scholarly journals Strengths and potential pitfalls of hay-transfer for ecological restoration revealed by RAD-seq analysis in floodplain Arabis species

2018 ◽  
Author(s):  
Hannes Dittberner ◽  
Christian Becker ◽  
Wen-Biao Jiao ◽  
Korbinian Schneeberger ◽  
Norbert Hölzel ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ecological Restoration ◽  
Habitat Restoration ◽  
De Novo ◽  
Flood Plain ◽  
Intraspecific Diversity ◽  
Close Relative ◽  
Its Sequencing ◽  
Adaptive Potential ◽  
Local Material

AbstractAchieving high intraspecific genetic diversity is a critical goal in ecological restoration as it increases the adaptive potential and long-term resilience of populations. Thus, we investigated genetic diversity within and between pristine sites in a fossil floodplain and compared it to sites restored by hay-transfer between 1997 and 2014. RAD-seq genotyping revealed that the stenoecious flood-plain species Arabis nemorensis is co-occurring with individuals that, based on ploidy, ITS-sequencing and morphology, probably belong to the close relative Arabis sagittata, which has a documented preference for dry calcareous grasslands but has not been reported in floodplain meadows. We show that hay-transfer maintains genetic diversity for both species. Additionally, in A. sagittata, transfer from multiple genetically isolated pristine sites resulted in restored sites with increased diversity and admixed local genotypes. In A. nemorensis, transfer did not create novel admixture dynamics because genetic diversity between pristine sites was less differentiated. Thus, the effects of hay-transfer on genetic diversity also depend on the genetic makeup of the donor communities of each species, especially when local material is mixed. Our results demonstrate the efficiency of hay-transfer for habitat restoration and emphasize the importance of pre-restoration characterization of micro-geographic patterns of intraspecific diversity of the community to guarantee that restoration practices reach their goal, i.e. maximize the adaptive potential of the entire restored plant community. Overlooking these patterns may alter the balance between species in the community. Additionally, our comparison of summary statistics obtained from de novo and reference-based RAD-seq pipelines shows that the genomic impact of restoration can be reliably monitored in species lacking prior genomic knowledge.

scholarly journals Genetic Consequences of Fence Confinement in a Population of White-Tailed Deer

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 126
Author(s):  
Emily K. Latch ◽  
Kenneth L. Gee ◽  
Stephen L. Webb ◽  
Rodney L. Honeycutt ◽  
Randy W. DeYoung ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Wildlife Management ◽  
Field Observations ◽  
Adaptive Potential ◽  
Population Isolation ◽  
Potential Benefits ◽  
Wildlife Populations ◽  
Mtdna Diversity

Fencing wildlife populations can aid wildlife management goals, but potential benefits may not always outweigh costs of confinement. Population isolation can erode genetic diversity and lead to the accumulation of inbreeding, reducing viability and limiting adaptive potential. We used microsatellite and mitochondrial DNA data collected from 640 white-tailed deer confined within a 1184 ha fence to quantify changes in genetic diversity and inbreeding over the first 12 years of confinement. Genetic diversity was sustained over the course of the study, remaining comparable to unconfined white-tailed deer populations. Uneroded genetic diversity suggests that genetic drift is mitigated by a low level of gene flow, which supports field observations that the fence is not completely impermeable. In year 9 of the study, we observed an unexpected influx of mtDNA diversity and drop in inbreeding as measured by FIS. A male harvest restriction imposed that year increased male survival, and more diverse mating may have contributed to the inbreeding reduction and temporary genetic diversity boost we observed. These data add to our understanding of the long-term impacts of fences on wildlife, but also highlight the importance of continued monitoring of confined populations.

