Positive selection drives population differentiation in the skeletal genes in modern humans

During the course of evolution, the human skeletal system has evolved rapidly leading to an incredible array of phenotypic diversity, including variations in height and bone mineral density. However, the genetic basis of this phenotypic diversity and the relatively rapid tempo of evolution have remained largely undocumented. Here, we discover that skeletal genes exhibit a significantly greater level of population differentiation among humans compared with other genes in the genome. The pattern is exceptionally evident at amino acid-altering sites within these genes. Divergence is greater between Africans and both Europeans and East Asians. In contrast, relatively weak differentiation is observed between Europeans and East Asians. SNPs with higher levels of differentiation have correspondingly higher derived allele frequencies in Europeans and East Asians. Thus, it appears that positive selection has operated on skeletal genes in the non-African populations and this may have been initiated with the human colonization of Eurasia. In conclusion, we provide genetic evidence supporting the rapid evolution of the human skeletal system and the associated diversity of phenotypes.

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.

Lack of mtDNA control region variation in Hainan Eld's deer: Consequence of a recent population bottleneck?

We find no genetic variation at 550bp of mtDNA control region among 55 Hainan Eld's deer in an island population that has suffered recent population contractions. Congeneric species show high levels of variation at this locus. We use a simulation approach to test the likelihood of various bottleneck scenarios, and show, in the context of what is known about the recent demographic history of this population, that there are credible scenarios for a bottleneck driven by hunting pressure in the 1960s that could account for the lack of variation at this locus.

Status of hilsa (Tenualosa ilisha) management in the Bay of Bengal: an assessment of population risk and data gaps for more effective regional management

Assessment of country status papers on hilsa fisheries presented at the BOBP – IGO Chittagong, Bangladesh 2010. Assessment of status hilsa management in Bangladesh, India and Myanmar. Brief recommendations of potential follow-up activities that could enhance management. Risk assessment of hilsa in each country with Productivity Susceptibility Analysis (PSA). Summary of new approach to assess ecological risk.

Impact of common carp, Cyprinus carpio (L.) and Nile tilapia, Oreochromis niloticus (L.) on arthropods population, zoobenthos and weeds in rice-fish culture

An experiment was carried out in the fields of the Agronomy Field Laboratory, Bangladesh Agricultural University, Mymensingh, Bangladesh to determine the impact of common carp (Cyprinus carpio) and tilapia (Oreochromis niloticus) culture on arthropod population, zoobenthos and weeds of rice field. The treatments were: (1) rice combined with mono sex tilapia, (2) rice combined with common carp, (3) rice combined with a mixed culture of mono sex tilapia and common carp and (4) rice alone. It was observed that tilapia significantly reduced the number of arthropods, green leafhoppers and white leafhoppers in the rice-fish production systems. Benthos analysis revealed significant effects of fish culture on the abundance of molluscs, oligochaete worms and chironomid larvae. Lowest number of benthos was obtained in the treatments with common carp and significant reduction of the weed biomass was observed, especially in the tilapia containing plots. Based on the results of the study it can be suggested that common carp may play an important role in controlling of benthic organisms, while tilapia might be more effective to control terrestrial arthropods and weeds.

Distribution of plankton population in shrimp ghers of Bagherhat, Bangladesh

Analysis of plankton sample recorded a total of 5 classes’ phytoplankton viz Bacillariophyceae, Chlorophyceae, Cyanophyceae, Dinophyceae, and Polyhymenophorea. Total 50 phytoplankton species were identified. Among the phytoplankton 18 species belonged to Bacillariophyceae, 12 to Chlorophyceae, 8 to Cyanophyceae, 7 to Dinophyceae, and 5 to Polyhymenophorea. Bacillariophyceae was the dominant group of phytoplankton throughout the study period. Toxin producing dinoflagelates were recorded from the shrimp ghers. A total of 11 kinds of different zooplankton genera were recorded, 4 of which were belonged to Copepoda, 3 to Cladocera, 3 to Rotifera and 1 to Decapoda. Copepoda was the dominant group among the zooplankton which was followed by Rotifera and Decapoda. Temperature varied from 27°C to 32°C, transparency 24.5-29.6 cm and pH 6.7 to 9. Salinity fluctuated from 12 to 32.5‰ in both ghers. PO sub(4)-P and NO sub(3)-N ranged from 0.9 to 4.2 ppm.

