Effects of taxon sampling on molecular dating for within-genus divergence events, when deep fossils are used for calibration

A universal method of molecular dating that can be applied to all families and genera regardless of their fossil records, or lack thereof, is highly desirable. A possible method for eudicots is to use a large phylogeny calibrated using deep fossils including tricolpate pollen as a fixed （124 mya） calibration point. This method was used to calculate node ages within three species-poor disjunct basal eudicot genera, Caulophyllum, Podophyllum and Pachysandra, and sensitivity of these ages to effects such as taxon sampling were then quantified. By deleting from one to three accessions related to each genus in 112 different combinations, a confidence range describing variation due only to taxon sampling was generated. Ranges for Caulophyllum, Podophyllum and Pachysandra were 8.4-10.6, 7.6-20.0, and 17.6-25.0 mya, respectively. However, the confidence ranges calculated using bootstrapping were much wider, at 3-19, 0-32 and 11-32 mya, respectively. Furthermore, deleting 10 adjacent taxa had a large effect in Pachysandra only, indicating that undersampling effects are significant among Buxales. Changes to sampling density in neighboring clades, or to the position of the fixed fossil calibration point had small to negligible effects. Non-parametric rate smoothing was more sensitive to taxon sampling effects than was penalized likelihood. The wide range for Podophyllum, compared to the other two genera, was probably due to a high degree of rate heterogeneity within this genus. Confidence ranges calculated by this method could be narrowed by sampling more individuals within the genus of interest, and by sequencing multiple DNA regions from all species in the phylogeny.     

A Dispersal and Vicariance Analysis of the Genus Caragana Fabr.

The genus Caragana Fabr., consisting of approximately 70 species, has a temperate Asian distribution and occurs mainly in the drought and cold regions of the northwestern and southwestern Tibetan Plateau of China. The distribution pattern of the genus was investigated using dispersal-vicariance analysis （DIVA）, The results indicate that vicariance versus dispersal plays a major role in the evolution of the genus and that short-distance dispersal also exists. There is no fossil record of this genus. Therefore, Caragana is inferred as an advanced taxon in terms of its limited temperate Asian distribution. Based on the morphological variation and ecological adaptation in Caragana, the generic speciation is postulated to be related to the uplifting of the Tibetan Plateau and to the increasing arid conditions of Central Asian lands since the Neogene. The Mongolian Plateau and the Tibetan Plateau are hypothesized as the barriers of vicariance between East Asia and western Central Asia.     

The geographic polymorphisms of Y chromosome at YAP locus among 25 ethnic groups in Yunnan, China

Little is known of the origin and the earliest migratory routes of the eastern Asia populations. Many researchers suggested that modern humans in eastern Asia originated from Africa[1,2], and the migratory routes spread from western to eastern Asia along southern mainland of Asia[3]. Eastern Asia was one of the few regions with relatively abundant hominid fossils, especially Yun-nan Province of China, the home of Ramapithecus and Yuanmou Man. Yuanmou Man was the oldest hominid fossil[4]. …     

Addition of Ptyas nigromarginata （Blyth, 1854） （Squamata： Colubridae） to the Snake Fauna of Thailand with Preliminary Remarks on Its Distribution

The first record of Ptyas nigromarginata(Blyth,1854) from Thailand and a new record from China are reported.Literature and internet sources were searched for previous records of this species to establish its geographic and altitudinal distributions in Asia.The distribution in India was adapted to the new state division of the northern part of the country.The results show that the species almost exclusively occurs in hill evergreen and montane forests of the Himalayan foothills and mountain ranges continuous with it,at altitudes of 1000–2300 m above sea level.     

NEW RECORDS OF CROTONIOIDEA FROM CHINA, WITH DESCRIPTION OF A NEW SPECIES OF ALLONOTHRUS (AGARI: ORIBAIDA)

A majority of known species of Crotonioidea inhabit leaf litter or upper soil horizons, where they feed on fungi or decomposing higher plant material; some inhabit specialized rnicro-habitats, such as tree, bog or spring. The superfamily encompasses, approximately 400 species representing 32 genera in nine families. Although this superfamily is relatively well known in the European and Soviet part of the Palearctic region, it is almost unknown in China.This paper reports 29 species of crotonioid mites in China representing 13 genera in 6 families. Among them one species is described as new and 27 species are recorded for the first time from China.     

