MOLECULAR PHYLOGENETICS AND EVOLUTION 致力于让达尔文的梦想触手可及——“拥有每个伟大自然王国的相当真实的系谱树。”该杂志为分子研究提供了一个论坛，促进我们对系统发育和进化的理解，进一步发展系统发育学上更准确的分类学分类，并最终为所有分支的生命线带来统一的分类。如果系统地理学研究提供了卓越的理论或经验进展，将考虑出版。

Molecular Phylogenetics and Evolution is dedicated to making Darwin's dream a reality—"to have a reasonably accurate phylogenetic tree for every great kingdom of nature." This journal provides a forum for molecular research, enhancing our understanding of phylogenetics and evolution, advancing more accurate taxonomic classifications in phylogenetics, and ultimately providing a unified classification for all branches of life. Research in systematic biogeography that offers significant theoretical or empirical advancements will be considered for publication.

《Molecular Phylogenetics and Evolution》致力于实现达尔文的梦想——“拥有每个伟大自然王国的真实系谱树。”该杂志为分子研究提供了一个论坛，促进我们对系统发育和进化的理解，推动系统发育学上更准确的分类学发展，并最终为所有生命的分支提供统一的分类。如果系统地理学研究在理论或经验上有显著进展，将考虑发表相关成果。

Molecular Phylogenetics and Evolution

Ginkgo biloba is one of the most famous and therefore intensively studied living fossils. The Ginkgoaceae was suggested to have originated in the early Permian approximately 280mya, and at the height of their worldwide radiation consisted of least 16 genera that were distributed in temperate forests. However, China's G. biloba is the only species of this genus which has survived until today. Using a phylogeographical approach we analyzed the history of this remnant from the past. G. biloba is native to China and has been distributed less than 300 years ago by humans throughout all temperate regions of the world. Separate from this human influence, native Chinese populations of G. biloba have been affected by the cycles of glaciation and deglaciation of the Pleistocene era, similar to many other global plant species. We used molecular markers from the nuclear (AFLPs) and plastid genomes (trnK intron, trnS-trnG intergenic spacer), and based on these data, glacial survival of Gingko populations within two refugia in Southwestern and Eastern China, respectively, is suggested. Specifically, for the first time, this study provides evidence of the existence of a refuge area in Eastern China on the West Tianmu Mountains. We can not support any extensive postglacial range expansion from these refuge areas. Furthermore, AFLP data indicate substantial genetic differentiation among populations from Southwestern, Eastern and Central China. We also hypothesize that this evidence supports that as a long-lived dioecious plant, G. biloba displays high levels of intra-populational genetic diversity that have been maintained in most populations, regardless if they are native or reforested stands. Furthermore, we provide evidence that planted trees from Europe, Japan, Korea and America were introduced multiple times from Eastern China.

Wei Gong

Chuan Chen

Christoph Dobes

Cheng-Xin Fu

Marcus A Koch

Molecular phylogenetics and evolution

Mol Phylogenet Evol

Phylogeography of a living fossil: pleistocene glaciations forced Ginkgo biloba L. (Ginkgoaceae) into two refuge areas in China with limited subsequent postglacial expansion.

Stag beetles (family Lucanidae Latreille, 1804) are one of the earliest branching lineages of scarab beetles that are characterized by the striking development of the male mandibles. Despite stag beetles' popularity among traditional taxonomists and amateur collectors, there has been almost no study of lucanid relationships and evolution. Entomologists, including Jeannel (1942), have long recognized resemblance between the austral stag beetles of the tribes Chiasognathini, Colophonini, Lamprimini, Pholidotini, Rhyssonotini, and Streptocerini, but this hypothesis of their close relationship across the continents has never been tested. To gain further insight into lucanid phylogeny and biogeography, we reconstructed the first molecular phylogeny of world stag beetles using DNA sequences from mitochondrial 16S rDNA, nuclear 18S and 28S rDNA, and the nuclear protein-coding (NPC) gene wingless for 93 lucanid species representing all extant subfamilies and 24 out of the 27 tribes, together with 14 representative samples of other early branching scarabaeoid families and two staphyliniform beetle families as outgroups. Both Bayesian inference (BI) and maximum likelihood inference (MLI) strongly supported the monophyly of Lucanidae sensu lato that includes Diphyllostomatidae. Within Lucanidae sensu stricto, the subfamilies Lucaninae and Lampriminae appeared monophyletic under both methods of phylogenetic inferences; however, Aesalinae and Syndesinae were found to be polyphyletic. A time-calibrated phylogeny based on five fossil data estimated the origin of crown group Lucanidae as circa 160 million years ago (MYA). Divergence between the Neotropical and Australasian groups of the Chiasognathini was estimated to be circa 47MYA, with the South African Colophonini branching off from the ancient Chiasognathini lineage around 87MYA. Another Gondwanan relationship was recovered between the Australasian Eucarteria and the Neotropical Casignetus, which diverged circa 58MYA. Lastly, as Jeannel's hypothesis predicted, divergence within Lampriminae between the Australasian Lamprima and the Neotropical Streptocerus was estimated to be circa 37MYA. The split of these lineages were generally concordant with the pattern of continental break-up of the super-continent Gondwana, and our biogeographic reconstructions based on the dispersal-extinction-cladogenesis model (DEC) corroborate our view that the divergences in these austral lineages were caused by vicariance events following the Gondwanan break-up. In addition, the phylogenetic position and geographic origin of the Hawaiian genus Apterocyclus was revealed for the first time. Overall, our results provide the framework toward studying lucanid relationships and divergence time estimates, which allowed for more accurate biogeographic explanations and discussions on ancestral lucanids and the evolutionary origin of the enlarged male mandibles.

