DOI: 10.5061/dryad.gxd2547sq
title: Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales

description: The macroevolutionary processes that have shaped biodiversity across the
 temperate realm remain poorly understood and may have resulted from
 evolutionary dynamics related to diversification rates, dispersal rates,
 and colonization times, closely coupled with Cenozoic climate change. We
 integrated phylogenomic, environmental ordination, and macroevolutionary
 analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle
 the evolutionary processes that have contributed to high species diversity
 within and across temperate biomes. Our results show independent
 colonization of environmentally similar but geographically separated
 temperate regions mainly during the Oligocene, consistent with the global
 expansion of temperate biomes. High global, regional, and local temperate
 diversity was the result of high in situ diversification rates,
 rather than high immigration rates or accumulation time, except for
 Southern China, which was colonized much earlier than other regions. The
 relatively common lineage dispersals out of temperate hotspots highlights
 strong source-sink dynamics across the cosmopolitan distribution of
 Rhamnaceae. The proliferation of temperate environments since the
 Oligocene may have provided the ecological opportunity for rapid in situ
 diversification of Rhamnaceae across the temperate realm. Our study
 illustrates the importance of high in situ diversification rates for the
 establishment of modern temperate biomes and biodiversity hotspots across
 spatial scales.
description: We sampled 574 Rhamnaceae species, three species of Elaeagnaceae
 and one species each of Barbeyaceae and Dirachmaceae (Rosales). Leaf
 material was collected from the following herbaria: A, AD, BRI, CAS, F,
 KUN, MEL, MO, NY, OS, PERTH, TEX, and US as well as from the field. Total
 DNA was extracted using a modified CTAB method. We use
 hybridization enrichment sequencing (Hyb-seq) to capture 100 low-copy
 nuclear genes. Raw sequenced reads were cleaned and filtered as follows:
 Illumina adapter sequence artifacts were trimmed, low-quality reads were
 discarded, and low-quality read ends were trimmed using TRIMMOMATIC
 v0.32 . Assembly of the processed nuclear reads was performed using
 HybPiper v1.2. Each gene missing &gt; 75% of the sampled species was
 excluded. As a result, 89 loci were kept for further analysis.
 The sequences of each targeted gene region were initially aligned
 using MAFFT using default settings. To reduce errors in our alignments
 (i.e., gap-heavy and ambiguously aligned sites), we cleaned the original
 alignment of each gene using ‘pxclsq’ in phyx, removing alignment columns
 with &lt; 30% occupancy. Finally, we got 89 cleaned
 alignments.
description: # Rapid in-situ diversification rates in Rhamnaceae explain the parallel
 evolution of high diversity in temperate biomes from global to local
 scales ### Dataset
 Summary: The dataset pertains to the research on the "Rapid in situ
 diversification rates in Rhamnaceae explain the parallel evolution of high
 diversity in temperate biomes from global to local scales". It
 encompasses genetic information extracted from 574 Rhamnaceae species,
 along with three species of Elaeagnaceae and one species each of
 Barbeyaceae and Dirachmaceae (Rosales). Experimental Procedures and
 Results: * **Data Collection:** Leaf material was gathered from multiple
 herbaria and the field. Total DNA extraction was performed via a modified
 CTAB method. * **Sequencing and Processing:** Hybridization enrichment
 sequencing (Hyb-seq) was used to capture 100 low-copy nuclear genes. Raw
 sequenced reads underwent cleaning and filtering processes, which included
 trimming Illumina adapter sequence artifacts, discarding low-quality
 reads, and trimming low-quality read ends using TRIMMOMATIC v0.32.
 Assembly of processed nuclear reads was executed using HybPiper v1.2. Each
 gene missing &gt; 75% of the sampled species was excluded. As a result, 89
 loci were kept for further analysis. * **Sequence Alignment and
 Cleaning:** The sequences of 89 genes were aligned using MAFFT, following
 which the original alignments were cleaned to reduce errors, removing
 gap-heavy and ambiguously aligned sites. To reduce errors in our
 alignments (i.e., gap-heavy and ambiguously aligned sites), the original
 alignment of each gene was cleaned using ‘pxclsq’ in phyx, removing
 alignment columns with &lt; 30% occupancy. ### Description of Data
 Structure: The dataset consists of 89 cleaned alignments after processing.