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Knief U, Müller IA, Stryjewski KF, Metzler D, Sorenson MD, Wolf JBW. Evolution of chromosomal inversions across an avian radiation. Mol Biol Evol 2024:msae092. [PMID: 38743589 DOI: 10.1093/molbev/msae092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/05/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
Chromosomal inversions are structural mutations that can play a prominent role in adaptation and speciation. Inversions segregating across species boundaries (trans-species inversions) are often taken as evidence for ancient balancing selection or adaptive introgression but can also be due to incomplete lineage sorting (ILS). Using whole-genome resequencing data from 18 populations of 11 recognized munia species in the genus Lonchura (N = 176 individuals), we identify four large para- and pericentric inversions ranging in size from 4 to 20 Mb. All four inversions co-segregate across multiple species and predate the numerous speciation events associated with the rapid radiation of this clade across the prehistoric Sahul (Australia, New Guinea) and Bismarck Archipelago. Using coalescent theory, we infer that trans-specificity is improbable for neutrally segregating variation despite substantial ILS characterizing this young radiation. Instead, maintenance of all three autosomal inversions (chr1, chr5, chr6) is best explained by selection acting along eco-geographic clines not observed for the collinear parts of the genome. In addition, the large sex chromosome inversion largely aligns with species boundaries and shows signatures of repeated positive selection for both alleles. This study provides evidence for trans-species inversion polymorphisms involved in both adaptation and speciation. It further highlights the importance of informing selection inference using a null model of neutral evolution derived from the collinear part of the genome.
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Affiliation(s)
- Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
- Evolutionary Biology & Ecology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Ingo A Müller
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 11418 Stockholm, Sweden
- Division of Systematics and Evolution, Department of Zoology, Stockholm University, 11418 Stockholm, Sweden
| | | | - Dirk Metzler
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
| | | | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
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Fröhlich M, van Noordwijk MA, Mitra Setia T, van Schaik CP, Knief U. Wild and captive immature orangutans differ in their non-vocal communication with others, but not with their mothers. Behav Ecol Sociobiol 2024; 78:12. [PMID: 38235053 PMCID: PMC10789664 DOI: 10.1007/s00265-023-03426-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/19/2024]
Abstract
Abstract In many group-living species, individuals are required to flexibly modify their communicative behaviour in response to current social challenges. To unravel whether sociality and communication systems co-evolve, research efforts have often targeted the links between social organisation and communicative repertoires. However, it is still unclear which social or interactional factors directly predict communicative complexity. To address this issue, we studied wild and zoo-housed immature orangutans of two species to assess the impact of the socio-ecological setting on the production of non-vocal signal repertoires. Specifically, we compared repertoire size, dyadic repertoire similarity, and number of social goals (i.e. observer's estimate of the signaller's intended interaction outcome) for communicative interactions with mothers versus other conspecifics, controlling for critical individual and environmental factors. In this small sample of immature orangutans, wild-captive contrasts were statistically significant only for other-directed repertoires, but not for mother-directed repertoires, and not for the number of social goals that immatures communicated towards. While the repertoires of individuals living in the same research setting were more similar than those living in contrasting settings, this difference was most pronounced for other-directed repertoires of the less socially tolerant orangutan species. These results suggest that the boosted interactional opportunities in captivity rather than mere differences in environmental affordances or communicative needs drive the wild-captive contrast in orangutan communicative repertoires. Overall, this fine-grained analysis of repertoires further underscores that not only a species' social organisation but also the targeted audience may have a profound impact on communicative behaviour. Significance statement Navigating a dynamic social environment often requires flexible signal use. While it has repeatedly been shown that the social organisation and structure of species predict the complexity of their communication systems, the mechanisms underlying these relationships are largely unknown. Because targeted studies to assess this issue in great apes are difficult, we take an alternative approach here: we compare the same species living in the wild and in artificial habitats in captivity. This contrast allows a direct test of how repertoires respond to the relevant difference in socio-ecological conditions. Our results show that the diversity of interaction partners (i.e. social opportunities), but not the diversity of social goals (i.e. possible interaction outcomes) or the broader physical opportunities (i.e. safe ground use), predict the size and consistency of wild and captive signalling repertoires. Supplementary Information The online version contains supplementary material available at 10.1007/s00265-023-03426-3.
