Holocene history of the El Niño phenomenon as recorded in flood sediments of northern coastal Peru

EXTRACT (SEE PDF FOR FULL ABSTRACT): The Holocene history of flooding in northern coastal Peru is believed to be a proxy record for the El Niño phenomenon. A recently completed set of 30 radiocarbon dates on overbank flood deposits and a tsunami deposit from the Casma region (Figure 1 and Table 1) establishes a chronology for the largest events that have occurred during the last 3500 years. ... The data presented here indicate that events much larger than the one in 1982-1983 may occur with a frequency of about once every 1000 years.

Life history of prawns: a review of recent studies with special reference to Indian species

The paper contains a brief review of the studies on the life histories of Indian species of prawns chiefly belonging to the family Penaeidae. References to similar work carried out outside India are furnished where significant variations have been observed. The three main larval stages viz., Nauplius, Protozoea and Zoea (Mysis) and their important characteristics, including modes of locomotion, are described. The post-larval development of one species that has been studied in detail (Metapenaeus dobsoni) is indicated in outline. Some aspects of the bionomics of these prawns, especially breeding and migration, are also briefly dealt with in view of their relevance in their life cycle. An outline of the life histories of some Palaemonid prawns of both fresh water and marine habitats is added at the end and the need for well- planned investigations in regard to species of such economic value as Palaemon carcinus (Macrobrachium rosenbergii) is indicated.

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

Evolutionary history of the mtDNA 9-bp deletion in Chinese populations and its relevance to the peopling of east and southeast Asia

In total, 1218 Chinese from twelve ethnic groups and nine Han geographic groups were screened for the mtDNA 9-bp deletion motif. The frequency of the 9-bp deletion in all samples was 14.7% but ranged from 0% to 32% in the various ethnic groups. Three individuals had a triplication of the 9-bp segment. Phylogenetic and demographic analyses of the mtDNA hypervariable segment 1 (HVS1) sequences suggest that the 9-bp deletion occurred more than once in China. The majority of the Chinese deletion:haplotypes (about 90%) have a common origin as a mutational event following an initial expansion of modem humans in eastern Asia. Other deletion haplotypes and the three haplotypes with a 9-bp triplication may have arisen independently in the Chinese, presumably by replication error. HVS1 haplotype analysis suggests two possible migration routes of the 9-bp deletion in east and southeast Asia. Both migrations originated in China with one route leading to the Pacific Islands via Taiwan, the other to southeast Asia and possibly the Nicobar Islands. Along both routes of peopling, a decrease in HVS1 diversity of the mtDNA haplotypes is observed. The "Polynesian motif (16217T/C, 16247A/G, and 16261C/T)" and the 16140T/C, 16266C/A, or C/G polymorphisms appear specific to each migration route.

Mitochondrial DNA variation, effective female population size and population history of the endangered Chinese sturgeon, Acipenser sinensis

The anadromous Chinese sturgeon (Acipenser sinensis), mainly endemic to the Yangtze River in China, is an endangered fish species. The natural population has declined since the Gezhouba Dam blocked its migratory route to the spawning grounds in 1981. In the near future, the completion of the Three Gorges Dam, the world's largest hydroelectric project, may further impact this species by altering the water flow of the Yangtze River. Little is currently known about the population genetic structure of the Chinese sturgeon. In this study, DNA sequence data were determined from the control region (D-loop) of the mitochondrial genome of adult sturgeons (n = 106) that were collected between 1995-2000. The molecular data were used to investigate genetic variation, effective female population size and population history of the Chinese sturgeon in the Yangtze River. Our results indicate that the reduction in abundance did not change genetic variation of the Chinese sturgeon, and that the population underwent an expansion in the past. AMOVA analysis indicated that 98.7% of the genetic variability occurred within each year's spawning populations, the year of collection had little influence on the diversity of annual temporary samples. The relative large effective female population size (N-ef) indicates that good potential exists for the recovery of this species in the future. Strikingly, the ratio of N-ef to the census female population size (N-f) is unusually high (0.77-0.93). This may be the result of a current bottleneck in the population of the Chinese sturgeon that is likely caused by human intervention.

Genetic diversity and population history of golden monkeys (Rhinopithecus roxellana)

Golden monkey (Rhinopithecus roxellana), namely the snub-nosed monkey, is a well-known endangered primate, which distributes only in the central part of mainland China. As an effort to understand the current genetic status as well as population history of this species, we collected a sample of 32 individuals from four different regions, which cover the major habitat of this species. Forty-four allozyme loci were surveyed in our study by allozyme electrophoresis, none of which was found to be polymorphic. The void of polymorphism compared with that of other nonhuman primates is surprising particularly considering that the current population size is many times larger than that of some other endangered species. Since many independent loci are surveyed in this Study, the most plausible explanation for our observation is that the population has experienced a recent bottleneck. We used a coalescent approach to explore various scenarios of population bottleneck and concluded that the most recent bottleneck could have happened within the last 15,000 years. Moreover, the proposed simulation approach could be useful to researchers who need to analyze the non- or low-polymorphism data.

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

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.

Ecology and life history of penaeid shrimps

Fourteen species of penaeid shrimps with commercial value in Batan Bay and Tigbauan-Guimbal waters were identified as follows: Penaeus monodon, P.semisulcatus, P.japonicus, Metapenaeus ensis, M.burkenroadi, M.endeavouri, Metapenaeopsis palmensis, M.stridulans, Trachypenaeus fulvus, and Parapenaeus longipes. Among the 14 penaeids, P.semisulcatus, M.ensis and M.palmensis were found to be the dominant species within each genus. There are seven existing fishing gears for shrimping in the Batan Bay and Tigbauan-Guimbal waters: fish corrals, lift net, filter net, gill net, skimming net, baby trawler and commercial trawler. In general, female penaeids are larger than males. The largest P.monodon female measured was 81 mm in carapace length with 23 g in body weight. The largest male measuring 59 mm in carapace length with 119 g of body weight was caught in Batan Bay. Judging from spermatozoa occurrence on both sexes of P.monodon, the biological minimum size for male is 37 mm in carapace length and 49 mm for female. A total of 133 Penaeus postlarvae obtained from the offshore were identified by comparison with those reared in the laboratory. The postlarvae of P.japonicus-latisulcatus complex were quite dominant (60 . 2%), followed by P.semisulcatus (18 . 0%), and P.merguiensis-indicus complex (17 . 3%). The number of P.monodon postlarvae was relatively small (4 . 5%). The modal carapace length of P.monodon postlarvae from the offshore was 1 . 3 mm with three or four dorsal and no ventral spines on the rostrum, while P.monodon fry from the shoreline had 2 . 3 mm with five or six dorsal and one or two ventral spines.

Developmental and ecological stages in the life history of milkfish Chanos chanos Forsskal

Seven stages in the life history of the milkfish C. chanos , are recognized and suggested: A, embryonic; B, yolksac larval; C, larval; D, postlarval; E, juvenile; F, subadult; G. adult. An outline is presented of the life history. It is concluded that the milkfish, throughout the known stages of their life history are well adapted and equipped for optimal survival. High swimming performance, broad flexibility in feeding habits, high adaptability to a wide range of physicochemical conditions of the environment are but a few of the adaptations. The main driving force in all developmental stages is the evolutionary response to food distribution and availability followed by predation pressure.

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.