Sang Il Kim

Brian D Farrell

Phylogeny of world stag beetles (Coleoptera: Lucanidae) reveals a Gondwanan origin of Darwin's stag beetle.

世界锹甲虫（鞘翅目：Lucanidae）的系统发育揭示了达尔文锹甲虫的冈瓦纳起源。

Inversions of the origin of replication (ORI) in mitochondrial genomes produce asymmetrical mutational pressures that can cause strong base composition skews. Due to skews often being overlooked, the total number of crustacean lineages that underwent ORI events remains unknown. We analysed skews, cumulative skew plots, conserved sequence motifs, and mitochondrial architecture of all 965 available crustacean mitogenomes (699 unique species). We found indications of an ORI in 159 (22.7%) species, and mapped these to 23 ORI events: 16 identified with confidence and 7 putative (13 newly proposed, and for 5 we improved the resolution). Two ORIs occurred at or above the order level: Isopoda and Copepoda. Shifts in skew plots are not a precise tool for identifying the replication mechanism. We discuss how ORIs can produce mutational bursts in mitogenomes and show how these can interfere with various types of evolutionary studies. Phylogenetic analyses were plagued by artefactual clustering, and ORI lineages exhibited longer branches, a higher number of synonymous substitutions, higher mutational saturation, and higher compositional heterogeneity. ORI events also affected codon usage and protein properties. We discuss how this may have caused erroneous interpretation of data in previous studies that did not account for skew patterns.

Ivan Jakovlić

Hong Zou

Xu-Mao Zhao

Jin Zhang

Gui-Tang Wang

Dong Zhang

Evolutionary history of inversions in directional mutational pressures in crustacean mitochondrial genomes: Implications for evolutionary studies.

甲壳类线粒体基因组中倒位在定向突变压力下的演化历史：对进化研究的启示。

We announce the release of Reconstruct Ancestral State in Phylogenies (RASP), a user-friendly software package for inferring historical biogeography through reconstructing ancestral geographic distributions on phylogenetic trees. RASP utilizes the widely used Statistical-Dispersal Vicariance Analysis (S-DIVA), the Dispersal-Extinction-Cladogenesis (DEC) model (Lagrange), a Statistical DEC model (S-DEC) and BayArea. It provides a graphical user interface (GUI) to specify a phylogenetic tree or set of trees and geographic distribution constraints, draws pie charts on the nodes of a phylogenetic tree to indicate levels of uncertainty, and generates high-quality exportable graphical results. RASP can run on both Windows and Mac OS X platforms. All documentation and source code for RASP is freely available at http://mnh.scu.edu.cn/soft/blog/RASP.

Yan Yu

Alan J Harris

Christopher Blair

Xingjin He

RASP (Reconstruct Ancestral State in Phylogenies): a tool for historical biogeography.

RASP（在系统发育中重建祖先状态）：历史生物地理学工具。

In this study, mitochondrial sequences were used to investigate the relationships among the major lineages of Arthropoda. The data matrix used for the analyses includes 84 taxa and 3918 nucleotides representing six mitochondrial protein-coding genes (atp6 and 8, cox1-3, and nad2). The analyses of nucleotide composition show that a reverse strand-bias, i.e., characterized by an excess of T relative to A nucleotides and of G relative to C nucleotides, was independently acquired in six different lineages of Arthropoda: (1) the honeybee mite (Varroa), (2) Opisthothelae spiders (Argiope, Habronattus, and Ornithoctonus), (3) scorpions (Euscorpius and Mesobuthus), (4) Hutchinsoniella (Cephalocarid), (5) Tigriopus (Copepod), and (6) whiteflies (Aleurodicus and Trialeurodes). Phylogenetic analyses confirm that these convergences in nucleotide composition can be particularly misleading for tree reconstruction, as unrelated taxa with reverse strand-bias tend to group together in MP, ML, and Bayesian analyses. However, the use of a specific model for minimizing effects of the bias, the "Neutral Transition Exclusion" (NTE) model, allows Bayesian analyses to rediscover most of the higher taxa of Arthropoda. Furthermore, the analyses of branch lengths suggest that three main factors explain accelerated rates of substitution: (1) genomic rearrangements, including duplication of the control region and gene translocation, (2) parasitic lifestyle, and (3) small body size. The comparisons of Bayesian Bootstrap percentages show that the support for many nodes increases when taxa with long branches are excluded from the analyses. It is therefore recommended to select taxa and genes of the mitochondrial genome for inferring phylogenetic relationships among arthropod lineages. The phylogenetic analyses support the existence of a major dichotomy within Arthropoda, separating Pancrustacea and Paradoxopoda. Basal relationships between Pancrustacean lineages are not robust, and the question of Hexapod monophyly or polyphyly cannot be answered with the available mitochondrial sequences. Within Paradoxopoda, Chelicerata and Myriapoda are each found to be monophyletic, and Endeis (Pycnogonida) is, surprisingly, associated with Acari.

