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., Di Febbraro, M., & Raia, P.(2018). A new method for testing evolutionary rate variation and shifts in phenotypic evolution. Methods in Ecology and Evolution, 9: 974-983.<doi:10.1111/2041-210X.12954>
multiple regression version of RRphylo
Serio, C., Castiglione, S., Tesone, G., Piccolo, M., Melchionna, M., Mondanaro, A., Di Febbraro, M., & Raia, P.(2019). Macroevolution of toothed whales exceptional relative brain size. Evolutionary Biology, 46: 332-342.<doi:10.1007/s11692-019-09485-7>
Melchionna, M., Mondanaro, A., Serio, C., Castiglione, S., Di Febbraro, M., Rook, L.,Diniz-Filho,J.A.F., 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<doi:10.1093/biolinnean/blz161>
Ancestral state integration in RRphylo (RRphylo-noder)
Castiglione, S., Serio, C., Mondanaro, A., Melchionna, M., Carotenuto, F., Di Febbraro, M., Profico, A., Tamagnini, D., & Raia, P. (2020). Ancestral State Estimation with Phylogenetic Ridge Regression. Evolutionary Biology, 47: 220-232.<doi:10.1007/s11692-020-09505-x>
search.trend
Castiglione, S., Serio, C., Mondanaro, A., Di Febbraro, M., 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. doi.org/10.1371/journal.pone.0210101
search.conv
Castiglione, S., Serio, C., Tamagnini, D., Melchionna, M., Mondanaro, A., Di Febbraro, M., 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.<doi:10.1371/journal.pone.0226949>
fix.poly
Castiglione, S., Serio, C., Piccolo, M., Mondanaro, A., Melchionna, M., Di Febbraro, M., 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.<doi: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, L.M., 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.<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.<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.<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},
doi = {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},
doi = {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},
doi = {10.1093/biolinnean/blz161},
}
@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},
doi = {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},
doi = {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},
doi = {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},
doi = {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},
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},
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},
doi = {10.1111/pala.12588},
}