Convergent patterns of gene expression and protein evolution associated with adaptation to desert environments in rodents

Desert specialization has arisen multiple times across rodents and is often associated with a suite of convergent phenotypes, including modification of the kidneys to mitigate water loss. However, the extent to which phenotypic convergence in desert rodents is mirrored at the molecular level is unknown. Here, we sequenced kidney mRNA and assembled transcriptomes for three pairs of rodent species to search for convergence in gene expression and amino acid sequence associated with adaptation to deserts. We conducted phylogenetically-independent comparisons between a desert specialist and a non-desert relative in three families representing ∼70 million years of evolution. Overall, patterns of gene expression faithfully recapitulated the phylogeny of these six taxa. However, we found that 8.6% of all genes showed convergent patterns of expression evolution between desert and non-desert taxa, a proportion that is much higher than expected by chance. In addition to these convergent changes, we observed many species-pair specific changes in gene expression indicating that different instances of adaptation to deserts include a combination of unique and shared changes. Patterns of protein evolution revealed a small number of genes showing evidence of positive selection, the majority of which did not show convergent changes in gene expression. Overall, our results suggest convergent changes in gene regulation play a primary role in the complex trait of desert adaptation in rodents.

Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics

Lichens are symbiotic associations resulting from interactions among fungi (primary and secondary mycobionts), algae and/or cyanobacteria (primary and secondary photobionts), and specific elements of the bacterial microbiome associated with the lichen thallus. The question of what is a species, both concerning the lichen as a whole and its main fungal component, the primary mycobiont, has faced many challenges throughout history and has reached new dimensions with the advent of molecular phylogenetics and phylogenomics. In this paper, we briefly revise the definition of lichens and the scientific and vernacular naming conventions, concluding that the scientific, Latinized name usually associated with lichens invariably refers to the primary mycobiont, whereas the vernacular name encompasses the entire lichen. Although the same lichen mycobiont may produce different phenotypes when associating with different photobionts or growing in axenic culture, this discrete variation does not warrant the application of different scientific names, but must follow the principle "one fungus = one name". Instead, broadly agreed informal designations should be used for such discrete morphologies, such as chloromorph and cyanomorph for lichens formed by the same mycobiont but with either green algae or cyanobacteria. The taxonomic recognition of species in lichen-forming fungi is not different from other fungi and conceptual and nomenclatural approaches follow the same principles. We identify a number of current challenges and provide recommendations to address these. Species delimitation in lichen-forming fungi should not be tailored to particular species concepts but instead be derived from empirical evidence, applying one or several of the following principles in what we call the LPR approach: lineage (L) coherence vs. divergence (phylogenetic component), phenotype (P) coherence vs. divergence (morphological component), and/or reproductive (R) compatibility vs. isolation (biological component). Species hypotheses can be established based on either L or P, then using either P or L (plus R) to corroborate them. The reliability of species hypotheses depends not only on the nature and number of characters but also on the context: the closer the relationship and/or similarity between species, the higher the number of characters and/or specimens that should be analyzed to provide reliable delimitations. Alpha taxonomy should follow scientific evidence and an evolutionary framework but should also offer alternative practical solutions, as long as these are scientifically defendable. Taxa that are delimited phylogenetically but not readily identifiable in the field, or are genuinely cryptic, should not be rejected due to the inaccessibility of proper tools. Instead, they can be provisionally treated as undifferentiated complexes for purposes that do not require precise determinations. The application of infraspecific (gamma) taxonomy should be restricted to cases where there is a biological rationale, i.e., lineages of a species complex that show limited phylogenetic divergence but no evidence of reproductive isolation. Gamma taxonomy should not be used to denote discrete phenotypical variation or ecotypes not warranting the distinction at species level. We revise the species pair concept in lichen-forming fungi, which recognizes sexually and asexually reproducing morphs with the same underlying phenotype as different species. We conclude that in most cases this concept does not hold, but the actual situation is complex and not necessarily correlated with reproductive strategy. In cases where no molecular data are available or where single or multi-marker approaches do not provide resolution, we recommend maintaining species pairs until molecular or phylogenomic data are available. This recommendation is based on the example of the species pair Usnea aurantiacoatra vs. U. antarctica, which can only be resolved with phylogenomic approaches, such as microsatellites or RADseq. Overall, we consider that species delimitation in lichen-forming fungi has advanced dramatically over the past three decades, resulting in a solid framework, but that empirical evidence is still missing for many taxa. Therefore, while phylogenomic approaches focusing on particular examples will be increasingly employed to resolve difficult species complexes, broad screening using single barcoding markers will aid in placing as many taxa as possible into a molecular matrix. We provide a practical protocol how to assess and formally treat taxonomic novelties. While this paper focuses on lichen fungi, many of the aspects discussed herein apply generally to fungal taxonomy. The new combination Arthonia minor (Lücking) Lücking comb. et stat. nov. (Bas.: Arthonia cyanea f. minor Lücking) is proposed.

