Lessons from a natural experiment: Allopatric morphological divergence and sympatric diversification in the Midas cichlid species complex are largely influenced by ecology in a deterministic way

Explaining why some lineages diversify while others do not and how are key objectives in evolutionary biology. Young radiations of closely related species derived from the same source population provide an excellent opportunity to disentangle the relative contributions of possible drivers of diversification. In these settings, lineage‐specific effects are shared and can be ruled out. Moreover, the relevant demographic and ecological parameters can be estimated accurately. Midas cichlid fish in Nicaragua have repeatedly colonized several crater lakes, diverged from the same source populations, and, interestingly, diversified in some of them but not others. Here, using the most comprehensive molecular and geometric morphometric data set on Midas cichlids to date (∼20,000 SNPs, 12 landmarks, ∼700 individuals), we aim to understand why and how crater lake populations diverge and why some of them are more prone to diversify in sympatry than others. Taking ancestor‐descendant relationships into account, we find that Midas cichlids diverged in parallel from their source population mostly—but not exclusively—by evolving more slender body shapes in all six investigated crater lakes. Admixture among crater lakes has possibly facilitated this process in one case, but overall, admixture and secondary waves of colonization cannot predict morphological divergence and intralacustrine diversification. Instead, morphological divergence is larger the more dissimilar a crater lake is compared to the source lake and happens rapidly after colonization followed by a slow‐down with time. Our data also provide some evidence that founder effects may positively contribute to divergence. The depth of a crater lake is positively associated with variation in body shapes (and number of species), presumably by providing more ecological opportunities. In conclusion, we find that parallel morphological divergence in allopatry and the propensity for diversification in sympatry across the entire Midas cichlid fish radiation is partly predictable and mostly driven by ecology.publishe

A new Merluccius polli reference genome to investigate the effects of global change in West African waters

Genome resources have become crucial to assess genome-wide level of variation as well as to detect adaptive variation. This is particularly important for studying diversity in marine species inhabiting regions highly affected by accelerated climate warming and pollution, also known as global change. A greater awareness of the impacts of global change is urgently needed to ensure sustainable marine fisheries. Despite recent efforts, there are still many gaps in fish reference genomes, both geographical and taxonomic. Here, we sequence, assemble and annotate the genome of Merluccius polli. The total length of this new assembly (~582 Kb, N50 = 168Kb) is approximately 40% longer and much less fragmented than a previous version. Even though it might not be intrinsic of this species, low level of heterozygosity (1.16 SNPs/Kb) and low proportion of repeat content (9.21%) was found in this genome. This hake species has a wide latitudinal distribution; therefore, it is exposed to a changing temperature gradient and to a variety of contaminants in part of its distribution along West African coast. Special emphasis was laid on the identification and characterization of candidate genes known to respond to different stressors (depth, temperature, hypoxia, and heavy metals) happening along its geographical distribution. A total of 68 of the selected candidate genes known to be associated with responses to these stressors were found in the current assembly of the genome, and their predicted sequence can be considered as full-length. Therefore, it is expected that this genome would serve as a tool to further investigations of global change in one of the most stressed marine regions in the planet

Considerations of Efficiency and Distributive Justice in Multidimensional Poverty Measurement

