Assembly dynamics of East Asian subtropical evergreen broadleaved forests: New insights from the dominant Fagaceae trees

The dominant species of a biome can be regarded as its genuine indicator. Evergreen broadleaved forests (EBLFs) in subtropical East Asia harbor high levels of species biodiversity and endemism and are vital to regional carbon storage and cycling. However, the historical assembly of this unique biome is still controversial. Fagaceae is the most essential family in East Asian subtropical EBLFs and its dominant species are vital for the existence of this biome. Here, we used the dominant Fagaceae species to shed light on the dynamic process of East Asian subtropical EBLFs over time. Our results indicate high precipitation in summer and low temperature in winter are the most influential climatic factors for the distribution of East Asian subtropical EBLFs. Modern East Asian subtropical EBLFs did not begin to appear until 23 Ma, subsequently experienced a long-lasting development in the Miocene and markedly deteriorated at about 4 Ma, driven jointly by orogenesis and paleoclimate. We also document that there is a lag time between when one clade invaded the region and when its members become dominant species within the region. This study may improve our ability to predict and mitigate the threats to biodiversity of East Asian subtropical EBLFs and points to a new path for future studies involving multidisciplinary methods to explore the assembly of regional biomes.     

鄂西南两个自然保护区亚热带常绿落叶阔叶混交林类型及其常绿和落叶物种组成结构分析

为深入研究亚热带常绿落叶阔叶混交林的生物多样性维持机制, 合理保护与利用此类森林植被, 以鄂西南两个自然保护区——星斗山和木林子典型的亚热带常绿落叶阔叶混交林为研究对象, 在野外样方调查的基础上进行了群落数量分类和排序, 分析了常绿和落叶物种比例随群落类型及环境因子变化的规律。研究结果表明: (1)将鄂西南两个自然保护区的亚热带常绿落叶阔叶混交林划分为5个群落类型: 即青冈-翅柃+尖连蕊茶(Cyclobalanopsis glauca-Eurya alata + Camellia cuspidata)群落(I)、川陕鹅耳枥+青冈-翅柃(Carpinus fargesiana + Cyclobalanopsis glauca-Eurya alata)群落(II)、川陕鹅耳枥+青冈-水马桑(Carpinus fargesiana + Cyclobalanopsis glauca-Weigela japonica)群落(III)、光叶水青冈+多脉青冈-翅柃(Fagus lucida + Cyclobalanopsis multinervis-Eurya alata)群落(IV)和川陕鹅耳枥+交让木+包果柯-翅柃(Carpinus fargesiana + Daphniphyllum macropodum + Lithocarpus cleistocarpus-Eurya alata)群落(V); (2)常绿和落叶物种的丰富度、多度、胸高断面积及重要值等指标随群落类型而变化。在群落II、III和V中落叶物种占优势, 而在群落I和IV中二者无显著差异; (3)各类型群落在小径级(1-5 cm)内落叶物种的丰富度大于常绿物种, 但多度、胸高断面积和重要值大都小于常绿物种。在中径级(5-10 cm)内, 群落I和群落IV的各项指标都表现为常绿物种大于落叶物种, 而群落II、群落III和群落V的则相反。在大径级(≥ 10 cm)内, 各群落类型的落叶物种都占显著优势, 其各项指标大于常绿物种; (4)海拔、坡度、坡向、土壤氮含量和土壤磷含量是影响各群落类型内常绿和落叶物种比例变化的主导因子。     

A fossil-calibrated relaxed clock for Ephedra indicates an Oligocene age for the divergence of Asian and New World clades and Miocene dispersal into South America

Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions （amphitropical range）. Great heterogeneity in the substitution rates of Gnetales （Ephedra, Gnetum, and Welwitschia） has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species （and 7736 aligned nucleotides） to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil-based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long-distance dispersal, but finer-scale studies are needed to test this hypothesis.     

Phylogeography of the magpie-robin species complex (Aves: Turdidae: Copsychus) reveals a Philippine species, an interesting isolating barrier and unusual dispersal patterns in the Indian Ocean and Southeast Asia

Aim The oriental magpie‐robin (Copsychus saularis) of South and Southeast Asia is a phenotypically variable species that appears to be closely related to two endemic species of the western Indian Ocean: the Madagascar magpie‐robin (Copsychus albospecularis) and the Seychelles magpie‐robin (Copsychus sechellarum). This unusual distribution led us to examine evolutionary relationships in magpie‐robins, and also the taxonomic significance of their plumage variation, via a molecular phylogenetic and population genetic analysis of C. saularis and C. albospecularis. Location Southern Asia from Nepal across Indochina to southern China, and the Indian Ocean from Madagascar to the Greater Sunda and Philippine islands. Methods We sequenced 1695 nucleotides of mitochondrial DNA comprising the complete second subunit of the nicotinamide adenine dinucleotide dehydrogenase (ND2) gene and 654 bases of the cytochrome c oxidase subunit I (COI) region in 51 individuals of eight C. saularis subspecies, 10 individuals of C. albospecularis (one subspecies) and single individuals of two other Copsychus species as outgroups. The data were analysed phylogenetically, with maximum likelihood, Bayesian, relaxed clock and parsimony methods, and geographically for patterns of genetic diversity. Results Phylogenetic analysis indicated that C. albospecularis lies within the nominal C. saularis, making C. saularis polyphyletic. Malagasy and non‐Philippine Asian populations form a monophyletic group that is sister to a clade of Philippine populations. Within non‐Philippine Asian populations, two groups are evident: black‐bellied birds in the eastern Greater Sunda islands and white‐bellied birds in the western Sundas and on mainland Asia. Main conclusions The phylogeny of magpie‐robins suggests a novel pattern of dispersal and differentiation in the Old World. Ancestral magpie‐robins appear to have spread widely among islands of the Indian Ocean in the Pliocene, probably aided by their affinity for coastal habitats. Populations subsequently became isolated in island groups, notably the Philippines, Madagascar and the Greater Sundas, leading to speciation in all three areas. Isolation in the Philippines may have been aided by competitive exclusion of C. saularis from Palawan by a congener, the white‐vented shama (Copsychus niger). In the Greater Sundas, white‐bellied populations appear to have invaded Borneo and Java recently, where they hybridize with resident black‐bellied birds.     

