12 research outputs found

    Divergence values and time estimates of mtDNA haplogroup T1 and its subclades obtained by using maximum likelihood (ML) and ρ statistics.

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    a<p>These correspond to the T1 complete mtDNA sequences shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone-0038601-g001" target="_blank">Figure 1</a>. Additional information regarding each mtDNA is provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone-0038601-t002" target="_blank">Table 2</a>.</p>b<p>Average number of base substitutions in the mtDNA coding region (between nps 364 and 15791) from the ancestral sequence type.</p>c<p>Estimate of the time to the most recent common ancestor of each clade, using a mutation rate estimate of 3,172 years per substitution in the whole coding region (15,428 bp) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone.0038601-Achilli1" target="_blank">[8]</a>.</p

    Tree of Complete Bovine mtDNA Sequences Belonging to Haplogroup T1.

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    <p>This tree was built as previously described <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone.0038601-Achilli1" target="_blank">[8]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone.0038601-Bonfiglio1" target="_blank">[11]</a>. The position of the Bovine Reference Sequence (BRS) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone.0038601-Anderson1" target="_blank">[23]</a> is indicated for reading off-sequence motifs. Divergence time estimates are those obtained using ML as reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone-0038601-t003" target="_blank">Table 3</a>. Branches display mutations with numbers according to the BRS; they are transitions unless a base is explicitly indicated for transversions (to A, G, C, or T) or a suffix for indels (+, d) and should be read as if the BRS was an artificial root. Recurrent mutations are underlined; back mutations at positions that separate the T1 tree from the BRS are prefixed with the superscript @. Note that the reconstruction of recurrent mutations in the control region is ambiguous in a number of cases. Heteroplasmy is marked with a suffix (h). The numbering of sequences is the same as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone-0038601-t002" target="_blank">Table 2</a>. The orange line connecting T1e and T1f to nps 16050 and 16113 reflects the uncertainty of their classification as quasi-sister taxa of sub-haplogroups T1a to T1d and implies the possibility that either one or the other or both might well descend from a T1â€Č2â€Č3â€Č – T1 intermediate (see Discussion for more details). Note that a potential affiliation of sequence #44 within sub-haplogroup T1e should be also considered (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#s2" target="_blank">Results</a>). The pie charts summarize the typing results of the survey performed on our entire dataset of 281 T1 mtDNAs (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone-0038601-t001" target="_blank">Table 1</a>) with diagnostic T1 sub-haplogroups markers. The numbers of mtDNAs for each sub-haplogroup are shown and include the 54 mtDNAs completely sequenced in this study, but not those previously published (#3, 4, 10, 22, 23, 29, 37, 46, 49 and 62) (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone-0038601-t002" target="_blank">Table 2</a>). Colors in the pie charts indicate geographical origins.</p

    List of T1 complete mitochondrial genomes analyzed in this study.

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    a<p>ID numbers are those reported in the phylogeny of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone-0038601-g001" target="_blank">Figure 1</a>.</p>b<p>Illumina sequencing.</p>c<p>Sanger sequencing.</p>d<p>Completely sequenced with both Illumina and Sanger approaches.</p>e<p>A potential affiliation within sub-haplogroup T1e should also be considered.</p

