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Increased microgastropoda sampling give new insights into the phylogenetic relationships of Littorinoidea (Littorinimorpha) 增加对微小腹足纲动物的取样,为了解 Littorinoidea(Littorinimorpha)的系统发育关系提供了新的视角。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-08 DOI: 10.1016/j.ympev.2024.108139

Littorinoidea is one of the most diverse radiations and the most successful group that evolutionary transitions from marine to terrestrial within Littorinimorpha. With such an unmatched diversity, few phylogenetic investigations have attempted to understand their evolutionary relationships, and existing research has primarily focused on typical intertidal species. To address this gap, we conducted the first phylogenomic analysis of the Littorinoidea, leveraging 35 transcriptomes to investigate their internal relationships. Our analyses revealed significant revisions necessary within the Littorinoidea: 1) Pomatias appears distantly related to Littorinidae, suggesting a potential ancestral origin outside of Littorinoidea, challenging traditional classification. The homology of penial innervation within Littorinoidea warrants reevaluation. 2) Lacuna’s placement indicates a close relationship with Naticidae, prompting consideration for its removal from Littorinidae. 3) Based on the current phylogenetic research, Peasiella may belong to a distinct family separate from Littorinidae. 4) Our findings support revising the placement of Pteropods within the Littorinimorpha, which is situated phylogenetically between the families Littorinoidea and Naticoidea. Additionally, we highlight the impact of site heterogeneity and evolutionary rate variation on phylogenetic inference. Our study provides a robust phylogenomic framework for the Littorinoidea, emphasizing the importance of including microgastropoda taxa in molecular phylogenetic reconstructions of gastropod subgroups.

Littorinoidea是Littorinimorpha中从海洋向陆地进化过渡最成功、最多样化的类群之一。由于其多样性无与伦比,很少有系统发育研究试图了解它们的进化关系,现有的研究主要集中在典型的潮间带物种上。为了填补这一空白,我们利用 35 个转录组研究了 Littorinoidea 的内部关系,首次进行了系统发生组分析。我们的分析揭示了Littorinoidea内部需要进行的重大修订:1)Pomatias似乎与Littorinidae关系疏远,表明其祖先可能起源于Littorinoidea之外,这对传统分类提出了挑战。Littorinoidea内阴茎神经支配的同源性值得重新评估。2) Lacuna 的位置表明其与 Naticidae 关系密切,因此应考虑将其从 Littorinidae 中剔除。3) 根据目前的系统发育研究,Peasiella 可能属于一个独立的科,与 Littorinidae 区分开来。4) 我们的研究结果支持修改翼足目在 Littorinimorpha 科中的位置,该科在系统发育上位于 Littorinoidea 科和 Naticoidea 科之间。此外,我们还强调了地点异质性和进化速度变化对系统发生推断的影响。我们的研究为腹足纲提供了一个稳健的系统发生学框架,强调了将小腹足纲类群纳入腹足亚群分子系统发生重建的重要性。
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引用次数: 0
The impact of geographic isolation and host shifts on population divergence of the rare cicada Subpsaltria yangi 地理隔离和寄主迁移对珍稀蝉类 "扬子蝉 "种群分化的影响。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-08 DOI: 10.1016/j.ympev.2024.108146
Yunxiang Liu , Christopher H. Dietrich , Cong Wei

The contributions of divergent selection and spatial isolation to population divergence are among the main focuses of evolutionary biology. Here we employed integrated methods to explore genomic divergence, demographic history and calling-song differentiation in the cicada Subpsaltria yangi, and compared the genotype and calling-song phenotype of different populations occurring in distinct habitats. Our results indicate that this species comprises four main lineages with unique sets of haplotypes and calling-song structure, which are distinctly associated with geographic isolation and habitats. The populations occurring on the Loess Plateau underwent substantial expansion at ∼0.130–0.115 Ma during the Last Interglacial. Geographic distance and host shift between pairs of populations predict genomic divergence, with geographic distance and acoustical signal together explaining > 60% of the divergence among populations. Differences in calling songs could reflect adaptation of populations to novel environments with different host plants, habitats and predators, which may have resulted from neutral divergence at the molecular level followed by natural selection. Geomorphic barriers and climate oscillations associated with Pleistocene glaciation may have been primary factors in shaping the population genetic structure of this species. Ultimately this may couple with a host shift in leading toward allopatric speciation in S. yangi, i.e., isolation by distance. Our findings improve understanding of divergence in allopatry of herbivorous insects, and may inform future studies on the molecular mechanisms underlying the association between genetic/phenotypic changes and adaptation of insects to novel niches and host plants.