The larva of Sericostoma galeatum Rambur 1842 (Trichoptera: Sericostomatidae), based on French material

The present paper describes the previously unknown larva of Sericostoma galeatum based on French material. Information on the morphology of the larva is given, and the most important morphological characters are illustrated. Sericostoma galeatum is very close to the S. personatum / S. flavicorne species pair and cannot be separated yet from those confusing congeners. With respect to the distribution, S. galeatum is confined to the French, Italian, and Swiss western Alps and the Apennines. In addition, ecological information is provided.

Contribution to the bryoflora of Australia, V. Radula tonitrua sp. nov. from Queensland

Study of two recognised geographic lineages within Radula novae-hollandiae sens. lat. have resulted in the detection of morphological differences between individuals from the Queensland Wet Tropics, and those from New South Wales. Individuals from the Wet Tropics have perianths that are shorter at maturity (1.6–2.0 v. 3.8–4.4 mm), leaf lobes that usually bear numerous marginal gemmae, and leaf-lobules that are smaller and more quadrate. The morphological differences, particularly in perianth length, were not fully appreciated previously and provide evidence supporting the recognition of the Queensland Wet Tropics lineage as a distinct and new species, Radula tonitrua, which is here described. The degree of phylogenetic divergence and fixed molecular difference between R. tonitrua and R. novae-hollandiae, are comparable with the separation observed between R. ocellata and R. pulchella, another species pair exhibiting the same geographic disjunction.

Usnea nipparensis and U. sinensis form a ‘species pair ’ presuming morphological, chemical and molecular phylogenetic data

Phylogenetic relationships between Usnea nipparensis and U. sinensis, caperatic acid containing Usnea species, were examined based on ITS rDNA, and the phylogenetic position of U. nipparensis was inferred based on multi-locus gene analysis using ITS rDNA, nuLSU, and MCM7. Although U. nipparensis and U. sinensis have a sorediate and an esorediate shrubby thallus, respectively, and in general look quite different, other detailed morphological and chemical features are similar. Analysis of the ITS rDNA sequences suggests their close relationship, but also confirms the independence of both species, and that they most likely form a ‘species pair’ based on morphological, chemical and molecular phylogenetic data. Phylogenetic trees based on both multi-locus gene and ITS rDNA alone strongly support that U. nipparensis and U. angulata belong to the same clade.

Three new species of Synergini wasps from same galls on Lithocarpus glaber (Thunb.) in Hunan, China (Hymenoptera, Cynipidae)

Three new species of the tribe Synergini (Hymenoptera, Cynipidae), i.e., Lithosaphonecrus arcoverticus Liu, Zhu et Pang, sp. n. Lithosaphonecrus decarinatus Liu, Zhu et Pang, sp. n. and Saphonecrus emarginatus Liu, Zhu et Pang, sp. n. are described from Hunan, China. The three species have emerged from the same galls collected on Lithocarpus glaber (Thunb.) in December, June, and April, respectively. Phylogenetic reconstruction of Synergini based on mtDNA COI and rRNA 28S D2 genes resolved two independent monophyletic clades exclusively associated with Lithocarpus plant hosts, i.e., the genus Lithosaphonecus and the lithocarpii species complex of Saphonecrus. The three species each have a sister relationship with a congener in Taiwan, an island off the southeastern coast of continental China. This recurrent disjunct distribution and relatively low COI sequence variation between the sister species in each species pair are considered attributable to the formation of the Taiwan Strait in Holocene ca 10,000 years ago. We also discussed the possible speciation mechanism for Lithosaphonecrus due to seasonality and topography in subtropical China. Finally, we addressed the need for conservation consideration in urbanization planning.