Molecular phylogeny of the nettle family (Urticaceae) inferred from multiple loci of three genomes and extensive generic sampling.

Abstract:

:Urticaceae is one of the larger Angiosperm families, but relationships within it remain poorly known. This study presents the first densely sampled molecular phylogeny of Urticaceae, using maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) to analyze the DNA sequence data from two nuclear (ITS and 18S), four chloroplast (matK, rbcL, rpll4-rps8-infA-rpl36, trnL-trnF) and one mitochondrial (matR) loci. We sampled 169 accessions representing 122 species, representing 47 of the 54 recognized genera within Urticaceae, including four of the six sometimes separated as Cecropiaceae. Major results included: (1) Urticaceae including Cecropiaceae was monophyletic; (2) Cecropiaceae was biphyletic, with both lineages nested within Urticaceae; (3) Urticaceae can be divided into four well-supported clades; (4) previously erected tribes or subfamilies were broadly supported, with some additions and alterations; (5) the monophyly of many genera was supported, whereas Boehmeria, Pellionia, Pouzolzia and Urera were clearly polyphyletic, while Urtica and Pilea each had a small genus nested within them; (6) relationships between genera were clarified, mostly with substantial support. These results clarify that some morphological characters have been overstated and others understated in previous classifications of the family, and provide a strong foundation for future studies on biogeography, character evolution, and circumscription of difficult genera.

journal_name

Mol Phylogenet Evol

authors

Wu ZY,Monro AK,Milne RI,Wang H,Yi TS,Liu J,Li DZ

doi

10.1016/j.ympev.2013.06.022

subject

Has Abstract

pub_date

2013-12-01 00:00:00

pages

814-27

issue

3

eissn

1055-7903

issn

1095-9513

pii

S1055-7903(13)00262-5

journal_volume

69

pub_type

杂志文章
  • Understanding the colonization history of the Galápagos flycatcher (Myiarchus magnirostris).

    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

    authors: Sari EH,Parker PG

    更新日期:2012-05-01 00:00:00

  • Phylogeny and temporal diversification of the New World pond turtles (Emydidae).

    abstract::We present a comprehensive multigene phylogeny and time tree for the turtle family Emydidae. Our phylogenetic analysis, based on 30 nuclear and four mitochondrial genes (23,330 total base pairs) sequenced for two individuals for each of the currently recognized species of the subfamily Emydinae and two species from ea...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2016.07.007

    authors: Spinks PQ,Thomson RC,McCartney-Melstad E,Shaffer HB

    更新日期:2016-10-01 00:00:00

  • Phylogenetic analyses of key developmental genes provide insight into the complex evolution of seeds.

    abstract::Gene duplication plays a decisive role in organismal diversification and in the appearance of novel structures. In plants the megagametophyte covered by the integuments, which after fertilization becomes the seed constitutes a novel structure: the ovule. In Arabidopsis thaliana, genetic mechanisms regulating ovule dev...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2020.106778

    authors: Zumajo-Cardona C,Ambrose BA

    更新日期:2020-06-01 00:00:00

  • Molecular phylogeny of hybridizing species from the genus Spartina Schreb. (Poaceae).

    abstract::Interspecific hybridization events have been reported in the genus Spartina Schreb. (Poaceae), involving the east American species Spartina alterniflora, and including either introgression (e.g., with the western American Spartina foliosa) or allopolyploid speciation (e.g., with the Euro-African Spartina maritima). Mo...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.2001.1064

    authors: Baumel A,Ainouche ML,Bayer RJ,Ainouche AK,Misset MT

    更新日期:2002-02-01 00:00:00

  • Phylogenetic relationships of the Asian palm civets (Hemigalinae & Paradoxurinae, Viverridae, Carnivora).

    abstract::The Viverridae (Mammalia, Carnivora), one of the least studied groups of carnivorans, include two subfamilies of Asian palm civets: Hemigalinae and Paradoxurinae. The relationships between and within these two subfamilies have never been thoroughly tested using an extensive molecular sample set. In this study, we gath...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2008.03.026

    authors: Patou ML,Debruyne R,Jennings AP,Zubaid A,Rovie-Ryan JJ,Veron G

    更新日期:2008-06-01 00:00:00

  • Beyond phylogeny: pelecaniform and ciconiiform birds, and long-term niche stability.