Alexandre Hassanin

Phylogeny of Arthropoda inferred from mitochondrial sequences: strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution.

基于线粒体序列的节肢动物系统发育：限制模式和替换速率多次变化误导效应的策略。

Alexander A. Stewart

John J. Wiens

A time-calibrated salamander phylogeny including 765 species and 503 genes

一个包含765个物种和503个基因的时间校准蝾螈系统发育树

Silas Bossert

Felipe V. Freitas

Alain Pauly

Gengping Zhu

David W. Crowder

Michael C. Orr

James B. Dorey

Elizabeth A. Murray

Phylogeny, antiquity, and niche occupancy of Trinomia (Hymenoptera: Halictidae), an Afrotropical endemic genus of Nomiinae

三新属（膜翅目：准蜂科）的系统发育、古老性及生态位占据：一个非洲热带特有的诺米蜂亚科属

The family-level placement of the species Pacificana cockayni Hogg, 1904 (Araneae, Miturgidae) has been ambiguous for over a century, with the monotypic genus initially placed in Agelenidae, later transferred to Amaurobioidinae (Anyphaenidae), and presently in Miturgidae. A recent work describing the male and molecular data consisting of a single mitochondrial gene, cytochrome c oxidase subunit I, confirmed that the species is part of the marronoid clade; however, these data did not result in conclusive family-level placement. Here, we use low-coverage whole genome sequencing (lcWGS) combined with data from the Sequence Read Archive to infer a phylogeny from ultraconserved elements (UCEs) and six legacy Sanger loci. Indications of potential family placements from prior work and the topologies from this study support a transfer of Pacificana Hogg, 1904 to Cycloctenidae Simon, 1898 (new family placement).

Jacob A Gorneau

Franklyn Cala-Riquelme

Sarah C Crews

Katherine O Montana

Joseph C Spagna

Cor J Vink

Lauren A Esposito

Mystery on the Bounty: The family-level status of Pacificana cockayni Hogg, 1904 (Araneae)

赏金之谜：太平洋纳科卡克尼（Hogg, 1904）（蜘蛛目）的科级地位

Qi Chen

Min Deng

Xuan Dai

Wei Wang

Xing Wang

Liu-Sheng Chen

Guo-Hua Huang

Retraction notice to “Phylogenomic data exploration with increased sampling provides new insights into the higher-level relationships of butterflies and moths (Lepidoptera)” [Mol. Phylogenet. Evol. 197 (2024) 108113]

撤稿通知：“通过增加采样对蝴蝶和蛾类（鳞翅目）的高级关系进行系统基因组数据探索的新见解” [分子系统发育与进化 197 (2024) 108113]

In the present study, we used DNA sequences from three mitochondrial (COI, Cytb, and nd2) and one nuclear (RAG2) marker, to perform species delimitation analyses (ABGD, GMYC, BPP, and bPTP) within Sturisoma to test the validity of currently recognized and potential new species for the genus. Additionally, a historical biogeographic analysis was carried out to test the age and centers of origin for species of the genus. Results found here indicate a high degree of genetic divergence with overlapping morphological characteristics suggesting a greater diversity than previously proposed for the genus. All valid species currently included in Sturisoma were confirmed here, and one potentially undescribed species was recovered. Based on genetic distances, geographical patterns and historical biogeography, the diversification of the group could be related to dispersal events from Western to Eastern Amazonia resulting in sympatric species that are highly divergent genetically but conservative morphologically. The lower (eastern) Amazonas and the Orinoco River basins were identified as the main centers of origin for the genus, with an approximate age of origin of 13 Mya, during the Miocene. The diversity of the genus is likely to be even higher because the Amazon River is a hotspot of hidden biodiversity.

Alejandro Londoño-Burbano

Marcelo R Britto

Species delimitation and historical biogeography of Sturisoma Swainson, 1838 (Loricariidae: Loricariinae): Hidden diversity along the Amazon River

Sturisoma Swainson, 1838（甲鲶科：甲鲶亚科）的物种界定与历史生物地理学：亚马孙河流域的隐匿多样性

Abbreviation	Mol. Phylogenet. Evol.
Journal Impact	3.79
Quartiles(Global)	GENETICS & HEREDITY(Q2)

ISSN	1055-7903, 1095-9513
h-index	177
Top Journals	Yes

Publication Information	Publisher: Academic Press Inc.，Publishing cycle: Monthly，Journal Type: journal，Open Access Journals: No
Basic data	Year of publication: 1992，Proportion of original research papers: 99.04%，Self Citation Rate:11.10%， Gold OA Rate: 31.95%
Average review cycle	网友分享经验：平均12.0个月
Average recruitment ratio	网友分享经验：约37.5%

Molecular Phylogenetics and Evolution

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