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Hans Ellegren - One of the best experts on this subject based on the ideXlab platform.
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variation in the Z Chromosome to autosomes ratio of genetic diversity across birds and its relationship to the fast Z effect
2019Co-Authors: Homa Papoli Yazdi, Paulina Bolivar, Carina F Mugal, Hans EllegrenAbstract:Variation in the Z Chromosome to Autosomes Ratio of Genetic Diversity across Birds and its Relationship to the Fast-Z effect
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emergence of male biased genes on the chicken Z Chromosome sex Chromosome contrasts between male and female heterogametic systems
Genome Research, 2011Co-Authors: Hans EllegrenAbstract:Selection shapes genome evolution at the DNA sequence level, mainly manifested in changes in the primary structure of genes and other functional elements. A long-standing question in evolutionary biology is whether the organiZation of genes, their location in different regions of the genome, is also subject to selection (Hurst et al. 2004). A candidate case would be the genomic organiZation of sexually antagonistic genes, i.e., genes beneficial to one sex but either detrimental or neutral to the other (Rice 1992; Rice and Chippindale 2001; van Doorn 2009). Theoretical arguments imply that such genes are only expected to occur if the benefits accrued to one sex outweigh the disadvantages imposed to the other. However, there is an important exception to this prediction that relates to the special mode of inheritance and organiZation of sex Chromosomes, and to cost-benefit scenarios associated with sex-linkage. For example, as far as partially or fully dominant mutations are considered, theory predicts that it should be easier for an antagonistic gene favorable to one sex to evolve on a sex Chromosome that is more often present in that sex than in the other, since net selection will then be positive (Rice 1984; Charlesworth et al. 1987). This leads to the expectation that female-beneficial genes should be over-represented, and male-beneficial genes under-represented, on the X-Chromosome in male-heterogametic organisms. In practice, it is difficult on a large scale to determine whether genes are or have been sexually antagonistic. Several investigators have therefore used sex-biased gene expression as a proxy for sexual antagonism (see Ellegren and Parsch 2007); sex-biased gene expression may potentially represent the resolution of past sexual antagonism (e.g., Mank and Ellegren 2009). This line of thinking has been integrated with several observations of a non-random genomic distribution of genes with sex-biased expression. In Drosophila, male-biased genes are under-represented on the X (Parisi et al. 2003; Sturgill et al. 2007; Vicoso and Charlesworth 2009). If this is translated into an under-representation of male-beneficial genes on X, it would be consistent with theory for partly or fully dominant mutations (Rice 1984). In Caenorhabditis elegans, sperm-enriched genes are nearly absent from the X-Chromosome (Reinke et al. 2000). In mammals, the picture is more complex. Female-biased genes expressed in ovary and placenta are over-represented on the mouse X-Chromosome (Khil et al. 2004), also as expected for dominant mutations. However, male-biased genes expressed in early stages of spermatogenesis are in excess on the mouse X as well (Khil et al. 2004), although genes expressed later during male meiosis are, in fact, under-represented on the X (Khil et al. 2004). Several alternative explanations to the non-random distribution of sex-biased genes have therefore been suggested (Rogers et al. 2003; Meisel et al. 2009), including escape from meiotic sex Chromosome inactivation (MSCI) by genes needed to be expressed during spermatogenesis (Hense et al. 2007; PotrZebowski et al. 2008; Vibranovski et al. 2009a). A limitation in the abovementioned empirical studies is that they survey the overall present-day gene content of different chromosomal categories rather than specifically focusing on the characteristics of those new genes that evolved in different regions of the genome (cf. Zhang et al. 2010). However, the arguments for the probability of evolution of sexually antagonistic alleles in different chromosomal categories can also be applied to different scenarios of movement of genes between sex Chromosomes and autosomes (Moyle et al. 2010). Relevant in this context are empirical data on traffic of retrogenes between autosomes and the X-Chromosome in mammals and Drosophila (Betran et al. 2002; Emerson et al. 2004; Vibranovski et al. 2009b), in particular, a pattern that has been referred to as “out-of-X movement.” It has been noted that many retrotransposed gene copies moving from the X-Chromosome to autosomes have acquired sex-biased gene expression and are mainly expressed in testis (Bradley et al. 2004). In the seminal study by Emerson et al. (2004), it was hypothesiZed that natural selection has favored the preservation of genes with male-biased function that move from the X-Chromosome to autosomes: “One model of sexual antagonism (Wu and Yujun Xu 2003) predicts that gene copies that benefit males at a cost to females would be more likely found on the autosomes than on the X-Chromosome.” Note again that sex-biased gene expression is taken as a proxy for sexual antagonism. A potentially interesting contrast in testing an adaptive scenario for the genomic distribution of new sex-biased genes is to study organisms with female heterogamety (males ZZ, females ZW). In this case, male-beneficial genes in which new mutations are at least partly dominant may be expected to accumulate on the Z-Chromosome, rather than on autosomes, because Z is two-thirds of the time in males. With