Species delimitation in Amana (Liliaceae): transcriptomes battle with evolutionary complexity.

Species delimitation has long been a subject of controversy, and there are many alternative concepts and approaches used to define species in plants. The genus Amana (Liliaceae), known as "East Asian tulips" has a number of cryptic species and a huge genome size (1C = 21.48-57.35 pg). It also is intriguing how such a spring ephemeral genus thrives in subtropical areas. However, phylogenetic relationships and species delimitation within Amana are challenging. Here we included all species and 84 populations of Amana, which are collected throughout its distribution range. A variety of methods were used to clarify its species relationships based on a combination of morphological, ecological, genetic, evolutionary and phylogenetic species concepts. This evidence supports the recognition of at least 12 species in Amana. Moreover, we explored the complex evolutionary history within the genus and detected several historical hybridization and introgression events based on phylogenetic trees (transcriptomic and plastid), phylonetworks, admixture and ABBA-BABA analyses. Morphological traits have undergone parallel evolution in the genus. This spring ephemeral genus might have originated from a temperate region, yet finally thrives in subtropical areas, and three hypotheses about its adaptive evolution are proposed for future testing. In addition, we propose a new species, Amana polymorpha, from eastern Zhejiang Province, China. This research also demonstrates that molecular evidence at the genome level (such as transcriptomes) has greatly improved the accuracy and reasonability of species delimitation and taxon classification.

Phylogenomics and integrative taxonomy reveal two new species of Amana (Liliaceae).

Until now the genus Amana (Liliaceae), known as 'East Asian tulips', has contained just seven species. In this study, a phylogenomic and integrative taxonomic approach was used to reveal two new species, Amana nanyueensis from Central China and A. tianmuensis from East China. A. nanyueensis resembles Amana edulis in possessing a densely villous-woolly bulb tunic and two opposite bracts, but differs in its leaves and anthers. Amana tianmuensis resembles Amana erythronioides in possessing three verticillate bracts and yellow anthers, but differs in aspects of its leaves and bulbs. These four species are clearly separated from each other in principal components analysis based on morphology. Phylogenomic analyses based on plastid CDS further support the species delimitation of A. nanyueensis and A. tianmuensis and suggests they are closely related to A. edulis. Cytological analysis shows that A. nanyueensis and A. tianmuensis are both diploid (2n = 2x = 24), different from A. edulis, which is either diploid (northern populations) or tetraploid (southern populations, 2n = 4x = 48). The pollen morphology of A. nanyueensis is similar to other Amana species (single-groove germination aperture), but A. tianmuensis is quite different because of the presence of a sulcus membrane, which creates the illusion of double grooves. Ecological niche modelling also revealed a niche differentiation between A. edulis, A. nanyueensis and A. tianmuensis.

Bulliform Phytolith Size of Rice and Its Correlation With Hydrothermal Environment: A Preliminary Morphological Study on Species in Southern China.

In the last decade, our understanding of rice domestication has improved by new archaeological findings using advanced analytical techniques such as morphological and morphometric analyses on rice grains, spikelet bases and phytoliths, and ancient DNA analysis on rice remains. Previous studies have considered the size of rice bulliform phytoliths as a proxy for tracking the domestication process. These phytoliths are often abundant and well preserved in sediments, and their shape is under the control of numerous genes, which may shift toward larger sizes by genetic mutation in domestication. Therefore, it has been assumed that the bulliforms of domesticated rice are usually larger than those of wild ones; however, morphometric data supporting this assumption are lacking in the literature, thereby requiring additional evidence to test its veracity. In this study, the vertical and horizonal lengths of bulliform phytoliths were measured in four rice species (domesticated Oryza sativa and wild Oryza rufipogon, Oryza officinalis, and Oryza meyeriana) from different regions of southern China. We found that the bulliform morphometric data of wild and domesticated rice overlapped and that there was no statistically significant difference between them. Therefore, bulliform size could not be used as a diagnostic indicator to distinguish domesticated rice from wild species and is a supporting rather than conclusive proxy for determining the domesticated status of rice in archaeological research. We further found that larger rice bulliform sizes likely occurred at the locations with higher temperature, precipitation, and water levels, indicating hydrothermal environment is an alternative factor influencing the size of rice bulliform phytoliths. For further archaeological use of an increasing size trend of bulliform phytoliths to reveal the process of rice domestication, we present some suggestions for controlling the influence of hydrothermal factors. Even so, the combination of bulliform phytolith size with other established criteria is strongly suggested to provide precise identification of wild and domesticated rice in future research.

