How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.info:eu-repo/semantics/publishedVersio

The era of reference genomes in conservation genomics

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics

The era of reference genomes in conservation genomics

info:eu-repo/semantics/publishedVersio

The era of reference genomes in conservation genomics

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics

How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics

Ecological and Evolutionary Consequences of Color- and Trophic Polymorphisms in Cichlid Fishes

How the exuberant diversity on our planet arose is still a question of central interest in biology. Rapidly diversifying species complexes that experience adaptive radiation have always been prime study targets to infer the underlying mechanisms of divergence. Young species-rich systems that display ongoing diversification in multiple replicates are of particular relevance, because different stages of divergence are likely to be found, ranging from incipient speciation to stable species assemblages consisting of multiple reproductively isolated species. In that framework, various studies focusing on phenotypic variation, on the interaction of phenotype and environment, and consequently of adaptation to different environments have produced manifold insights into the ecological and evolutionary processes leading to diversification. The presence of discontinuous variation in trophic characters or in coloration has by many investigators not only been regarded as an efficient mechanism to achieve a relaxation of intraspecific competition, but also as a signal of ongoing diversification processes. This doctoral thesis entitled “Ecological and Evolutionary Consequences of Color- and Trophic Polymorphisms in Cichlid Fishes” is aimed at advancing the still limited understanding of the underlying processes leading to the evolution and maintenance of biological diversity. With more than 2,000 described species, cichlid fishes are one of nature’s most biologically diverse groups. Eco-morphologically similar species and color morphs can be observed among independent lineages. Consequently, cichlids are an excellent model for studying the biological, evolutionary, and ecological factors that promote biodiversity and the genesis of new species. The central line of research being addressed throughout this thesis investigates ecological consequences of trophic and color polymorphisms and assesses their maintenance as well as their putative role in lineage diversification in two study systems of cichlid fishes: Midas cichlids from Nicaragua and Perissodus microlepis, a scale-eating cichlid from Lake Tanganyika. Midas cichlids notably occur in the Nicaraguan great lakes and in some small and isolated crater lakes that have been colonized from the great lakes. In some crater lakes Midas cichlids have further diversified and new species have evolved within short time periods, making them prone to study diversification processes. Also, the crater lake populations are often considered being “evolutionary replicates” or “independent laboratories of evolution”. In several crater lakes diversification takes place along the Abstract 12 benthic-limnetic axis and most populations are also color-polymorphic. The most comprehensive project focuses on the gold/dark color polymorphism in the Midas cichlid species complex (Amphilophus citrinellus spp.). Using a comparative approach that bases on extensive field collections of Midas cichlids, a substantial degree of ecological differentiation between color morphs is revealed. The differentiation is consistent throughout the species complex. From a common garden approach it is inferred, that eco-morphological differentiation between color morphs in the wild is likely partly genetically determined. This is an innovative finding in adaptive radiation research. The correlation of ecology and coloration presumably contributes to the maintenance of this color polymorphism over time through niche partitioning and additionally exhibits great potential to facilitate sympatric diversification processes, given the reported color assortative mating. In a subproject related to coloration, color differential predation by a major Midas cichlid predator (Parachromis managuensis) was revealed using color variants of the common Goldfish that are similar to gold and dark Midas cichlid color morphs. A highly increased attack risk was observed for the Goldfish variant that is similar to the Midas cichlid gold morph. The putative role of color differential predation in maintaining the color polymorphism throughout the evolutionary replicates is discussed. Another project aims at detecting intraspecific diversification along the benthic-limnetic axis in one of the youngest crater lakes of Nicaragua. In each of two older crater lakes multiple Midas cichlid species can be found, that are characteristically diverse along the benthic-limnetic axis. Substantial variability and individual specialization was found in this young Midas cichlid population. This may hint at the incipient evolution of a trophic resource polymorphism and possibly at imminent diversification along the benthic-limnetic axis. The second case study involved the scale eating cichlid Perissodus microlepis from Lake Tanganyika that is famous for its asymmetric mouth morphology. In some textbooks this species is referred to as an example of a stunning trophic specialization, and of the role of negative frequency-dependent selection in the maintenance of an intraspecific trophic polymorphism. Perissodus microlepis attacks its prey mostly from behind and snatches scales from the prey fish flanks. It is assumed that through the possession of asymmetric mouth morphologies scale-eating from the prey fish flanks is facilitated. So far, this trophic polymorphism has mainly been described as a dimorphic trait, i.e. left (L-morph) or right (R-morph) with no intermediate morphologies. It is thought that L-morphs prefer to attack the right flanks of their prey fish whereas RAbstract 13 morphs rather attack the left prey fish flanks. The maintenance of this polymorphism is thought to be achieved because the prey fish would be more alert against the relatively more often attacked body flank. Hence the common scale-eater morph would suffer a disadvantage, and consequently the rare morph will be favored and eventually increase in frequency. Mouth asymmetry in this species is thought to be determined by two alleles at a single locus, (R is dominant over L and R is homozygous lethal). The pattern of disassortative mating between mouth morphs has been invoked to compensate the reported lethality of the individuals carrying two copies of the dominant R-allele. One project contributing to this thesis is aimed at shedding light on a recently developing controversial debate, that relates to the distribution of morphological variation (discrete vs. continuous) and to the mating pattern (disassortative vs. random) of this species. Mouth asymmetry in an extensive sample of wild-caught specimens was quantitatively assessed and the mating pattern was reinvestigated. In contrast to previous reports continuously distributed mouth morphologies were found in several populations and random mating was observed. These findings are concordant with that of other recent studies and question the original claims that have been outlined above. In particular they hint at significant environmental contributions to the shaping of morphological laterality in this species. However, given the large geographic distances between our sampling sites and those of previous studies, that have initially coined this textbook example, it is still conceivable that geographic aspects play a role. Additional aspects come from a behavioral perspective: Using wild-caught adult scale-eaters and their natural prey, we predicted the direction of lateralized attack behavior from morphology in the field. In the laboratory, strong behavioral lateralization was found in at most weakly asymmetric laboratory-raised juvenile fish, with respect to morphology. This suggests that morphological asymmetry might be governed by behavioral handedness in this species, somewhat underlining the role of phenotypic plasticity in bringing about morphological asymmetry in this species, that has recently been invoked in the controversial debate surrounding this system. Overall, this thesis reveals various patterns of ecological diversification based on trophic- and color polymorphisms in cichlid fishes and describes the dynamics of maintenance and the putative role of such polymorphisms in lineage diversification, therefore adding to the understanding of phenotypic evolution in the biodiversity of life