Genetic diversity study of Caspian brown trout (Salmo trutta caspius Kessler, 1877) population in five rivers in the southern part of Caspian Sea, Iran

For study the genetic diversity of Caspian brown trout population in five rivers in the southern part of Caspian Sea in Iran 182 number generators in the fall and winter of 1390 were collected in Chalus, Sardab Rud, Cheshmeh Kileh, Kargan Rud and Astara rivers. Then about 3-5 g of soft and fresh tissue from the bottom fin fish removed and were fixed in ethanol 96°. Genomic DNA was extracted by using ammonium acetate, then quantity and quality of the extracted DNA were determined by using spectrophotometry and horizontal electrophoresis in 1% agarose gel. The polymerase chain reaction was performed by using 16 SSR primers and sequencing primers (D-Loop) and the quality of PCR products amplified by SSR method were performed by using horizontal electrophoresis in 2% agarose gel. Alleles and their sizes were determined by using vertical electrophoresis in 6% polyacrylamide gel and silver nitrate staining method. Gel images were recorded by gel documentarian, the bands were scored by using Photo- Capt software and statistical analysis was performed by using Gene Alex and Pop Gene software. Also the PCR sequencing products after quality assessment by usinghorizontal electrophoresis in 1.5% agarose gel were purified and sent to South Korea Bioneer Corporation for sequencing. Sequencing was performed by chain termination method and the statistical analysis was performed by using Bio- Edit, Mega, Arlequin and DNA SP software. The SSR method, 5 pairs of primers produced polymorphic bands and the average real and effective number of alleles were calculated 5.60±1.83 and 3.87±1.46 in the Cheshmeh Kileh river and 7.60±1.75 and 5.48±1.32 in the Karganrud river and the mean observed and expected heterozygosity were calculated 0.44 ±0.15 and 0.52 ±0.16 in the Cheshmeh Kileh river and 0.50 ±0.11 and 0.70±0.13 in the Karganrud river. Analysis of Molecular Variance results showed that significant differences in genetic diversity between and within populations and between and within individuals in the studied rivers (P<0.01). The sequencing method identified 35 different haplotype, the highest number of polymorphic position (251) and haplotype (14) were observed in the Chalus river. The highest mean observed number of alleles (2.24±0.48) was calculated in the Sardabrud river, the highest mean observed heterozygosity (1.00±0.03) was calculated in the Chalus river and the highest mean nucleotide diversity (0.13±0.07) was observed in the Sardabrud river and mean haplotype diversity was obtained (1) in three studied rivers. The overall results show that there are no same population of this fish in the studied rivers and Karganrud and Chalus rivers in the SSR and sequencing methods had the highest levels of genetic diversity.

The zooplankton population structure and their trend of variations in the southern of Caspian Sea (Iranian waters)