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Affiliation(s)
- Marlen Fröhlich
- Palaeoanthropology, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - Maria A. van Noordwijk
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
- Comparative Socioecology Research Group, Max Planck Institute of Animal Behavior, Konstanz, Germany
| | - Tatang Mitra Setia
- Fakultas Biologi, Universitas Nasional, 12520 Jakarta Selatan, Indonesia
| | - Carel P. van Schaik
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
- Comparative Socioecology Research Group, Max Planck Institute of Animal Behavior, Konstanz, Germany
- Center for the Interdisciplinary Study of Language Evolution (ISLE), University of Zurich, Zurich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Ulrich Knief
- Evolutionary Biology and Ecology, Faculty of Biology, University of Freiburg, Freiburg, Germany
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Catalán A, Merondun J, Knief U, Wolf JBW. Chromatin accessibility, not 5mC methylation covaries with partial dosage compensation in crows. PLoS Genet 2023; 19:e1010901. [PMID: 37747941 PMCID: PMC10575545 DOI: 10.1371/journal.pgen.1010901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/13/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
The evolution of genetic sex determination is often accompanied by degradation of the sex-limited chromosome. Male heterogametic systems have evolved convergent, epigenetic mechanisms restoring the resulting imbalance in gene dosage between diploid autosomes (AA) and the hemizygous sex chromosome (X). Female heterogametic systems (AAf Zf, AAm ZZm) tend to only show partial dosage compensation (0.5 < Zf:AAf < 1) and dosage balance (0.5
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Affiliation(s)
- Ana Catalán
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Justin Merondun
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Ulrich Knief
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
- Evolutionary Biology & Ecology,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jochen B. W. Wolf
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
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Pei Y, Forstmeier W, Knief U, Kempenaers B. Weak antagonistic fitness effects can maintain an inversion polymorphism. Mol Ecol 2023. [PMID: 37118648 DOI: 10.1111/mec.16963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 04/30/2023]
Abstract
The study of chromosomal inversion polymorphisms has received much recent attention, particularly in cases where inversions have drastic effects on phenotypes and fitness (e.g. lethality of homozygotes). Less attention has been paid to the question of the maintenance of inversion polymorphisms that show only weak effects. Here, we study the maintenance of such an inversion polymorphism that links 250 genes on chromosome Tgu11 in the zebra finch (Taeniopygia guttata). Based on data from over 6000 captive birds, we estimated the effects of this inversion on a wide range of fitness-related traits. We found that, compared with the ancestral allele A, the inverted allele D had small additive beneficial effects on male siring success and on female fecundity. These fitness-enhancing effects may explain the initial spread of the derived D allele (allele frequency 53%). However, individuals that were homozygous for D had a slightly lower survival rate, which may explain why the D allele has not spread to fixation. We used individual-based simulations to examine how an inversion polymorphism with such antagonistic fitness effects behaves over time. Our results indicate that polymorphisms become stabilized at an intermediate allele frequency if the inversion links an additively beneficial allele of small effect size to a recessive weakly deleterious mutation, overall resulting in weak net heterosis. Importantly, this conclusion remains valid over a wide range of selection coefficients against the homozygous DD (up to lethality), suggesting that the conditions needed to maintain the polymorphism may frequently be met. However, the simulations also suggest that in our zebra finch populations, the estimated recessive deleterious effect of the D allele (on survival in captivity) is not quite large enough to prevent fixation of the D allele in the long run. Estimates of fitness effects from free-living populations are needed to validate these results.
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Affiliation(s)
- Yifan Pei
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Institute for Evolutionary Biology and Ecology, University of Bonn, Bonn, Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
- Evolutionary Biology and Ecology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
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Fröhlich M, van Schaik CP, van Noordwijk MA, Knief U. Individual variation and plasticity in the infant-directed communication of orang-utan mothers. Proc Biol Sci 2022; 289:20220200. [PMID: 35582800 PMCID: PMC9114970 DOI: 10.1098/rspb.2022.0200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Between-individual variation in behavioural expression, such as social responsiveness, has been shown to have important eco-evolutionary consequences. However, most comparative research on non-human primate communication has focused on species- or population-level variation, while among- and within-individual variation has been largely ignored or considered as noise. Here, we apply a behavioural reaction norm framework to repeated observations of mother-offspring interactions in wild and zoo-housed orang-utans (Pongo abelii, P. pygmaeus) to tease apart variation on the individual level from population-level and species-level differences. Our results showed that mothers not only differed in the composition of their infant-directed gestural repertoires, but also in communicative tactics, such as gestural redoings (i.e. persistence) and responsiveness to infants' requests. These differences remained after controlling for essential moderators, including species, setting, parity and infant age. Importantly, mothers differed in how they adjusted their behaviour across social contexts, making a strong case for investigating within-individual variation. Our findings highlight that partitioning behavioural variation into its within-individual, between-individual and environmental sources allows us to estimate the extent of plastic responses to the immediate environment in great ape communication.
