Why Do Some Lineages Radiate While Others Do Not? Perspectives for Future Research on Adaptive Radiations.

Understanding the processes that drive phenotypic diversification and underpin speciation is key to elucidating how biodiversity has evolved. Although these processes have been studied across a wide array of clades, adaptive radiations (ARs), which are systems with multiple closely related species and broad phenotypic diversity, have been particularly fruitful for teasing apart the factors that drive and constrain diversification. As such, ARs have become popular candidate study systems for determining the extent to which ecological features, including aspects of organisms and the environment, and inter- and intraspecific interactions, led to evolutionary diversification. Despite substantial past empirical and theoretical work, understanding mechanistically how ARs evolve remains a major challenge. Here, we highlight a number of understudied components of the environment and of lineages themselves, which may help further our understanding of speciation and AR. We also outline some substantial remaining challenges to achieving a detailed understanding of adaptation, speciation, and the role of ecology in these processes. These major challenges include identifying factors that have a causative impact in promoting or constraining ARs, gaining a more holistic understanding of features of organisms and their environment that interact resulting in adaptation and speciation, and understanding whether the role of these organismal and environmental features varies throughout the radiation process. We conclude by providing perspectives on how future investigations into the AR process can overcome these challenges, allowing us to glean mechanistic insights into adaptation and speciation.

Mitogenomes do not substantially improve phylogenetic resolution in a young non-model adaptive radiation of freshwater gastropods.

BACKGROUND: Species flocks in ancient lakes, and particularly those arising from adaptive radiation, make up the bulk of overall taxonomic and morphological diversity in these insular ecosystems. For these mostly young species assemblages, classical mitochondrial barcoding markers have so far been key to disentangle interspecific relationships. However, with the rise and further development of next-generation sequencing (NGS) methods and mapping tools, genome-wide data have become an increasingly important source of information even for non-model groups. RESULTS: Here, we provide, for the first time, a comprehensive mitogenome dataset of freshwater gastropods endemic to Sulawesi and thus of an ancient lake invertebrate species flock in general. We applied low-coverage whole-genome sequencing for a total of 78 individuals including 27 out of the 28 Tylomelania morphospecies from the Malili lake system as well as selected representatives from Lake Poso and adjacent catchments. Our aim was to assess whether mitogenomes considerably contribute to the phylogenetic resolution within this young species flock. Interestingly, we identified a high number of variable and parsimony-informative sites across the other 'non-traditional' mitochondrial loci. However, although the overall support was very high, the topology obtained was largely congruent with previously published single-locus phylogenies. Several clades remained unresolved and a large number of species was recovered polyphyletic, indicative of both rapid diversification and mitochondrial introgression. CONCLUSIONS: This once again illustrates that, despite the higher number of characters available, mitogenomes behave like a single locus and thus can only make a limited contribution to resolving species boundaries, particularly when introgression events are involved.

The genetics of niche-specific behavioral tendencies in an adaptive radiation of cichlid fishes.

Behavior is critical for animal survival and reproduction, and possibly for diversification and evolutionary radiation. However, the genetics behind adaptive variation in behavior are poorly understood. In this work, we examined a fundamental and widespread behavioral trait, exploratory behavior, in one of the largest adaptive radiations on Earth, the cichlid fishes of Lake Tanganyika. By integrating quantitative behavioral data from 57 cichlid species (702 wild-caught individuals) with high-resolution ecomorphological and genomic information, we show that exploratory behavior is linked to macrohabitat niche adaptations in Tanganyikan cichlids. Furthermore, we uncovered a correlation between the genotypes at a single-nucleotide polymorphism upstream of the AMPA glutamate-receptor regulatory gene cacng5b and variation in exploratory tendency. We validated this association using behavioral predictions with a neural network approach and CRISPR-Cas9 genome editing.

Revision of the cichlid fish genus Gnathochromis (Teleostei: Cichlidae) from Lake Tanganyika with the description of a new genus Jabarichromis gen. nov.

