Peter Holland

Peter Holland
University of Oxford | OX · Department of Zoology

MA PhD DSc FLS FMBA FRS

About

280
Publications
58,363
Reads
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20,906
Citations
Introduction
Skills and Expertise
Additional affiliations
October 2002 - present
University of Oxford
Position
  • Professor
August 1994 - September 2002
University of Reading
Position
  • Professor of Zoology
October 1987 - July 1994
University of Oxford
Position
  • Researcher

Publications

Publications (280)
Article
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Author Summary We have examined gene duplication in a set of ancient genes used in patterning of animal embryos: the Hox genes. These genes code for proteins that bind DNA and switch on or off other genes, and they are very similar between distantly related animal species. Butterflies and moths, however, have additional Hox genes whose origin and...
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Over the past 200 years, almost every invertebrate phylum has been proposed as a starting point for evolving vertebrates. Most of these scenarios are outdated, but several are still seriously considered. The short-range transition from ancestral invertebrate chordates (similar to amphioxus and tunicates) to vertebrates is well accepted. However, lo...
Article
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BackgroundA central goal of evolutionary biology is to link genomic change to phenotypic evolution. The origin of new transcription factors is a special case of genomic evolution since it brings opportunities for novel regulatory interactions and potentially the emergence of new biological properties. ResultsWe demonstrate that a group of four home...
Article
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The sand rat Psammomys obesus is a gerbil species native to deserts of North Africa and the Middle East, and is constrained in its ecology because high carbohydrate diets induce obesity and type II diabetes that, in extreme cases, can lead to pancreatic failure and death. We report the sequencing of the sand rat genome and discovery of an unusual,...
Article
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Background: The homeobox genes Pdx and Cdx are widespread across the animal kingdom and part of the small ParaHox gene cluster. Gene expression patterns suggest ancient roles for Pdx and Cdx in patterning the through-gut of bilaterian animals although functional data are available for few lineages. To examine evolutionary conservation of Pdx and C...
Article
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Eutherian Totipotent Cell Homeobox (ETCHbox) genes are mammalian-specific PRD-class homeobox genes with conserved expression in the preimplantation embryo but fast-evolving and highly divergent sequences. Here we exploit an ectopic expression approach to examine the role of bovine ETCHbox genes and show that ARGFX and LEUTX homeodomain proteins upr...
Article
We present a genome assembly from an individual male Catocala fraxini (the Clifden nonpareil; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 781 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. The mitochondrial genome was also assem...
Article
We present a genome assembly from an individual female Noctua pronuba (the large yellow underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 529 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled. The mitochondrial genome was also assembled...
Article
We present a genome assembly from an individual female Autographa gamma (the silver Y; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 373 megabases in span. The majority of the assembly (99.65%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The mitochondrial genome was also asse...
Article
We present a genome assembly from an individual female Phlogophora meticulosa (the angle shades; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 539 megabases in span. The majority of the assembly, 95.17%, is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Some unassigned scaffolds are ident...
Article
We present a genome assembly from an individual male Xestia xanthographa (the square-spot rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 934 megabases in span. The majority of the assembly (99.94%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.
Article
We present a genome assembly from an individual female Phalera bucephala (the buff-tip; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 933 megabases in span. The majority of the assembly, 99.27%, is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.
Article
We present a genome assembly from an individual male Mimas tiliae (the lime hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 478 megabases in span. The complete assembly is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled.
Article
We present a genome assembly from an individual female Noctua fimbriata (the broad-bordered yellow underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 574 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled.
Article
We present a genome assembly from an individual male Notocelia uddmanniana (the bramble shoot moth; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 794 megabases in span. The majority of the assembly, 99.96%, is scaffolded into 28 chromosomal pseudomolecules, with the Z sex chromosome assembled.
Article
We present a genome assembly from an individual male Notodonta dromedarius (iron prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 342 megabases in span. The majority of the assembly, 99.35%, is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.
Article
We present a genome assembly from an individual male Pheosia tremula (the swallow prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 290 megabases in span. The majority of the assembly, 99.94%, is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.
Article
We present a genome assembly from an individual male Euproctis similis (the yellow-tail; Arthropoda; Insecta; Lepidoptera; Lymantriidae). The genome sequence is 508 megabases in span. Over 99% of the assembly is scaffolded into 22 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome, 15.5 kb in length,...
Article
We present a genome assembly from an individual male Abrostola tripartita (the spectacle; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 381 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.
Article
We present a genome assembly from an individual female Acronicta aceris (the sycamore; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 466 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.
Article
We present a genome assembly from an individual male Amphipyra berbera (Svensson’s copper underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 582 megabases in span. The majority (99.97%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.
Article
We present a genome assembly from an individual male Spilosoma lubricipeda (the white ermine; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 587 megabases in span. The majority of the assembly is scaffolded into 30 chromosomal pseudomolecules, with the Z sex chromosome assembled.
Article
We present a genome assembly from an individual male Thyatira batis (the peach-blossom moth; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 315 megabases in span. The majority of the assembly (99.68%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. The mitochondrial genome was also asse...
Article
Supergenes are regions of suppressed recombination that may span hundreds of genes and can control variation in key ecological phenotypes. Since genetic analysis is made impossible by the absence of recombination between genes, it has been difficult to establish how individual genes within these regions contribute to supergene-controlled phenotypes...
Article
