged, molars were shown to be important discriminators, Mesopithecus was confirmed as a colobine (as expected) and found to be closer to Asian species than to African ones, and the odd-nosed colobines were found to share more dental similarities with Mesopithecus than other colobines. The last finding is in contrast to previous studies, in which it was proposed that M. pentelicus is morphologically closely related to the African colobus and the gray langur (Semnopithecus).     

Widespread mito‐nuclear discordance with evidence for introgressive hybridization and selective sweeps in Lycaeides

We investigated the extent and potential cause(s) of mitochondrial introgression within the polytypic North American Lycaeides species complex (Lepidoptera). By comparing population genetic structure based on mitochondrial DNA (COI and COII) and nuclear DNA (251 polymorphic amplified fragment length polymorphism markers), we detected substantial mito‐nuclear discordance, primarily involving a single mitochondrial haplotype (h01), which is likely due to mitochondrial introgression between differentiated Lycaeides populations and/or species. We detected reduced mitochondrial genetic diversity relative to nuclear genetic diversity in populations where mitochondrial haplotype h01 occurs, suggesting that the spread of this haplotype was facilitated by selection. We found no evidence that haplotype h01 is associated with increased fitness (in terms of survival to eclosion, fresh adult weight, and adult longevity) in a polymorphic Lycaeides melissa population. However, we did find a positive association between mitochondrial haplotype h01 and infection by the endoparasitic bacterium Wolbachia in one out of three lineages tested. Linkage disequilibrium between mitochondrial haplotype h01 and Wolbachia infection status may have resulted in indirect selection favouring the spread of haplotype h01 in at least one lineage of North American Lycaeides. These results illustrate the potential for introgressive hybridization to produce substantial mito‐nuclear discordance and demonstrate that an individual's mitochondrial and nuclear genome may have strikingly different evolutionary histories resulting from non‐neutral processes and intrinsic differences in the inheritance and biology of these genomes.     

杯萼海桑和格氏海桑自然杂交的分子证据

Interspecific hybridization has been frequently observed in the mangrove genus Sonneratia. However, no natural hybridization has been reported between Sonneratia alba and S. griffithii to date, despite their overlapping distribution in the coast of Andaman Sea. In this study, cysteine proteinase inhibitor gene (cpi) from the nuclear genome, and two intergenic spacers (trnL-trnF and trnV-trnM) from the chloroplast genome, were sequenced to determine whether natural hybridization took place between the two species. Our results revealed two distinct types of cpi sequences from the putative hybrid matching those acquired from S. griffithii and S. alba, respectively. Sequencing of the chloroplast trnL-trnF and trnV-trnM regions showed that S. alba differed from S. griffithii by one nucleotide in each region, and the putative hybrid had the identical sequences with S. griffithii. Molecular data demonstrated clearly that there indeed existed natural hybridization between S. alba and S. griffithii, and that S. griffithii was the maternal parent in this hybridization event.     

Bi‐parentally inherited species‐specific markers identify hybridization between rainbow trout and cutthroat trout subspecies

Eight polymerase chain reaction primer sets amplifying bi‐parentally inherited species‐specific markers were developed that differentiate between rainbow trout (Oncorhynchus mykiss) and various cutthroat trout (O. clarki) subspecies. The primers were tested within known F₁ and first generation hybrid backcrosses and were shown to amplify codominantly within hybrids. Heterozygous individuals also amplified a slower migrating band that was a heteroduplex, caused by the annealing of polymerase chain reaction products from both species. These primer sets have numerous advantages for native cutthroat trout conservation including statistical genetic analyses of known crosses and simple hybrid identification.     

