Leaf evolution in Southern Hemisphere conifers tracks the angiosperm ecological radiation

The angiosperm radiation has been linked to sharp declines in gymnosperm diversity and the virtual elimination of conifers from the tropics. The conifer family Podocarpaceae stands as an exception with highest species diversity in wet equatorial forests. It has been hypothesized that efficient light harvesting by the highly flattened leaves of several podocarp genera facilitates persistence with canopy-forming angiosperms, and the angiosperm ecological radiation may have preferentially favoured the diversification of these lineages. To test these ideas, we develop a molecular phylogeny for Podocarpaceae using Bayesian-relaxed clock methods incorporating fossil time constraints. We find several independent origins of flattened foliage types, and that these lineages have diversified predominantly through the Cenozoic and therefore among canopy-forming angiosperms. The onset of sustained foliage flattening podocarp diversification is coincident with a declining diversification rate of scale/needle-leaved lineages and also with ecological and climatic transformations linked to angiosperm foliar evolution. We demonstrate that climatic range evolution is contingent on the underlying state for leaf morphology. Taken together, our findings imply that as angiosperms came to dominate most terrestrial ecosystems, competitive interactions at the foliar level have profoundly shaped podocarp geography and as a consequence, rates of lineage diversification.     

Integrating Early Cretaceous fossils into the phylogeny of living angiosperms:Magnoliidae and eudicots

Over the past 25 years, discoveries of Early Cretaceous fossil flowers, often associated with pollen and sometimes with vegetative parts, have revolutionized our understanding of the morphology and diversity of early angiosperms. However, few of these fossils have been integrated into the increasingly robust phylogeny of living angiosperms based primarily on molecular data. To remedy this situation, we have used a morphological dataset for living basal angiosperms (including basal eudicots and monocots) to assess the most parsimonious positions of early angiosperm fossils on cladograms of Recent plants, using constraint trees that represent the current range of hypotheses on higher-level relationships, and concentrating on Magnoliidae (the clade including Magnoliales, Laurales, Canellales, and Piperales) and eudicots. In magnoliids, our results confirm proposed relationships of Archaeanthus (latest Albian?) to Magnoliaceae, Endressinia (late Aptian) to Magnoliales (the clade comprising Degeneria, Galbulimima, Eupomatia, and Annonaceae), and Walkeripollis pollen tetrads (late Barremian?) to Win-teraceae, but they indicate that Mauldinia (early Cenomanian) was sister to both Lauraceae and Hernandiaceae rather than to Lauraceae alone. Among middle Albian to early Cenomanian eudicots, we confirm relationships of Nelumbites to Nelumbo, platanoid inflorescences and Sapindopsis to Platanaceae, and Spanomera to Buxaceae. With the possible exception of Archaeanthus, these fossils are apparently not crown group members of living families but rather stem relatives of one or more families.     

基于5 993个核基因的被子植物系统发育关系研究

系统发育关系的构建对被子植物分类及进化研究非常重要。长期以来,被子植物系统发育的研究,大多使用质体基因、线粒体基因或少数保守的单拷贝核基因。该研究从已注释基因组或转录组中搜集88种被子植物(包含58目)的核基因集;通过对其进行同源基因聚类及去旁系同源基因,获得了5 993个一对一的直系同源基因家族(即对于每个基因家族,每种植物最多一条序列,最少包含50个物种);使用截取各种不同数目基因集的DNA或氨基酸序列,采用串联法(concatenation)和溯祖法(coalescence),共构建了20棵进化树。比较这些进化树,虽然大部分结果支持APG IV中描述的被子植物主要支系之间的关系[(真双子叶植物,单子叶植物),木兰类植物],但真双子叶植物内部各目分支的演化关系与APG IV有一个很大的不同,即认为檀香目和石竹目是蔷薇类植物的姊妹群。基于这些进化树,估算了被子植物各目分支的分化时间,结果表明被子植物的起源时间为237.78百万年前(95%置信区间为202.6～278.08),与主流观点认为的225百万年至240百万年前一致。以上结果为构建进化树提供了一种可行性策略,这种方法允许使用基...     

