Genomic insights into zokors' phylogeny and speciation in China

Genomic structural variation is associated with hypoxia adaptation in high-altitude zokors

Zokors, an Asiatic group of subterranean rodents, originated in lowlands and colonized high-elevational zones following the uplift of the Qinghai-Tibet plateau about 3.6 million years ago. Zokors live at high elevation in subterranean burrows and experience hypobaric hypoxia, including both hypoxia (low oxygen concentration) and hypercapnia (elevated partial pressure of CO2). Here we report a genomic analysis of six zokor species (genus Eospalax) with different elevational ranges to identify structural variants (deletions and inversions) that may have contributed to high-elevation adaptation. Based on an assembly of a chromosome-level genome of the high-elevation species, Eospalax baileyi, we identified 18 large inversions that distinguished this species from congeners native to lower elevations. Small-scale structural variants in the introns of EGLN1, HIF1A, HSF1 and SFTPD of E. baileyi were associated with the upregulated expression of those genes. A rearrangement on chromosome 1 was associated with altered chromatin accessibility, leading to modified gene expression profiles of key genes involved in the physiological response to hypoxia. Multigene families that underwent copy-number expansions in E. baileyi were enriched for autophagy, HIF1 signalling and immune response. E. baileyi show a significantly larger lung mass than those of other Eospalax species. These findings highlight the key role of structural variants underlying hypoxia adaptation of high-elevation species in Eospalax.

Four new complete mitochondrial genomes of Gobioninae fishes (Teleostei: Cyprinidae) and their phylogenetic implications

The subfamily Gobioninae is one of the most diverse fish groups within Cyprinidae. Their taxonomy and phylogenetic relationships are not completely resolved. In this study, the complete mitochondrial genomes (mitogenome) of four Gobioninae species (Microphysogobio elongatus, Microphysogobio chinssuensis, Gobio rivuloides and Rhinogobio nasutus) were sequenced and compared. The mitogenomes of four species ranges from 16603 bp to 16609 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. Most PCGs had significant codon usage bias. Except for the tRNASer (GCT), all the nucleotide substitutions of tRNA loops higher than the stems could fold into a stable secondary structure. The nucleotide compositions of Gobioninae mitogenome were biased toward A/T, and NAD4 was subjected to low purification selection and had a faster evolution rate among 13 PCGs. Bayesian inference and maximum likelihood phylogenetic analyses showed the consistent results. The four sequenced species clustered together with their congener species. However, more samples and mitogenome data are needed to untangle the phylogenetic relationships among genera Microphysogobio, Romanogobio, Hugobio, Biwia and Platysmacheilus.

Insights into the phylogenetic relationships and species boundaries of the Myricaria squamosa complex (Tamaricaceae) based on the complete chloroplast genome

Myricaria plants are widely distributed in Eurasia and are helpful for windbreak and embankment protection. Current molecular evidence has led to controversy regarding species boundaries within the Myricaria genus and interspecific phylogenetic relationships between three specific species-M. bracteata, M. paniculata and M. squamosa-which have remained unresolved. This study treated these three unresolved taxa as a species complex, named the M. squamosa complex. The genome skimming approach was used to determine 35 complete plastome sequences and nuclear ribosomal DNA sequences for the said complex and other closely related species, followed by de novo assembly. Comparative analyses were conducted across Myricaria to identify the genome size, gene content, repeat type and number, SSR (simple sequence repeat) abundance, and codon usage bias of chloroplast genomes. Tree-based species delimitation results indicated that M. bracteata, M. paniculata and M. squamosa could not be distinguished and formed two monophyletic lineages (P1 and P2) that were clustered together. Compared to plastome-based species delimitation, the standard nuclear DNA barcode had the lowest species resolution, and the standard chloroplast DNA barcode and group-specific barcodes delimitated a maximum of four out of the five species. Plastid phylogenomics analyses indicated that the monophyletic M. squamosa complex is comprised of two evolutionarily significant units: one in the western Tarim Basin and the other in the eastern Qinghai-Tibet Plateau. This finding contradicts previous species discrimination and promotes the urgent need for taxonomic revision of the threatened genus Myricaria. Dense sampling and plastid genomes will be essential in this effort. The super-barcodes and specific barcode candidates outlined in this study will aid in further studies of evolutionary history.

Analysis of the distribution pattern of the ectomycorrhizal fungus Cenococcum geophilum under climate change using the optimized MaxEnt model

Cenococcum geophilum (C. geophilum) is a widely distributed ectomycorrhizal fungus that plays a crucial role in forest ecosystems worldwide. However, the specific ecological factors influencing its global distribution and how climate change will affect its range are still relatively unknown. In this study, we used the MaxEnt model optimized with the kuenm package to simulate changes in the distribution pattern of C. geophilum from the Last Glacial Maximum to the future based on 164 global distribution records and 17 environmental variables and investigated the key environmental factors influencing its distribution. We employed the optimal parameter combination of RM = 4 and FC = QPH, resulting in a highly accurate predictive model. Our study clearly shows that the mean temperature of the coldest quarter and annual precipitation are the key environmental factors influencing the suitable habitats of C. geophilum. Currently, appropriate habitats of C. geophilum are mainly distributed in eastern Asia, west-central Europe, the western seaboard and eastern regions of North America, and southeastern Australia, covering a total area of approximately 36,578,300 km2 globally. During the Last Glacial Maximum and the mid-Holocene, C. geophilum had a much smaller distribution area, being mainly concentrated in the Qinling-Huaihe Line region of China and eastern Peninsular Malaysia. As global warming continues, the future suitable habitat for C. geophilum is projected to shift northward, leading to an expected expansion of the suitable area from 9.21% to 21.02%. This study provides a theoretical foundation for global conservation efforts and biogeographic understanding of C. geophilum, offering new insights into its distribution patterns and evolutionary trends.

