Corticotropin-Releasing Hormone (CRH) gene family duplications in Lampreys correlate with two early vertebrate genome doublings

The ancestor of gnathostomes (jawed vertebrates) is generally considered to have undergone two rounds of whole genome duplication (WGD). The timing of these WGD events relative to the divergence of the closest relatives of the gnathostomes, the cyclostomes, has remained contentious. Lampreys and hagfishes are extant cyclostomes whose gene families can shed light on the relationship between the WGDs and the cyclostome-gnathostome divergence. Previously, we have characterized in detail the evolution of the gnathostome corticotropin-releasing hormone (CRH) family and found that its five members arose from two ancestral genes that existed before the WGDs. The two WGDs resulted, after secondary losses, in one triplet consisting of CRH1, CRH2, and UCN1, and one pair consisting of UCN2 and UCN3. All five genes exist in representatives for cartilaginous fishes, ray-finned fishes, and lobe-finned fishes. Differential losses have occurred in some lineages. We present here analyses of CRH-family members in lamprey and hagfish by comparing sequences and gene synteny with gnathostomes. We found five CRH-family genes in each of two lamprey species (Petromyzon marinus and Lethenteron camtschaticum) and two genes in a hagfish (Eptatretus burgeri). Synteny analyses show that all five lamprey CRH-family genes have similar chromosomal neighbors as the gnathostome genes. The most parsimonious explanation is that the lamprey CRH-family genes are orthologs of the five gnathostome genes and thus arose in the same chromosome duplications. This suggests that lampreys and gnathostomes share the same two WGD events and that these took place before the lamprey-gnathostome divergence.Portuguese Foundation for Science and Technology: UIDB/04326/2020info:eu-repo/semantics/publishedVersio

Ancient Grandeur of the Vertebrate Neuropeptide Y System Shown by the Coelacanth Latimeria chalumnae

The neuropeptide Y (NPY) family receptors and peptides have previously been characterized in several tetrapods, teleost fishes, and in a holocephalan cartilaginous fish. This has shown that the ancestral NPY system in the jawed vertebrates consisted of the peptides NPY and peptide YY (PYY) and seven G-protein-coupled receptors named Y1-Y8 (Y3 does not exist). The different vertebrate lineages have subsequently lost or gained a few receptor genes. For instance, the human genome has lost three of the seven receptors while the zebrafish has lost two and gained two receptor genes. Here we describe the NPY system of a representative of an early diverging lineage among the sarcopterygians, the West Indian Ocean coelacanth Latimeria chalumnae. The coelacanth was found to have retained all seven receptors from the ancestral jawed vertebrate. The receptors display the typical characteristics found in other vertebrates. Interestingly, the coelacanth was found to have the local duplicate of the PYY gene, called pancreatic polypeptide, previously only identified in tetrapods. Thus, this duplication took place very early in the sarcopterygian lineage, before the origin of tetrapods. These findings confirm the ancient complexity of the NPY system and show that mammals have lost more NPY receptors than any other vertebrate lineage. The coelacanth has all three peptides found in tetrapods and has retained the ancestral jawed vertebrate receptor repertoire with neither gains or losses

Unexpected multiplicity of QRFP receptors in early vertebrate evolution

The neuropeptide QRFP, also called 26RFa, and its G protein-coupled receptor GPR103 have been identified in all vertebrates investigated. In mammals, this peptide-receptor pair has been found to have several effects including stimulation of appetite. Recently, we reported that a QRFP peptide is present in amphioxus, Branchiostoma floridae, and we also identified a QRFP receptor (QRFPR) that mediates a functional response to sub-nanomolar concentrations of the amphioxus peptide as well as short and long human QRFP (Xu et al., submitted). Because the ancestral vertebrate underwent two tetraploidizations, it might be expected that duplicates of the QRFP gene and its receptor gene may exist. Indeed, we report here the identification of multiple vertebrate QRFPR genes. Three QRFPR genes are present in the coelacanth Latimeria chalumnae, representing an early diverging sarcopterygian lineage. Three QRFPR genes are present in the basal actinopterygian fish, the spotted gar. Phylogenetic and chromosomal analyses show that only two of these receptor genes are orthologous between the two species, thus demonstrating a total of four distinct vertebrate genes. Three of the QRFPR genes resulted from the early vertebrate tetraploidizations and were copied along with syntenic neuropeptide Y receptor genes. The fourth QRFPR gene may be an even older and distinct lineage. Because mammals and birds have only a single QRFPR gene, this means that three genes have been lost in these lineages, and at least one of these was lost independently in mammals and birds because it is still present in a turtle. In conclusion, these results show that the QRFP system gained considerable complexity in the early stages of vertebrate evolution and still maintains much of this in some lineages, and that it has been secondarily reduced in mammals