A fossil‐calibrated relaxed clock for Ephedra indicates an Oligocene age for the divergence of Asian and New World clades and Miocene dispersal into South America

Abstract Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions (amphitropical range). Great heterogeneity in the substitution rates of Gnetales (Ephedra, Gnetum, and Welwitschia) has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species (and 7736 aligned nucleotides) to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil‐based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long‐distance dispersal, but finer‐scale studies are needed to test this hypothesis.     

A new genus and species of abyssal sponge commonly encrusting polymetallic nodules in the Clarion-Clipperton Zone,East Pacific Ocean

The Clarion-Clipperton Zone (CCZ) in the East Pacific is a vast region targeted for deep-sea mineral exploration, for which there are almost no published taxonomic data. Here we describe Plenaster craigi gen. nov. sp. nov. from depths of ～4000 m in the eastern CCZ polymetallic nodule province. Despite over 40 years of intense exploration in the area, we reveal that P. craigi sp. nov. is the most abundant sponge and the most common metazoan encrusting on nodules in our study area at the eastern CCZ. It has a mean abundance of 15.3 ± 8.9 individuals per m² across 11 stations in a 30 × 30 km study site nested within the Singapore exploration area. The white encrusting sponge is filled with spheroxyasters with occasional styles protruding the surface. Plenaster craigi sp. nov. is morphologically similar to genera from three different families in two orders: Timea (Timeidae; Tethyida); Hemiasterella and Leptosastra (Hemiasterellidae; Tethyida); and Paratimea (Stelligeridae; Axinellida). However, based on the molecular (COI and 28S) phylogenetic trees generated in this study, P. craigi sp. nov. was located in the Order Axinellida and appeared to be distant to Timea, Hemiasterella, Leptosastra, and Paratimea. We propose a new genus for our material to be placed provisionally in the family Stelligeridae, as it is the only family in the order Axinellida whose members possess euasters. This provisional placement may change when sequences of the type specimens of these genera and advanced phylogenetic reconstruction methods become available in the future. However, we have shown clearly that Plenaster gen. nov. is unique and distinct from all currently known taxa. Plenaster craigi sp. nov. being an abundant metazoan encrusting on nodule and easily identified filter-feeding animal is a potentially indicator species for future mining impacts in the eastern CCZ, and possibly across the entire CCZ.

LSID: urn:lsid:zoobank.org:act:99D2DDBA-4643-4752-8C8A-AFF314E6B6E3     

A new species of Dasypodidae (Xenarthra: Cingulata) from the late Miocene of northwestern South America: implications in the Dasypodini phylogeny and diversity

A new species of dasypodid armadillo (Xenarthra, Cingulata), Anadasypus aequatorianus, from the late Miocene of Ecuador is described. The remains were collected in sediments of the Letrero Formation, Nabón Basin, which is part of several intermontane basins related to Andean uplift. The genus represents the oldest record of Dasypodini, which also encompasses Propraopus (Pleistocene–early Holocene) and Dasypus (?Miocene–Recent). The new species is based on several osteoderms, which show more derived features than Anadasypus hondanus, from the middle Miocene of Colombia. In order to test the affinities of A. aequatorianus within Dasypodini, we conducted a cladistic analysis of 24 morphological characters for 10 taxa. The most parsimonious tree supports the generic attribution of the new species and places Anadasypus basal to Propraopus and Dasypus, agreeing with the stratigraphic evidence. The faunas from tropical Andean areas differ noticeably from the better-known assemblages of the classic South American sequences. In the case of dasypodines, their geochronological distribution shows that they were historically restricted to tropical and subtropical environments and the main cladogenetic events of the group probably occurred at lower latitudes. In this context, the taxon described herein fills important temporal and geographic gaps of early Neogene armadillos from intertropical areas.http://www.zoobank.org/urn:lsid:zoobank.org:pub:9DC76603-D831-4E68-BE55-90113228E0F4     

A phylogeographical study of the Turnip mosaic virus population in East Asia reveals an 'emergent' lineage in Japan

The genetic structure of populations of Turnip mosaic virus (TuMV) in East Asia was assessed by making host range and gene sequence comparisons of 118 isolates utilizing a population genetic approach. Most, but not all, isolates collected from Brassica plants in China infected only Brassica plants, whereas those from Japan infected both Brassica and Raphanus (BR) plants. Analyses of the positions of recombination sites in five regions of the genomes (one third of the full sequence) of the many recombinant isolates were fully congruent with the results of phylogenetic analysis, and at least one recombination type pattern was shared between Chinese and Japanese populations. One lineage of nonrecombinant isolates from the basal-BR lineage was found in 2000 in Kyushu, Japan but none in China, and have since been found over the whole island. The sudden expansion of this basal-BR population was strongly supported by calculations showing the deviations from the neutral equilibrium model for the individual geographical lineages with overall lack of nucleotide diversity, and by analysis of mismatch distribution. Our study shows that the recent Chinese and Japanese TuMV isolates are part of the same population but are discrete lineages.