Lab-reared 3 month old juvenile Perissodus microlepis fish

Mouth asymmetry (mouth bending angle) and PC-1 scores (geometric and morphometric analysis) of laboratory-reared 3 month old juvenile Perissodus microlepis fis

Lab-reared 7 month old juvenile Perissodus microlepis fish

Mouth asymmetry (mouth bending angle), PC-1 scores (geometric and morphometric analysis) and body size (total length) of laboratory-reared 7 month old juvenile Perissodus microlepis fis

Data from: Mouth asymmetry in the textbook example of scale-eating cichlid fish is not a discrete dimorphism after all

Individuals of the scale-eating cichlid fish, Perissodus microlepis, from Lake Tanganyika tend to have remarkably asymmetric heads that are either left-bending or right-bending. The ‘left’ morph opens its mouth markedly towards the left and preferentially feeds on the scales from the right side of its victim fish and the ‘right’ morph bites scales from the victims’ left side. This striking dimorphism made these fish a textbook example of their astonishing degree of ecological specialization and as one of the few known incidences of negative frequency-dependent selection acting on an asymmetric morphological trait, where left and right forms are equally frequent within a species. We investigated the degree and the shape of the frequency distribution of head asymmetry in P. microlepis to test whether the variation conforms to a discrete dimorphism, as generally assumed. In both adult and juvenile fish, mouth asymmetry appeared to be continuously and unimodally distributed with no clear evidence for a discrete dimorphism. Mixture analyses did not reveal evidence of a discrete or even strong dimorphism. These results raise doubts about previous claims, as reported in textbooks, that head variation in P. microlepis represents a discrete dimorphism of left- and right-bending forms. Based on extensive field sampling that excluded ambiguous (i.e. symmetric or weakly asymmetric) individual adults, we found that left and right morphs occur in equal abundance in five populations. Moreover, mate pairing for 51 wild caught pairs was random with regard to head laterality, calling into question reports that this laterality is maintained through disassortative mating