To cite RRphylo implementations and auxilliary functions in publications use:
RRphylo package, search.shift, and auxilliary functions
Castiglione S, Tesone G, Piccolo M, Melchionna M, Mondanaro A, Serio C, Febbraro MD, Raia P (2018). “A new method for testing evolutionary rate variation and shifts in phenotypic evolution.” Methods in Ecology and Evolution, 9, 974-983. https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12954.
multiple regression version of RRphylo
Serio C, Castiglione S, Tesone G, Piccolo M, Melchionna M, Mondanaro A, Febbraro MD, Raia P (2019). “Macroevolution of toothed whales exceptional relative brain size.” Evolutionary Biology, 46, 332-342. https://link.springer.com/article/10.1007/s11692-019-09485-7.
Melchionna M, Mondanaro A, Serio C, Castiglione S, Febbraro MD, Rook L, Diniz-Filho JA, Manzi G, Profico A, Sansalone G, Raia P (2020). “Macroevolutionary trends of brain mass in Primates.” Biological Journal of the Linnean Society, 129, 14-25. https://academic.oup.com/biolinnean/advance-article/doi/10.1093/biolinnean/blz161/5614248.
Ancestral state integration in RRphylo (RRphylo-noder)
Castiglione S, Serio C, Mondanaro A, Melchionna M, Carotenuto F, Febbraro MD, Profico A, Tamagnini D, Raia P (2020). “Ancestral State Estimation with Phylogenetic Ridge Regression.” Evolutionary Biology, 47, 220-232. https://link.springer.com/article/10.1007/s11692-020-09505-x.
search.trend
Castiglione S, Serio C, Mondanaro A, Febbraro MD, Profico A, Girardi G, Raia P (2019). “Simultaneous detection of macroevolutionary patterns in phenotypic means and rate of change with and within phylogenetic trees including extinct species.” PLoS ONE, 14, e0210101. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0210101.
search.conv
Castiglione S, Serio C, Tamagnini D, Melchionna M, Mondanaro A, Febbraro MD, Profico A, Piras P, Barattolo F, Raia P (2019). “A new, fast method to search for morphological convergence with shape data.” PLoS ONE, 14, e0226949. https://doi.org/10.1371/journal.pone.0226949.
fix.poly
Castiglione S, Serio C, Piccolo M, Mondanaro A, Melchionna M, Febbraro MD, Sansalone G, Wroe S, Raia P (2020). “The influence of domestication, insularity and sociality on the tempo and mode of brain size evolution in mammals.” Biological Journal of the Linnean Society, 132, 221-231. https://doi.org/10.1093/biolinnean/blaa186.
conv.map
Melchionna M, Profico A, Castiglione S, Serio C, Mondanaro A, Modafferi M, Tamagnini D, Maiorano L, Raia P, Witmer LM, Wroe S, Sansalone G (2021). “A method for mapping morphological convergence on three-dimensional digital models: the case of the mammalian sabre-tooth.” Palaeontology, 64, 573–584. https://onlinelibrary.wiley.com/doi/10.1111/pala.12542.
rate.map
Castiglione S, Melchionna M, Profico A, Sansalone G, Modafferi M, Mondanaro A, Wroe S, Piras P, Raia P (2021). “Human face-off: a new method for mapping evolutionary rates on three-dimensional digital models.” Palaeontology, 65, e12582. https://onlinelibrary.wiley.com/doi/10.1111/pala.12582.
tree.merger
Castiglione S, Serio C, Mondanaro A, Melchionna M, Raia P (2022). “Fast Production of Large, Time-Calibrated Informal Supertrees with tree.merger.” Palaeontology, 65, e12588. https://onlinelibrary.wiley.com/doi/10.1111/pala.12588.