    Genotypes v1

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    Microsatellite genotypes from 81 cattle populations typed with 19 markers. British and Continental European; Blue: Indian Zebu. SPANISH. Betizu (BET), Toro de Lidia (TL), Menorquina (MEN), Alistana (ALS), Sayaguesa (SAY), Tudanca (TUD), Asturiana de los Valles (ASV), Asturiana de las Montañas (ASM), Retinta (RET), Morucha (MOR), Avileña (AVI), Pirenaica (PIRM), Rubia Gallega (RGA), Mallorquina (MALL), Monchina (MON), Serrana de Teruel (STE), Parda de Montaña (PM), Bruna de los Pirineos (BRP), Pasiega (PAS), Berrenda en Colorado (BC), Berrenda en Negro (BN), Marismeña (MAR), Pajuna (PAJ), Negra Andaluza (NAN), Vaca Canaria (VCA), Vaca Palmera (PAL); PORTUGUESE. Alentejana (ALT), Arouquesa (ARO), BarrosĂŁ (BARR), Brava de Lide (BRAV), Cachena (CACH), Garvonesa (GARV), Marinhoa (MARI), Maronesa (MARO), Mertolenga (MERT), Minhota (MINH), Mirandesa (MIRA), Preta (PRET), Ramo Grande (RG); CREOLE. GuabalĂĄ (GUA), GuaymĂ­ (GY), Texas Longhorn (TLH), Criollo Poblano (CPO), Criollo de Baja California (CBC), Criollo de Chihuahua (CHU), Criollo de Nayarit (CNY), Criollo de Chiapas (CHI), Blanco Orejinegro (BON), Caqueteño (CAQ), Sanmartinero (SM), Romosinuano (RMS), Costeño con Cuernos (CCC), Chino Santandereano (CH), Velasquez (VEL), Lucerna (LUC), HartĂłn del Valle (HV), Criollo Casanareño (CC), Criollo Ecuatoriano (EC), Criollo Uruguayo (CUR), Pampa Chaqueño (PA), Criollo Pilcomayo (PIL), Criollo Argentino (CARG), Criollo PatagĂłnico (PAT), CaracĂș (CAR), Cubano (CUB), Siboney (SIB); ZEBU: Gyr (GYR), Brahman (BRH), Sindi (SIN), Guzerat (GUZ), Nelore (NEL), Zebu Cubano (CUZ); Other EUROPEAN. Friesian (FRI), Hereford (HER), Brown Swiss (BSW), Aberdeen Angus (AA), British White (BWC), Charolais (CHAR), Jersey (JER), Limousin (LIM), Shorthorn (SH)

    Neighbor-net dendrogram constructed from the Reynolds genetic distances among 81 cattle breeds.

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    <p>Yellow: Creole; Green: Iberian; Pink: British and Continental European; Blue: Indian Zebu. <b><i>SPANISH</i></b>. Betizu (BET), Toro de Lidia (TL), Menorquina (MEN), Alistana (ALS), Sayaguesa (SAY), Tudanca (TUD), Asturiana de los Valles (ASV), Asturiana de las Montañas (ASM), Retinta (RET), Morucha (MOR), Avileña (AVI), Pirenaica (PIRM), Rubia Gallega (RGA), Mallorquina (MALL), Monchina (MON), Serrana de Teruel (STE), Parda de Montaña (PM), Bruna de los Pirineos (BRP), Pasiega (PAS), Berrenda en Colorado (BC), Berrenda en Negro (BN), Marismeña (MAR), Pajuna (PAJ), Negra Andaluza (NAN), Vaca Canaria (VCA), Vaca Palmera (PAL); <b><i>PORTUGUESE</i></b>. Alentejana (ALT), Arouquesa (ARO), BarrosĂŁ (BARR), Brava de Lide (BRAV), Cachena (CACH), Garvonesa (GARV), Marinhoa (MARI), Maronesa (MARO), Mertolenga (MERT), Minhota (MINH), Mirandesa (MIRA), Preta (PRET), Ramo Grande (RG); <b><i>CREOLE</i></b>. GuabalĂĄ (GUA), GuaymĂ­ (GY), Texas Longhorn (TLH), Criollo Poblano (CPO), Criollo de Baja California (CBC), Criollo de Chihuahua (CHU), Criollo de Nayarit (CNY), Criollo de Chiapas (CHI), Blanco Orejinegro (BON), Caqueteño (CAQ), Sanmartinero (SM), Romosinuano (RMS), Costeño con Cuernos (CCC), Chino Santandereano (CH), Velasquez (VEL), Lucerna (LUC), HartĂłn del Valle (HV), Criollo Casanareño (CC), Criollo Ecuatoriano (EC), Criollo Uruguayo (CUR), Pampa Chaqueño (PA), Criollo Pilcomayo (PIL), Criollo Argentino (CARG), Criollo PatagĂłnico (PAT), CaracĂș (CAR), Cubano (CUB), Siboney (SIB); <b><i>ZEBU</i></b>: Gyr (GYR), Brahman (BRH), Sindi (SIN), Guzerat (GUZ), Nelore (NEL), Zebu Cubano (CUZ); Other <b><i>EUROPEAN.</i></b> Friesian (FRI), Hereford (HER), Brown Swiss (BSW), Aberdeen Angus (AA), British White (BWC), Charolais (CHAR), Jersey (JER), Limousin (LIM), Shorthorn (SH).</p
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