Phenology.bib

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@article{CHADWICK2006,
author = {CHADWICK, F R EDE R ICK M. S LAT ER And S J ORME ROD},
doi = {10.1111/j.1365-2486.2006.01156.x},
file = {:Users/Ty/Documents/Mendeley Desktop/CHADWICK{\_}2006{\_}Inter- and intraspecific differences in climatically mediated phenological change in coexisting Triturus species.pdf:pdf},
journal = {Global Change Biology},
keywords = {5 december 2005,amphibian,breeding,climate change,migration,newt,phenological asynchrony,phenology,received 27 may 2004,revised version received 21,september 2005 and accepted,triturus helveticus,triturus vulgaris},
pages = {1069--1078},
title = {{Inter- and intraspecific differences in climatically mediated phenological change in coexisting Triturus species}},
year = {2006}
}
@article{Visser2010,
abstract = {Phenology refers to the periodic appearance of life-cycle events and currently receives abundant attention as the effects of global change on phenology are so apparent. Phenology as a discipline observes these events and relates their annual variation to variation in climate. But phenology is also studied in other disciplines, each with their own perspective. Evolutionary ecologists study variation in seasonal timing and its fitness consequences, whereas chronobiologists emphasize the periodic nature of life-cycle stages and their underlying timing programmes (e.g. circannual rhythms). The (neuro-) endocrine processes underlying these life-cycle events are studied by physiologists and need to be linked to genes that are explored by molecular geneticists. In order to fully understand variation in phenology, we need to integrate these different perspectives, in particular by combining evolutionary and mechanistic approaches. We use avian research to characterize different perspectives and to highlight integration that has already been achieved. Building on this work, we outline a route towards uniting the different disciplines in a single framework, which may be used to better understand and, more importantly, to forecast climate change impacts on phenology.},
annote = {Intro







- some species show extreme reliability in year-to-year phenology (i.e. birds) while others show great variation between years. 
- temperate zone, temperature usually the best predictor of phenology.
- needed -- ability to predict phenology shifts well outside the current projected range of observed data to address climate change. Hence, we need a unified framework that incorporates an ecological and evolutionary prospective. 
- look up -- cirannual thythms.







Different Perspectives







-Phenologists -- record life-cycle events over long periods of time and relate the inter-annual variations to climatic variables.
- focus on seasonal recurrence in its own right.
- focus on first individuals or population mean rather than variation among individuals of the population.
- Individual approach -- The date that something happens is a phenotype and should be treated accordingly.
- variation in date will be the result of phenotypic plastisity and is this shaped by the interaction between the genotype and the environment.
- Evolutionary ecologist -- refer to it as "seasonal timing." Emphasize variation among individuals within years and between years. 
- "birds have been selected for their ability to have their chicks in the nest at the time of peak food abundance." -- I think the link to evolution is correct, but I don't think it has as much to do with food as it does with temperature. 
- have birds evoloved the ability to CORRECTLY interpret proximate cues (interpreted well before the actual breeding event) to hit a particular optimal date?
- cues should provide the ability to predict the future environment under which the phenotype will be selected. Including: conspecific and multi-trophic interactions. 
- these cues must actually be a suite of cues on a multi-dimensional enivronmental axis. 
- Mainly study organisms in the wild to observe fitness benifits and selection events on timing.
- Physiologists -- how do the changes within annual cycles causally come about? How can environmental cues adjust morphology, physiology, and behaviour over an annual schedule?
- strong emphasis on photoperiod. 
- hypothalamo-pituitary-honadal (HPG) axis is the well studied mechanism for translating photoperiod cues to behavioral action in birds.
- shown that temp, social, moisture, and food availability cues are also important, but the mechanism for translation is not as well known as the HPG axis.
- most of this work is done at the individual behavioral level, in a lab.
- test usually conducted under controlled temp (usually warmer than natural conditions and constant) with a heavy bias toward males rather than females (because females usually don't reach full reproductive maturity in captivity). 
- one useful proxy used in field experiments is gonadal development rather than actual egg laying. 
- Chronobiologist -- focus on internal timing programmes that enable organisms to cope with, and anticipate, geophysical cycles in the enivronment.
- this is the internal clock that persists even without external cues. 
-work on daily or yearly cycles
- seperate period (length of cycle) from phase (time when that cycle occurs). 
- less interested in variation between years or individuals 
- focus on avvual cycle and variation over the year.
- events occur based on the interplay between internal time-structuring and environmental cues. 
- seasonal clock determines how sensitive an animal is to external cues. The individual will respond to cues during some times of the year and not others. 
- for birds -- the circadian clock internally references 24 hours for the bird to compare the photoperiod to, to determine if a day is "long" (larger proportion of 24) or "short" (smaller proportion of 24). 
- If the bird is in the correct phase for photostimulation, a cascade of gene expression starts. 
- includes citations for comparisons of this process between different taxa. 
- Molecular Geneticist -- what are the genes controlling timing and how do those genes vary between individuals.
- have shown that a latitudinal gradient exists in the mean repeat lenght (more repeats at hight lats) exists in the one known candidate gene for timing. 
- females with shorter repeat lengths layed eggs earlier. 
- these studies completely absent in wild birds. 
- OTL studies are monitoring gene expression to try to find the genes controlling these cycles. Looking at both the genes that do the work and the genes that set that work into motion. 