Last Glacial Maximum, early Holocene and modern environments of the northern South China Sea region: Insight from SEM analysis of Oak (Quercus) pollen.

Oak (Quercus) pollen was identified at the infra-generic (i.e. sub-genus to species) utilizing Scanning Electron Microscope (SEM) images of modern (i.e. 18 species from southern China) and fossil pollen grains from northern South China Sea (SCS) marine and terrestrial sediments. Key morphological characteristics of Quercus exine sculpture were used to separate the pollen into evergreen and deciduous groups, with this distinction applied to the fossil oak pollen from the Last Glacial Maximum (LGM) and early Holocene periods. The presence of Quercus pollen from the modern Pearl River and northern SCS suggests long distance transport from inland temperate to tropical regions surrounding the SCS. Fossil oak pollen from terrestrial and marine sediments from the northern SCS region suggests different pollen representation between these two sedimentary environments, with the terrestrial site dominated by evergreen Quercus types and the marine location showing greater representation of deciduous oak species. The presence of both evergreen and deciduous oak pollen in the LGM age marine sediments suggests only moderate cooling during this time period, while the dramatic increase of deciduous Quercus pollen in the marine core, as well as generally higher pollen influx values, reflects greater fluvial discharge, which in turn is linked to increased precipitation in the region during the early Holocene period.

Morphological diversity of Quercus fossil pollen in the northern South China Sea during the last glacial maximum and its paleoclimatic implication.

We aimed to obtain high resolution vegetation data and climate information about the LGM in the inland of the northern SCS based on key pollen types. Dominant Quercus fossil pollen grains in the core from the continental shelf of the northern SCS have been identified at the infrageneric level by using scanning electron microscopy. Based on tectum ornamentation, we recognized five sculpture types of Quercus pollen, namely, rodlike, rodlike masked, rodlike vertical, verrucate and micro-verrucate. Such a high diversity of Quercus fossil pollen types indicated that broadleaved forests were widely distributed in the inland along the northern SCS and included species of the subgenera Cyclobalanopsis and Quercus, of which subgenus Cyclobalanopsis populations were highly dominant. Low abundance of deciduous Quercus pollen probably derived from temperate-subtropical forests, while abundant evergreen pollen types of subgenura Quercus and Cyclobalanopsis, as well as other pollen of broadleaved taxa in the pollen assemblages, strongly suggest that the inland has been covered by dense subtropical forests. Consequently, the warm and humid subtropical climate prevailed during the LGM in the inland along the northern SCS. Our results shed new light on regional climatic conditions during the LGM in eastern Asia based on high diversity of Quercus fossil pollen in marine deposits from northern SCS.

A grazing Gomphotherium in Middle Miocene Central Asia, 10 million years prior to the origin of the Elephantidae.

Feeding preference of fossil herbivorous mammals, concerning the coevolution of mammalian and floral ecosystems, has become of key research interest. In this paper, phytoliths in dental calculus from two gomphotheriid proboscideans of the middle Miocene Junggar Basin, Central Asia, have been identified, suggesting that Gomphotherium connexum was a mixed feeder, while the phytoliths from G. steinheimense indicates grazing preference. This is the earliest-known proboscidean with a predominantly grazing habit. These results are further confirmed by microwear and isotope analyses. Pollen record reveals an open steppic environment with few trees, indicating an early aridity phase in the Asian interior during the Mid-Miocene Climate Optimum, which might urge a diet remodeling of G. steinheimense. Morphological and cladistic analyses show that G. steinheimense comprises the sister taxon of tetralophodont gomphotheres, which were believed to be the general ancestral stock of derived "true elephantids"; whereas G. connexum represents a more conservative lineage in both feeding behavior and tooth morphology, which subsequently became completely extinct. Therefore, grazing by G. steinheimense may have acted as a behavior preadaptive for aridity, and allowing its lineage evolving new morphological features for surviving later in time. This study displays an interesting example of behavioral adaptation prior to morphological modification.

Identification of host plant use of adults of a long-distance migratory insect, Mythimna separata.

