Shunping He

The distribution and economic losses of alien species invasion to China

Invasive alien species have become one of the most serious environmental issues in the world. Data of taxon, origin, pathway, and environmental impacts of invasive alien microorganisms, invertebrates, amphibians and reptiles, fish, birds, mammals, herbs, trees, and, marine organisms in terrestrial, aquatic, and marine ecosystems of China were analyzed during 2001 and 2003, based on literature retrieval and field survey. There were 283 invasive alien species in China, and the number of species of invasive alien microorganisms, aquatic plants, terrestrial plants, aquatic invertebrates, terrestrial invertebrates, amphibians and reptiles, fish, and mammals were 19, 18, 170, 25, 33, 3, 10, and 5, respectively. The proportion of invasive alien species originated from America, Europe, Asia, Africa, and Oceania were 55.1, 21.7, 9.9, 8.1, and 0.6%, respectively. Methods for estimation of direct economic losses to agriculture, forestry, stockbreeding, fishery, road and water transportation, storage, water conservancy, environment and public facilities, and human health were established. Methods for estimation of indirect economic losses caused by invasive alien species to service functions of forest ecosystems, agricultural ecosystems, grassland ecosystems, and wetland ecosystems were also established. The total economic losses caused by invasive alien species to China were to the time of USD 14.45 billion, with direct and indirect economic losses accounting for 16.59% and 83.41% of total economic losses, respectively.

Molecular phylogenetics of the family Cyprinidae (Actinopterygii : Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: Further evidence from a nuclear gene of the systematic chaos in the family

The family Cyprinidae is the largest freshwater fish group in the world, including over 200 genera and 2100 species. The phylogenetic relationships of major clades within this family are simply poorly understood, largely because of the overwhelming diversity of the group; however, several investigators have advanced different hypotheses of relationships that pre- and post-date the use of shared-derived characters as advocated through phylogenetic systematics. As expected, most previous investigations used morphological characters. Recently, mitochondrial DNA (mtDNA) sequences and combined morphological and mtDNA investigations have been used to explore and advance our understanding of species relationships and test monophyletic groupings. Limitations of these studies include limited taxon sampling and a strict reliance upon maternally inherited mtDNA variation. The present study is the first endeavor to recover the phylogenetic relationships of the 12 previously recognized monophyletic subfamilies within the Cyprinidae using newly sequenced nuclear DNA (nDNA) for over 50 species representing members of the different previously hypothesized subfamily and family groupings within the Cyprinidae and from other cypriniform families as outgroup taxa. Hypothesized phylogenetic relationships are constructed using maximum parsimony and Basyesian analyses of 1042 sites, of which 971 sites were variable and 790 were phylogenetically informative. Using other appropriate cypriniform taxa of the families Catostomidae (Myxocyprinus asiaticus), Gyrinocheilidae (Gyrinocheilus aymonieri), and Balitoridae (Nemacheilus sp. and Beaufortia kweichowensis) as outgroups, the Cyprinidae is resolved as a monophyletic group. Within the family the genera Raiamas, Barilius, Danio, and Rasbora, representing many of the tropical cyprinids, represent basal members of the family. All other species can be classified into variably supported and resolved monophyletic lineages, depending upon analysis, that are consistent with or correspond to Barbini and Leuciscini. The Barbini includes taxa traditionally aligned with the subfamily Cyprininae sensu previous morphological revisionary studies by Howes (Barbinae, Labeoninae, Cyprininae and Schizothoracinae). The Leuciscini includes six other subfamilies that are mainly divided into three separate lineages. The relationships among genera and subfamilies are discussed as well as the possible origins of major lineages.

Inferring the Tree of Life of the order Cypriniformes, the earth's most diverse clade of freshwater fishes: Implications of varied taxon and character sampling

