Reciprocal chromosome painting illuminates the history of genome evolution of the domestic cat, dog and human

Domestic cats and dogs are important companion animals and model animals in biomedical research. The cat has a highly conserved karyotype, closely resembling the ancestral karyotype of mammals, while the dog has one of the most extensively rearranged mammalian karyotypes investigated so far. We have constructed the first detailed comparative chromosome map of the domestic dog and cat by reciprocal chromosome painting. Dog paints specific for the 38 autosomes and the X chromosomes delineated 68 conserved chromosomal segments in the cat, while reverse painting of cat probes onto red fox and dog chromosomes revealed 65 conserved segments. Most conserved segments on cat chromosomes also show a high degree of conservation in G-banding patterns compared with their canine counterparts. At least 47 chromosomal fissions (breaks), 25 fusions and one inversion are needed to convert the cat karyotype to that of the dog, confirming that extensive chromosome rearrangements differentiate the karyotypes of the cat and dog. Comparative analysis of the distribution patterns of conserved segments defined by dog paints on cat and human chromosomes has refined the human/cat comparative genome map and, most importantly, has revealed 15 cryptic inversions in seven large chromosomal regions of conserved synteny between humans and cats.

Genetic diversity and population history of the red panda (Ailurus fulgens) as inferred from mitochondrial DNA sequence variations

The red panda (Ailurus fulgens) is one of the flagship species in worldwide conservation and is of special interest in evolutionary studies due to its taxonomic uniqueness. We sequenced a 236-bp fragment of the mitochondrial D-loop region in a sample of 5

The ADH1B Arg47His polymorphism in East Asian populations and expansion of rice domestication in history

Background: The emergence of agriculture about 10,000 years ago marks a dramatic change in human evolutionary history. The diet shift in agriculture societies might have a great impact on the genetic makeup of Neolithic human populations. The regionally restricted enrichment of the class I alcohol dehydrogenase sequence polymorphism (ADH1BArg47His) in southern China and the adjacent areas suggests Darwinian positive selection on this genetic locus during Neolithic time though the driving force is yet to be disclosed. Results: We studied a total of 38 populations (2,275 individuals) including Han Chinese, Tibetan and other ethnic populations across China. The geographic distribution of the ADH1B*47His allele in these populations indicates a clear east-to-west cline, and it is dominant in south-eastern populations but rare in Tibetan populations. The molecular dating suggests that the emergence of the ADH1B*47His allele occurred about 10,000 similar to 7,000 years ago. Conclusion: We present genetic evidence of selection on the ADH1BArg47His polymorphism caused by the emergence and expansion of rice domestication in East Asia. The geographic distribution of the ADH1B*47His allele in East Asia is consistent with the unearthed culture relic sites of rice domestication in China. The estimated origin time of ADH1B*47His allele in those populations coincides with the time of origin and expansion of Neolithic agriculture in southern China.

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

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.

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.

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.

The effect of food concentration on the life history of three types of Brachionus calyciflorus females

The effect of food concentration on the life history of three types of Brachionus calciflorus females (amictic, unfertilized mictic and fertilized mictic female) was studied with replicated individual cultures at 25 degrees and at four food concentrations (1.5, 3.0, 6.0 and 9.0 x 10(6) cells mL(-1)) of Scenedesmus obliquus. There were highly significant effects of both food concentration and female type, independently and in interaction on the duration of juvenile period of the rotifer, but neither a;ere the effects on the duration of post-reproductive period and mean life-span. The duration of juvenile period of unfertilized mictic female at the food concentration of 9.0 x 10(6) cells mL(-1) was the longest among all the food concentration-female type combinations. Both food concentration and female type influenced significantly the duration of reproductive period and the number of eggs produced by each type of female per life cycle, respectively. There was, however, no significant interaction between food level and female type. Among the three types of females, the number of eggs produced by an unfertilized mictic female was the largest. and that of a fertilized mictic female was the smallest.

Characterization of the life history of Bangia fuscopurpurea (Bangiaceae, Rhodophyta) in connection with its cultivation in China

Bangia fuscopurpurea (Rhodophyta) was cultivated in Putian (Fujian province, China). The characteristics of the life history concerned with cultivation were investigated and the cultivation procedure was presented. The gametophytic phase (thallus) and the sporophytic phase (conchocelis) occurred alternately in the life history of B. fuscopurpurea. Young thalli produced archeospores, and the number depended on the environmental factors. Temperature affected the number of archeospore release and percent of germination, and photo flux density (PFD) mainly affected the time of spore release and germination. Thalli matured from December to February and developed into the conchocelis phase through sexual reproduction. The conchocelis grown in shells had three developmental stages: vegetative conchocelis, conchosporangiall formation and conchospore formation. Pit-connections were present in the first 2 stages but absent after conchospore formation. Vegetative conchocelis and conchosporangial. branches can transform into each other. However, conchospores only developed into the gametophytic phase. Cultivation of B. fuscopurpurea was based on characterization of the life history, consisting of 3 steps: zygotospores collection, indoor cultivation of conchocelis and outdoor cultivation of thalli. Young thalli that developed from conchospores produced numerous archeospores before December. Over 90% of the crop was from the development of archeospores. The results indicated that conchosporelings were a good source of archeospores, and the development of the large quantity of archeospores acted as a more prevailing means to increase the population size. (C) 2008 Elsevier B.V. All rights reserved.

Life history strategies of Calanus sinicus in the southern Yellow Sea in summer

Ecological and physiological features of the planktonic copepod Calanus sinicus in the southern Yellow Sea in summer were studied to reveal its life history strategy. From the coastal shallow waters to the central part of the southern Yellow Sea, a shift of the stage composition occurs from being dominated by the egg-nauplius stage to being dominated by the fifth copepodite (CV) stage. Most CVs reside in the Yellow Sea Cold Water Mass (YSCWM), where both temperature and food abundance are low. CVs in the YSCWM have longer body lengths, heavier body weights and higher carbon contents than those outside the YSCWM. Onboard incubations show that the development of CVs in the YSCWM is suspended. Energy conservation, development suspension and lack of diel vertical migration (DVM) behavior suggest a diapause status for the CVs in the YSCWM, although vertical distribution patterns indicate the CV individuals are not fully synchronous in physiology and development. This adaptive oversummering strategy would help C. sinicus to live through the warm and food-limited summer in the central part of the southern Yellow Sea; both low temperature and low food supply are necessary for CV to maintain the resting state in the YSCWM. Calanus sinicus exhibits different life history strategies in different regions of the southern Yellow Sea in summer.