Integration toward a single framework







- evolution is the primary controlling force. phenotype controlled by selection.
-relatively small changes in reproduction date have large fitness consequences. 
-because fitness consequences depend on a species' ecology, and the particular environment, "there is no single mechanism that fits all species."
-- I don't think this is exactly true... I'm trying to define the environment 
within with species or individual 
compete and set their date.
-a crucial step is taking account of variation between species or populations, as well as between individuals with a population. 
- 



















































animals must use cues to predict selection



















































. 
- so, the animal will use a cue that predicts indirect effects. i.e. precip -{\textgreater} grass -{\textgreater} food source.
- quails require a combined reduction in temperature and photoperiod to stop reproduction entirely. 
- the same temperature can have a stronger effect on a species during longer photoperiod than shorter photoperiod. 
- in very long photoperiods, individuals can breed under very low abient temperatures. 
- if things go wrong and you lay out of optimal zone or a severe weather event takes place, then individuals may switch to an emergency life-history stage. 
- phenotypic reaction norm -- a distribution where the breadth determines how broadly selection can act on a trait and the hight determines how strongly selection can act on a trait. 
- selection can not act on the translation and response to cues, not on date itself. probably also works on a suite of traits rather than a specific one.
-- similarities to spatial movement. 
We sense our location based on cues, 
not the location itself.
- the cues do not happen in the same environment as the reproduction. Again, prediction. 
- 














only if the environment of selection is predicted by an environmental variable can it serve as a predictive cue














. 








- Blue tit case study.








- Outlook -- where to go from here.
- climate change is effecting phenology, but how and why?
- If climate change affets the environmental variables that serve as cues differently from the from the environmental variables that form the environment at the time of selection, then the response to climate change will no longer be adaptive. Cues lose their predictive value. 
- for things to survive climate change, their phenotypic plasticity must be greater than the change in the environment.
- does learning play a role over the lifetime of individuals? probably...},
author = {Visser, M.E. and Caro, S.P.},
doi = {10.1098/rstb.2010.0111},
file = {:Users/Ty/Documents/Mendeley Desktop/Visser, Caro{\_}2010{\_}Phenology, seasonal timing and circannual rhythms towards a unified framework.pdf:pdf},
issn = {1471-2970},
journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
keywords = {avian reproduction,circannual rhythms,molecular genetics,phenology,reproductive physiology,seasonal timing},
month = {oct},
number = {1555},
pages = {3113--3127},
pmid = {20819807},
title = {{Phenology, seasonal timing and circannual rhythms: towards a unified framework}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20819807 http://rstb.royalsocietypublishing.org/content/365/1555/3113.short},
volume = {365},
year = {2010}
}
@article{Schaik1993,
author = {van Schaik, CP and Terborgh, JW},
file = {:Users/Ty/Documents/Mendeley Desktop/Schaik, Terborgh{\_}1993{\_}The phenology of tropical forests adaptive significance and consequences for primary consumers.pdf:pdf},
journal = {Annual Review of Ecology and},
title = {{The phenology of tropical forests: adaptive significance and consequences for primary consumers}},
url = {http://www.jstor.org/stable/2097183},
volume = {0},
year = {1993}
}
@article{Forkner2008,
author = {Forkner, RE and Marquis, RJ and Lill, John T. and {Le Corff}, Josiane},
doi = {10.1111/j.1365-2311.2007.00976.x},
file = {:Users/Ty/Documents/Mendeley Desktop/Forkner et al.{\_}2008{\_}Timing is everything Phenological synchrony and population variability in leaf-chewing herbivores of Quercus.pdf:pdf},
journal = {Ecological {\ldots}},
keywords = {budburst,lepidoptera,plant phenology,population dynamics,quercus},
pages = {276--285},
title = {{Timing is everything ? Phenological synchrony and population variability in leaf-chewing herbivores of Quercus}},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2311.2007.00976.x/full},
volume = {33},
year = {2008}
}
@article{Tuff2009,
author = {Tuff, Ty},
file = {:Users/Ty/Documents/Mendeley Desktop/Tuff{\_}2009{\_}EBIO Phenology grant.pdf:pdf},
journal = {North},
title = {{EBIO Phenology grant}},
year = {2009}
}
@article{Schleip2008a,
author = {Schleip, Christoph and Rutishauser, This and Luterbacher, J{\"{u}}rg and Menzel, Annette},
doi = {10.1029/2007JG000646},
file = {:Users/Ty/Documents/Mendeley Desktop/Schleip et al.{\_}2008{\_}Time series modeling and central European temperature impact assessment of phenological records over the last 250(2).pdf:pdf;:Users/Ty/Documents/Mendeley Desktop/Schleip et al.{\_}2008{\_}Time series modeling and central European temperature impact assessment of phenological records over the last 250 ye.pdf:pdf},
issn = {0148-0227},
journal = {Journal of Geophysical Research},
month = {dec},
number = {G4},
pages = {1--13},
title = {{Time series modeling and central European temperature impact assessment of phenological records over the last 250 years}},
url = {http://www.agu.org/pubs/crossref/2008/2007JG000646.shtml},
volume = {113},
year = {2008}
}
@article{Wilczek2010a,
annote = {-under climate change --
- spring phenological events have advanced far further and more consistently than autumn events.
- disrupted trophic interactions as different taxa respond differently to warming.
- there are studies linking phenology shifts to extinction vs. persistence 
- plants develop faster in the spring if they have experience a colder winter. 
-- they have a good figure that looks like mine for day length plus one for temp.
- precipitation my help determine the length of the growing season (my thought, not fact) more than just the date of starting. 
- these guys are hinting at some of my ideas.
- specific genetic pathways (like the axis in birds) well known in Arabidopsis thaliana