The phylogenetic relationships of species are fundamental to any biological investigation, including all evolutionary studies. Accurate inferences of sister group relationships provide the researcher with an historical framework within which the attributes or geographic origin of species (or supraspecific groups) evolved. Taken out of this phylogenetic context, interpretations of evolutionary processes or origins, geographic distributions, or speciation rates and mechanisms, are subject to nothing less than a biological experiment without controls. Cypriniformes is the most diverse clade of freshwater fishes with estimates of diversity of nearly 3,500 species. These fishes display an amazing array of morphological, ecological, behavioral, and geographic diversity and offer a tremendous opportunity to enhance our understanding of the biotic and abiotic factors associated with diversification and adaptation to environments. Given the nearly global distribution of these fishes, they serve as an important model group for a plethora of biological investigations, including indicator species for future cli- matic changes. The occurrence of the zebrafish, Danio rerio, in this order makes this clade a critical component in understanding and predicting the relationship between mutagenesis and phenotypic expressions in vertebrates, including humans. With the tremendous diversity in Cypriniformes, our understanding of their phylogenetic relationships has not proceeded at an acceptable rate, despite a plethora of morphological and more recent mo- lecular studies. Most studies are pre-Hennigian in origin or include relatively small numbers of taxa. Given that analyses of small numbers of taxa for molecular characters can be compromised by peculiarities of long-branch attraction and nodal-density effect, it is critical that significant progress in our understanding of the relationships of these important fishes occurs with increasing sampling of species to mitigate these potential problems. The recent Cypriniformes Tree of Life initiative is an effort to achieve this goal with morphological and molecular (mitochondrial and nuclear) data. In this early synthesis of our understanding of the phylogenetic relationships of these fishes, all types of data have contributed historically to improving our understanding, but not all analyses are complementary in taxon sampling, thus precluding direct understanding of the impact of taxon sampling on achieving accurate phylogenetic inferences. However, recent molecular studies do provide some insight and in some instances taxon sampling can be implicated as a variable that can influence sister group relationships. Other instances may also exist but without inclusion of more taxa for both mitochondrial and nuclear genes, one cannot distinguish between inferences being dictated by taxon sampling or the origins of the molecular data.

The status and causes of alien species invasion in China

Data of classification, origin, pathway and environmental impacts of invasive alien micro-organisms, invertebrates, amphibians and reptiles, fish, birds, mammals, weeds, trees, and marine organisms in terrestrial, aquatic and marine ecosystems of China, were analyzed, based on literature retrieval, field survey and consultation. Some 283 invasive alien species were recorded in China, including 19 invasive alien micro-organisms, 18 aquatic plants, 170 terrestrial plants, 25 aquatic invertebrates, 33 terrestrial invertebrates, 3 amphibians and reptiles, 10 fish, and 5 mammals. Of the invasive alien species, 55.1% originated from North and South America, 21.7% from Europe, 9.9% from Asia, 8.1% from Africa and 0.6% from Oceania. Many institutions and individuals in China lack adequate knowledge of ecological and environmental consequences caused by invasive alien species, with some ignorance of the dangerous invasion in the introduction of alien species. For instance, 50.0% of invasive alien plants were intentionally introduced as pasture, feedingstuff, ornamental plants, textile plants, medicinal plants, vegetables, or lawn plants, 25% of alien invasive animals were intentionally introduced for cultivation, ornament, or biological control, In addition, more efforts are being made in the introduction of alien species, and little attention is paid on the management of introduced alien species, which may cause their escape into natural environment and potential threats to the environment. There were also gaps in quarantine system in China. All microorganisms were unintentionally introduced, through timber, seedling, flowerpot, or soil; 76.3% of alien invasive animals invaded through commodity or transportation facility because of the failure of quarantine. Therefore, quarantine measures should be strictly implemented; and meanwhile the intentional introduction of alien species should be strictly managed and a system of risk assessment should be implemented.

Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces: Cypriniformes) inferred from cytochrome b sequences

Complete mitochondrial cytochrome b sequences of 54 species, including 18 newly sequenced, were analyzed to infer the phylogenetic relationships within the family Cyprinidae in East Asia. Phylogenetic trees were generated using various tree-building methods, including Neighbor-joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods, with Myxocyprinus asiaticus (family Catostomidae) as the designated outgroup. The results from NJ and ML methods were mostly similar, supporting some existing subfamilies within Cyprinidae as monophyletic, such as Cultrinae, Xenocyprinae and Gobioninae (including Gobiobotinae). However, genera within the subfamily “Danioninae” did not form a monophyletic group. The subfamily Leuciscinae was divided into two unrelated groups: the “Leuciscinae” in East Asia forming as a monophyletic group together with Cultrinae and Xenocyprinae, while the Leuciscinae in Europe, Siberia, and North America as another monophyletic group. The monophyly of subfamily Cyprininae sensu Howes was supported by NJ and ML trees and is basal in the tree. The position of Acheilognathinae, a widely accepted monophyletic group represented by Rhodeus sericeus, was not resolved.

Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei: Cypriniformes).

The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A>T, C>G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA.

The Phylogenetic Relationships of the Gobioninae (Teleostei: Cyprinidae) Inferred from Mitochondrial Cytochrome b Gene Sequences

The Gobioninae are a group of morphologically and ecologically diverse Eurasian freshwater cyprinid fishes. The intergeneric relationships of this group are unresolved and the possible monophyly of this subfamily remains to be established. We used complete mitochondrial cytochrome b gene sequences from most genera within the gobionine group, in addition to a selection of cyprinid outgroups, to investigate the possible monophyly of this group and resolve the interrelationships within the group. Our results support the monophyly of the Gobioninae and identify four monophyletic groups within the subfamily; the Hemibarbus group, the Sarcocheilichthys group, the Gobio group, and the Pseudogobio group. The morphologically aberrant genera Gobiobotia, Xenophysogobio and Gobiocypris are included in the Gobioninae, with the latter a sister group of Gnathopogon.

