Conservation genetics of South American aquatic mammals: an overview of gene diversity, population structure, phylogeography, non-invasive methods and forensics

Eastern South America, or what is today Brazilian territory, poses interesting questions about the early human occupation of the Americas. Three totally distinct and contemporaneous lithic technologies, dated between 11,000 and 10,000 14C BP, are present in different portions of the country: the Umbu tradition in the south, with its formal bifacial industry, with well-retouched scrapers and bifacial points; the Itaparica tradition in the central-west / northwest, totally unifacial, whose only formal artifacts are limaces; and the "Lagoa Santa" industry, completely lacking any formal artifacts, composed mainly of small quartz flakes. Our data suggests that these differences are not related to subsistence or raw-material constraints, but rather to different cultural norms and transmission of strongly divergent chaînes opératoires. Such diversity in material culture, when viewed from a cultural transmission (CT) theory standpoint, seems at odds with a simple Clovis model as the origin of these three cultural traditions given the time elapsed since the first Clovis ages and the expected population structure of the early South American settlers.

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South American Aquatic Mammals

Encyclopedia of Marine Mammals ◽

10.1016/b978-0-12-373553-9.00243-1 ◽

2009 ◽

pp. 1071-1076 ◽

Cited By ~ 2

Author(s):

Enrique A. Crespo

Keyword(s):

South American ◽

Aquatic Mammals

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Analysis of Genetic Diversity and Population Structure of Some Bangladeshi Rice Landraces and HYV

Journal of Scientific Research ◽

10.3329/jsr.v4i3.10416 ◽

2012 ◽

Vol 4 (3) ◽

pp. 757-767 ◽

Cited By ~ 1

Author(s):

M. M. Hassan ◽

A. K. M. Shamsuddin ◽

M. M. Islam ◽

K. Khatun ◽

J. Halder

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Distance ◽

Gene Diversity ◽

Allele Number ◽

Rice Landraces ◽

Efficient Management ◽

Ssr Loci ◽

Pattern Of Variation ◽

Rice Improvement

Information on the patterns of genetic variation and population structure is essential for rational use and efficient management of germplasms. It helps in monitoring germplasm and can also be used to predict potential genetic gains. Therefore, in the present study genetic diversity of 59 rice genotypes were assessed using 8 simple sequence repeat (SSR) primers. By the DNA profiling, a total of 114 alleles were detected. Allele number per/locus ranged from 9 to 27, with an average of 14.25. Average polymorphism information content (PIC) value was 0.857 with lowest 0.767 to highest 0.857. Mean gene diversity over all SSR loci was 0.870 with a range from 0.792 to 0.948. Fst values for each locus varied from 0.071 to 0.262. Genetic distance between the variety pair ranged from 0.33 to 1.0. The lowest genetic distance was found between Rajashili and Kumragori (2). Cluster and principal coordinate analysis (PCoA) analysis revealed similar pattern of variation. Marker RM11300 was found most polymorphic and robust among the accessions and can be widely used for rice germplasm characterization. The exclusive variability and unique feature of germplasm found in this study can be a gateway for both domestic and global rice improvement.© 2012 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved.doi: http://dx.doi.org/10.3329/jsr.v4i3.10416 J. Sci. Res. 4 (3), 757-767 (2012)

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Genetic diversity and population structure of Vigna exilis and Vigna grandiflora (Phaseoleae, Fabaceae) from Thailand based on microsatellite variation

Botany ◽

10.1139/cjb-2013-0029 ◽

2013 ◽

Vol 91 (10) ◽

pp. 653-661 ◽

Cited By ~ 4

Author(s):