    abstract::Phylogenetic trees are a starting point for the study of further evolutionary and ecological questions. We show that for avian evolutionary relationships, improved taxon sampling, longer sequences and additional data sets are giving stability to the prediction of the grouping of pelecaniforms and ciconiiforms, thus al...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.03.021

    authors: Gibb GC,Kennedy M,Penny D

    更新日期:2013-08-01 00:00:00

  • Parsimony analysis as a specific kind of homology estimation and the implications for character weighting.

    abstract::"Remane-Hennigian systematists" still reject parsimony analysis for phylogenetics, because homology or apomorphy analyses are not included. In contrast, "pattern cladists" regard homology as a deductive concept after applying a parsimony test of character congruence. However, as in molecular phylogeny, selection of "g...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1998.0496

    authors: Haszprunar G

    更新日期:1998-06-01 00:00:00

  • Phylogeny of Drosophila and related genera: conflict between molecular and anatomical analyses.

    abstract::Drosophila species are extensively used in biological research; yet, important phylogenetic relationships within the genus and with related genera remain unresolved. The combined data for three genes (Adh, Sod, and Gpdh) statistically resolves outstanding issues. We define the genus Drosophila inclusively so as to inc...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1999.0657

    authors: Kwiatowski J,Ayala FJ

    更新日期:1999-11-01 00:00:00

  • Phylogeny and character behavior in the family Lemuridae.

    abstract::A phylogenetic analysis of the family Lemuridae was accomplished using multiple gene partitions and morphological characters. The results of the study suggest that several nodes in the lemurid phylogeny can be robustly resolved; however, the relationships of the species within the genus Eulemur are problematically non...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1999.0723

    authors: Wyner Y,DeSalle R,Absher R

    更新日期:2000-04-01 00:00:00

  • Out of Africa: The origins of the protozoan blood parasites of the Trypanosoma cruzi clade found in bats from Africa.

    abstract::Understanding geographic patterns of interaction between hosts and parasites can provide useful insight into the evolutionary history of the organisms involved. However, poor taxon sampling often hinders meaningful phylogenetic descriptions of groups of parasites. Trypanosome parasites that constitute the Trypanosoma ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2019.106705

    authors: Clément L,Dietrich M,Markotter W,Fasel NJ,Monadjem A,López-Baucells A,Scaravelli D,Théou P,Pigeault R,Ruedi M,Christe P

    更新日期:2020-04-01 00:00:00

  • A test of morphological hypotheses for tribal and subtribal relationships of Aphidinae (Insecta: Hemiptera: Aphididae) using DNA sequences.

    abstract::Aphidinae is the most diverse major lineage of aphids (Aphididae). Aphidinae currently dominate the temperate, northern-hemisphere fauna, but only since the late Tertiary, and few species are native to the southern hemisphere. The success of Aphidinae may be linked to the evolution of an unusual life cycle, host alter...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2005.04.035

    authors: von Dohlen CD,Rowe CA,Heie OE

    更新日期:2006-02-01 00:00:00

  • The scale of divergence: a phylogenetic appraisal of intercontinental allopatric speciation in a passively dispersed freshwater zooplankton genus.

    abstract::Molecular studies have enlightened our understanding of freshwater zooplankton biogeography, yet questions remain regarding the scale and commonality of geographic speciation. Here, we present a mtDNA-based phylogenetic hypothesis for 92 Daphnia species from all seven continents, with a focus on North and South Americ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2008.11.026

    authors: Adamowicz SJ,Petrusek A,Colbourne JK,Hebert PD,Witt JD

    更新日期:2009-03-01 00:00:00

  • Not always young: The first vertebrate ancient origin of true parthenogenesis found in an Amazon leaf litter lizard with evidence of mitochondrial haplotypes surfing on the wave of a range expansion.

    abstract::In vertebrates, true parthenogenesis is found only in squamate reptiles and (mostly) originates via interspecific hybridization after secondary contact. In many cases, parthenogenesis is followed by an increase of ploidy, resulting in triploid lineages. Phylogenetic analyses derived from nuclear and maternally inherit...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2019.01.023

    authors: Brunes TO,da Silva AJ,Marques-Souza S,Rodrigues MT,Pellegrino KCM

    更新日期:2019-06-01 00:00:00

  • Dispersing towards Madagascar: Biogeography and evolution of the Madagascan endemics of the Spermacoceae tribe (Rubiaceae).