Ab den 1980er Jahren entwickelte Amartya Sen eine neue Wohlfahrtstheorie: den Capability Approach (Sen, 1979; 1985; 1992; 1999; 2009). Dabei ersetzen Capabilities und Functionings, d.h. das, was Personen tatsächlich in der Lage sind zu tun und zu sein, den traditionellen Einkommensansatz. Armut ist im Capability Approach das Unvermögen, ein bestimmtes Minimum an zentralen Capabilities zu erreichen, die benötigt werden, um das Leben nach den eigenen Vorstellungen zu gestalten. Der Capability Approach hat so viele interessante Eigenschaften, besonders in Bezug auf die Armutsmessung, dass er zunehmend Einfluss in der Wohlfahrtsökonomie gewinnt. Diese Entwicklung wird durch empirische Untersuchungen gefördert, die zeigen, dass dieser multidimensionale Ansatz zur Armutsmessung deutlich andere Ergebnisse generiert als der traditionelle Einkommensansatz (vgl. Klasen, 2000, Alkire und Santos, 2010, Figari, 2012). Der derzeitige multidimensionale Ansatz hat jedoch eine methodische Schwäche: Ungleichheit zwischen Armutsdimensionen wird entweder als Korrelationssensitivität definiert – womit Effizienz aber nicht Verteilungsgerechtigkeit berücksichtigt wird – oder als die Verteilung multipler Mangelerscheinungen in einer Gesellschaft – womit Verteilungsgerechtigkeit aber nicht Effizienz berücksichtigt wird. Die ersten beiden Kapitel dieser Dissertation widmen sich der Behebung dieser methodischen Schwäche. Dazu wird Ungleichheit zwischen Dimensionen zunächst als „korrelationssensitive Verteilung multipler Mangelerscheinungen in einer Gesellschaft“ definiert. Die ersten beiden Kapitel operationalisieren diese erweiterte Definition für den Fall ordinaler und kardinaler Armutsindices. Im Einzelnen wird ein neues Axiom für den ordinalen sowie den kardinalen Fall eingeführt, das das Ausmaß, mit dem ein Ungleichheitsfördernder Tausch Armut sinken (oder steigen) lässt, von der Beziehung zwischen den Armutsdimensionen abhängig macht. Diese Neuerung wird benutzt um eine neue Klasse ordinaler bzw. kardinaler Armutsindices herzuleiten. Diese zwei Klassen sind die ersten additiven Armutsindices die in der Lage sind, sowohl Ungleichheit als auch Korrelationssensitivität zu erfassen. Das dritte Kapitel nutzt das deutsche sozio-ökonomische Panel um zwei ordinale Armutsindices für Deutschland vorzuschlagen, die auf der zuvor entwickelten Methode basieren: den „Deutschen Korrelationssensitiven Armutsindex“ und den „Subjektiven Korrelationssensitiven Armutsindex“. Die beiden Indices werden mit dem offiziellen deutschen Armutsmaß, der Armutsgefährdungsquote, über Dimensionen, Regionen und über die Zeit hinweg verglichen. Die Resultate zeigen vor allem eines: die signifikanten Unterschiede in der Beurteilung von Armut und Armutstrends die durch die verschiedenen Indices versursacht werden und den hohen Mehrwert den die Operationalisierung des Capability Approachs darstellt

Contrasting signatures of genomic divergence during sympatric speciation

Population genomic analyses of Midas cichlid fishes in young Nicaraguan crater lakes suggest that sympatric speciation is promoted by polygenic architectures. The transition from 'well-marked varieties' of a single species into 'well-defined species'-especially in the absence of geographic barriers to gene flow (sympatric speciation)-has puzzled evolutionary biologists ever since Darwin(1,2). Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process(3). Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs(4), but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories(5). Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry.Peer reviewe

Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range

notes: PMCID: PMC2882343© 2010 Griffiths et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Anadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range.European Union INTERREG IIIB programme (Atlantic Salmon Arc Project [ASAP], Project No. 040)

Two fish in a pod. Mislabelling on board threatens sustainability in mixed fisheries

Accuracy in reporting captures is a key element to achieve fisheries sustainability. However, identification of the catches might be a challenge when two or more species are morphologically similar and caught jointly, like the mixed fisheries of black hakes in East Atlantic African waters. Black hakes (Merluccius senegalensis and M. polli) are tough to differentiate without previous training due to their high morphological resemblance. The two species are managed as a single stock, although the biological differences between them suggest the need of a separate management. In this study, a total of 806 black hakes were visually identified by fishers on deck of fishing vessels operating in Mauritania and Senegal waters, then assigned to a species by sequencing 450bp of the Mitochondrial Control Region. Comparing the results with visual identification we found 31.4% of the total catch were incorrectly labelled on board by the fishermen. The accuracy of the fishers' identification depended on the depth of capture and on fish size, larger individuals caught from deeper waters being more correctly assigned to M. polli. Mislabelling biased to M. polli suggests that M. senegalensis, already catalogued as endangered, is being underreported, which could endanger the conservation of this species and threaten the sustainability of black hake fisheries. Our results highlight the need for separate evaluation of the stocks in mixed fisheries for morphologically similar fish. Thus, monitoring through DNA barcoding in the very first step of the seafood chain surveys would improve accurate species delimitation and reduce its impact on the correct assessment of the stocks.info:eu-repo/semantics/publishedVersio

A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.)

Atlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon

Estructura genética de poblaciones de merluzas americanas y trazabilidad de productos pesqueros

