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Evaluating Intraspecific Variation and Interspecific Diversity: comparing humans and fish species  [PDF]
Bradly Alicea
Quantitative Biology , 2008,
Abstract: The analysis of eight molecular datasets involving human and teleost examples along with morphological samples from several groups of Neotropical electric fish (Order: Gymnotiformes) were used in this thesis to test the dynamics of both intraspecific variation and interspecific diversity. In terms of investigating molecular interspecific diversity among humans, two experimental exercises were performed. A cladistic exchange experiment tested for the extent of discontinuity and interbreeding between H. sapiens and neanderthal populations. As part of the same question, another experimental exercise tested the amount of molecular variance resulting from simulations which treated neanderthals as being either a local population of modern humans or as a distinct subspecies. Finally, comparisons of hominid populations over time with fish species helped to define what constitutes taxonomically relevant differences between morphological populations as expressed among both trait size ranges and through growth patterns that begin during ontogeny. Compared to the subdivision found within selected teleost species, H. sapiens molecular data exhibited little variation and discontinuity between geographical regions. Results of the two experimental exercises concluded that neanderthals exhibit taxonomic distance from modern H. sapiens. However, this distance was not so great as to exclude the possibility of interbreeding between the two subspecific groups. Finally, a series of characters were analyzed among species of Neotropical electric fish. These analyses were compared with hominid examples to determine what constituted taxonomically relevant differences between populations as expressed among specific morphometric traits that develop during the juvenile phase.
DNA Methylation Alterations at 5′-CCGG Sites in the Interspecific and Intraspecific Hybridizations Derived from Brassica rapa and B. napus  [PDF]
Wanshan Xiong, Xiaorong Li, Donghui Fu, Jiaqin Mei, Qinfei Li, Guanyuan Lu, Lunwen Qian, Yin Fu, Joseph Onwusemu Disi, Jiana Li, Wei Qian
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0065946
Abstract: DNA methylation is an important regulatory mechanism for gene expression that involved in the biological processes of development and differentiation in plants. To investigate the association of DNA methylation with heterosis in Brassica, a set of intraspecific hybrids in Brassica rapa and B. napus and interspecific hybrids between B. rapa and B. napus, together with parental lines, were used to monitor alterations in cytosine methylation at 5′-CCGG sites in seedlings and buds by methylation-sensitive amplification polymorphism analysis. The methylation status of approximately a quarter of the methylation sites changed between seedlings and buds. These alterations were related closely to the genomic structure and heterozygous status among accessions. The methylation status in the majority of DNA methylation sites detected in hybrids was the same as that in at least one of the parental lines in both seedlings and buds. However, the association between patterns of cytosine methylation and heterosis varied among different traits and between tissues in hybrids of Brassica, although a few methylation loci were associated with heterosis. Our data suggest that changes in DNA methylation at 5′-CCGG sites are not associated simply with heterosis in the interspecific and intraspecific hybridizations derived from B. rapa and B. napus.
The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements
Tomàs Marques-Bonet, Ze Cheng, Xinwei She, Evan E Eichler, Arcadi Navarro
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-384
Abstract: Here we take the opposite view and focus on SDs. We analyze several of the features of SDs, including the rates of intraspecific divergence between paralogous copies of human SDs and of interspecific divergence between human SDs and chimpanzee DNA. We study how divergence measures relate to chromosomal rearrangements, while considering other factors that affect evolutionary rates in single copy DNA.We find that interspecific SD divergence behaves similarly to divergence of single-copy DNA. In contrast, old and recent paralogous copies of SDs do present different patterns of intraspecific divergence. Also, we show that some relatively recent SDs accumulate in regions that carry inversions in sister lineages.Initial analyses of the human genome sequence have showed that ~5% of the human genome is composed by interspersed segmental duplications (SDs) [1]. SDs can be defined as blocks of DNA ranging from 1–400 kb in length, with copies found in multiple sites and that typically share high sequence similarity (> 90%). The distribution of these duplications is non-uniform within and among chromosomes, with a tendency to cluster in pericentromeric and subtelomeric regions [2-7] and in the breakpoints of chromosomal rearrangements [8-12]Duplications have both functional and structural effects [1,2,6,7,9,13-15]. Their functional consequences are very diverse. First, by predisposing chromosomal architectures to be rearranged by non-allelic homologous recombination [7,12,16-18], SDs constitute genetic risk factors for many diseases (e.g. Prader-Willi, Williams-Beuren Syndromes, juvenile nephronophtisis or spinal muscular atrophy). Second, SDs are related to genic evolution because they produce duplications of coding sequences that can lead to genes with new functions [7,19-25]. Finally, rates of evolution of duplicated genes are accelerated just after the duplication event [26]. These accelerations could be due to an increase of mutation rates after duplication, the relaxation
Chromosomes of Theridiidae spiders (Entelegynae): interspecific karyotype diversity in Argyrodes and diploid number intraspecific variability in Nesticodes rufipes
Stavale, Leila Miguel;Schneider, Marielle Cristina;Araujo, Douglas;Brescovit, Antonio Domingos;Cella, Doralice Maria;
Genetics and Molecular Biology , 2010, DOI: 10.1590/S1415-47572010005000076
Abstract: theridiidae is a derived family within the araneoidea clade. in contrast to closely related groups, the 2n(male) = 20+x1x2 with acro/telocentric chromosomes is the most widespread karyotype among the theridiid spiders. in this work, the cytogenetic analysis of argyrodes elevatus revealed original chromosome features different from those previously registered for theridiidae, including the presence of 2n(male) = 20+x with meta/submetacentric chromosomes. most individuals of nesticodes rufipes showed family conserved karyotype characteristics. however, one individual had a 2n(male) = 24 due to the presence of an extra chromosome pair, which exhibited regular behavior and reductional segregation during meiosis. after silver staining, mitotic cells exhibited nors localized on the terminal regions of the short arms of pairs 2, 3, and 4 of a. elevatus and on the terminal regions of long arms of pair 4 of n. rufipes. the comparative analysis with data from phylogenetically related species allowed the clarification of the origin of the interspecific and intraspecific chromosome variability observed in argyrodes and in n. rufipes, respectively.
Intraspecific and interspecific competition of Japanese yew (Taxus cuspidata)
天然东北红豆杉(Taxus cuspidata)种内和种间竞争

