Baskin resources and ISI spp. searches

[DeirdreLoughnan]

@lizzieinvancouver @FrederikBaumgarten @dbuona I started looking at some citations referenced in the Baskin book for our OSPREE spp:

1. Acer campestre: C Cites Toth & Garett 1989, which is a "Tree planters notes Vol 4 No 3" from the Reforestation, Nurseries, and Genetic resources (not available on ISI). The publication actually includes data for four of our OSPREE species. They apply four stratification treatments and pericarp removal and report percent germination.

I got no search results for this species when I searched ISI with "Acer campestre AND germination AND seed dormancy"

I will look up a few more of their references for other species, but this is an interesting start!

[DeirdreLoughnan]

Next steps:

1. Look up five references for specific genera (or all available if fewer) based on tables primarily on pages 700 (shrubs) or 715 (deciduous trees): a. what kind of literature are they referencing (grey vs white)? b. do any references include more than one species? c. do they include information on chilling and germination temperatures and key response variables (germination rates, percent germination, etc.) c. are there better references than those cited by the Baskin reference?

2. ISI search of your species and terms like "seed germination" and "seed dormancy" (optional task depending on outcome of above)

Based on the number of species per genera: @FrederikBaumgarten: Prunus and Betula @lizzieinvancouver: Quercus and Viburnum @DeirdreLoughnan: Acer and Picea @dbuona: Ulmus and Populus

[DeirdreLoughnan]

@lizzieinvancouver @FrederikBaumgarten @dbuona Our aim is to have these searches done by Friday December 8th

[lizzieinvancouver]

@DeirdreLoughnan @dbuona @FrederikBaumgarten I added a file for this task see here. Please use it!

[lizzieinvancouver]

Here are the species:

"Acer_barbinerve"               "Acer_campestre"               
  [5] "Acer_ginnala"                  "Acer_negundo"                  "Acer_pensylvanicum"            "Acer_platanoides"             
  [9] "Acer_pseudoplatanus"           "Acer_rubrum"                   "Acer_saccharinum"              "Acer_saccharum"               
 [13] "Acer_tataricum"

"Betula_alleghaniensis"        
 [29] "Betula_ermanii"                "Betula_lenta"                  "Betula_nana"                   "Betula_occidentalis"          
 [33] "Betula_papyrifera"             "Betula_pendula"                "Betula_pendula,pubescens"      "Betula_populifolia"  
"Picea_abies"                   "Picea_breweriana"              "Picea_engelmannii"            
[137] "Picea_glauca"                  "Picea_glehnii"                 "Picea_jezoensis"               "Picea_mariana"                
[141] "Picea_pungens"                 "Picea_sitchensis"
 "Populus_balsamifera"           "Populus_deltoides"            
[153] "Populus_grandidentata"         "Populus_koreana"               "Populus_tremula"               "Populus_tremuloides"          
[157] "Populus_trichocarpa"
[177] "Quercus_alba"                  "Quercus_bicolor"               "Quercus_coccifera"             "Quercus_ellipsoidalis"        
[181] "Quercus_faginea"               "Quercus_ilex"                  "Quercus_petraea"               "Quercus_pubescens"            
[185] "Quercus_robur"                 "Quercus_rubra"                 "Quercus_shumardii"             "Quercus_velutina"
"Ulmus_americana"               "Ulmus_glabra"                  "Ulmus_laevis"                  "Ulmus_macrocarpa"             
[241] "Ulmus_minor"                   "Ulmus_parvifolia"              "Ulmus_pumila"                  "Ulmus_villosa"                
[245] "Vaccinium_ashei"               "Vaccinium_corymbosum"          "Vaccinium_myrtilloides"        "Viburnum_betulifolium"        
[249] "Viburnum_buddleifolium"        "Viburnum_carlesii"             "Viburnum_cassinoides"          "Viburnum_lantanoides"         
[253] "Viburnum_opulus"               "Viburnum_plicatum"  

[lizzieinvancouver]

Just noting some of my progress (plus updates later) here so I can pick this up later. I am working on Quercus. I started with Quercus robur in B2 and found one of the three refs that I looked up was on Google Scholar as a result, which was the Woody Plant Seed Manual (Bonner, USDA). It has a great chapter (which includes flowering months and seed dispersal months ... wonder if we should scrape this ... we might be able to do it in PERL, but I sort of doubt It).

