Evidence for relaxed selection of mitogenome in rapid-flow cyprinids

Transcriptomic data support phylogenetic congruence and reveal genomic changes associated with the repeated evolution of annualism in aplocheiloid killifishes (Cyprinodontiformes)

Repeated evolution of novel life histories that are correlated with ecological variables offers opportunities to study convergence in genetic, developmental, and metabolic features. Nearly half of the 800 species of Aplocheiloid killifishes, a clade of teleost fishes with a circumtropical distribution, are "annual" or seasonal species that survive in ephemeral bodies of water that desiccate and are unfeasible for growth, reproduction, or survival for weeks to months every year. But the repeated evolution of adaptations that are key features of the annual life history among these fishes remains poorly known without a robust phylogenetic framework. We present a large-scale phylogenomic reconstruction of aplocheiloid killifishes evolution using newly sequenced transcriptomes obtained from a diversity of killifish lineages representing putative independent origins of annualism. Ancestral state estimation shows that developmental dormancy (diapause), a key trait of the killifish annual life cycle, may have originated up to seven times independently among African and South American lineages. To further explore the genetic basis of this unique trait, we measure changes in evolutionary rates among orthologous genes across the killifish tree of life by quantifying codon evolution using dN/dS ratios. We show that some genes have higher dN/dS ratios in lineages leading to species with annual life history. Many of them constitute key developmental genes or nuclear-encoded metabolic genes that control oxidative phosphorylation. Lastly, we compare these genes with higher ω to genes previously associated to developmental dormancy and metabolic shifts in killifishes and other vertebrates, and thereby identify molecular evolutionary signatures of repeated transitions to extreme environments.

Comparisons of chemosensory gene repertoires in human and non-human feeding Anopheles mosquitoes link olfactory genes to anthropophily

We investigate the genetic basis of anthropophily (human host use) in a non-model mosquito species group, the Anopheles farauti complex from the southwest Pacific. This complex has experienced multiple transitions from anthropophily to zoophily, contrasting with well-studied systems (the global species Aedes aegypti and the African Anopheles gambiae complex) that have evolved to be specialist anthropophiles. By performing tests of selection and assessing evolutionary patterns for >200 olfactory genes from nine genomes, we identify several candidate genes associated with differences in anthropophily in this complex. Based on evolutionary patterns (phylogenetic relationships, fixed amino acid differences, and structural differences) as well as results from selection analyses, we identify numerous genes that are likely to play an important role in mosquitoes’ ability to detect humans as hosts. Our findings contribute to the understanding of the evolution of insect olfactory gene families and mosquito host preference as well as having potential applied outcomes.

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Genomes of Anopheles mosquitoes with differing host preferences were sequenced

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Evolutionary comparisons were performed on >200 insect chemosensory genes

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These comparisons revealed candidate genes involved in human feeding

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Two of the main candidates identified were co-receptor Ir8a and Or75

The phylogeographical pattern of the Amur minnow Rhynchocypris lagowskii (Cypriniformes: Cyprinidae) in the Qinling Mountains

In this study, the phylogeographical pattern of the Amur minnow (Rhynchocypris lagowskii) widely distributed in the cold freshwaters of the Qinling Mountains was examined. A total of 464 specimens from 48 localities were sequenced at a 540-bp region of the mitochondrial cytochrome b (Cytb) gene, and 69 haplotypes were obtained. The mean ratio of the number of synonymous and nonsynonymous substitutions per site (dN/dS) was 0.028 and indicated purifying selection. Haplotype diversity (h) and nucleotide diversity (π) of natural populations of R. lagowskii varied widely between distinct localities. Phylogenetic trees based on Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods, and network analysis showed five well-differentiated lineages, but these did not completely correspond to localities and geographic distribution. Meanwhile, analysis of molecular variances (AMOVA) indicated the highest proportion of genetic variation was attributed to the differentiation between populations rather than by our defined lineages. In addition, there was no significant correlation between the pairwise Fst values and geographic distance (p > .05). Based on the molecular clock calibration, the time to the most recent common ancestor (TMRCA) was estimated to have emerged from the Late Miocene to the Early Pleistocene. Finally, the results of demographic history based on the neutrality test, mismatch distribution, and Bayesian skyline plot (BSP) analyses showed that collectively, the populations were stable during the Pleistocene while one lineage (lineage E) probably underwent a slight contraction during the Middle Pleistocene and a rapid expansion from the Middle to the Late Pleistocene. Therefore, the study suggests the current phylogeographical pattern of R. lagowskii was likely shaped by geological events that led to vicariance followed by dispersal and secondary contact, river capture, and climatic oscillation during the Late Miocene to the Early Pleistocene in the Qinling Mountains.

Patterns of Natural Selection on Mitochondrial Protein-Coding Genes in Lungless Salamanders: Relaxed Purifying Selection and Presence of Positively Selected Codon Sites in the Family Plethodontidae

There are two distinct lungless groups in caudate amphibians (salamanders and newts) (the family Plethodontidae and the genus Onychodactylus, from the family Hynobiidae). Lunglessness is considered to have evolved in response to environmental and/or ecological adaptation with respect to oxygen requirements. We performed selection analyses on lungless salamanders to elucidate the selective patterns of mitochondrial protein-coding genes associated with lunglessness. The branch model and RELAX analyses revealed the occurrence of relaxed selection (an increase of the dN/dS ratio = ω value) in most mitochondrial protein-coding genes of plethodontid salamander branches but not in those of Onychodactylus. Additional branch model and RELAX analyses indicated that direct-developing plethodontids showed the relaxed pattern for most mitochondrial genes, although metamorphosing plethodontids had fewer relaxed genes. Furthermore, aBSREL analysis detected positively selected codons in three plethodontid branches but not in Onychodactylus. One of these three branches corresponded to the most recent common ancestor, and the others corresponded with the most recent common ancestors of direct-developing branches within Hemidactyliinae. The positive selection of mitochondrial protein-coding genes in Plethodontidae is probably associated with the evolution of direct development.