Y chromosome evolution in the subgenus Mus (genus Mus).

Abstract A 305 base pair DNA sequence isolated from the Y chromosome of the inbred mouse strain C57BL/10 was used to investigate the pattern and tempo of evolution of Y chromosome DNA sequences for five species in the subgenus Mus, including Mus spretus, Mus hortulanus, Mus abbotti, Mus musculus and Mus domesticus. Variation in hybridization patterns between species was characterized by differences in fragment lengths of both intensely and faintly hybridizing fragments, whereas variation in hybridization patterns within species was characterized primarily by differences in fragment lengths of faintly hybridizing fragments. Phylogenetic analyses were conducted based on fragment size variation within and among species. Phylogenetic relationships inferred from these analyses partly agree with the phylogenetic relationships obtained from biochemical and mitochondrial DNA data. We conclude that a set of DNA sequences common to the Y chromosomes of a closely related group of species in the subgenus Mus has evolved rapidly as reflected by sequence divergence and sequence amplification.

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A repeated segment on the mouse Y chromosome is composed of retroviral-related, Y-enriched and Y-specific sequences.

Genetics ◽

10.1093/genetics/122.1.181 ◽

1989 ◽

Vol 122 (1) ◽

pp. 181-192

Author(s):

E M Eicher ◽

K W Hutchison ◽

S J Phillips ◽

P K Tucker ◽

B K Lee

Keyword(s):

Y Chromosome ◽

Dna Sequences ◽

Inbred Mouse ◽

Inbred Mouse Strain ◽

Phage Library ◽

Mus Spretus ◽

Lambda Phage ◽

Isolation And Characterization ◽

Repeated Segment

Abstract We report the isolation and characterization of two recombinant clones containing DNA derived from the Y chromosome of the C57BL/10 inbred mouse strain. Both clones were isolated from a lambda phage library derived from a partial EcoRI digest of C57BL/10 male DNA using the murine retrovirus M720. Characterization of these clones showed they were derived from a repeated segment present on the C57BL/10J Y chromosome that contains sequences found elsewhere in the genome. In addition, one clone contained a sequence, designated YB10, that is unique to the Y chromosome and present in approximately 500 copies on the C57BL/10J Y chromosome. Analysis of Southern blots containing DNAs prepared from females and males of representative species from four subgenera of Mus probed with pYB10 and the 3'LTR from one of the Y-associated retroviruses (MuRVY) revealed that, with the exception of a single fragment observed in both female and male DNA of Mus saxicola, hybridization to pYB10 was observed only to male DNA of the species Mus spretus, Mus hortulanus, Mus musculus, Mus domesticus and Mus abbotti. In addition, the pattern and intensity of hybridization to YB10 and the MuRVY-LTR indicated that sequence of divergence was followed by amplification of Y chromosome sequences containing YB10 and MuRVY. The divergence and amplification occurred separately in each of the ancestral lineages leading to M. spretus, M. hortulanus, M. abbotti, M. musculus and M. domesticus. We suggest that acquisition and amplification of DNA sequences by the mammalian Y chromosome has contributed to its evolution and may imply that the mammalian Y chromosome is evolving at a faster rate than the rest of the genome.

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Epigenetic control of mammalian centromere protein binding: does DNA methylation have a role?

Journal of Cell Science ◽

10.1242/jcs.109.9.2199 ◽

1996 ◽

Vol 109 (9) ◽

pp. 2199-2206

Author(s):

A.R. Mitchell ◽

P. Jeppesen ◽

L. Nicol ◽

H. Morrison ◽

D. Kipling

Keyword(s):

Dna Sequences ◽

Satellite Dna ◽

Inbred Mouse ◽

Inbred Mouse Strain ◽

Chromosome 1 ◽

Satellite Sequences ◽

E Protein ◽

Minor Satellite ◽

Internal Block ◽

Terminal Block

Chromosome 1 of the inbred mouse strain DBA/2 has a polymorphism associated with the minor satellite DNA at its centromere. The more terminal block of satellite DNA sequences on this chromosome acts as the centromere as shown by the binding of CREST ACA serum, anti-CENP-B and anti-CENP-E polyclonal sera. Demethylation of the minor satellite DNA sequences accomplished by growing cells in the presence of the drug 5-aza-2′-deoxycytidine results in a redistribution of the CENP-B protein. This protein now binds to an enlarged area on the more terminal block and in addition it now binds to the more internal block of minor satellite DNA sequences on chromosome 1. The binding of the CENP-E protein does not appear to be affected by demethylation of the minor satellite sequences. We present a model to explain these observations. This model may also indicate the mechanism by which the CENP-B protein recognises specific sites within the arrays of minor satellite DNA on mouse chromosomes.

