Genetic structure and differentiation of Reaumuria soongorica (Pall.) Maxim population from the desert of Fukang, Xinjiang, were assessed by means of random amplified polymorphic DNA (RAPD) markers. High genetic diver...Genetic structure and differentiation of Reaumuria soongorica (Pall.) Maxim population from the desert of Fukang, Xinjiang, were assessed by means of random amplified polymorphic DNA (RAPD) markers. High genetic diversity and differentiation were revealed in the population of R soongorica by 15 random primers. One hundred and thirty-six individuals from seven subpopulations were sampled in the study. Seventy-one loci have been detected, and among them 69 were polymorphic. The mean proportion of polymorphic loci (PPB) was 97.18%. The analyses of Shannon information index (0.307 5), Nei's gene diversity (0.312 7) and G(ST)(0.312 0) indicated that there were more genetic variations within the subpopulations than those among the subpopulations. The results of AMOVA analysis showed that 61.58% of the genetic variations existed within subpopulations, and 38.02% among the subpopulations. The gene flow among the subpopulations of R soongorica (Nm = 1.102 8) was much less than that of the common anemophytes (Nm = 5.24), so genetic differentiation among the subpopulations occurred to some extent. Additionally, through the use of clustering and the correlation analyses, we found that the genetic structure of natural population of R soongorica was related to some ecological factors (soil factors mainly) of the oasis-desert transition zone. The genetic diversity level of R soongorica had negative correlation with the content of total soil P and Cl significantly (P < 0.05). On the contrary, it had significant positive correlation with CO32- (P < 0.05), showing that the distribution of the individuals of R soongorica in the sampled areas correlates with certain soluble salt. Furthermore, the genetic diversity of the natural population of R soongorica increased with the decreasing of the content of soil organic matters, water, total N and total P in soil. The paper concluded that the microenvironment ecological factors played an important role in the adaptive evolution of R soongorica population.展开更多
Seagrass research in China is still in its infancy. Even though there has been progress recently, there is still a great deal of research needed to gain a better understanding of seagrass. In this article we review an...Seagrass research in China is still in its infancy. Even though there has been progress recently, there is still a great deal of research needed to gain a better understanding of seagrass. In this article we review and discuss the advances in seagrass research in China from two aspects: (1) seagrass species and their distribution; (2) seagrass research in China, including studies on their taxonomy, ecology, photosynthesis, applications in aquaculture, salt-tolerance mechanisms and other research topics. A total of 18 seagrass species belonging to 8 genera are distributed in nine provinces and regions in China (including Hong Kong and Taiwan), as well as the Xisha and Nansha Archipelagos. They can be divided into two groups: a North China Group and a South China Group. Based on the seagrass distribution, the Chinese mainland coast can be divided into three sections: North China Seagrass Coast, Middle China Seagrass Coast, and South China Seagrass Coast. Ecological studies include research on seagrass communities, nutrient cycling in seagrass ecosystems, genetic diversity, pollution ecology and research in the key regions of Shandong, Guangdong, Guangxi, and Hainan. Seagrass species and their locations, community structure, ecological evaluation, epiphytes, ecological functions and threats in the key regions are also summarized. Other studies have focused on remote sensing of seagrass, threatened seagrass species of China, and pollen morphology of Halophila ovalis.展开更多
Oplegnathusfasciatus （rock bream） is a commercial rocky reef fish species in East Asia that has been considered for aquaculture. We estimated the population genetic diversity and population structure of the species ...Oplegnathusfasciatus （rock bream） is a commercial rocky reef fish species in East Asia that has been considered for aquaculture. We estimated the population genetic diversity and population structure of the species along the coastal waters of China using fluorescent-amplifed fragment length polymorphisms technology. Using 53 individuals from three populations and four pairs of selective primers, we amplified 1 264 bands, 98.73% of which were polymorphic. The Zhoushan population showed the highest Nei＇s genetic diversity and Shannon genetic diversity. The results of analysis of molecular variance （AMOVA） showed that 59.55% of genetic variation existed among populations and 40.45% occurred within populations, which indicated that a significant population genetic structure existed in the species. The pairwise fixation index Fst ranged from 0.20 to 0.63 and were significant after sequential Bonferroni correction. The topology of an unweighted pair group method with arithmetic mean tree showed two significant genealogical branches corresponding to the sampling locations of North and South China. The AMOVA and STRUCTURE analyses suggested that the O.fasciatus populations examined should comprise two stocks.展开更多
