Genomic Signatures for Species-Specific Adaptation in Lake Victoria Cichlids Derived from Large-Scale Standing Genetic Variation

Paleopteran molecular clock: Time drift and recent acceleration

Applying BEAST v1.10.4, we constructed a Bayesian Inference tree comprising 322 taxa, primarily representing Paleoptera (Odonata and Ephemeroptera; Pterygota), Zygentoma and Archaeognatha (Apterygota; paraphyly), and Neoptera (Plecoptera; Pterygota), based on a 2685 bp sequence dataset. Our analyses revealed that robust dating required the incorporation of both Quaternary and pre-Quaternary dates. To achieve this, our dating incorporated a 1.55 Ma (Quaternary) geological event (the formation of the Ryukyu Islands) and a set of chronologically well-founded fossil dates, spanning from up to 400 Ma (Devonian) for the stem Archaeognatha, 320 Ma (Carboniferous) for the crown of Paleoptera, 300 Ma (Carboniferous) for the crown Ephemeroptera, and 280 Ma (Permian) for the crown Odonata, down to 1.76 Ma (Quaternary) for Calopteryx japonica, encompassing a total of 22 calibration points (events: 6, fossils: 16; Quaternary: 7, pre-Quaternary: 15). The resulting dated tree aligns with previous research, albeit with some dates being overestimated. This overestimation was mainly due to the lack of Quaternary calibration and the exclusive dependence on pre-Quaternary calibration, though the application of maximum age constraints also played a role. Our minimum age dating demonstrates that the molecular clock did not uniformly progress, rendering rate dating an inapplicable approach. We observed that the base substitution rate is time-dependent, with an exponential increase evident from around 20 Ma (Miocene) to the present time, exceeding an order of magnitude. The extensive radiation and speciation of Insecta and Paleoptera, potentially resulting from the severe climatic changes associated with the Quaternary, including the commencement of glacial and interglacial cycles, may have significantly contributed to this increase in base substitution rates. Additionally, we identified a potential peak in base substitution rates during the Carboniferous period, around 320 million years ago, possibly corresponding to the Late Paleozoic Ice Age.

Severe Bottleneck Impacted the Genomic Structure of Egg-Eating Cichlids in Lake Victoria

Within 15,000 years, the explosive adaptive radiation of haplochromine cichlids in Lake Victoria, East Africa, generated 500 endemic species. In the 1980s, the upsurge of Nile perch, a carnivorous fish artificially introduced to the lake, drove the extinction of more than 200 endemic cichlids. The Nile perch predation particularly harmed piscivorous cichlids, including paedophages, cichlids eat eggs and fries, which is an example of the unique trophic adaptation seen in African cichlids. Here, aiming to investigate past demographic events possibly triggered by the invasion of Nile perch and the subsequent impacts on the genetic structure of cichlids, we conducted large-scale comparative genomics. We discovered evidence of recent bottleneck events in 4 species, including 2 paedophages, which began during the 1970s to 1980s, and population size rebounded during the 1990s to 2000s. The timing of the bottleneck corresponded to the historical records of endemic haplochromines" disappearance and later resurgence, which is likely associated with the introduction of Nile perch by commercial demand to Lake Victoria in the 1950s. Interestingly, among the 4 species that likely experienced bottleneck, Haplochromis sp. "matumbi hunter," a paedophagous cichlid, showed the most severe bottleneck signatures. The components of shared ancestry inferred by ADMIXTURE suggested a high genetic differentiation between matumbi hunter and other species. In contrast, our phylogenetic analyses highly supported the monophyly of the 5 paedophages, consistent with the results of previous studies. We conclude that high genetic differentiation of matumbi hunter occurred due to the loss of shared genetic components among haplochromines in Lake Victoria caused by the recent severe bottleneck.

Chromosome-Scale Genome Assembly of the Freshwater Snail Semisulcospira habei from the Lake Biwa Drainage System

Semisulcospira habei is a freshwater snail species endemic to the Lake Biwa drainage and belongs to a species group radiated within the lake system. We report the chromosome-scale genome assembly of S. habei, including eight megascaffolds larger than 150 Mb. The genome assembly size is about 2.0 Gb with an N50 of 237 Mb. There are 41,547 protein-coding genes modeled by ab initio gene prediction based on the transcriptome data set, and the BUSCO completeness of the annotated genes was 92.2%. The repeat elements comprise approximately 76% of the genome assembly. The Hi-C contact map showed seven well-resolved scaffolds that correspond to the basic haploid chromosome number of S. habei inferred from the preceding karyotypic study, while it also exhibited one scaffold with a complicated mosaic pattern that is likely to represent the complex of multiple supernumerary chromosomes. The genome assembly reported here represents a high-quality genome resource in disentangling the genomic background of the adaptive radiation of Semisulcospira and also facilitates evolutionary studies in the superfamily Cerithioidea.