Late Pliocene diversity and distribution of Drynaria(Polypodiaceae) in western Yunnan explained by forest vegetation and humid climates

The palaeodiversity of flowering plants in Yunnan has been extensively interpreted from both a molecular and fossil perspective. However, for cryptogamic plants such as ferns, the palaeodiversity remains poorly known. In this study, we describe a new ferny fossil taxon, Drynaria lanpingensis sp. nov. Huang,Su et Zhou(Polypodiaceae), from the late Pliocene of northwestern Yunnan based on fragmentary frond and pinna with in situ spores. The frond is pinnatifid and the pinnae are entirely margined. The sori are arranged in one row on each side of the primary vein. The spores have a semicircular to bean-shaped equatorial view and a tuberculate surface. Taken together with previously described fossils, there are now representatives of three known fossil taxa of Drynaria from the late Pliocene of western Yunnan.These finds suggest that Drynaria diversity was considerable in the region at that time. As Drynaria is a shade-tolerant plant, growing preferably in wet conditions in the understory of forests, its extensive existence may indicate forest vegetation and humid climates in western Yunnan during the late Pliocene.This is in line with results from floristic investigations and palaeoclimatic reconstructions based on fossil floras.     

First Record of the Gekkonid Genus Cnemaspis Strauch, 1887 from Gunung Mulu National Park,Northern Sarawak,East Malaysia may Represent an Undescribed Species

We provide confirmed photographic evidence for the previously overlooked occurrence of the polyphyletic Asian gecko genus Cnemaspis from Gunung Mulu National Park, the world-renowned UNESCO natural heritage site in northern Sarawak, East Malaysia. This new record from Sarawak province represents a remarkable range extension for Cnemaspis cf. kendallii by 550 km to the northeast and denotes the most northern occurrence of the genus in Borneo. Our new finding makes it very likely that these gekkonid lizards also inhabit appropriate limestone karst habitats in adjacent Sabah, Brunei, and Kalimantan. Given the visible differences in the Mulu specimen compared to those from the remaining distribution range on Borneo and the Malaysian Peninsula together with the fact that numerous Cnemaspis species are restricted to small areas, it seems plausible that another undescribed, rather cryptic and possibly locally endemic Bornean species is involved. Lastly, the new record contributes to the importance of the Mulu National Park as a major conservation area in East Malaysia of international concerns.     

Inferring the biogeographic origins of inter‐continental disjunct endemics using a Bayes‐DIVA approach

The arcto‐Tertiary relictual flora is comprised of many genera that occur non‐contiguously in the temperate zones of eastern Asia, Europe, eastern North America, and western North America. Within each distributional area, species are typically endemic and may thus be widely separated from closely related species within the other areas. It is widely accepted that this common pattern of distribution resulted from of the fragmentation of a once more‐continuous arcto‐Tertiary forest. The historical biogeographic events leading to the present‐day disjunction have often been investigated using a phylogenetic approach. Limitations to these previous studies have included phylogenetic uncertainty and uncertainty in ancestral range reconstructions. However, the recently described Bayes‐DIVA method handles both types of uncertainty. Thus, we used Bayes‐DIVA analysis to reconstruct the stem lineage distributions for 185 endemic lineages from 23 disjunct genera representing 17 vascular plant families. In particular, we asked whether endemic lineages within each of the four distributional areas more often evolved from (1) widespread ancestors, (2) ancestors dispersed from other areas, or (3) endemic ancestors. We also considered which of these three biogeographic mechanisms may best explain the origins of arcto‐Tertiary disjunct endemics in the neotropics. Our results show that eastern Asian endemics more often evolved from endemic ancestors compared to endemics in Europe and eastern and western North America. Present‐day endemic lineages in the latter areas more often arose from widespread ancestors. Our results also provide anecdotal evidence for the importance of dispersal in the biogeographic origins of arcto‐Tertiary species endemic in the neotropics.     

Species-level phylogeography and evolutionary history of the hyperdiverse marine gastropod genus Conus

Phylogenetic and paleontological analyses are combined to reveal patterns of species origination and divergence and to define the significance of potential and actual barriers to dispersal in Conus, a species-rich genus of predatory gastropods distributed throughout the world's tropical oceans. Species-level phylogenetic hypotheses are based on nucleotide sequences from the nuclear calmodulin and mitochondrial 16S rRNA genes of 138 Conus species from the Indo-Pacific, eastern Pacific, and Atlantic Ocean regions. Results indicate that extant species descend from two major lineages that diverged at least 33 mya. Their geographic distributions suggest that one clade originated in the Indo-Pacific and the other in the eastern Pacific + western Atlantic. Impediments to dispersal between the western Atlantic and Indian Oceans and the central and eastern Pacific Ocean may have promoted this early separation of Indo-Pacific and eastern Pacific + western Atlantic lineages of Conus. However, because both clades contain both Indo-Pacific and eastern Pacific + western Atlantic species, migrations must have occurred between these regions; at least four migration events took place between regions at different times. In at least three cases, incursions between regions appear to have crossed the East Pacific Barrier. The paleontological record illustrates that distinct sets of Conus species inhabited the Indo-Pacific, eastern Pacific + western Atlantic, and eastern Atlantic + former Tethys Realm in the Tertiary, as is the case today. The ranges of <1% of fossil species (N=841) spanned more than one of these regions throughout the evolutionary history of this group.     

