Abstract:
:Because of its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconic regions which include nine multi-copy gene families. These gene families are expressed exclusively in testes and usually implicated in spermatogenesis. Here, to gain a better understanding of the role of the Y chromosome in human evolution and in determining sexually dimorphic traits, we studied ampliconic gene copy number variation in 100 males representing ten major Y haplogroups world-wide. Copy number was estimated with droplet digital PCR. In contrast to low nucleotide diversity observed on the Y in previous studies, here we show that ampliconic gene copy number diversity is very high. A total of 98 copy-number-based haplotypes were observed among 100 individuals, and haplotypes were sometimes shared by males from very different haplogroups, suggesting homoplasies. The resulting haplotypes did not cluster according to major Y haplogroups. Overall, only two gene families (RBMY and TSPY) showed significant differences in copy number among major Y haplogroups, and the haplogroup of a male could not be predicted based on his ampliconic gene copy numbers. Finally, we did not find significant correlations either between copy number variation and individual's height, or between the former and facial masculinity/femininity. Our results suggest rapid evolution of ampliconic gene copy numbers on the human Y, and we discuss its causes.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Ye D,Zaidi AA,Tomaszkiewicz M,Anthony K,Liebowitz C,DeGiorgio M,Shriver MD,Makova KDdoi
10.1093/gbe/evy086subject
Has Abstractpub_date
2018-05-01 00:00:00pages
1333-1350issue
5issn
1759-6653pii
4990384journal_volume
10pub_type
杂志文章abstract::By comparing the patterns of evolution in the coding and upstream noncoding regions of yeast ribosomal protein (RP) genes duplicated in a genome duplication, we find that although nonsynonymous sites in the coding sequences show strong evidence for the fixation of recent gene conversion events, similar patterns are le...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evq067
更新日期:2010-01-01 00:00:00
abstract::To fulfill their physiological functions, bile acids are conjugated with amino acids. In humans, conjugation is catalyzed by bile acid coenzyme A: amino acid N-acyltransferase (BAAT), an enzyme with a highly conserved catalytic triad in its active site. Interestingly, the conjugated amino acids are highly variable amo...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz238
更新日期:2019-11-01 00:00:00
abstract::All living organisms require protein degradation to terminate biological processes and remove damaged proteins. One such machine is the 20S proteasome, a specialized barrel-shaped and compartmentalized multicatalytic protease. The activity of the 20S proteasome generally requires the binding of regulators/proteasome a...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv068
更新日期:2015-05-04 00:00:00
abstract::The hundreds of endemic species of cichlid fishes in the East African Great Lakes Tanganyika, Malawi, and Victoria are a prime model system in evolutionary biology. With five genomes currently being sequenced, eastern African cichlids also represent a forthcoming genomic model for evolutionary studies of genotype-to-p...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr047
更新日期:2011-01-01 00:00:00
abstract::Selection modulates gene sequence evolution in different ways by constraining potential changes of amino acid sequences (purifying selection) or by favoring new and adaptive genetic variants (positive selection). The number of nonsynonymous differences in a pair of protein-coding sequences can be used to quantify the ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evp030
更新日期:2009-08-13 00:00:00
abstract::Bacterial degraders of chlorophenoxy herbicides have been isolated from various ecosystems, including pristine environments. Among these degraders, the sphingomonads constitute a prominent group that displays versatile xenobiotic-degradation capabilities. Four separate sequencing strategies were required to provide th...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx185
更新日期:2017-09-01 00:00:00
abstract::The effect of homologous recombination (HR) on the evolution of microbial genomes remains contentious as competing hypotheses seek to explain the evolutionary dynamics of microbial species. Evidence for HR between microbial genomes is widespread, and this process has been proposed to act as a cohesive force that can c...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr110
更新日期:2011-01-01 00:00:00
abstract::Kallikrein related peptidase 8 (KLK8; also called neuropsin) is a serine protease that plays distinct roles in the skin and hippocampus. In the skin, KLK8 influences keratinocyte proliferation and desquamation, and activates antimicrobial peptides in sweat. In the hippocampus, KLK8 affects memory acquisition. Here, we...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx239
更新日期:2017-11-01 00:00:00
abstract::Population-level differences in the number of copies of genes resulting from gene duplication and loss have recently been recognized as an important source of variation in eukaryotes. However, except for a small number of cases, the phenotypic effects of this variation are unknown. Data from the Saccharomyces Genome R...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evq043
更新日期:2010-01-01 00:00:00
abstract::In 1957, an invasive and highly defensive honey bee began to spread across Brazil. In the previous year, Brazilian researchers hoped to produce a subtropical-adapted honey bee by crossing local commercial honey bees (of European origin) with a South African honey bee subspecies (Apis mellifera scutellata; an A-lineage...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa128
更新日期:2020-08-01 00:00:00
abstract::piRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. More...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa064
更新日期:2020-05-01 00:00:00
abstract::Theory suggests that biological modularity and robustness allow for maintenance of fitness under mutational change, and when this change is adaptive, for evolvability. Empirical demonstrations that these traits promote evolvability in nature remain scant however. This is in part because modularity, robustness, and evo...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr046
更新日期:2011-01-01 00:00:00