The cichlid species flock from Lake Tanganyika is a well-studied system for evolutionary biology research because its species assemblage shows a high degree of endemism and is a product of adaptive radiation. While our understanding of the evolutionary history of Lake Tanganyika cichlids has advanced tremendously over the past decades, their taxonomy received considerably less attention, despite numerous taxonomic misplacements (e.g., polyphyletic genera and species) that have been revealed by phylogenetic studies. One prominent example of a polyphyletic genus is Gnathochromis, which includes two distantly related species, belonging to two different tribes. To resolve this issue, here we present a taxonomic revision based on an extensive morphological dataset obtained from a comprehensive taxon sampling including 587 specimens from 63 taxa. We introduce a new monotypic genus, Jabarichromis gen. nov. for Gnathochromis pfefferi, a member of the tribe Tropheini, thereby separating it from the type species of Gnathochromis, G. permaxillaris. As a result, the genus Gnathochromis, which belongs to the tribe Limnochromini, is rendered monophyletic. Further, we provide an additional character to distinguish the recently described genus Shuja, which also belongs to the Tropheini, from its former mostly riverine congeners.

Host adaptive radiation is associated with rapid virus diversification and cross-species transmission in African cichlid fishes.

Adaptive radiations are generated through a complex interplay of biotic and abiotic factors. Although adaptive radiations have been widely studied in the context of animal and plant evolution, little is known about how they impact the evolution of the viruses that infect these hosts, which in turn may provide insights into the drivers of cross-species transmission and hence disease emergence. We examined how the rapid adaptive radiation of the cichlid fishes of African Lake Tanganyika over the last 10 million years has shaped the diversity and evolution of the viruses they carry. Through metatranscriptomic analysis of 2,242 RNA sequencing libraries, we identified 121 vertebrate-associated viruses among various tissue types that fell into 13 RNA and 4 DNA virus groups. Host-switching was commonplace, particularly within the Astroviridae, Metahepadnavirus, Nackednavirus, Picornaviridae, and Hepacivirus groups, occurring more frequently than in other fish communities. A time-calibrated phylogeny revealed that hepacivirus diversification was not constant throughout the cichlid radiation but accelerated 2-3 million years ago, coinciding with a period of rapid cichlid diversification and niche packing in Lake Tanganyika, thereby providing more closely related hosts for viral infection. These data depict a dynamic virus ecosystem within the cichlids of Lake Tanganyika, characterized by rapid virus diversification and frequent host jumping, and likely reflecting their close phylogenetic relationships that lower the barriers to cross-species virus transmission.

Diversity and evolution of the vertebrate chemoreceptor gene repertoire.

Chemoreception - the ability to smell and taste - is an essential sensory modality of most animals. The number and type of chemical stimuli that animals can perceive depends primarily on the diversity of chemoreceptors they possess and express. In vertebrates, six families of G protein-coupled receptors form the core of their chemosensory system, the olfactory/pheromone receptor gene families OR, TAAR, V1R and V2R, and the taste receptors T1R and T2R. Here, we study the vertebrate chemoreceptor gene repertoire and its evolutionary history. Through the examination of 1,527 vertebrate genomes, we uncover substantial differences in the number and composition of chemoreceptors across vertebrates. We show that the chemoreceptor gene families are co-evolving, highly dynamic, and characterized by lineage-specific expansions (for example, OR in tetrapods; TAAR, T1R in teleosts; V1R in mammals; V2R, T2R in amphibians) and losses. Overall, amphibians, followed by mammals, are the vertebrate clades with the largest chemoreceptor repertoires. While marine tetrapods feature a convergent reduction of chemoreceptor numbers, the number of OR genes correlates with habitat in mammals and birds and with migratory behavior in birds, and the taste receptor repertoire correlates with diet in mammals and with aquatic environment in fish.

Ancient DNA is preserved in fish fossils from tropical lake sediments.

Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now-extinct diversity. Time-structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high-throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1 mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia.