the same argument, female-beneficial genes would be expected to become less abundant on the Z-Chromosome. These opposing predictions compared to systems of male heterogamety are helpful for the general argument because they allow distinguishing the expected effects of heterogamety from any other difference that pertain to autosomes and sex Chromosomes. Female heterogamety is found in a diverse range of organisms. All birds are female heterogametic, and the same applies to all butterflies. A ZW sex Chromosome system is also present in individual lineages of reptiles, amphibians, fishes, and crustaceans. Although draft genome sequences of a few female heterogametic bird species (chicken, Gallus gallus [International Chicken Genome Sequencing Consortium 2004]; Zebra finch, Taeniopygia guttata [Warren et al. 2010]; and turkey [Dalloul et al. 2010]) and one moth (silkworm, Bombyx mori [Mita et al. 2004; Xia et al. 2004]) have been reported, the coverage of the Z-Chromosome has generally not been sufficient for a comprehensive analysis of gene content. However, the recent sequencing to near completion of the chicken Z-Chromosome (Bellott et al. 2010) provides a framework for a test of the emergence of new genes on sex Chromosomes in a female heterogametic system. The chicken Z-Chromosome is 80 Mb in siZe and contains about 1000 genes. The female-specific W-Chromosome is less well characteriZed, but it is considerably smaller, mostly non-recombining, and contains a limited number of paralogs (gametologs) to Z-linked genes as well as some female-specific genes (Ellegren 2000; International Chicken Genome Sequencing Consortium 2004). The avian ZW and the mammalian XY sex Chromosomes evolved independently from different pairs of autosomes present in a vertebrate ancestor (Fridolfsson et al. 1998; Nanda et al. 1999; Bellott et al. 2010). They thereby offer parallel biological replicates to the study of sex Chromosome evolution and the associated question of genome organiZation potentially driven by selectively favorable gene acquisitions.
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no evidence for Z Chromosome rearrangements between the pied flycatcher and the collared flycatcher as judged by gene based comparative genetic maps
Molecular Ecology, 2010Co-Authors: Niclas Backstrom, Anna Qvarnstrom, Eleftheria Palkopoulou, Hans EllegrenAbstract:Revealing the genetic basis of reproductive isolation is fundamental for understanding the speciation process. Chromosome speciation models propose a role for chromosomal rearrangements in promoting the build up of reproductive isolation between diverging populations and empirical data from several animal and plant taxa support these models. The pied flycatcher and the collared flycatcher are two closely related species that probably evolved reproductive isolation during geographical separation in Pleistocene glaciation refugia. Despite the short divergence time and current hybridiZation, these two species demonstrate a high degree of intrinsic post-Zygotic isolation and previous studies have shown that traits involved in mate choice and hybrid viability map to the Z-Chromosome. Could rearrangements of the Z-Chromosome between the species explain their reproductive isolation? We developed high coverage Z-Chromosome linkage maps for both species, using gene-based markers and large-scale SNP genotyping. Best order maps contained 57-62 gene markers with an estimated average density of one every 1-1.5 Mb. We estimated the recombination rates in flycatcher Z-Chromosomes to 1.1-1.3 cM/Mb. A comparison of the maps of the two species revealed extensive co-linearity with no strong evidence for chromosomal rearrangements. This study does therefore not provide support the idea that sex Chromosome rearrangements have caused the relatively strong post-Zygotic reproductive isolation between these two Ficedula species.
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the chicken gallus gallus Z Chromosome contains at least three nonlinear evolutionary strata
Genetics, 2008Co-Authors: Hans EllegrenAbstract:Birds have female heterogamety with Z and W sex Chromosomes. These evolved from different autosomal precursor Chromosomes than the mammalian X and Y. However, previous work has suggested that the pattern and process of sex Chromosome evolution show many similarities across distantly related organisms. Here we show that stepwise restriction of recombination between the protosex Chromosomes of birds has resulted in regions of the chicken Z Chromosome showing discrete levels of divergence from W homologs (gametologs). The 12 genes analyZed fall into three levels of estimated divergence values, with the most recent divergence (dS = 0.18–0.21) displayed by 6 genes in a region on the Z Chromosome corresponding to the interval 1–11 Mb of the assembled genome sequence. Another 4 genes show intermediate divergence (dS = 0.27–0.38) and are located in the interval 16–53 Mb. Two genes (at positions 42 and 50 Mb) with higher dS values are located proximal to the most distal of the 4 genes with intermediate divergence, suggesting an inversion event. The distribution of genes and their divergence indicate at least three evolutionary strata, with estimated times for cessation of recombination between Z and W of 132–150 (stratum 1), 71–99 (stratum 2), and 47–57 (stratum 3) million years ago. An inversion event, or some other form of intrachromosomal rearrangement, subsequent to the formation of strata 1 and 2 has scrambled the gene order to give rise to the nonlinear arrangement of evolutionary strata currently seen on the chicken Z Chromosome. These observations suggest that the progressive restriction of recombination is an integral feature of sex Chromosome evolution and occurs also in systems of female heterogamety.