Genetic diversity of fringed brome (Bromus ciliatus) as determined by amplified fragment length polymorphism

2005 ◽  
Vol 83 (10) ◽  
pp. 1322-1328 ◽  
Author(s):  
Yong-Bi Fu ◽  
Bruce E. Coulman ◽  
Yasas S.N. Ferdinandez ◽  
Jacques Cayouette ◽  
Paul M. Peterson
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Habitat Restoration ◽  
Fragment Length Polymorphism ◽  
Natural Populations ◽  
Germplasm Conservation ◽  
Amplified Fragment Length Polymorphism ◽  
Large Area ◽  
Geographic Origins

Fringed brome ( Bromus ciliatus L.) is found in native stands throughout a large area of North America. Little is known about the genetic diversity of this species. The amplified fragment length polymorphism (AFLP) technique was applied to assess the genetic diversity of 16 fringed brome populations sampled in Canada from the provinces of Alberta, British Columbia, Quebec, and Saskatchewan. Four AFLP primer pairs were employed to screen 82 samples with four to six samples per population and 83 polymorphic AFLP bands scored for each sample. The frequencies of the scored bands in all assayed samples ranged from 0.01 to 0.99 and averaged 0.53. Analysis of molecular variance revealed that 52.6% of the total AFLP variation resided among the 16 populations and 20.6% among the four provinces. The five Quebec populations appeared to be genetically the most diverse and distinct. The AFLP variability observed was significantly associated with the geographic origins of the fringed brome populations. These findings are useful for sampling fringed brome germplasm from natural populations for germplasm conservation and should facilitate the development of genetically diverse regional cultivars for habitat restoration and revegetation.

scholarly journals Low-Bias RNA Sequencing of the HIV-2 Genome from Blood Plasma

2018 ◽  
Vol 93 (1) ◽  
Author(s):  
Katherine L. James ◽  
Thushan I. de Silva ◽  
Katherine Brown ◽  
Hilton Whittle ◽  
Stephen Taylor ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Blood Plasma ◽  
De Novo ◽  
A Priori ◽  
Pcr Amplification ◽  
Hiv Vaccine ◽  
Whole Genome ◽  
Plasma Samples ◽  
Target Enrichment ◽  
Rna Seq

ABSTRACTAccurate determination of the genetic diversity present in the HIV quasispecies is critical for the development of a preventative vaccine: in particular, little is known about viral genetic diversity for the second type of HIV, HIV-2. A better understanding of HIV-2 biology is relevant to the HIV vaccine field because a substantial proportion of infected people experience long-term viral control, and prior HIV-2 infection has been associated with slower HIV-1 disease progression in coinfected subjects. The majority of traditional and next-generation sequencing methods have relied on target amplification prior to sequencing, introducing biases that may obscure the true signals of diversity in the viral population. Additionally, target enrichment through PCR requiresa priorisequence knowledge, which is lacking for HIV-2. Therefore, a target enrichment free method of library preparation would be valuable for the field. We applied an RNA shotgun sequencing (RNA-Seq) method without PCR amplification to cultured viral stocks and patient plasma samples from HIV-2-infected individuals. Libraries generated from total plasma RNA were analyzed with a two-step pipeline: (i)de novogenome assembly, followed by (ii) read remapping. By this approach, whole-genome sequences were generated with a 28× to 67× mean depth of coverage. Assembled reads showed a low level of GC bias, and comparison of the genome diversities at the intrahost level showed low diversity in the accessory genevpxin all patients. Our study demonstrates that RNA-Seq is a feasible full-genomede novosequencing method for blood plasma samples collected from HIV-2-infected individuals.IMPORTANCEAn accurate picture of viral genetic diversity is critical for the development of a globally effective HIV vaccine. However, sequencing strategies are often complicated by target enrichment prior to sequencing, introducing biases that can distort variant frequencies, which are not easily corrected for in downstream analyses. Additionally, detaileda priorisequence knowledge is needed to inform robust primer design when employing PCR amplification, a factor that is often lacking when working with tropical diseases localized in developing countries. Previous work has demonstrated that direct RNA shotgun sequencing (RNA-Seq) can be used to circumvent these issues for hepatitis C virus (HCV) and norovirus. We applied RNA-Seq to total RNA extracted from HIV-2 blood plasma samples, demonstrating the applicability of this technique to HIV-2 and allowing us to generate a dynamic picture of genetic diversity over the whole genome of HIV-2 in the context of low-bias sequencing.

scholarly journals Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in Northwest China

2018 ◽  
Author(s):  
Yanfen Zhao ◽  
Hongxiang Zhang ◽  
Borong Pan ◽  
Mingli Zhang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic ◽  
Divergence Time ◽  
Northwest China ◽  
Northwestern China ◽  
Intraspecific Diversity ◽  
Early Pleistocene ◽  
Helan Mountains ◽  
The Impact