Comparative proteomic analysis between fifth‐instar nymphs and adults of Asian citrus psyllid Diaphorina citri

Asian citrus psyllid Diaphorina citri Kuwayama is extremely problematic worldwide, particularly where Huanglongbing (HLB) disease, the most serious and devastating of citrus diseases, is found. The threat is a result of its ability to transmit the causal agent of HLB, Candidatus Liberibacter asiaticus (CLas) bacterium. Improvements in proteomics, mass spectrometry, bioinformatics tools and gene ontology annotation facilitate the mapping and large‐scale identification and quantification of proteins. To date, only a few comparative proteomic studies report the developmental proteomic changes of hemimetabolous and plant–disease vector insects. Two‐dimensional gel electrophoresis analysis of D. citri total protein is able to detect qualitative and quantitative developmental differences. Liquid chromatography‐tandem mass spectrometry identifies 89 protein spots. Most proteins are metabolism and bioenergetics‐related. Nineteen protein spots are found to be implicated in stress/defence/immunity; 7 in development regulation; 9 in nervous system functions; 4 in the reproductive system; 23 in cytoskeleton and muscle organization; and 4 in movement, flight and other processes. Significant increases in the level of proteins related to structural constitution of the skeleton, stress/defence/immunity, reproduction system, muscles, locomotion and flight are found in adults, consistent with the fact that D. citri is a hemimetabolous insect, whereas proteins involved in developmental regulation are higher in the nymphal stage. The identification of these variably expressed proteins between the nymph and adult stages, linked with the basis of their physiological roles, will lead to a better understanding of the factors influencing development in D. citri and the regulation of some crucial metabolic pathways. It may also help to identify targets for genetic manipulation using RNA interference or other techniques to disrupt Asian citrus psyllid development, lifespan or its ability to transmit CLas.     

Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf‐feeding monkey (Pygathrix nemaeus)

Faecal samples are of great value as a non‐invasive means to gather information on the genetics, distribution, demography, diet and parasite infestation of endangered species. Direct shotgun sequencing of faecal DNA could give information on these simultaneously, but this approach is largely untested. Here, we used two faecal samples to characterize the diet of two red‐shanked doucs langurs (Pygathrix nemaeus) that were fed known foliage, fruits, vegetables and cereals. Illumina HiSeq produced ~74 and 67 million paired reads for these samples, of which ~10 000 (0.014%) and ~44 000 (0.066%), respectively, were of chloroplast origin. Sequences were matched against a database of available chloroplast ‘barcodes’ for angiosperms. The results were compared with ‘metabarcoding’ using PCR amplification of the P6 loop of trnL. Metagenomics identified seven and nine of the likely 16 diet plants while six and five were identified by metabarcoding. Metabarcoding produced thousands of reads consistent with the known diet, but the barcodes were too short to identify several plant species to genus. Metagenomics utilized multiple, longer barcodes that combined had greater power of identification. However, rare diet items were not recovered. Read numbers for diet species in metagenomic and metabarcoding data were correlated, indicating that both are useful for determining relative sequence abundance. Metagenomic reads were uniformly distributed across the chloroplast genomes; thus, if chloroplast genomes were used as reference, the precision of identifications and species recovery would improve further. Metagenomics also recovered the host mitochondrial genome and numerous intestinal parasite sequences in addition to generating data useful for characterizing the microbiome.     

Genetic evidence for multiple events of hybridization between wolves and domestic dogs in the Iberian Peninsula