Visual opsin gene expression evolution in the adaptive radiation of cichlid fishes of Lake Tanganyika.

Tuning the visual sensory system to the ambient light is essential for survival in many animal species. This is often achieved through duplication, functional diversification, and/or differential expression of visual opsin genes. Here, we examined 753 new retinal transcriptomes from 112 species of cichlid fishes from Lake Tanganyika to unravel adaptive changes in gene expression at the macro-evolutionary and ecosystem level of one of the largest vertebrate adaptive radiations. We found that, across the radiation, all seven cone opsins-but not the rhodopsin-rank among the most differentially expressed genes in the retina, together with other vision-, circadian rhythm-, and hemoglobin-related genes. We propose two visual palettes characteristic of very shallow- and deep-water living species, respectively, and show that visual system adaptations along two major ecological axes, macro-habitat and diet, occur primarily via gene expression variation in a subset of cone opsin genes.

Genomics of cold adaptations in the Antarctic notothenioid fish radiation.

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.

Species diversity and phylogeography of the Australoheros autrani group (Teleostei, Cichlidae) in eastern Brazil.

Cichlid fishes are an important model system in evolutionary biology, primarily because of their exceptional diversity. However, while some cichlid assemblages, such as the ones of the African Great Lakes, have received considerable attention, others are not well studied, including many riverine species. Here, we focus on the Australoheros autrani species group and first report a new record of Australoheros in the upper Paranaíba River drainage, extending the known distribution range of this genus. Through Bayesian inference and maximum likelihood phylogenetic analyses of the mitochondrial cytochrome b gene of these specimens as well as available sequences, we assigned the newly discovered population to Australoheros barbosae. We corroborate the monophyly of the A. autrani species group and the presence of three species in the upper/middle Paraíba do Sul River basin as well as molecular diagnostic characters for each. Finally, we provide evidence for a recent expansion of A. barbosae. Supplementary Information: The online version contains supplementary material available at 10.1007/s10228-022-00888-9.

The history and organization of the Workshop on Population and Speciation Genomics.

With the advent of high-throughput genome sequencing, bioinformatics training has become essential for research in evolutionary biology and related fields. However, individual research groups are often not in the position to teach students about the most up-to-date methodology in the field. To fill this gap, extended bioinformatics courses have been developed by various institutions and provide intense training over the course of two or more weeks. Here, we describe our experience with the organization of a course in one of the longest-running extended bioinformatics series of workshops, the Evomics Workshop on Population and Speciation Genomics that takes place biennially in the UNESCO world heritage town of Ceský Krumlov, Czech Republic. We list the key ingredients that make this workshop successful in our view, explain the routine for workshop organization that we have optimized over the years, and describe the most important lessons that we have learned from it. We report the results of a survey conducted among past workshop participants that quantifies measures of effective teaching and provide examples of how the workshop setting has led to the cross-fertilisation of ideas and ultimately scientific progress. We expect that our account may be useful for other groups aiming to set up their own extended bioinformatics courses.

No evidence for sex chromosomes in natural populations of the cichlid fish Astatotilapia burtoni.

Sex determination (SD) is not conserved among teleost fishes and can even differ between populations of the same species. Across the outstandingly species-rich fish family Cichlidae, more and more SD systems are being discovered. Still, the picture of SD evolution in this group is far from being complete. Lake Tanganyika and its affluent rivers are home to Astatotilapia burtoni, which belongs to the extremely successful East African cichlid lineage Haplochromini. Previously, in different families of an A. burtoni laboratory strain, an XYW system and an XY system have been described. The latter was also found in a second laboratory strain. In a laboratory-reared family descending from a population of the species' southern distribution, a second XY system was discovered. Yet, an analysis of sex chromosomes for the whole species distribution is missing. Here, we examined the genomes of 11 natural populations of A. burtoni, encompassing a wide range of its distribution, for sex-linked regions. We did not detect signs of differentiated sex chromosomes and also not the previously described sex chromosomal systems present in laboratory lines, suggesting different SD systems in the same species under natural and (long-term) artificial conditions. We suggest that SD in A. burtoni is more labile than previously assumed and consists of a combination of non-genetic, polygenic, or poorly differentiated sex chromosomes.

Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations.

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.].

Towards the phylogenetic placement of the enigmatic African genus Prolabeops Schultz, 1941.

The small cyprinid genus Prolabeops Schultz, 1941 is restricted to the Nyong and Sanaga River systems in Cameroon. In the past, the genus had been suggested to be either a member of the Labeoninae, Torinae or the Smiliogastrinae mainly on the basis of morphological similarities, and it is nowadays considered as incertae sedis within the Cypriniformes. This study provides the first attempt to reveal the phylogenetic position of Prolabeops using molecular data. For this purpose, the authors sequenced a large fraction of the mitochondrial genome (c. 13,600 bp), including all mitochondrial protein coding genes, of two Prolabeops melanhypopterus specimens and an additional four Enteromius specimens. The large-scale phylogenetic analysis was based on an alignment including all mitochondrial protein coding genes of 902 specimens representing c. 899 cypriniform species. Prolabeops was clearly recovered within the African Smiliogastrinae, forming a weakly supported clade together with Enteromius jae, Enteromius hulstaerti and Barboides gracilis. The study data underline the urgent need of a thorough taxonomic revision of the small African barbs collectively placed in the genus Enteromius.

Molecular evolution and depth-related adaptations of rhodopsin in the adaptive radiation of cichlid fishes in Lake Tanganyika.

The visual sensory system is essential for animals to perceive their environment and is thus under strong selection. In aquatic environments, light intensity and spectrum differ primarily along a depth gradient. Rhodopsin (RH1) is the only opsin responsible for dim-light vision in vertebrates and has been shown to evolve in response to the respective light conditions, including along a water depth gradient in fishes. In this study, we examined the diversity and sequence evolution of RH1 in virtually the entire adaptive radiation of cichlid fishes in Lake Tanganyika, focusing on adaptations to the environmental light with respect to depth. We show that Tanganyikan cichlid genomes contain a single copy of RH1. The 76 variable amino acid sites detected in RH1 across the radiation were not uniformly distributed along the protein sequence, and 31 of these variable sites show signals of positive selection. Moreover, the amino acid substitutions at 15 positively selected sites appeared to be depth-related, including three key tuning sites that directly mediate shifts in the peak spectral sensitivity, one site involved in protein stability and 11 sites that may be functionally important on the basis of their physicochemical properties. Among the strongest candidate sites for deep-water adaptations are two known key tuning sites (positions 292 and 299) and three newly identified variable sites (37, 104 and 290). Our study, which is the first comprehensive analysis of RH1 evolution in a massive adaptive radiation of cichlid fishes, provides novel insights into the evolution of RH1 in a freshwater environment.

Tracing evolutionary decoupling of oral and pharyngeal jaws in cichlid fishes.

Evolutionary innovations can facilitate diversification if the novel trait enables a lineage to exploit new niches or by expanding character space. The elaborate pharyngeal jaw apparatus of cichlid fishes is often referred to as an evolutionary "key innovation" that has promoted the spectacular adaptive radiations in these fishes. This goes back to the idea that the structural and functional independence of the oral and pharyngeal jaws for food capturing and food processing, respectively, permitted each jaw type to follow independent evolutionary trajectories. This "evolutionary decoupling" is thought to have facilitated novel trait combinations and, hence, ecological specialization, ultimately allowing more species to coexist in sympatry. Here, we test the hypotheses of evolutionary decoupling of the oral and pharyngeal jaws in the massive adaptive radiation of cichlid fishes in African Lake Tanganyika. Based on phylogenetic comparative analyses of oral jaw morphology and lower pharyngeal jaw shape across most of the ∼240 cichlid species occurring in that lake, we show that the two jaws evolved coupled along the main axes of morphological variation, yet most other components of these trait complexes evolved largely independently over the course of the radiation. Further, we find limited correlations between the two jaws in both overall divergence and evolutionary rates. Moreover, we show that the two jaws were evolutionary decoupled at a late stage of the radiation, suggesting that decoupling contributed to micro-niche partitioning and the associated rapidly increasing trophic diversity during this phase.