分化选择和空间隔离对种群分化的贡献是进化生物学的重点之一。在此,我们采用综合方法探讨了蝉Subpsaltria yangi的基因组分化、人口历史和叫声分化,并比较了发生在不同栖息地的不同种群的基因型和叫声表型。我们的研究结果表明,该物种由四个主要品系组成,具有独特的单倍型和叫声结构,这些单倍型和叫声结构与地理隔离和栖息地有明显的关联。发生在黄土高原的种群在末次冰期的 0.130-0.115 Ma 之间经历了大幅扩张。成对种群之间的地理距离和宿主迁移预示着基因组的分化,地理距离和声学信号共同解释了种群间大于60%的分化。叫声的差异可能反映了种群对不同寄主植物、栖息地和捕食者的新环境的适应,这可能是分子水平的中性分化和自然选择的结果。与更新世冰川作用有关的地貌障碍和气候振荡可能是形成该物种种群遗传结构的主要因素。最终,这可能会与宿主的转变相结合,导致 S. yangi 的同域物种分化,即通过距离实现隔离。我们的发现加深了人们对食草昆虫异地种群分化的理解,并可能为今后研究昆虫基因/表型变化与适应新的生境和寄主植物之间联系的分子机制提供信息。
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引用次数: 0
A comprehensive molecular phylogeny of the terrestrial Parasitengona (Acariformes, Prostigmata) provides insights into the evolution of their metamorphosis, invasion into aquatic habitats and classification 陆生寄生天牛(蛛形纲,原尾目)的综合分子系统发育为了解其变态、入侵水生栖息地和分类的进化过程提供了见解。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-08 DOI: 10.1016/j.ympev.2024.108147
Samuel G.S. Costa , Andrei Tolstikov , Alireza Saboori , Dante Batista-Ribeiro , Javad Noei , Mark S. Harvey , Matthew D. Shaw , Pavel B. Klimov , Zhi-Qiang Zhang , Almir R. Pepato

Parasitengona (velvet mites, chiggers and water mites) is a highly diverse and globally distributed mite lineage encompassing over 11,000 described species, inhabiting terrestrial, freshwater and marine habitats. Certain species, such as chiggers (Trombiculidae), have a great medical and veterinary importance as they feed on their vertebrate hosts and vector pathogens. Despite extensive previous research, the classification of Parasitengona is still contentious, particularly regarding the boundaries between superfamilies and families, exacerbated by the absence of a comprehensive phylogeny. The ontogeny of most Parasitengona is distinct by the presence of striking metamorphosis, with parasitic larvae being heteromorphic compared to the predatory free-living deutonymphs and adults. The enigmatic superfamily Allotanaupodoidea is an exception, with larvae and active post-larval stages being morphologically similar, suggesting that the absence of metamorphosis may be either an ancestral state or a secondary reversal. Furthermore, there is disagreement in the literature on whether Parasitengona had freshwater or terrestrial origin. Here, we inferred phylogenetic relationships of Parasitengona (89 species, 36 families) and 307 outgroups using five genes (7,838 nt aligned). This phylogeny suggests a terrestrial origin of Parasitengona and a secondary loss of metamorphosis in Allotanaoupodoidea. We recovered the superfamily Trombidioidea (Trombidioidea sensu lato) as a large, well-supported, higher-level clade including 10 sampled families. We propose a new classification for the terrestrial Parasitengona with three new major divisions (epifamilies) of the superfamily Trombidioidea: Trombelloidae (families Audyanidae, Trombellidae, Neotrombidiidae, Johnstonianidae, Chyzeriidae); Trombidioidae (Microtrombidiidae, Neothrombiidae, Achaemenothrombiidae, Trombidiidae, Podothrombiidae); and Trombiculoidae (=Trombiculidae sensu lato). Adding them to previously recognized superfamilies Allotanaupodoidea, Amphotrombioidea, Calyptostomatoidea, Erythraeoidea, Tanaupodoidae and Yurebilloidae.