Table 4 has cold strat, germ temps with germ rates and % germination, but all ranges so I plan to look up these refs for the table: Dirr and Heuser (1987), Korstian (1927), Larsen (1963), Olson (1974), Swingle (1939)

1. Dirr MA, Heuser CW Jr. 1987. The reference manual of woody plant propagation: from seed to tissue culture. Athens, GA:Varsity Press. 239 p. -- NEED to go look at non-circ copy at library.
2. Korstian CF. 1927. Factors controlling germination and early survival in oaks. For. Bull. 19. New Haven, CT: Yale University School of Forestry. 115 p. -- Downloaded, has lots of tables we could scrape.
3. Larsen HS. 1963. Effects of soaking in water on acorn germination of four southern oaks. Forest Science 9: 236–241 -- ignoring for now.
4. Olson DF Jr. 1974. Quercus L., oak. In: Schopmeyer CS, tech. coord. Seeds of woody plants in the United States. Agric. Handbk. 450. Washington, DC: USDA Forest Service: 692–703. -- ordered
5. Swingle CF, comp. 1939. Seed propagation of trees, shrubs, and forbs for conservation planting. SCS-TP-27. Washington, DC: USDA Soil Conservation Service. 195 p -- found it, downloaded it, lots of but I don't think much of it was controlled temperatures so not sure ... need to look at it again.

I also found one ref that had several of our Quercus species in one paper, but only looked at smoke/fire or high temperatures.

[DeirdreLoughnan]

I conducted my search today and pushed notes for Acer and Picea.

In general I found most papers to only include one species and to only report or have figures for percent germination.

But I did have difficulty finding a lot of the Baskin & Baskin references. I also noticed that when species occur in more than one table in their book, they sometimes give different references.

[lizzieinvancouver]

Now working on Viburnum, though not sure how many of our species B2 has ... I have found Viburnum betulifolium and cassinoides with these refs in B2 (they mention V opulus in Ch 12 but I have yet to find it in a table):

• Wang et al, 2009d; Wang, J.-H., Du, G.-Z., Cui, X.-L., Zheng, X.-F., Qi, W., 2009d. Germination characteristics of 61 common woody species from the eastern Qinghai-Tibet Plateau of China and their life history corre- lates. Zhi. Sheng. Xue. 33, 171
  179. -- found it, it's in Chinese and it does not have our Viburnum species.
• Baskin et al.,unpubl. -- oy!
• Gill & Pogge, 1974 -- Gill, J.D., Pogge, F.L., 1974. Parthenocissus Planch. Creeper. In: Schopmeyer C.S. (Ed.), (Technol. Coord.). Seeds of woody plants in the United States. USDA. Forest Service. Agriculture Handbook No. 450. pp 568
  571. -- requested a copy

Actually seems like the Woody Plant Seed Manual again is pretty good ... It refers to the Gill & Pogge that I ordered and:

Vines RA. 1960. Trees, shrubs and woody vines of the Southwest. Austin: University of Texas Press. 1104 p. ... which I just ordered via Document Delivery (at UBC, I think it's maybe offsite?)

[dbuona]

Quick question: Are we interested in non-dormant species that have no chilling in experiments? All Populus and about half of the Ulmus species in Baskin & Baskin are ND. The data from the Ulmus that have chilling treatments and PD are in .

In: Schopmeyer C.S. (Ed.), (Technol. Coord.). Seeds of woody plants in the United States. USDA. Forest Service. Agriculture Handbook No. 450. pp 568�571.

I also requested a copy from UMass library, but I won't be able to pick it up until next Tuesday so I am not sure how helpful it will be.

[lizzieinvancouver]

@dbuona I think we just want all OSPREE spp we can get, right? I thought the mix of dormant and ND was interesting for our spp.

Remind me we should also discuss today if we want to scrape the additional tables in Woody Plant Manual USDA.

And for anyone looking up Dirr and Heuser, I went to the library Wednesday to look at it and it's not useful to us (methinks). I will aim to upload photos later....

[DeirdreLoughnan]

@FrederikBaumgarten @lizzieinvancouver @dbuona

I created a new folder within the egret paper folder for Baskin references.

