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Abstract Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, here we generate and analyse new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes. 

Abstract African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate the relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as the sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system. [African cichlids; Blenniiformes; Gene tree heterogeneity; Hybrid assembly; Phylogenetic network; Pseudocrenilabrinae; Species tree.] 

Abstract. The Neogene and Quaternary are characterized by enormous changes in globalclimate and environments, including global cooling and the establishment ofnorthern high-latitude glaciers. These changes reshaped global ecosystems,including the emergence of tropical dry forests and savannahs that are foundin Africa today, which in turn may have influenced the evolution of humansand their ancestors. However, despite decades of research we lack long,continuous, well-resolved records of tropical climate, ecosystem changes,and surface processes necessary to understand their interactions andinfluences on evolutionary processes. Lake Tanganyika, Africa, contains themost continuous, long continental climate record from the mid-Miocene(∼10 Ma) to the present anywhere in the tropics and has longbeen recognized as a top-priority site for scientific drilling. The lake issurrounded by the Miombo woodlands, part of the largest dry tropical biomeon Earth. Lake Tanganyika also harbors incredibly diverse endemic biotaand an entirely unexplored deep microbial biosphere, and it provides textbookexamples of rift segmentation, fault behavior, and associated surfaceprocesses. To evaluate the interdisciplinary scientific opportunities thatan ICDP drilling program at Lake Tanganyika could offer, more than 70scientists representing 12 countries and a variety of scientificdisciplines met in Dar es Salaam, Tanzania, in June 2019. The teamdeveloped key research objectives in basin evolution, source-to-sinksedimentology, organismal evolution, geomicrobiology, paleoclimatology,paleolimnology, terrestrial paleoecology, paleoanthropology, andgeochronology to be addressed through scientific drilling on LakeTanganyika. They also identified drilling targets and strategies, logisticalchallenges, and education and capacity building programs to be carried outthrough the project. Participants concluded that a drilling program at LakeTanganyika would produce the first continuous Miocene–present record fromthe tropics, transforming our understanding of global environmental change,the environmental context of human origins in Africa, and providing adetailed window into the dynamics, tempo and mode of biologicaldiversification and adaptive radiations. 

Vertebrate vision is accomplished through light-sensitive photopigments consisting of an opsin protein bound to a chromophore. In dim light, vertebrates generally rely on a single rod opsin [rhodopsin 1 (RH1)] for obtaining visual information. By inspecting 101 fish genomes, we found that three deep-sea teleost lineages have independently expanded their RH1 gene repertoires. Among these, the silver spinyfin (Diretmus argenteus) stands out as having the highest number of visual opsins in vertebrates (two cone opsins and 38 rod opsins). Spinyfins express up to 14 RH1s (including the most blueshifted rod photopigments known), which cover the range of the residual daylight as well as the bioluminescence spectrum present in the deep sea. Our findings present molecular and functional evidence for the recurrent evolution of multiple rod opsin–based vision in vertebrates.