Sampling Strategy and Potential Utility of Indels for DNA Barcoding of Closely Related Plant Species:A Case Study in Taxus

Although DNA barcoding has become a useful tool for species identification and biodiversity surveys in plant sciences, there remains little consensus concerning appropriate sampling strategies and the treatment of indels. To address these two issues, we sampled 39 populations for nine Taxus species across their entire ranges, with two to three individuals per population randomly sampled. We sequenced one core DNA barcode (matK) and three supplementary regions (trnH-psbA, trnL-trnF and ITS) for all samples to test the effects of sampling design and the utility of indels. Our results suggested that increasing sampling within-population did not change the clustering of individuals, and that meant within-population P-distances were zero for most populations in all regions. Based on the markers tested here, comparison of methods either including or excluding indels indicated that discrimination and nodal support of monophyletic groups were significantly increased when indels were included. Thus we concluded that one individual per population was adequate to represent the within-population variation in these species for DNA barcoding, and that intra-specific sampling was best focused on representing the entire ranges of certain taxa. We also found that indels occurring in the chloroplast trnL-trnF and trnH-psbA regions were informative to differentiate among for closely related taxa barcoding, and we proposed that indel-coding methods should be considered for use in future for closed related plant species DNA barcoding projects on or below generic level

Using <i>Mid</i>dRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species

Microsatellites are highly polymorphic markers which have been used in a wide range of genetic studies. In recent years, various sources of next-generation sequencing data have been used to develop new microsatellite loci, but compared with the more common shotgun genomic sequencing or transcriptome data, the potential utility of RAD-seq data for microsatellite ascertainment is comparatively under-used. In this study, we employed MiddRAD-seq data to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. Of 8,823,053 clean reads generated for ten individuals of a population, 94,851 (?1%) contained microsatellite motifs. These corresponded to 2,993 unique loci, of which 526 (?18%) exhibited polymorphism. Of which, 237 were suitable for designing microsatellite primer pairs, and 128 loci were randomly selected for PCR validation and microsatellite screening. Out of the 128 primer pairs, 16 loci gave clear, reproducible patterns, and were then screened and characterized in 24 individuals from two populations. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD dataauthorsversionPeer reviewe

DialCoT Meets PPO: Decomposing and Exploring Reasoning Paths in Smaller Language Models

Chain-of-Thought (CoT) prompting has proven to be effective in enhancing the reasoning capabilities of Large Language Models (LLMs) with at least 100 billion parameters. However, it is ineffective or even detrimental when applied to reasoning tasks in Smaller Language Models (SLMs) with less than 10 billion parameters. To address this limitation, we introduce Dialogue-guided Chain-of-Thought (DialCoT) which employs a dialogue format to generate intermediate reasoning steps, guiding the model toward the final answer. Additionally, we optimize the model's reasoning path selection using the Proximal Policy Optimization (PPO) algorithm, further enhancing its reasoning capabilities. Our method offers several advantages compared to previous approaches. Firstly, we transform the process of solving complex reasoning questions by breaking them down into a series of simpler sub-questions, significantly reducing the task difficulty and making it more suitable for SLMs. Secondly, we optimize the model's reasoning path selection through the PPO algorithm. We conduct comprehensive experiments on four arithmetic reasoning datasets, demonstrating that our method achieves significant performance improvements compared to state-of-the-art competitors.Comment: Accepted to EMNLP 202

Amentotaxus × hybridia (Taxaceae), a new natural Amentotaxus hybrid from southeast Yunnan province, China

During floristic surveys of Taxaceae in Hekou County, Yunnan Province, China, a putative natural hybrid between A. yunnanensis H.L. Li and A. hekouensis L.M. Gao was collected. Morphological and molecular evidence confirms its status as a natural hybrid. Amentotaxus × hybridia L.M. Gao has linear or linear-lanceolate leaves 6–13 cm × 1.0–1.5 cm, white stomatal bands with 34–40 rows on abaxial side, 2.5–3.5 mm, slightly wider than leaf margins; 3–6 seeds borne at the base of the branchlet, peduncle 1.3–1.6 cm long with 3–4 rows of persistent basal bracts

Biogeographic history of the pantropical family Gesneriaceae with a focus on the Indian plate and diversification through the Old World