Hybridization between wild species and their domestic counterparts may represent a major threat to natural populations. However, high genetic similarity between the hybridizing taxa makes the detection of hybrids a difficult task and may hinder attempts to assess the impact of hybridization in conservation biology. In this work, we used a combination of 42 autosomal microsatellites together with Y-chromosome microsatellite-defined haplotypes and mtDNA sequences to investigate the occurrence and dynamics of wolf-dog hybridization in the Iberian Peninsula. To do this, we applied a variety of Bayesian analyses and a parallel set of simulation studies to evaluate (i) the differences between Iberian wolves and dogs, (ii) the frequency and geographical distribution of hybridization and (iii) the directionality of hybridization. First, we show that Iberian wolves and dogs form two well-differentiated genetic entities, suggesting that introgressive hybridization is not a widespread phenomenon shaping both gene pools. Second, we found evidence for the existence of hybridization that is apparently restricted to more peripheral and recently expanded wolf populations. Third, we describe compelling evidence suggesting that the dynamics of hybridization in wolf populations is mediated by crosses between male dogs and female wolves. More importantly, the observation of a population showing the occurrence of a continuum of hybrid classes forming mixed packs may indicate that we have underestimated hybridization. If future studies confirm this pattern, then an intriguing avenue of research is to investigate how introgression from free-ranging domestic dogs is enabling wolf populations to adapt to the highly humanized habitats of southern Europe while still maintaining their genetic differentiation.     

Frequency of hybridization between Ostrinia nubilalis E‐and Z‐pheromone races in regions of sympatry within the United States

Female European corn borer, Ostrinia nubilalis, produce and males respond to sex pheromone blends with either E‐ or Z‐Δ11‐tetradecenyl acetate as the major component. E‐ and Z‐race populations are sympatric in the Eastern United States, Southeastern Canada, and the Mediterranean region of Europe. The E‐ and Z‐pheromone races of O. nubilalis are models for incipient species formation, but hybridization frequencies within natural populations remain obscure due to lack of a high‐throughput phenotyping method. Lassance et al. previously identified a pheromone gland‐expressed fatty‐acyl reductase gene (pgfar) that controls the ratio of Δ11‐tetradecenyl acetate stereoisomers. We identified three single nucleotide polymorphism (SNP) markers within pgfar that are differentially fixed between E‐ and Z‐race females, and that are ≥98.2% correlated with female pheromone ratios measured by gas chromatography. Genotypic data from locations in the United States demonstrated that pgfar‐z alleles were fixed within historically allopatric Z‐pheromone race populations in the Midwest, and that hybrid frequency ranged from 0.00 to 0.42 within 11 sympatric sites where the two races co‐occur in the Eastern United States (mean hybridization frequency or heterozygosity (H_O) = 0.226 ± 0.279). Estimates of hybridization between the E‐ and Z‐races are important for understanding the dynamics involved in maintaining race integrity, and are consistent with previous estimates of low levels of genetic divergence between E‐ and Z‐races and the presence of weak prezygotic mating barriers.     

Genetic evidence for spatio‐temporal changes in the dispersal patterns of two sympatric African colobine monkeys

Western black‐and‐white colobus and Temmink's red colobus are two forest‐dependent African primates with similar ecological requirements, often found in sympatry. Their most striking difference lies in their social system: black‐and‐white colobus live in small groups with mainly male‐mediated dispersal but where females can also disperse, whereas red colobus live in larger groups with males described as philopatric. To investigate whether genetic evidence supports the reported patterns of dispersal based on observational data, we examined eight black‐and‐white and six red colobus social groups from Cantanhez National Park, Guinea‐Bissau. Microsatellite markers revealed a lack of sex‐biased dispersal for black‐and‐white colobus. Gene flow, mainly mediated by females, better explained the genetic patterns found in red colobus, with some evidence for less extensive male dispersal. In contrast to the microsatellite data, low mitochondrial diversity for the black‐and‐white colobus suggests that historical and/or long‐range male‐mediated gene flow might have been favored. In red colobus, the co‐existence of three divergent mitochondrial haplogroups suggests that the Cantanhez population contains a secondary contact zone between divergent lineages that evolved in allopatry. Female‐biased dispersal in this species may be a major factor contributing to the colonization by such differentiated mitochondrial lineages in the region. Overall, we find evidence for a spatio‐temporal change in the dispersal patterns of the colobus monkeys of Cantanhez, with mitochondrial DNA indicating dispersal by mainly a single sex and microsatellite data suggesting that recently both sexes appear to be dispersing within the population. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.     