Corresponding BibTeX entries:
@Article{,
title = {A new method for testing evolutionary rate variation and
shifts in phenotypic evolution.},
author = {Silvia Castiglione and Gianmarco Tesone and Martina
Piccolo and Marina Melchionna and Alessandro Mondanaro and
Carmela Serio and Mirko Di Febbraro and Pasquale Raia},
journal = {Methods in Ecology and Evolution},
year = {2018},
volume = {9},
pages = {974-983},
url =
{https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12954},
}
@Article{,
title = {Macroevolution of toothed whales exceptional relative
brain size.},
author = {Carmela Serio and Silvia Castiglione and Gianmarco Tesone
and Martina Piccolo and Marina Melchionna and Alessandro
Mondanaro and Mirko Di Febbraro and Pasquale Raia},
journal = {Evolutionary Biology},
year = {2019},
volume = {46},
pages = {332-342},
url =
{https://link.springer.com/article/10.1007/s11692-019-09485-7},
}
@Article{,
title = {Macroevolutionary trends of brain mass in Primates.},
author = {Marina Melchionna and Alessandro Mondanaro and Carmela
Serio and Silvia Castiglione and Mirko Di Febbraro and Lorenzo
Rook and José Alexandre Diniz-Filho and Giorgio Manzi and Antonio
Profico and Gabriele Sansalone and Pasquale Raia},
journal = {Biological Journal of the Linnean Society},
year = {2020},
volume = {129},
pages = {14-25},
url =
{https://academic.oup.com/biolinnean/advance-article/doi/10.1093/biolinnean/blz161/5614248},
}
@Article{,
title = {Ancestral State Estimation with Phylogenetic Ridge
Regression},
author = {Silvia Castiglione and Carmela Serio and Alessandro
Mondanaro and Marina Melchionna and Francesco Carotenuto and
Mirko Di Febbraro and Antonio Profico and Davide Tamagnini and
Pasquale Raia},
journal = {Evolutionary Biology},
year = {2020},
volume = {47},
pages = {220-232},
url =
{https://link.springer.com/article/10.1007/s11692-020-09505-x},
}
@Article{,
title = {Simultaneous detection of macroevolutionary patterns in
phenotypic means and rate of change with and within phylogenetic
trees including extinct species.},
author = {Silvia Castiglione and Carmela Serio and Alessandro
Mondanaro and Mirko Di Febbraro and Antponio Profico and Giorgia
Girardi and Pasquale Raia},
journal = {PLoS ONE},
year = {2019},
volume = {14},
pages = {e0210101},
url =
{https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0210101},
}
@Article{,
title = {A new, fast method to search for morphological convergence
with shape data.},
author = {Silvia Castiglione and Carmela Serio and Davide Tamagnini
and Marina Melchionna and Alessandro Mondanaro and Mirko Di
Febbraro and Antonio Profico and Paolo Piras and Filippo
Barattolo and Pasquale Raia},
journal = {PLoS ONE},
year = {2019},
volume = {14},
pages = {e0226949},
url = {https://doi.org/10.1371/journal.pone.0226949},
}
@Article{,
title = {The influence of domestication, insularity and sociality
on the tempo and mode of brain size evolution in mammals.},
author = {Silvia Castiglione and Carmela Serio and Martina Piccolo
and Alessandro Mondanaro and Marina Melchionna and Mirko Di
Febbraro and Gabriele Sansalone and Stephen Wroe and Pasquale
Raia},
journal = {Biological Journal of the Linnean Society},
year = {2020},
volume = {132},
pages = {221-231},
url = {https://doi.org/10.1093/biolinnean/blaa186},
}
@Article{,
title = {A method for mapping morphological convergence on
three-dimensional digital models: the case of the mammalian
sabre-tooth},
author = {Marina Melchionna and Antonio Profico and Silvia
Castiglione and Carmela Serio and Alessandro Mondanaro and Maria
Modafferi and Davide Tamagnini and Luigi Maiorano and Pasquale
Raia and Lawrence M. Witmer and Stephen Wroe and Gabriele
Sansalone},
journal = {Palaeontology},
year = {2021},
volume = {64},
pages = {573–584},
url = {https://onlinelibrary.wiley.com/doi/10.1111/pala.12542},
}
@Article{,
title = {Human face-off: a new method for mapping evolutionary
rates on three-dimensional digital models},
author = {Silvia Castiglione and Marina Melchionna and Antonio
Profico and Gabriele Sansalone and Maria Modafferi and Alessandro
Mondanaro and Stephen Wroe and Paolo Piras and Pasquale Raia},
journal = {Palaeontology},
year = {2021},
volume = {65},
pages = {e12582},
url = {https://onlinelibrary.wiley.com/doi/10.1111/pala.12582},
}
@Article{,
title = {Fast Production of Large, Time-Calibrated Informal
Supertrees with tree.merger},
author = {Silvia Castiglione and Carmela Serio and Alessandro
Mondanaro and Marina Melchionna and Pasquale Raia},
journal = {Palaeontology},
year = {2022},
volume = {65},
pages = {e12588},
url = {https://onlinelibrary.wiley.com/doi/10.1111/pala.12588},
}