We present a genome assembly from an individual female Laothoe populi (the poplar hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 576 megabases in span. The majority of the assembly is scaffolded into 29 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.
Article
We present a genome assembly from an individual female Hypena proboscidalis (the snout; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 637 megabases in span. The majority of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.
Article
We present a genome assembly from an individual male Euproctis similis (the yellow-tail; Arthropoda; Insecta; Lepidoptera; Lymantriidae). The genome sequence is 508 megabases in span. The majority of the assembly is scaffolded into 22 chromosomal pseudomolecules, with the Z sex chromosome assembled.
Article
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Gerbils are a subfamily of rodents living in arid regions of Asia and Africa. Recent studies have shown that several gerbil species have unusual amino acid changes in the PDX1 protein, a homeodomain transcription factor essential for pancreatic development and β-cell function. These changes were linked to strong GC-bias in the genome that may be ca...
Article
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The majority of homeobox genes are highly conserved across animals, but the eutherian-specific ETCHbox genes, embryonically expressed and highly divergent duplicates of CRX , are a notable exception. Here we compare the ETCHbox genes of 34 mammalian species, uncovering dynamic patterns of gene loss and tandem duplication, including the presence of...
Article
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Hox and ParaHox genes encode transcription factors with similar expression patterns in divergent animals. The Pdx ( Xlox ) homeobox gene, for example, is expressed in a sharp spatial domain in the endodermal cell layer of the gut in chordates, echinoderms, annelids and molluscs. The significance of comparable gene expression patterns is unclear bec...
Article
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Background Two gerbil species, sand rat ( Psammomys obesus ) and Mongolian jird ( Meriones unguiculatus ), can become obese and show signs of metabolic dysregulation when maintained on standard laboratory diets. The genetic basis of this phenotype is unknown. Recently, genome sequencing has uncovered very unusual regions of high guanine and cytosin...
Article
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The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfish Sanderia malayensis and Rhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like ge...
Article
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The aCristina Guijarro-Clarkenimal kingdom shows an astonishing diversity, the product of over 550 million years of animal evolution. The current wealth of genome sequence data offers an opportunity to better understand the genomic basis of this diversity. Here we analyse a sampling of 102 whole genomes including >2.6 million protein sequences. We...
Article
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
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Recombination increases the local GC-content in genomic regions through GC-biased gene conversion (gBGC). The recent discovery of a large genomic region with extreme GC-content in the fat sand rat Psammomys obesus provides a model to study the effects of gBGC on chromosome evolution. Here, we compare the GC-content and GC-to-AT substitution pattern...
Article
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ETCHbox genes are fast-evolving homeobox genes present only in eutherian (placental) mammals which originated by duplication and divergence from a conserved homeobox gene, Cone-rod homeobox (CRX). While expression and function of CRX are restricted to the retina in eutherian mammals, ETCHbox gene expression is specific to preimplantation embryos. T...
Article
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Background: The evolution of the head was one of the key events that marked the transition from invertebrates to vertebrates. With the emergence of structures such as eyes and jaws, vertebrates evolved an active and predatory life style and radiated into diversity of large-bodied animals. These organs are moved by cranial muscles that derive embry...
Article
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Several processes can lead to strong GC skew in localized genomic regions. In most cases, GC skew should not affect conserved amino acids because natural selection will purge deleterious alleles. However, in the gerbil subfamily of rodents, several conserved genes have undergone radical alteration in association with strong GC skew. An extreme exam...
Article
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Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes a...
Article
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Aim We have investigated the phylogeography and genetic structure of the Speckled Wood butterfly (Pararge aegeria) across its entire distribution range and studied its dispersal both on mainland and across sea straits. The apparent lack of gene flow between Sardinia and Corsica was further investigated by means of mating experiments. Location Euro...
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Understanding the emergence of the Animal Kingdom is one of the major challenges of modern evolutionary biology. Many genomic changes took place along the evolutionary lineage that gave rise to the Metazoa. Recent research has revealed the role that co-option of old genes played during this transition, but the contribution of genomic novelty has no...
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Background: ETCHbox genes are eutherian-specific homeobox genes expressed during preimplantation development at a time when the first cell lineage decisions are being made. The mouse has an unusual repertoire of ETCHbox genes with several gene families lost in evolution and the remaining two, Crxos and Obox, greatly divergent in sequence and numbe...
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The cloning and embryonic expression analysis of an amphioxus Hox gene in 1992 marked the start of molecular analysis of cephalochordate development. Other papers quickly followed, including a description of the amphioxus Hox gene cluster in 1994, fuelling a resurgence of interest in a long-forgotten animal. I describe the academic background, labo...
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Analysis of genome sequences within a phylogenetic context can give insight into the mode and tempo of gene and protein evolution, including inference of gene ages. This can reveal whether new genes arose on particular evolutionary lineages and were recruited for new functional roles. Here, we apply MCL clustering with all-versus-all reciprocal BLA...
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Background The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification are often temporally separated from WGD. Salmonid fish, whose ancestor underwent WGD by autotetraploidization ~95 million year...
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The NANOG homeobox gene plays a pivotal role in self-renewal and maintenance of pluripotency in human, mouse and other vertebrate embryonic stem cells, and in pluripotent cells of the blastocyst inner cell mass. There is a poorly studied and atypical homeobox locus close to the Nanog gene in some mammals which could conceivably be a cryptic paralog...
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Gene duplications and gene losses have been frequent events in the evolution of animal genomes, with the balance between these two dynamic processes contributing to major differences in gene number between species. After gene duplication, it is common for both daughter genes to accumulate sequence change at approximately equal rates. In some cases,...