The next genera for us to get references for are: @lizzieinvancouver: Tilia, Rhododendron, Syringa @FrederikBaumgarten: Sorbus, Larix, Lonicera @dbuona: Fraxinus, Fagus, Pyrus @DeirdreLoughnan: Pinus, Salix, Ribes

[lizzieinvancouver]

@DeirdreLoughnan Thanks! (I am jealous of @dbuona assigned genera.)

[lizzieinvancouver]

Full species list:

> sort(unique(paste(d$genus, d$species)))
  [1] "Abies alba"                    "Abies homolepis"              
  [3] "Acer barbinerve"               "Acer campestre"               
  [5] "Acer ginnala"                  "Acer negundo"                 
  [7] "Acer pensylvanicum"            "Acer platanoides"             
  [9] "Acer pseudoplatanus"           "Acer rubrum"                  
 [11] "Acer saccharinum"              "Acer saccharum"               
 [13] "Acer tataricum"                "Actinidia deliciosa"          
 [15] "Aesculus flava"                "Aesculus hippocastanum"       
 [17] "Aesculus parviflora"           "Alnus glutinosa"              
 [19] "Alnus incana"                  "Alnus maximowiczii"           
 [21] "Alnus rubra"                   "Amelanchier alnifolia"        
 [23] "Amelanchier florida"           "Amelanchier laevis"           
 [25] "Amorpha fruticosa"             "Aronia melanocarpa"           
 [27] "Berberis dielsiana"            "Betula alleghaniensis"        
 [29] "Betula ermanii"                "Betula lenta"                 
 [31] "Betula nana"                   "Betula occidentalis"          
 [33] "Betula papyrifera"             "Betula pendula"               
 [35] "Betula pendula,pubescens"      "Betula populifolia"           
 [37] "Betula pubescens"              "Buddleja albiflora"           
 [39] "Buddleja alternifolia"         "Buddleja davidii"             
 [41] "Caragana pygmaea"              "Carpinus betulus"             
 [43] "Carpinus laxiflora"            "Carpinus monbeigiana"         
 [45] "Carya cordiformis"             "Carya laciniosa"              
 [47] "Carya ovata"                   "Castanea sativa"              
 [49] "Cedrus libani"                 "Celtis caucasica"             
 [51] "Celtis laevigata"              "Celtis occidentalis"          
 [53] "Cephalanthus occidentalis"     "Cercidiphyllum japonicum"     
 [55] "Cercidiphyllum magnificum"     "Cercis canadensis"            
 [57] "Cercis chinensis"              "Cladrastis lutea"             
 [59] "Cornus alba"                   "Cornus kousa"                 
 [61] "Cornus mas"                    "Corylopsis sinensis"          
 [63] "Corylopsis spicata"            "Corylus avellana"             
 [65] "Corylus cornuta"               "Corylus heterophylla"         
 [67] "Corylus sieboldiana"           "Decaisnea fargesii"           
 [69] "Deutzia gracilis"              "Deutzia scabra"               
 [71] "Elaeagnus ebbingei"            "Eleutherococcus senticosus"   
 [73] "Eleutherococcus setchuenensis" "Eleutherococcus sieboldianus" 
 [75] "Euonymus europaeus"            "Euonymus latifolius"          
 [77] "Fagus crenata"                 "Fagus engleriana"             
 [79] "Fagus grandifolia"             "Fagus orientalis"             
 [81] "Fagus sylvatica"               "Forsythia ovata"              
 [83] "Forsythia suspensa"            "Fraxinus americana"           
 [85] "Fraxinus chinensis"            "Fraxinus excelsior"           
 [87] "Fraxinus latifolia"            "Fraxinus nigra"               
 [89] "Fraxinus ornus"                "Fraxinus pennsylvanica"       
 [91] "Ginkgo biloba"                 "Hamamelis japonica"           
 [93] "Hamamelis vernalis"            "Hamamelis virginiana"         
 [95] "Heptacodium miconioides"       "Hibiscus syriacus"            
 [97] "Hydrangea arborescens"         "Hydrangea involucrata"        
 [99] "Hydrangea serrata"             "Ilex mucronata"               
[101] "Juglans ailantifolia"          "Juglans cinerea"              
[103] "Juglans regia"                 "Juglans spp"                  
[105] "Kalmia angustifolia"           "Larix decidua"                
[107] "Larix gmelinii"                "Larix kaempferi"              
[109] "Larix laricina"                "Larix laricinia"              
[111] "Ligustrum tschonoskii"         "Liquidambar orientalis"       
[113] "Liquidambar styraciflua"       "Liriodendron tulipifera"      
[115] "Lonicera alpigena"             "Lonicera caerulea"            
[117] "Lonicera canadensis"           "Lonicera maximowiczii"        
[119] "Lyonia ligustrina"             "Malus domestica"              
[121] "Malus pumila"                  "Metasequoia glyptostroboides" 
[123] "Nothofagus antarctica"         "Nyssa sylvatica"              
