Abstract:
:Fishes of the order Myctophiformes (Teleostei; Scopelomorpha) comprise over half of all deep-sea biomass, and are a critical component of marine ecosystems worldwide. Members of the family Myctophidae, within Myctophiformes, form the majority of species diversity within the order (∼250 species, 33 genera, 2 subfamilies), and are further known for their diverse bioluminescent traits, comprised of distinct cranial, postcranial, and caudal luminous systems that is perhaps the most elaborate among all vertebrates. These features make myctophids particularly compelling from both economic and scientific perspectives, yet no studies have sampled these fishes at a density appropriate for addressing any questions requiring a phylogenetic hypothesis as input. This study therefore presents a seven-locus molecular phylogeny of the order, sampling over 50% of all nominal myctophid species. This taxon sampling triples the representation of the next most comprehensive analysis, and reveals several new and well-supported hypotheses of relationships, in addition to supporting traditional hypotheses based on combined morphological data. This analysis shows that the slendertailed myctophids Gonichthys, Centrobranchus, Loweina, and Tarletonbeania are rendered non-monophyletic by a polyphyletic Myctophum; the enigmatic, monotypic genus Notolychnus valdiviae is nested within tribe Lampanyctini; the genus Diaphus is divided into at least two clades, with the suborbital (So) group recovered as monophyletic with strong support; and the genera Lampanyctus and Nannobrachium are recovered as non-monophyletic. These molecular results highlight the potential of myctophids as a premier model system for the application of modern comparative methods to studies of deep-sea evolution.
journal_name
Mol Phylogenet Evoljournal_title
Molecular phylogenetics and evolutionauthors
Denton JSdoi
10.1016/j.ympev.2014.02.009subject
Has Abstractpub_date
2014-07-01 00:00:00pages
270-92eissn
1055-7903issn
1095-9513pii
S1055-7903(14)00060-8journal_volume
76pub_type
杂志文章abstract::Identifying patterns of introgression across the tree of life is foundational to understanding general mechanisms that govern the impacts of gene flow on the speciation process. There are few vertebrate groups in which hybridization is associated with as large a diversity of outcomes as in North American whiptail liza...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2018.12.016
更新日期:2019-03-01 00:00:00
abstract::Sequence data from the noncoding region separating the plastid genes atpbeta and rbcL were gathered for 27 epacrid taxa, representing all previously recognized infrafamilial groups, and four outgroup taxa (Ericaceae), to address several persistent phylogenetic questions in the group. Parsimony analyses were conducted ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1006/mpev.2000.0794
更新日期:2000-08-01 00:00:00
abstract::The North Atlantic red alga Mastocarpus stellatus is characterized by two life histories (sexual-type and direct-type), which correspond to two geographically isolated breeding groups. These features enable M. stellatus to be an interesting model to investigate how environmental shift and apomictic propagation have in...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2015.10.029
更新日期:2016-01-01 00:00:00
abstract::Allopolyploid speciation is widespread in plants, yet the molecular requirements for successful orchestration of coordinated gene expression for two divergent and reunited genomes are poorly understood. Recent studies in several plant systems have revealed that allopolyploid genesis under both synthetic and natural co...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章,评审
doi:10.1016/s1055-7903(03)00213-6
更新日期:2003-12-01 00:00:00
abstract::The genes for nine ribosomal proteins, L24, L5, S14, S8, L6, L18, S5, L30, and L15, have been isolated and sequenced from the spc operon in the archaeon (Crenarchaeota) Sulfolobus acidocaldarius, and the putative amino acid sequence of the proteins coded by these genes has been determined. In addition, three other gen...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1006/mpev.1998.0607
更新日期:1999-07-01 00:00:00
abstract::Nucleotide sequences of the nuclear c-mos gene and the mitochondrial cytochrome b and ND2 genes were used to assess the monophyly of Sibley and Monroe's [Distribution and Taxonomy of Birds of the World, Yale University Press, New Haven, 1990] Muscicapoidea superfamily. The relationships and monophyly of major lineages...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/s1055-7903(03)00191-x
更新日期:2004-02-01 00:00:00
abstract::A species flock of the freshwater isopod genus Eophreatoicus Nicholls lives in seeps, springs and perched aquifers at the base of the Arnhem Plateau and associated sandstone outliers in Australia's Northern Territory. These species have been found to have surprisingly high levels of genetic divergence and narrow range...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2009.02.001