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Affiliation(s)
- Marlen Fröhlich
- Paleoanthropology, Institute for Archaeological Sciences, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany,Department of Anthropology, University of Zurich, Zurich, Switzerland
| | - Carel P. van Schaik
- Department of Anthropology, University of Zurich, Zurich, Switzerland,Comparative Socioecology Research Group, Max Planck Institute of Animal Behavior, Konstanz, Germany,Center for the Interdisciplinary Study of Language Evolution (ISLE), University of Zurich, Zurich, Switzerland,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Maria A. van Noordwijk
- Department of Anthropology, University of Zurich, Zurich, Switzerland,Comparative Socioecology Research Group, Max Planck Institute of Animal Behavior, Konstanz, Germany
| | - Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
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Pei Y, Forstmeier W, Ruiz-Ruano FJ, Mueller JC, Cabrero J, Camacho JPM, Alché JD, Franke A, Hoeppner M, Börno S, Gessara I, Hertel M, Teltscher K, Knief U, Suh A, Kempenaers B. Occasional paternal inheritance of the germline-restricted chromosome in songbirds. Proc Natl Acad Sci U S A 2022; 119:e2103960119. [PMID: 35058355 PMCID: PMC8794876 DOI: 10.1073/pnas.2103960119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 11/06/2021] [Indexed: 11/29/2022] Open
Abstract
Songbirds have one special accessory chromosome, the so-called germline-restricted chromosome (GRC), which is only present in germline cells and absent from all somatic tissues. Earlier work on the zebra finch (Taeniopygia guttata castanotis) showed that the GRC is inherited only through the female line-like the mitochondria-and is eliminated from the sperm during spermatogenesis. Here, we show that the GRC has the potential to be paternally inherited. Confocal microscopy using GRC-specific fluorescent in situ hybridization probes indicated that a considerable fraction of sperm heads (1 to 19%) in zebra finch ejaculates still contained the GRC. In line with these cytogenetic data, sequencing of ejaculates revealed that individual males from two families differed strongly and consistently in the number of GRCs in their ejaculates. Examining a captive-bred male hybrid of the two zebra finch subspecies (T. g. guttata and T. g. castanotis) revealed that the mitochondria originated from a castanotis mother, whereas the GRC came from a guttata father. Moreover, analyzing GRC haplotypes across nine castanotis matrilines, estimated to have diverged for up to 250,000 y, showed surprisingly little variability among GRCs. This suggests that a single GRC haplotype has spread relatively recently across all examined matrilines. A few diagnostic GRC mutations that arose since this inferred spreading suggest that the GRC has continued to jump across matriline boundaries. Our findings raise the possibility that certain GRC haplotypes could selfishly spread through the population via occasional paternal transmission, thereby outcompeting other GRC haplotypes that were limited to strict maternal inheritance, even if this was partly detrimental to organismal fitness.
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Affiliation(s)
- Yifan Pei
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany;
| | - Wolfgang Forstmeier
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany;
| | - Francisco J Ruiz-Ruano
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, United Kingdom;
- Department of Organismal Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University SE-752 36 Uppsala, Sweden
| | - Jakob C Mueller
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Josefa Cabrero
- Department of Genetics, University of Granada E-18071 Granada, Spain
| | | | - Juan D Alché
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council E-18008 Granada, Spain
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel 24118 Kiel, Germany
| | - Marc Hoeppner
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel 24118 Kiel, Germany
| | - Stefan Börno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics 14195 Berlin, Germany
| | - Ivana Gessara
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Moritz Hertel
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Kim Teltscher
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich D-82152 Planegg-Martinsried, Germany
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, United Kingdom;
- Department of Organismal Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University SE-752 36 Uppsala, Sweden
| | - Bart Kempenaers
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
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Metzler D, Knief U, Peñalba JV, Wolf JBW. Assortative mating and epistatic mating-trait architecture induce complex movement of the crow hybrid zone. Evolution 2021; 75:3154-3174. [PMID: 34694633 DOI: 10.1111/evo.14386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/06/2021] [Indexed: 12/20/2022]
Abstract
Hybrid zones provide a window into the evolutionary processes governing species divergence. Yet, the contribution of mate choice to the temporal and spatial stability of hybrid zones remains poorly explored. Here, we investigate the effects of assortative mating on hybrid-zone dynamics by means of a mathematical model parameterized with phenotype and genotype data from the hybrid zone between all-black carrion and gray-coated hooded crows. In the best-fit model, narrow clines of the two mating-trait loci were maintained by a moderate degree of assortative mating inducing pre- and postzygotic isolation via positive frequency-dependent selection. Epistasis between the two loci induced hybrid-zone movement in favor of alleles conveying dark plumage followed by a shift in the opposite direction favoring gray-coated phenotypes ∼ 1 200 generations after secondary contact. Unlinked neutral loci diffused near-unimpeded across the zone. These results were generally robust to the choice of matching rule (self-referencing or parental imprinting) and effects of genetic drift. Overall, this study illustrates under which conditions assortative mating can maintain steep clines in mating-trait loci without generalizing to genome-wide reproductive isolation. It further emphasizes the importance of the genetic mating-trait architecture for spatio-temporal hybrid-zone dynamics.