Seismic Signaling for Detection of Empty Tunnels in the Plateau Zokor, Eospalax baileyi

There are considerable challenges involved in studying the behavior of subterranean rodents owing to the underground nature of their ecotope. Seismic communication plays a crucial role in the behavior of subterranean rodents, particularly solitary ones. The plateau zokor (Eospalax baileyi), a solitary subterranean rodent species endemic to the Qinghai−Tibet Plateau, will usually occupy empty neighboring tunnels in order to extend their territory. Little is known, however, about the process of territorial occupation or the function of animal communication when occupation is taking place. Based on previous studies of subterranean rodent communication, we hypothesized that plateau zokors use seismic signals to detect neighboring tunnels and then occupy them when it was found their neighbors were absent. To test this, we placed artificial tunnels close to active original zokor tunnels to simulate the availability of an empty neighboring tunnel, and then the seismic signals when a zokor chose to occupy the empty artificial tunnel were recorded. The results showed that the frequency of zokors occupying artificial empty tunnels within 48 h was 7/8, In all of these instances, the zokors generated seismic signals before and after occupation of the empty artificial tunnel. The number of seismic signals generated by the zokors increased significantly (p = 0.024) when they detected and occupied the artificial tunnels, compared to those generated in their original tunnels without the presence of an artificial tunnel alongside. Inside the original tunnels, the inter-pulse time interval of the seismic signals was significantly higher (p < 0.001), the peak frequency of these signals was significantly higher (p < 0.01), and the energy of the signals was significantly lower (p = 0.006), compared with those when an artificial tunnel was positioned next to the original. The results of this study suggest that plateau zokors first generate seismic signals to detect empty neighboring tunnels and that they are empty. In the absence of neighbor plateau zokors, they occupy the empty tunnels to extend their own territory.

Sympatric Speciation in Mole Rats and Wild Barley and Their Genome Repeatome Evolution: A Commentary

The theories of sympatric speciation (SS) and coding and noncoding (cd and ncd =repeatome)  genome function are still contentious. Studies on SS in our two new models, "Evolution Canyon" and "Evolution Plateau", in Israel, divergent microclimatically and geologically-edaphically, respectively, indicated that in ecologically divergent microsites SS is a common speciation model across life from bacteria to mammals. Genomically, the intergenic ncd repeatome was and is still regarded by many biologists as "selfish," "junk," and non-functional. In contrast, it is considered by the encyclopedia of DNA elements discovery as biochemically functional and regulatory, and the transposable elements were considered earlier by Barbara McClintock as "controlling elements" of genes. Remarkably, it is found that repeated elements can statistically identify significantly, the five species of subterranean mole rats of Spalax ehrenbergi superspecies adapted to increasingly arid climatic trend southward in Israel. Moreover, it is first discovered in the SS studies in two distant taxa, subterranean mole rats and wild barley, and later also in spiny mice in Israel and subterranean zokors in China, that the noncoding repeatome is genomically mirroring the image of the protein-coding genome in divergent ecologies. It is shown that this mirroring image is statistically significant both within and between the ecologically divergent taxa supporting the hypothesis that much of the repeatome might be regulatory and selected as the protein-coding genome by the same ecological stresses.

The Complex and Well-Developed Morphological and Histological Structures of the Gastrointestinal Tract of the Plateau Zokor Improve Its Digestive Adaptability to High-Fiber Foods

The morphological and histological traits of the gastrointestinal tract (GIT) enable the animal to perform some specific functions that enhance the species’ adaptability to environments. The plateau zokor (Eospalax baileyi) is a subterranean rodent that mainly forages on plant roots in the Qinghai-Tibet Plateau, but little is known about the mechanism by which the plateau zokor digests roots that have high fiber contents. In this study, we used comparative anatomy methods to compare the morphological and histological traits of the GIT of both the plateau zokor and the plateau pika (Ochotona curzoniae), a small, fossorial lagomorph that forages aboveground plant parts, in order to clarify the traits of the plateau zokor’s GIT and to understand its adaptations to high-fiber foods. The results showed that the foods which plateau zokors eat have a higher fiber content than those which the plateau pikas eat. The plateau zokor has a double-chambered and hemi-glandular stomach (the tubular glands are only in the gastric corpus II, and the gastric fundus is keratinized), whereas the plateau pika has a simple, wholly glandular stomach. The gross morphological indicators (organ index and relative length) of the GIT were significantly lower in the plateau zokor than they were in the plateau pika (p < 0.001). However, the thickness of the gastric corpus II mucosal layer and the gastric fundus muscle layer are significantly higher in the plateau zokor than they are in the plateau pika (p < 0.001), and the thickness of each layer of intestinal tissue is higher in the plateau zokor than it is in the plateau pika. Additionally, the small intestinal villi also are higher and wider in the plateau zokor than they are in the plateau pika. Our results suggest that instead of adapting to digest the high-fiber diet by expanding the size of the GIT, the plateau zokor has evolved a complex stomach and a well-developed gastrointestinal histological structure, and that these specialized GIT structures are consistent with an optimal energy-economy evolutionary adaptation strategy.