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genetic mapping in a natural population of collared flycatchers ficedula albicollis conserved synteny but gene order rearrangements on the avian Z Chromosome
Genetics, 2006Co-Authors: Niclas Backstrom, Lars Gustafsson, Anna Qvarnstrom, Mikael Brandstrom, Hans H Cheng, Hans EllegrenAbstract:Data from completely sequenced genomes are likely to open the way for novel studies of the genetics of nonmodel organisms, in particular when it comes to the identification and analysis of genes responsible for traits that are under selection in natural populations. Here we use the draft sequence of the chicken genome as a starting point for linkage mapping in a wild bird species, the collared flycatcher—one of the most well-studied avian species in ecological and evolutionary research. A pedigree of 365 flycatchers was established and genotyped for single nucleotide polymorphisms in 23 genes selected from (and spread over most of) the chicken Z Chromosome. All genes were also found to be located on the Z Chromosome in the collared flycatcher, confirming conserved synteny at the level of gene content across distantly related avian lineages. This high degree of conservation mimics the situation seen for the mammalian X Chromosome and may thus be a general feature in sex Chromosome evolution, irrespective of whether there is male or female heterogamety. Alternatively, such unprecedented chromosomal conservation may be characteristic of most Chromosomes in avian genome evolution. However, several internal rearrangements were observed, meaning that the transfer of map information from chicken to nonmodel bird species cannot always assume conserved gene orders. Interestingly, the rate of recombination on the Z Chromosome of collared flycatchers was only ∼50% that of chicken, challenging the widely held view that birds generally have high recombination rates.
Glennpeter Saetre - One of the best experts on this subject based on the ideXlab platform.
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increased divergence but reduced variation on the Z Chromosome relative to autosomes in ficedula flycatchers differential introgression or the faster Z effect
Ecology and Evolution, 2012Co-Authors: Silje Hogner, Stein Are Saether, Thomas Borge, Torbjorn Bruvik, Arild Johnsen, Glennpeter SaetreAbstract:Recent multilocus studies of congeneric birds have shown a pattern of elevated interspecific divergence on the Z Chromosome compared to the autosomes. In contrast, intraspecifically, birds exhibit less polymorphism on the Z Chromosome relative to the autosomes. We show that the four black-and-white Ficedula flycatcher species show greater genetic divergence on the Z Chromosome than on the autosomes, and that the ratios of intraspecific polymorphism at Z-linked versus autosomal markers are below the neutral expectation of 75%. In all species pairs, we found more fixed substitutions and fewer shared polymorphisms on the Z Chromosome than on the autosomes. Finally, using isolation with migration (IMa) models we estimated gene flow among the four closely related flycatcher species. The results suggest that different pattern of evolution of Z Chromosomes and autosomes is best explained by the faster-Z hypothesis, since the estimated long-term gene flow parameters were close to Zero in all comparisons.
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sex Chromosome linked species recognition and evolution of reproductive isolation in flycatchers
Science, 2007Co-Authors: Stein Are Saether, Thomas Borge, Glennpeter Saetre, Gunilla Andersson, Chris Wiley, Nina Svedin, Thor VeenAbstract:Interbreeding between species (hybridiZation) typically produces unfit offspring. Reduced hybridiZation should therefore be favored by natural selection. However, this is difficult to accomplish because hybridiZation also sets the stage for genetic recombination to dissociate species-specific traits from the preferences for them. Here we show that this association is maintained by physical linkage (on the same Chromosome) in two hybridiZing Ficedula flycatchers. By analyZing the mating patterns of female hybrids and cross-fostered offspring, we demonstrate that species recognition is inherited on the Z Chromosome, which is also the known location of species-specific male plumage traits and genes causing low hybrid fitness. Limited recombination on the Z Chromosome maintains associations of Z-linked genes despite hybridiZation, suggesting that the sex Chromosomes may be a hotspot for adaptive speciation.
