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Rubin, Carl-Johan
Publications (10 of 52) Show all publications
Kurland, S., Wheat, C. W., Mancera, M. d., Kutschera, V. E., Hill, J., Andersson, A., . . . Laikre, L. (2019). Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species. Ecology and Evolution, 9(19), 11448-11463
Open this publication in new window or tab >>Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species
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2019 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 9, no 19, p. 11448-11463Article in journal (Refereed) Published
Abstract [en]

Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual-based single nucleotide polymorphisms [SNPs]) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F-ST) between the two introduced populations exceeds that of the naturally sympatric populations (F-ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ (pi over bar approximate to 0.002 and pi over bar approximate to 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.

Place, publisher, year, edition, pages
WILEY, 2019
Keywords
genetic diversity, genome sequencing, population genomics, Salmo trutta, salmonid, single nucleotide polymorphism
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-399013 (URN)10.1002/ece3.5646 (DOI)000487783000001 ()31641485 (PubMedID)
Funder
Swedish Research Council FormasKnut and Alice Wallenberg Foundation, 2014.0278Carl Tryggers foundation Swedish Agency for Marine and Water Management
Available from: 2019-12-13 Created: 2019-12-13 Last updated: 2019-12-13Bibliographically approved
Qanbari, S., Rubin, C.-J., Maqbool, K., Weigend, S., Weigend, A., Geibel, J., . . . Andersson, L. (2019). Genetics of adaptation in modern chicken. PLoS Genetics, 15(4), Article ID e1007989.
Open this publication in new window or tab >>Genetics of adaptation in modern chicken
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2019 (English)In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 4, article id e1007989Article in journal (Refereed) Published
Abstract [en]

We carried out whole genome resequencing of 127 chicken including red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken (Gallus gallus domesticus). We uncovered >21 million high quality SNPs of which 34% are newly detected variants. This panel comprises >115,000 predicted amino-acid altering substitutions as well as 1,100 SNPs predicted to be stop-gain or -loss, several of which reach high frequencies. Signatures of selection were investigated both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during domestication and breed development. Contrasting wild and domestic chicken we confirmed selection at the BCO2 and TSHR loci and identified 34 putative sweeps co-localized with ALX1, KITLG, EPGR, IGF1, DLK1, JPT2, CRAMP1, and GLI3, among others. Analysis of enrichment between groups of wild vs. commercials and broilers vs. layers revealed a further panel of candidate genes including CORIN, SKIV2L2 implicated in pigmentation and LEPR, MEGF10 and SPEF2, suggestive of production-oriented selection. SNPs with marked allele frequency differences between wild and domestic chicken showed a highly significant deficiency in the proportion of amino-acid altering mutations (P<2.5x10(-6)). The results contribute to the understanding of major genetic changes that took place during the evolution of modern chickens and in poultry breeding. Author summary Domestic chickens (Gallus gallus domesticus) provide a critical resource for animal proteins for human nutrition worldwide. Chickens were primarily domesticated from the red jungle fowl (Gallus gallus gallus), a bird that still runs wild in most of Southeast Asia. Human driven selection during domestication and subsequent specialization into meat type (broilers) and egg layer (layers) birds has left detectable signatures of selection within the genome of modern chicken. In this study, we performed whole genome sequencing of 127 chicken including the red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken. Analysis of selection provided a comprehensive list of several tens of independent loci that are likely to have contributed to domestication or improving production. SNP by SNP comparison of allele frequency between groups of wild and domestic chicken showed a highly significant deficiency of the proportion of amino acid altering mutations. This implies that commercial birds have undergone purifying selection reducing the frequency of deleterious variants.

Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE, 2019
National Category
Genetics and Breeding in Agricultural Sciences
Identifiers
urn:nbn:se:uu:diva-385576 (URN)10.1371/journal.pgen.1007989 (DOI)000466866000009 ()31034467 (PubMedID)
Funder
German Research Foundation (DFG), QA55/1-1
Available from: 2019-06-17 Created: 2019-06-17 Last updated: 2019-06-17Bibliographically approved
McCoy, A. M., Beeson, S. K., Rubin, C.-J., Andersson, L., Caputo, P., Lykkjen, S., . . . McCue, M. E. (2019). Identification and validation of genetic variants predictive of gait in standardbred horses. PLoS Genetics, 15(5), Article ID e1008146.
Open this publication in new window or tab >>Identification and validation of genetic variants predictive of gait in standardbred horses
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2019 (English)In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 5, article id e1008146Article in journal (Refereed) Published
Abstract [en]