LIU Tong,LI Yun-Ling,ZHOU Zhi-Qiang,HU Hai-Qing,

生态学报 , 2007,
Abstract: Intraspecific and interspecific competitions are important relationships of plants. We analyzed competition intensity using field data for 95 Japanese yew (Taxus cuspidata) target trees and 980 individuals of competing species by using the competition index (CI) in Muling Nature Reserve of eastern Heilongjiang Province. The intraspecific competition of Japanese yew population was weak, accounting for 4 percent of total competition, and the main stress to the Japanese yew population came from interspecific competition, which accounted for 96 percent of the total. The main competitors were the dominant species of the zonal vegetation types,including Abies nephrolepis, Tilia amurensis, Acer mono and Pinus koraiensis. The competition intensity of Japanese yew declined with increasing DBH, and the stress was more intense for trees less than 20 cm in DBH. The relationship between competition intensity and DBH of target trees followed the equation CI=AD-B.
Regional Yield Evaluation of the Interspecific Hybrids (O. glaberrimax O. sativa) and Intraspecific (O. sativa x O. sativa) Lowland Rice  [PDF]
M. Sie,Y. Sere,S. Sanyang,L.T. Narteh
Asian Journal of Plant Sciences , 2008,
Abstract: The immense potential of the lowlands in West and Central Africa for durable intensification of rice cropping have not been realised due to biotic and abiotic constraints. There is a need to replace existing rice varieties with others that are better adapted to the lowland conditions. After the success of the upland interspecific varieties, Africa Rice Center (WARDA) and its partners developed NERICA varieties suitable for irrigated and rainfed lowlands. The stable varieties resulting from this work were evaluated under preliminary yield trials in eight countries at 19 sites. The entries included 61 interspecific (O. glaberrima x O. sativa indica) varieties and 9 intraspecific (O. sativa indica x O. sativa indica) varieties. The aim of the study is to introduce new lowland NERICAs through a participatory approach and to identify ideotypes that are adapted to lowland conditions. Variations did exist among the 73 rice varieties with respect to the five traits that were evaluated. Total number of tillers, panicle number and flowering dates were observed to greatly influence the yield among the 73 varieties that were evaluated. A principal components plot clustering analysis were used to group the accessions. The interspecific varieties formed the most interesting group and have a better capacity for adaptation to the diversity of lowlands. They have acceptable yields, sometimes higher than those of intraspecific varieties and checks. Thus, most lowland NERICAs varieties tested in three ecologies could produce more than 5 t ha-1. The results obtained were quite encouraging and showed that, the varieties possess good agronomic traits that are well adapted to intensified lowland rice farming. The recent naming of some of these interspecific varieties as NERICA-L (New Rice for Africa Lowland) by Africa Rice Center has confirmed that they compare well with the traditional varieties. Thus, from this study, we now have a new set of interspecific varieties that are adapted to lowland conditions and which the national research programs can use in various tests for satisfying farmers` needs.
Intraspecific and Interspecific competition analysis of community dominant plant populations based on Voronoi diagram

