Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs.

This corrects the article DOI: 10.1038/hdy.2015.89.

Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs.

Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs-Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates >135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.

Effect of ewe birth litter size and estimation of genetic parameters on ewe reproductive life traits.

Ewe lifetime productivity has economic implications for producers because shorter lifetime productivity results in less profit. Productive years of ewes from extensive, range-based systems of the United States West are generally less than ewes from more temperate regions of the United States. Accordingly, ewes from range-based systems, especially those employing shed-lambing strategies, have been selected for increased litter size to offset decreased lifetime productivity. However, the relationship of the ewe's birth litter size (ELSB) has not been considered a potential contributor to lifetime productivity. Longevity (number of productive years, n = 1 per population) and stayability (probability to survive to the next age; ages 2-7 years, n = 6 per population) were investigated to understand ELSB effects on productive life. Columbia, Polypay, Rambouillet, and Targhee breeds were used in this study. Across-breed (n = 11 550) and within-breed (Columbia, n = 4 398; Polypay, n = 4 534; Rambouillet, n = 5 922; Targhee, n = 6 482) analyses were used. Depending on the population, records spanned from 1950 to 2008, where ewe's birth year was included as a fixed effect in the animal model using restricted maximum likelihood estimation procedures. Fixed effects investigated included ELSB (single-, twin-, or triplet-born) and ewe breed (across-breed analyses only). Regardless of trait or population used, heritability ranged from 0.06 ± 0.02 to 0.34 ± 0.03, where stayability at younger ages had the highest estimates. The breed effect was significant in all across-breed analyses (0.0001 ≤ P ≤ 0.038; n = 7), where Polypay, a breed selected for accelerated lambing and increased fertility, averaged shorter productive life or had a lower probability of survival to the next age compared with other breeds (longevity: 0.009 ≤ P ≤ 0.223; stayability: 0.000 ≤ P ≤ 0.842). The ELSB was significant in 60% (n = 5) and 37% (n = 30) of longevity and stayability analyses, respectively. Except for Targhee, all analyses showed ewes born in smaller litter sizes were associated with longer productive lives or higher probability of surviving to the next age, particularly in across-breed analyses (e.g., longevity: single- vs twin-born ewes, P = 0.004; vs triplet-born ewes, P = 0.003). This study provides evidence that increasing prolificacy in ewes from extensive, range-based production systems may impact productive life. Due to the low heritability of these traits, additional investigation into modeling these traits with dominance effects and litter size needs to be conducted.

In vivo expression of mRNA for the Ca++-binding protein SPARC (osteonectin) revealed by in situ hybridization.

In situ hybridization is used to survey the tissue-specific and developmental expression of the cloned mouse gene Sparc, coding for a protein homologous to the bovine Ca++-binding protein, osteonectin. High levels of SPARC RNA are found in osteoblasts and odontoblasts. In addition, high grain counts are associated with a variety of other cell types in the embryo and newborn mouse, including parietal endoderm, deciduum, whisker follicles (connective tissue sheath), peripheral nerve trunk, skin (dermis), and stomach (submucosa). Spatially restricted but high levels of SPARC mRNA are also seen in the adult adrenal glands, testis, and ovary. This pattern of differential gene expression demands a reassessment of the function originally proposed for osteonectin, and predicts a much wider role for the protein in a variety of biological processes.

Vertebrate evolution: something fishy about Hox genes.

The complete Hox gene complement of the Japanese pufferfish has now been determined, together with the genomic organisation of all four Hox gene clusters. One of the many surprises is that this strange fish has lost an unusually large number of Hox genes.

Evidence for 14 homeobox gene clusters in human genome ancestry.

The arrangement of Hox genes into physical clusters is fundamental to the patterning of animal body plans. Other homeobox genes are often described as dispersed, with only occasional examples of linkage reported, such as the amphioxus ParaHox and Drosophila 93D/E clusters. This clustering is unlikely to be the derived condition, as the genes of the ParaHox and 93D/E clusters are phylogenetically widespread. To assess whether clustering is retained in mammals, and to infer its history, we considered the distribution of ANTP superclass homeobox genes in human and mouse genomes. We postulate four ancient arrays of ANTP superclass genes in animal genomes, denoted 'extended Hox' (Hox, Evx and Mox), NKL (including NK1, NK3, NK4, Lbx, Tlx, Emx, Vax, Hmx, NK6, Msx), ParaHox (Cdx, Xlox, Gsx) and EHGbox (En, HB9, Gbx). Each of these duplicated in the ancestry of the human genome to yield four Hox, four NKL, four ParaHox and at least two EHGbox clusters or arrays. Two of the human NKL clusters (four in mouse) have subsequently been split by chromosome rearrangement, as has one human EHGbox array. We date all cluster duplications to early chordate evolution and infer that three clusters (Hox, NKL, EHGbox) resided on the same chromosome before duplication.

Hsp70 sequences indicate that choanoflagellates are closely related to animals.