Several horse breeds have been specifically selected for the ability to exhibit alternative patterns of locomotion, or gaits. A premature stop codon in the gene DMRT3 is permissive for gaitedness across breeds. However, this mutation is nearly fixed in both American Standardbred trotters and pacers, which perform a diagonal and lateral gait, respectively, during harness racing. This suggests that modifying alleles must influence the preferred gait at racing speeds in these populations. A genome-wide association analysis for the ability to pace was performed in 542 Standardbred horses (n = 176 pacers, n = 366 trotters) with genotype data imputed to similar to 74,000 single nucleotide polymorphisms (SNPs). Nineteen SNPs on nine chromosomes (ECA1, 2, 6, 9, 17, 19, 23, 25, 31) reached genome-wide significance (p < 1.44 x 10(-6)). Variant discovery in regions of interest was carried out via whole-genome sequencing. A set of 303 variants from 22 chromosomes with putative modifying effects on gait was genotyped in 659 Standardbreds (n = 231 pacers, n = 428 trotters) using a high-throughput assay. Random forest classification analysis resulted in an out-of-box error rate of 0.61%. A conditional inference tree algorithm containing seven SNPs predicted status as a pacer or trotter with 99.1% accuracy and subsequently performed with 99.4% accuracy in an independently sampled population of 166 Standardbreds (n = 83 pacers, n = 83 trotters). This highly accurate algorithm could be used by owners/trainers to identify Standardbred horses with the potential to race as pacers or as trotters, according to the genotype identified, prior to initiating training and would enable fine-tuning of breeding programs with designed matings. Additional work is needed to determine both the algorithm's utility in other gaited breeds and whether any of the predictive SNPs play a physiologically functional role in the tendency to pace or tag true functional alleles.

Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE, 2019
National Category
Genetics and Breeding in Agricultural Sciences
Identifiers
urn:nbn:se:uu:diva-387964 (URN)10.1371/journal.pgen.1008146 (DOI)000470208000034 ()31136578 (PubMedID)
Available from: 2019-06-27 Created: 2019-06-27 Last updated: 2019-06-27Bibliographically approved
Andrade, P., Pinho, C., Perez i de lanuza, G., Afonso, S., Brejcha, J., Rubin, C.-J., . . . Carneiro, M. (2019). Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard. Proceedings of the National Academy of Sciences of the United States of America, 116(12), 5633-5642
Open this publication in new window or tab >>Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard
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2019 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 12, p. 5633-5642Article in journal (Refereed) Published
Abstract [en]

Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard (Podarcis muralis), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions near genes associated with pterin [sepiapterin reductase (SPR)] and carotenoid [beta-carotene oxygenase 2 (BCO2)] metabolism, demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been coopted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles, and haplotype analysis revealed abundant transspecific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.

Keywords
Podarcis muralis, carotenoid pigmentation, pterin pigmentation, balanced polymorphism, introgression
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-381075 (URN)10.1073/pnas.1820320116 (DOI)000461679000067 ()30819892 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 2017-02907Swedish Research Council, E0446501EU, Horizon 2020, PTDC/BIA-EVL/30288/2017 -NORTE -01-0145-FEDER-30288EU, Horizon 2020, PTDC/BIA-EVL/30288/2017 -NORTE -01-0145-FEDER-30288EU, FP7, Seventh Framework Programme, 286431Swedish Research Council
Available from: 2019-04-23 Created: 2019-04-23 Last updated: 2019-04-23Bibliographically approved
Felkel, S., Vogl, C., Rigler, D., Dobretsberger, V., Chowdhary, B. P., Distl, O., . . . Wallner, B. (2019). The horse Y chromosome as an informative marker for tracing sire lines. Scientific Reports, 9, Article ID 6095.
Open this publication in new window or tab >>The horse Y chromosome as an informative marker for tracing sire lines
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2019 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 6095Article in journal (Refereed) Published
Abstract [en]

Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'crown haplogroup' in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse 'Galopin', born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago.