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Monophyly of Verbascum (Scrophularieae : Scrophulariaceae): evidence from nuclear and plastid phylogenetic analyses

Australian Journal of Botany ◽

10.1071/bt14159 ◽

2014 ◽

Vol 62 (8) ◽

pp. 638 ◽

Cited By ~ 2

Author(s):

Farrokh Ghahremaninejad ◽

Mehrshid Riahi ◽

Melina Babaei ◽

Faride Attar ◽

Lütfi Behçet ◽

...

Keyword(s):

Molecular Markers ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Molecular Data ◽

Nrdna Its ◽

Starting Point ◽

High Species Diversity ◽

Phylogenetic Estimation

Verbascum is one of the main genera of Scrophulariaceae, but delimitation and phylogenetic relationships of this genus are unclear and have not yet been studied using DNA sequences. Here, using four selected molecular markers (nrDNA ITS and the plastid spacers trnS/G, psbA-trnH and trnY/T), we present a phylogeny of Verbascum and test previous infrageneric taxonomic hypotheses as well as its monophyly with respect to Scrophularia. We additionally discuss morphological variation and the utility of morphological characters as predictors of phylogenetic relationships. Our results show that while molecular data unambiguously support the circumscription of Verbascum inferred from morphology, they prove to be of limited utility in resolving infrageneric relationships, suggesting that Verbascum ‘s high species diversity is due to rapid and recent radiation. Our work provides phylogenetic estimation of the genus Verbascum using molecular data and can serve as a starting point for future investigations of Verbascum and relatives.

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Novel structural organisation of a Mus musculus DBA/2 chromosome shows a fixed position for the centromere

Journal of Cell Science ◽

10.1242/jcs.106.1.79 ◽

1993 ◽

Vol 106 (1) ◽

pp. 79-85 ◽

Cited By ~ 3

Author(s):

A.R. Mitchell ◽

L. Nicol ◽

P. Malloy ◽

D. Kipling

Keyword(s):

Dna Sequences ◽

Inbred Mouse ◽

Inbred Mouse Strain ◽

Chromosome 1 ◽

Sequence Motif ◽

Major Satellite ◽

Satellite Sequences ◽

Minor Satellite ◽

Apparent Similarity ◽

Terminal Block

Chromosome 1 of the inbred mouse strain DBA/2 shows an unusual polymorphism associated with its centromeric satellite DNA sequences. The minor satellite array has undergone amplification and is present as two blocks separated by major satellite sequences. Both minor satellite blocks appear to carry the sequence motif necessary for CENP-B protein binding. Despite this apparent similarity the functional centromere, as defined by the location of CREST antigens, appears to form only within the more terminal block. The two blocks also vary in that sister chromatid association only occurs with this more terminal block.

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Molecular and morphological diagnostic markers for the Himalayan Ips DeGeer species (Coleoptera: Curculionidae: Scolytinae)

Zootaxa ◽

10.11646/zootaxa.3128.1.2 ◽

2011 ◽

Vol 3128 (1) ◽

pp. 47 ◽

Cited By ~ 4

Author(s):

ABDUL A. BUHROO ◽

FERENC LAKATOS

Keyword(s):

Dna Sequences ◽

Bark Beetles ◽

Phylogenetic Analyses ◽

Sequence Divergence ◽

Morphological Characters ◽

The Body ◽

Specific Sequence ◽

Haplotype Variation ◽

Mitochondrial Cytochrome Oxidase ◽

I Gene

Morphological and molecular analyses of Ips bark beetles collected in the eastern and northwestern Himalayan area resulted in the diagnosis of three species—Ips stebbingi, I. longifolia and I. schmutzenhoferi. These three species can be distinguished by morphological characters, including the frontal setae, the body size and the shape and position of the spines on the elytral declivity. DNA sequences of the mitochondrial Cytochrome Oxidase I gene were analyzed to detect haplotype variation within each of the species. A phylogenetic analysis was performed on our data plus data from GenBank. Considerable amount of intra-specific sequence divergence was found in I. longifolia, ranging between 0.2%−2.5%. Intra-specific sequence divergence in I. stebbingi ranged from 0.2%−1.1% and in I. schmutzenhoferi it varied by 0.2%. Interspecific sequence divergence was high among the three species: 7.4−8.6% between I. longifolia and I. stebbingi, 11.9−12.2% between I. stebbingi and I. schmutzenhoferi, and 11.5−12.6% between I. longifolia and I. schmutzenhoferi. Phylogenetic analyses revealed Himalayan Ips species to be monophyletic and unrelated to other Asian species. Ips stebbingi and I. longifolia were sister taxa and I. schmutzenhoferi was distinguished from I. stebbingi.