Adults of many insect species often become contaminated with pollen grains when feeding. Identification of plant hosts for M. separata moths could increase our understanding of their geographic origin and the coevolution of M. separata moths and their host plants. However, identifying the diet of noctuid moths using traditional direct observation is limited by their nocturnal and flight habits. In this study, we used core barcode markers and pollen morphology to identify pollen species. We found pollen from 13 plant species belonging to nine families on trapped M. separata moths, mainly from Angiosperm, Dicotyledoneae. Pollen was found on 14.4% and 12.3% of females and males, respectively, and the amount of pollen transported varied with the body part, with the most pollen on the proboscis. We were able to determine from this that the moths visited woody plants more than herbaceous plants, but not significantly so, and that they carried more pollen earlier in the migration season. In this study, we clarified the species and frequencies of pollen deposition on M. separata moths. These findings improve our understanding of the coevolution of the moths and their host plants. Identification of plant hosts for adult moths provides a new means of studying noctuid moth-host plant interactions, and informs the development of more efficient management practices for M. separata.

Host Plants Identification for Adult Agrotis ipsilon, a Long-Distance Migratory Insect.

In this study, we determined the host relationship of Agrotis ipsilon moths by identifying pollen species adhering them during their long-distance migration. Pollen carried by A. ipsilon moths was collected from 2012 to 2014 on a small island in the center of the Bohai Strait, which is a seasonal migration pathway of this pest species. Genomic DNA of single pollen grains was amplified by using whole genome amplification technology, and a portion of the chloroplast rbcL sequence was then amplified from this material. Pollen species were identified by a combination of DNA barcoding and pollen morphology. We found 28 species of pollen from 18 families on the tested moths, mainly from Angiosperm, Dicotyledoneae. From this, we were able to determine that these moths visit woody plants more than herbaceous plants that they carry more pollen in the early and late stages of the migration season, and that the amounts of pollen transportation were related to moth sex, moth body part, and plant species. In general, 31% of female and 26% of male moths were found to be carrying pollen. Amounts of pollen on the proboscis was higher for female than male moths, while the reverse was true for pollen loads on the antennae. This work provides a new approach to study the interactions between noctuid moth and their host plants. Identification of plant hosts for adult moths furthers understanding of the coevolution processes between moths and their host plants.

A diverse paleobiota in early eocene Fushun amber from China.

Paleogene arthropod biotas have proved important for tracing the faunal turnover and intercontinental faunal interchange driven by climatic warming and geodynamic events [1-5]. Despite the large number of Paleogene fossil arthropods in Europe and North America [5-8], little is known about the typical Asian (Laurasia-originated) arthropod biota. Here, we report a unique amber biota (50-53 million years ago) from the Lower Eocene of Fushun in northeastern China, which fills a large biogeographic gap in Eurasia. Fushun amber is derived from cupressaceous trees, as determined by gas chromatography-mass spectrometry, infrared spectroscopy, and paleobotanical observations. Twenty-two orders and more than 80 families of arthropods have been reported so far, making it among the most diverse amber biotas. Our results reveal that an apparent radiation of ecological keystone insects, including eusocial, phytophagous, and parasitoid lineages, occurred at least during the Early Eocene Climatic Optimum. Some insect taxa have close phylogenetic affinities to those from coeval European ambers, showing a biotic interchange between the eastern and western margins of the Eurasian landmass during the Early Paleogene.

500-year climate cycles stacking of recent centennial warming documented in an East Asian pollen record.

Here we presented a high-resolution 5350-year pollen record from a maar annually laminated lake in East Asia (EA). Pollen record reflected the dynamics of vertical vegetation zones and temperature change. Spectral analysis on pollen percentages/concentrations of Pinus and Quercus, and a temperature proxy, revealed ~500-year quasi-periodic cold-warm fluctuations during the past 5350 years. This ~500-year cyclic climate change occurred in EA during the mid-late Holocene and even the last 150 years dominated by anthropogenic forcing. It was almost in phase with a ~500-year periodic change in solar activity and Greenland temperature change, suggesting that ~500-year small variations in solar output played a prominent role in the mid-late Holocene climate dynamics in EA, linked to high latitude climate system. Its last warm phase might terminate in the next several decades to enter another ~250-year cool phase, and thus this future centennial cyclic temperature minimum could partially slow down man-made global warming.