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Affiliation(s)
- Dirk Metzler
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, Munich, 80539, Germany
| | - Ulrich Knief
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, Munich, 80539, Germany
| | - Joshua V Peñalba
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, Munich, 80539, Germany
| | - Jochen B W Wolf
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, Munich, 80539, Germany
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Knief U, Forstmeier W, Kempenaers B, Wolf JBW. A sex chromosome inversion is associated with copy number variation of mitochondrial DNA in zebra finch sperm. R Soc Open Sci 2021; 8:211025. [PMID: 34540261 PMCID: PMC8437020 DOI: 10.1098/rsos.211025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
The propulsion of sperm cells via movement of the flagellum is of vital importance for successful fertilization. While the exact mechanism of energy production for this movement varies between species, in avian species energy is thought to come predominantly from the mitochondria located in the sperm midpiece. Larger midpieces may contain more mitochondria, which should enhance the energetic capacity and possibly promote mobility. Due to an inversion polymorphism on their sex chromosome TguZ, zebra finches (Taeniopygia guttata castanotis) exhibit large within-species variation in sperm midpiece length, and those sperm with the longest midpieces swim the fastest. Here, we test through quantitative real-time PCR in zebra finch ejaculates whether the inversion genotype has an effect on the copy number of mitochondrial DNA (mtDNA). We find that zebra finches carrying the derived allele (correlated with longer sperm midpieces) have more copies of the mtDNA in their ejaculates than those homozygous for the ancestral allele (shorter midpieces). We suggest downstream effects of mtDNA copy number variation on the rate of adenosine triphosphate production, which in turn may influence sperm swimming speed and fertilization success. Central components of gamete energy metabolism may thus be the proximate cause for a fitness-relevant genetic polymorphism, stabilizing a megabase-scale inversion at an intermediate allele frequency in the wild.
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Affiliation(s)
- Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, Planegg-Martinsried 82152, Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen 82319, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen 82319, Germany
| | - Jochen B. W. Wolf
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, Planegg-Martinsried 82152, Germany
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Weissensteiner MH, Bunikis I, Catalán A, Francoijs KJ, Knief U, Heim W, Peona V, Pophaly SD, Sedlazeck FJ, Suh A, Warmuth VM, Wolf JBW. Author Correction: Discovery and population genomics of structural variation in a songbird genus. Nat Commun 2021; 12:3163. [PMID: 34017009 PMCID: PMC8138003 DOI: 10.1038/s41467-021-23640-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Matthias H Weissensteiner
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden. .,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany. .,Department of Biology, Pennsylvania State University, 310 Wartik Lab, PA, 16802, USA.
| | - Ignas Bunikis
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815752 37, Uppsala, Sweden
| | - Ana Catalán
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | | | - Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Wieland Heim
- Institute of Landscsape Ecology, University of Münster, Heisenbergstrasse 2, 48149, Münster, Germany
| | - Valentina Peona
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.,Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden
| | - Saurabh D Pophaly
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.,Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center at Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Alexander Suh
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.,Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Vera M Warmuth
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Jochen B W Wolf
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden. .,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
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Knief U, Forstmeier W, Pei Y, Wolf J, Kempenaers B. A test for meiotic drive in hybrids between Australian and Timor zebra finches. Ecol Evol 2020; 10:13464-13475. [PMID: 33304552 PMCID: PMC7713956 DOI: 10.1002/ece3.6951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/14/2020] [Accepted: 09/28/2020] [Indexed: 12/16/2022] Open
Abstract
Meiotic drivers have been proposed as a potent evolutionary force underlying genetic and phenotypic variation, genome structure, and also speciation. Due to their strong selective advantage, they are expected to rapidly spread through a population despite potentially detrimental effects on organismal fitness. Once fixed, autosomal drivers are cryptic within populations and only become visible in between-population crosses lacking the driver or corresponding suppressor. However, the assumed ubiquity of meiotic drivers has rarely been assessed in crosses between populations or species. Here we test for meiotic drive in hybrid embryos and offspring of Timor and Australian zebra finches-subspecies that have evolved in isolation for about two million years-using 38,541 informative transmissions of 56 markers linked to either centromeres or distal chromosome ends. We did not find evidence for meiotic driver loci on specific chromosomes. However, we observed a weak overall transmission bias toward Timor alleles at centromeres in females (transmission probability of Australian alleles of 47%, nominal p = 6 × 10-5). While this is in line with the centromere drive theory, it goes against the expectation that the subspecies with the larger effective population size (i.e., the Australian zebra finch) should have evolved the more potent meiotic drivers. We thus caution against interpreting our finding as definite evidence for centromeric drive. Yet, weak centromeric meiotic drivers may be more common than generally anticipated and we encourage further studies that are designed to detect also small effect meiotic drivers.