寄生螨(绒螨、恙螨和水螨)种类繁多,分布于全球各地,包括 11,000 多个已描述的物种,栖息于陆地、淡水和海洋栖息地。某些种类,如恙螨(Trombiculidae),以脊椎动物宿主和病原体媒介为食,因此在医学和兽医学方面具有重要意义。尽管之前进行了大量研究,但寄生虫分类仍存在争议,尤其是超科和科之间的界限,而缺乏全面的系统发育则加剧了这一争议。大多数寄生藤壶虫的本体发育都有显著的变态现象,寄生幼虫与捕食性的自由生活的脱虫和成虫相比具有异形性。神秘的超科 Allotanaupodoidea 是一个例外,其幼虫和活跃的后幼虫阶段在形态上相似,这表明没有变态可能是一种祖先状态,也可能是一种继发性逆转。此外,关于 Parasitengona 是起源于淡水还是陆地,文献中也存在分歧。在此,我们利用 5 个基因(7838 nt 对齐)推断了 Parasitengona(89 种,36 科)和 307 个外群的系统发生关系。该系统发育表明,Parasitengona起源于陆生,Allotanaoupodoidea次生失去了变态过程。我们复原了超科 Trombidioidea(Trombidioidea sensu lato),它是一个大型的、支持良好的、更高层次的支系,包括 10 个采样科。我们为陆生寄生虫提出了一个新的分类法,即在超科 Trombidioidea 中划分出三个新的主要分支(外科):Trombelloidae(Audyanidae科、Trombellidae科、Neotrombidiidae科、Johnstonianidae科、Chyzeriidae科);Trombidioidae(Microtrombidiidae科、Neothrombiidae科、Achaemenothrombiidae科、Trombidiidae科、Podothrombiidae科);以及Trombiculoidae(=Trombiculidae sensu lato)。将它们加入之前已被确认的超科 Allotanaupodoidea、Amphotrombioidea、Calyptostomatoidea、Erythraeoidea、Tanaupodoidae 和 Yurebilloidae。
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引用次数: 0
A multiscale analysis of coralline algae Lithophylloideae (Corallinophycidae, Rhodophyta) shedding new light on understanding cryptic diversity 对珊瑚藻类石珊瑚科(Corallinophycidae,Rhodophyta)的多尺度分析为了解隐蔽多样性提供了新的视角。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-07 DOI: 10.1016/j.ympev.2024.108140

Cryptic diversity abounds in many biological species, posing challenges to our understanding of biological diversity, conservation and management. Taking the common coralline algae, the subfamily Lithophylloideae as an illustration, this study delved into the implications of cryptic diversity through global-level phylogenetic and geographical analysis based upon Lithophylloideae molecular data worldwide, as well as a multi-locus time-calibrated phylogeny to elucidate their possible evolutionary process. The multiscale analysis revealed the polyphyly in current concept of the genus Lithophyllum. Geographic isolation resulting from the Tethys terminal event (TTE) has led to two distinct distribution regions for this so-called cosmopolitan genus: one regionally distributed along European coasts/Mediterranean that should include the taxonomical Lithophyllum; others widely distributed, particularly among pan-tropic waters, suggesting at least five groups to be rediscovered within the subfamily Lithophylloideae. Meanwhile, the cryptic genus Titanoderma, lacking morphological identification features with Lithophyllum, exhibited differences in distribution and evolutionary patterns consistent with their ecological habits, thus supporting their separation. This study provided useful hints for cryptic diversity, which advocated an integrative thinking to investigating global cryptic diversity and exploring the broad linkages between phylogenetic relationships and evolutionary origin, biogeography, morphological and ecological traits to achieve a more comprehensive understanding of biodiversity.