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contrasting patterns of polymorphism and divergence on the Z Chromosome and autosomes in two ficedula flycatcher species
Genetics, 2005Co-Authors: Thomas Borge, Matthew T Webster, Gunilla Andersson, Glennpeter SaetreAbstract:In geographic areas where pied and collared flycatchers (Ficedula hypoleuca and F. albicollis) breed in sympatry, hybridiZation occurs, leading to gene flow (introgression) between the two recently diverged species. Notably, while such introgression is observable at autosomal loci it is apparently absent at the Z Chromosome, suggesting an important role for genes on the Z Chromosome in creating reproductive isolation during speciation. To further understand the role of Z-linked loci in the formation of new species, we studied genetic variation of the two species from regions where they live in allopatry. We analyZed patterns of polymorphism and divergence in introns from 9 Z-linked and 23 autosomal genes in pied and collared flycatcher males. Average variation on the Z Chromosome is greatly reduced compared to neutral expectations based on autosomal diversity in both species. We also observe significant heterogeneity between patterns of polymorphism and divergence at Z-linked loci and a relative absence of polymorphisms that are shared by the two species on the Z Chromosome compared to the autosomes. We suggest that these observations may indicate the action of recurrent selective sweeps on the Z Chromosome during the evolution of the two species, which may be caused by sexual selection acting on Z-linked genes. Alternatively, reduced variation on the Z Chromosome could result from substantially higher levels of introgression at autosomal than at Z-linked loci or from a complex demographic history, such as a population bottleneck.
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recurrent selective sweeps on the Z Chromosome characteriZe the evolutionary history of two closely related flycatcher species ficedula hypoleuca and f albicollis
2004Co-Authors: Thomas Borge, Matthew T Webster, Gunilla Andersson, Glennpeter SaetreAbstract:In this thesis, different genetic tools are used to investigate pre- and postZygotic barriers to gene exchange and their role in speciation in the pied flycatcher (Ficedula hypoleuca) and the collared flycatcher (F. albicollis). This species complex consists of four genetically distinct clades that apparently diverged in allopatry (I). Sequencing of introns from autosomal and Z-linked genes from the two species reveals signs of selection on the Z-Chromosome. Sexual selection acting on Z-linked genes might explain this pattern (II). By using large-scale genotyping of single nucleotide polymorphisms (SNPs), introgression is observed at autosomal- but not Z-linked loci, mostly from the pied- to the collared flycatcher. Male plumage characters and genes involved in hybrid fitness are largely mapped to the Z-Chromosome (III). By studying mate choice of female hybrids I show that there is a link between female preferences and the Z Chromosome (IV). The rate of introgression in island versus clinal hybrid Zones is consistent with regional differences in hybrid fertility. Asymmetric gene flow from allopatry on the islands may oppose reinforcement, leading to introgression and a partial breakdown of postZygotic isolation. Adaptive introgression may explain the high rate of introgression observed at one of the genetic markers (V). For late breeding female collared flycatchers it appears to be adaptive to use pied flycatchers as social fathers but conspecific males as genetic fathers. Additionally, females in mixed species pairs may reduce hybridiZation costs by producing an excess of male hybrid offspring that are more fertile than females (VI). In conclusion, the Z-Chromosome appears to play a major role in flycatcher speciation. Sexual selection and reinforcement are important mechanisms in the divergence of these birds. However, gene flow from allopatry, introgression of adaptive genes and adaptive hetrospecific pairing by late breeding collared flycatcher females may work in the opposite direction.
Shigeki Mizuno - One of the best experts on this subject based on the ideXlab platform.
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the male hypermethylation mhm region on the chicken Z Chromosome female specific transcription and its biological implication
2004Co-Authors: Mika Teranishi, Shigeki MizunoAbstract:The human DM-related transcript 1 (DMRT1) and DMRT2 genes are located at the distal region of Chromosome 9p24.3 and suggested to be involved in the differentiation of testis in a dosage dependent manner, because XY individuals hemiZygous for these genes exhibit a high frequency of XY feminiZation (Raymond et al., 1999a). In mouse embryos, the expression of DMRT1 gene is first detected by RT-PCR at E9.5, the earliest stage of genital ridge formation, and its expression in genital ridges and in early gonads, as detected by RT-PCR and in situ hybridiZation, continues until E14.5 in both male and female embryos. At E15.5, its expression in the female declines significantly and becomes testis-specific in adults (Raymond et al., 1999b). In chickens, a single DMRT1 gene is located on the short arm of the Z Chromosome, expressed in genital ridges of both male and female embryos at as early as stage 19 (~3-day) (Raymond et al., 1999b) but later its expression becomes male (testis)-specific as in mammals (this study; Figure 2A,B). In early chicken embryos at stages 25–31 (4.5- to 7-day), the level of DMRT1 mRNA is about 2-fold higher in males than in females (Raymond et al., 1999b and this study), which might have been attained by the absence of a mechanism to shut off the transcription on one of the Z Chromosomes in males (Kuroda et al., 2001). It has been speculated that the apparently dosage-dependent expression of the DMRT1 gene in early chicken embryos may have a role in the sex determination (Raymond et al., 1999b). The exclusive expression of the DMRT1 gene in adult testis both in mammals and birds may also suggest that its gene expression is required for some essential functions in the differentiated testis.