No evidence for a trade‐off between sperm length and male premating weaponry

Male ornaments and armaments that mediate success in mate acquisition and ejaculate traits influencing competitive fertilization success are under intense sexual selection. However, relative investment in these pre‐ and post‐copulatory traits depends on the relative importance of either selection episode and on the energetic costs and fitness gains of investing in these traits. Theoretical and empirical work has improved our understanding of how precopulatory sexual traits and investments in sperm production covary in this context. It has recently also been suggested that male weapon size may trade off with sperm length as another post‐copulatory sexual trait, but the theoretical framework for this suggestion remains unclear. We evaluated the relationship between precopulatory armaments and sperm length, previously reported in ungulates, in five taxa as well as meta‐analytically. Within and between taxa, we found no evidence for a negative or positive relationship between sperm length and male traits that are important in male–male contest competition. It is important to consider pre‐ and post‐copulatory sexual selection together to understand fitness, and to study investments in different reproductive traits jointly rather than separately. A trade‐off between pre‐ and post‐copulatory sexual traits may not manifest itself in sperm length but rather in sperm number or function. Particularly in large‐bodied taxa such as ungulates, sperm number is more variable interspecifically and likely to be under more intense selection than sperm length. We discuss our and the previous results in this context.     

Oligocene–Neogene fossil history of Asian endemic conifer genera in Japan and Korea

Temporal and spatial changes of ten conifer genera that are endemic to East Asia were analyzed based on fossil data from humid temperate forests in the Japanese Islands and Korean Peninsula to elucidate the phytogeographic history, and to understand differences between those genera eliminated from the Japanese Islands and those that remained extant. All these genera, except for Thujopsis, have existed in the area since the Paleogene and remained in the Japanese islands after initial separation from the continent at the early–middle Miocene. Fossil representatives of locally extinct six genera have tendencies to adapt to wider ranges of climatic conditions than their modern relatives. Metasequoia, Glyptostrobus, and Taiwania began to change their distributions since the late Miocene possibly through habitat partitioning. Keteleeria, Pseudolarix, and Cunninghamia appeared to have expanded their habitat toward warmer conditions during the mid‐Miocene Climatic Optimum and then became restricted to warmer forest vegetation by the end of Pliocene. Overall changes in their distribution can be explained by climatic effects. On the contrary, three genera endemic to Japan (Sciadopitys, Cryptomeria, and Thujopsis) followed clearly different trends from the others. Cryptomeria and Thujopsis were especially adapted to cooler‐temperate climate and they retained their habitat areas in the northern part of Japan. During the late Miocene–Pliocene, the islands connected with the Eurasian continent again, which probably acted as a corridor for warm‐adapted genera to disperse southwest. Current data suggest that ecological requirements of each genus might be essential to determine whether they could survive on the Japanese Islands.     

Genetic evidence for natural hybridization and apparent introgression between freshwater snail species (Viviparus ater and V. contectus)

We examined six allozyme markers and shell morphology to study gene flow between the naturally sympatric freshwater snail species Viviparus ater and V. contectus in Lake Garda, Italy, using offspring from experimental crosses and snails collected from natural populations. Hybrid offspring obtained from experimental crosses and hybrids collected from natural populations were heterozygous at four or five out of five diagnostic loci. Shell morphology was a poor predictor of the hybrid status of individual snails. Backcrossed offspring from experimentally bred hybrids and either of the parental species morphologically resembled the parental species. There was no evidence of segregation distortion at the six loci. Linkage analysis revealed one pair of linked loci (GPI and PNP). These cross experiments indicated a Mendelian type hybrid system in which gene introgression may occur. F₁ hybrids were found at four out of six sampling sites of Lake Garda, Italy. Local frequencies of F₁ hybrids ranged from 0% to 1.6% (estimated average = 0.74%) of the total population including both species. Alleles typical of V. ater were found at low frequencies in V. contectus at all six sampling sites. Alleles typical of V. contectus were found at low frequencies in V. ater at three out of six sampling sites. This is consistent with the hypothesis of introgression in both directions.     