更新日期:2009-05-01 00:00:00
abstract::We analyzed 2995 base pairs of nucleotide sequence data (nuclear beta-fibrinogen intron 7 and mitochondrial cytochrome b and ND2 genes), using parsimony and model-based approaches to infer phylogenetic relationships of the woodpeckers and allies, yielding novel hypotheses for several critical gaps in the knowledge of ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2006.02.021
更新日期:2006-08-01 00:00:00
abstract::The field of phylogenetics is changing rapidly with the application of high-throughput sequencing to non-model organisms. Cost-effective use of this technology for phylogenetic studies, which often include a relatively small portion of the genome but several taxa, requires strategies for genome partitioning and sequen...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2014.02.007
更新日期:2014-06-01 00:00:00
abstract::The longhorn bee tribe Eucerini (Hymenoptera: Apidae) is a diverse, widely distributed group of solitary bees that includes important pollinators of both wild and agricultural plants. About half of the species in the tribe are currently assigned to the genus Eucera and to a few other related genera. In this large genu...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2017.10.007
更新日期:2018-02-01 00:00:00
abstract::Stratiomyidae is a cosmopolitan family of Brachycera (Diptera) that contains over 2800 species. This study focused on the relationships of members of the subfamily Clitellariinae, which has had a complicated taxonomic history. To investigate the monophyly of the Clitellariinae, the relationships of its genera, and the...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2006.09.006
更新日期:2007-05-01 00:00:00
abstract::The Common Bush-Tanager (Chlorospingus ophthalmicus) is distributed in Neotropical cloud-forests from Mexico to Argentina and contains 25 subspecies divided into eight subspecies groups based on biogeography, eye coloration, presence of a postocular spot and chest band. All of Central America is occupied by a single s...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2008.02.004
更新日期:2008-05-01 00:00:00
abstract::Diversification of the California icthyofauna has been greatly influenced by a complex geomorphological history and past fluctuations in climate regimes. This complex history has resulted in areas of high endemism for a number of taxa. Here we present data on the two species in the genus Lavinia, the California roach ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2008.11.028
更新日期:2009-05-01 00:00:00
abstract::Phylogenetic relationships within the bryozoan order Cheilostomata are currently uncertain, with many morphological hypotheses proposed but scarcely tested by independent means of molecular analysis. This research uses DNA sequence data across five loci of both mitochondrial and nuclear origin from 91 species of cheil...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2011.07.005
更新日期:2011-11-01 00:00:00
abstract::Symbiotic nitrogen fixing bacteria-known as rhizobia-harbour a set of nodulation (nod) genes that control the synthesis of modified lipo-chitooligosaccharides, called Nod factors that are required for legume nodulation. The nodA gene, which is essential for symbiosis, is responsible for the attachment of the fatty aci...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/S1055-7903(03)00255-0
更新日期:2004-03-01 00:00:00
abstract::As circumscribed by Drude, the umbellifer subfamily Hydrocotyloideae posed a major hindrance to resolving the phylogeny of order Apiales. Previous studies have suggested its polyphyly, but have not had sufficient sampling to address the issue fully. To put an end to the out-dated concept of Hydrocotyloideae, we invest...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2009.06.010
更新日期:2009-10-01 00:00:00
abstract::All taxa endemic to the Qinghai-Tibet Plateau are hypothesized to have originated in situ or from immediately adjacent areas because of the relatively recent formation of the plateau since the Pliocene, followed by the large-scaled biota extinction and recession caused by the Quaternary ice sheet. However, identificat...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/s1055-7903(02)00039-8
更新日期:2002-06-01 00:00:00
abstract::Nucleotide sequences of the small subunit ribosomal RNA (18S) gene were used to investigate evolutionary relationships within the Fungi. The inferred tree topologies are in general agreement with traditional classifications in the following ways: (1) the Chytridiomycota and Zygomycota appear to be basal groups within ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/1055-7903(92)90020-h
更新日期:1992-09-01 00:00:00