Caspian Sea has gone under a lot of changes due to human influences and the unwanted presence of a ctenophora Menomiopsis leidyi which has greatly changed the structure of planktons in the last recent years. Therefore, this study was carried out in order to determine these changes in the zooplankton community. the Sampling was done in 8 transacts in Astara, Anzali, Sefidrood, Tonekaboun, Noushahr, Babolsar, Amirabad and Bandar Torkaman coastal waters at 5 different depths including 5, 10, 20, 50 and 100 m. Sampling was carried out in four seasons of spring, summer, autumn and winter during 2008, 2009 and 2010 on board of R/V Gilan. Altogether, 12 species of zooplankton were identified in 2008, 22 species in 2009 and 14 species in 2010. The zooplankton included four groups: copepoda (4 species), cladocera (8species), rotatoria (10 species) and protozoa (2 species).The increase of diversity in 2009 was due to cladocera and rotatoria groups. The abundance of zooplankton in the spring was 5074 + 7807 ind/m3 more than other season in 2008. The abundance of copepoda in the summer reached the highest value of 3332 ind/m3 and since autumn the abundance gradually decreases and in the winter reached to the lowest value. The most abundance of cladocera was 797 ind/m3 in winter and decreased in summer and autumn. The abundance of rotatoria was 2189 ind/m3 in winter. rotifera and copepoda consisted the main population of Zooplanktons in the winter. The results of 2009 and 2010 showed that the abundance of zooplankton in winter was 2.6 fold of autumn, 1.6 fold of summer and 1.1 fold (1/9 fold in 2010)of spring. After increasing increased of temperature, phytoplankton, and zooplankton in summer, M.leidyi increased too. In the autumn M. leidyi reached to the highest rate and decreased zooplankton. The maximum population of zooplankton was in the layer 0-20 m and in the layer more than 20 meters, the abundance of zooplankton decreased very much. In 216 2008, 2009 and 2010, the abundance of zooplankton was 87, 77 and 77 percent in the layer 0-20 m respectively. In this study, the thermocline was observed in the layer 10 – 20 meters in the spring, that formed a thin layer but in the summer it was in the layer 20 to 50 meters. Temperature decreased between 11 to 15 oC in this layer. The variation of temperature between surfaces to bottom was 10 to 13 oC in spring, 19 to 21 in summer, about 9 oC in autumn and maximum 3 oC in winter. The most biomass of zooplankton was in the west. The biomass of zooplankton in central west and east of Southern of Caspian Sea was 54 %, 22 % and 24 % respectively in 2008, in 2009 was 48%, 33% and 20% respectively and in 2010 was 54 %, 29 % and 16 % respectively .The biomass decreased from west to east. The model of zooplankton designed by principal component analysis (PCA)and linear regression for Southern of Caspian Sea.

Biological characteristics and determination of population dynamic parameters of Sphyraena jello in the coastal waters of Province Bushehr- Persian Gulf

Sphyraena jello, Pick handle Barracuda, is amongst the highly valuable and main commercial fisheries resources in the southern waters of Iran. Given such an economically significant position, this study, being conducted in 2006-2007, attempts to investigate its biological habit and characteristics in Iran’s water of the Persian Gulf. For the sampling purpose, three major landings namely Bushehr, Deylam and Genaveh were selected to obtain samples from commercial catches. The sampling is composed of 655 males and 515 females during a twelve month period. By studying the feeding through the counting method, it is revealed that, Liza subviridis characterized by %42.8 and Sepia pharaonis by %8.4 made the highest and lowest stomach content respectively. The findings showed that male fish in smaller size will mature sooner than females’ specimen but this gender ratio or proportion was not significantly different except during October and September. Such a difference between male and female in different months could be originated from longer residing of female group in spawning ground compared to male group. The previous spawning lasted during September –October, and there was a peak of spawning in feeding in August. The lowest fat proportion for both male and female genders was reported 0.10 and 0.11 respectively in October; but the highest level of condition factor was reported to be 0.59 and 0.63 during November and June.

The study of biological characteristic and population dynamic of Caspian vimba (Vimba vimba persa), in coastal waters of Caspian Sea (Mazandaran Province)

