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  • 1
    Online Resource
    Online Resource
    Origin matters: Using a local reference genome improves measures in population genomics
    Wiley ; 2023
    In:  Molecular Ecology Resources Vol. 23, No. 7 ( 2023-10), p. 1706-1723
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 23, No. 7 ( 2023-10), p. 1706-1723
    Abstract: Genome sequencing enables answering fundamental questions about the genetic basis of adaptation, population structure and epigenetic mechanisms. Yet, we usually need a suitable reference genome for mapping population‐level resequencing data. In some model systems, multiple reference genomes are available, giving the challenging task of determining which reference genome best suits the data. Here, we compared the use of two different reference genomes for the three‐spined stickleback ( Gasterosteus aculeatus ), one novel genome derived from a European gynogenetic individual and the published reference genome of a North American individual. Specifically, we investigated the impact of using a local reference versus one generated from a distinct lineage on several common population genomics analyses. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we demonstrate that genetic distance among samples and the reference genomes impacts downstream analyses. Using a local reference genome increased mapping efficiency and genotyping accuracy, effectively retaining more and better data. Despite comparable distributions of the metrics generated across the genome using SNP data (i.e. π, Tajima's D and F ST ), window‐based statistics using different references resulted in different outlier genes and enriched gene functions. A marker‐based analysis of DNA methylation distributions had a comparably high overlap in outlier genes and functions, yet with distinct differences depending on the reference genome. Overall, our results highlight how using a local reference genome decreases reference bias to increase confidence in downstream analyses of the data. Such results have significant implications in all reference‐genome‐based population genomic analyses.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.v23.7
    DOI: 10.1111/1755-0998.13838
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Inconsistent patterns of body size evolution in co‐occurring island reptiles
    Wiley ; 2018
    In:  Global Ecology and Biogeography Vol. 27, No. 5 ( 2018-05), p. 538-550
    Details
    In: Global Ecology and Biogeography, Wiley, Vol. 27, No. 5 ( 2018-05), p. 538-550
    Abstract: Animal body sizes are often remarkably variable across islands, but despite much research we still have a poor understanding of both the patterns and the drivers of body size evolution. Theory predicts that interspecific competition and predation pressures are relaxed on small, remote islands, and that these conditions promote body size evolution. We studied body size variation across multiple insular populations of 16 reptile species co‐occurring in the same archipelago and tested which island characteristics primarily drive body size evolution, the nature of the common patterns, and whether co‐occurring species respond in a similar manner to insular conditions. Location Aegean Sea islands. Time period 1984–2016. Major taxa studied Reptiles. Methods We combined fieldwork, museum measurements and a comprehensive literature survey to collect data on nearly 10,000 individuals, representing eight lizard and eight snake species across 273 islands. We also quantified a large array of predictors to assess directly the effects of island area, isolation (both spatial and temporal), predation and interspecific competition on body size evolution. We used linear models and meta‐analyses to determine which predictors are informative for all reptiles, for lizards and snakes separately, and for each species. Results Body size varies with different predictors across the species we studied, and patterns differ within families and between lizards and snakes. Each predictor influenced body size in at least one species, but no general trend was recovered. As a group, lizards are hardly affected by any of the predictors we tested, whereas snake size generally increases with area and with competitor and predator richness, and decreases with isolation. Main conclusions No factor emerges as a predominant driver of Aegean reptile sizes. This contradicts theories of general body size evolutionary trajectories on islands. We conclude that overarching generalizations oversimplify patterns and processes of reptile body size evolution on islands. Instead, species’ autecology and island particularities interact to drive the course of size evolution.
    Type of Medium: Online Resource
    ISSN: 1466-822X , 1466-8238
    URL: Issue
    URL: Article
    DOI: 10.1111/geb.2018.27.issue-5
    DOI: 10.1111/geb.12716
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 1479787-2
    detail.hit.zdb_id: 2021283-5
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Linking epigenetics and biological conservation: Towards a conservation epigenetics perspective
    Wiley ; 2020
    In:  Functional Ecology Vol. 34, No. 2 ( 2020-02), p. 414-427
    Details
    In: Functional Ecology, Wiley, Vol. 34, No. 2 ( 2020-02), p. 414-427
    Abstract: Biodiversity conservation is a global issue where the challenge is to integrate all levels of biodiversity to ensure the long‐term evolutionary potential and resilience of biological systems. Genetic approaches have largely contributed to conservation biology by defining “conservation entities” accounting for their evolutionary history and adaptive potential, the so‐called evolutionary significant units (ESUs). Yet, these approaches only loosely integrate the short‐term ecological history of organisms. Here, we argue that epigenetic variation, and more particularly DNA methylation, represents a molecular component of biodiversity that directly links the genome to the environment. As such, it provides the required information on the ecological background of organisms for an integrative field of conservation biology. We synthesize knowledge about the importance of epigenetic mechanisms in (a) orchestrating fundamental development alternatives in organisms, (b) enabling individuals to respond in real‐time to selection pressures and (c) improving ecosystem stability and functioning. Using practical examples in conservation biology, we illustrate the relevance of DNA methylation (a) as biomarkers of past and present environmental stress events as well as biomarkers of physiological conditions of individuals; (b) for documenting the ecological structuring/clustering of wild populations and hence for better integrating ecology into ESUs; (c) for improving conservation translocations; and (d) for studying landscape functional connectivity. We conclude that an epigenetic conservation perspective will provide environmental managers the possibility to refine ESUs, to set conservation plans taking into account the capacity of organisms to rapidly cope with environmental changes, and hence to improve the conservation of wild populations. A free Plain Language Summary can be found within the Supporting Information of this article.
