Target capture has emerged as an important tool for phylogenetics and population genetics in nonmodel taxa. Whereas developing taxon‐specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly developed target capture set for Bromeliaceae, a large and ecologically diverse plant family with highly variable diversification rates. The set targets 1776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon‐specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon‐specific set results in higher enrichment success across the entire family; however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, for example the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon‐specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.

Aim: Understanding patterns of tropical plant diversity and their vulnerability to anthropogenic disturbance at different spatial scales remains a great challenge in ecology and conservation. Here, we study how the effects of forest-use intensity on vascular epiphyte diversity vary along a tropical elevational gradient.Location: 3,500-m elevational gradient along the eastern slopes of Cofre de Perote, Mexico. Methods:We studied the effects of forest-use intensity on alpha, beta and gamma diversity of vascular epiphyte assemblages in old-growth, degraded and secondary forests at eight study sites at 500-m intervals along the elevational gradient. At each elevation and in each of the three forest-use intensity levels, we established five 400-m 2 plots yielding a total of 120 plots.Results: Interactive effects of elevation and forest-use intensity strongly impacted local-scale patterns of vascular epiphyte diversity. Species diversity peaked at 500 as well as 1,500 m above sea level, which deviates from the previously reported humpshaped pattern. In most cases, alpha diversity did not differ significantly among forest-use intensity levels. However, gamma diversity was always lower in secondary forests compared to old-growth forests across the entire elevational gradient. Within each elevational belt, beta diversity was dominated by species turnover along the forest-use intensity gradient in the lowlands and declined with increasing elevation, where community composition became increasingly nested. Along the elevational gradient, the spatial turnover of vascular epiphyte community composition was similar among forest-use intensity levels. Main conclusions:Our results reveal a strong interaction between forest-use intensity and elevation, making it difficult to extrapolate findings from one elevational belt to another. Our findings highlight the value of old-growth forest for epiphyte diversity, but also show that degraded and secondary forests-depending on the elevational belt-may maintain a high species diversity and thus play an important role in conservation planning.

Vascular epiphytes are a diverse and conspicuous component of biodiversity in tropical and subtropical forests. Yet, the patterns and drivers of epiphyte assemblages are poorly studied in comparison with soil-rooted plants. Current knowledge about diversity patterns of epiphytes mainly stems from local studies or floristic inventories, but this information has not yet been integrated to allow a better understanding of large-scale distribution patterns. EpIG-DB, the first database on epiphyte assemblages at the continental scale, resulted from an exhaustive compilation of published and unpublished inventory data from the Neotropics. The current version of EpIG-DB consists of 463,196 individual epiphytes from 3,005 species, which were collected from a total of 18,148 relevés (host trees and 'understory' plots). EpIG-DB reports the occurrence of 'true' epiphytes, hemiepiphytes and nomadic vines, including information on their cover, abundance, frequency and biomass. Most records (97%) correspond to sampled host trees, 76% of them aggregated in forest plots. The data is stored in a TURBOVEG database using the most up-to-date checklist of vascular epiphytes. A total of 18 additional fields were created for the standardization of associated data commonly used in epiphyte ecology (e.g. by considering different sampling methods). EpIG-DB currently covers six major biomes across the whole latitudinal range of epiphytes in the Neotropics but welcomes data globally. This novel database provides, for the first time, unique biodiversity data on epiphytes for the Neotropics and unified guidelines for future collection of epiphyte data. EpIG-DB will allow exploration of new ways to study the community ecology and biogeography of vascular epiphytes. K E Y W O R D S biodiversity, community ecology, database, forest plot, hemiepiphytes, Neotropics, nomadic vines, taxonomic diversity, vascular epiphytes, vegetation relevé 520 |

QuestionLand‐use change and intensification are currently the most pervasive threats to tropical biodiversity. Yet, their effects on biodiversity change with elevation are unknown. Here, we examine how tree diversity and community composition vary with elevation and how the effects of forest use intensity on tree diversity and community composition change within elevations.LocationEastern slopes of the Cofre de Perote mountain, state of Veracruz, Mexico.MethodsWe assessed tree diversity and composition using a sampling design in which elevation was crossed with three levels of forest use intensity: old‐growth, degraded, and secondary forests. We established 120 20 m × 20 m forest plots, located at eight sites between 0 m and 3,545 m. At each site, five replicate plots were inventoried for each level of forest use intensity.ResultsOur analyses revealed an interactive effect between elevation and forest use intensity affecting tree diversity and community composition along the elevational gradient. Contrasting effects of forest use intensity within elevation resulted in tree diversity following a low‐plateau pattern for old‐growth and a bimodal pattern for degraded and secondary forests. Along the entire elevational gradient, there were 217 tree species distributed within 154 genera and 80 families. Species accumulation curves revealed that forests at 0 m and 1,500 m elevation showed differences in species richness among forest use intensities. In contrast, species richness did not differ between old‐growth forest and the other forest use intensities in five of the eight studied elevations. In terms of community composition, secondary forests differed from old‐growth and degraded forests.ConclusionOur results suggest that the interactive effects of elevation and forest use intensity change tree diversity patterns and community composition along a tropical elevational gradient. Degraded forests were similar to old‐growth forests in terms of species diversity and composition, suggesting that they may act as a safeguard of tree diversity in human‐dominated tropical landscapes.

Target capture emerged as an important tool for phylogenetics and population genetics in non-model taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly-developed target capture set for Bromeliaceae, a large and ecologically-diverse plant family with highly variable diversification rates. The set targets 1,776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon-specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon-specific set results in higher enrichment success across the entire family. However, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, e.g. the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon-specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.