Ancient standing genetic variation facilitated the adaptive radiation of Lake Victoria cichlids

Cichlid fishes are textbook examples of explosive speciation and adaptive radiation, providing a great opportunity to understand how the genomic substrate yields extraordinary species diversity. Recently, we performed comparative genomic analyses of three Lake Victoria cichlids to reveal the genomic substrates underlying their rapid speciation and adaptation. We found that long divergent haplotypes derived from large-scale standing genetic variation, which originated before the adaptive radiation of Lake Victoria cichlids, may have contributed to their rapid diversification. In addition, the present study on genomic data from other East African cichlids suggested the reuse of alleles that may have originated in the ancestral lineages of Lake Tanganyika cichlids during cichlid evolution. Therefore, our results highlight that the primary factor that could drive repeated adaptive radiation across East African cichlids was allelic reuse from standing genetic variation to adapt to their own specific environment. In this report, we summarize the main results and discuss the evolutionary mechanisms of cichlids, based on our latest findings.

Mitogenomic Characterization of Cameroonian Endemic Coptodon camerunensis (Cichliformes: Cichlidae) and Matrilineal Phylogeny of Old-World Cichlids

The mitogenomic evolution of old-world cichlids is still largely incomplete in Western Africa. In this present study, the complete mitogenome of the Cameroon endemic cichlid, Coptodon camerunensis, was determined by next-generation sequencing. The mitogenome was 16,557 bp long and encoded with 37 genes (13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region). The C. camerunensis mitogenome is AT-biased (52.63%), as exhibited in its congener, Coptodon zillii (52.76% and 53.04%). The majority of PCGs start with an ATG initiation codon, except COI, which starts with a GTG codon and five PCGs and ends with the TAA termination codon and except seven PCGs with an incomplete termination codon. In C. camerunensis mitogenome, most tRNAs showed classical cloverleaf secondary structures, except tRNA-serine with a lack of DHU stem. Comparative analyses of the conserved blocks of two Coptodonini species control regions revealed that the CSB-II block was longer than other blocks and contained highly variable sites. Using 13 concatenated PCGs, the mitogenome-based Bayesian phylogeny easily distinguished all the examined old-world cichlids. Except for Oreochromini and Coptodinini tribe members, the majority of the taxa exhibited monophyletic clustering within their respective lineages. C. camerunensis clustered closely with Heterotilapia buttikoferi (tribe Heterotilapiini) and had paraphyletic clustering with its congener, C. zillii. The Oreochromini species also displayed paraphyletic grouping, and the genus Oreochromis showed a close relationship with Coptodinini and Heterotilapiini species. In addition, illustrating the known distribution patterns of old-world cichlids, the present study is congruent with the previous hypothesis and proclaims that prehistoric geological evolution plays a key role in the hydroclimate of the African continent during Mesozoic, which simultaneously disperses and/or colonizes cichlids in different ichthyological provinces and Rift Lake systems in Africa. The present study suggests that further mitogenomes of cichlid species are required, especially from western Africa, to understand their unique evolution and adaptation.

Selection-driven trait loss in independently evolved cavefish populations

Laboratory studies have demonstrated that a single phenotype can be produced by many different genotypes; however, in natural systems, it is frequently found that phenotypic convergence is due to parallel genetic changes. This suggests a substantial role for constraint and determinism in evolution and indicates that certain mutations are more likely to contribute to phenotypic evolution. Here we use whole genome resequencing in the Mexican tetra, Astyanax mexicanus, to investigate how selection has shaped the repeated evolution of both trait loss and enhancement across independent cavefish lineages. We show that selection on standing genetic variation and de novo mutations both contribute substantially to repeated adaptation. Our findings provide empirical support for the hypothesis that genes with larger mutational targets are more likely to be the substrate of repeated evolution and indicate that features of the cave environment may impact the rate at which mutations occur.

Three problems in the genetics of speciation by selection

Speciation is the process by which barriers to gene flow evolve between populations. Although we now know that speciation is largely driven by natural selection, knowledge of the agents of selection and the genetic and genomic mechanisms that facilitate divergence is required for a satisfactory theory of speciation. In this essay, we highlight three advances/problems in our understanding of speciation that have arisen from studies of the genes and genomic regions that underlie the evolution of reproductive isolation. First, we describe how the identification of “speciation” genes makes it possible to identify the agents of selection causing the evolution of reproductive isolation, while also noting that the link between the genetics of phenotypic divergence and intrinsic postzygotic reproductive barriers remains tenuous. Second, we discuss the important role of recombination suppressors in facilitating speciation with gene flow, but point out that the means and timing by which reproductive barriers become associated with recombination cold spots remains uncertain. Third, we establish the importance of ancient genetic variation in speciation, although we argue that the focus of speciation studies on evolutionarily young groups may bias conclusions in favor of ancient variation relative to new mutations.