Site-Based Estimation of Ancestral Range of Species

Usage

calc_sbears(
  x,
  phy,
  coords,
  method = c("single_site", "disp_assembly"),
  w_slope = 5,
  min_disp_prob = 0.8,
  compute.node.by.sites = FALSE,
  make.node.label = FALSE
)

Arguments

x: Matrix object with community/assemblage composition. Rows represent sites and columns represents species.
phy: A phylogenetic tree of phylo class object.
coords: A rectangular object (it can be a matrix, data.frame or tibble) containing two columns, one with longitude and another with latitude coordinates in this order.
method: character indicating how ancestral range probabilities are computed. The options are "single_site" or "disp_assembly"
w_slope: A scalar representing the slope of the dispersal kernel function.
compute.node.by.sites: Logical, TRUE (default) computes a matrix of node occurrence by site.
make.node.label: Logical, if TRUE (default) the nodes of the phylogeny will be named as the letter "N" preceding node number

Value

a list with three elements. reconstruction is the result of ancestral . area reconstruction; phylogeny is the matrix containing the occurrence of nodes in sites and joint.phylo.obs is the joint occurrence of nodes and species in phylogenetic tree.

Details

SBEARS (Site-Based Estimation of Ancestral Range of Species) is a method for ancestral state reconstruction of species geographic ranges. It operates at fine spatial resolution and does not require predefined discrete biogeographic areas. The method estimates ancestral ranges under a maximum likelihood framework, using site-level occurrence information.

the method used to compute ancestral range probabilities can be single_site or disp_assembly. For both methods SBEARS use the function fastAnc to reconstruct the the ancestral ranges. In single_site each site is taken as a binary categorical trait representing the presence (state 1) or the absence (state 0) of every species in the site, which is reconstructed along the nodes of the phylogeny. In disp_assembly option the single site reconstruction is carried out, producing a matrix describing standardized probabilities of occurrence of each node at each site. The difference here is that an additional step is performed to compute the probability of a cell being colonized by an ancestral species originating from a focal cell. The probability of colonization decreases increasing the distance from the focal cell. This probability of an ancestral species to disperse from a cell to any other can be defined using a dispersal kernel function proposed by Gravel et al (2006).

References

Gravel D., Canhan C.D., Beaudet M. and Messier C. Reconciling niche and neutrality: the continuum hypothesis. 2006. Ecology Letters doi:10.1111/j.1461-0248.2006.00884.x