许多生物物种都存在隐蔽多样性,这对我们理解生物多样性、保护和管理提出了挑战。本研究以常见的珊瑚藻--石花菜亚科为例,通过基于全球石花菜属分子数据的全球系统发育和地理分析,以及多焦点时间校准系统发育,深入探讨了隐性多样性的意义,以阐明其可能的进化过程。多尺度分析揭示了当前石莲花属概念中的多态性。特提斯末端事件(TTE)导致的地理隔离使这一所谓的世界性属种形成了两个不同的分布区域:一个区域分布在欧洲海岸/地中海沿岸,应包括分类学上的石花菜属;另一个区域分布广泛,尤其是在泛热带水域,表明在石花菜亚科中至少有五个类群有待重新发现。同时,与石花菜缺乏形态学识别特征的隐生属Titanoderma在分布和进化模式上表现出与生态习性一致的差异,从而支持了它们的分离。该研究为隐性多样性的研究提供了有益的启示,提倡以综合的思维来研究全球隐性多样性,探索系统发生关系与进化起源、生物地理学、形态学和生态学特征之间的广泛联系,从而更全面地认识生物多样性。
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引用次数: 0
Reassessing the phylogeny of Cyphophthalmi with phylogenomics: A UCE-based phylogeny of mite harvesters (Opiliones) 利用系统发生组学重新评估栉水母的系统发生:基于 UCE 的螨类收割机(Opiliones)系统发育。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-06 DOI: 10.1016/j.ympev.2024.108143
Shahan Derkarabetian , Ligia R. Benavides , Gonzalo Giribet

Cyphophthalmi (the mite harvesters) are a group of Opiliones with broad interest due to their species being classic examples of short-range endemics and displaying model biogeographical patterns for poor dispersers. Cyphophthalmi phylogeny has received attention using morphology, Sanger-based sequencing data, or transcriptomics. Here we turn to a new type of data, ultraconserved elements (UCEs) and provide a first phylogeny for the entire suborder Cyphophthalmi using such data and including representatives from 36 of the 46 currently recognized genera. Phylogenetic analysis of four occupancy matrices (50%, 75%, 90% and 95%), for a total of 840, 567, 129, and 23 loci, respectively, yielded a well resolved phylogeny with monophyly of Pettalidae, Parasironidae, Stylocellidae and Troglosironidae. However, Neogoveidae appeared paraphyletic with respect to Ogoveidae in all datasets and to Troglosironidae in some, and the traditional Sironidae, which was monophyletic, now appeared paraphyletic with respect to the recently erected family Parasironidae. Our phylogenomic results using UCE data resolve the position of several problematic genera (e.g., Pettalus) and add support to other parts of the tree that received low support in Sanger-based phylogenies. Our work also stresses the possibility to add museum samples to phylogenies although methods for optimizing DNA yield from such small-bodied specimens need further improvement. Finally, this backbone phylogeny demonstrates the feasibility of an all-species phylogeny using UCEs for Cyphophthalmi, and by extension, for all Opiliones.

栉水母(螨类收割机)是一类具有广泛兴趣的裸盖目动物,因为它们的物种是短程特有物种的典型代表,并显示了贫散生物的生物地理模式。利用形态学、基于 Sanger 的测序数据或转录组学,栉水母的系统发育受到了关注。在此,我们将目光转向一种新型数据--超保守元素(UCEs),并利用此类数据首次为整个栉水母亚目提供了一个系统发育图,其中包括目前公认的 46 个属中 36 个属的代表。通过对四个占有率矩阵(50%、75%、90%和 95%)(分别为 840、567、129 和 23 个位点)进行系统进化分析,得出了 Pettalidae、Parasironidae、Stylocellidae 和 Troglosironidae 的单系系统进化。然而,在所有数据集中,Neogoveidae 与 Ogoveidae 和在某些数据集中与 Troglosironidae 都是旁系,而传统的 Sironidae 是单系的,现在与新近建立的 Parasironidae 科是旁系。我们利用 UCE 数据进行的系统发生结果解决了几个有问题的属(如 Pettalus)的位置问题,并为系统树的其他部分提供了支持,而这些部分在基于 Sanger 的系统发生中支持率较低。我们的工作还强调了将博物馆样本添加到系统发生中的可能性,尽管从这种小体型标本中优化 DNA 产率的方法还需要进一步改进。最后,这一骨干系统发生证明了利用 UCE 对酞鲤进行全物种系统发生的可行性,进而也证明了利用 UCE 对所有欧皮隆类动物进行全物种系统发生的可行性。
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引用次数: 0
Phylogenomic insights into the historical biogeography, character-state evolution, and species diversification rates of Cypripedioideae (Orchidaceae) 通过系统发生组学深入了解兰科(Cypripedioideae)植物的历史生物地理学、特征进化和物种多样化率。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-06 DOI: 10.1016/j.ympev.2024.108138
Min Liao , Jun-Yi Zhang , Yu Feng , Zong-Xin Ren , Heng-Ning Deng , Bo Xu