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Phylogenetic relationships of Chacodelphys (Marsupialia: Didelphidae: Didelphinae) based on “ancient” DNA sequences

Journal of Mammalogy ◽

10.1093/jmammal/gyv197 ◽

2015 ◽

Vol 97 (2) ◽

pp. 394-404 ◽

Cited By ~ 4

Author(s):

Juan F. Díaz-Nieto ◽

Sharon A. Jansa ◽

Robert S. Voss

Keyword(s):

Soft Tissue ◽

Ancient Dna ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Morphological Character ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sister Taxon ◽

Evolutionary Relationships ◽

Fresh Material

Abstract Morphological character data are inadequate to resolve the evolutionary relationships of the didelphid genus Chacodelphys , which previous phylogenetic analyses have alternatively suggested might be the sister taxon of Lestodelphys and Thylamys (tribe Thylamyini) or of Monodelphis (tribe Marmosini) in the subfamily Didelphinae. Because fresh material of Chacodelphys is unavailable, we extracted DNA from microscopic fragments of soft tissue adhering to the 95-year-old holotype skull of C. formosa. Phylogenetic analyses of the resulting sequence data convincingly resolve Chacodelphys as the sister taxon of Cryptonanus , a genus with which it had not previously been thought to be closely related. This novel clade ( Chacodelphys + Cryptonanus ) belongs to an unnamed thylamyine lineage with Gracilinanus and Lestodelphys + Thylamys , but relationships among these taxa remain to be convincingly resolved. Los análisis basados en caracteres morfológicos han sido inadecuados para resolver las relaciones evolutivas del género marsupial didélfido Chacodelphys . Previos análisis filogenéticos han sugerido como hipótesis alternativas que Chacodelphys sea el grupo hermano de Lestodelphys y Thylamys (tribu Thylamyini) o de Monodelphis (tribu Marmosini), todos estos géneros pertenecientes a la subfamilia Didelphinae. Debido a la ausencia de material fresco de Chacodelphys , extrajimos ADN de fragmentos microscópicos de tejido adherido al cráneo de 95 años del holotipo de C. formosa . Análisis filogenéticos de las secuencias obtenidas resuelven convincentemente la posición filogenética de Chacodelphys como el taxón hermano de Cryptonanus , un género con el cual nunca antes se había pensado que estuviera cercanamente relacionado. Aunque reconocemos a este nuevo clado ( Chacodelphys + Cryptonanus ) junto con Gracilinanus y Lestodelphys + Thylamys pertenecientes a un linaje sin nombre, las relaciones entre estas taxa siguen sin estar convincentemente resueltas.

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Annonaceae substitution rates: a codon model perspective

Revista Brasileira de Fruticultura ◽

10.1590/s0100-29452014000500013 ◽

2014 ◽

Vol 36 (spe1) ◽

pp. 108-117 ◽

Cited By ~ 1

Author(s):

Lars Willem Chatrou ◽

Michael David Pirie ◽

Robin Van Velzen ◽

Freek Theodoor Bakker

Keyword(s):

Dna Sequences ◽

Phylogenetic Trees ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sequence Divergence ◽

High Ratio ◽

Molecular Dating ◽

Codon Model ◽

Synonymous Substitutions ◽

Branch Lengths

The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.

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A Phylogenetic Investigation of the New Zealand Pteridaceae Ferns

10.26686/wgtn.16934449.v1 ◽

2021 ◽

Author(s):

◽

Whitney L M Bouma

Keyword(s):

New Zealand ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Native Species ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Taxonomic Confusion ◽

