Differential population structuring and demographic history of two closely related fish species, Japanese sea bass (Lateolabrax japonicus) and spotted sea bass (Lateolabrax maculatus) in Northwestern Pacific

The Quaternary cold periods in the Northwestern Pacific are thought to have heavily influenced the amount and distribution of intraspecific genetic variation in marine fishes. To estimate the demographic history and genetic structure of Lateolabrax macula

Revealing the History of Sheep Domestication Using Retrovirus Integrations

The domestication of livestock represented a crucial step in human history. By using endogenous retroviruses as genetic markers, we found that sheep differentiated on the basis of their "retrotype" and morphological traits dispersed across Eurasia and Afr

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication(1,2). To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data(3). Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.

Population structure and history in East Asia

Archaeological, anatomical, linguistic, and genetic data have suggested that there is an old and significant boundary between the populations of north and south China. We use three human genetic marker systems and one human-carried virus to examine the north/south distinction. We find no support for a major north/south division in these markers; rather, the marker patterns suggest simple isolation by distance.

A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution

Nectogaline shrews are a major component of the small mammalian fauna of Europe and Asia, and are notable for their diverse ecology, including utilization of aquatic habitats. So far, molecular phylogenetic analyses including nectogaline species have been unable to infer a well-resolved, well-supported phylogeny, thus limiting the power of comparative evolutionary and ecological analyses of the group. Here, we employ Bayesian phylogenetic analyses of eight mitochondrial and three nuclear genes to infer the phylogenetic relationships of nectogaline shrews. We subsequently use this phylogeny to assess the genetic diversity within the genus Episoriculus, and determine whether adaptation to aquatic habitats evolved independently multiple times. Moreover, we both analyze the fossil record and employ Bayesian relaxed clock divergence dating analyses of DNA to assess the impact of historical global climate change on the biogeography of Nectogalini. We infer strong support for the polyphyly of the genus Episoriculus. We also find strong evidence that the ability to heavily utilize aquatic habitats evolved independently in both Neomys and Chimarrogale + Nectogale lineages. Our Bayesian molecular divergence analysis suggests that the early history of Nectogalini is characterized by a rapid radiation at the Miocene/Pliocene boundary, thus potentially explaining the lack of resolution at the base of the tree. Finally, we find evidence that nectogalines once inhabited northern latitudes, but the global cooling and desiccating events at the Miocene/Pliocene and Pliocene/Pleistocene boundaries and Pleistocene glaciation resulted in the migration of most Nectogalini lineages to their present day southern distribution. (C) 2010 Elsevier Inc. All rights reserved.

Reconstructing the evolutionary history of China: A caveat about inferences drawn from ancient DNA

The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modem data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (similar to 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modem populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.

The Genomes of Oryza sativa: A history of duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped superscaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000 - 40,000. Only 2% - 3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism ( SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Diatom community succession in the recent history of a eutrophic Yunnan Plateau lake, Lake Dianchi, in subtropical China

Fish introduction, eutrophication and disappearance of aquatic vegetation are important disturbances of aquatic ecosystems, especially in plateau lakes, which are generally considered to be very vulnerable. Fish were introduced to Lake Dianchi, a eutrophic plateau lake in southwest China, in the late 1950s and 1970s. After the introduction, invasive fish became the dominant species, and the total fish yield increased. Meanwhile, the trophic level of Lake Dianchi had a tendency to increase in the past decades because of the increases in human activities in the watershed area. In addition, the area of aquatic vegetation decreased from more than 90 to 1.8% of the lake area from the 1950s to 2000. This study investigated the effects of fish introduction, eutrophication and aquatic vegetation on the diatom community of Lake Dianchi by examining the changes of microfossil diatom assemblage and abundance. Results showed that the absolute abundance and diatom assemblages changed after fish were introduced. The endemic species, Cyclotella rohomboideo-elliptica, disappeared with the introduction of fish and increasing trophic levels after 1958. Fragilaria crotonensis entered into the lake with the introduction of fish and gradually thrived in the lake after 1958. Diatom species numbers also decreased gradually from 21 to 9 from the past to present. Epiphytic diatoms disappeared with the decrease of aquatic vegetation after 1985. Our study indicated that eutrophication was the most important process determining diatom abundance, and fish introduction was a secondary process determining diatom abundance, while aquatic vegetation had a more important role in structuring the diatom community in this eutrophic plateau lake.

Multiple invasions of europe by east asian cobitid loaches (Teleostei : Cobitidae)

While it has been widely suggested that freshwater fishes from East Asia invaded the western Palaearctic, details about this process are largely unknown. Here, using the cytochrome b gene, we evaluated the phylogenetic relationships of a small group of Eurasian primary freshwater fishes (Cobitidae), which are widely distributed and species rich in East Asia and Europe, with the purpose of inferring their invasion process of Europe from East Asia. Though phylogenetic relationships of cobitids were not well resolved, our analysis could identify three sister groups formed by the European and East Asian cobitids, which brought new insights into the biogeography of the genera Cobitis, Misgurnus, and Sabanejewia. The present results support the view that Asian cobitid fishes may have invaded Europe at least five times independently, and once reverse colonization of European cobitids to East Asia could also be found. Ancestral Sabanejewia might have been the first cobitids to cross Siberia and invade the EMZS (Euro-Mediterranean zoogeographic subregion) about 33.54 million years ago (MYA). One lineage of Cobitis and the ancestor of Misgurnus fossilis (Linnaeus) almost in the same time invaded the Europe, responding to 16.71 MYA and 16.59 MYA, respectively. Three different lineages of Cobitis were found to have invaded the EMZS from East Asia, and once reverse invasion to East Asia occurred to one subclade of European Cobitis. And our data also suggest that the diversity of East Asian cobitid fishes, especially of the genus Cobitis, is greatly underestimated.

