Phenotype-environment correlations in a putative whitefish adaptive radiation

1. The adaptive radiation of fishes into benthic (littoral) and pelagic (lentic) morphs in post-glaciallakes has become an important model system for speciation. Although these systems are well stud-ied, there is little evidence of the existence of morphs that have diverged to utilize resources in theremaining principal lake habitat, the profundal zone.
2. Here, we tested phenotype-environment correlations of three whitefish (Coregonus lavaretus)morphs that have radiated into littoral, pelagic and profundal niches in northern Scandinavianlakes. We hypothesized that morphs in such trimorphic systems would have a morphology adaptedto one of the principal lake habitats (littoral, pelagic or profundal niches). Most whitefish popula-tions in the study area are formed by a single (monomorphic) whitefish morph, and we furtherhypothesized that these populations should display intermediate morphotypes and niche utiliza-tion. We used a combination of traditional (stomach content, habitat use, gill raker counts) andmore recently developed (stable isotopes, geometric morphometrics) techniques to evaluate pheno-type-environment correlations in two lakes with trimorphic and two lakes with monomorphicwhitefish.
3. Distinct phenotype-environment correlations were evident for each principal niche in whitefishmorphs inhabiting trimorphic lakes. Monomorphic whitefish exploited multiple habitats, hadintermediate morphology, displayed increased variance in gillraker-counts, and relied significantlyon zooplankton, most likely due to relaxed resource competition.
4. We suggest that the ecological processes acting in the trimorphic lakes are similar to each other,and are driving the adaptive evolution of whitefish morphs, possibly leading to the formation ofnew species.

Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Scripting automation e modelli bayesiani: Applicazioni cliniche in radioterapia e sviluppo di tecniche innovative per adaptive radiation therapy

La presente ricerca consiste nel validare ed automatizzare metodiche di Adaptive Radiation Therapy (ART), che hanno come obiettivo la personalizzazione continua del piano di trattamento radioterapico in base alle variazioni anatomiche e dosimetriche del paziente. Tali variazioni (casuali e/o sistematiche) sono identificabili mediante l’utilizzo dell’imaging diagnostico. Il lavoro svolto presso la struttura di Fisica Medica dell’Azienda Ospedaliera Universitaria del Policlinico di Modena, si inserisce in un progetto del Ministero della Salute del bando Giovani Ricercatori dal titolo: “Dose warping methods for IGRT and ADAPTIVERT: dose accumulation based on organ motion and anatomical variations of the patients during radiation therapy treatments”. Questa metodica si sta affermando sempre più come nuova opportunità di trattamento e, per tale motivo, nasce l’esigenza di studiare e automatizzare processi realizzabili nella pratica clinica, con un utilizzo limitato di risorse. Si sono sviluppati script che hanno permesso l’automazione delle operazioni di Adaptive e deformazioni, raccogliendo i dati di 51 pazienti sottoposti a terapia mediante Tomotherapy. L’analisi delle co-registrazioni deformabili delle strutture e delle dosi distribuite, ha evidenziato criticità del software che hanno reso necessario lo sviluppo di sistemi di controllo dei risultati, per facilitare l’utente nella revisione quotidiana dei casi clinici. La letteratura riporta un numero piuttosto limitato di esperienze sulla validazione e utilizzo su larga scala di questi tools, per tale motivo, si è condotto un esame approfondito della qualità degli algoritmi elastici e la valutazione clinica in collaborazione di fisici medici e medici radioterapisti. Sono inoltre stati sviluppati principi di strutturazione di reti Bayesiane, che consentono di predirre la qualità delle deformazioni in diversi ambiti clinici (H&N, Prostata, Polmoni) e coordinare il lavoro quotidiano dei professionisti, identificando i pazienti, per i quali sono apprezzabili variazioni morfo-dosimetriche significative. Da notare come tale attività venga sviluppata automaticamente durante le ore notturne, sfruttando l’automation come strumento avanzato e indipendente dall’operatore. Infine, il forte sviluppo, negli ultimi anni della biomeccanica applicata al movimento degli organi (dimostrato dalla numerosa letteratura al riguardo), ha avuto come effetto lo sviluppo, la valutazione e l’introduzione di algoritmi di deformazione efficaci. In questa direzione, nel presente lavoro, si sono analizzate quantitivamente le variazioni e gli spostamenti delle parotidi, rispetto all’inizio del trattamento, gettando le basi per una proficua linea di ricerca in ambito radioterapico.

Population genomic tests of models of adaptive radiation in Lake Victoria Region cichlid fish

Adaptive radiation is usually thought to be associated with speciation, but the evolution of intraspecific polymorphisms without speciation is also possible. The radiation of cichlid fish in Lake Victoria (LV) is perhaps the most impressive example of a recent rapid adaptive radiation, with 600+ very young species. Key questions about its origin remain poorly characterized, such as the importance of speciation versus polymorphism, whether species persist on evolutionary time scales, and if speciation happens more commonly in small isolated or in large connected populations. We used 320 individuals from 105 putative species from Lakes Victoria, Edward, Kivu, Albert, Nabugabo and Saka, in a radiation-wide amplified fragment length polymorphism (AFLP) genome scan to address some of these questions. We demonstrate pervasive signatures of speciation supporting the classical model of adaptive radiation associated with speciation. A positive relationship between the age of lakes and the average genomic differentiation of their species, and a significant fraction of molecular variance explained by above-species level taxonomy suggest the persistence of species on evolutionary time scales, with radiation through sequential speciation rather than a single starburst. Finally the large gene diversity retained from colonization to individual species in every radiation suggests large effective population sizes and makes speciation in small geographical isolates unlikely.