Unexpected multiplicity of QRFP receptors in early vertebrate evolution

The neuropeptide QRFP, also called 26RFa, and its G protein-coupled receptor GPR103 have been identified in all vertebrates investigated. In mammals, this peptide-receptor pair has been found to have several effects including stimulation of appetite. Recently, we reported that a QRFP peptide is present in amphioxus, Branchiostoma floridae, and we also identified a QRFP receptor (QRFPR) that mediates a functional response to sub-nanomolar concentrations of the amphioxus peptide as well as short and long human QRFP (Xu et al., submitted). Because the ancestral vertebrate underwent two tetraploidizations, it might be expected that duplicates of the QRFP gene and its receptor gene may exist. Indeed, we report here the identification of multiple vertebrate QRFPR genes. Three QRFPR genes are present in the coelacanth Latimeria chalumnae, representing an early diverging sarcopterygian lineage. Three QRFPR genes are present in the basal actinopterygian fish, the spotted gar. Phylogenetic and chromosomal analyses show that only two of these receptor genes are orthologous between the two species, thus demonstrating a total of four distinct vertebrate genes. Three of the QRFPR genes resulted from the early vertebrate tetraploidizations and were copied along with syntenic neuropeptide Y receptor genes. The fourth QRFPR gene may be an even older and distinct lineage. Because mammals and birds have only a single QRFPR gene, this means that three genes have been lost in these lineages, and at least one of these was lost independently in mammals and birds because it is still present in a turtle. In conclusion, these results show that the QRFP system gained considerable complexity in the early stages of vertebrate evolution and still maintains much of this in some lineages, and that it has been secondarily reduced in mammals

Evolution of the Insulin-Like Growth Factor Binding Protein (IGFBP) Family

The evolution of the IGF binding protein (IGFBP) gene family has been difficult to resolve. Both chromosomal and serial duplications have been suggested asmechanisms for the expansion of this gene family. We have identified and annotated IGFBP sequences from a wide selection of verte-brate species as well as Branchiostoma floridae and Ciona intestinalis. By combining detailed sequence analysis with sequence-based phylogenies and chromosome information, we arrive at the following scenario: the ancestral chordate IGFBP gene underwent a local gene duplication, resulting in a gene pair adjacent to a HOX cluster. Subsequently, the gene family expanded in the twobasal vertebrate tetraploidization (2R) resulting in the six IGFBP types that are presently found in placental mammals. The teleost fish ancestor underwent a third tetraploidization (3R) that further expanded the IGFBP repertoire. The five sequenced teleost fish genomes retain 9–11 of IGFBP genes. This scenario is supported by the phylogenies of three adjacent gene families in the HOX gene regions, namely the epidermal growth factor receptors (EGFR) and the Ikaros and distal-less (DLX) transcription factors. Our sequence comparisons show that several im-portant structural components in the IGFBPs are ancestral vertebrate features that have bee

Table paralogon 1 in teleosts

Table containing information about the nAChR neighboring gene families included in the analysis of nAChR paralogon 1 in relation to 3R event in teleosts. First, information about genome assembly versions used are listed, then the following information about the neighboring gene families is provided: species, HGNC/ZFIN/Flybase symbol name, chromosome or genomic scaffold position, Ensembl ID or NCBI accession number, taxa ID and additional comments regarding sequence update date on NCBI or if there has been manual edits of the original Ensembl or NCBI sequence. There is one page per family, presented in alphabetical order