- photoperiod pathways among the most ancient genes in plants. 
- look up -{\textgreater} external coincidence model
- though many of the phenology genes are highly conserved, the genes regulating the interpretation and interaction with environmental cues may be species or group specific.
- look up -{\textgreater} orthologous genes
- got to section 4(b) and gave up due to boredum. suggest finishing sometime.},
author = {Wilczek, AM},
doi = {10.1098/rstb.2010.0128},
file = {:Users/Ty/Documents/Mendeley Desktop/Wilczek{\_}2010{\_}Genetic and physiological bases for phenological responses to current and predicted climates.pdf:pdf},
issn = {0962-8436},
journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
keywords = {genetic architecture,life-history evolution,local adaptation,phenology,seasonal timing},
month = {sep},
number = {1555},
pages = {3129--3147},
title = {{Genetic and physiological bases for phenological responses to current and predicted climates}},
url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2010.0128 http://rstb.royalsocietypublishing.org/content/365/1555/3129.short},
volume = {365},
year = {2010}
}
@article{Post2008,
author = {Post, E.S. and Pedersen, C. and Wilmers, C.C. and Forchhammer, M.C.},
file = {:Users/Ty/Documents/Mendeley Desktop/Post et al.{\_}2008{\_}Phenological sequences reveal aggregate life history response to climatic warming.pdf:pdf},
journal = {Ecology},
keywords = {arctic,betula nana,cerastium alpinum,climate change,global warming,phenology,salix},
number = {2},
pages = {363--370},
publisher = {Eco Soc America},
title = {{Phenological sequences reveal aggregate life history response to climatic warming}},
url = {http://www.esajournals.org/doi/abs/10.1890/06-2138.1},
volume = {89},
year = {2008}
}
@article{Kudo2008,
author = {Kudo, Gaku and Ida, Takashi Y. and Tani, Tomokazu},
file = {:Users/Ty/Documents/Mendeley Desktop/Kudo, Ida, Tani{\_}2008{\_}Linkages Between Phenology, Pollination, Photosynthesis, and Reproduction in Deciduous Forest Understory Plants.pdf:pdf},
journal = {Ecology},
keywords = {deciduous forest,flowering phenology,fruit set,light availability,photosynthetic rate,pollination,seasonal dynamics,understory herbs},
number = {2},
pages = {321--331},
title = {{Linkages Between Phenology, Pollination, Photosynthesis, and Reproduction in Deciduous Forest Understory Plants.}},
volume = {89},
year = {2008}
}
@article{Visser2005,
author = {Visser, Marcel E and Both, Christiaan},
doi = {10.1098/rspb.2005.3356},
file = {:Users/Ty/Documents/Mendeley Desktop/Visser, Both{\_}2005{\_}Shifts in phenology due to global climate change the need for a yardstick Shifts in phenology due to global climate c.pdf:pdf},
journal = {B, Proc R Soc},
keywords = {climate change,food chains,mistiming,phenology},
number = {October 2009},
pages = {2561--2569},
title = {{Shifts in phenology due to global climate change : the need for a yardstick Shifts in phenology due to global climate change : the need for a yardstick}},
year = {2005}
}
@article{Neill2008,
author = {Neill, J D and Keith, D A and Akgakaya, H R and Rafter, M A and Railsback, B L and Rylands, A B and Mitteimeier, R A and Mittemeier, C G},
file = {:Users/Ty/Documents/Mendeley Desktop/Neill et al.{\_}2008{\_}reference list.pdf:pdf},
journal = {Sciences-New York},
title = {reference list},
year = {2008}
}