    abstract::Despite the close proximity of the African mainland, dispersal of plant lineages towards Madagascar remains intriguing. The composition of the Madagascan flora is rather mixed and shows besides African representatives, also floral elements of India, Southeast Asia, Australia, and the Neotropics. Due to its proportiona...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2015.10.024

    authors: Janssens SB,Groeninckx I,De Block PJ,Verstraete B,Smets EF,Dessein S

    更新日期:2016-02-01 00:00:00

  • Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade.

    abstract::The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined anal...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2020.106960

    authors: Natusch DJD,Esquerré D,Lyons JA,Hamidy A,Lemmon AR,Lemmon EM,Riyanto A,Keogh JS,Donnellan S

    更新日期:2020-09-18 00:00:00

  • Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: evidence for a misleading mitochondrial gene tree.

    abstract::It has proven remarkably difficult to obtain a well-resolved and strongly supported phylogeny for horned lizards (Phrynosoma) because of incongruence between morphological and mitochondrial DNA sequence data. We infer the phylogenetic relationships among all 17 extant Phrynosoma species using >5.1 kb of mtDNA (12S rRN...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2005.12.016

    authors: Leaché AD,McGuire JA

    更新日期:2006-06-01 00:00:00

  • Phylogenetic relationships of Mesoamerican spider monkeys (Ateles geoffroyi): Molecular evidence suggests the need for a revised taxonomy.

    abstract::Mesoamerican spider monkeys (Ateles geoffroyi sensu lato) are widely distributed from Mexico to northern Colombia. This group of primates includes many allopatric forms with morphologically distinct pelage color and patterning, but its taxonomy and phylogenetic history are poorly understood. We explored the genetic re...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2014.08.025

    authors: Morales-Jimenez AL,Cortés-Ortiz L,Di Fiore A

    更新日期:2015-01-01 00:00:00

  • Phylogenetic analysis revealed reticulate evolution of allotetraploid Elymus ciliaris.

    abstract::Increasing evidence has shown the complex and dynamic nature of polyploids. Two single copy nuclear genes were used to explore genome evolutionary dynamics and the origin of tetraploid E. ciliaris: the phosphoglycerate kinase (PGK1) and the second largest subunit of RNA polymerase II (RPB2) together with a chloroplast...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.06.023

    authors: Hu Q,Yan C,Sun G

    更新日期:2013-12-01 00:00:00

  • Delimitation of cryptic species drastically reduces the geographical ranges of marine interstitial ghost-worms (Stygocapitella; Annelida, Sedentaria).

    abstract::The recognition of cryptic species concealed in traditionally established species may reveal new biogeographical patterns and alter the understanding of how biodiversity is geographically distributed. This is particularly relevant for marine ecosystems where the incidence of cryptic species is high and where species d...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2019.106663

    authors: Cerca J,Meyer C,Purschke G,Struck TH

    更新日期:2020-02-01 00:00:00

  • Phylogeny of the leafy liverwort Ptilidium: cryptic speciation and shared haplotypes between the Northern and Southern Hemispheres.

    abstract::The small, phylogenetically isolated liverwort genus Ptilidium has been regarded as of cool-Gondwanic origin with the bipolar, terrestrial Ptilidium ciliare giving rise to the Northern Hemisphere epiphytes Ptilidium pulcherrimum and Ptilidium californicum. This hypothesis is examined using a dataset including three ch...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2010.10.002

    authors: Kreier HP,Feldberg K,Mahr F,Bombosch A,Schmidt AR,Zhu RL,von Konrat M,Shaw B,Shaw AJ,Heinrichs J

    更新日期:2010-12-01 00:00:00

  • Systematics of New World monkeys (Platyrrhini, Primates) based on 16S mitochondrial DNA sequences: a comparative analysis of different weighting methods in cladistic analysis.

    abstract::In order to investigate the effects of different weighting methods on a phylogeny reconstruction based on DNA sequences and to evaluate the phylogenetic information content of various secondary structures, a fragment of the large ribosomal mitochondrial gene (16S) was sequenced from 13 species of New World monkeys, th...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1995.1041

    authors: Horovitz I,Meyer A

    更新日期:1995-12-01 00:00:00

  • The intraspecific genetic variability of siliceous and calcareous Gentiana species is shaped by contrasting demographic and re-colonization processes.