abstract::The Galápagos archipelago has never been connected to any continental land masses, so it is of interest to know the colonization and diversification history of its endemic species. We analyzed the phylogenetic placement of the endemic Galápagos flycatcher, M. magnirostris, within Myiarchus by using the genes ND2 and c...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2011.10.023
更新日期:2012-05-01 00:00:00
abstract::A lot is known about the evolution and architecture of plastid, mitochondrial, and nuclear genomes, but surprisingly little is known about their relative rates of mutation. Most available relative-rate data come from seed plants, which, with few exceptions, have a mitochondrial mutation rate that is lower than those o...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2014.07.001
更新日期:2014-10-01 00:00:00
abstract::Porpoises (Phocoenidae), dolphins (Delphinidae), and the two species of Monodontidae (beluga and narwhal) together constitute the superfamily Delphinoidea. Although there is extensive evidence supporting the monophyly of this superfamily, previous studies involving morphology, as well as sequence analysis of mitochond...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1006/mpev.1999.0751
更新日期:2000-05-01 00:00:00
abstract::Next-generation genomic sequencing promises to quickly and cheaply resolve remaining contentious nodes in the Tree of Life, and facilitates species-tree estimation while taking into account stochastic genealogical discordance among loci. Recent methods for estimating species trees bypass full likelihood-based estimate...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2014.08.023
更新日期:2014-12-01 00:00:00
abstract::All spiders produce silk and use it for various functions throughout their lives, but not all spiders produce the same silks, or use them for the same functions. These functions may include building shelters, protecting eggs, and trapping prey. The "RTA clade" of spiders (grass spiders, jumping-spiders, wolf spiders, ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2007.08.008
更新日期:2008-01-01 00:00:00
abstract::Influenza A virus infects a wide range of hosts including birds, humans, pigs, horses, and other mammals. Because hosts differ in immune system structure and demography, it is therefore expected that host populations leave different imprints on the viral genome. In this study, we investigated the evolutionary trajecto...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2010.04.039
更新日期:2010-08-01 00:00:00
abstract::A combined molecular (18S rDNA, 28S rDNA, 16S rDNA and COI) and morphological analysis of the benthic phyllodocids is presented for the first time. Nineteen phyllodocids and two outgroup taxa are assessed using parsimony, maximum likelihood and Bayesian analyses. We demonstrate high degrees in homoplasy in the traditi...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2007.04.015
更新日期:2007-10-01 00:00:00
abstract::There have been many studies on the chemistry of mammalian pancreatic ribonucleases (ribonucleases 1), but the functional biology of this family of homologous proteins is still largely unknown. Many studies have been performed on the molecular evolution and properties of this enzyme from species belonging to a large n...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/s1055-7903(03)00014-9
更新日期:2003-06-01 00:00:00
abstract::Trichomycteridae is the second most diverse family of the order Siluriformes, its members are widely distributed through the freshwaters of Central and South America, exhibiting an exceptional ecological and phenotypic disparity. The most diverse subfamily, Trichomycterinae, represented mainly by the genus Trichomycte...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2017.07.007
更新日期:2017-10-01 00:00:00
abstract::Even though Brazil is the world leader in amphibian diversity, a significant part of its richness remains unknown or hidden under cryptic taxa. Here, we used model-based species delimitation in an integrative taxonomic approach, by gathering molecular and morphometric data to assess cryptic taxa within the monkey frog...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2018.11.022
更新日期:2019-03-01 00:00:00
abstract::Eight current species of snakes of the Bothrops neuwiedi group are widespread in South American open biomes from northeastern Brazil to southeastern Argentina. In this paper, 140 samples from 93 different localities were used to investigate species boundaries and to provide a hypothesis of phylogenetic relationships a...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2013.10.003
更新日期:2014-02-01 00:00:00
abstract::Snakes of the subfamily Boinae are found in Madagascar, the Papuan-Pacific Islands, and the Neotropics. It has been suggested that genera within each of these particular areas do not form monophyletic groups. Further, it was proposed that the New World Boa constrictor is more closely related to boine genera in Madagas...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2004.08.017
更新日期:2005-01-01 00:00:00