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Affiliation(s)
- Ulrich Knief
- Department of Behavioural Ecology and Evolutionary GeneticsMax Planck Institute for OrnithologySeewiesenGermany
- Division of Evolutionary BiologyFaculty of BiologyLudwig Maximilian University of MunichPlanegg‐MartinsriedGermany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary GeneticsMax Planck Institute for OrnithologySeewiesenGermany
| | - Yifan Pei
- Department of Behavioural Ecology and Evolutionary GeneticsMax Planck Institute for OrnithologySeewiesenGermany
| | - Jochen Wolf
- Division of Evolutionary BiologyFaculty of BiologyLudwig Maximilian University of MunichPlanegg‐MartinsriedGermany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary GeneticsMax Planck Institute for OrnithologySeewiesenGermany
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11
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Fröhlich M, Kunz J, Fryns C, Falkner S, Rukmana E, Schuppli M, Knief U, Utami Atmoko SS, Schuppli C, van Noordwijk MA. Social interactions and interaction partners in infant orang-utans of two wild populations. Anim Behav 2020. [DOI: 10.1016/j.anbehav.2020.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Weissensteiner MH, Bunikis I, Catalán A, Francoijs KJ, Knief U, Heim W, Peona V, Pophaly SD, Sedlazeck FJ, Suh A, Warmuth VM, Wolf JBW. Discovery and population genomics of structural variation in a songbird genus. Nat Commun 2020; 11:3403. [PMID: 32636372 PMCID: PMC7341801 DOI: 10.1038/s41467-020-17195-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/16/2020] [Indexed: 02/07/2023] Open
Abstract
Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.
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Affiliation(s)
- Matthias H Weissensteiner
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
- Department of Biology, Pennsylvania State University, 310 Wartik Lab, University Park, PA, 16802, USA.
| | - Ignas Bunikis
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, 752 37, Uppsala, Sweden
| | - Ana Catalán
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | | | - Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Wieland Heim
- Institute of Landscsape Ecology, University of Münster, Heisenbergstrasse 2, 48149, Münster, Germany
| | - Valentina Peona
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden
| | - Saurabh D Pophaly
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center at Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Alexander Suh
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Vera M Warmuth
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Jochen B W Wolf
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
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13
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Knief U, Bossu CM, Wolf JBW. Extra-pair paternity as a strategy to reduce the costs of heterospecific reproduction? Insights from the crow hybrid zone. J Evol Biol 2020; 33:727-733. [PMID: 32069366 DOI: 10.1111/jeb.13607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/22/2020] [Accepted: 02/17/2020] [Indexed: 12/30/2022]
Abstract
Within hybrid zones of socially monogamous species, the number of mating opportunities with a conspecific can be limited. As a consequence, individuals may mate with a heterospecific (social) partner despite possible fitness costs to their hybrid offspring. Extra-pair copulations with a conspecific may thus arise as a possible post hoc strategy to reduce the costs of hybridization. We here assessed the rate of extra-pair paternity in the hybrid zone between all-black carrion crows (Corvus (corone) corone) and grey hooded crows (C. (c.) cornix) and tested whether extra-pair paternity (EPP) was more likely in broods where parents differed in plumage colour. The proportion of broods with at least one extra-pair offspring and the proportion of extra-pair offspring were low overall (6.98% and 2.90%, respectively) with no evidence of hybrid broods having higher EPP rates than purebred nests.