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absence of Z Chromosome inactivation for five genes in male chickens
Chromosome Research, 2001Co-Authors: Yukiko Kuroda, Tetsuya Hori, Nozomu Arai, Mariko Arita, Mika Teranishi, Masahiko Harata, Shigeki MizunoAbstract:In order to examine if Z-Chromosome inactivation, which is analogous to X-Chromosome inactivation in mammals, takes place in male birds having ZZ sex Chromosomes, five Z-linked genes of chickens which are expressed in both sexes in certain tissues were selected: i.e. genes for growth hormone receptor, nicotinic acetylcholine receptor β3, aldolase B, β1,4-galactosyltransferase I, and iron-responsive element-binding protein (also known as cytosolic aconitase). Antisense or sense riboprobe was prepared from an intronic sequence of each gene and subjected to fluorescence in situ hybridiZation to nascent transcripts of each gene in a nucleus. Each antisense riboprobe hyridiZed to two spots of nascent RNA which corresponded to its gene loci on the two Z Chromosomes in a majority of nuclei in a tissue of the male. The efficiency of detection of two spots per nucleus was comparable to that for the glyceraldehyde-3-phosphate dehydrogenase gene, an autosomal housekeeping gene. These results suggest strongly that Z-Chromosome inactivation, i.e. virtual silence of transcription at one of the alleles, does not take place for these five Z-linked genes in male chickens.
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Differentiation of Z and W Chromosomes Revealed by Replication Banding and FISH Mapping of Sex-Chromosome-linked DNA Markers in the Cassowary (Aves, Ratitae)
Chromosome Research, 1999Co-Authors: Chizuko Nishida-umehara, Shigeki Mizuno, Atushi Fujiwara, Akira Ogawa, Syuiti Abe, Michihiro C. YoshidaAbstract:We identified sex Chromosomes of the double-wattled cassowary (Casuarius casuarius) by a replication banding method. The acrocentric Z Chromosome, the fifth largest pair in males and slightly smaller W Chromosome show no sign of heterochromatiniZation and share a nearly identical banding pattern in the distal half of the long arm. These Chromosomes were further characteriZed by FISH with three probes linked either to Z or W Chromosome in most avian species examined thus far. Contrary to the situation in the chicken, we obtained positive signals with Z-specific ZOV3 and W-specific EE0.6 in the distal region of both Z and W Chromosomes. However, IREBP signals localiZed to the proximal half of the Z Chromosome were not detected on the W Chromosome. Thus, structural rearrangements such as deletions and inversions might have been the initial step of W Chromosome differentiation from an ancestral homomorphic pair in this species.
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sexing the oriental white stork ciconia boyciana by pcr using a single plucked feather as a source of dna
Japanese Journal of Ornithology, 1998Co-Authors: Koichi Murata, Yuichiro Itoh, Akira Ogawa, Shigeki MizunoAbstract:A small amount of DNA extracted from a single plucked contour feather from four captive young Oriental White Storks Ciconia boyciana, a sexually monomorphic bird, was used for gender determination by the method of polymerase chain reaction (PCR) based on its sex Chromosome-specific DNA sequences, the 0.6-kb Xba I -HindIII fragment(XH0.6) on the W Chromosome and the region homologous to the XH0.6sequence (XH0.6-RSM) on the Z Chromosome. After the agarose gel electrophoresis of the PCR products, two bands which correspond to the W and Z Chromosome-specific fragments were observed from the female DNA. By contrast only one Z Chromosome-specific fragment was observed from the male DNA. These results were consistent with those obtained by Southern blot hybridiZation using the DNA from red blood cells and the discriminant analysis of body measurements. This PCR method using a single feather is easy, fast, accurate, and also relatively stress-less to the birds which are not used to being handled for sampling. It will become one of useful tools in the captive propagation program and reintroduction plan for the C. boyciana, a special natural monument of Japan.