[125] "Oemleria cerasiformis"         "Olea europaea"                
[127] "Orixa japonica"                "Ostrya carpinifolia"          
[129] "Ostrya virginiana"             "Paeonia rockii"               
[131] "Parrotia persica"              "Parrotiopsis jaquemontiana"   
[133] "Photinia villosa"              "Picea abies"                  
[135] "Picea breweriana"              "Picea engelmannii"            
[137] "Picea glauca"                  "Picea glehnii"                
[139] "Picea jezoensis"               "Picea mariana"                
[141] "Picea pungens"                 "Picea sitchensis"             
[143] "Pieris japonica"               "Pinus banksiana"              
[145] "Pinus contorta"                "Pinus nigra"                  
[147] "Pinus strobus"                 "Pinus sylvestris"             
[149] "Pinus taeda"                   "Pinus wallichiana"            
[151] "Populus balsamifera"           "Populus deltoides"            
[153] "Populus grandidentata"         "Populus koreana"              
[155] "Populus tremula"               "Populus tremuloides"          
[157] "Populus trichocarpa"           "Prinsepia sinensis"           
[159] "Prinsepia uniflora"            "Prunus avium"                 
[161] "Prunus cerasifera"             "Prunus cerasus"               
[163] "Prunus insititia"              "Prunus padus"                 
[165] "Prunus pensylvanica"           "Prunus persica"               
[167] "Prunus salicina"               "Prunus serotina"              
[169] "Prunus serrulata"              "Prunus tenella"               
[171] "Pseudotsuga menziesii"         "Ptelea trifoliata"            
[173] "Pyrus communis"                "Pyrus elaeagnifolia"          
[175] "Pyrus pyrifolia"               "Pyrus ussuriensis"            
[177] "Quercus alba"                  "Quercus bicolor"              
[179] "Quercus coccifera"             "Quercus ellipsoidalis"        
[181] "Quercus faginea"               "Quercus ilex"                 
[183] "Quercus petraea"               "Quercus pubescens"            
[185] "Quercus robur"                 "Quercus rubra"                
[187] "Quercus shumardii"             "Quercus velutina"             
[189] "Rhamnus alpina"                "Rhamnus cathartica"           
[191] "Rhamnus frangula"              "Rhododendron canadense"       
[193] "Rhododendron dauricum"         "Rhododendron mucronulatum"    
[195] "Rhododendron prinophyllum"     "Rhododendron simsii"          
[197] "Ribes alpinum"                 "Ribes divaricatum"            
[199] "Ribes glaciale"                "Ribes nigrum"                 
[201] "Robinia pseudoacacia"          "Rosa hugonis"                 
[203] "Rosa majalis"                  "Rosa spp"                     
[205] "Rubus idaeus"                  "Salix gracilistyla"           
[207] "Salix pulchra"                 "Salix repens"                 
[209] "Salix smithiana"               "Sambucus nigra"               
[211] "Sambucus pubens"               "Sambucus tigranii"            
[213] "Sinowilsonia henryi"           "Sorbus aria"                  
[215] "Sorbus aucuparia"              "Sorbus commixta"              
[217] "Sorbus decora"                 "Sorbus intermedia"            
[219] "Sorbus torminalis"             "Spiraea canescens"            
[221] "Spiraea chamaedryfolia"        "Spiraea japonica"             
[223] "Spirea alba"                   "Stachyurus praecox"           
[225] "Stachyurus sinensis"           "Symphoricarpos albus"         
[227] "Syringa josikaea"              "Syringa reticulata"           
[229] "Syringa villosa"               "Syringa vulgaris"             
[231] "Tilia americana"               "Tilia cordata"                
[233] "Tilia dasystyla"               "Tilia japonica"               
[235] "Tilia platyphyllos"            "Toona sinensis"               
[237] "Ulmus americana"               "Ulmus glabra"                 
[239] "Ulmus laevis"                  "Ulmus macrocarpa"             
[241] "Ulmus minor"                   "Ulmus parvifolia"             
[243] "Ulmus pumila"                  "Ulmus villosa"                
[245] "Vaccinium ashei"               "Vaccinium corymbosum"         
[247] "Vaccinium myrtilloides"        "Viburnum betulifolium"        
[249] "Viburnum buddleifolium"        "Viburnum carlesii"            
[251] "Viburnum cassinoides"          "Viburnum lantanoides"         
[253] "Viburnum opulus"               "Viburnum plicatum"            
[255] "Vitis vinifera"                "Weigela coraeensis"           
[257] "Weigela florida"               "Weigela maximowiczii

