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We thankMelanie Schneider and Christine Baumgartner for support with molecular work, Martin Irestedt for help with DNA extractions for the 10X samples, Shouwen Ma for discussion on microscopic image processing, Keren Sadanandan for discussion on tanglegram analysis, and Katrin Martin, Isabel Schmelcher, Claudia Scheicher, Sonja Bauer, Edith Bodendorfer, Jane Didsbury, Annemarie Gr_otsch, Andrea Kortner, Petra Neubauer, Frances Weigel, and Barbara W_orle for animal care and help with breeding zebra finches. We thank Frank R_o ss ler for providing the castanotis x guttata hybrid male, and Leo Joseph and the Australian National Wildlife Collection for providing testis and liver samples from a wild T. g. castanotis individual. We thank Leo Joseph, Julie Blommaert, Octavio Palacios, Simone Fouch~e, and three anonymous reviewers for comments on the manuscript. Some of the computations were performed on resources provided by the Swedish National Infrastructure for Computing through the Uppsala Multidisciplinary Center for Advanced Computational Science. We acknowledge support from the National Genomics Infrastructure in Stockholm funded by Science for Life Laboratory, the Knut and AliceWallenberg Foundation, and the Swedish Research Council. This research was supported by the Max Planck Society (to B.K.), the Swedish Research Council Formas (2017-01597 and 2020-04436 to A.S.), and the Swedish Research Council Vetenskapsr~adet (2016-05139 to A.S.). Y.P. was part of the International Max Planck Research School for Organismal Biology. F.J.R.-R. was supported by a postdoctoral fellowship from Sven och Lilly Lawskis fond and a Marie Curie Individual Fellowship (875732)., 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., National Genomics Infrastructure in Stockholm - Science for Life Laboratory, Knut & Alice Wallenberg Foundation, Swedish Research Council, European Commission, Max Planck Society, Foundation CELLEX, Swedish Research Council Swedish Research Council Formas 2017-01597 2020-04436, Swedish Research Council 2016-05139, Sven och Lilly Lawskis fond, European Commission 875732

Satellite DNA (satDNA) is an abundant class of tandemly repeated noncoding sequences, showing high rate of change in sequence, abundance, and physical location. However, the mechanisms promoting these changes are still controversial. The library model was put forward to explain the conservation of some satDNAs for long periods, predicting that related species share a common collection of satDNAs, which mostly experience quantitative changes. Here, we tested the library model by analyzing three satDNAs in ten species of Schistocerca grasshoppers. This group represents a valuable material because it diversified during the last 7.9 Myr across the American continent from the African desert locust (Schistocerca gregaria), and this thus illuminates the direction of evolutionary changes. By combining bioinformatic and cytogenetic, we tested whether these three satDNA families found in S. gregaria are also present in nine American species, and whether differential gains and/or losses have occurred in the lineages. We found that the three satDNAs are present in all species but display remarkable interspecies differences in their abundance and sequences while being highly consistent with genus phylogeny. The number of chromosomal loci where satDNA is present was also consistent with phylogeny for two satDNA families but not for the other. Our results suggest eminently chance events for satDNA evolution. Several evolutionary trends clearly imply either massive amplifications or contractions, thus closely fitting the library model prediction that changes are mostly quantitative. Finally, we found that satDNA amplifications or contractions may influence the evolution of monomer consensus sequences and by chance playing a major role in driftlike dynamics. Fil: Palacios-Gimenez, Octavio M.. Uppsala Universitet; Suecia Fil: Milani, Diogo. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil Fil: Song, Hojun. Texas A&M University; Estados Unidos Fil: Marti, Dardo Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentina Fil: López-León, Maria D.. Universidad de Granada; España Fil: Ruiz-Ruano, Francisco J.. Uppsala Universitet; Suecia Fil: Camacho, Juan Pedro M.. Universidad de Granada; España Fil: Cabral-de-Mello, Diogo C.. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil

Additional file 4: Dataset 3. Coverage levels of the 21 protein-coding genes found in the A. scabripinnis and A. paranae B chromosomes. gDNA coverage is shown as number of copies. Additionally, we add a track showing the position of the B-specific SNPs found in the A. scabripinnis libraries. The dotted lines delimit the CDS region and the shaded zones indicate the regions amplified in the qPCR experiments. The coverage pattern attributed to each gene can be found in the Table 1.