Steady diversification of derived liverworts under Tertiary climatic fluctuations

Tropical forests contain the majority of extant plant diversity and their role as a cradle and/or museum of biodiversity is an important issue in our attempts to assess the long-term consequences of global climate change for terrestrial biomes. Highly diverse groups of liverworts are an often ignored but extremely common element in rainforests, and thus their evolution may shed light on the ecological robustness of rainforest biomes to climate fluctuations. We record a remarkable constant accumulation of diversity through time for the most species-rich family of liverworts, Lejeuneaceae, inferred by divergence time estimates. The observed pattern supports the recently developed concept of a dual role of the tropics as both a museum and a cradle of biodiversity.     

The platypus is in its place: nuclear genes and indels confirm the sister group relation of monotremes and Therians

Morphological data supports monotremes as the sister group of Theria (extant marsupials + eutherians), but phylogenetic analyses of 12 mitochondrial protein-coding genes have strongly supported the grouping of monotremes with marsupials: the Marsupionta hypothesis. Various nuclear genes tend to support Theria, but a comprehensive study of long concatenated sequences and broad taxon sampling is lacking. We therefore determined sequences from six nuclear genes and obtained additional sequences from the databases to create two large and independent nuclear data sets. One (data set I) emphasized taxon sampling and comprised five genes, with a concatenated length of 2,793 bp, from 21 species (two monotremes, six marsupials, nine placentals, and four outgroups). The other (data set II) emphasized gene sampling and comprised eight genes and three proteins, with a concatenated length of 10,773 bp or 3,669 amino acids, from five taxa (a monotreme, a marsupial, a rodent, human, and chicken). Both data sets were analyzed by parsimony, minimum evolution, maximum likelihood, and Bayesian methods using various models and data partitions. Data set I gave bootstrap support values for Theria between 55% and 100%, while support for Marsupionta was at most 12.3%. Taking base compositional bias into account generally increased the support for Theria. Data set II exclusively supported Theria, with the highest possible values and significantly rejected Marsupionta. Independent phylogenetic evidence in support of Theria was obtained from two single amino acid deletions and one insertion, while no supporting insertions and deletions were found for Marsupionta. On the basis of our data sets, the time of divergence between Monotremata and Theria was estimated at 231-217 MYA and between Marsupialia and Eutheria at 193-186 MYA. The morphological evidence for a basal position of Monotremata, well separated from Theria, is thus fully supported by the available molecular data from nuclear genes.     

新疆裂腹鱼类的系统发生关系及物种分化时间

文章采用线粒体COI、ND4、16S rRNA基因联合数据分析了新疆分布的裂腹鱼类4属10个种或亚种的分子系统发育,并通过鲤亚科的分化时间、黄河上游和青海湖隔离的地质时间来校正分子钟,进而探讨了裂腹鱼类分化时间与塔里木盆地周边地区主要地质事件和气候变化的关系。结果发现,扁吻鱼属未能形成独立的分支,与塔里木裂腹鱼、厚唇裂腹鱼聚在一起。进一步基于COI基因序列,利用Kimura双参数模型计算遗传距离,发现扁吻鱼属和裂腹鱼属间的遗传距离未达到属间区别,扁吻鱼可能是裂腹鱼属内特化的物种;聚类分析结果不同于裂腹鱼属的形态学分类方法,不支持裂腹鱼属鱼类的亚属划分;原始等级裂腹鱼类(包括裂腹鱼属和扁吻鱼属)两个族群的分化时间(8.18 Ma)与新疆裸重唇鱼和斑重唇鱼的分化时间(7.67 Ma)均发生于晚中新世,这可能与8Ma左右青藏高原北缘和北天山抬升、塔里木盆地气候干旱化等重大地质事件和气候转型导致青藏高原北缘(昆仑山)和北天山水系间出现分离相关。而塔里木盆地裂腹鱼属鱼类现今的分布格局可能与第四纪喜马拉雅运动使盆地形成西高东低的地势、罗布泊成为塔里木盆地周边高山发源河流的汇水中心相关。     

Radiation of the ,,Drosophila“ subgenus (Drosophilidae,Diptera) in the Neotropics