The term ＂forgotten city＂ was mentioned by researchers to denominate some colonial Brazilian settlements and cities which seem to have the same characteristics that demonstrate they were hidden along the years and t...The term ＂forgotten city＂ was mentioned by researchers to denominate some colonial Brazilian settlements and cities which seem to have the same characteristics that demonstrate they were hidden along the years and that have the same atmosphere as they used to in their past life, i.e., they have the same traditional type of urban configuration produced at the origin of the city. This paper brings into discussion this character of this city, using as an example the city of Laranjeiras, one of the oldest cities of the State of Sergipe, which had a great and rich trade of sugar, besides significant cultural and political activities, being known as ＂Brazilian Athens＂ in the 19th century. Then, Laranjeiras decayed and stopped growing along the 20th century. However, it has had a good perspective to develop again with insertion of new different activities recently. The initial Portuguese planning to villages in Brazil followed specific rules and had a systematic assistance, what discards the myth that many Brazilian cities were born and grown up as a spontaneous form without planning. Studying some factors deeply, as spatial configuration, settlement localization and urban grid, it can be possible to point some recognizable elements which demonstrate that some cities were built to be forgotten. The methodology used for the analysis of Laranjeiras presents many historic, economic and cultural aspects related to the spatial-syntactic studies （Space Syntax Theory）, bringing to light some interesting thoughts about urban form and social life.展开更多
Half-smooth tongue sole (Cynoglossus semilaevis) is a promising species for aquaculture in China.The wild population of C. semilaevis is under threat from environmental factors. Microsatellite markers are very suitabl...Half-smooth tongue sole (Cynoglossus semilaevis) is a promising species for aquaculture in China.The wild population of C. semilaevis is under threat from environmental factors. Microsatellite markers are very suitable for assessing genetic diversity. Four microsatellite-enriched libraries of half smooth tongue sole (Cynoglossus semilaevis) were constructed,from which 57 polymorphic microsatellites were isolated and characterized.The polymorphism of these microsatellites was assessed by genotyping in 30 individual fish.The number of alleles ranged from 2 to 11, with an average of 4.614 alleles per locus.The values of observed and expected heterozygosities ranged from 0.1000 to 1.0000 and from 0.0966 to 0.8847 respectively. Polymorphism information content (PIC) ranged from 0.0905 to 0.862.These markers would be useful for population structure assessment,genetic linkage map construction and parentage analysis for this species.展开更多
Chaotic genetic patchiness （CGP） refers to surprising patterns of spatial and temporal genetic structure observed in some marine species at a scale where genetic variation should be efficiently homogenized by gene f...Chaotic genetic patchiness （CGP） refers to surprising patterns of spatial and temporal genetic structure observed in some marine species at a scale where genetic variation should be efficiently homogenized by gene flow via larval dispersal. Here we review and discuss 4 mechanisms that could generate such unexpected patterns： selection, sweepstakes reproductive success, collective dispersal, and temporal shifts in local population dynamics. First, we review examples where genetic differentiation at specific loci was driven by diversifying selection, which was historically the first process invoked to explain CGP. Second, we turn to neutral demographic processes that may drive genome-wide effects, and whose effects on CGP may be enhanced when they act together. We discuss how sweepstakes reproductive success accelerates genetic drift and can thus generate genetic structure, provided that gene flow is not too strong. Collective dispersal is another mechanism whereby genetic structure can be maintained regardless of dispersal intensity, because it may prevent larval cohorts from becoming entirely mixed. Theoretical analyses of both the sweepstakes and the collective dispersal ideas are presented. Finally, we discuss an idea that has received less attention than the other ones just mentioned, namely temporal shifts in local population dynamics.展开更多
