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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...conservation does not fall within the scope of Ohno's original prediction (Ohno 1967) as intrachromosomal rearrangements presumably would not disrupt dosage levels to the same degree as would interchromosomal translocations. Linkage conservation is also not as pervasive as the conservation of gene content...
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Resource: Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation
- Kang Du,
- Martin Pippel,
- Susanne Kneitz,
- Romain Feron,
- Irene da Cruz,
- Sylke Winkler,
- Brigitta Wilde,
- Edgar G. Avila Luna,
- Gene Myers,
- Yann Guiguen,
- Constantino Macias Garcia,
- and Manfred Schartl
Genome Res. March 2022 32: 583-594; Published in Advance January 26, 2022, doi:10.1101/gr.275826.121
...on the Y was identified covering 80% of Chromosome 20, allowing some first inferences on the recent origin and a candidate male sex determining gene. Genome-wide transcriptomics uncovered sex-specific differences in brain gene expression with an enrichment for neurosteroidogenesis and testis genes in males...
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LETTER: The Origin of Human Chromosome 1 and Its Homologs in Placental Mammals
- William J. Murphy,
- Lutz Frönicke,
- Stephen J. O'Brien,
- and Roscoe Stanyon
Genome Res. August 2003 13: 1880-1888; Published in Advance July 17, 2003, doi:10.1101/gr.1022303
...The Origin of Human Chromosome 1 and Its Homologs in Placental Mammals William J. Murphy 1 , 3 , 4 , Lutz Frönicke 2 , 3 , Stephen J. O'Brien 1 , and Roscoe Stanyon 2 1 Laboratory of Genomic Diversity, National Cancer...
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Research: Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals
- Yoshihito Niimura,
- Atsushi Matsui,
- and Kazushige Touhara
Genome Res. September 2014 24: 1485-1496; Published in Advance July 22, 2014, doi:10.1101/gr.169532.113
...both elephant and non-elephant genes in a phylogenetic gene tree of a candidate OGG. If a clade contained elephant genes and genes from other species, those elephant and non-elephant genes were likely tohave originated froma single ancestral gene in the MRCA of placental mammals, and therefore...
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Research: Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes
- Eskeatnaf Mulugeta,
- Evelyne Wassenaar,
- Esther Sleddens-Linkels,
- Wilfred F.J. van IJcken,
- Edith Heard,
- J. Anton Grootegoed,
- Walter Just,
- Joost Gribnau,
- and Willy M. Baarends
Genome Res. September 2016 26: 1202-1210; Published in Advance August 10, 2016, doi:10.1101/gr.201665.115
...; for more detailed analyses of E. lutescens and E. talpinus, see Supplemental Fig. S1). Phylogeographical data, as well as the palaeogeographical history of the area near the Caspian Sea where the animals have their habitats (www. iucnredlist.org) (Fig. 1B), are in agreement with such a phylogenetic origin...
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Platypus Special/Letter: Origin of INSL3-mediated testicular descent in therian mammals
- Jae-Il Park,
- Jenia Semyonov,
- Chia Lin Chang,
- Wei Yi,
- Wesley Warren,
- and Sheau Yu Teddy Hsu
Genome Res. June 2008 18: 974-985; Published in Advance May 7, 2008, doi:10.1101/gr.7119108
...chromosome 19p13 fragment. (**) The co-orthologous relationship of the zebrafish RFLC2 gene on chromosome 24 to the pufferfish counterparts was determined based on sequence similarity analysis. INSL3 is a therian mammal-specific signature protein In addition to revealing the origin of relaxin family genes...
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Platypus Special/Letter: Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes
- Frédéric Veyrunes,
- Paul D. Waters,
- Pat Miethke,
- Willem Rens,
- Daniel McMillan,
- Amber E. Alsop,
- Frank Grützner,
- Janine E. Deakin,
- Camilla M. Whittington,
- Kyriena Schatzkamer,
- Colin L. Kremitzki,
- Tina Graves,
- Malcolm A. Ferguson-Smith,
- Wes Warren,
- and Jennifer A. Marshall Graves
Genome Res. June 2008 18: 965-973; Published in Advance May 7, 2008, doi:10.1101/gr.7101908
...Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes Frédéric Veyrunes 1 , 2 , 6 , Paul D. Waters 1 , 6 , 7 , Pat Miethke 1 , Willem Rens 2 , Daniel McMillan 1 , Amber E. Alsop 1 , Frank...
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Research: Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
- Stefan Washietl,
- Manolis Kellis,
- and Manuel Garber
Genome Res. April 2014 24: 616-628; Published in Advance January 15, 2014, doi:10.1101/gr.165035.113
..., with 73% of lincRNAs in cow, 58% in mouse, and 54% in rat, showing >30% exonic alignment. This fraction is well below that of mRNAs but clearly above random regions (Table 1; Supplemental Fig. 3). LincRNA expression across mammals To detect the expression of homologous lincRNAs in other species, we...
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LETTER: Phylogenetic Footprint Analysis of IGF2 in Extant Mammals
- Jennifer R. Weidman,
- Susan K. Murphy,
- Catherine M. Nolan,
- Fred S. Dietrich,
- and Randy L. Jirtle
Genome Res. September 2004 14: 1726-1732; doi:10.1101/gr.2774804
..., O.A., and O'Brien, S.J. 2001 . Molecular phylogenetics and the origins of placental mammals. Nature 409 : 614 -618. ↵ Murrell, A., Heeson, S., Bowden, L., Constancia, M., Dean, W., Kelsey, G., and Reik, W. 2001 . An intragenic methylated region in the imprinted Igf2 gene augments transcription. EMBO...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...of transposable element origination and high inactivity compared to other vertebrates. Beyond providing a reference point for comparative vertebrate genomic studies, the new gar s illuminate a structural component of slow genomic evolution in living fossils and molecular mechanisms that may underlie exceptional...

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