Genetic structure and demographic history of the endangered and endemic schizothoracine fish Gymnodiptychus pachycheilus in Qinghai-Tibetan Plateau.

The endangered schizothoracine fish Gymnodiptychus pachycheilus is endemic to the Qinghai-Tibetan Plateau (QTP), but very little genetic information is available for this species. Here, we accessed the current genetic divergence of G. pachycheilus population to evaluate their distributions modulated by contemporary and historical processes. Population structure and demographic history were assessed by analyzing 1811-base pairs of mitochondrial DNA from 61 individuals across a large proportion of its geographic range. Our results revealed low nucleotide diversity, suggesting severe historical bottleneck events. Analyses of molecular variance and the conventional population statistic FST (0.0435, P = 0.0215) confirmed weak genetic structure. The monophyly of G. pachycheilus was statistically well-supported, while two divergent evolutionary clusters were identified by phylogenetic analyses, suggesting a microgeographic population structure. The consistent scenario of recent population expansion of two clusters was identified based on several complementary analyses of demographic history (0.096 Ma and 0.15 Ma). This genetic divergence and evolutionary process are likely to have resulted from a series of drainage arrangements triggered by the historical tectonic events of the region. The results obtained here provide the first insights into the evolutionary history and genetic status of this little-known fish.

The complete mitochondrial genome of Gobio huanghensis (Cypriniformes: Cyprinidae) in the Yellow River, China.

Gobio huanghensis, a member of the eponymous genus within the Cyprinidae, family of the Cypriniformes order, is an endemic fish species found exclusively in the upper reaches of the Yellow River, spanning from Yinchuan to Lanzhou. This study presents the first comprehensive report of the complete mitochondrial genome sequence of G. huanghensis, encompassing 16,604 base pairs (bp) with a nucleotide composition of 26.3% cytosine (C), 17.6% guanine (G), 29.4% adenine (A), and 26.7% thymine (T). In congruence with other species in the Gobio genus, its mitochondrial genome comprises 37 genes, including two ribosomal RNA genes, 13 protein-coding genes (PCGs), and 22 transfer RNA genes. Notably, COX1 initiates with the start codon GTG, distinct from the typical ATG start codon of other PCGs. The mitogenome exhibits four types of stop codons: TAA, TAG, TA-, and T--. Phylogenetic analyses, grounded in complete mitochondrial sequences, position G. huanghensis at the forefront of one of two major clusters within the genus Gobio, corroborating existing morphological classifications. These findings offer valuable theoretical insights for the taxonomic classification, conservation, and population genetics of G. huanghensis.

Unrecognized diversity, genetic structuring, and phylogeography of the genus Triplophysa (Cypriniformes: Nemacheilidae) sheds light on two opposite colonization routes during Quaternary glaciation that occurred in the Qilian Mountains.

In recent years, the influence of historical geological and climatic events on the evolution of flora and fauna in the Tibetan Plateau has been a hot research topic. The Qilian Mountain region is one of the most important sources of biodiversity on the Qinghai-Tibet Plateau. Many species existed in the region during the Pleistocene glacial oscillation, and the complex geographical environment provided suitable conditions for the survival of local species. The shrinkage, expansion, and transfer of the distribution range and population size of species have significant effects on genetic diversity and intraspecific differentiation. To reveal the effects of geological uplift and climate oscillation on the evolution of fish populations in the Qilian Mountains, we investigated the genetic structure, phylogenetic relationship, and phylogeographical characteristics of genus Triplophysa species in the Qilian Mountains using the mitochondrial DNA gene (COI), three nuclear genes (RAG1, sRH, and Myh6) and 11 pairs of nuclear microsatellite markers. We collected 11 species of genus Triplophysa living in the Qilian Mountains, among which Triplophysa hsutschouensis and Triplophysa papillosolabiata are widely distributed in the rivers on the northern slope of the Qilian Mountains. There was a high degree of lineage differentiation among species, and the genetic diversity of endemic species was low. The different geographical groups of T. papillosolabiata presented some allogeneic adaptation and differentiation, which was closely related to the changes in the river system. Except for the population expansion event of T. hsutschouensis during the last glacial period of the Qinghai-Tibet Plateau (0.025 MYA), the population sizes of other plateau loach species remained stable without significant population expansion. Starting from the east and west sides of the Qilian Mountains, T. hsutschouensis, and T. papillosolabiata showed two species colonization routes in opposite directions. The geological events of the uplift of the Qinghai-Tibet Plateau and the climatic oscillation of the Quaternary glaciation had a great influence on the genetic structure of the plateau loach in the Qilian Mountains, which promoted the genetic differentiation of the plateau loach and formed some unique new species. The results of this study have important guiding significance for fish habitat protection in the Qilian Mountains.