Origin of Gymnocypris przewalskii and phylogenetic history of Gymnocypris eckloni (Teleostei : Cyprinidae)

The origins and phylogenetic patterns were assessed for G. przewalskii and G. eckloni by analyzing the complete mtDNA cytochrome b gene sequence (1140bp). Phylogenetic analyses further supported that there were three mtDNA lineages (A-C) identified in G. przewalskii and G. eckloni, demonstrating that outer rakers of the first gill have little significance in the phylogeny of the Gymnocypris fishes. The network established showed that G. eckloni of the Yellow River specific haplotype A1 was a founder and it radiated all haplotypes of G. przewalskii which suggested G. przewalskii might only originate from one of two maternals of G. eckloni from the Yellow River. Fs test and mismatch analysis showed at least two expansion events in the population of G. przewalskii about 0.2734 Ma and 0.0658 Ma, while G. eckloni from Qaidam Basin could have experienced severe bottleneck effect about 0.0693 Ma. The population expansion was detected in subclades A1 and A21 with the most recent common ancestor (TMRCA) about 0.2308 +/- 0.01 Ma and 0.1319 +/- 0.015 Ma, respectively, which were within the geological age range of "Gonghe Movement" event that caused the separation of Lake Qinghai from the upper Yellow River. These results suggested the effect of the fish diversification by rapid uplift of the Qinghai-Tibetan Plateau in the Late Pleistocene.

Changes in the life history of Abbottina fivularis in Lake Fuxian

After invading Lake Fuxian, China, Abbottina rivularis showed marked changes in its life history traits, including alterations in annuli formation, extension to the length of the breeding season, and an increase in fecundity and growth rate. The results are explained in the context of the enemy release hypothesis. (c) 2007 The Authors. Journal compilation (c) 2007 The Fisheries Society of the British Isles.

Rearing of Procypris rabaudi during early life-history stages

The early life-history of Chinese rock carp Procypris rabaudi was investigated during a 56-day rearing period: 318 artificially propagated P. rabaudi larvae were reared throughout metamorphosis in a small-scale recirculation system (345 L water volume, 10 x 18 L rearing tanks, 150 L storage and filter compartment with bioballs, 20-30 larvae L-1) at the Institute of Hydrobiology, Wuhan, Hubei Province, China. The newly hatched larvae had an initial total length of 8.93 +/- 0.35 mm SD (n = 10) at 3 days post-hatch and reached an average total length of 33.29 mm (+/- 1.88 mm SD, n = 10) 56 days after hatching. Length increment averaged 0.45 mm day(-1), resulting in a mean growth of 24.4 mm within the 56-day period. High mortality rates of up to 92% derived from an introduced fungus infection and subsequent treatment stress with malachite green. Our results indicate that Chinese rock carp can be raised successfully from artificially fertilized eggs. We therefore assume this species to be a candidate for commercial aquaculture.

The costs and benefits in an unusual symbiosis: experimental evidence that bitterling fish (Rhodeus sericeus) are parasites of unionid mussels in Europe

Interspecific symbiotic relationships involve a complex network of interactions, and understanding their outcome requires quantification of the costs and benefits to both partners. We experimentally investigated the costs and benefits in the relationship between European bitterling fish (Rhodeus sericeus) and freshwater mussels that are used by R. sericeus for oviposition. This relationship has hitherto been thought mutualistic, on the premise that R. sericeus use mussels as foster parents of their embryos while mussels use R. sericeus as hosts for their larvae. We demonstrate that R. sericeus is a parasite of European mussels, because it (i) avoids the cost of infection by mussel larvae and (ii) imposes a direct cost on mussels. Our experiments also indicate a potential coevolutionary arms race between bitterling fishes and their mussel hosts; the outcome of this relationship may differ between Asia, the centre of distribution of bitterling fishes, and Europe where they have recently invaded.

Life history and production of Sphaerium lacustre (Mollusca : Sphaeriidae) in a shallow subtropical Chinese lake

A fingernail clam, Sphaerium lacustre, was studied in subtropical Lake Donghu from June 1999 to May 2000. The S. lacustre population was characterized by a single annual reproduction period starting in March and ending in October; the population comprised three size groups, of which the 1999 cohort was dominant. The annual average density and biomass were 100.2 ind./m(2) and 12.11 g/m(2), respectively The annual production was 43.02 wet weight g/m(2), and the corresponding annual production/biomass ratio was 3.55.

Life history characteristics of three types of females in Brachionus calyciflorus Pallas (Rotifera) fed different algae

This study describes the life history characteristics of amictic, unfertilized mictic and fertilized mictic females of the rotifer Brachionus calyciflorus cultured individually on two different algae at 0.1 mg ml(-1) food concentration and 27 degreesC. The duration of the juvenile period of amictic females was significantly shorter on Chlorella pyrenoidosa Chick than on Scenedesmus obliquus Kutz or both algae together. The duration of the juvenile period of unfertilized mictic females was significantly longer, and the number of eggs produced by amictic females was significantly larger on Chlorella pyrenoidosa than on S. obliquus. When fed the same type of alga, the duration of the juvenile period of the fertilized mictic females was the longest among the three types of females, and the durations of the reproductive period of the amictic females and the post-reproductive period of the fertilized mictic females were longer than, or equal to those of the other two types of females, respectively. The number of eggs produced by an unfertilized mictic female was the largest among the three types of females, and that of amictic females was larger than or equal to that of fertilized mictic females, depending on the type of diet.