This study was conducted to determine reproduction characteristics, diet regime, age structure and population dynamics parameters of the vimba vimba persa (Pallas, 1811) in Mazandaran waters of the Caspian Sea, from October 2008 to September 2009. A total of 994 specimens were monthly collected by beach seine and cast net from six fish landings of Ramsar, Tonekabon, Chaloos, Mahmood Abad, Sari and Behshahr. Biometric characters were measured for each specimen at the laboratory. Scales were used for age determination. Sex determination and fecundity were determined. Population dynamic parameters as well as stock assessment including cohort analysis were estimated using FISAT software. The finding showed that the mean of fork length and body weight of the Caspian Vimba were 168.4±2.6 mm and 71.94±32.24 g respectively. Strong correlation was found between these two variables (a= 0.012; b = 3.047; r2 = 0.955). 92 specimens were studied from the fecundity point of view. This species was found to have more abundance in spring (esp. Apr-May). The samples composed of 397(42.6%) male, 537(57.4%) female; Overall sex ratio (M: F =1: 1.35) was significantly different from the expected 1:1 ratio (p ≤0.05). The advanced stages of maturity (4th & 5th) were found in April and May. The highest Gonadosomatic Index in female was in May and the lowest one was in July. This fish is therefore a spring spawner. The maximum absolute and relative fecundities were 34640 and 260.9, respectively; the minimum absolute and relative fecundities were 5400 and 94.5 respectively. The averages of absolute and relative fecundities were 17198±7710 and 171.85±48.8, respectively. Coefficient vacuity index was 59.2% which indicates that this fish is mesophagous. Among of living creature consumes by Caspian Vimba mollusks, 76 arthropods, worms, plants, detritus and fishes were found 32.9% , 26.7% , 13.4% , 17% , 4.4% and 1.6% respectively. The infinite fork lengths were 261 mm for females, 25mm for males and 261 mm for both sexes respectively. For population growth and mortality parameters; K ( 0.28 per year for both sexes, 0.3 per year for males, 0.33 per year for females); t0 ( -0.65 year for both sexes, -0.23 year in females, -0.51 year in males ); Φ' ( 2.28 ); Z ( 0.98 per year ); M ( 0.59 per year); F ( 0.39 per year) and Exploitation coefficient was 0.4. The analysis showed that total biomass and MSY were 1336 and 528.8 tonnes respectively.

Evaluation of some biological indices and population dynamic of "Saurida tumbil" in the northern Persian Gulf and Oman Sea

The Great lizardfish is one of the commercial demersal fishes in the Persian Gulf and Oman Sea. In this study the food preference index (FPI), Fullness index (FI) and stomach contents of Saurida tumbil were evaluated to assess the quantity and kind of food which this species consumes in the study area. The samples were collected monthly from commercial bottom trawl fisheries in main fishing grounds of eastern Strait of Hormuz. A total of 346 specimens were collected during years 2009-2010 of which 269 specimens were female and 77 specimens were male. The minimum and maximum total length were 161 and 590 mm, respectively with the highest frequency in length group of 350-370mm. Results showed that 20.9% of stomachs were full, 18.9% were semi-full and 60.2% were empty. The main stomach contents (FPI=80.2%) were fishes and minor stomach contents (FPI=25.7%) were crustacean (Specially crab and shrimp) and cephalopods were found as random food. The minimum and maximum FIs were 2.5 and 42.5 in December and September respectively; and the overall CV was 60.2. The results indicate that this fish is a relatively frugal species which consumes fishes as main food and there is no difference in feeding of male and female.

Biological characteristics and determination of population dynamics parameters of Nemipterus japonicus in the coastal waters of Province Bushehr, Persian Gulf

This study was conducted to determine biological characteristics and population dynamics parameters of threadfin bream (Nemipterus japonicus) in Persian Gulf (Bushehr Province), during November 2006 and October 2007. The minimum and maximum specimens were 75-273 mm FL and their weight was 7.6 - 351.9 g. Based on the exponential relationship between fork length and weight, slope (b) for individuals, males and females was 2.987321, 2.992546 and 3.007314, respectively. The emptiness value (V) was 45.6% and it shows that N. japonicus is a moderate feeder. The results of Fp indicates that crustacean with 78.2% are main foods, mollusca (27.7%), fishes (20.7%), polychaeta (19.2%) and Foraminifera (11.7%) were identified as minor foods and phytoplanktons (9.9%), nematoda(8.0%), echinodermata (2.3%) and sea weeds (0.3%) were random foods. The reproduction studies showed the spawning season extended within 2 peaks, from April- May and September and main spawning occurs in spring season.The mean absolute and relative fecundities were 472388±42633 and 3817±293 (X±SE), respectively. The maximum, minimum and mean of oocyte diameter were 0.448, 0.022 and 0.221mm (SE=0.071), respectively.The fork length at 50% maturity estimated to be 20.25 cm for females. The growth coefficient (K) , length infinity (L∞ ) and ɸ' was estimated 0.42/yr , 34.17 cm and 2.69, respectively. The coefficient of total mortality, fishing mortality, natural mortality and E was 1.37, 0.43, 0.94 and 0.31, respectively.

