分子系統(tǒng)遺傳學(xué)和進(jìn)化致力于使達(dá)爾文的夢想觸手可及——“擁有每個大自然王國相當(dāng)真實的系譜樹。”該雜志為分子研究提供了一個論壇，促進(jìn)我們對系統(tǒng)發(fā)育和進(jìn)化的理解，進(jìn)一步發(fā)展系統(tǒng)發(fā)育上更精確的分類，并最終為所有的分支生命線帶來統(tǒng)一的分類。如果系統(tǒng)地理學(xué)研究提供了特殊的理論或?qū)嵶C進(jìn)展，將考慮出版。該雜志鼓勵多學(xué)科的文章，特別是在領(lǐng)域，如生物信息學(xué)，計算生物學(xué)，分子生物學(xué)和有機(jī)體生物學(xué)，是有興趣的社區(qū)的系統(tǒng)和進(jìn)化生物學(xué)家。此外,報告新發(fā)現(xiàn)或見解的進(jìn)化過程和機(jī)制上表達(dá)了在分子水平上是受歡迎的,就像那些處理重建從分子進(jìn)化歷史數(shù)據(jù)的方法(如描述的新的或更強(qiáng)大的計算機(jī)算法從同源核苷酸或氨基酸序列構(gòu)建系統(tǒng)發(fā)育樹)。對分子進(jìn)化機(jī)制和過程的深入理解，將有助于建立更精確的分子進(jìn)化模型，從而有助于開發(fā)更好的算法，從序列數(shù)據(jù)重建進(jìn)化歷史。基于少數(shù)分類單元、單個分子標(biāo)記或使用基于密碼子的方法測試達(dá)爾文選擇陽性的論文，但在缺乏實驗證據(jù)的情況下，即所謂的選擇氨基酸變化導(dǎo)致適應(yīng)性表型效應(yīng)，將不被接受。

Molecular Phylogenetics and Evolution is dedicated to bringing Darwin's dream within grasp - to "have fairly true genealogical trees of each great kingdom of Nature." The journal provides a forum for molecular studies that advance our understanding of phylogeny and evolution, further the development of phylogenetically more accurate taxonomic classifications, and ultimately bring a unified classification for all the ramifying lines of life. Phylogeographic studies will be considered for publication if they offer EXCEPTIONAL theoretical or empirical advances.The journal encourages articles that are multidisciplinary, especially in areas, such as bioinformatics, computational biology, molecular biology, and organismic biology, that are of interest to the community of systematic and evolutionary biologists. In addition, presentations of new findings on or insights into evolutionary processes and mechanisms as expressed at the molecular level are welcome, as are those that deal with the methodology of reconstructing evolutionary history from molecular data (such as descriptions of new or more powerful computer algorithms for constructing phylogenetic trees from orthologous nucleotide or aminoacid sequences). A deeper understanding of the mechanisms and processes of molecular evolution should lead to more accurate models of molecular evolution, which in turn should facilitate the development of better algorithms for reconstructing evolutionary history from sequence data.Papers based on few taxa, single molecular markers, or that use codon-based methods to test for positive Darwinian selection, but in the absence of experimental evidence that allegedly selected amino acid changes cause an adaptive phenotypic effect, will not be accepted.