    abstract::The Ciminalis section of Gentiana comprises seven species, two of them growing on siliceous substrates (G. alpina and G. acaulis), the other ones being calcareous taxa (G. clusii, G. angustifolia, G. ligustica, G. occidentalis and G. dinarica). A total of 515 individuals from 183 populations over the entire Ciminalis ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.09.022

    authors: Christe C,Caetano S,Aeschimann D,Kropf M,Diadema K,Naciri Y

    更新日期:2014-01-01 00:00:00

  • Analyzing the functional divergence of Slo1 and Slo3 channel subfamilies.

    abstract::Slo1 and Slo3 encode close paralogues of the Slo potassium (K+) channels family. Despite their evolutionary relatedness, Slo1 and Slo3 channels show marked functional differences and evolutionary dynamics. Whereas Slo1 is a highly conserved and widely expressed channel, Slo3 is a rapidly evolving channel restricted to...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2018.12.026

    authors: Vicens A,Vinuesa P,Arenas M,Treviño CL

    更新日期:2019-04-01 00:00:00

  • Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid loci.

    abstract::The phylogeny of Celastraceae subfamily Hippocrateoideae (∼ 100 species and 19 genera in the Old and New World tropics) was inferred using morphological characters together with plastid (matK, trnL-F) and nuclear (ITS and 26S rDNA) genes. The subfamily is easily recognized by the synapomorphies of transversely flatten...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2011.02.017

    authors: Coughenour JM,Simmons MP,Lombardi JA,Yakobson K,Archer RH

    更新日期:2011-05-01 00:00:00

  • Nuclear and mitochondrial DNA evidence of polyphyly in the avian superfamily Muscicapoidea.

    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

    authors: Voelker G,Spellman GM

    更新日期:2004-02-01 00:00:00

  • Return flight to the Canary Islands--the key role of peripheral populations of Afrocanarian blue tits (Aves: Cyanistes teneriffae) in multi-gene reconstructions of colonization pathways.

    abstract::Afrocanarian blue tits (Cyanistes teneriffae) have a scattered distribution on the Canary Islands and on the North African continent. To date, the Canary Islands have been considered the species' main Pleistocene evolutionary center, but their colonization pathways remain uncertain. We set out to reconstruct a dated m...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.02.010

    authors: Päckert M,Martens J,Hering J,Kvist L,Illera JC

    更新日期:2013-05-01 00:00:00

  • Phylogeny, species limits, and biogeography of the Brazilian lizards of the genus Eurolophosaurus (Squamata: Tropiduridae) as inferred from mitochondrial DNA sequences.

    abstract::Phylogenetic relationships and divergence times for 10 populations of the three recognized "species" of Brazilian lizards of genus Eurolophosaurus were estimated from 1229bp of cyt b, COI, 12S, and 16S rRNA mitochondrial gene segments. Eurolophosaurus is monophyletic and the basal split within the genus separates E. d...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2007.10.022

    authors: Passoni JC,Benozzati ML,Rodrigues MT

    更新日期:2008-02-01 00:00:00

  • Molecular genetic aspects of tetraploidy in the common carp Cyprinus carpio.

    abstract::Genome duplications are believed to have occurred on multiple occasions in vertebrate evolution. Studies of duplicate gene loci in tetraploid animals may reveal important general aspects of gene duplication, an important mode of gene evolution in metazoans. The common carp Cyprinus carpio has twice as many chromosomes...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1994.1007

    authors: Larhammar D,Risinger C

    更新日期:1994-03-01 00:00:00

  • Molecular phylogeny of the Neotropical fish genus Tetragonopterus (Teleostei: Characiformes: Characidae).

    abstract::Tetragonopterinae encompasses characid species of the genus Tetragonopterus, which are widely distributed throughout east of the Andes in South America. While taxonomy has recently clarified the species diversity and molecular evidence strongly supports the monophyly of Tetragonopterus, no interspecific relationship s...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2015.10.022

    authors: Melo BF,Benine RC,Silva GSC,Avelino GS,Oliveira C

    更新日期:2016-01-01 00:00:00

  • From America to Eurasia: a multigenomes history of the genus Abies.

    abstract::The origin of conifer genera, the main components of mountain temperate and boreal forests, was deemed to arise in the Mesozoic, although paleontological records and molecular data point to a recent diversification, presumably related to Neogene cooling. The geographical area(s) where the modern lines of conifers emer...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2018.03.009

    authors: Semerikova SA,Khrunyk YY,Lascoux M,Semerikov VL

    更新日期:2018-08-01 00:00:00