Cypripedioideae (slipper orchids; Orchidaceae) currently consist of ∼200 herbaceous species with a strikingly disjunctive distribution in tropical and temperate regions of both hemispheres. In this study, an updated phylogeny with representatives from all five cypripedioid genera was presented based on maximum likelihood and Bayesian inference of plastome and low-copy nuclear genes. Phylogenomic analyses indicated that each genus is monophyletic, but some relationships (e.g., those among Cypripedium sects. Acaulia, Arietinum, Bifolia, Flabellinervia, Obtusipetala and Palangshanensia) conflict with those in previous studies based on Sanger data. Cypripedioideae appeared to have arisen in South America and/or the adjacent Qinghai-Tibet Plateau and Hengduan Mountains ∼35 Mya. We inferred multiple dispersal events between East Asia and North America in Cypripedium, and between mainland Southeast Asia and the Malay Archipelago in Paphiopedilum. In the Americas, divergences among four genera (except Cypripedium) occurred around 31–20 Mya, long before the closure of the Isthmus of Panama, indicating the importance of long-distance dispersal. Evolutionary patterns between morphological and plastome character evolution suggested several traits, genome size and NDH genes, which are likely to have contributed to the success of slipper orchids in alpine floras and low-elevation forests. Species diversification rates were notably higher in epiphytic clades of Paphiopedilum than in other, terrestrial cypripedioids, paralleling similar accelerations associated with epiphytism in other groups. This study also suggested that sea-level fluctuations and mountain-building processes promoted the diversification of the largest genera, Paphiopedilum and Cypripedium.

拖鞋兰科(Cypripedioideae;Orchidaceae)目前有 200 多个草本物种,分布在两个半球的热带和温带地区,具有明显的不连续性。本研究根据质体基因和低拷贝核基因的最大似然法和贝叶斯推断法,提出了一个最新的系统发生图,其中包括所有五个蝶形花属的代表物种。系统发生组分析表明,每个属都是单系的,但有些关系(如 Cypripedium sects.Acaulia、Arietinum、Bifolia、Flabellinervia、Obtusipetala 和 Palangshanensia)与之前基于 Sanger 数据的研究结果相冲突。Cypripedioideae似乎起源于南美洲和/或邻近的青藏高原和横断山脉∼35 Mya。我们推断Cypripedium在东亚和北美之间、Paphiopedilum在东南亚大陆和马来群岛之间有多次扩散事件。在美洲,4个属之间的分化发生在31-20万年左右,远远早于巴拿马地峡的关闭,这表明了远距离扩散的重要性。形态和质体特征之间的进化模式表明,基因组大小和NDH基因等几种性状很可能有助于拖鞋兰在高山植物区系和低海拔森林中取得成功。木犀草属附生支系的物种多样化率明显高于其他陆生蝶形花科植物,这与其他类群中与附生相关的类似加速现象类似。这项研究还表明,海平面波动和造山运动促进了最大的属--木槿属和芹菜属--的多样化。
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引用次数: 0
Phylogenomics and biogeography of sawflies and woodwasps (Hymenoptera, Symphyta) 锯蝇和木蝉(膜翅目,同翅目)的系统发生组学和生物地理学。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-05 DOI: 10.1016/j.ympev.2024.108144
Saskia Wutke , Stephan M. Blank , Jean-Luc Boevé , Brant C. Faircloth , Frank Koch , Catherine R. Linnen , Tobias Malm , Gengyun Niu , Marko Prous , Nathan M. Schiff , Stefan Schmidt , Andreas Taeger , Lars Vilhelmsen , Niklas Wahlberg , Meicai Wei , Tommi Nyman