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Affiliation(s)
- Ulrich Knief
- Division of Evolutionary Biology, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Christen M Bossu
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany.,Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
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14
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Knief U, Bossu CM, Saino N, Hansson B, Poelstra J, Vijay N, Weissensteiner M, Wolf JBW. Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone. Nat Ecol Evol 2019; 3:570-576. [PMID: 30911146 PMCID: PMC6445362 DOI: 10.1038/s41559-019-0847-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/18/2019] [Indexed: 12/22/2022]
Abstract
The evolution of genetic barriers opposing inter-specific gene flow is key to the origin of new species. Drawing from information of over 400 admixed genomes sourced from replicate transects across the European hybrid zone between all-black carrion crows and grey-coated hooded crows, we decipher the interplay between phenotypic divergence and selection at the molecular level. Over 68% of plumage variation was explained by epistasis between the gene NDP and a ~2.8 Mb region on chromosome 18 with suppressed recombination. Both pigmentation loci showed evidence for divergent selection resisting introgression. This study reveals how few, large-effect loci can govern prezygotic isolation and shield phenotypic divergence from gene flow.
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Affiliation(s)
- Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany
| | - Christen M Bossu
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Institute of the Environment and Sustainability, Center for Tropical Research, University of California, Los Angeles, CA, USA
| | - Nicola Saino
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
| | - Jelmer Poelstra
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Biology Department, Duke University, Durham, NC, USA
| | - Nagarjun Vijay
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Matthias Weissensteiner
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany.,Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany. .,Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.
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15
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Zollinger SA, Dorado-Correa A, Goymann W, Forstmeier W, Knief U, BastidasUrrutia AM, Brumm H. Traffic noise exposure depresses plasma corticosterone and delays offspring growth in breeding zebra finches. Conserv Physiol 2019; 7:coz056. [PMID: 31620292 PMCID: PMC6788579 DOI: 10.1093/conphys/coz056] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/02/2019] [Accepted: 07/17/2019] [Indexed: 05/21/2023]
Abstract
The impact of human activity on the acoustic environment is overwhelming, with anthropogenic noise reaching even remote areas of the planet. The World Health Organization has identified noise pollution as one of the leading environmental health risks in humans, and it has been linked to a myriad of short- and long-term health effects in exposed individuals. However, less is known about the health effects of anthropogenic noise exposure on animals. We investigated long- and short-term effects of traffic noise on zebra finches breeding in small communal aviaries, using a repeated measures design. Birds bred in both noise and no-noise conditions, and we measured baseline plasma glucocorticoid levels before, during and after breeding. In addition, we assayed immune function, measured reproductive success and offspring growth and compared rates of extra-pair paternity of breeding adults. Breeding birds had significantly lower baseline plasma corticosterone levels when exposed to traffic noise than when they were not exposed to noise playback. In addition, the nestlings reared during noise exposure were lighter than nestlings of the same parents when breeding in control conditions. Our results suggest that traffic noise poses a more severe hurdle to birds at more vulnerable stages of their life history, such as during reproductive events and ontogeny. While chronic exposure to traffic noise in our birds did not, by itself, prove to be a sufficient stressor to cause acute effects on health or reproductive success in exposed individuals, it did result in disruptions to normal glucocorticoid profiles and delayed offspring growth. However, animals living in urban habitats are exposed to a multitude of anthropogenic disturbances, and it is likely that even species that appear to be thriving in noisy environments may suffer cumulative effects of these multiple disturbances that may together impact their fitness in urban environments.
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Affiliation(s)
- Sue Anne Zollinger
- Department of Natural Sciences, Manchester Metropolitan University, John Dalton East, Chester Street, Manchester M1 5GD, UK
- Communication and Social Behaviour Group, Max Planck Institute for Ornithology, EberhardGwinnerStrasse 1, 82319 Seewiesen, Germany
- Corresponding author: Department of Natural Sciences, Manchester Metropolitan University, Manchester M1 5GD, UK.