Over 130 years ago, James-Clark noted a remarkable structural similarity between the feeding cells of sponges (choanocytes) and a group of free-living protists, the choanoflagellates. Both cell types possess a single flagellum surrounded by a collar of fine tentacles. The similarity led to the hypothesis that sponges, and, by implication, other animals, evolved from choanoflagellate-like ancestors. Phylogenetic analysis of ribosomal DNA neither supports nor refutes this hypothesis. Here, we report the sequence of an hsp70 gene and pseudogene from the freshwater choanoflagellate Monosiga ovata. These represent the first nuclear-encoded protein-coding sequences reported for any choanoflagellate. We find that Monosiga and most bilaterian hsp70 genes have high GC contents that may distort phylogenetic tree construction; therefore, protein sequences were used for phylogenetic reconstruction. Our analyses indicate that Monosiga is more closely related to animals than to fungi. We infer that animals and at least some choanoflagellates are part of a clade that excludes the fungi. This is consistent with the origin of animals from a choanoflagellate-like ancestor.

Estimation of Hox gene cluster number in lampreys.

Hox gene clusters are linked arrays of related homeobox genes with important roles in patterning the main body axis of animal embryos. Almost all invertebrates analyzed in detail, including a cephalochordate, have a single Hox gene cluster. In contrast, mammals have four such clusters inferred to have arisen by duplication. Data from other jawed vertebrates, including teleost fish, suggest they have at least four Hox gene clusters, implying that cluster duplication dates to very early in vertebrate evolution. Lampreys descended from one of the earliest vertebrate lineages and are thus critical in dating the duplication events. Here we analyze the Hox gene complement of a freshwater lamprey, Lampetra, using degenerate PCR. By analysis of the DNA sequences, deduced protein sequences, and by comparison to previous data from the distantly related sea lamprey, we conclude that lampreys have approximately 21 Hox genes from paralogous groups 1-10, plus a group 13 Hox gene. The data support the presence of three Hox gene clusters in lampreys more strongly than they support the presence of one, two or four gene clusters. We discuss how this situation may have arisen in evolution.

Cloning and evolutionary analysis of msh-like homeobox genes from mouse, zebrafish and ascidian.

The homeobox is a relatively conserved 180-nucleotide-long sequence characterizing a large and phylogenetically wide-spread family of putative regulatory genes, many of which have been implicated in the control of embryonic development. The Drosophila melanogaster muscle segment homeobox (msh) gene contains a homeobox which is markedly divergent from that of any other characterized D. melanogaster gene, yet very similar to that of the mouse Hox-7.1 gene [Robert et al., EMBO J. 8 (1989) 91-100; Hill et al., Genes Develop. 3 (1989) 26-37]. To elucidate the evolutionary relationship between these two genes, and hence facilitate comparative analyses, it is necessary to determine the number of msh-like genes in the two species, and to characterize any msh gene duplication events which may have occurred since their divergence. To address these questions, I have employed the polymerase chain reaction to amplify, clone and sequence msh-related homeobox genes from two divergent vertebrate species (mouse and zebrafish), one ascidian (Ciona intestinalis), and D. melanogaster. Sequence determination of 91 recombinant clones resulted in the identification of three msh-like genes from mouse and three from zebrafish, but only one each from C. intestinalis and D. melanogaster. Sequence analyses suggest that multiple msh gene duplications occurred in the lineage leading to vertebrates, after the divergence of the ascidia.

Cloning and analysis of an HMG gene from the lamprey Lampetra fluviatilis: gene duplication in vertebrate evolution.

Evolution has shaped the organisation of vertebrate genomes, including the human genome. To shed further light on genome history, we have cloned and analysed an HMG gene from lamprey, representing one of the earliest vertebrate lineages. Genes of the HMG1/2 family encode chromosomal proteins that bind DNA in a non-sequence-specific manner, and have been implicated in a variety of cellular processes dependent on chromatin structure. They are characterised by two copies of a conserved motif, the HMG box, followed by an acidic C-terminal region. We report here the cloning of a cDNA clone from the river lamprey Lampetra fluviatilis containing a gene with two HMG boxes and an acidic tail; we designate this gene LfHMG1. Molecular phylogenetic analysis shows that LfHMG1 is descended from a gene ancestral to mammalian HMG1 and HMG2. This implies that there was a duplication event in the HMG1/2 gene family, that occurred after the divergence of the jawed and jawless fishes, 450 million years ago. This conclusion supports and refines the hypothesis that there was a period of extensive gene duplication early in vertebrate evolution. We also show that the HMG1/2 family originated before the protostomes and deuterostomes diverged, over 525 million years ago.

Conservation of engrailed-like homeobox sequences during vertebrate evolution.