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Predominant expression of a Z-Chromosome-linked immunoglobulin superfamily gene, ZOV3, in steroidogenic cells of ovarian follicles and in embryonic gonads of chickens
Differentiation; research in biological diversity, 1997Co-Authors: Ryota Kunita, Osamu Nakabayashi, Tateki Kikuchi, Shigeki MizunoAbstract:A cDNA clone, pZOV3, was isolated from the cDNA library of immature chicken ovaries and its gene was mapped to the middle of the short arm of the Z Chromosome. The cDNA sequence suggests that ZOV3 is a novel member of the immunoglobulin superfamily. cDNA clones of homologues of chicken ZOV3 were also obtained from Japanese quail and pigeon. Northern blot hybridiZation suggests that the high-level expression of the ZOV3 gene is restricted to the gonads: embryonic, immature and mature ovaries, and embryonic and immature testes. Western blot analysis and immunocytological detection using specific polyclonal antibodies against amino- and carboxyl-terminal regions of ZOV3 demonstrate that ZOV3 is a plasma membrane-bound glycoprotein that exists in granulosa cells and islets of cells in the theca externa layer of ovarian follicles. The latter islets coincide with those producing estradiol-17β. In male and female embryos, production of ZOV3 is first prominent in medullary and seminiferous codes, respectively, of developing gonads. Then, after hatching, it is shifted to the cortex surrounding the primitive follicles in the ovary or is continued weakly in the primary seminiferous tubules in the testis. Expression of the ZOV3 gene and production of ZOV3 are no longer detectable in the mature testis. ZOV3 is unique among the immunoglobulin superfamily proteins in that it is produced predominantly in gonads. Its possible role in differentiation or maintenance of steroidogenic cells in an ovarian follicle is discussed.
James R Walters - One of the best experts on this subject based on the ideXlab platform.
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support for faster and more adaptive Z Chromosome evolution in two divergent lepidopteran lineages
Evolution, 2021Co-Authors: Andrew J Mongue, Megan E Hansen, James R WaltersAbstract:The rate of divergence for Z or X Chromosomes is usually observed to be greater than autosomes, but the proposed evolutionary causes for this pattern vary, as do empirical results from diverse taxa. Even among moths and butterflies (Lepidoptera), which generally share a single-origin Z Chromosome, the handful of available studies give mixed support for faster or more adaptive evolution of the Z Chromosome, depending on the species assayed. Here, we examine the molecular evolution of Z Chromosomes in two additional lepidopteran species: the Carolina sphinx moth and the monarch butterfly, the latter of which possesses a recent chromosomal fusion yielding a segment of newly Z-linked DNA. We find evidence for both faster and more adaptive Z Chromosome evolution in both species, though this effect is strongest in the neo-Z portion of the monarch sex Chromosome. The neo-Z is less male-biased than expected of a Z Chromosome, and unbiased and female-biased genes drive the signal for adaptive evolution here. Together these results suggest that male-biased gene accumulation and haploid selection have opposing effects on long-term rates of adaptation and may help explain the discrepancies in previous findings as well as the repeated evolution of neo-sex Chromosomes in Lepidoptera. This article is protected by copyright. All rights reserved.
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ZZ top faster and more adaptive Z Chromosome evolution in two lepidoptera
bioRxiv, 2020Co-Authors: Andrew J Mongue, Megan E Hansen, James R WaltersAbstract:The rate of divergence for Z or X Chromosomes is theoretically predicted to be greater than autosomes, but the possible explanations for this pattern vary, as do empirical results from diverse taxa. Even among moths and butterflies (Lepidoptera), which generally share a single-origin Z Chromosome, the handful of available studies give mixed support for faster or more adaptive evolution of the Z Chromosome, depending on the species assayed. Here, we examine the molecular evolution of Z Chromosomes in two additional lepidopteran species: the Carolina sphinx moth and the monarch butterfly, the latter of which possesses a recent chromosomal fusion yielding a segment of newly Z-linked DNA. We find evidence for both faster and more adaptive Z Chromosome evolution in both species, though this effect is strongest in the neo-Z portion of the monarch sex Chromosome. The neo-Z is less male-biased than expected of a Z Chromosome, and unbiased and female-biased genes drive the signal for adaptive evolution here. Together these results suggest that male-biased gene accumulation and haploid selection have opposing effects on long-term rates of adaptation and may help explain the discrepancies in previous findings as well as the repeated evolution of neo-sex Chromosomes in Lepidoptera.
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dichotomy of dosage compensation along the neo Z Chromosome of the monarch butterfly
Current Biology, 2019Co-Authors: Patrick Reilly, Peter Andolfatto, James J Lewis, Robert D Reed, James R WaltersAbstract:Summary Mechanisms of sex Chromosome dosage compensation (SCDC) differ strikingly among animals. In Drosophila flies, Chromosome-wide transcription is doubled from the single X Chromosome in hemiZygous (XY) males, whereas in Caenorhabditis nematodes, expression is halved for both X copies in homoZygous (XX) females [ 1 , 2 ]. Unlike other female-heterogametic (WZ female and ZZ male) animals, moths and butterflies exhibit sex Chromosome dosage compensation patterns typically seen only in male-heterogametic species [ 3 ]. The monarch butterfly carries a newly derived Z Chromosome segment that arose from an autosomal fusion with the ancestral Z [ 4 ]. Using a highly contiguous genome assembly, we show that gene expression is balanced between sexes along the entire Z Chromosome but with distinct modes of compensation on the two segments. On the ancestral Z segment, depletion of H4K16ac corresponds to nearly halving of biallelic transcription in males, a pattern convergent to nematodes. Conversely, the newly derived Z segment shows a Drosophila-like mode of compensation, with enriched H4K16ac levels corresponding to doubled monoallelic transcription in females. Our work reveals that, contrary to the expectation of co-opting regulatory mechanisms readily in place, the evolution of plural modes of dosage compensation is also possible along a single sex Chromosome within a species.