National Category
Genetics and Breeding in Agricultural Sciences
Identifiers
urn:nbn:se:uu:diva-382849 (URN)10.1038/s41598-019-42640-w (DOI)000464495800019 ()30988347 (PubMedID)
Available from: 2019-05-22 Created: 2019-05-22 Last updated: 2019-05-22Bibliographically approved
Rafati, N., Blanco-Aguiar, J. A., Rubin, C.-J., Sayyab, S., Sabatino, S., Afonso, S., . . . Carneiro, M. (2018). A genomic map of clinal variation across the European rabbit hybrid zone. Molecular Ecology, 27(6), 1457-1478
Open this publication in new window or tab >>A genomic map of clinal variation across the European rabbit hybrid zone
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2018 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 6, p. 1457-1478Article in journal (Refereed) Published
Abstract [en]

Speciation is a process proceeding from weak to complete reproductive isolation. In this continuum, naturally hybridizing taxa provide a promising avenue for revealing the genetic changes associated with the incipient stages of speciation. To identify such changes between two subspecies of rabbits that display partial reproductive isolation, we studied patterns of allele frequency change across their hybrid zone using whole-genome sequencing. To connect levels and patterns of genetic differentiation with phenotypic manifestations of subfertility in hybrid rabbits, we further investigated patterns of gene expression in testis. Geographic cline analysis revealed 253 regions characterized by steep changes in allele frequency across their natural region of contact. This catalog of regions is likely to be enriched for loci implicated in reproductive barriers and yielded several insights into the evolution of hybrid dysfunction in rabbits: (i) incomplete reproductive isolation is likely governed by the effects of many loci, (ii) protein-protein interaction analysis suggest that genes within these loci interact more than expected by chance, (iii) regulatory variation is likely the primary driver of incompatibilities, and (iv) large chromosomal rearrangements appear not to be a major mechanism underlying incompatibilities or promoting isolation in the face of gene flow. We detected extensive misregulation of gene expression in testis of hybrid males, but not a statistical overrepresentation of differentially expressed genes in candidate regions. Our results also did not support an X chromosome-wide disruption of expression as observed in mice and cats, suggesting variation in the mechanistic basis of hybrid male reduced fertility among mammals.

Place, publisher, year, edition, pages
John Wiley & Sons, 2018
Keywords
Speciation, reproductive isolation, expression, hybrid
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-314393 (URN)10.1111/mec.14494 (DOI)000430183100010 ()29359877 (PubMedID)
Funder
EU, European Research Council, SFRH/BPD/65464/2009EU, FP7, Seventh Framework Programme, 286431
Note

Title in thesis list of papers: The early stages of species formation revealed by a genomic map of clinal variation across the European rabbit hybrid zone

Available from: 2017-02-02 Created: 2017-02-02 Last updated: 2018-06-19Bibliographically approved
Reimer, C., Rubin, C.-J., Sharifi, A. R., Ha, N.-T. -., Weigend, S., Waldmann, K.-H. -., . . . Simianer, H. (2018). Analysis of porcine body size variation using re-sequencing data of miniature and large pigs. BMC Genomics, 19, Article ID 687.
Open this publication in new window or tab >>Analysis of porcine body size variation using re-sequencing data of miniature and large pigs
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2018 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 19, article id 687Article in journal (Refereed) Published
Abstract [en]

Background: Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in "SweepFinder", to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely F-ST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F-2 individuals from a cross of Goettingen Minipigs and large pigs. Results: Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F-2 cross-breds. Conclusion: The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono-or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region.

Place, publisher, year, edition, pages
BMC, 2018
Keywords
Goettingen Minipig, Whole genome resequencing, Body size, X-chromosomal QTL
National Category
Genetics Genetics and Breeding in Agricultural Sciences
Identifiers
urn:nbn:se:uu:diva-366733 (URN)10.1186/s12864-018-5009-y (DOI)000445495200002 ()30231878 (PubMedID)
Funder
European Science Foundation (ESF)
Available from: 2018-12-11 Created: 2018-12-11 Last updated: 2018-12-11Bibliographically approved
Felkel, S., Vogl, C., Rigler, D., Jagannathan, V., Leeb, T., Fries, R., . . . Wallner, B. (2018). Asian horses deepen the MSY phylogeny. Animal Genetics, 49(1), 90-93
Open this publication in new window or tab >>Asian horses deepen the MSY phylogeny
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2018 (English)In: Animal Genetics, ISSN 0268-9146, E-ISSN 1365-2052, Vol. 49, no 1, p. 90-93Article in journal (Refereed) Published
Abstract [en]

Humans have shaped the population history of the horse ever since domestication about 5500years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 +/- 872years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages.