Anochar Kaewwongwal ◽

Arunee Jetsadu ◽

Prakit Somta ◽

Sompong Chankaew ◽

Peerasak Srinives

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Allelic Richness ◽

Gene Diversity ◽

In Situ Conservation ◽

Natural Populations ◽

Microsatellite Variation ◽

Genetic Clusters ◽

Simple Sequence

The objective of this research was to determine the genetic diversity and population structure of natural populations of two rare wild species of Asian Vigna (Phaseoleae, Fabaceae), Vigna exilis Tateishi & Maxted and Vigna grandiflora (Prain) Tateishi & Maxted, from Thailand. Employing 21 simple sequence repeat markers, 107 and 85 individuals from seven and five natural populations of V. exilis and V. grandiflora, respectively, were analyzed. In total, the markers detected 196 alleles for V. exilis and 219 alleles for V. grandiflora. Vigna exilis populations showed lower average values in number of alleles, allelic richness, observed heterozygosity, gene diversity, and outcrossing rate than V. grandiflora populations, namely 58.00% versus 114.60%, 51.96% versus 74.80%, 0.02% versus 0.18%, 0.40% versus 0.66%, and 3.24% versus 17.41%, respectively. Pairwise FST among populations demonstrated that V. exilis was much more differentiated than V. grandiflora. Analysis of molecular variance revealed that 41.83% and 15.06% of total variation resided among the populations of V. exilis and V. grandiflora, respectively. Seven and two genetic clusters were detected for V. grandiflora and V. exilis by STRUCTURE analysis. Our findings suggest that different strategies are required for in situ conservation of the two species. All V. exilis populations, or as many as possible, should be conserved to protect genetic resources of this species, while a few V. grandiflora populations can capture the majority of its genetic variation.

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Population Structure and Molecular Characterization of Nigerian Field Genebank Collections of Cacao, Theobroma cacao L.

Silvae Genetica ◽

10.1515/sg-2010-0039 ◽

2010 ◽

Vol 59 (1-6) ◽

pp. 273-285 ◽

Cited By ~ 8

Author(s):

P. O. Aikpokpodion ◽

M. Kolesnikova-Allen ◽

V. O. Adetimirin ◽

M. J. Guiltinan ◽

A. B. Eskes ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Large Scale ◽

Gene Diversity ◽

Hybrid Population ◽

Population Variance ◽

F1 Hybrid ◽

Germplasm Collections ◽

Inadequate Knowledge ◽

Genebank Collections

Abstract Inadequate knowledge of the population structure and diversity present often hamper the efficient use of germplasm collections. Using a high through-put system, twelve microsatellite loci were used to analyze genetic diversity and population structure in a national field genebank repository of 243 cacao accessions grouped into 11 populations based on their known sources. Based on multi-locus profiles, the Bayesian method was used for individual assignment to verify membership in each population, determine mislabeling and ancestry of some important accessions used in breeding program. A total of 218 alleles was revealed with a mean number of 18.2 alleles per locus. Gene diversity (He = 0.70) and allelic richness (4.34 alleles per locus) were highest in the F1 hybrid population. Differential mating system was suggested as responsible for the observed deficit and excess of heterozygotes observed among the populations. Analysis of molecular variance showed that within-population variance accounted for 63.0% of the total variance while the rest 37% was accounted for by the among-population variance. Cluster dendrogram based on UPGMA revealed two main subsets. The first group was made up of the Amelonado/Trinitario ancestry and the other of Nanay/Parinari ancestry. We found that Nanay and Parinari populations were the major source of Upper Amazon genes utilized while a large proportion of genetic diversity in the field genebank remained under-utilized in development of improved cultivars released to farmers in Nigeria. This study showed that the presence of alleles of the Upper Amazon Forasteros (Nanay, Parinari and Iquitos Mixed Calabacillo) genetic materials in the locally available accessions predated the formal large scale introduction of Upper Amazon materials in 1944. This is the first report of population structure of field genebank collections of cacao in Nigeria since more than seven decades of formal cacao breeding research.

