Local origin or external input: modern horse origin in East Asia.

BACKGROUND: Despite decades of research, the horse domestication scenario in East Asia remains poorly understood. RESULTS: The study identified 16 haplogroups with fine-scale phylogenetic resolution using mitochondrial genomes of 317 horse samples. The time to the most recent common ancestor of the 16 haplogroups ranges from [0.8-3.1] thousand years ago (KYA) to [7.9-27.1] KYA. With combined analyses of the mitochondrial control region for 35 extant Przewalski's horses, 3544 modern and 203 ancient horses across the world, researchers provide evidence for that East Asian prevalent haplogroups Q and R were indigenously domesticated or they were involved in numerous distinct genetic components from wild horses in the southern part of East Asia. These events of haplotypes Q and R occurred during 4.7 to 16.3 KYA and 2.1 to 11.5 KYA, respectively. The diffusion of preponderant European haplogroups L from west to East Asia is consistent with the external gene input. Furthermore, genetic differences were detected between northern East Asia and southern East Asia cohorts by Principal Component Analysis, Analysis of Molecular Variance test, the χ2 test and phylogeographic analyses. CONCLUSIONS: All results suggest a complex picture of horse domestication, as well as geographic pattern in East Asia. Both local origin and external input occurred in East Asia horse populations. And besides, there are at least two different domestication or hybridization centers in East Asia.

Microscopic and Submicroscopic Gradient Variation of Olfactory Systems among Six Sinocyclocheilus Species Living in Different Environments.

The fish genus Sinocyclocheilus contains many different species that inhabit diverse natural environments, such as surface water layer, cave, or intermediate. As a result of these different habitats there are some differences in their sensory systems. Microscopic and submicroscopic structures of olfactory systems in six representative species of Sinocyclocheilus were studied, including one surface-dwelling species (S. grahami), two intermediate species (S. jii and S. macrophthalmus) and three cave-dwelling species (S. brevibarbatus, S. anshuiensis, and S. tianlinensis). Due to adaptive evolution under extreme environmental conditions, cave-dwelling species have more developed olfactory systems. We observed that, compared with surface-dwelling species, the olfactory sac of the cave-dwelling Sinocyclocheilus species has the following characteristics: higher density of cilia, greater length of sensory cilia, many other special structures (micro-ridge, olfactory islet, rod cilia). These results reveal different levels of olfactory system development, consistent with the view that that cave-dwelling species have more developed olfactory systems than intermediate and surface-dwelling species.

Effects of multiple N, P, and K fertilizer combinations on strawberry growth and the microbial community.

Nitrogen (N), phosphorus (P), and potassium (K) exert various effects on strawberry (Fragaria ananassa Duchesne) yields. In this study, we employed an orthogonal experimental design (T1-T9) with three fertilization treatments (N, P, and K) at three levels to identify an optimal fertilization scheme for strawberry cultivation. The effects of fertilizer combinations the rhizosphere soil microbial community were also explored by using bacterial full-length 16S rRNA and fungal ITS (internal transcribed spacer) sequencing (30 samples for each analysis). The results showed that the average plant height and leaf area of the fertilized groups were 24.6% and 41.6% higher than those of the non-fertilized group (T0). After 60 d of planting, the sucrase activity in the T6 group increased by 76.67% compared to the T0 group, with phosphate fertilizer exerting a more significant impact on sucrase activity. The T6 treatment group had the highest alpha diversity index among bacterial and fungal microorganisms, and had a different microbial community structure compared with the control group. The most abundant bacterial taxa in the strawberry rhizosphere soil were Proteobacteria, Bacteroidota, and Acidobacteriota, and the most abundant fungal phyla were Monoblepharomycota, Glomeromycota, and Mucoromycota. Application of the optimal combined fertilizer treatment (T6) significantly increased the abundance of Proteobacteria and altered the abundance of Gemmatimonas compared to other treatment groups. Notably, Gemmatimonas abundance positively correlated with strawberry plant height and soil N, P, and K levels. These findings indicated that the relative abundance of beneficial bacteria could be enhanced by the application of an optimal fertilizer ratio, ultimately improving strawberry agronomic traits.

Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences.

Molecular studies on donkey mitochondrial sequences have clearly defined two distinct maternal lineages involved in domestication. However, domestication histories of these two lineages remain enigmatic. We therefore compared several population characteristics between these two lineages based on global sampling, which included 171 sequences obtained in this study (including Middle Asian, East Asian, and African samples) plus 536 published sequences (including European, Asian, and African samples). The two lineages were clearly separated from each other based on whole mitochondrial genomes and partial non-coding displacement loop (D-loop) sequences, respectively. The Clade I lineage experienced an increase in population size more than 8 000 years ago and shows a complex haplotype network. In contrast, the population size of the Clade II lineage has remained relatively constant, with a simpler haplotype network. Although the distribution of the two lineages was almost equal across the Eurasian mainland, they still presented discernible but complex geographic bias in most parts of Africa, which are known as their domestication sites. Donkeys from sub-Saharan Africa tended to descend from the Clade I lineage, whereas the Clade II lineage was dominant along the East and North coasts of Africa. Furthermore, the migration routes inferred from diversity decay suggested different expansion across China between the two lineages. Altogether, these differences indicated non-simultaneous domestication of the two lineages, which was possibly influenced by the response of pastoralists to the desertification of the Sahara and by the social expansion and trade of ancient humans in Northeast Africa, respectively.