The complete mitochondrial genome sequence and phylogenetic position of Gobio coriparoides.

In this paper, we determined the complete mitochondrial DNA (mtDNA) sequence of Gobio coriparoides and analyzed its phylogenetic position. The complete mitogenome is 16,604 bp in length. It consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. Among the 37 genes, 28 were encoded on the heavy strand, while 9 were encoded on the light strand. The overall base composition was 28.97% for A, 18.06% for G, 26.54% for T, and 26.43% for C, with a higher A + T content (55.51%). There are some overlaps existing in G. coriparoides mitochondrial genome. The neighbor-joining (NJ) phylogenetic tree based on whole mitogenome sequences supported that G. coriparoides is the closest to G. cynocephalus. This result will provide a basic reference for understanding the genetic structure, molecular evolution, and phylogeny of G. coriparoides and related species.

Expression-Invariant Age Estimation Using Structured Learning.

In this paper, we investigate and exploit the influence of facial expressions on automatic age estimation. Different from existing approaches, our method jointly learns the age and expression by introducing a new graphical model with a latent layer between the age/expression labels and the features. This layer aims to learn the relationship between the age and expression and captures the face changes which induce the aging and expression appearance, and thus obtaining expression-invariant age estimation. Conducted on three age-expression datasets (FACES , Lifespan and NEMO ), our experiments illustrate the improvement in performance when the age is jointly learnt with expression in comparison to expression-independent age estimation. The age estimation error is reduced by 14.43, 37.75 and 9.30 percent for the FACES, Lifespan and NEMO datasets respectively. The results obtained by our graphical model, without prior-knowledge of the expressions of the tested faces, are better than the best reported ones for all datasets. The flexibility of the proposed model to include more cues is explored by incorporating gender together with age and expression. The results show performance improvements for all cues.

Learning to Recognize Human Activities Using Soft Labels.

Human activity recognition system is of great importance in robot-care scenarios. Typically, training such a system requires activity labels to be both completely and accurately annotated. In this paper, we go beyond such restriction and propose a learning method that allow labels to be incomplete and uncertain. We introduce the idea of soft labels which allows annotators to assign multiple, and weighted labels to data segments. This is very useful in many situations, e.g., when the labels are uncertain, when part of the labels are missing, or when multiple annotators assign inconsistent labels. We formulate the activity recognition task as a sequential labeling problem. Latent variables are embedded in the model in order to exploit sub-level semantics for better estimation. We propose a max-margin framework which incorporate soft labels for learning the model parameters. The model is evaluated on two challenging datasets. To simulate the uncertainty in data annotation, we randomly change the labels for transition segments. The results show significant improvement over the state-of-the-art approach.

Characterization of the complete mitochondrial genome of Gymnocypris chilianensis (Teleostei: Cypriniformes: Cyprinidae).

The complete mitochondrial DNA sequence of Gymnocypris chilianensis was determined and analyzed. The mitogenome of G. chilianensis is 16,667 bp long, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The gene order of mitogenome is identical to that observed in most other vertebrates. The complete mitogenome sequence information of G. chilianensis can provide useful data for further studies on molecular systematic, taxonomic status, stock evaluation and conservation genetics.

Sequence and organization of the complete mitochondrial genome of Schizothorax davidi (Teleostei: Cypriniformes: Cyprinidae).

In this study, we determined the complete mitochondrial genome sequence of Schizothorax davidi. The length of the genome is 16,577 bp, which contains 13 protein coding genes, 22 transfer RNAs, two ribosomal RNAs, and two non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The complete mitochondrial DNA sequence of S. davidi provides useful genetic markers for the studies on molecular systematic, population genetics, and phylogeography.

Extracting 3D layout from a single image using global image structures.

Extracting the pixel-level 3D layout from a single image is important for different applications, such as object localization, image, and video categorization. Traditionally, the 3D layout is derived by solving a pixel-level classification problem. However, the image-level 3D structure can be very beneficial for extracting pixel-level 3D layout since it implies the way how pixels in the image are organized. In this paper, we propose an approach that first predicts the global image structure, and then we use the global structure for fine-grained pixel-level 3D layout extraction. In particular, image features are extracted based on multiple layout templates. We then learn a discriminative model for classifying the global layout at the image-level. Using latent variables, we implicitly model the sublevel semantics of the image, which enrich the expressiveness of our model. After the image-level structure is obtained, it is used as the prior knowledge to infer pixel-wise 3D layout. Experiments show that the results of our model outperform the state-of-the-art methods by 11.7% for 3D structure classification. Moreover, we show that employing the 3D structure prior information yields accurate 3D scene layout segmentation.