Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales|植物进化数据集|遗传研究数据集

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 relat..., 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 > 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 site..., , # 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, discardi...