| | - Adriana Dorado-Correa
- Communication and Social Behaviour Group, Max Planck Institute for Ornithology, EberhardGwinnerStrasse 1, 82319 Seewiesen, Germany
| | - Wolfgang Goymann
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, EberhardGwinnerStrasse 1, 82319 Seewiesen, Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, EberhardGwinnerStrasse 1, 82319 Seewiesen, Germany
| | - Ulrich Knief
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, EberhardGwinnerStrasse 1, 82319 Seewiesen, Germany
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, Grosshaderner Strasse 2, 82152 PlaneggMartinsried, Germany
| | - Ana María BastidasUrrutia
- Biodiversity and Global Change Lab, Terrestrial Ecology Research Group, Technical University of Munich, HansCarlvonCarlowitzPlatz 2, 85354 Freising, Germany
| | - Henrik Brumm
- Communication and Social Behaviour Group, Max Planck Institute for Ornithology, EberhardGwinnerStrasse 1, 82319 Seewiesen, Germany
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16
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Forstmeier W, Ihle M, Opatová P, Martin K, Knief U, Albrechtová J, Albrecht T, Kempenaers B. Testing the phenotype-linked fertility hypothesis in the presence and absence of inbreeding. J Evol Biol 2017; 30:968-976. [DOI: 10.1111/jeb.13062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/02/2017] [Indexed: 12/14/2022]
Affiliation(s)
- W. Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
| | - M. Ihle
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
| | - P. Opatová
- Department of Botany and Zoology; Faculty of Science; Masaryk University; Brno Czech Republic
- External Research Facility Studenec; Institute of Vertebrate Biology; Czech Academy of Sciences; Brno Czech Republic
| | - K. Martin
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
| | - U. Knief
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
| | - J. Albrechtová
- External Research Facility Studenec; Institute of Vertebrate Biology; Czech Academy of Sciences; Brno Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague Czech Republic
| | - T. Albrecht
- External Research Facility Studenec; Institute of Vertebrate Biology; Czech Academy of Sciences; Brno Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague Czech Republic
| | - B. Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
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17
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Knief U, Schielzeth H, Backström N, Hemmrich‐Stanisak G, Wittig M, Franke A, Griffith SC, Ellegren H, Kempenaers B, Forstmeier W. Association mapping of morphological traits in wild and captive zebra finches: reliable within, but not between populations. Mol Ecol 2017; 26:1285-1305. [DOI: 10.1111/mec.14009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 12/05/2016] [Accepted: 12/21/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Ulrich Knief
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
| | - Holger Schielzeth
- Department of Population Ecology Friedrich Schiller University Jena 07743 Jena Germany
| | - Niclas Backström
- Department of Ecology and Genetics Uppsala University 752 36 Uppsala Sweden
| | | | - Michael Wittig
- Institute of Clinical Molecular Biology Christian‐Albrechts‐University 24105 Kiel Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology Christian‐Albrechts‐University 24105 Kiel Germany
| | - Simon C. Griffith
- Department of Biological Sciences Macquarie University Sydney NSW 2109 Australia
- School of Biological, Earth & Environmental Sciences University of New South Wales Sydney NSW 2057 Australia
| | - Hans Ellegren
- Department of Ecology and Genetics Uppsala University 752 36 Uppsala Sweden
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
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18
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Knief U, Hemmrich-Stanisak G, Wittig M, Franke A, Griffith SC, Kempenaers B, Forstmeier W. Fitness consequences of polymorphic inversions in the zebra finch genome. Genome Biol 2016; 17:199. [PMID: 27687629 PMCID: PMC5043542 DOI: 10.1186/s13059-016-1056-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/05/2016] [Indexed: 12/21/2022] Open
Abstract
Background Inversion polymorphisms constitute an evolutionary puzzle: they should increase embryo mortality in heterokaryotypic individuals but still they are widespread in some taxa. Some insect species have evolved mechanisms to reduce the cost of embryo mortality but humans have not. In birds, a detailed analysis is missing although intraspecific inversion polymorphisms are regarded as common. In Australian zebra finches (Taeniopygia guttata), two polymorphic inversions are known cytogenetically and we set out to detect these two and potentially additional inversions using genomic tools and study their effects on embryo mortality and other fitness-related and morphological traits. Results Using whole-genome SNP data, we screened 948 wild zebra finches for polymorphic inversions and describe four large (12–63 Mb) intraspecific inversion polymorphisms with allele frequencies close to 50 %. Using additional data from 5229 birds and 9764 eggs from wild and three captive zebra finch populations, we show that only the largest inversions increase embryo mortality in heterokaryotypic males, with surprisingly small effect sizes. We test for a heterozygote advantage on other fitness components but find no evidence for heterosis for any of the inversions. Yet, we find strong additive effects on several morphological traits. Conclusions The mechanism that has carried the derived inversion haplotypes to such high allele frequencies remains elusive. It appears that selection has effectively minimized the costs associated with inversions in zebra finches. The highly skewed distribution of recombination events towards the chromosome ends in zebra finches and other estrildid species may function to minimize crossovers in the inverted regions. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1056-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ulrich Knief
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany. .,Current address: Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, 82152, Planegg-Martinsried, Germany.