    Type of Medium: Online Resource
    ISSN: 0269-8463 , 1365-2435
    URL: Issue
    URL: Article
    DOI: 10.1111/fec.v34.2
    DOI: 10.1111/1365-2435.13429
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2020307-X
    detail.hit.zdb_id: 619313-4
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Tail regeneration alters the digestive performance of lizards
    Wiley ; 2021
    In:  Journal of Evolutionary Biology Vol. 34, No. 4 ( 2021-04), p. 671-679
    Details
    In: Journal of Evolutionary Biology, Wiley, Vol. 34, No. 4 ( 2021-04), p. 671-679
    Abstract: Tissue regeneration is a fundamental evolutionary adaptation, which is well known in lizards that can regenerate their entire tail. However, numerous parameters of this process remain poorly understood. Lizard tail serves many functions. Thus, tail autotomy comes with many disadvantages and the need for quick regeneration is imperative. To provide the required energy and materials for caudal tissue building, lizards are expected to undergo a number of physiological and biochemical adjustments. Previous research showed that tail regeneration induces changes in the digestive process. Here, we investigated if and how tail regeneration affects the digestive performance in five wall lizard species deriving from mainland and island sites and questioned whether the association of tail regeneration and digestion is affected by species relationships or environmental features, including predation pressure. We expected that lizards from high predation environments would regenerate their tail faster and modify accordingly their digestive efficiency, prioritizing the digestion of proteins; the main building blocks for tissue repair. Second, we anticipated that the general food shortage on islands would inhibit the process. Our findings showed that all species shifted their digestive efficiency, as predicted. Elongation rate was higher in sites with stronger predation regime and this was also applied to the rate with which protein digestion raised. Gut passage time increases during regeneration so as to improve the nutrient absorbance, but among the islanders, the pace was more intense. The deviations between species should be attributed to the different ecological conditions prevailing on islands rather than to their phylogenetic relationships.
    Type of Medium: Online Resource
    ISSN: 1010-061X , 1420-9101
    URL: Issue
    URL: Article
    DOI: 10.1111/jeb.v34.4
    DOI: 10.1111/jeb.13769
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 92624-3
    detail.hit.zdb_id: 1465318-7
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Ecological explanations to island gigantism: dietary niche divergence, predation, and size in an endemic lizard
    Wiley ; 2015
    In:  Ecology Vol. 96, No. 8 ( 2015-08), p. 2077-2092
    Details
    In: Ecology, Wiley, Vol. 96, No. 8 ( 2015-08), p. 2077-2092
    Abstract: Although rapid evolution of body size on islands has long been known, the ecological mechanisms behind this island phenomenon remain poorly understood. Diet is an important selective pressure for morphological divergence. Here we investigate if selection for novel diets has contributed to the multiple independent cases of island gigantism in the Skyros wall lizard ( Podarcis gaigeae ) and if diet, predation, or both factors best explain island gigantism. We combined data on body size, shape, bite force, and realized and available diets to address this. Several lines of evidence suggest that diet has contributed to the island gigantism. The larger islet lizards have relatively wider heads and higher bite performance in relation to mainland lizards than would be expected from size differences alone. The proportions of consumed and available hard prey are higher on islets than mainland localities, and lizard body size is significantly correlated with the proportion of hard prey. Furthermore, the main axis of divergence in head shape is significantly correlated with dietary divergence. Finally, a model with only diet and one including diet and predation regime explain body size divergence equally well. Our results suggest that diet is an important ecological factor behind insular body size divergence, but could be consistent with an additional role for predation.
    Type of Medium: Online Resource
    ISSN: 0012-9658 , 1939-9170
    URL: Article
    URL: Article
    DOI: 10.1890/14-1996.1
    DOI: 10.1890/14-1996.1.sm
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 1797-8
    detail.hit.zdb_id: 2010140-5
    SSG: 12
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