A molecular timeline for the origin of photosynthetic eukaryotes

The appearance of photosynthetic eukaryotes (algae and plants) dramatically altered the Earth's ecosystem, making possible all vertebrate life on land, including humans. Dating algal origin is, however, frustrated by a meager fossil record. We generated a plastid multi-gene phylogeny with Bayesian inference and then used maximum likelihood molecular clock methods to estimate algal divergence times. The plastid tree was used as a surrogate for algal host evolution because of recent phylogenetic evidence supporting the vertical ancestry of the plastid in the red, green, and glaucophyte algae. Nodes in the plastid tree were constrained with six reliable fossil dates and a maximum age of 3,500 MYA based on the earliest known eubacterial fossil. Our analyses support an ancient (late Paleoproterozoic) origin of photosynthetic eukaryotes with the primary endosymbiosis that gave rise to the first alga having occurred after the split of the Plantae (i.e., red, green, and glaucophyte algae plus land plants) from the opisthokonts sometime before 1,558 MYA. The split of the red and green algae is calculated to have occurred about 1,500 MYA, and the putative single red algal secondary endosymbiosis that gave rise to the plastid in the cryptophyte, haptophyte, and stramenopile algae (chromists) occurred about 1,300 MYA. These dates, which are consistent with fossil evidence for putative marine algae (i.e., acritarchs) from the early Mesoproterozoic (1,500 MYA) and with a major eukaryotic diversification in the very late Mesoproterozoic and Neoproterozoic, provide a molecular timeline for understanding algal evolution.     

河南省被子植物分布新记录

通过野外调查和标本鉴定,报道了河南被子植物分布新记录3种,分别为单花红丝线〔Lycianthes lysimachioides （Wall.） Bitter〕、狭齿水苏（Stachys pseudophlomis C. Y. Wu）、白花蝇子草〔Silene latifolia subsp. alba （Mill.） Greuter & Burdet〕。单花红丝线所在的红丝线属〔Lycianthes （Dunal） Hassl.〕为河南省分布新记录属。上述新记录的凭证标本存放于河南宝天曼保护区标本室。     

福建省被子植物分布新记录

在闽东地区的植被调查中,发现福建省被子植物地理分布新记录属1个:虉草属(Phalaris Linn.);新记录种4个,分别是虉草(Phalaris arundinacea Linn.)、浙江虎耳草(Saxifraga zhejiangensis Z. Wei. et Y. B. Chang)、莼菜(Brasenia schreberi J. P. Gmel.)和斑地锦(Euphorbia maculate Linn.)。标本存放于宁德师范学院植物标本室(NDTC)。     

The age of the crown group of passerine birds and its evolutionary significance – molecular calibrations versus the fossil record

Based on calibrations of molecular phylogenies and biogeographic considerations, it has been argued that the basal divergences of crown group Passeriformes occurred in the late Cretaceous, following the break-up of eastern Gondwana. Some implications of this hypothesis have, however, not yet been adequately addressed. In particular, a Cretaceous divergence of crown group passerines would imply an unprecedented evolutionary stasis for more than 80 million years in one of the most species-rich group of endothermic vertebrates. The temporal distribution and phylogenetic affinities of northern hemispheric fossils further conflicts with current hypotheses on the historical biogeography of passerines, and is in better concordance with a Cenozoic divergence of crown group Passeriformes.     

A 'living fossil' eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau

We report the discovery of an enigmatic, small eel-like fish from a 35 m-deep fringing-reef cave in the western Pacific Ocean Republic of Palau that exhibits an unusual suite of morphological characters. Many of these uniquely characterize the Recent members of the 19 families comprising the elopomorph order Anguilliformes, the true eels. Others are found among anguilliforms only in the Cretaceous fossils, and still others are primitive with respect to both Recent and fossil eels. Thus, morphological evidence explicitly places it as the most basal lineage (i.e. the sister group of extant anguilliforms). Phylogenetic analysis and divergence time estimation based on whole mitogenome sequences from various actinopterygians, including representatives of all eel families, demonstrate that this fish represents one of the most basal, independent lineages of the true eels, with a long evolutionary history comparable to that of the entire Anguilliformes (approx. 200 Myr). Such a long, independent evolutionary history dating back to the early Mesozoic and a retention of primitive morphological features (e.g. the presence of a premaxilla, metapterygoid, free symplectic, gill rakers, pseudobranch and distinct caudal fin rays) warrant recognition of this species as a 'living fossil' of the true eels, herein described as Protanguilla palau genus et species nov. in the new family Protanguillidae.     