Species Specific

<p>The fern family Pteridaceae is among the largest fern families in New Zealand. It comprises 17 native species among five genera. Traditionally the classification of Pteridaceae was based on morphological characters. The advent of molecular technology, now makes is possible to test these morphology-based classifications. The Pteridaceae has previously been subjected to phylogenetic analyses; however representatives from New Zealand and the South Pacific have never been well represented in these studies. This thesis research aimed to investigate the phylogenetic relationships of the New Zealand Pteridaceae, as well as, the phylogenetic relationships of the New Zealand species to their overseas relatives. The DNA sequences of several Chloroplast loci (e.g. trnL-trnF locus, rps4 and rps4-trnS IGS, atpB, and rbcL) were determined and the phylogenetic relationships of the New Zealand Pteridaceae and several species-specific question within the genus Pellaea and Adiantum were investigated. Results presented in this thesis confirm previously published phylogenetics of the Pteridaceae, which show the resolution of five major clades, i.e.,cryptogrammoids, ceratopteridoids, pteridoids, cheilanthoids, and the adiantoids. The addition of the New Zealand species revealed a possible South West Pacific groups formed by the respective genera, where New Zealand species were generally more related to one another than to overseas relatives. Within the New Zealand Pellaea, the analysis of the trnL-trnF locus sequence data showed that the morphologically-intermediate plants P. aff. falcata, responsible for taxonomic confusion, were more closely related to P. rotundifolia than to P. falcata. Furthermore, the species collected on the Kermadec Islands, previously thought to be P. falcata, are genetically distinct from the Australian P. falcata and they could constitute a new species. Adiantum hispidulum, which is polymorphic for two different hair types being used to distinguish them as different species, was also reinvestigated morphologically and molecularly. Morphological inspection of hairs revealed three hair types as opposed to the previous thought two, and furthermore, they correspond to three different trnL-trnF sequences haplotypes.</p>

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Nectria-related fungi causing dieback and canker diseases in China, with Neothyronectria citri sp. nov. described

MycoKeys ◽

10.3897/mycokeys.56.36079 ◽

2019 ◽

Vol 56 ◽

pp. 49-66

Author(s):

Qin Yang ◽

Wen-Yan Chen ◽

Ning Jiang ◽

Cheng-Ming Tian

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Molecular Data ◽

Bright Yellow

To clarify phylogenetic relationships amongst Nectria, Neothyronectria and Thyronectria in Nectriaceae, we examined detailed morphological characters and performed phylogenetic analyses of a concatenated dataset, based on the ITS, LSU, tef1 and tub2 DNA sequences of fungal specimens in China. Four species of nectria-related fungi were identified, i.e. Nectriadematiosa, N.pseudotrichia, Neothyronectriacitri and Thyronectriapinicola. The newly described species, Neothyronectriacitri, is characterised by its ascomatal wall with bright yellow scurf, unitunicate asci, each with 4-spored and ascospores allantoid to short-cylindrical, uniseriate, muriform, hyaline to slightly yellowish-brown. This species has affinities with other one known species of Neothyronectria and can be distinguished by molecular data.

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Molecular phylogeny and divergence time estimates in pennatulaceans (Cnidaria: Octocorallia: Pennatulacea)

Scientia Marina ◽

10.3989/scimar.05067.28a ◽

2020 ◽

Vol 84 (4) ◽

pp. 317-330

Author(s):

Francisco J. García-Cárdenas ◽

Mónica Núñez-Flores ◽

Pablo J. López-González

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Morphological Characters ◽

Nuclear Markers ◽

Divergence Time Estimates ◽

Time Estimates ◽

Soft Bottoms

Pennatulaceans are an important component of benthic marine communities usually related to soft bottoms. Despite their important ecological role, as yet little is known about their origin and divergence time. The first attempts to establish phylogenetic relationships among genera date from the early 20th century, when only morphological characters were available. In the last decade, phylogenetic analyses based on mitochondrial DNA sequences from a selected number of species have proposed a different hypothetical ancestor for this group, but their intergeneric relationships remain obscure. The present study is based on a combination of mitochondrial and nuclear markers (mtMutS, Cox1 and 28S rDNA), adding new molecular information about the phylogenetic relationships among the pennatulacean genera, including 38 new sequences belonging to 13 different species. Some of the phylogenetic relationships inferred in the present study question the current classification of sea pens based on morphology (at different taxonomic levels), clearly indicating that the two main groups Sessiliflorae and Subselliflorae, some of their main families (e.g. Pennatulidae, Umbellulidae, Virgulariidae) and some genera (e.g. Umbellula, Veretillum) are non-monophyletic. In addition, the veretillids, traditionally considered the most primitive pennatulaceans, are not shown as the earliest-diverging taxon. Moreover, an analysis of divergence time performed here suggested that the origin of the pennatulaceans dates from the Lower Cretaceous (Berriasian, ~144 Ma), in agreement with their sparsely known fossil record, while the initial divergence of most extant genera occurred in the Oligocene and Miocene times.

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