Climactic fluctuations during the Quaternary played a crucial role in genetic diversity and population genetic structure of many plant species in northwestern China. In order to understand the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Two chloroplast DNA intergenic spacers (trnH-psbA and rpoB-trnC) were used to sequence 269 individuals from 27 populations and seven haplotypes were identified. Genetic structure and demographic characteristics were estimated using AMOVA, neutrality tests, and mismatch distribution analyses. The divergence times between the seven haplotypes were estimated using Beast. Our results revealed high levels of total genetic diversity (HT = 0.673±0.0869) and low levels of average within-population genetic diversity (HS = 0.033±0.0214). The analysis of molecular variance indicated major genetic differentiation among the three groups: northern, central, and eastern group. The species distribution modeling and demographic analysis indicated that P. lanata has not experience a recent range expansion. The divergence time within P. lanata occurred between the early Pleistocene and the late Pleistocene, which coincides with aridification and the expansion of the deserts in northwestern China that resulted in species diversification and habitat fragmentation. In addition, we speculate that the deserts and the Helan Mountains acted as effective geographic barriers that led to intraspecific diversity.

scholarly journals Genetic and Genomic Resources to Study Natural Variation in Brassica rapa

2020 ◽  
Author(s):  
Ping Lou ◽  
Scott Woody ◽  
Kathleen Greenham ◽  
Robert VanBuren ◽  
Marivi Colle ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Natural Variation ◽  
De Novo ◽  
Coat Color ◽  
Current Knowledge ◽  
Genomic Structure ◽  
Close Relative ◽  
Structure Variation ◽  
Genomic Resources ◽  
Ril Population

ABSTRACTThe globally important crop Brassica rapa, a close relative of Arabidopsis, is an excellent system for modeling our current knowledge of plant growth on a morphologically diverse crop. The long history of B. rapa domestication across Asia and Europe provides a unique collection of locally adapted varieties that span large climatic regions with various abiotic and biotic stress tolerance traits. This diverse gene pool provides a rich source of targets with the potential for manipulation towards the enhancement of productivity of crops both within and outside the Brassicaceae. To expand the genetic resources available to study natural variation in B. rapa, we constructed an Advanced Intercross Recombinant Inbred (AI-RIL) population using B. rapa subsp. trilocularis (Yellow Sarson) R500 and the B. rapa subsp. parachinensis (Cai Xin) variety L58. Our current understanding of genomic structure variation across crops suggests that a single reference genome is insufficient for capturing the genetic diversity within a species. To complement this AI-RIL population and current and future B. rapa genomic resources, we generated a de novo genome assembly of the B. rapa subsp. trilocularis (Yellow Sarson) variety R500, the maternal parent of the AI-RIL population. The genetic map for the R500 x L58 population generated using this de novo genome was used to map QTL for seed coat color and revealed the improved mapping resolution afforded by this new assembly.

scholarly journals Intraspecific Diversity of Fission Yeast Mitochondrial Genomes

2019 ◽  
Vol 11 (8) ◽  
pp. 2312-2329 ◽  
Author(s):  
Yu-Tian Tao ◽  
Fang Suo ◽  
Sergio Tusso ◽  
Yan-Kai Wang ◽  
Song Huang ◽  
...  
Keyword(s):  
Fission Yeast ◽  
Population Genomics ◽  
De Novo ◽  
Model Organism ◽  
Nuclear Genome ◽  
Intraspecific Diversity ◽  
Future Research ◽  
Data Sets ◽  
Diversity Pattern ◽  
Mitochondrial Introns

Abstract The fission yeast Schizosaccharomyces pombe is an important model organism, but its natural diversity and evolutionary history remain under-studied. In particular, the population genomics of the S. pombe mitochondrial genome (mitogenome) has not been thoroughly investigated. Here, we assembled the complete circular-mapping mitogenomes of 192 S. pombe isolates de novo, and found that these mitogenomes belong to 69 nonidentical sequence types ranging from 17,618 to 26,910 bp in length. Using the assembled mitogenomes, we identified 20 errors in the reference mitogenome and discovered two previously unknown mitochondrial introns. Analyzing sequence diversity of these 69 types of mitogenomes revealed two highly distinct clades, with only three mitogenomes exhibiting signs of inter-clade recombination. This diversity pattern suggests that currently available S. pombe isolates descend from two long-separated ancestral lineages. This conclusion is corroborated by the diversity pattern of the recombination-repressed K-region located between donor mating-type loci mat2 and mat3 in the nuclear genome. We estimated that the two ancestral S. pombe lineages diverged about 31 million generations ago. These findings shed new light on the evolution of S. pombe and the data sets generated in this study will facilitate future research on genome evolution.