Population Genetic Structure of the Yangtze Finless Porpoise (Neophocaena phocaenoides asiaeorientalis): Implications for Management and Conservation

Understanding the population genetic structure is a prerequisite for conservation of a species. The degree of genetic variability characteristic of the mitochondrial DNA control region has been widely exploited in studies of population genetic structure and can be useful in identifying meaningful population subdivisions. To estimate the genetic profile of the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis), an endangered freshwater population endemic to China, the complete mtDNA control region was examined in 39 individuals belonging to seven different stocks inhabiting the middle and lower reaches of the Yangtze River. Very low genetic diversity was found (nucleotide diversity 0.0011± 0.0002 and haplotypic diversity 0.65± 0.05). The mtDNA genetic pattern of the Yangtze population appears to indicate a founder event in its evolutionary history and to support the marine origin for this population. Analyses by Fst and Φst yielded statistically significant population genetic structure (Fst = 0.44, P < 0.05; Φst = 0.36, P < 0.05). These results may have significant implications for the management and conservation of the Yangtze finless porpoise in the future.

The uplift of Qinghai-Xizang (Tibet) Plateau and the vicariance speciation of glyptosternoid fishes (Siluriformes: Sisoridae)

Based on the phylogenetic and biogeographical studies of the glyptosternoid fishes in Qinghai-Tibet area, the following hypothesis is proposed: the speciation of this group has a direct relationship with the three uplift intervals of the Qinghai-Tibet Plateau. This process was explained by the theory of vicariance of biogeography. The ancestor of this group was similar toBagarus and/orGlyptothorax, which still have a wide distribution. At the moment when the Tethys sea closed, the Indian tectonic plate collided with the Eurasian tectonic plate, so theGlyptothorax-like andBagarus-like ancestors entered Eurasia and gradually became widely distributed. After the Pleistocene, with the enforced colliding, the gradual uplift of the Qinghai-Tibet Plateau brought about the current water environment, and the Glyptosternoids were generated fromGlyptothorax-like fish under this environment. The presentGlyptosternum, distributed across the Himalayas is the ancestor of Glyptosternoids. In the three uplift intervals of the plateau, the water system of this region was separated gradually andGlyptosternum-like ancestor was isolated in different rivers and evolved into various species. All this resulted in the speciation and formation of the biogeographical pattern of glyptosternoids.

Molecular phylogenetics of Gymnocypris (Teleostei: Cyprinidae) in Lake Qinghai and adjacent drainages

Abstract149 complete mitochondrial DNA (mtDNA) cytochrome b (Cyt b) genes (1140 bp) of Gymnocypris przewalskii, Gymnocypris eckloni and Gymnocypris scolistomus from the Lake Qinghai, Yellow River and Qaidam Basin were sequenced and analyzed. Consistent dendrogram indicated that the samples collected from the same species do not constitute a separate monophyletic group and all the samples were grouped into three highly divergent lineages (A, B and C). Among them, Lineage A contained all samples of G. przewalskii from the Lake Qinghai and partial samples of the G. eckloni from the Yellow River. Lineage B contained the remaining samples of G. eckloni from the Yellow River. Lineage C was composed of a monophyletic group by G. eckloni from the Qaidam Basin. Analysis of molecular variance (AMOVA) indicated that most of genetic variations were detected within these three mtDNA lineages (93.12%), suggesting that there are three different lineages of Gymnocypris in this region. Our Cyt b sequence data showed that G. przewalskii was not a polytypic species, and G. scolistomus was neither an independent species nor a subspecies of G. eckloni. The divergent mtDNA lineages of G. eckloni from the Yellow River suggested that gene flow between the different populations was restricted to a certain extent by several gorges on the upper reach of the Yellow River. Lineage B of G. eckloni might be the genetic effect from the ancestor which was incorporated with the endemic schizothoracine fishes when the headward erosion of the Yellow River reached to its current headwaters of late. The G. eckloni from Basin Qaidam was a monophyletic group (lineage C) and Fst values within G. eckloni from the Yellow River were higher than 0.98, suggesting that the gene flow has been interrupted for a long time and the G. eckloni from Basin Qaidam might have been evolved into different species by ecology segregation. The correlation between the rakers number of Gymnocypris and population genetic variation was not significant. All Gymnocypris populations exhibited a low nucleotide diversity (π = 0.00096–0.00485). Therefore the Gymnocypris populations from Basin Qaidam could have experienced severe bottleneck effect in history. Our result suggested Gymnocypris populations of Basin Qaidam should give a high priority in conservation programs.