里白科植物的系统发育和分歧时间估计——基于叶绿体三个基因序列的证据

里白科(Gleicheniaceae)是古老的真蕨类植物,最早的化石记录可追溯到石炭纪。现存类群的属级分类和系统演化关系一直存在很大的分歧,为了进一步探讨该类群的起源演化,文中运用最大简约法和贝叶斯演绎方法对18种代表现存里白科植物全部6属(包括新测的12种)的叶绿体3个编码基因序列(atpB,rbcL和rps4)进行分析,探讨其主要分类群(属级)的系统演化关系。结果显示,里白科植物为一个单系群,由3个分支构成:里白属(Diplopterygium Nakai)和Gleichenia japonica构成一个分支;芒萁属(Dicranopteris Bernh.)和Gleichenella pec-tinata构成另一个分支;假芒萁属(Sticherus C.Presl)与单种属Stromatopteris Mettenius及Gleichenia dicarpa构成第三个分支。用宽松分子钟方法推测里白科主要类群的起源时间为:现代里白科植物起源于早白垩世(111—140Ma),其主要分支类群随后发生多样性分化,里白属和芒萁属的快速辐射演化均发生在古近纪(40—64Ma,36—50Ma)。起源时间的估算结果暗示化石种三叠里白Diplopterygium triassica不应归入现代里白属,其归属需要重新考虑。     

The recognition of ancestors

The recognition of ancestors is problematic using cladistic logic alone because monophyletic groups (clades) are defined by shared derived characters (synapomorphies) which their ancestors must have lacked. Nevertheless, ancestors possess three key attributes. They belong within a larger, paraphyletic group. They will be morphologically most similar to their immediate descendants, and they evolved before any and all of their descendants. Recognition of ancestors requires both morphological and stratigraphic data and, in practice, the task is to reduce the size of the paraphyletic group within which the ancestor must lie. All ancestor‐descendant relationships are phylogenetic hypotheses. Despite the legendary incompleteness of the fossil record, testing the validity of available data is far more difficult for character analysis than for stratigraphy.     

Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals

O''Leary et al. (O''Leary et al. 2013 Science 339, 662–667. (doi:10.1126/science.1229237)) performed a fossil-only dating analysis of mammals, concluding that the ancestor of placentals post-dated the Cretaceous–Palaeogene boundary, contradicting previous palaeontological and molecular studies that placed the ancestor in the Cretaceous. They incorrectly used fossil ages as species divergence times for crown groups, while in fact the former should merely form minimum-age bounds for the latter. Statistical analyses of the fossil record have shown that crown groups are significantly older than the oldest ingroup fossil, so that fossils do not directly reflect the true ages of clades. Here, we analyse a 20 million nucleotide genome-scale alignment in conjunction with a probabilistic interpretation of the fossil ages from O''Leary et al. Our combined analysis of fossils and molecules demonstrates that Placentalia originated in the Cretaceous.     

Estimating primate divergence times by using conditioned birth-and-death processes

The fossil record provides a lower bound on the primate divergence time of 54.8 million years ago, but does not provide an explicit estimate for the divergence time itself. We show how the pattern of diversification through the Cenozoic can be combined with a model for speciation to give a distribution for the age of the primates. The primate fossil record, the number of extant primate species, and information about the structure of the primate phylogenetic tree are combined to provide an estimate for the joint distribution of the primate and anthropoid divergence times. To take this information into account, we derive the structure of the birth-and-death process conditioned to have a subtree originate at a particular point in time. This process has a size-biased law and has an immortal line running from the root of the tree to the root of the subtree, with species on the spine having modified offspring and length distributions. We conclude that it is not possible, with this model, to rule out a Cretaceous origin for the primates.     

多凿齿蜥类(Squamata,Polyglyphanodontia)的分类学与系统发育学综述*

多凿齿蜥类(Squamata, Polyglyphanodontia)是晚白垩世时有鳞类中的优势类群之一, 地理分布广, 体形大小迥异, 形态多样性高。特别表现为多样且独特的牙齿形态, 如横向凿状牙齿和类似哺乳动物臼齿的多尖型牙齿。多凿齿蜥类在经历了晚白垩世的繁盛之后却在白垩纪末和恐龙、翼龙以及有鳞类中的沧龙共同灭绝。近年来多凿齿蜥类化石已报道的属种众多(共计60余种), 但因其兼具臼齿蜥类和鬣蜥类的形态特征、早期研究描述简略和图版不足, 多凿齿蜥类的成员组成、该类群在有鳞类中的系统位置以及类群内的系统关系还存在争议。本研究较全面地梳理了曾归入多凿齿蜥类的属种的分类学和该类群的系统发育学分析结果, 讨论了多凿齿蜥类的定义以及该类群内的形态多样性。