RADseq resolves the phylogeny of Hawaiian Myrsine (Primulaceae) and provides evidence for hybridization

The Hawaiian radiation of Myrsine (primrose family, Primulaceae) is the only one among the ten most species‐rich Hawaiian plant lineages that has never been included in a phylogenetic analysis. Our study is based on a RADseq dataset of nearly all Hawaiian Myrsine species and a Sanger sequencing dataset based on a worldwide sampling of Myrsine and related genera. Myrsine as a whole might be paraphyletic with respect to the monotypic Macaronesian genera Heberdenia and Pleiomeris, whereas Hawaiian Myrsine is resolved as monophyletic. The Sanger sequencing proved to be insufficient to resolve the Hawaiian lineage, whereas RADseq fully resolved the relationships with high support. Hawaiian Myrsine consists of three main lineages, of which one contains the majority of species and is mainly confined to Kauaʻi, and the other two lineages primarily consist of few widespread species. Although phylogenetic reconstructions delivered fully resolved and supported tree topologies, Quartet Sampling and HyDe analyses reveal phylogenetic incongruence throughout the phylogeny and provide the first molecular evidence of extensive hybridization in the lineage.     

Comparative analysis of intrinsic skin aging between Caucasian and Asian subjects by slide‐free in vivo harmonic generation microscopy

Phenotypical and functional differences in the intrinsic skin aging process of individuals between Caucasians and Asians have generated considerable interest in dermatology and cosmetic industry. Most of the studies focused on the stratum corneum, and in some other studies inter‐individual differences overwhelms the racial difference. None of the studies comparatively analyzes the difference from the histopathological point of view. Here we report our harmonic generation microscopy study to analyze the difference of intrinsic aging between Caucasian and Asian skin from a histopathological point of view. As a result, the cellular and nuclear areas of basal cells in Caucasian subjects were found to increase at the same rate as the Asian subjects, ideal for scoring age. The maximum thickness of the viable epidermis, the dermal papilla (DP) volume per unit area and the depth of the DP zone in Caucasians were found to decrease at faster rates than those in Asians.     

Integrative analysis provides multi‐omics evidence for the pathogenesis of placenta percreta

Pernicious placenta previa with placenta percreta (PP) is a catastrophic condition during pregnancy. However, the underlying pathogenesis remains unclear. In the present study, the placental tissues of normal cases and PP tissues of pernicious placenta previa cases were collected to determine the expression profile of protein‐coding genes, miRNAs, and lncRNAs through sequencing. Weighted gene co‐expression network analysis (WGCNA), accompanied by miRNA target prediction and correlation analysis, were employed to select potential hub protein‐coding genes and lncRNAs. The expression levels of selected protein‐coding genes, Wnt5A and MAPK13, were determined by quantitative PCR and immunohistochemical staining, and lncRNA PTCHD1‐AS and PAPPA‐AS1 expression levels were determined by quantitative PCR and fluorescence in situ hybridization. The results indicated that 790 protein‐coding genes, 382 miRNAs, and 541 lncRNAs were dysregulated in PP tissues, compared with normal tissues. WGCNA identified coding genes in the module (ME) black and ME turquoise modules that may be involved in the pathogenesis of PP. The selected potential hub protein‐coding genes, Wnt5A and MAPK13, were down‐regulated in PP tissues, and their expression levels were positively correlated with the expression levels of PTCHD1‐AS and PAPPA‐AS1. Further analysis demonstrated that PTCHD1‐AS and PAPPA‐AS1 regulated Wnt5A and MAPK13 expression by interacting with specific miRNAs. Collectively, our results provided multi‐omics data to better understand the pathogenesis of PP and help identify predictive biomarkers and therapeutic targets for PP.