The Drosophila melanogaster developmental gene engrailed (en) is a member of a distinct subfamily of homeobox genes with a wide phylogenetic distribution. Here we report the use of reduced stringency polymerase chain reaction (PCR) to amplify and clone 8 genes related to en from 5 vertebrate species, including representatives of the most ancient vertebrate lineages. Nucleotide and deduced amino acid sequence comparisons between mouse, toad, zebrafish, lamprey and hagfish genes reveal extensive evolutionary conservation, and suggests that 2 en-like genes have been retained in most vertebrate lineages.

Cloning of segment polarity gene homologues from the unsegmented brachiopod Terebratulina retusa (Linnaeus).

We have used the polymerase chain reaction (PCR) to amplify, clone and sequence homologues of the Drosophila segment polarity genes engrailed (en), cubitus interruptus Dominant (ciD) and wingless (wg) from the genome of the brachiopod, Terebratulina retusa (Linnaeus). The deduced translation products of brachiopod en and ciD share high levels of sequence identity with their Drosophila homologues. The brachiopod wg-related clone is divergent from Drosophila wg, although clearly a member of the wg/Wnt gene family. These results indicate that structural diversity of Drosophila segment polarity genes has been evolutionarily conserved in a divergent, ancient and unsegmented animal phylum.

Molecular genetic analysis of sperm competition in the damselfly Ischnura elegans (Vander Linden).

Sperm competition can be a powerful selective force in the evolution of mating systems. Several odonate species have attracted study to assess the extent and mechanism of last-male sperm precedence. Members of the genus Ischnura (Zygoptera) display a particularly interesting range of mating systems, and Ischnura elegans was selected for study. Polymorphic microsatellites were cloned, sequenced and used to determine paternity of I. elegans larvae, to reveal patterns of sperm precedence. More than 3000 larvae, collected from both wild and captively bred I. elegans females, were typed for one or two microsatellite loci and paternity was determined by comparison with parental genotypes. Microsatellite typing showed that most wild-caught females had mated with several males. Analysis of offspring from females which mated in captivity showed that multiple-matings result in a large proportion of last-male sperm precedence (mean value for immediate last male precedence is 0.79 +/- 0.2 (+/- s.d.; n = 11, range = 0.44-1)). There is appreciable variation in the extent and patterns of immediate and longer-term precedence, which could reflect differences in male sperm removal ability or selective use of sperm by females.

The effect of gene duplication on homology.

Genes related by gene duplication within an organism's evolutionary lineage are termed paralogues; genes related by speciation are orthologues. It is generally agreed that orthologous genes must be compared when using DNA sequences to reconstruct the evolutionary history of organisms. There is an important exception: information from paralogous genes can reveal the root position of a phylogenetic tree. The duplicated rDNA genes of arrow worms provide an example. Gene duplication is also relevant when comparing gene expression between taxa; for example, when trying to identify homologous roles of genes. When gene duplication occurred after lineage divergence, single orthologues no longer exist, and comparison is complicated. This is a particular problem when comparing roles of vertebrate and invertebrate genes. Amphioxus and ascidian genes can be useful in such situations, since they diverged before extensive gene duplication in the vertebrate lineage. Using Otx and Pax as examples, I show how examination of amphioxus or ascidian genes reveals patterns of gene divergence after duplication, assisting the identification of homologous gene functions. Given the problems of comparing duplicated genes between species, the time is ripe for the introduction of additional terminology to elaborate on the concepts of paralogy and orthology.

On the recollection of specific- and partial-source information.

Memory judgments can be based on information that is more or less specific with respect to the source of an item. The authors introduce a procedure and multinomial model for measuring specific- and partial-source information. In 2 experiments, participants heard words spoken by 4 different voices: 2 male voices and 2 female voices. During the test, participants were required to remember who spoke the test items (e.g., Male 1, Male 2, Female 1, Female 2, or new word). Participants often remembered information about the gender of the source (i.e., partial-source information) when they did not remember information that identified the source itself (i.e., specific-source information). Dividing attention during retrieval impaired participants' memory for specific-source information (i.e., voice information) but did not affect memory for partial-source information (i.e., gender information).

The effects of combining sanctions and rehabilitation for driving under the influence: an evaluation of the New Jersey Alcohol Countermeasures Program.

In contrast to many other state Driving under the Influence (DUI) programs developed in the United States in the 1970s as alternatives to traditional sanctions, the New Jersey Alcohol Countermeasures Program combined sanctions with mandatory education/rehabilitation for offenders. Three components were evaluated: DUI education, "treatment," and Alcoholics Anonymous. For 2,734 first and repeat offenders participating in this program between 1979 and 1982, the program was effective in reducing DUI recidivism for program completers (66% while licensed and 51% while suspended) compared with noncompleters, but it was less effective in reducing subsequent moving violations while licensed (20% compared with noncompleters) and accidents while licensed (18% compared with noncompleters). Completers had higher rates of violations and accidents while suspended (9% compared with noncompleters). A small group of repeat offenders, missassigned to DUI education, had higher post conviction rates of negative driving events than those of comparable offenders assigned to "treatment" or Alcoholics Anonymous, indicating that for these offenders the latter interventions were more effective.