Invasive species are considered one of the greatest threats to native ecosystems, second only to habitat loss and frag- mentation. Despite this, the temporal dynamics of invasions are poorly understood, with most stud...Invasive species are considered one of the greatest threats to native ecosystems, second only to habitat loss and frag- mentation. Despite this, the temporal dynamics of invasions are poorly understood, with most studies focusing on a single time point, providing us with only a snapshot of the biology and genetics of the invader. We investigated the invasion of Lord Howe Island by the delicate skink Lampropholis delicata and assessed the introduction history and genetic structure of this species over a 5-year period. Using genetic data taken from 2007, and again in 2011/12, we examined changes in the population genetic struc- ture （whether new haplotypes had been introduced to the island, and shifts in haplotype frequencies） of the species on the island between these two time points. No new haplotypes were introduced to the island between 2007 and 2011/12; however, significant shifts in haplotype frequencies across the island were detected. We conclude that the delicate skink is expanding its range into the southern regions of the island and that the haplotype frequencies on Lord Howe Island are still in a state of highly dynamic flux. Our study highlights the importance of considering invasions as dynamic and studying them in such a way that enable us to better manage their impacts展开更多
When incompletely isolated taxa coexist in a patchy environment （e.g. mosaic hybrid zones, host-race complexes）, patterns of variation may differ between selected traits/genes and neutral markers. While the genetic ...When incompletely isolated taxa coexist in a patchy environment （e.g. mosaic hybrid zones, host-race complexes）, patterns of variation may differ between selected traits/genes and neutral markers. While the genetic structure of selected traits/loci tends to coincide with habitat variables （producing Genetic-Environment Association or GEA）, genetic differentiation at neutral loci unlinked to any selected locus rather depends on geographic connectivity at a large scale （e.g. Isolation- By-Distance or IBD）, although these loci often display GEA at a small scale. This discrepancy has been repeatedly taken as evi- dence for parallel primary divergence driven by local adaptation. We argue that this interpretation needs to be addressed more thoroughly by considering the alternative hypothesis that speciation was initiated in allopatry and secondary introgression has subsequently erased the signal of past differentiation at neutral loci. We present a model of neutral introgression after secondary contact in a mosaic hybrid zone, which describes how GEAs dissipate with time and how neutral variation self-organizes accord- ing to the environmental and geographic structures. We show that although neutral loci can be affected by environmental selection they are often more affected by history and connectivity： the neutral structure retains the initial geographic separation more than it correlates with the environment during the colonization and introgression phases, and then converges to a migration-drift balance, the most frequent outcome of which is GEA at a local scale but IBD at a large scale. This is the exact pattern usually attributed to parallel ecological speciation. Introgression is heterogeneous in space and depends on the landscape structure （e.g. it is faster in small patches, which are more impacted by immigration）. Furthermore, there is no directionality in the association and it is possi- ble to observe reversed GEAs between distant regions. We argue that the history of differentiation should ideally be reconstructed with selected loci or neutral loci linked to them, not neutral ones, and review some case studies for which the hypothesis of a long co-existence of co-adapted genetic backgrounds might have been refuted too hastily [Current Zoology 59 （1）： 72-86, 2013].展开更多
文摘Genetic structure and differentiation of Reaumuria soongorica (Pall.) Maxim population from the desert of Fukang, Xinjiang, were assessed by means of random amplified polymorphic DNA (RAPD) markers. High genetic diversity and differentiation were revealed in the population of R soongorica by 15 random primers. One hundred and thirty-six individuals from seven subpopulations were sampled in the study. Seventy-one loci have been detected, and among them 69 were polymorphic. The mean proportion of polymorphic loci (PPB) was 97.18%. The analyses of Shannon information index (0.307 5), Nei's gene diversity (0.312 7) and G(ST)(0.312 0) indicated that there were more genetic variations within the subpopulations than those among the subpopulations. The results of AMOVA analysis showed that 61.58% of the genetic variations existed within subpopulations, and 38.02% among the subpopulations. The gene flow among the subpopulations of R soongorica (Nm = 1.102 8) was much less than that of the common anemophytes (Nm = 5.24), so genetic differentiation among the subpopulations occurred to some extent. Additionally, through the use of clustering and the correlation analyses, we found that the genetic structure of natural population of R soongorica was related to some ecological factors (soil factors mainly) of the oasis-desert transition zone. The genetic diversity level of R soongorica had negative correlation with the content of total soil P and Cl significantly (P < 0.05). On the contrary, it had significant positive correlation with CO32- (P < 0.05), showing that the distribution of the individuals of R soongorica in the sampled areas correlates with certain soluble salt. Furthermore, the genetic diversity of the natural population of R soongorica increased with the decreasing of the content of soil organic matters, water, total N and total P in soil. The paper concluded that the microenvironment ecological factors played an important role in the adaptive evolution of R soongorica population.
