Molecular phylogeny and trait evolution in an ancient terrestrial arthropod lineage: Systematic revision and implications for ecological divergence (Collembola, Tomocerinae)

The first chromosome-level genome assembly of Entomobrya proxima Folsom, 1924 (Collembola: Entomobryidae)

The Entomobryoidea, the largest superfamily of Collembola, encompasses over 2,000 species in the world. However, the lack of high-quality genomes hinders our understanding of the evolution and ecology of this group. This study presents a chromosome-level genome of Entomobrya proxima by combining PacBio long reads, Illumina short reads, and Hi-C data. The genome has a size of 362.37 Mb, with a scaffold N50 size of 57.67 Mb, and 97.12% (351.95 Mb) of the assembly is located on six chromosomes. The BUSCO analysis of our assembly indicates a completeness of 96.1% (n = 1,013), including 946 (93.4%) single-copy BUSCOs and 27 (2.7%) duplicated BUSCOs. We identified that the genome contains 22.16% (80.06 Mb) repeat elements and 20,988 predicted protein-coding genes. Gene family evolution analysis of E. proxima identified 177 gene families that underwent significant expansions, which were primarily associated with detoxification and metabolism. Moreover, our inter-genomic synteny analysis showed strong chromosomal synteny between E. proxima and Sinella curviseta. Our study provides valuable genomic information for comprehending the evolution and ecology of Collembola.

Mitogenome selection in the evolution of key ecological strategies in the ancient hexapod class Collembola

A longstanding question in evolutionary biology is how natural selection and environmental pressures shape the mitochondrial genomic architectures of organisms. Mitochondria play a pivotal role in cellular respiration and aerobic metabolism, making their genomes functionally highly constrained. Evaluating selective pressures on mitochondrial genes can provide functional and ecological insights into the evolution of organisms. Collembola (springtails) are an ancient hexapod group that includes the oldest terrestrial arthropods in the fossil record, and that are closely associated with soil environments. Of interest is the diversity of habitat stratification preferences (life forms) exhibited by different species within the group. To understand whether signals of positive selection are linked to the evolution of life forms, we analysed 32 published Collembola mitogenomes in a phylomitogenomic framework. We found no evidence that signatures of selection are correlated with the evolution of novel life forms, but rather that mutations have accumulated as a function of time. Our results highlight the importance of nuclear-mitochondrial interactions in the evolution of collembolan life forms and that mitochondrial genomic data should be interpreted with caution, as complex selection signals may complicate evolutionary inferences.

Chromosomal-level genome assembly of the springtail Tomocerus qinae (Collembola: Tomoceridae)

The family Tomoceridae is among the earliest derived collembolan lineages, thus is of key importance in understanding the evolution of Collembola. Here, we assembled a chromosome-level genome of one tomocerid species Tomocerus qinae by combining Nanopore long reads and Hi-C data. The final genome size was 334.44 Mb with the scaffold/contig N50 length of 71.85/13.94 Mb. BUSCO assessment indicated that 96.80% of complete arthropod universal single-copy orthologs (n = 1,013) were present in the assembly. The repeat elements accounted for 26.11% (87.26 Mb) and 494 noncoding RNAs were identified in the genome. A total of 20,451 protein-coding genes were predicted, which captured 96.0% (973) BUSCO genes. Gene family evolution analyses identified 4,825 expanded gene families of T. qinae, among them, 47 experienced significant expansions, and these significantly expanded gene families mainly involved in proliferation and growth. This study provides an important genomic resource for future evolution and comparative genomics analyses of Collembola.

The Coume Ouarnède System, a Hotspot of Subterranean Biodiversity in Pyrenees (France)

Located in Northern Pyrenees, in the Arbas massif, France, the system of the Coume Ouarnède, also known as Réseau Félix Trombe—Henne Morte, is the longest and the most complex cave system of France. The system, developed in massive Mesozoic limestone, has two distinct resurgences. Despite relatively limited sampling, its subterranean fauna is rich, composed of a number of local endemics, terrestrial as well as aquatic, including two remarkable relictual species, Arbasus caecus (Simon, 1911) and Tritomurus falcifer Cassagnau, 1958. With 38 stygobiotic and troglobiotic species recorded so far, the Coume Ouarnède system is the second richest subterranean hotspot in France and the first one in Pyrenees. This species richness is, however, expected to increase because several taxonomic groups, like Ostracoda, as well as important subterranean habitats, like MSS (“Milieu Souterrain Superficiel”), have not been considered so far in inventories. Similar levels of subterranean biodiversity are expected to occur in less-sampled karsts of central and western Pyrenees.

An updated phylogenetic and biogeographic analysis based on genome skimming data reveals convergent evolution of shrubby habit in Clematis in the Pliocene and Pleistocene

Convergent evolution, often viewed as the inevitable outcome of natural selection, has received special attention since the time of Darwin. Clematis is well known for its climbing habit, but it has some shrubby species, known as sect. Fruticella s.l. The shrubby Clematis species are distributed in the dry habitats of Central Asia and adjacent areas showing possible convergent evolution. In this study, we assembled the complete plastome and nuclear ribosomal DNA (nrDNA) sequences of 56 Clematis species, representing most sections and covering most of the shrubby species, to reconstruct their evolutionary histories. Using both maximum likelihood and Bayesian methods, the plastome and nrDNA datasets generated similar, but not identical, phylogenetic relationships, which are better resolved than in previous studies. Then, molecular dating, historical range reconstruction, and character optimization analyses were conducted based on this updated phylogenetic framework. All the morphological characters widely used for taxonomy were shown to have evolved multiple times. Molecular dating inferred that Clematis diverged from its sister in the mid Miocene, and all six major clades of Clematis originated during the late Miocene, with a species radiation during the Pliocene to Pleistocene. The results clearly showed that the shrubby habit evolved independently in four lineages of Clematis in Asia. We also revealed that the shrubby lineages have emerged since the very beginning of Pliocene. Asian monsoon variation in the Pliocene and glacial period fluctuation in the Pleistocene may be the driving forces for the origin and diversification of the shrubby Clematis in Central Asia and adjacent dry areas.