| | - Georg Hemmrich-Stanisak
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW, 2057, Australia
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany
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19
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Knief U, Forstmeier W. Mapping centromeres of microchromosomes in the zebra finch (Taeniopygia guttata) using half-tetrad analysis. Chromosoma 2016; 125:757-68. [PMID: 26667931 PMCID: PMC5023761 DOI: 10.1007/s00412-015-0560-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/12/2015] [Accepted: 11/13/2015] [Indexed: 12/24/2022]
Abstract
Centromeres usually consist of hundreds of kilobases of repetitive sequence which renders them difficult to assemble. As a consequence, centromeres are often missing from assembled genomes and their locations on physical chromosome maps have to be inferred from flanking sequences via fluorescence in situ hybridization (FISH). Alternatively, centromere positions can be mapped using linkage analyses in accidentally triploid individuals formed by half-tetrads (resulting from the inheritance of two chromatids from a single meiosis). The current genome assembly of the zebra finch (Taeniopygia guttata) comprises 32 chromosomes, but only for the ten largest chromosomes centromere positions have been mapped using FISH. We here map the positions of most of the remaining centromeres using half-tetrad analyses. For this purpose, we genotyped 37 zebra finches that were triploid or tetraploid due to inheritance errors (and mostly died as embryos) together with their parents at 64 microsatellite markers (at least two per chromosome). Using the information on centromere positions on the ten largest chromosomes, we were able to identify 12 cases of non-disjunction in maternal meiosis I and 10 cases of non-disjunction in maternal meiosis II. These 22 informative cases allowed us to infer centromere positions on additional 19 microchromosomes in reference to the current genome assembly. This knowledge will be valuable for studies of chromosome evolution, meiotic drive and species divergence in the avian lineage.
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Affiliation(s)
- Ulrich Knief
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany
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20
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Lindholm AK, Dyer KA, Firman RC, Fishman L, Forstmeier W, Holman L, Johannesson H, Knief U, Kokko H, Larracuente AM, Manser A, Montchamp-Moreau C, Petrosyan VG, Pomiankowski A, Presgraves DC, Safronova LD, Sutter A, Unckless RL, Verspoor RL, Wedell N, Wilkinson GS, Price TA. The Ecology and Evolutionary Dynamics of Meiotic Drive. Trends Ecol Evol 2016; 31:315-326. [DOI: 10.1016/j.tree.2016.02.001] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/29/2016] [Accepted: 02/01/2016] [Indexed: 12/24/2022]
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Knief U, Schielzeth H, Ellegren H, Kempenaers B, Forstmeier W. A prezygotic transmission distorter acting equally in female and male zebra finchesTaeniopygia guttata. Mol Ecol 2015; 24:3846-59. [DOI: 10.1111/mec.13281] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/13/2015] [Accepted: 06/17/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Ulrich Knief
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Eberhard-Gwinner-Str. 82319 Seewiesen Germany
| | - Holger Schielzeth
- Department of Evolutionary Biology; Bielefeld University; Morgenbreede 45 33615 Bielefeld Germany
| | - Hans Ellegren
- Department of Evolutionary Biology; Uppsala University; Norbyvägen 18D 752 36 Uppsala Sweden
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Eberhard-Gwinner-Str. 82319 Seewiesen Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Eberhard-Gwinner-Str. 82319 Seewiesen Germany
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22
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Knief U, Hemmrich-Stanisak G, Wittig M, Franke A, Griffith SC, Kempenaers B, Forstmeier W. Quantifying realized inbreeding in wild and captive animal populations. Heredity (Edinb) 2015; 114:397-403. [PMID: 25585923 DOI: 10.1038/hdy.2014.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 11/10/2014] [Accepted: 11/14/2014] [Indexed: 12/19/2022] Open
Abstract
Most molecular measures of inbreeding do not measure inbreeding at the scale that is most relevant for understanding inbreeding depression-namely the proportion of the genome that is identical-by-descent (IBD). The inbreeding coefficient FPed obtained from pedigrees is a valuable estimator of IBD, but pedigrees are not always available, and cannot capture inbreeding loops that reach back in time further than the pedigree. We here propose a molecular approach to quantify the realized proportion of the genome that is IBD (propIBD), and we apply this method to a wild and a captive population of zebra finches (Taeniopygia guttata). In each of 948 wild and 1057 captive individuals we analyzed available single-nucleotide polymorphism (SNP) data (260 SNPs) spread over four different genomic regions in each population. This allowed us to determine whether any of these four regions was completely homozygous within an individual, which indicates IBD with high confidence. In the highly nomadic wild population, we did not find a single case of IBD, implying that inbreeding must be extremely rare (propIBD=0-0.00094, 95% CI). In the captive population, a five-generation pedigree strongly underestimated the average amount of realized inbreeding (FPed=0.013<propIBD=0.064), as expected given that pedigree founders were already related. We suggest that this SNP-based technique is generally useful for quantifying inbreeding at the individual or population level, and we show analytically that it can capture inbreeding loops that reach back up to a few hundred generations.
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Affiliation(s)
- U Knief
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - G Hemmrich-Stanisak
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - M Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - A Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - S C Griffith
- 1] Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia [2] School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - B Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - W Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
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