Speciation dynamics and extent of parallel evolution along a lake-stream environmental contrast in African cichlid fishes.

Understanding the dynamics of speciation is a central topic in evolutionary biology. Here, we investigated how morphological and genomic differentiation accumulated along the speciation continuum in the African cichlid fish Astatotilapia burtoni. While morphological differentiation was continuously distributed across different lake-stream population pairs, we found that there were two categories with respect to genomic differentiation, suggesting a "gray zone" of speciation at ~0.1% net nucleotide divergence. Genomic differentiation was increased in the presence of divergent selection and drift compared to drift alone. The quantification of phenotypic and genetic parallelism in four cichlid species occurring along a lake-stream environmental contrast revealed parallel and antiparallel components in rapid adaptive divergence, and morphological convergence in species replicates inhabiting the same environments. Furthermore, we show that the extent of parallelism was higher when ancestral populations were more similar. Our study highlights the complementary roles of divergent selection and drift on speciation and parallel evolution.

Dynamics of sex chromosome evolution in a rapid radiation of cichlid fishes.

Sex is a fundamental trait determined by environmental and/or genetic factors, including sex chromosomes. Sex chromosomes are studied in species scattered across the tree of life, yet little is known about tempo and mode of sex chromosome evolution among closely related species. Here, we examine sex chromosome evolution in the adaptive radiation of cichlid fishes in Lake Tanganyika. Through the analysis of male and female genomes from 244 cichlid taxa (189 described species with 5 represented with two local variants/populations; 50 undescribed species) and of 396 multitissue transcriptomes from 66 taxa, we identify signatures of sex chromosomes in 79 taxa, involving 12 linkage groups. We find that Tanganyikan cichlids have the highest rates of sex chromosome turnover and heterogamety transitions known to date. We show that sex chromosome recruitment is not at random. Moreover convergently emerged sex chromosomes in cichlids support the "limited options" hypothesis of sex chromosome evolution.

The Visual Opsin Gene Repertoires of Teleost Fishes: Evolution, Ecology, and Function.

Visual opsin genes expressed in the rod and cone photoreceptor cells of the retina are core components of the visual sensory system of vertebrates. Here, we provide an overview of the dynamic evolution of visual opsin genes in the most species-rich group of vertebrates, teleost fishes. The examination of the rich genomic resources now available for this group reveals that fish genomes contain more copies of visual opsin genes than are present in the genomes of amphibians, reptiles, birds, and mammals. The expansion of opsin genes in fishes is due primarily to a combination of ancestral and lineage-specific gene duplications. Following their duplication, the visual opsin genes of fishes repeatedly diversified at the same key spectral-tuning sites, generating arrays of visual pigments sensitive to the ultraviolet to red spectrum of light. Species-specific opsin gene repertoires correlate strongly with underwater light habitats, ecology, and color-based sexual selection.

The non-gradual nature of adaptive radiation.

Adaptive radiation is a major source of biodiversity. Still, many aspects of this evolutionary process remain poorly understood. Our recent integrative examination of the cichlid adaptive radiation in African Lake Tanganyika provides new insights into the process of explosive diversification. The in-depth phylogenetic comparative analysis of nearly all species occurring in that lake permitted us to trace patterns of eco-morphological evolution throughout the phylogenetic history of the radiation and revealed that it occurred in a non-gradual manner, in the form of time-shifted bursts of accelerated evolution. The temporal pattern of divergence along different axes of morphological evolution provides empirical support for a scenario that potentially unifies two popular models of adaptive radiation, the "early burst model" and the "stages model".