scholarly journals Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health

2019 ◽  
Vol 6 (4) ◽  
pp. 810-824 ◽  
Author(s):  
Elaine A Ostrander ◽  
Guo-Dong Wang ◽  
Greger Larson ◽  
Bridgett M vonHoldt ◽  
Brian W Davis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Architecture ◽  
Evolutionary History ◽  
De Novo ◽  
Mammalian Species ◽  
Aging Behavior ◽  
Extended Pedigrees ◽  
Geographical Variability ◽  
Whole Genomes

ABSTRACT Dogs are the most phenotypically diverse mammalian species, and they possess more known heritable disorders than any other non-human mammal. Efforts to catalog and characterize genetic variation across well-chosen populations of canines are necessary to advance our understanding of their evolutionary history and genetic architecture. To date, no organized effort has been undertaken to sequence the world's canid populations. The Dog10K Consortium (http://www.dog10kgenomes.org) is an international collaboration of researchers from across the globe who will generate 20× whole genomes from 10 000 canids in 5 years. This effort will capture the genetic diversity that underlies the phenotypic and geographical variability of modern canids worldwide. Breeds, village dogs, niche populations and extended pedigrees are currently being sequenced, and de novo assemblies of multiple canids are being constructed. This unprecedented dataset will address the genetic underpinnings of domestication, breed formation, aging, behavior and morphological variation. More generally, this effort will advance our understanding of human and canine health.

Phylogeny and mtDNA phylogeography of two widespread European pond skater species (Hemiptera-Heteroptera: Gerridae: Gerris Fabricius)

2006 ◽  
Vol 37 (3) ◽  
pp. 335-350 ◽  
Author(s):  
Jakob Damgaard
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Dna Sequence ◽  
Sequence Data ◽  
Close Relative ◽  
Individual Species ◽  
Widespread Species ◽  
Dna Sequence Data ◽  
Central Asian ◽  
Species Groups

AbstractThis study addresses the phylogenetic relationships within and between two widespread Palaearctic pond skater species, Gerris costae and G. thoracicus, by including new DNA sequence data from the Central Asian G. sahlbergi, traditionally assigned as a close relative of G. costae. The results support the assignment of G. costae and G. thoracicus to two individual species groups that are not closely related, but also that G. sahlbergi is nested within G. costae (including subspecies costae, fieberi and poissoni) thus suggesting a new subspecific rank as G. c. sahlbergi. A broad geographical sampling of mitochondrial DNA from populations of G. thoracicus and G. costae (incl. G. c. sahlbergi) shows that the two species are strikingly similar in terms of genetic diversity and lack of geographical substructure, thus adding further evidence for the G. costae group comprising a single, widespread species.

scholarly journals Long-term molecular evolutionary rate determines intraspecific genetic diversity

2019 ◽  
Author(s):  
Jiaqi Wu ◽  
Takahiro Yonezawa ◽  
Hirohisa Kishino
Keyword(s):  
Genetic Diversity ◽  
De Novo ◽  
Early Stage ◽  
Morphological Evolution ◽  
Biological Traits ◽  
Gene Trees ◽  
Intraspecific Genetic Diversity ◽  
Molecular Evolutionary Rates ◽  
Species Specific

AbstractWhat determines genetic diversity and how it connects to the various biological traits is unknown. In this work, we offer answers to these questions. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual genomes of human, chimpanzee, gorilla, mouse and dog/wolf, we found that intraspecific genetic diversity is determined by long-term molecular evolutionary rates, rather than de novo mutation rates. This relationship was established during the early stage of mammalian evolution. Expanding this new finding, we developed a method to detect fluctuations of species-specific selection on genes as the deviations of intra-species genetic diversity predicted from long-term rates. We show that the evolution of epithelial cells, rather than of connective tissue, mainly contributes to morphological evolution of different species. For humans, evolution of the immune system and selective sweeps subjected by infectious diseases are most representative of adaptive evolution.

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