Maximum likelihood tree nAChR gene family

The phylogenetic maximum likelihood tree of the nAChR genes in nexus format. The tree topology is supported by a non-parametric Ultra-Fast Bootstrap (UFBoot) and approximate Likelihood-Ratio Test (aLRT) with 1000 replicates. For simplicity only UFBoot values are shown. The taxa ID contains the species, the localization of the gene (chromosome/scaffold/contig number) and a number indicating the order on the chromosome/scaffold/contig if several genes are located on the same one. The taxa ID of human and zebrafish genes with annotated HGNC or ZFIN names, respectively, also contain these names. The assigned taxa ID and sequence information details are provided in Additional file 4

Table paralogon 1

Table containing information about the nAChR neighboring gene families included in the analysis of the nAChR paralogon 1. First, information about genome assembly versions used are listed, then the following information about the neighboring gene families is provided: species, HGNC/ZFIN/Flybase symbol name, chromosome or genomic scaffold position, Ensembl ID or NCBI accession number, taxa ID and additional comments regarding sequence update date on NCBI or if there has been manual edits of the original Ensembl or NCBI sequence. There is one page per family, presented in alphabetical order

aLRT SH-like trees paralogon 5

Phylogenetic aLRT SH-like tree of the neighboring gene families included in analysis of nAChR paralogon 5. There is one neighboring gene family per page in alphabetical order. Taxa ID and sequence information details are provided in the table below

Selektiivisestä yliopistosta valmistumisen vaikutus alku-uran tuloihin teknillisellä alalla

Koulutuksen laadun vaikutuksia yksilöiden työmarkkinatulemiin on tutkittu maailmalla paljon, mutta Suomessa aihealueen tutkimus on toistaiseksi ollut vähäistä. Tutkielma pyrkii paikkaamaan tätä aukkoa tutkimalla asiaa Suomen teknillisten yliopistojen saralla. Käytännössä tarkastellaan eroavatko selektiivisestä metropolialueen teknillisestä yliopistosta valmistuneiden alku-urien tulot muista teknillisistä yliopistoista valmistuneiden tuloista. Tutkimuskysymyksen tarkasteluun käytetään aineistoa, joka muodostuu vuosina 2000 2004 DIA-yhteishaussa hakeneista sekä heidän tulotiedoistaan vuoteen 2012 asti. Se sisältää yhteensä 223628 valintaryhmä hakukohde vuosi-havaintoa. Käytössä oleva aineisto mahdollistaa tutkimuskysymyksen tarkastelun käyttäen fuzzy regressioepäjatkuvuusmenetelmää (FRD). Siinä hyödynnetään selektiivisen yliopiston sisäänpääsyrajoilla esiintyvää epäjatkuvuutta kyseisestä yliopistosta valmistumisen todennäköisyydessä. Saatujen tulosten perusteella selektiivisestä yliopistosta valmistumisen tulovaikutukset ovat suuria (noin 20%) ja positiivisia, mutta eivät tilastollisesti merkitseviä. Verrattuna muihin pohjoismaisiin tutkimustuloksiin saatu preemio on erittäin suuri, mutta toisaalta yhdenpitävä siinä suhteessa, ettei se ole tilastollisesti merkitsevä. Erot muihin pohjoismaisiin tutkimustuloksiin saattavat selittyä sillä, että tutkielma on ensimmäisiä, jossa koulutuksen laadun vaikutuksia tutkitaan alan sisällä. Muita mahdollisia syitä ansiopreemion suuruuteen on esimerkiksi se, että selektiivisestä teknillisestä yliopistosta valmistuneet päätyvät tulosten perusteella muita todennäköisemmin asumaan Uudellemaalle, jossa tuottavuus ja myös tulot ovat muutenkin muuta maata korkeammat. Tulosten perusteella selektiivisestä teknillisestä yliopistosta valmistuneet myös työskentelevät sekä opintojensa aikana, että tulojen havaintohetkellä muista teknillisistä yliopistoista valmistuneita enemmän