TANG Meng-Ping,CHEN Yong-Gang,SHI Yong-Jun,ZHOU Guo-Mo,ZHAO Min-Shui,

生态学报 , 2007,
Abstract: One plot that represents typical evergreen broad-leaved forests was established and surveyed in Tianmu Mountain National Nature Reserve, Zhejiang Province, and the plot size was 100 m × 100 m. Each tree was located in terms of x-, y-, and z-coordinates using a total station and the dominant plant populations were determined based on the dominance index analysis method. Then, V_Hegyi competition index based on Voronoi diagram was put forward, and three competition indices including Hegyi, APA and V_Hegyi were compared. Finally, the new competition index V_Hegyi was applied to analyze intraspecific and interspecific competition of dominant species. The results show that in the evergreen broadleaf forest that was studied, there are eleven dominant tree species, including Cyclobalanopsis myrsinaefolia, Cyclobalanopsis glauca, Lithocarpus brevicaudatus, Litsea coreana, Quercus fabri, Litsea auriculata, Pistacia chinensis, Zelkova schneideriana, Cunninghamia lanceolata, Liquidambar formosana and Dalbergia hupeana. The comparison and analysis imply that V_Hegyi not only overcomes the shortcoming in the inconsistency of measure units used to determine the competition based on fixed radius circles, but also can be used to make intraspecific and interspecific competition analysis and leads to stable rank of competition. Thus, V_Hegyi is superior to Hegyi and APA, and applicable for dominant tree species competition analysis. In the evergreen broadleaf forest, the intraspecific competition is fiercer than the interspecific competition. The dominant tree species whose intraspecific competition is the fiercest, Cyclobalanopsis myrsinaefolia, Cyclobalanopsis glauca and Lithocarpus brevicaudatus, also possess the cruelest interspecific competition. On the contrary, both intraspecific and interspecific competition of the tree species including Litsea coreana, Quercus fabri, Litsea auriculata, Pistacia chinensis, Zelkova schneideriana, Cunninghamia lanceolata, Liquidambar formosana and Dalbergia hupeana, are weak. Most of the dominant tree species have one main competitor, but few have more than three. Cyclobalanopsis myrsinaefolia is the absolutely dominant tree species and shows the fiercest intraspecific competition and at the same time, it is also the strongest competitor of other dominant tree species.
Study on Intraspecific and Interspecific Competition in Abies fargesii on Taibai Mountain

DUAN Ren-Yan,WANG Xiao-An,HUANG Min-Yi,TU Yun-Bo,WANG Chao,

植物科学学报 , 2007,
Abstract: The improved competition index and method of qualify the competition zone reflecting objectively the competition and growth pattern of Abies fargesii were selected.The results showed that:with the increase of the size and the distance,the intraspecific competition intensity decreased,because of the population density regulation during self-thinning.In the community,the competition intensity of interspecific was more excessive than that of intraspecific.The order of competition intensity was Larix chinensis-A.fargesii>A.fargesii-A.fargesii>Betula utilis-A.fargesii>other species-A.fargesii.The relationship between competition intensity and individual growth of objective tree followed closely the following equation CI=AD-B,and the changing of competition intensity was very small when the diameter of the objective tree growed to 25 cm.The improved method could simulate and predict the intraspecific and interspecific competition of A.fargesii efficiently.
Intraspecific and Interspecific Competition of Rhizophora stylosa in Techeng Isle of Zhanjiang

- , 2015, DOI: doi:10.3969/j.issn.1001-7461.2015.03.12
Abstract: 利用Hegyi提出的单木竞争指数模型分析湛江市特呈岛红海兰混交群落种内和种间竞争指数。结果表明,红海兰种内种间竞争指数随着林木径级增大而减少;径级在3.0~3.9 cm时受到的竞争强度最大;种内竞争远大于种间竞争;种间竞争强度的顺序为海榄雌>木榄>秋茄树;红海兰种内、种间和林分竞争强度服从幂函数关系。
Using intraspecific and interspecific competition of Rhizophora stylosa occurring in Techeng Isle of Zhanjiang were analyzed by using Hegyi’s competition index model for individual tree. The results showed that intraspecific and interspecific competition index of R. stylosa reduced with the increase in diameter scale of the trees. The competitive intensity reached the maximum when the diameter class was between 3.0 cm and 3.9 cm. The intraspecific competition was much larger than interspecific competition.The order of interspecific competition was listed as:Avicennia marina>Bruguiera gymnorrhiza>Kandelia candel. The intraspecific and interspecific, as well as forest stand competitive intensities of R. stylosa matched the power function CI=ADB
Tonic immobility in terrestrial isopods: intraspecific and interspecific variability  [cached]
Aline Quadros,Priscila Bugs,Paula Beatriz de Araujo
ZooKeys , 2012, DOI: 10.3897/zookeys.176.2355
Abstract: Many arthropods, including terrestrial isopods, are capable of entering a state of tonic immobility upon a mechanical disturbance. Here we compare the responses to mechanical stimulation in three terrestrial isopods Balloniscus glaber, B. sellowii and Porcellio dilatatus. We applied three stimuli in a random order and recorded whether each individual was responsive (i.e. showed tonic immobility) or not and the duration of the response. In another trial we related the time needed to elicit tonic immobility and the duration of response of each individual. Balloniscus sellowii was the least responsive species and P. dilatatus was the most, with 23% and 89% of the tested individuals, respectively, being responsive. Smaller B. sellowii were more responsive than larger individuals. Porcellio dilatatus responded more promptly than the Balloniscus spp. but it showed the shortest response. Neither sex, size nor the type of stimulus explained the variability found in the duration of tonic immobility. These results reveal a large variability in tonic immobility behavior, even between closely related species, which seems to reflect a species-specific response to predators with different foraging modes.
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