abstract::Nuclear-encoded pentatricopeptide repeat (PPR) proteins are site-specific factors for C-to-U RNA editing in plant organelles coevolving with their targets. Losing an editing target by C-to-T conversion allows for eventual loss of its editing factor, as recently confirmed for editing factors CLB19, CRR28, and RARE1 tar...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz032
更新日期:2019-03-01 00:00:00
abstract::Homologous recombination is a major driver of bacterial speciation. Genetic divergence and host association are important factors influencing homologous recombination. Here, we study these factors for Campylobacter fetus, which shows a distinct intraspecific host dichotomy. Campylobacter fetus subspecies fetus (Cff) a...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy048
更新日期:2018-03-01 00:00:00
abstract::Although pooled-population sequencing has become a widely used approach for estimating allele frequencies, most work has proceeded in the absence of a proper statistical framework. We introduce a self-sufficient, closed-form, maximum-likelihood estimator for allele frequencies that accounts for errors associated with ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu085
更新日期:2014-04-30 00:00:00
abstract::Many organisms have a global mechanism for dosage compensation (DC) operating along the entire male X chromosome, which equalizes gene expression on the male X with that on the two Xs in females and/or on autosomes. At the initial stage of sex chromosome evolution, however, gene-by-gene (or localized) DC may also be n...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy148
更新日期:2018-08-01 00:00:00
abstract::The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effect...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt083
更新日期:2013-01-01 00:00:00
abstract::The root-knot nematodes (genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species, most of which are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture. While understanding...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx201
更新日期:2017-10-01 00:00:00
abstract::The loss of Y-linked genes during sex chromosome evolution creates a potentially deleterious low gene dosage in males. Recent studies have reported different strategies of dosage compensation. Unfortunately, most of these studies investigated taxa with comparatively old sex chromosome systems, which may limit insights...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv013
更新日期:2015-01-23 00:00:00
abstract::Because natural selection is likely to act on multiple genes underlying a given phenotypic trait, we study here the potential effect of ongoing and past selection on the genetic diversity of human biological pathways. We first show that genes included in gene sets are generally under stronger selective constraints tha...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv083
更新日期:2015-05-13 00:00:00
abstract::The precise localization of CaV2 voltage-gated calcium channels at the synapse active zone requires various interacting proteins, of which, Rab3-interacting molecule or RIM is considered particularly important. In vertebrates, RIM interacts with CaV2 channels in vitro via a PDZ domain that binds to the extreme C-termi...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa097
更新日期:2020-08-01 00:00:00
abstract::Sequencing of the complete mitochondrial genome of the soft coral Paraminabea aldersladei (Alcyoniidae) revealed a unique gene order, the fifth mt gene arrangement now known within the cnidarian subclass Octocorallia. At 19,886 bp, the mt genome of P. aldersladei is the second largest known for octocorals; its gene co...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evs074
更新日期:2012-01-01 00:00:00
abstract::The nuclear pore complex (NPC) is a large macromolecular assembly situated within the pores of the nuclear envelope. Through interactions between its subcomplexes and import proteins, the NPC mediates the transport of molecules into and out of the nucleus and facilitates dynamic chromatin regulation and gene expressio...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz029
更新日期:2019-03-01 00:00:00
abstract::Primary metabolism is essential to plants for growth and development, and secondary metabolism helps plants to interact with the environment. Many plant metabolites are industrially important. These metabolites are produced by plants through complex metabolic pathways. Lack of knowledge about these pathways is hinderi...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv217
更新日期:2015-11-10 00:00:00
abstract::Short interspersed elements (SINEs) are non-autonomous retrotransposons. Although they usually show fast evolutionary rates, in some instances highly conserved domains (HCDs) have been observed in elements with otherwise divergent sequences and from distantly related species. Here, we document the life history of two ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx094
更新日期:2017-06-01 00:00:00
abstract::Arbuscular mycorrhizal fungi (AMF) represent an ecologically important and evolutionarily intriguing group of symbionts of land plants, currently thought to have propagated clonally for over 500 Myr. AMF produce multinucleate spores and may exchange nuclei through anastomosis, but meiosis has never been observed in th...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr089
更新日期:2011-01-01 00:00:00
abstract::Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lo...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz053
更新日期:2019-04-01 00:00:00
abstract::Hemerythrins and hemocyanins are respiratory proteins present in some of the most ecologically diverse animal lineages; however, the precise evolutionary history of their enzymatic domains (hemerythrin, hemocyanin M, and tyrosinase) is still not well understood. We survey a wide dataset of prokaryote and eukaryote gen...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt102
更新日期:2013-01-01 00:00:00
abstract::Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insert...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw302
更新日期:2017-02-01 00:00:00
abstract::Parasitoid wasps are among the most speciose animals, yet have relatively few available genomic resources. We report a draft genome assembly of the wasp Diachasma alloeum (Hymenoptera: Braconidae), a host-specific parasitoid of the apple maggot fly Rhagoletis pomonella (Diptera: Tephritidae), and a developing model fo...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz205
更新日期:2019-10-01 00:00:00