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Aim: Phylogenies are increasingly used in community ecology, biogeography and macroecology. However, sourcing a phylogeny comprising the entire species pool for a focal region can be difficult. Typically, a bespoke phylogeny must be created requiring considerable data manipulation and the use of many standalone software packages. Here we present a suite of methodological tools within the popular R environment that help to build molecular phylogenies appropriate for ecological studies with a regional focus. Innovation: Our R package regPhylo provides a pipeline to construct a Bayesian posterior distribution of time‐calibrated trees suitable to address ecological questions. The novel contributions of regPhylo include options to: use prior phylogenetic knowledge through flexible topological constraints; include spatial metadata in sourcing DNA sequences; and include taxa without DNA sequences and then infer consequent phylogenetic uncertainty. Specifically, regPhylo helps researchers: retrieve DNA sequences; enhance available metadata; select DNA sequences based on their length or spatial proximity to the region of study; align sequences; and perform quality control. Output from the pipeline is a file ready to run in the Bayesian tree reconstruction software beast2, appropriate for estimating time‐calibrated trees and including phylogenetic uncertainty for downstream analyses. Main conclusions: Overall, regPhylo improves the integration of popular standalone phylogenetic software into the flexible R environment. It provides a novel approach to include topological constraints based on prior knowledge, include taxa without DNA sequences, and select spatially appropriate DNA sequences. When coupled with a Bayesian tree‐building process, our approach provides estimates of uncertainty in both topology and branch lengths. We demonstrate the utility of the package by constructing a posterior distribution of time‐calibrated phylogenies for the New Zealand marine ray‐finned fishes (Actinopterygii) providing the unprecedented opportunity to include phylogenetic information in downstream ecological analyses for marine fishes in this region. [ABSTRACT FROM AUTHOR]

Aim Three broad mechanisms have been proposed to explain geographic variation in species range size: habitat area/heterogeneity, climate seasonality and long-term climate variability. However, it has proved difficult to disentangle their relative role, particularly as temperature seasonality often covaries with the amplitude of long-term temperature oscillations. Here, we shed new light onto this debate by providing the first continental-scale analysis of range size and beta diversity in groundwater habitats, where taxa are not exposed to latitudinal variation in temperature seasonality. Location Europe. Methods We compiled and mapped occurrence data for 1570 groundwater crustacean species. Generalized regression models were used to test for latitudinal variation in geographic range size and to assess the relative role of the three broad mechanisms in shaping present-day patterns of range size. We partitioned beta diversity into its spatial turnover and nestedness components and analysed their latitudinal variation across Europe. Results Median range size increases with latitude above 43° N and the range size of individual species is positively correlated to latitude, even after accounting for phylogenetic effects. Long-term temperature variability accounted for a substantially higher variation in median range size of groundwater crustaceans across Europe than precipitation seasonality and habitat heterogeneity, including aquifer area, elevation range, climatic rarity and productive energy. Spatial turnover contributes significantly more to beta diversity in southern regions characterized by stable historic climates than it does in northern Europe. Main conclusions Our findings add support to the historic climate hypothesis which suggests that patterns of increasing range size and decreasing species turnover at higher latitudes in the Palaearctic region are primarily driven by long-term temperature oscillations rather than by climatic seasonality and the availability and heterogeneity of habitats. [ABSTRACT FROM AUTHOR]