The Gesneriaceae consists of around 150 genera and c. 3750 species with a predominantly tropical and subtropical distribution across all continents. Although previous studies have proposed an American origin of Gesneriaceae, the biogeographic history of this pantropical plant family is still unclear, particularly in the Old World. To address this, we assembled the most comprehensively sampled matrix of Gesneriaceae with 143 Gesneriaceae genera and 355 species, including key samples from Sri Lanka analysed here for the first time. We generated molecular phylogenies based on four plastid gene regions (ndhF, matK, rps16 and trnL-F), obtained fossil-calibrated trees, and reconstructed ancestral areas and dispersal routes using Bayesian methods. Our results confirm the origin for the family in the Early Palaeocene (67. Ma) in the region of present-day Central America &amp; Andean South America, and that diversity in the Old World originated from a long-distance dispersal event from South America around 59 Ma, most likely to the Indian plate, which was an island at the time. This lineage then dispersed to Malesia and later East Asia, which would ultimately become a major centre of diversity and source of many dispersals to other regions. Our results thus highlight the Indian plate as a likely key player in the early diversification of Old World Gesneriaceae, even though it is now more diverse elsewhere, and hence offer novel insights into this plant family’s dispersal routes and areas of diversification in the Old World

The Ras Superfamily of Small GTPases in Non-neoplastic Cerebral Diseases

The small GTPases from the Ras superfamily play crucial roles in basic cellular processes during practically the entire process of neurodevelopment, including neurogenesis, differentiation, gene expression, membrane and protein traffic, vesicular trafficking, and synaptic plasticity. Small GTPases are key signal transducing enzymes that link extracellular cues to the neuronal responses required for the construction of neuronal networks, as well as for synaptic function and plasticity. Different subfamilies of small GTPases have been linked to a number of non-neoplastic cerebral diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), intellectual disability, epilepsy, drug addiction, Huntington’s disease (HD), amyotrophic lateral sclerosis (ALS) and a large number of idiopathic cerebral diseases. Here, we attempted to make a clearer illustration of the relationship between Ras superfamily GTPases and non-neoplastic cerebral diseases, as well as their roles in the neural system. In future studies, potential treatments for non-neoplastic cerebral diseases which are based on small GTPase related signaling pathways should be explored further. In this paper, we review all the available literature in support of this possibility

Determinants of genetic structure in a highly heterogeneous landscape in southwest China

Intra-specific genetic diversity is a fundamental component of biodiversity, and is key to species adaptation and persistence. However, significant knowledge gaps still exist in our understanding of the patterns of genetic diversity and their key determinants. Most previous investigations mainly utilized single-species and/or a limited number of explanatory variables; so here we mapped the patterns of plastid genetic diversity within 15 plant species, and explored the key determinants shaping these patterns using a wide range of variables. Population-level cpDNA sequence data for 15 plant species from the Longitudinal Range Gorge Region (LRGR), southwest China, were retrieved from literature and used to estimate haplotype diversity (H(D)) and population pairwise genetic differentiation (F(ST)) indices. Genetic diversity and divergence landscape surfaces were then generated based on the H(D) and F(ST), respectively, to clarify the patterns of genetic structure in the region. Subsequently, we analyzed the relationships between plastid genetic diversity and 16 explanatory variables (classified as anthropogenic, climatic, and topographic). We found that the highest genetic diversity occurred in the Yulong Mountain region, with a significant proportion (~74.81%) of the high diversity land area being located outside of protected areas. The highest genetic divergence was observed approximately along the 25°N latitudinal line, with notable peaks in the western and eastern edges of the LRGR. Genetic diversity (H(D)) was weakly but significantly positively correlated with both Latitude (lat) and Annual Mean Wet Day Frequency (wet), yet significantly negatively correlated with all of Longitude (long), Annual Mean Cloud Cover Percent (cld), Annual Mean Anthropogenic Flux (ahf), and Human Footprint Index (hfp). A combination of climatic, topographic, and anthropogenic factors explained a significant proportion (78%) of genetic variation, with topographic factors (lat and long) being the best predictors. Our analysis identified areas of high genetic diversity (genetic diversity “hotspots”) and divergence in the region, and these should be prioritized for conservation. This study contributes to a better understanding of the features that shape the distribution of plastid genetic diversity in the LRGR and thus would inform conservation management efforts in this species-rich, but vulnerable region