Comparative transcriptomic analysis reveals the mechanism of leech environmental adaptation.

The medicinal leeches have been widely utilized in medical procedures for thousands of years. Recently, there were more and more transcriptomes of leech published online including the medicinal leech (Hirudo medicinalis) and some other leeches. However, leech's genetic backgrounds are still largely unknown. In this report, transcriptomes of three phylogenetically close leeches (Poecilobdella javanica, Whitmania pigra, and Haemadipsa cavatuses) were established by RNA-seq technique for studying their genetic mechanisms of environmental adaption. Over 110 million high-quality reads were generated and assembled into unique transcriptome (reads = 200 bp). 27,138 out of de novo assembled transcripts (41.77%) were assigned to one or more GO terms. Additionally, the transcripts were detected in 217 predicted KEGG pathways. The enriched genes were involved in protein metabolism, GPCRs and pathogen-resistant pathways. The results showed that the great variations existed in gene expression of olfactory transduction pathway among three leech species. The comparisons of leech species hinted at the underlying mechanism of leeches adapting well in various environments. Our study will provide useful rationales for future studies of leeches and other annelid species.

The complete mitochondrial genome sequence of Sinocyclocheilus jii (Cypriniformes: Cyprinidae) and phylogenetic implications.

In this study, we first determined the complete mitochondrial genome sequence of Sinocyclocheilus jii, which is an endemic species to Southwestern China. The complete mitochondrial genome is 16,577 bp in length, consisting of 37 genes coding for 13 proteins, two rRNAs, 22 tRNAs, and one control region. Its gene arrangement pattern was identical to that of most vertebrates. Phylogenetic analysis using mitochondrial genomes of 11 species showed that nine Sinocyclocheilus species clustered as one monophyletic clade and S. jii was the most basal species on the phylogenetic tree of the Sinocyclocheilus fishes.

DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals.

Mitochondrial DNA (mtDNA) is widely used in various genetic studies of domesticated animals. Many applications require comprehensive knowledge about the phylogeny of mtDNA variants. Herein, we provide the most up-to-date mtDNA phylogeny (i.e. haplogroup tree or matrilineal genealogy) and a standardized hierarchical haplogroup nomenclature system for domesticated cattle, dogs, goats, horses, pigs, sheep, yaks and chickens. These high-resolution mtDNA haplogroup trees based on 1240 complete or near-complete mtDNA genome sequences are available in open resource DomeTree (http://www.dometree.org). In addition, we offer the software MitoToolPy (http://www.mitotool.org/mp.html) to facilitate the mtDNA data analyses. We will continuously and regularly update DomeTree and MitoToolPy.

Dispersal of the Japanese pine sawyer, Monochamus alternatus (Coleoptera: Cerambycidae), in mainland China as inferred from molecular data and associations to indices of human activity.

The Japanese pine sawyer, Monochamus alternatus Hope (Coleoptera: Cerambycidae), is an important forest pest as well as the principal vector of the pinewood nematode (PWN), Bursaphelenchus xylophilus (Steiner et Buhrer), in mainland China. Despite the economic importance of this insect-disease complex, only a few studies are available on the population genetic structure of M. alternatus and the relationship between its historic dispersal pattern and various human activities. The aim of the present study was to further explore aspects of human activity on the population genetic structure of M. alternatus in mainland China. The molecular data based on the combined mitochondrial cox1 and cox2 gene fragments from 140 individuals representing 14 Chinese populations yielded 54 haplotypes. Overall, a historical (natural) expansion that originated from China's eastern coast to the western interior was revealed by the haplotype network, as well as several recent, long-distant population exchanges. Correlation analysis suggested that regional economic status and proximity to marine ports significantly influenced the population genetic structure of M. alternatus as indicated by both the ratio of shared haplotypes and the haplotype diversity, however, the PWN distribution in China was significantly correlated with only the ratio of shared haplotypes. Our results suggested that the modern logistical network (i.e., the transportation system) in China is a key medium by which humans have brought about population exchange of M. alternatus in mainland China, likely through inadvertent movement of infested wood packaging material associated with trade, and that this genetic exchange was primarily from the economically well-developed east coast of China, westward, to the less-developed interior. In addition, this study demonstrated the existence of non-local M. alternatus in new PWN-infested localities in China, but not all sites with non-local M. alternatus were infested with PWN.

[Progress on the degeneration mechanism of cave fishes' eyes].

Attempts to understand the degeneration of the eyes in cave fish has largely been explained by either various extents of gradual degeneration, ranging from partial to total loss, observed in various species or by acceleration of loss caused by dark environments. However, neither the theory of biological evolution developed by Charles Darwin nor the neutral theory of molecular evolution formulated by Kimura Motoo adequately explains these phenomena. Recent trends in utilizing multidisciplinary research, however, have yielded better results, helping reveal a more complex picture of the mechanisms of degeneration. Here, we summarize the current progress of the research via morphology and anatomy, development biology, animal behavior science and molecular genetics, and offer some perspectives on the ongoing research into the development and degeneration of eyes in cave fish.