Place, publisher, year, edition, pages
WILEY, 2018
Keywords
Equus, breeding, paternal lineage, Y chromosome, haplotype, ancestry, diversity, history, oriental origin
National Category
Genetics and Breeding in Agricultural Sciences
Identifiers
urn:nbn:se:uu:diva-348388 (URN)10.1111/age.12635 (DOI)000425119400011 ()29333704 (PubMedID)
Available from: 2018-04-16 Created: 2018-04-16 Last updated: 2018-04-16Bibliographically approved
Brusini, I., Carneiro, M., Wang, C., Rubin, C.-J., Ring, H., Afonso, S., . . . Andersson, L. (2018). Changes in brain architecture are consistent with altered fear processing in domestic rabbits. Proceedings of the National Academy of Sciences of the United States of America, 115(28), 7380-7385
Open this publication in new window or tab >>Changes in brain architecture are consistent with altered fear processing in domestic rabbits
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 28, p. 7380-7385Article in journal (Refereed) Published
Abstract [en]

The most characteristic feature of domestic animals is their change in behavior associated with selection for tameness. Here we show, using high-resolution brain magnetic resonance imaging in wild and domestic rabbits, that domestication reduced amygdala volume and enlarged medial prefrontal cortex volume, supporting that areas driving fear have lost volume while areas modulating negative affect have gained volume during domestication. In contrast to the localized gray matter alterations, white matter anisotropy was reduced in the corona radiata, corpus callosum, and the subcortical white matter. This suggests a compromised white matter structural integrity in projection and association fibers affecting both afferent and efferent neural flow, consistent with reduced neural processing. We propose that compared with their wild ancestors, domestic rabbits are less fearful and have an attenuated flight response because of these changes in brain architecture.

National Category
Psychology Radiology, Nuclear Medicine and Medical Imaging
Identifiers
urn:nbn:se:uu:diva-355452 (URN)10.1073/pnas.1801024115 (DOI)000438050900076 ()29941556 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilThe Swedish Brain FoundationEuropean Social Fund (ESF)
Available from: 2018-06-29 Created: 2018-06-29 Last updated: 2018-09-25Bibliographically approved
Makino, T., Rubin, C.-J., Carneiro, M., Axelsson, E., Andersson, L. & Webster, M. T. (2018). Elevated proportions of deleterious genetic variation in domestic animals and plants. Genome Biology and Evolution, 10(1), 276-290
Open this publication in new window or tab >>Elevated proportions of deleterious genetic variation in domestic animals and plants
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2018 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 10, no 1, p. 276-290Article in journal (Refereed) Published
Abstract [en]

A fraction of genetic variants segregating in any population are deleterious, which negatively impacts individual fitness. The domestication of animals and plants is associated with population bottlenecks and artificial selection, which are predicted to increase the proportion of deleterious variants. However, the extent to which this is a general feature of domestic species is unclear. Here we examine the effects of domestication on the prevalence of deleterious variation using pooled whole-genome resequencing data from five domestic animal species (dog, pig, rabbit, chicken and silkworm) and two domestic plant species (rice and soybean) compared to their wild ancestors. We find significantly reduced genetic variation and increased proportion of nonsynonymous amino acid changes in all but one of the domestic species. These differences are observable across a range of allele frequencies, both common and rare. We find proportionally more SNPs in highly conserved elements in domestic species and a tendency for domestic species to harbour a higher proportion of changes classified as damaging. Our findings most likely reflect an increased incidence of deleterious variants in domestic species, which is most likely attributable to population bottlenecks that lead to a reduction in the efficacy of selection. An exception to this pattern is displayed by European domestic pigs, which do not show traces of a strong population bottleneck and probably continued to exchange genes with wild boar populations after domestication. The results presented here indicate that an elevated proportion of deleterious variants is a common, but not ubiquitous, feature of domestic species.

Place, publisher, year, edition, pages
Oxford University Press, 2018
Keywords
artificial selection, domestication, effective population size, mutational load, natural selection, population bottleneck
National Category
Evolutionary Biology Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-339437 (URN)10.1093/gbe/evy004 (DOI)000424893500020 ()29325102 (PubMedID)
Available from: 2018-01-18 Created: 2018-01-18 Last updated: 2018-04-10Bibliographically approved
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