Phylogeny and biogeography of the flowering plant genus Styrax (Styracaceae) based on chloroplast DNA restriction sites and DNA sequences of the internal transcribed spacer region

Phylogenetic relationships within the flowering plant genus Styrax were investigated with DNA sequence data from the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) and with chloroplast DNA restriction site data from the genes trnK, rpoC1, and rpoC2. The data sets from each genome were analyzed separately and in combination with parsimony methods. The results strongly support the monophyly of each of the four series of the genus but provide little phylogenetic resolution among them. Reticulate evolution may at least partly explain discordance between the molecular phylogenetic estimates and a prior morphological estimate within series Cyrta. The historical biogeography of the genus was inferred with unweighted parsimony character optimization of trees recovered from a combined ITS and morphological data set, after a series of combinability tests for data set congruence was conducted. The results are consistent with the fossil record in supporting a Eurasian origin of Styrax. The nested phylogenetic position of the South American members of the genus within those from southern North America and Eurasia suggests that the boreotropics hypothesis best explains the amphi-Pacific tropical disjunct distribution occurring within section Valvatae. The pattern of relationship recovered among the species of section Styrax ((western North America + western Eurasia) (eastern North America + eastern Eurasia)) is rare among north-temperate Tertiary forest relicts. The monophyly of the group of species from western North America and western Eurasia provides qualified support for the Madrean-Tethyan hypothesis, which posits a Tertiary floristic connection among the semiarid regions in which these taxa occur. A single vicariance event between eastern Asia and eastern North America accounts for the pattern of relationship among intercontinental disjuncts in series Cyrta.     

Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Bracbypodium distacbyon

This work evaluates the phenotypic response of the model grass （Brachypodium distacbyon （L.） P. Beauv.） to nitrogen and phosphorus nutrition using a combination of imaging techniques and destructive harvest of shoots and roots. Reference line Bd21-3 was grown in pots using 11 phosphorus and 11 nitrogen concentrations to establish a dose-response curve. Shoot biovolume and biomass, root length and biomass, and tissue phosphorus and nitrogen concentrations increased with nutrient concentration. Shoot biovolume, estimated by imaging, was highly correlated with dry weight （R2 〉 0.92） and both biovolume and growth rate responded strongly to nutrient availability. Higher nutrient supply increased nodal root length more than other root types. Photochemical efficiency was strongly reduced by low phosphorus concentrations as early as 1 week after germination, suggesting that this measurement may be suitable for high throughput screening of phosphorus response. In contrast, nitrogen concentration had little effect on photochemical efficiency. Changes in biovolume over time were used to compare growth rates of four accessions in response tonitrogen and phosphorus supply. We demonstrate that a time series image-based approach coupled with mathematical modeling provides higher resolution of genotypic response to nutrient supply than traditional destructive techniques and shows promise for high throughput screening and determina- tion of genomic regions associated with superior nutrient use efficiency.     

Genealogy and phylogeography of Cyprinid fish Labeo rohita （Hamilton, 1822） inferred from ATPase 6 and 8 mitochondrial DNA gene analysis

ATPase 6/8 gene （842 bp） of mitochondrial DNA was sequenced in Labeo rohita samples （n = 253） collected from nine rivers belonging to four river basins; Indus, Ganges, Brahmaputra and Mahanadi. Analysis revealed 44 haplotypes with high haplotype diversity （Hd） 0.694 and low nucleotide diversity （π） 0.001. The within population variation was larger （83.44%） than among population differences （16.56%）. The mean Fsv value （0.166; P 〈 0.05） for overall populations revealed moderate level of genetic structuring in the wild L. rohita populations. The haplotype network presented a single clade for wild L. rohita population, from different rivers. Negative values for Fu＇s index （Fs）, mismatch distribution analysis indicated period of expansion in L. rohita population. The time after recent expansion was estimated for each population, between 0.042 to 0.167 mya. The pattern of Isolation by Distance （IBD） was not significant （r = -0.113, P 〈 0.287）, when all the sampling locations were compared （Mantel test）, however, when an outlier （Indus, Brahmaputra and Mahanadi） was removed from the whole population set, a clear positive correlation between pairwise Fsv and geographic distance （Km） was seen. The analysis of data demonstrated that ATPase6/8 gene polymorphism is a potential marker to understand genetic population structure of wild L. rohita existing in different rivers. The study identified population substructure in wild L. rohita with common ancestral origin [Current Zoology 60 （4）： 460--471, 2014].     