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Genetic population structure of mangrove jack, Lutjanus argentimaculatus (Forsskål)

Marine and Freshwater Research ◽

10.1071/mf02142 ◽

2003 ◽

Vol 54 (2) ◽

pp. 127 ◽

Cited By ~ 20

Author(s):

Jennifer R. Ovenden ◽

Raewyn Street

Keyword(s):

Population Structure ◽

Gene Flow ◽

Allelic Variation ◽

Gene Diversity ◽

Haplotype Diversity ◽

Genetic Population Structure ◽

Western Coast ◽

Base Pairs ◽

Genetic Population ◽

Lutjanus Argentimaculatus

Translocations of mangrove jack, Lutjanus argentimaculatus (Forsskål 1775), to increase angling opportunities in artificial impoundments are foreshadowed in Queensland. To evaluate genetic population structure before translocations occur, mangrove jack were collected from three sites on the Queensland coast and from one site on the north-western coast of Western Australia. Allelic variation at four dinucleotide microsatellite loci was high: gene diversity (heterozygosity) ranged from 0.602 to 0.930 and allelic counts from 10 to 24. Genetic differentiation among collection sites was weak: estimates of FST were 0.002 for all four sites, and less (FST = 0.001) across a major biogeographical boundary (the Torres Strait region). Nucleotide sequence from two mitochondrial regions (control, 375 base pairs, and ATPase, 415 base pairs) was obtained from a subset of the Australian and additional Indo-Pacific (Indonesian and Samoan) mangrove jack. Haplotype diversity was high (control region, 33 haplotypes for 34 fish; ATPase region, 13 haplotypes for 56 fish). Phylogenetic analysis of mitochondrial DNA sequence data could not discern a relationship between tree topology and geography. These results suggest that mangrove jack in Queensland, and possibly throughout Australia, experience high levels of gene flow. The artificial gene flow caused by permitted translocations is unlikely to exceed natural levels. Fine-scale ecological matching between donor and recipient populations may increase stocking success, and is important if translocation is needed as a species recovery tool in the future.

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Population structure of nuclear and mitochondrial DNA variation among South American Burmeister’s porpoises (Phocoena spinipinnis)

Conservation Genetics ◽

10.1007/s10592-005-4988-9 ◽

2005 ◽

Vol 6 (3) ◽

pp. 431-443 ◽

Cited By ~ 23

Author(s):

Sabrina Rosa ◽

Michel C. Milinkovitch ◽

Koen Van Waerebeek ◽

Jehanne Berck ◽

Jorge Oporto ◽

...

Keyword(s):

Mitochondrial Dna ◽

Population Structure ◽

South American ◽

Dna Variation

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Genetic diversity, population structure and association analysis in coconut (Cocos nucifera L.) germplasm using SSR markers

Plant Genetic Resources ◽

10.1017/s1479262117000119 ◽

2017 ◽

Vol 16 (2) ◽

pp. 156-168 ◽

Cited By ~ 6

Author(s):

S. Geethanjali ◽

J. Anitha Rukmani ◽

D. Rajakumar ◽

P. Kadirvel ◽

P.L. Viswanathan

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Association Analysis ◽

Gene Diversity ◽

Cocos Nucifera ◽

Germplasm Collection ◽

Yield Component ◽

Chromosome 1 ◽

Genetic Structuring ◽

Model Based Clustering

AbstractA world-wide coconut germplasm collection (79 genotypes) was analyzed for genetic diversity and population structure based on 48 simple sequence repeat (SSR) loci. The genotypes displayed moderately high amount of genetic diversity, which was strongly structured according to geographical origins. Number of SSR alleles ranged from 2 to 7 with an average of 4.1 per locus. Gene diversity (expected heterozygosity) estimates ranged from 0.162 to 0.811 with a mean of 0.573. Polymorphism information content values ranged from 0.149 to 0.785 with an average of 0.522. Hierarchical clustering analysis grouped the genotypes into two major clusters with two sub-groups in each, which corresponded with the geographic origins. The first cluster comprised of ‘Tall’ genotypes originated from Indo-Atlantic and South Asia regions. The second cluster comprised mostly of ‘Dwarf’ genotypes and some Tall genotypes which originated from Indo-Pacific and South-East Asia regions. Model-based clustering by STRUCTURE analysis also supported the presence of clear genetic structuring in the collection with two major populations (K = 2) and four sub-populations (K = 4). The proportion of SSR locus-pairs in linkage disequilibrium was low (2.4%). Association analysis in a subset of 44 genotypes detected a single SSR locus, CnCir73 (chromosome 1) putatively associated with fruit yield component traits, which corresponded with a previously mapped quantitative trait locus in coconut.

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