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conserved patterns of sex Chromosome dosage compensation in the lepidoptera wZ ZZ insights from a moth neo Z Chromosome
Genome Biology and Evolution, 2017Co-Authors: James R Walters, Douglas C KnippleAbstract:Where previously described, patterns of sex Chromosome dosage compensation in the Lepidoptera (moths and butterflies) have several unusual characteristics. Other female-heterogametic (ZW/ZZ) species exhibit female Z-linked expression that is reduced compared with autosomal expression and male Z expression. In the Lepidoptera, however, Z expression typically appears balanced between sexes but overall reduced relative to autosomal expression, that is Z ≈ ZZ < AA. This pattern is not easily reconciled with theoretical expectations for the evolution of sex Chromosome dosage compensation. Moreover, conflicting results linger due to discrepancies in data analyses and tissues sampled among lepidopterans. To address these issues, we performed RNA-seq to analyZe sex Chromosome dosage compensation in the codling moth, Cydia pomonella, which is a species from the earliest diverging lepidopteran lineage yet examined for dosage compensation and has a neo-Z Chromosome resulting from an ancient Z:autosome fusion. While supported by intraspecific analyses, the Z ≈ ZZ < AA pattern was further evidenced by comparative study using autosomal orthologs of C. pomonella neo-Z genes in outgroup species. In contrast, dosage compensation appears to be absent in reproductive tissues. We thus argue that inclusion of reproductive tissues may explain the incongruence from a prior study on another moth species and that patterns of dosage compensation are likely conserved in the Lepidoptera. Notably, this pattern appears convergent with patterns in eutherian mammals (X ≈ XX < AA). Overall, our results contribute to the notion that the Lepidoptera present challenges both to classical theories regarding the evolution of sex Chromosome dosage compensation and the emerging view of the association of dosage compensation with sexual heterogamety.
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convergent patterns of sex Chromosome dosage compensation between lepidopteran species wZ ZZ and eutherian mammals xx xy insights from a moth neo Z Chromosome
bioRxiv, 2015Co-Authors: James R Walters, Douglas C KnippleAbstract:In contrast to XX/XY species, Z-linked expression is overall reduced in female WZ/ZZ species compared to males or the autosomal expression. This pattern (Z<ZZ≈AA) has been consistently reported in all the WZ/ZZ taxa examined so far, with the singular exception of the insect order of Lepidoptera (moths and butterflies). However, conflicting results linger in this taxon due to discrepancies in data analyses and tissues sampled. To address this issue, we analyZed dosage compensation in the codling moth Cydia pomonella (Tortricidae) using tissues that represent different levels of sexual divergence. C. pomonella is the most basal lepidopteran species yet examined for dosage compensation and has a neo-Z Chromosome resulting from an ancient Z:autosome translocation. We based our analyses on RNAseq and de novo transcriptome data from C. pomonella, as well as scrutiny into investigations of other lepidopteran species. Our evidence supports that the lepidopterans share a pattern (Z≈ZZ
Niclas Backstrom - One of the best experts on this subject based on the ideXlab platform.
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multilayered tuning of dosage compensation and Z Chromosome masculiniZation in the wood white leptidea sinapis butterfly
Genome Biology and Evolution, 2019Co-Authors: Lars Josef Hook, Luis Leal, Venkat Talla, Niclas BackstromAbstract:In species with genetic sex determination, dosage compensation can evolve to equal expression levels of sex-linked and autosomal genes. Current knowledge about dosage compensation has mainly been derived from male-heterogametic (XX/XY) model organisms, whereas less is understood about the process in female-heterogametic systems (ZZ/ZW). In moths and butterflies, downregulation of Z-linked expression in males (ZZ) to match the expression level in females (ZW) is often observed. However, little is known about the underlying regulatory mechanisms, or if dosage compensation patterns vary across ontogenetic stages. In this study, we assessed dynamics of Z-linked and autosomal expression levels across developmental stages in the wood white (Leptidea sinapis). We found that although expression of Z-linked genes in general was reduced compared with autosomal genes, dosage compensation was actually complete for some categories of genes, in particular sex-biased genes, but equaliZation in females was constrained to a narrower gene set. We also observed a noticeable convergence in Z-linked expression between males and females after correcting for sex-biased genes. Sex-biased expression increased successively across developmental stages, and male-biased genes were enriched on the Z-Chromosome. Finally, all five core genes associated with the ribonucleoprotein dosage compensation complex male-specific lethal were detected in adult females, in correspondence with a reduction in the expression difference between autosomes and the single Z-Chromosome. We show that tuning of gene dosage is multilayered in Lepidoptera and argue that expression balance across chromosomal classes may predominantly be driven by enrichment of male-biased genes on the Z-Chromosome and cooption of available dosage regulators.
