Phylogenomics: A Primer
暫譯: 系統基因組學：入門指南

系統發育基因組學：入門（第二版）是為了進階本科生和研究生生物學學生而設，特別是那些學習分子生物學、比較生物學、演化學、基因組學和生物多樣性的學生。本書解釋了儲存和操作基因組數據的基本概念、系統發育樹的構建、族群遺傳學、自然選擇、生命之樹、DNA 條碼技術以及宏基因組學。每章中包含的問題解決練習使學生能夠深入理解現代生物學家面臨的重要分子和演化問題，以及解決這些問題所需的工具。

Rob DeSalle is Curator at the Sackler Institute of Comparative Genomics in the Division of invertebrate Zoology at the American Museum of Natural History. DeSalle works in molecular systematics, microbial evolution, and genomics. His current research concerns the development of bioinformatic tools to handle large-scale genomics problems using phylogenetic systematic approaches. Dr. DeSalle has worked closely with colleagues from Cold Spring Harbor Labs, New York University, and the New York Botanical Garden on seed plant genomics and development of tools to establish gene family membership on a genome- wide scale. His group also focuses on microbial genomics, taxonomy, and systematics. In particular, they approach tree-of-life questions concerning microbial life using whole genome information.

Jeffrey Rosenfeld is Assistant Professor for Pathology and Laboratory Medicine and Assistant Professor of Pathology and Laboratory Medicine at the Robert Wood Johnson Medical School of Rutgers, The State University of New Jersey. He has extensive experience in the analysis of next-generation sequencing data. His doctoral research resulted in one of the earliest papers on ChIP-seq utilizing Illumina sequencing. He also performed an extensive analysis of the function of the H3K9me3 histone modification. After completing his doctorate, Dr. Rosenfeld began working as a research scientist in the laboratory of Dr. Todd Lencz at Zucker Hillside Hospital. He was in charge of all nextgeneration sequencing analysis at the hospital including family-based exome sequencing and RNA-seq of cerebrospinal fluid (CSF). He has studied the occurrence of multiple nucleotide polymorphisms (MNP) in the human genome and is supervising the study of non-traditional human variants such as MNPs and polymorphic SNPs for the 1000 Genomes Project. Recently, Dr. Rosenfeld joined the High Performance and Research Computing group at UMDNJ and he is playing a key role in assisting researchers across the university in processing their next-generation sequencing data. Dr. Rosenfeld also has an appointment as a Research Associate at the American Museum of Natural History where he works on whole-genome phylogenetics.

Michael Tessler is Adjunct Faculty in Ecology at Sterling College. He received his PhD from the Richard Gilder Graduate School, American Museum of Natural History. His research explores the evolution and ecology of overlooked organisms and includes phylogenetic research on terrestrial leeches, combining his collections from China and Cambodia with AMNH's legacy collections to produce a phylogenetic revision of all terrestrial leech groups. His dissertation focused on the evolution of leech anticoagulants and on how leeches process difficult to digest blood such as urea-packed shark blood, and the ways anticoagulants evolved in leech lineages that no longer drink blood and instead eat invertebrates.

**Rob DeSalle** 是美國自然歷史博物館無脊椎動物動物學部薩克勒比較基因組學研究所的策展人。DeSalle 專注於分子系統學、微生物進化和基因組學。他目前的研究涉及開發生物信息學工具，以使用系統發生學方法處理大規模基因組問題。DeSalle 博士與來自冷泉港實驗室、紐約大學和紐約植物園的同事密切合作，研究種子植物的基因組學以及開發工具以在全基因組範圍內確定基因家族成員。他的團隊還專注於微生物基因組學、分類學和系統學。特別是，他們使用全基因組信息來探討有關微生物生命的生命樹問題。

**Jeffrey Rosenfeld** 是羅伯特·伍德·約翰遜醫學院（Rutgers, The State University of New Jersey）病理學和實驗室醫學的助理教授。他在下一代測序數據分析方面擁有豐富的經驗。他的博士研究產生了利用 Illumina 測序的 ChIP-seq 早期論文之一。他還對 H3K9me3 組蛋白修飾的功能進行了廣泛的分析。完成博士學位後，Rosenfeld 博士開始在扎克醫院的 Todd Lencz 博士實驗室擔任研究科學家。他負責醫院內所有的下一代測序分析，包括基於家族的外顯子測序和腦脊髓液 (CSF) 的 RNA-seq。他研究了人類基因組中多核苷酸多態性 (MNP) 的出現，並監督 1000 基因組計畫中非傳統人類變異（如 MNP 和多態性 SNP）的研究。最近，Rosenfeld 博士加入了 UMDNJ 的高性能和研究計算小組，並在協助全校研究人員處理他們的下一代測序數據方面發揮了關鍵作用。Rosenfeld 博士還在美國自然歷史博物館擔任研究助理，從事全基因組系統發生學的研究。

**Michael Tessler** 是斯特林學院生態學的兼任教員。他在美國自然歷史博物館的理查德·吉爾德研究生院獲得博士學位。他的研究探索了被忽視生物的進化和生態，並包括對陸生水蛭的系統發生學研究，結合他在中國和柬埔寨的採集與 AMNH 的遺留收藏，對所有陸生水蛭群體進行系統發生學修訂。他的論文專注於水蛭抗凝劑的進化，以及水蛭如何處理難以消化的血液，例如含尿素的鯊魚血，以及抗凝劑在不再吸血而是以無脊椎動物為食的水蛭系譜中的進化方式。