We present a phylogenetic hypothesis for 72 ,,Drosophila“ species, constructed through analysis from the paralogous alpha methyldopa (amd) and dopa decarboxylase (ddc) nuclear genes (encompassing a total of 2015 base pairs). Our data support the subdivision of the paraphyletic subgenus ,,Drosophila“ into three main radiations (the immigrans‐tripunctata, the virilis‐repleta and the Hawaiian Drosophilidae), each of which is further subdivided to originate monophyletic ‘sub‐radiations’. Moreover, this study raises the possibility that the Zaprionus/Liodrosophila species encompass a fourth radiation within the subgenus ,,Drosophila“ phylogeny and provides temporal estimates for each of the postulated divergence events.     

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.     

Phylogenetic biogeography and taxonomy of disjunctly distributed bryophytes

More than 200 research papers on the molecular phylogeny and phylogenetic biogeography ofbryophytes have been published since the beginning of this millenium. These papers corroborated assumptions of a complex genetic structure of morphologically circumscribed bryophytes, and raised reservations against many morphologically justified species concepts, especially within the mosses. However, many molecular studies allowed for corrections and modifications of morphological classification schemes. Several studies reported that the phylogenetic structure of disjunctly distributed bryophyte species reflects their geographical ranges rather than morphological disparities. Molecular data led to new appraisals of distribution ranges and allowed for the reconstruction of refugia and migration routes. Intercontinental ranges of bryophytes are often caused by dispersal rather than geographical vicariance. Many distribution patterns of disjunct bryophytes are likely formed by processes such as short distance dispersal, rare long distance dispersal events, extinction, recolonization and diversification.     

Rapid diversification and not clade age explains high diversity in neotropical Adelpha butterflies

Latitudinal gradients in species richness are among the most well-known biogeographic patterns in nature, and yet there remains much debate and little consensus over the ecological and evolutionary causes of these gradients. Here, we evaluated whether two prominent alternative hypotheses (namely differences in diversification rate or clade age) could account for the latitudinal diversity gradient in one of the most speciose neotropical butterfly genera (Adelpha) and its close relatives. We generated a multilocus phylogeny of a diverse group of butterflies in the containing tribe Limenitidini, which has both temperate and tropical representatives. Our results suggest there is no relationship between clade age and species richness that could account for the diversity gradient, but that instead it could be explained by a significantly higher diversification rate within the predominantly tropical genus Adelpha. An apparent early larval host-plant shift to Rubiaceae and other plant families suggests that the availability of new potential host plants probably contributed to an increase in diversification of Adelpha in the lowland Neotropics. Collectively, our results support the hypothesis that the equatorial peak in species richness observed within Adelpha is the result of increased diversification rate in the last 10-15 Myr rather than a function of clade age, perhaps reflecting adaptive divergence in response to the dramatic host-plant diversity found within neotropical ecosystems.     

Diversification in a fluctuating island setting: rapid radiation of Ohomopterus ground beetles in the Japanese Islands

The Japanese Islands have been largely isolated from the East Asian mainland since the Early Pleistocene, allowing the diversification of endemic lineages. Here, we explore speciation rates and historical biogeography of the ground beetles of the subgenus Ohomopterus (genus Carabus) based on nuclear and mitochondrial gene sequences. Ohomopterus diverged into 15 species during the Pleistocene. The speciation rate was 1.92 Ma(-1) and was particularly fast (2.37 Ma(-1)) in a group with highly divergent genitalia. Speciation occurred almost solely within Honshu, the largest island with complex geography. Species diversity is highest in central Honshu, where closely related species occur parapatrically and different-sized species co-occur. Range expansion of some species in the past has resulted in such species assemblages. Introgressive hybridization, at least for mitochondrial DNA, has occurred repeatedly between species in contact, but has not greatly disturbed species distinctness. Small-island populations of some species were separated from main-island populations only after the last glacial (or the last interglacial) period, indicating that island isolation had little role in speciation. Thus, the speciation and formation of the Ohomopterus assemblage occurred despite frequent opportunities for secondary contact and hybridization and the lack of persistent isolation. This radiation was achieved without substantial ecological differentiation, but with marked differentiation in mechanical agents of reproductive isolation (body size and genital morphology).