La falta de barreras al flujo génico es característica en la mayoría de los ambientes habitados por los peces pelágicos marinos, por lo tanto se espera que las especies de peces marinos con gran capacidad de dispersión constituyan poblaciones más o menos panmícticas. Sin embargo, existe un número creciente de estudios que evidencian estructuración espacial en poblaciones de peces marinos. Durante las últimas décadas, uno de las principales retos de la genética en pesquerías ha sido la delimitación de los stocks (unidad clave para el manejo sostenible de las pesquerías). De este modo, una descripción detallada de la estructura poblacional es crucial para la conservación de los recursos naturales. A pesar que las merluzas se encuentran entre las especies de peces marinos comercialmente más explotadas, no existe demasiada información acerca de la estructura genética poblacional de las mismas. El objetivo principal de esta tesis fue evaluar la estructura genética poblacional de diferentes especies de merluzas americanas explotadas comercialmente, empleando tanto marcadores nucleares como mitocondriales. Otro de los objetivos de este trabajo fue el desarrollo de nuevos marcadores moleculares que permitieran distinguir las distintas especies de merluzas del género Merluccius, para ser aplicados en la detección de errores en la identificación de productos comerciales de merluzas. Se ha detectado un alto grado de hibridación introgresiva de tipo bidireccional, empleando microsatélites como marcadores moleculares, entre las dos especies de merluzas norteamericanas Merluccius albidus y M. bilinearis en el área de solapamiento entre sus rangos de distribución. A partir del desarrollo de nuevos marcadores microsatélites, se identificó los distintos patrones de estructuración genética poblacional en las especies de merluzas estudiadas, asociados con diferentes tipos de barreras al flujo génico. Se encontró una gran diferenciación genética entre poblaciones distantes de la merluza austral (M. australis) que habitan Nueva Zelanda y Sudamérica, probablemente asociada con corrientes que previenen la homogeneización entre las poblaciones. Diferencias genéticas sutiles, con la identificación de stocks singulares en las merluzas que habitan los golfos, han sido detectadas para M. hubbsi y M. bilinearis en el Atlántico Sur y Norte, respectivamente. El flujo génico asimétrico detectado entre los golfos y las poblaciones de mar abierto, indica que las poblaciones que habitan los golfos podrían estar actuando como fuente de variación genética para estas especies de merluzas. Finalmente, se encontró una variación genética reducida en el Océano Pacífico para Merluccius australis y Macruronus magellanicus, que podría estar asociado con una mayor explotación pesquera en esta área durante las últimas décadas. En el caso de Merluccius australis, se encontró una diferenciación significativa y un flujo génico asimétrico entre las poblaciones del océano Pacífico y el Atlántico. Se han podido identificar once especies del género Merluccius mediante la utilización de un nuevo marcador molecular basado en SNPs mitocondriales (mtSNPs). Se detectó un elevado nivel de error en la identificación de productos comerciales y desembarcos de merluzas, principalmente en especies que son explotadas de forma conjunta

Species-specific differences in adaptive phenotypic plasticity in an ecologically relevant trophic trait : hypertrophic lips in midas cichlid fishes

The spectacular species richness of cichlids and their diversity in morphology, coloration, and behavior have made them an ideal model for the study of speciation and adaptive evolution. Hypertrophic lips evolved repeatedly and independently in African and Neotropical cichlid radiations. Cichlids with hypertrophic lips forage predominantly in rocky crevices and it has been hypothesized that mechanical stress caused by friction could result in larger lips through phenotypic plasticity. To test the influence of the environment on the size and development of lips, we conducted a series of breeding and feeding experiments on Midas cichlids. Full-sibs of Amphilophus labiatus (thick-lipped) and Amphilophus citrinellus (thin-lipped) each were split into a control group which was fed food from the water column and a treatment group whose food was fixed to substrates. We found strong evidence for phenotypic plasticity on lip area in the thick-lipped species, but not in the thin-lipped species. Intermediate phenotypic values were observed in hybrids from thick- and thin-lipped species reared under “control” conditions. Thus, both a genetic, but also a phenotypic plastic component is involved in the development of hypertrophic lips in Neotropical cichlids. Moreover, species-specific adaptive phenotypic plasticity was found, suggesting that plasticity is selected for in recent thick-lipped species

Data from: Species-specific differences in adaptive phenotypic plasticity in an ecologically relevant trophic trait: hypertrophic lips in Midas cichlid fishes

The spectacular species richness of cichlids and their diversity in morphology, coloration, and behaviour have made them an ideal model for the study of speciation and adaptive evolution. Hypertrophic lips evolved repeatedly and independently in African and Neotropical cichlid radiations. Cichlids with hypertrophic lips forage predominantly in rocky crevices and it has been hypothesized that mechanical stress caused by friction could result in larger lips through phenotypic plasticity. To test the influence of the environment on the size and development of lips, we conducted a series of breeding and feeding experiments on Midas cichlids. Full-sibs of Amphilophus labiatus (thick-lipped) and A. citrinellus (thin-lipped) each were split into a control group which was fed food from the water column and a treatment group whose food was fixed to substrates. We found strong evidence for phenotypic plasticity on lip area in the thick-lipped species, but not in the thin-lipped species. Intermediate phenotypic values were observed in hybrids from thick- and thin-lipped species reared under “control” conditions. Thus, both a genetic, but also a phenotypic plastic component is involved in the development of hypertrophic lips in Neotropical cichlids. Moreover, species-specific adaptive phenotypic plasticity was found, suggesting that plasticity is selected for in recent thick-lipped species