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sex and species biased gene flow in a spotted eagle hybrid Zone
BMC Evolutionary Biology, 2011Co-Authors: Niclas Backstrom, Ulo ValiAbstract:Recent theoretical and empirical work points toward a significant role for sex-Chromosome linked genes in the evolution of traits that induce reproductive isolation and for traits that evolve under influence of sexual selection. Empirical studies including recently diverged (Pleistocene), short-lived avian species pairs with short generation times have found that introgression occurs on the autosomes but not on the Z-Chromosome. Here we study genetic differentiation and gene flow in the long-lived greater spotted eagle (Aquila clanga) and lesser spotted eagle (A. pomarina), two species with comparatively long generation times. Our data suggest that there is a directional bias in migration rates between hybridiZing spotted eagles in eastern Europe. We find that a model including post divergence gene flow fits our data best for both autosomal and Z-Chromosome linked loci but, for the Z-Chromosome, the rate is reduced in the direction from A. pomarina to A. clanga. The fact that some introgression still occurs on the Z-Chromosome between these species suggests that the differentiation process is in a more premature phase in our study system than in previously studied avian species pairs and that could be explained by a shorter divergence time and/or a longer average generation time in the spotted eagles. The results are in agreement with field observations and provide further insight into the role of sex-linked loci for the build-up of barriers to gene flow among diverging populations and species.
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no evidence for Z Chromosome rearrangements between the pied flycatcher and the collared flycatcher as judged by gene based comparative genetic maps
Molecular Ecology, 2010Co-Authors: Niclas Backstrom, Anna Qvarnstrom, Eleftheria Palkopoulou, Hans EllegrenAbstract:Revealing the genetic basis of reproductive isolation is fundamental for understanding the speciation process. Chromosome speciation models propose a role for chromosomal rearrangements in promoting the build up of reproductive isolation between diverging populations and empirical data from several animal and plant taxa support these models. The pied flycatcher and the collared flycatcher are two closely related species that probably evolved reproductive isolation during geographical separation in Pleistocene glaciation refugia. Despite the short divergence time and current hybridiZation, these two species demonstrate a high degree of intrinsic post-Zygotic isolation and previous studies have shown that traits involved in mate choice and hybrid viability map to the Z-Chromosome. Could rearrangements of the Z-Chromosome between the species explain their reproductive isolation? We developed high coverage Z-Chromosome linkage maps for both species, using gene-based markers and large-scale SNP genotyping. Best order maps contained 57-62 gene markers with an estimated average density of one every 1-1.5 Mb. We estimated the recombination rates in flycatcher Z-Chromosomes to 1.1-1.3 cM/Mb. A comparison of the maps of the two species revealed extensive co-linearity with no strong evidence for chromosomal rearrangements. This study does therefore not provide support the idea that sex Chromosome rearrangements have caused the relatively strong post-Zygotic reproductive isolation between these two Ficedula species.
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genetic mapping in a natural population of collared flycatchers ficedula albicollis conserved synteny but gene order rearrangements on the avian Z Chromosome
Genetics, 2006Co-Authors: Niclas Backstrom, Lars Gustafsson, Anna Qvarnstrom, Mikael Brandstrom, Hans H Cheng, Hans EllegrenAbstract:Data from completely sequenced genomes are likely to open the way for novel studies of the genetics of nonmodel organisms, in particular when it comes to the identification and analysis of genes responsible for traits that are under selection in natural populations. Here we use the draft sequence of the chicken genome as a starting point for linkage mapping in a wild bird species, the collared flycatcher—one of the most well-studied avian species in ecological and evolutionary research. A pedigree of 365 flycatchers was established and genotyped for single nucleotide polymorphisms in 23 genes selected from (and spread over most of) the chicken Z Chromosome. All genes were also found to be located on the Z Chromosome in the collared flycatcher, confirming conserved synteny at the level of gene content across distantly related avian lineages. This high degree of conservation mimics the situation seen for the mammalian X Chromosome and may thus be a general feature in sex Chromosome evolution, irrespective of whether there is male or female heterogamety. Alternatively, such unprecedented chromosomal conservation may be characteristic of most Chromosomes in avian genome evolution. However, several internal rearrangements were observed, meaning that the transfer of map information from chicken to nonmodel bird species cannot always assume conserved gene orders. Interestingly, the rate of recombination on the Z Chromosome of collared flycatchers was only ∼50% that of chicken, challenging the widely held view that birds generally have high recombination rates.