基金Supported by Guangxi Science Foundation (No. 0832030)Scientific Research Fund of Guangxi University (2008)+1 种基金UNDP/GEF/SCCBD Project (SCCBD/CPR/02/31)Guangxi Key Lab Fund (No. 07109007)
文摘Seagrass research in China is still in its infancy. Even though there has been progress recently, there is still a great deal of research needed to gain a better understanding of seagrass. In this article we review and discuss the advances in seagrass research in China from two aspects: (1) seagrass species and their distribution; (2) seagrass research in China, including studies on their taxonomy, ecology, photosynthesis, applications in aquaculture, salt-tolerance mechanisms and other research topics. A total of 18 seagrass species belonging to 8 genera are distributed in nine provinces and regions in China (including Hong Kong and Taiwan), as well as the Xisha and Nansha Archipelagos. They can be divided into two groups: a North China Group and a South China Group. Based on the seagrass distribution, the Chinese mainland coast can be divided into three sections: North China Seagrass Coast, Middle China Seagrass Coast, and South China Seagrass Coast. Ecological studies include research on seagrass communities, nutrient cycling in seagrass ecosystems, genetic diversity, pollution ecology and research in the key regions of Shandong, Guangdong, Guangxi, and Hainan. Seagrass species and their locations, community structure, ecological evaluation, epiphytes, ecological functions and threats in the key regions are also summarized. Other studies have focused on remote sensing of seagrass, threatened seagrass species of China, and pollen morphology of Halophila ovalis.
基金Supported by the National High Technology Research and Development Program of China(863 Program)(No.2012AA10A413-1)the STS(No.KFJ-EW-STS-060-STS)+5 种基金the Natural Science Foundation of Jiangsu Province(No.BK2012222)the Key Laboratory of East China Sea&Oceanic Fishery Resources Exploitation and Utilization,Ministry of Agriculture,China(No.K201204)the Promotive Research Fund for Excellent Young and Middle-Aged Scientists of Shandong Province(No.BS2012HZ025)the National Natural Science Foundation of China(No.41506170)the Technology Foundation for Selected Overseas Chinese ScholarMinistry of Personnel of China(No.2013.01)
文摘Oplegnathusfasciatus （rock bream） is a commercial rocky reef fish species in East Asia that has been considered for aquaculture. We estimated the population genetic diversity and population structure of the species along the coastal waters of China using fluorescent-amplifed fragment length polymorphisms technology. Using 53 individuals from three populations and four pairs of selective primers, we amplified 1 264 bands, 98.73% of which were polymorphic. The Zhoushan population showed the highest Nei＇s genetic diversity and Shannon genetic diversity. The results of analysis of molecular variance （AMOVA） showed that 59.55% of genetic variation existed among populations and 40.45% occurred within populations, which indicated that a significant population genetic structure existed in the species. The pairwise fixation index Fst ranged from 0.20 to 0.63 and were significant after sequential Bonferroni correction. The topology of an unweighted pair group method with arithmetic mean tree showed two significant genealogical branches corresponding to the sampling locations of North and South China. The AMOVA and STRUCTURE analyses suggested that the O.fasciatus populations examined should comprise two stocks.
文摘The term ＂forgotten city＂ was mentioned by researchers to denominate some colonial Brazilian settlements and cities which seem to have the same characteristics that demonstrate they were hidden along the years and that have the same atmosphere as they used to in their past life, i.e., they have the same traditional type of urban configuration produced at the origin of the city. This paper brings into discussion this character of this city, using as an example the city of Laranjeiras, one of the oldest cities of the State of Sergipe, which had a great and rich trade of sugar, besides significant cultural and political activities, being known as ＂Brazilian Athens＂ in the 19th century. Then, Laranjeiras decayed and stopped growing along the 20th century. However, it has had a good perspective to develop again with insertion of new different activities recently. The initial Portuguese planning to villages in Brazil followed specific rules and had a systematic assistance, what discards the myth that many Brazilian cities were born and grown up as a spontaneous form without planning. Studying some factors deeply, as spatial configuration, settlement localization and urban grid, it can be possible to point some recognizable elements which demonstrate that some cities were built to be forgotten. The methodology used for the analysis of Laranjeiras presents many historic, economic and cultural aspects related to the spatial-syntactic studies （Space Syntax Theory）, bringing to light some interesting thoughts about urban form and social life.
