Exploring the Concept of Lineage Diversity across North American Forests

Abstract

Lineage diversity can refer to the number of genetic lineages within species or to the number of deeper evolutionary lineages, such as genera or families, within a community or assemblage of species. Here, we study the latter, which we refer to as assemblage lineage diversity (ALD), focusing in particular on its richness dimension. ALD is of interest to ecologists, evolutionary biologists, biogeographers, and those setting conservation priorities, but despite its relevance, it is not clear how to best quantify it. With North American tree assemblages as an example, we explore and compare different metrics that can quantify ALD. We show that both taxonomic measures (e.g., family richness) and Faith’s phylogenetic diversity (PD) are strongly correlated with the number of lineages in recent evolutionary time, but have weaker correlations with the number of lineages deeper in the evolutionary history of an assemblage. We develop a new metric, time integrated lineage diversity (TILD), which serves as a useful complement to PD, by giving equal weight to old and recent lineage diversity. In mapping different ALD metrics across the contiguous United States, both PD and TILD reveal high ALD across large areas of the eastern United States, but TILD gives greater value to the southeast Coastal Plain, southern Rocky Mountains and Pacific Northwest, while PD gives relatively greater value to the southern Appalachians and Midwest. Our results demonstrate the value of using multiple metrics to quantify ALD, in order to highlight areas of both recent and older evolutionary diversity.

Evolutionary Diversity Peaks at Mid-Elevations Along an Amazon-to-Andes Elevation Gradient

“…The nuanced variation observed between PD and TILD is likely to be associated with the way each metric weights the different evolutionary depths. TILD gives equal weight to diversity across all the evolutionary depths of a phylogeny, while PD gives greater weight to more-recently diverged lineages (Dexter et al, 2019). Basically, the contrast in results between TILD and PD show that older evolutionary lineages (picked up by TILD, but not represented well by PD) are present across a broad range of elevations and only really drop out at the extremes of the gradient.…”

“…The elevational pattern for sesPD is a non-linear increase with elevation with a decrease at the highest elevations sampled (Figure 2C). However, it has been suggested that variation in standardized phylogenetic diversity metrics may be an artifact of variation in taxonomic richness (Sandel, 2018) and that sesPD may be a poor estimator of the richness dimension of diversity (Tucker et al, 2017;Dexter et al, 2019). These results must be put in the context of an analysis focused on trees.…”

“…(1) Faith's phylogenetic diversity (PD), the sum of all the branch lengths of a phylogeny for taxa in a community, including the root branch (Faith, 1992). PD is weighted toward diversity in recent evolutionary time (Dexter et al, 2019). (2) The standard effect size of phylogenetic diversity (sesPD), which is obtained by comparing the observed phylogenetic diversity versus.…”

“…Positive values of sesPD indicate greater phylogenetic diversity than expected given species richness, negative values indicate less diversity than expected. (3) time-integrated lineage diversity (TILD) which evenly weights phylogenetic diversity across recent and deep evolutionary time and is calculated by integrating the area under a lineage through time plot (sensu Yguel et al, 2016), after log-transforming the y-axis, or the number of lineages at each time point (Dexter et al, 2019). PD and sesPD were calculated using the "picante" package (Kembel et al, 2010), TILD was calculated using a new R function (Dexter et al, 2019; Supplementary Material).…”

“…In systems with complex climatic trends superimposed on elevation, such as tropical montane forests (TMF), the EDG is nuanced and not fully understood, particularly at middle elevations (Lieberman et al, 1996;Kessler, 2000;Nottingham et al, 2018). While many investigations of diversity variation focus on taxonomic measures such as, species richness, interest has expanded to include quantification of evolutionary diversity (e.g., Faith, 1992;Dexter et al, 2019), providing potential for a new temporal perspective to the EDG. Possible contrasts between evolutionary diversity and measures of current taxonomic richness have yet to be fully explored in the context of the EDG.…”