Phylogenomic approaches have recently helped elucidate various insect relationships, but large-scale comprehensive analyses on relationships within sawflies and woodwasps are still lacking. Here, we infer the relationships and long-term biogeographic history of these hymenopteran groups using a large dataset of 354 UCE loci collected from 385 species that represent all major lineages. Early Hymenoptera started diversifying during the Early Triassic ∼249 Ma and spread all over the ancient supercontinent Pangaea. We recovered Xyeloidea as a monophyletic sister group to other Hymenoptera and Pamphilioidea as sister to Unicalcarida. Within the diverse family Tenthredinidae, our taxonomically and geographically expanded taxon sampling highlights the non-monophyly of several traditionally defined subfamilies. In addition, the recent removal of Athalia and related genera from the Tenthredinidae into the separate family Athaliidae is supported. The deep historical biogeography of the group is characterised by independent dispersals and re-colonisations between the northern (Laurasia) and southern (Gondwana) palaeocontinents. The breakup of these landmasses led to ancient vicariance in several Gondwanan lineages, while interchange across the Northern Hemisphere has continued until the Recent. The little-studied African sawfly fauna is likewise a diverse mixture of groups with varying routes of colonization. Our results reveal interesting parallels in the evolution and biogeography of early hymenopterans and other ancient insect groups.

系统发生组学方法最近帮助阐明了各种昆虫的关系,但仍然缺乏对锯蝇和木蝉内部关系的大规模综合分析。在这里,我们利用从代表所有主要品系的 385 个物种中收集的 354 个 UCE 位点组成的大型数据集,推断了这些膜翅目昆虫类群的关系和长期生物地理历史。早期膜翅目昆虫在早三叠世(249 Ma)开始分化,遍布古老的盘古大陆。我们发现 Xyeloidea 是其他膜翅目的单系姊妹群,Pamphilioidea 是 Unicalcarida 的姊妹群。在种类繁多的天牛科(Tenthredinidae)中,我们在分类学和地理学上扩大了分类群的取样范围,突出了几个传统定义的亚科的非单系性。此外,最近将 Athalia 及相关属从 Tenthredinidae 科移入单独的 Athaliidae 科的观点也得到了支持。该类的深层历史生物地理学特征是在北部(劳拉西亚)和南部(冈瓦纳)古大陆之间的独立扩散和再殖民。这些大陆的解体导致了冈瓦纳的几个种系在远古时期的沧海桑田,而北半球的交流则一直持续到近代。非洲锯蝇动物群的研究很少,同样也是一个由不同殖民路线的群体组成的多样性混合体。我们的研究结果揭示了早期膜翅目昆虫和其他古老昆虫类群在进化和生物地理学方面有趣的相似之处。
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引用次数: 0
Tracing the genealogy origin of geographic populations based on genomic variation and deep learning 基于基因组变异和深度学习追溯地理种群的谱系起源。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-02 DOI: 10.1016/j.ympev.2024.108142
Bing Yang , Xin Zhou , Shanlin Liu

Assigning a query individual animal or plant to its derived population is a prime task in diverse applications related to organismal genealogy. Such endeavors have conventionally relied on short DNA sequences under a phylogenetic framework. These methods naturally show constraints when the inferred population sources are ambiguously phylogenetically structured, a scenario demanding substantially more informative genetic signals. Recent advances in cost-effective production of whole-genome sequences and artificial intelligence have created an unprecedented opportunity to trace the population origin for essentially any given individual, as long as the genome reference data are comprehensive and standardized. Here, we developed a convolutional neural network method to identify population origins using genomic SNPs. Three empirical datasets (an Asian honeybee, a red fire ant, and a chicken datasets) and two simulated populations are used for the proof of concepts. The performance tests indicate that our method can accurately identify the genealogy origin of query individuals, with success rates ranging from  93 % to 100 %. We further showed that the accuracy of the model can be significantly increased by refining the informative sites through FST filtering. Our method is robust to configurations related to batch sizes and epochs, whereas model learning benefits from the setting of a proper preset learning rate. Moreover, we explained the importance score of key sites for algorithm interpretability and credibility, which has been largely ignored. We anticipate that by coupling genomics and deep learning, our method will see broad potential in conservation and management applications that involve natural resources, invasive pests and weeds, and illegal trades of wildlife products.