基金supported by the 863 Project of China(2006AA10A403)the Natural Science Foundation of China(No.30972244)Taishan Scholar Project of Shandong Province,China
文摘Half-smooth tongue sole (Cynoglossus semilaevis) is a promising species for aquaculture in China.The wild population of C. semilaevis is under threat from environmental factors. Microsatellite markers are very suitable for assessing genetic diversity. Four microsatellite-enriched libraries of half smooth tongue sole (Cynoglossus semilaevis) were constructed,from which 57 polymorphic microsatellites were isolated and characterized.The polymorphism of these microsatellites was assessed by genotyping in 30 individual fish.The number of alleles ranged from 2 to 11, with an average of 4.614 alleles per locus.The values of observed and expected heterozygosities ranged from 0.1000 to 1.0000 and from 0.0966 to 0.8847 respectively. Polymorphism information content (PIC) ranged from 0.0905 to 0.862.These markers would be useful for population structure assessment,genetic linkage map construction and parentage analysis for this species.
文摘Chaotic genetic patchiness （CGP） refers to surprising patterns of spatial and temporal genetic structure observed in some marine species at a scale where genetic variation should be efficiently homogenized by gene flow via larval dispersal. Here we review and discuss 4 mechanisms that could generate such unexpected patterns： selection, sweepstakes reproductive success, collective dispersal, and temporal shifts in local population dynamics. First, we review examples where genetic differentiation at specific loci was driven by diversifying selection, which was historically the first process invoked to explain CGP. Second, we turn to neutral demographic processes that may drive genome-wide effects, and whose effects on CGP may be enhanced when they act together. We discuss how sweepstakes reproductive success accelerates genetic drift and can thus generate genetic structure, provided that gene flow is not too strong. Collective dispersal is another mechanism whereby genetic structure can be maintained regardless of dispersal intensity, because it may prevent larval cohorts from becoming entirely mixed. Theoretical analyses of both the sweepstakes and the collective dispersal ideas are presented. Finally, we discuss an idea that has received less attention than the other ones just mentioned, namely temporal shifts in local population dynamics.
文摘Invasive species are considered one of the greatest threats to native ecosystems, second only to habitat loss and frag- mentation. Despite this, the temporal dynamics of invasions are poorly understood, with most studies focusing on a single time point, providing us with only a snapshot of the biology and genetics of the invader. We investigated the invasion of Lord Howe Island by the delicate skink Lampropholis delicata and assessed the introduction history and genetic structure of this species over a 5-year period. Using genetic data taken from 2007, and again in 2011/12, we examined changes in the population genetic struc- ture （whether new haplotypes had been introduced to the island, and shifts in haplotype frequencies） of the species on the island between these two time points. No new haplotypes were introduced to the island between 2007 and 2011/12; however, significant shifts in haplotype frequencies across the island were detected. We conclude that the delicate skink is expanding its range into the southern regions of the island and that the haplotype frequencies on Lord Howe Island are still in a state of highly dynamic flux. Our study highlights the importance of considering invasions as dynamic and studying them in such a way that enable us to better manage their impacts
文摘When incompletely isolated taxa coexist in a patchy environment （e.g. mosaic hybrid zones, host-race complexes）, patterns of variation may differ between selected traits/genes and neutral markers. While the genetic structure of selected traits/loci tends to coincide with habitat variables （producing Genetic-Environment Association or GEA）, genetic differentiation at neutral loci unlinked to any selected locus rather depends on geographic connectivity at a large scale （e.g. Isolation- By-Distance or IBD）, although these loci often display GEA at a small scale. This discrepancy has been repeatedly taken as evi- dence for parallel primary divergence driven by local adaptation. We argue that this interpretation needs to be addressed more thoroughly by considering the alternative hypothesis that speciation was initiated in allopatry and secondary introgression has subsequently erased the signal of past differentiation at neutral loci. We present a model of neutral introgression after secondary contact in a mosaic hybrid zone, which describes how GEAs dissipate with time and how neutral variation self-organizes accord- ing to the environmental and geographic structures. We show that although neutral loci can be affected by environmental selection they are often more affected by history and connectivity： the neutral structure retains the initial geographic separation more than it correlates with the environment during the colonization and introgression phases, and then converges to a migration-drift balance, the most frequent outcome of which is GEA at a local scale but IBD at a large scale. This is the exact pattern usually attributed to parallel ecological speciation. Introgression is heterogeneous in space and depends on the landscape structure （e.g. it is faster in small patches, which are more impacted by immigration）. Furthermore, there is no directionality in the association and it is possi- ble to observe reversed GEAs between distant regions. We argue that the history of differentiation should ideally be reconstructed with selected loci or neutral loci linked to them, not neutral ones, and review some case studies for which the hypothesis of a long co-existence of co-adapted genetic backgrounds might have been refuted too hastily [Current Zoology 59 （1）： 72-86, 2013].