[lizzieinvancouver]

I uploaded photos from Dirr & Heuser (which is NOT a useful book) to the Baskin refs folder on Google Drive.

[DeirdreLoughnan]

@lizzieinvancouver I finished reviewing my three genera. Although I should perhaps do two more.

Of the four Salix spp in ospree, only one is mentioned in text in Baskin & Baskin and there are no references given. Similarly the four Ribes spp only have one with a reference and the copy I found was not in english.

But I was able to find 1-2 references for each of the Pinus spp.

[lizzieinvancouver]

Vines 1960: TREES, SHRUBS, AND WOODY VINES OF THE SOUTHWEST. -- also not a good resource. @DeirdreLoughnan Can you add a few notes on that here?

[lizzieinvancouver]

I am still waiting on a ton of gray papers I ordered ... but I think have done enough work to meet Monday. To prep for the meeting @dbuona @DeirdreLoughnan @FrederikBaumgarten please pull together any notes and add here or on your Excel file and, can you please write up 1-3 proposed methods we should do?

For example, to maximize species overlap with OSPREE species, we reviewed references for a subset of OSPREE species from each OSPREE general in Baskin and Baskin and searched on Google Scholar to obtain 1-2 relevant papers if possible.

Try to diversify your suggested methods even if you have a top pick!

[dbuona]

I found the literature in Baskin very hit or miss, and usually only one species per study with lots of other complicating factors (storage time, pericarp removal etc). I propose:

1. For ospree species: scrape tables in woody plant manual
2. Scrape propagation protocols from forest service and European equivalent (using recommended stratification level as a proxy for chill sensitivity).

Or Abandon the ospree connection, and look at chilling requirements more broadly in EGRET

[lizzieinvancouver]

@DeirdreLoughnan Suggested a flow set of approaches (she will add them here) with step 1 being to scrape the Woody Plant Manual @lizzieinvancouver will work with Selena on this.

If we ever decide to scrape suggested seed treatments, then we could potentially scrape from Dirr & Heuser book and/or Prairie Moon Nursery -- @dbuona will contact them now... And we should look around some too if we do this later.

Two pronged approach for this term on data ...

1. Scrape woody plant manual (well, see how it goes)
2. Clean the EGRET data with some question about cold strat across species in mind ... What is a (quantitative) chilling cue across species? How much cold strat do they need, are they getting enough and will they etc. (see ref 1; ref 2) so need to do some forecasting (and figure out what soil temperature data there is).

What % of studies varied cold strat or warm start (time or temperature) ... thinking on 2.

[lizzieinvancouver]

Some relevant papers about forecasting germination (relevant meaning they are about this topic broadly): Climate change and plant regeneration from seed

Cold stratification in winter is more than enough for seed dormancy-break of summer annuals in eastern North America: implications for climate change

Maybe ... Germination niche breadth and potential response to climate change differ among three North American perennials

[lizzieinvancouver]

@dbuona Friendly reminder to jot down meetings notes from last week here, before we forget. @DeirdreLoughnan and also friendly reminder to write up that flow path. Thank you both!

[DeirdreLoughnan]

My proposed path forward is the following flow path:

1. Does the woody plant manual have data for 50+ OSPREE species? Yes---Great, clean and analyze the data No---See 2.
2. Can we find a similar book that compliments what the woody plant manual did have? Yes---Great, clean and analyze data from both sources No---Go back to looking at the Baskin Robbins references and try to get 50 species worth of data

I was unable to find a similar guide as the Woody plant manual from the UK.

[lizzieinvancouver]

@lizzieinvancouver I need to close out this and related issues with good notes!

[lizzieinvancouver]

Closing this, see notes/otherSourcesSearchDec2023.md