将查询到的动物或植物个体归入其衍生种群是与生物系谱相关的各种应用中的首要任务。这些工作通常依赖于系统发育框架下的短 DNA 序列。当推断出的种群来源在系统发育结构上含糊不清时,这些方法自然会受到限制,这种情况下就需要信息量更大的遗传信号。最近,全基因组序列的生产和人工智能在成本效益方面取得的进展,为追溯任何给定个体的种群起源创造了前所未有的机会,只要基因组参考数据是全面和标准化的。在这里,我们开发了一种卷积神经网络方法,利用基因组 SNPs 来识别种群起源。我们使用了三个经验数据集(亚洲蜜蜂、红火蚁和鸡数据集)和两个模拟种群进行概念验证。性能测试表明,我们的方法可以准确识别查询个体的系谱起源,成功率从 > 93 % 到 100 % 不等。我们还进一步证明,通过 FST 过滤提炼信息位点,可以显著提高模型的准确性。我们的方法对与批量大小和历时相关的配置具有鲁棒性,而模型学习则得益于适当预设学习率的设置。此外,我们还解释了关键位点对于算法可解释性和可信度的重要性得分,而这一点在很大程度上被忽视了。我们预计,通过将基因组学与深度学习相结合,我们的方法将在涉及自然资源、入侵害虫和杂草以及野生动物产品非法贸易的保护和管理应用中发挥广泛的潜力。
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引用次数: 0
Evolutionary analysis of species-specific duplications in flatworm genomes 扁形虫基因组中物种特异性重复的进化分析。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-02 DOI: 10.1016/j.ympev.2024.108141
Mauricio Langleib , Javier Calvelo , Alicia Costábile , Estela Castillo , José F. Tort , Federico G. Hoffmann , Anna V. Protasio , Uriel Koziol , Andrés Iriarte

Platyhelminthes, also known as flatworms, is a phylum of bilaterian invertebrates infamous for their parasitic representatives. The classes Cestoda, Monogenea, and Trematoda comprise parasitic helminths inhabiting multiple hosts, including fishes, humans, and livestock, and are responsible for considerable economic damage and burden on human health. As in other animals, the genomes of flatworms have a wide variety of paralogs, genes related via duplication, whose origins could be mapped throughout the evolution of the phylum. Through in-silico analysis, we studied inparalogs, i.e., species-specific duplications, focusing on their biological functions, expression changes, and evolutionary rate. These genes are thought to be key players in the adaptation process of species to each particular niche. Our results showed that genes related with specific functional terms, such as response to stress, transferase activity, oxidoreductase activity, and peptidases, are overrepresented among inparalogs. This trend is conserved among species from different classes, including free-living species. Available expression data from Schistosoma mansoni, a parasite from the trematode class, demonstrated high conservation of expression patterns between inparalogs, but with notable exceptions, which also display evidence of rapid evolution. We discuss how natural selection may operate to maintain these genes and the particular duplication models that fit better to the observations. Our work supports the critical role of gene duplication in the evolution of flatworms, representing the first study of inparalogs evolution at the genome-wide level in this group.

扁形动物(Platyhelminthes),又称扁形动物,是双脊无脊椎动物门的一个分支,因其寄生代表而臭名昭著。绦虫纲(Cestoda)、单精虫纲(Monogenea)和吸虫纲(Trematoda)由寄生蠕虫组成,栖息在鱼类、人类和家畜等多种宿主体内,造成了巨大的经济损失和人类健康负担。与其他动物一样,扁形动物的基因组中也有各种各样的旁系亲属,即通过重复而相关的基因,它们的起源可以在整个扁形动物门的进化过程中找到。通过模拟分析,我们研究了内同源物,即物种特异性复制,重点关注它们的生物学功能、表达变化和进化速度。这些基因被认为是物种适应每个特定生态位过程中的关键角色。我们的研究结果表明,与特定功能术语相关的基因,如应激反应、转移酶活性、氧化还原酶活性和肽酶等,在内切类中的比例较高。这一趋势在不同类别的物种(包括自由生活物种)中是一致的。来自曼氏血吸虫(一种吸虫类寄生虫)的现有表达数据显示,内表型之间的表达模式高度一致,但也有明显的例外,这些例外也显示了快速进化的证据。我们讨论了自然选择是如何维持这些基因的,以及更适合观察结果的特定复制模型。我们的工作证明了基因复制在扁形虫进化过程中的关键作用,这是首次在全基因组水平上研究该类扁形虫的内表型进化。
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引用次数: 0
Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies) Museomics有助于解析雪雀(鸟类,百灵鸟科,Montifringilla及其同属鸟类)的系统发育。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-24 DOI: 10.1016/j.ympev.2024.108135
Safiqul Islam , Claire Peart , Christian Kehlmaier , Yue-Hua Sun , Fumin Lei , Andreas Dahl , Sylvia Klemroth , Dimitra Alexopoulou , Maria del Mar Delgado , Paola Laiolo , Juan Carlos Illera , Sebastian Dirren , Sabine Hille , Davaa Lkhagvasuren , Till Töpfer , Martin Kaiser , Axel Gebauer , Jochen Martens , Claudia Paetzold , Martin Päckert

Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, Pyrgilauda theresae. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (Montifringilla nivalis).

Our phylogenetic reconstructions unanimously refuted the previously suggested paraphyly of genus Pyrgilauda. Misplacement of one species-level taxon (Onychostruthus tazcanowskii) in previous snowfinch phylogenies was undoubtedly inferred from chimeric mitogenomes that included heterospecific sequence information. Furthermore, comparison of novel and previously generated sequence data showed that the presumed sister-group relationship between M. nivalis and the QTP endemic M. henrici was suggested based on flawed taxonomy. Our phylogenetic reconstructions based on genome-wide SNP data and on mitogenomes were largely congruent and supported reciprocal monophyly of genera Montifringilla and Pyrgilauda with monotypic Onychostruthus being sister to the latter. The Afghan endemic P. theresae likely originated from a rather ancient Pliocene out-of-Tibet dispersal probably from a common ancestor with P. ruficollis. Our extended trans-Palearctic sampling for the white-winged snowfinch, M. nivalis, confirmed strong lineage divergence between an Asian and a European clade dated to 1.5 – 2.7 million years ago (mya). Genome-wide SNP data suggested subtle divergence among European samples from the Alps and from the Cantabrian mountains.

博物馆收藏的历史标本提供了一个宝贵的材料来源,这些标本也来自偏远地区或冲突地区,而现在的科学家还很难接触到这些地区的标本。通过这项研究,我们利用阿富汗特有物种--阿富汗雪雀(Pyrgilauda theresae)的整张皮上的历史 DNA,提供了一个完整的雪雀分类群系统发育。为了解决以前的系统发育假说之间的强烈冲突,我们利用ddRAD测序技术为青藏高原(QTP)特有的所有现生雪雀物种和中西古北唯一雪雀物种(Montifringilla nivalis)的扩展种内取样生成了选定类群的新型有丝分裂基因组序列和全基因组SNP数据。我们的系统发育重建一致驳斥了之前提出的雪雀属(Pyrgilauda)旁系的观点。一个种级分类群(Onychostruthus tazcanowskii)在以前的雪雀系统发育中的错误定位无疑是由包含异特异性序列信息的嵌合有丝分裂基因组推断出来的。此外,对新的序列数据和以前产生的序列数据进行比较后发现,假定 M. nivalis 与 QTP 特有的 M. henrici 之间的姊妹群关系是基于有缺陷的分类学提出的。基于全基因组 SNP 数据和有丝分裂基因组的系统发育重建结果基本一致,支持 Montifringilla 属和 Pyrgilauda 属互为单系,单型的 Onychostruthus 是后者的姊妹属。阿富汗特有的P. theresae可能起源于上新世的一次相当古老的西藏外扩散,可能与P. ruficollis有共同的祖先。我们对白翅雪雀(M. nivalis)进行的跨北极采样证实,在距今150万-270万年前的一个亚洲支系和一个欧洲支系之间存在着强烈的世系分化。全基因组 SNP 数据表明,来自阿尔卑斯山和坎塔布里亚山脉的欧洲样本之间存在微妙的分化。
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引用次数: 0
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Molecular Phylogenetics and Evolution
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