Molecular mechanisms of insect adaptation to plant defense： Lessons learned from a Bruchid beetle

Plants can accumulate, constitutively and/or after induction, a wide variety of defense compounds in their tissues that confer resistance to herbivorous insects. The naturally occurring plant resistance gene pool can serve as an arsenal in pest management via transgenic approaches. As insect-plant interaction research rapidly advances, it has gradually become clear that the effects of plant defense compounds are determined not only by their toxicity toward target sites, but also by how insects respond to the challenge. Insect digestive tracts are not passive targets of plant defense, but often can adapt to dietary challenge and successfully deal with various plant toxins and anti-metabolites. This adaptive response has posed an obstacle to biotechnology-based pest control approaches, which underscores the importance of understanding insect adaptive mechanisms. Molecular studies on the impact of protease inhibitors on insect digestion have contributed significantly to our understanding of insect adaptation to plant defense. This review will focus on exposing how the insect responds to protease inhibitors by both qualitative and quantitative remodeling of their digestive proteases using the cowpea bruchid-soybean cysteine protease inhibitor N system.     

Evolution of deceit by worthless donations in a nuptial gift-giving spider

Males of the nursery web spider Pisaura mirabil usually offer an insect prey wrapped in white silk as a nuptial gift to facilitate copulation. Males exploit female foraging preferences in a sexual context as females feed on the gift during copula- tion. It is possible for males to copulate without a gift, however strong female preference for the gift leads to dramatically higher mating success for gift-giving males. Females are polyandrous, and gift-giving males achieve higher mating success, longer copulations, and increased sperm transfer that confer advantages in sperm competition. Intriguingly, field studies show that ap- proximately one third of males carry a worthless gift consisting of dry and empty insect exoskeletons or plant fragments wrapped in white silk. Silk wrapping disguises gift content and females are able to disclose gift content only after accepting and feeding on the gift, meanwhile males succeed in transferring sperm. The evolution of deceit by worthless gift donation may be favoured by strong intra-sexual competition and costs of gift-construction including prey capture, lost foraging opportunities and investment in silk wrapping. Females that receive empty worthless gifts terminate copulation sooner, which reduces sperm transfer and likely disadvantages males in sperm competition. The gift-giving trait may thus become a target of sexually antagonistic co-evolution, where deceit by worthless gifts leads to female resistance to the trait. We discuss factors such as female mating rate and intensity of sperm competition that may shape the evolution of male deception, and how ecological factors may influence the evolution and maintenance of worthless gifts as an evolutionarily stable alternative mating strategy by frequency dependent selection     

Uropygial gland volatiles may code for olfactory information about sex,individual, and species in Bengalese finches Lonchura striata

Over-shadowed by eye-catching vocal and visual signals, chemical communication has long been overlooked in birds. This study aimed at exploring whether volatile composition of the uropygial gland secretion （UGS） of birds was associated with the information about sex, individual and species. By using dichloromethane extraction and gas chromatography-mass spectrometry （GC-MS）, we analyzed the UGS volatiles of domesticated Bengalese finches （ Lonchura striata, Estrildiea） which is also known as white-rumped munias. We characterized 16 volatile molecules from the UGS, including eight n-alkanols, five diesters, an ester, an aldehyde and a fatty acid, and quantified them in terms of GC peak area percentages （relative abundances） . Among these compounds, hexadecanol and octadecanol were major components in both sexes. The former was richer in males than in females and the latter richer in females than in males, suggesting that they might be male and female pheromone candidates, respectively. The high inter-individual variations, in relative abundance, of the UGS volatiles implied that these compounds might carry information about individuality. The similarity between GC profiles of the UGS and wing feather from same individuals indicates that the birds might preen the secretion to their feathers to transmit chemical cues. Additionally, by comparing with three sympatric passerine species, i. e., zebra finches Taeniopygia guttata, yellow-bowed buntings Emberiza chrysophrys and rooks Corvus frugilegus, we found that the composition of C13 - C18 alkanols in the UGS might code for information about species. Our study also showed that quantitative differences （degree） of same UGS volatiles might be the key for the Bengalese finch to code for information about sex and individuality whereas both the kind and degree of UGS constituents could be utilized to code for information about species [ Current Zoology 55 （5）： 357-365, 2009].