Phylogeny and species delimitation of the C-genome diploid species in Oryza

The diploid Oryza species with C-genome type possesses abundant genes useful for rice improvement and provides parental donors of many tetraploid species with the C-genome (BBCC,CCDD).Despite extensive studies,the phylogenetic relationship among the C-genome species and the taxonomic status of some taxa remain controversial.In this study,we reconstructed the phylogeny of three diploid species with C-genome (Oryza officinalis,O.rhizomatis,and O.eichingeri) based on sequences of 68 nuclear single-copy genes.We obtained a fully resolved phylogenetic tree,clearly indicating the sister relationship of O.officinalis and O.rhizomatis,with O.eichingeri being the more divergent lineage.Incongruent phylogenies of the C-genome species found in previous studies might result from lineage sorting,introgression/hybridization and limited number of genetic markers used.We further applied a recently developed Bayesian species delimitation method to investigate the species status of the Sri Lankan and African O.eichingeri.Analyses of two datasets (68 genes with a single sample,and 10 genes with multiple samples) support the distinct species status of the Sri Lankan and African O.eichingeri.In addition,we evaluated the impact of the number of sampled individuals and loci on species delimitation.Our simulation suggests that sampling multiple individuals is critically important for species delimitation,particularly for closely related species.     

Genetic and morphological diversity of mouse lemurs (Microcebus spp.) in northern Madagascar: The discovery of a putative new species?

Tropical forests harbor extremely high levels of biological diversity and are quickly disappearing. Despite the increasingly recognized high rate of habitat loss, it is expected that new species will be discovered as more effort is put to document tropical biodiversity. Exploring under‐studied regions is particularly urgent if we consider the rapid changes in habitat due to anthropogenic activities. Madagascar is known for its extraordinary biological diversity and endemicity. It is also threatened by habitat loss and fragmentation. It holds more than 100 endemic primate species (lemurs). Among these, Microcebus (mouse lemurs) is one of the more diverse genera. We sampled mouse lemurs from several sites across northern Madagascar, including forests never sampled before. We obtained morphological data from 99 Microcebus individuals; we extracted DNA from tissue samples of 42 individuals and amplified two mitochondrial loci (cytb and cox2) commonly used for species identification. Our findings update the distribution of three species (Microcebus tavaratra, Microcebus arnholdi, and Microcebus mamiratra), including a major increase in the distribution area of M. arnholdi. We also report the discovery of a new Microcebus lineage genetically related to M. arnholdi. Several complementary approaches suggest that the newly identified Microcebus lineage might correspond to a new putative species, to be confirmed or rejected with additional data. In addition, morphological analyses showed (a) clear phenotypic differences between M. tavaratra and M. arnholdi, but no clear differences between the new Microcebus lineage and the sister species M. arnholdi; and (b) a significant correlation between climatic variables and morphology, suggesting a possible relationship between species identity, morphology, and environment. By integrating morphological, climatic, genetic, and spatial data of two northern Microcebus species, we show that the spatial distribution of forest‐dwelling species may be used as a proxy to reconstruct the past spatial changes in forest cover and vegetation type.     

Fine-scale cospeciation between Brachycaudus and Buchnera aphidicola: bacterial genome helps define species and evolutionary relationships in aphids

Aphids harbour an obligatory symbiont, Buchnera aphidicola, providing essential amino acids not supplied by their diet. These bacteria are transmitted vertically and phylogenic analyses suggest that they have 'cospeciated' with their hosts. We investigated this cospeciation phenomenon at a fine taxonomic level, within the aphid genus Brachycaudus. We used DNA-based methods of species delimitation in both organisms, to avoid biases in the definition of aphid and Buchnera species and to infer association patterns without the presumption of a specific interaction. Our results call into question certain 'taxonomic' species of Brachycaudus and suggest that B. aphidicola has diversified into independently evolving entities, each specific to a 'phylogenetic' Brachycaudus species. We also found that Buchnera and their hosts simultaneously diversified, in parallel. These results validate the use of Buchnera DNA data for inferring the evolutionary history of their host. The Buchnera genome evolves rapidly, making it the perfect tool for resolving ambiguities in aphid taxonomy. This study also highlights the usefulness of species delimitation methods in cospeciation studies involving species difficult to conceptualize--as is the case for bacteria--and in cases in which the taxonomy of the interacting organisms has not been determined independently and species definition depends on host association.     

云南西部实蝇的多样性

2005和2006年,在云南西部瑞丽、潞江坝、六库、保山、大理5个地区,采用信息素引诱法及被害瓜果内实蝇收集法对5个地区实蝇多样性进行分析.结果表明,5个地区实蝇丰富度的发生模式明显分为2种类型:瑞丽和潞江坝实蝇全年发生;六库、保山和大理实蝇季节性发生;瑞丽的实蝇种类丰富度最高,有20种,其次是潞江坝,11种,而保山、大理的实蝇种类丰富度低,分别为4种和3种;该区域实蝇优势种为桔小实蝇(Bactrocera dorsalis)和南亚果实蝇(B. tau);2年实蝇多样性指数均以六库最低,以潞江坝最高.各地实蝇种类相似性变化较大, 相似性系数在0.15～1.00 之间.结果为了解云南西部实蝇种类分布以及预防实蝇危害提供了基础数据.     

Sequence-based species delineation and molecular phylogenetics of the transitional Nearctic–Neotropical grasshopper genus Taeniopoda (Orthoptera,Romaleidae)

Taeniopoda is a genus of grasshoppers currently represented by 12 species distributed from southern USA to Panama, with most of them occurring along the transitional Nearctic–Neotropical region in central and southern Mexico. Despite being a small group of conspicuous, colourful species, the systematics of Taeniopoda has been largely neglected, including its phylogenetic affinity with the morphologically similar, monotypic genus Romalea. Here, we assessed the species limits in 11 of the species of Teniopoda based on two mitochondrial (mt) markers (COI, cyt b). Phylogenetic relationships were reconstructed adding two nuclear gene markers (28S, H3). A relaxed molecular clock analysis was performed based on the mt markers. We detected nuclear mt paralogues (numts) and the probable introgression of T. tamaulipensis mtDNA in specimens of T. eques from central Mexico. Between six and 14 species of Taeniopoda were delimited by the sequence-based approaches performed (COI divergence with thresholds of 1 and 2%; General Mixed Yule-Coalescent (GMYC) model). The GMYC and 1% threshold analyses with COI were more congruent with the currently recognized morphology-based taxonomy with 10 and 11 putative species, respectively. Four of these species were regarded as ‘stable’, since they were supported by at least one of the molecular analyses and by diagnostic morphological features. The species-based phylogeny recovered Taeniopoda as paraphyletic with respect to the monotypic genus Romalea. Three morphologically and geographically congruent major clades were recovered, two with species having a considerably elevated pronotal crest and one with its members having it less elevated. The origin and subsequent diversification of Taeniopoda were estimated to occur from the mid and late Miocene to Pliocene, respectively. The current species diversity in Taeniopoda was estimated to occur during the Pleistocene, which was probably influenced by the climatic oscillations that occurred during this period and the uplift of mountain ranges in Central America.