A new phylogeny for the genus Picea from plastid, mitochondrial, and nuclear sequences

Lockwood, Jared D.; Aleksić, J.; Zou, Jiabin; Wang, Jing; Liu, Jianquan; Renner, Susanne S.

doi:10.1016/j.ympev.2013.07.004

Cited by 109 publications

(158 citation statements)

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“…The distributions of P. abies and P. obovata and their hybrid zone are also shown. The distribution of P. abies is based on the Euforgen map (EUFORGEN 2009, www.euforgen.org) and that of P. obovata is taken from [3]. The approximate location of the hybrid zone was inferred by genotyping 99 populations at 13 nuclear SSR loci and three cpSSR loci (Y. Tsuda, T. Källman, M. Lascoux, L. Parducci, D. Politov, V. Semerikov, J.H.…”

Section: Resultsmentioning

confidence: 99%

Clinal Variation at Phenology-Related Genes in Spruce: Parallel Evolution in FTL2 and Gigantea?

et al. 2014

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Parallel clines in different species, or in different geographical regions of the same species, are an important source of information on the genetic basis of local adaptation. We recently detected latitudinal clines in SNPs frequencies and gene expression of candidate genes for growth cessation in Scandinavian populations of Norway spruce (Picea abies). Here we test whether the same clines are also present in Siberian spruce (P. obovata), a close relative of Norway spruce with a different Quaternary history. We sequenced nine candidate genes and 27 control loci and genotyped 14 SSR loci in six populations of P. obovata located along the Yenisei river from latitude 56°N to latitude 67°N. In contrast to Scandinavian Norway spruce that both departs from the standard neutral model (SNM) and shows a clear population structure, Siberian spruce populations along the Yenisei do not depart from the SNM and are genetically unstructured. Nonetheless, as in Norway spruce, growth cessation is significantly clinal. Polymorphisms in photoperiodic (FTL2) and circadian clock (Gigantea, GI, PRR3) genes also show significant clinal variation and/or evidence of local selection. In GI, one of the variants is the same as in Norway spruce. Finally, a strong cline in gene expression is observed for FTL2, but not for GI. These results, together with recent physiological studies, confirm the key role played by FTL2 and circadian clock genes in the control of growth cessation in spruce species and suggest the presence of parallel adaptation in these two species.I DENTIFYING the loci underlying the variation in quantitative traits and detecting the selection acting on them remains, to this day, one of the main challenges in biology (Rockman 2012;Marjoram et al. 2013). In his Nobel lecture Sidney Brenner (Brenner 2003) predicted that genome-wide association studies (GWAS) would become the main approach to identifying the genetic factors controlling complex traits. The past decade has amply vindicated Brenner's prediction: GWAS have blossomed and identified a large number of single nucleotide polymorphism (SNP) associated to various quantitative traits (Visscher et al. 2012). Limitations of GWAS have, however, started to become evident and different strategies have been offered to alleviate those (Rockman 2012;Marjoram et al. 2013;Vilhjalmsson and Nordborg 2013). In particular, GWAS have limited power unless very large data sets are used. They therefore remain prohibitively expensive, and often not so informative, for nonmodel organisms with limited or nascent genome resources such as conifers. In such organisms a more targeted strategy, combining population genetics, physiology, and expression studies of candidate genes remains a very fruitful approach, at least in the short term. We recently adopted such a strategy in an attempt to unravel the genetic basis of growth cessation, a trait of adaptive value with a strong and well-documented clinal variation, in Norway spruce (Picea abies) (Chen et al. 2012a and references therein). T...

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Section: Resultsmentioning

confidence: 99%

Clinal Variation at Phenology-Related Genes in Spruce: Parallel Evolution in FTL2 and Gigantea?

et al. 2014

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“…Small characters are weak CMA-bands. *After Hizume et al (1991) and **clades of Lockwood et al (2013). Column color of taxon shows distribution; pink is America, beige is Eurasia and Europa and pale green is Asia.…”

Section: Fluorescent Banding Pattern Of Chromosomes In Each Picea Taxonmentioning

confidence: 97%

“…These taxonomical treatments were somewhat complex and difficult to compare with the species alignment based on the CMA-band pattern. Recently several molecular phylogenetic studies were performed in Picea (Ran et al 2006, Bouillé et al 2011, Lockwood et al 2013. The molecular phylogenetic relationship (Fig.…”

Section: Comparative Analysis Of Cma-banded Karyotype Among Picea Taxamentioning

confidence: 99%

“…The molecular phylogenetic relationship (Fig. 3 in Lockwood et al 2013) seems the most reliable using sequences of three genomes. Picea species was monophyletic and three clades were recognized; Clade I Asian and three European species, Clade II have North American species, and Clade III had Asian and one American species.…”

Section: Comparative Analysis Of Cma-banded Karyotype Among Picea Taxamentioning

confidence: 99%

“…The genus Picea is one of genera in Pinaceae and composed of 40-50species, and distributing North Hemisphere (Farjon 1990(Farjon , 2001(Farjon , 2010Lockwood et al 2013). The karyotype study by smear or squash methods had been started in several conifers by Sax and Sax (1933).…”

Section: Introductionmentioning

confidence: 99%

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Chromosome banding in <i>Picea</i> IV. Comparative karyotype analysis of fluorescent band patterns in 25 taxa

Hizume¹

2017

Chromosome Botany

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ABSTRACT:In 25 taxa of Picea the somatic chromosomes were analyzed by a fluorescent banding technique using chromomycin A 3 (CMA) and DAPI. They had 2n=24 chromosome number and similar karyotypes among species. On metaphase chromosomes in each taxon the CMA-bands appeared at the interstitial and centromeric regions. DAPI-bands appeared on chromosomes of some species. The CMA-band pattern of each taxon was described after identification of most homologous chromosomes and compared among taxa. An alignment of species based on CMA-band pattern with some exception were coincident on their geographic distribution, and discussed on interspecific relationships, comparison to molecular phylogeny and DNA sequences corresponding to fluorescent bands.

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An overview of extant conifer evolution from the perspective of the fossil record

Leslie

Beaulieu

Holman

et al. 2018

American J of Botany

120

113

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Molecular phylogenies are useful for answering deep questions in conifer evolution if they depend on understanding relationships among extant lineages. Because of extinction, however, molecular datasets poorly sample diversity from periods much earlier than the Late Cretaceous. This fundamentally limits their utility for understanding deep patterns of character evolution and resolving the overall pattern of conifer phylogeny.

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A new phylogeny for the genus Picea from plastid, mitochondrial, and nuclear sequences

Cited by 109 publications

References 73 publications

Clinal Variation at Phenology-Related Genes in Spruce: Parallel Evolution in FTL2 and Gigantea?

Clinal Variation at Phenology-Related Genes in Spruce: Parallel Evolution in FTL2 and Gigantea?

Chromosome banding in <i>Picea</i> IV. Comparative karyotype analysis of fluorescent band patterns in 25 taxa

An overview of extant conifer evolution from the perspective of the fossil record

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