An efficient and rapid DNA minipreparation procedure suitable for PCR/SSR and RAPD analyses in tropical forest tree species

An efficient and rapid DNA minipreparation modified method for frozen samples was developed for five tropical tree species: Copaifera langsdorffii, Hymenaea courbaril, Eugenia uniflora, Tabebuia roseo alba and Cariniana estrellensis. This procedure that dispenses the use of liquid nitrogen, phenol and the addition of proteinase K, is an adaptation of the CTAB-based DNA extraction method. The modifications included the use of PVP to eliminate the polyphenols, only one chloroform-isoamyl alcohol step and the addition of RNase immediately after extraction with chloroform. The yields of the DNA samples ranged from 25.7 to 42.1 µg from 100 mg leaf tissue. The DNA samples extracted by this method were successfully used for PCR (SSR and RAPD) analyses in these five and other twelve tropical tree species.

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Classification of Tropical Forest Tree Species Using Meter-Scale Image Data

Remote Sensing ◽

10.3390/rs11121411 ◽

2019 ◽

Vol 11 (12) ◽

pp. 1411 ◽

Cited By ~ 1

Author(s):

Matthew Cross ◽

Ted Scambos ◽

Fabio Pacifici ◽

Orlando Vargas-Ramirez ◽

Rafael Moreno-Sanchez ◽

...

Keyword(s):

Tropical Forest ◽

Tree Species ◽

Near Infrared ◽

Single Species ◽

Forest Tree ◽

Tropical Tree ◽

Forest Composition ◽

Species Classification ◽

Tropical Tree Species

Accurate classification of tropical tree species is critical for understanding forest habitat, biodiversity, forest composition, biomass, and the role of trees in climate variability through carbon uptake. The aim of this study is to establish an accurate classification procedure for tropical tree species, specifically testing the feasibility of WorldView-3 (WV-3) multispectral imagery for this task. The specific study site is a defined arboretum within a well-known tropical forest research location in Costa Rica (La Selva Biological Station). An object-based classification is the basis for the analysis to classify six selected tree species. A combination of pre-processed WV-3 bands were inputs to the classification, and an edge segmentation process defined multi-pixel-scale tree canopies. WorldView-3 bands in the Green, Red, Red Edge, and Near-Infrared 2, particularly when incorporated in two specialized vegetation indices, provide high discrimination among the selected species. Classification results yield an accuracy of 85.37%, with minimal errors of commission (7.89%) and omission (14.63%). Shadowing in the satellite imagery had a significant effect on segmentation accuracy (identifying single-species canopy tops) and on classification. The methodology presented provides a path to better characterization of tropical forest species distribution and overall composition for improving biomass studies in a tropical environment.

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Sampling Tissue for DNA Analysis of Trees: Trunk Cambium as an Alternative to Canopy Leaves

Silvae Genetica ◽

10.1515/sg-2005-0038 ◽

2005 ◽

Vol 54 (1-6) ◽

pp. 265-269 ◽

Cited By ~ 39

Author(s):

N. Colpaert ◽

S. Cavers ◽

E. Bandou ◽

H. Caron ◽

G. Gheysen ◽

...

Keyword(s):

Dna Extraction ◽

Tree Species ◽

Dna Analysis ◽

Leaf Tissue ◽

Ground Level ◽

Tropical Tree ◽

Aflp Analysis ◽

Simple Method ◽

Tropical Tree Species ◽

High Concentrations

Abstract The number of studies of tropical tree species that use molecular tools is increasing, most of which collect leaf tissue for genomic DNA extraction. In tropical trees the canopy is not only frequently inaccessible, but also, once reached, the leaf tissue is often heavily defended against herbivory by high concentrations of anti-predation compounds, which may inhibit downstream applications, particularly PCR. Cambium tissue, accessed directly from the tree trunk at ground level, offers a readily accessible resource that is less hampered by the presence of defensive chemicals than leaf tissue. Here we describe a simple method for obtaining tissue from the cambial zone for DNA extraction and test the applicability of the method in a range of tropical tree species. The method was used successfully to extract DNA from 11 species in nine families. A subset of the DNA extracts was tested in more detail and proved to be highly suitable for AFLP analysis.

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An estimate of the number of tropical tree species

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1423147112 ◽

2015 ◽

Vol 112 (24) ◽

pp. 7472-7477 ◽

Cited By ~ 168

Author(s):

J. W. Ferry Slik ◽

Víctor Arroyo-Rodríguez ◽

Shin-Ichiro Aiba ◽

Patricia Alvarez-Loayza ◽

Luciana F. Alves ◽

...

Keyword(s):

Species Richness ◽

Tree Species ◽

Forest Tree ◽

Tropical Tree ◽

Tropical Tree Species ◽

As Species ◽

Tree Inventory ◽

Minimum Number ◽

Closed Canopy ◽

High Species Richness

The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher’s alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼40,000 and ∼53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼19,000–25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼4,500–6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa.

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