Population genetic structure of Rutilus frisii kutum in Caspian Sea using biometry and microsatellite molecular technique

In order to carry out Biometric studies, 75 samples were caught from 3 locations ( Tajan river, Sefidrud and Shirud) using Salic and the length (±1 mm) and weights (± 5 gr) of samples were determined. Using One-way ANOVA by SPPSS software, there wasn’t significant difference between locations in length and fecondity (P ≥0.01(, but there was significant difference between Shirud and tajan samples with sefidrud in weight ) P≤0.01(. In order to carry out genetic variation studies, 210 fish were caught from 3 different regions of the Iranian coastline (Khoshkrud, Tonekabon, Gorganrud) and 1 region in Azerbaijan (Waters of the Caspian Sea close to Kura River mouth) during 2008-2009 . Genomic DNA was extracted of fin using the phenol-chloroform. The quantity and quality of DNA from samples were assessed by spectrophptometer and 1% agarose gel electro-phoresis. PCR was carried out using 15 paired microsatellite primers. PCR products were separated on 8% polyacrylamide gels that were stained using silver nitrate. Molecular weight calculate using UVTech software. The recorded microsatellite genotypes were used as input data for the GENALEX software version 6 package in order to calculate allele and genotype frequencies, observed (Ho) and (He) expected heterozygosities and to test for deviations from Hardy-Weinberg equilibrium. Genetic distance between two populations was estimated from Nei standard genetic distance and genetic similarity index (Nei, 1972). Genetic differentiation between populations was also evaluated by the calculation of pairwise estimates of Fst and Rst values. From 15 SSR markers were used in this investigation, 9 of them were polymorph. Average of expected and observed heterozygosity was 0.54 and 0.49 respectively. Significant deviations from Hardy-Weinberg expectations were observed in all of location except Anzali lagoon- autumn in AF277576 and EF144125, Khoshkrud in EF144125 and Gorganrud and Kura in AF277576. Using Fst and Rst there was significant difference between locations ) P≤0.01(. According to Fst , the highest population differentiation (Fst= 0.217) was between Gorganrud and Khoshkrud that have the lowest Nm and the lowest (Fst= 0.086) was between Gorganrud and Tonekabon that have the highest Nm. Using Rst the highest population differentiation (Rst= 0.271) was between Tonekabon and spring Anzali lagoon and the lowest (Rst= 0.026) was between Tonekabon and Autumn Anzali 159 lagoon. Also the difference between Spring Anzali lagoon and Autumn Anzali lagoon was noticeable (Fst=0.15). AMOVA analysis with consideration of 2 sampling regions (Iran and Azerbaijan) and 7 sampling locations (Iran: Khoshkrud, Tonekabon, Gorganrud, Spring Anzali lagoon and Autumn Anzali lagoon ; Azerbaijan: the Kura mouth) revealed that almost all of the variance in data namely 83% )P≤0.01( was within locations, Genetic variances among locations was 14% )P≤0.01( and among regions was 3% )P≤0.01(. The genetic distance was the highest (0.646) between Gorganrud and Autumn Anzali lagoon populations, whereas the lowest distance (0.237) was between Gorganrud and Tonekabon River. Result obtained from the present study show that at least 2 different population of Rutilus frissi kutum are found in the Caspian sea,which are including the kura river population and the southern Caspian sea samples and it appears that there is more than one population in southern Caspian sea that should be attantioned in artifical reproduction Center and stoke rebilding.