Adaptive plasticity and genetic divergence in feeding efficiency during parallel adaptive radiation of whitefish (Coregonus spp.)

Parallel phenotypic divergence in replicated adaptive radiations could either result from parallel genetic divergence in response to similar divergent selec- tion regimes or from equivalent phenotypically plastic response to the repeated occurrence of contrasting environments. In post-glacial fish, repli- cated divergence in phenotypes along the benthic-limnetic habitat axis is commonly observed. Here, we use two benthic-limnetic species pairs of whitefish from two Swiss lakes, raised in a common garden design, with reciprocal food treatments in one species pair, to experimentally measure whether feeding efficiency on benthic prey has a genetic basis or whether it underlies phenotypic plasticity (or both). To do so, we offered experimental fish mosquito larvae, partially burried in sand, and measured multiple feed- ing efficiency variables. Our results reveal both, genetic divergence as well as phenotypically plastic divergence in feeding efficiency, with the pheno- typically benthic species raised on benthic food being the most efficient forager on benthic prey. This indicates that both, divergent natural selection on genetically heritable traits and adaptive phenotypic plasticity, are likely important mechanisms driving phenotypic divergence in adaptive radiation.

Experimental evidence for trait utility of gill raker number in adaptive radiation of a north temperate fish

North temperate fish in post-glacial lakes are textbook examples for rapid parallel adaptive radiation into multiple trophic specialists within individual lakes. Speciation repeatedly proceeded along the benthic – limnetic habitat axis, and benthic – limnetic sister species diverge in the number of gill rakers. Yet, the utility of different numbers of gill rakers for consuming benthic vs. limnetic food has only very rarely been experimentally demonstrated. We bred and raised families of a benthic – limnetic species pair of whitefish under common garden conditions to test whether these species (i) show heritable differentiation in feeding efficiency on zooplankton, and (ii) whether varia- tion in feeding efficiency is predicted by variation in gill raker numbers. We used zooplankton of three different size classes to investigate prey size dependency of divergence in feeding efficiency and to investigate the effect strength of variation in the number of gill rakers. Our results show strong interspecific differences in feeding efficiency. These differences are largest when fish were tested with the smallest zooplankton. Importantly, feeding efficiency is significantly positively correlated with the number of gill rakers when using small zooplankton, also when species identity is statistically controlled for. Our results support the hypothesis that a larger number of gill rakers are of adaptive significance for feeding on zooplankton and pro- vide one of the first experimental demonstrations of trait utility of gill raker number when fish feed on zooplankton. These results are consistent with the suggested importance of divergent selection driven feeding adaptation during adaptive radiation of fish in post-glacial lakes.

Hybridization and adaptive radiation

Whether interspecific hybridization is important as a mechanism that generates biological diversity is a matter of controversy. Whereas some authors focus on the potential of hybridization as a source of genetic variation, functional novelty and new species, others argue against any important role, because reduced fitness would typically render hybrids an evolutionary dead end. By drawing on recent developments in the genetics and ecology of hybridization and on principles of ecological speciation theory, I develop a concept that reconciles these views and adds a new twist to this debate. Because hybridization is common when populations invade new environments and potentially elevates rates of response to selection, it predisposes colonizing populations to rapid adaptive diversification under disruptive or divergent selection. I discuss predictions and suggest tests of this hybrid swarm theory of adaptive radiation and review published molecular phylogenies of adaptive radiations in light of the theory. Some of the confusion about the role of hybridization in evolutionary diversification stems from the contradiction between a perceived necessity for cessation of gene flow to enable adaptive population differentiation on the one hand [1], and the potential of hybridization for generating adaptive variation, functional novelty and new species 2, 3 and 4 on the other. Much progress in the genetics 5, 6, 7, 8 and 9 and ecology of hybridization 9, 10 and 11, and in our understanding of the role of ecology in speciation (see Glossary) 12, 13 and 14 make a re-evaluation timely. Whereas botanists traditionally stressed the diversity-generating potential of hybridization 2, 3 and 14, zoologists traditionally saw it as a process that limits diversification [1] and refer to it mainly in the contexts of hybrid zones (Box 1) and reinforcement of reproductive isolation [15]. Judging by the wide distribution of allopolyploidy among plants, many plant species might be of direct hybrid origin or descended from a hybrid species in the recent past [16]. The ability to reproduce asexually might explain why allopolyploid hybrid species are more common in plants than in animals. Allopolyploidy arises when meiotic mismatch of parental chromosomes or karyotypes causes hybrid sterility. Mitotic error, duplicating the karyotype, can restore an asexually maintained hybrid line to fertility. Although bisexual allopolyploid hybrid species are not uncommon in fish [17] and frogs [18], the difficulty with which allopolyploid animals reproduce, typically requiring gynogenesis[19], makes establishment and survival of allopolyploid animal species difficult.

The genomic substrate for adaptive radiation in African cichlid fish

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.