A comprehensive analysis of the whole mitochondrial genomes of the Schizothoracinae subfamily of the family Cyprinidae has been revealed for the first time. The species analyzed include Schizothorax ...niger, Schizothorax esocinus, Schizothorax labiatus and Schizothorax plagoistomus. The total mitochondrial DNA (mtDNA) length was determined to be 16585 bp, 16583 bp, 16582 bp and 16576 bp, respectively with 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding area genes. The combined mean base compositions of the four species were as follows: A: 29.91 % T: 25.47 % G: 17.65 % C 27.01 %. The range of the GC content is 45–44 %, respectively. All protein coding genes (PCGs) commenced with the typical ATG codon, except for the cytochrome c oxidase subunit 1 (COX1) gene with GTG. The analysis of vital amino acid biosynthesis genes (COX1, ATPase 6, ATPase 8) in four different species revealed no significant differences. All 13 PCGs had Ka/Ks ratios that were all lesser than one, demonstrating purifying selection on those molecules. These tRNA genes were predicted to fold into the typical cloverleaf secondary structures with normal base pairing and ranged in size from 66 to 75 nucleotides. Additionally, the phylogenetic tree analysis revealed that S. esocinus species that was most alike to S. labiatus. This study provides critical data for phylogenetic analysis of the Schizothoracinae subfamily, which will help to resolve taxonomic difficulties and identify evolutionary links. Detailed mtDNA data are an invaluable resource for studying genetic diversity, population structure, and gene flow. Understanding genetic makeup can help inform conservation plans, identify unique populations, and track genetic variation to ensure effective preservation.
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•First analysis of entire mitochondrial genomes in four Schizothoracinae species.•Each genome consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding sections.•The average base composition is 29.91 % A, 25.47 % T, 17.65 % G, and 27.01 % C, with a GC concentration of 44–45 %.•S. esocinus is most similar to S. labiatus, which helps resolve taxonomy difficulties and comprehend evolutionary relationships.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Abstract Panax vietnamensis Ha et Grushv. is a precious medicinal species native to the tropical forests of Vietnam. Due to habitat loss and over-harvesting, this species is endangered in Vietnam. To ...conserve the species, we investigated genetic variability and population structure using nine microsatellites for 148 individuals from seven populations across the current distribution range of P. vietnamensis in Vietnam. We determined a moderate genetic diversity within populations (HO = 0.367, HE = 0.437) and relatively low population differentiation (the Weir and Cockerham index of 0.172 and the Hedrick index of 0.254) and showed significant differentiation (P < 0.05), which suggested fragmented habitats, over-utilization and over-harvesting of P. vietnamensis. Different clustering methods revealed that individuals were grouped into two major clusters, which were associated with gene flow across the geographical range of P. vietnamensis. This study also detected that ginseng populations can have undergone a recent bottleneck. We recommend measures in future P. vietnamensis conservation and breeding programs.
Resumo Panax vietnamensis Ha et Grushv. é uma espécie medicinal preciosa nativa das florestas tropicais do Vietnã. Por causa da perda de hábitat e da colheita excessiva, essa espécie está ameaçada de extinção no Vietnã. Para conservá-la, investigamos a variabilidade genética e a estrutura populacional usando nove microssatélites para 148 indivíduos de sete populações em toda a distribuição atual de P. vietnamensis no Vietnã. Determinamos uma diversidade genética moderada dentro das populações (HO = 0,367 e HE = 0,437) e diferenciação populacional relativamente baixa (índice de Weir e Cockerham de 0,172 e índice de Hedrick de 0,254), com diferenciação significativa (P < 0,05), o que sugeriu fragmentação de hábitats, sobreutilização e sobre-exploração de P. vietnamensis. Diferentes métodos de agrupamento revelaram que os indivíduos foram agrupados em dois agrupamentos principais, que foram associados ao fluxo gênico em toda a área geográfica de P. vietnamensis. Este estudo também detectou que as populações de ginseng podem ter sofrido um gargalo recente. Recomendamos medidas em futuros programas de conservação e melhoramento de P. vietnamensis.
For half a century population genetics studies have put type II restriction endonucleases to work. Now, coupled with massively‐parallel, short‐read sequencing, the family of RAD protocols that wields ...these enzymes has generated vast genetic knowledge from the natural world. Here, we describe the first software natively capable of using paired‐end sequencing to derive short contigs from de novo RAD data. Stacks version 2 employs a de Bruijn graph assembler to build and connect contigs from forward and reverse reads for each de novo RAD locus, which it then uses as a reference for read alignments. The new architecture allows all the individuals in a metapopulation to be considered at the same time as each RAD locus is processed. This enables a Bayesian genotype caller to provide precise SNPs, and a robust algorithm to phase those SNPs into long haplotypes, generating RAD loci that are 400–800 bp in length. To prove its recall and precision, we tested the software with simulated data and compared reference‐aligned and de novo analyses of three empirical data sets. Our study shows that the latest version of Stacks is highly accurate and outperforms other software in assembling and genotyping paired‐end de novo data sets.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation ...biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.
The current rate of species extinction is rapidly approaching unprecedented highs, and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change, ...and ecological collapse. The field of conservation genetics aims at preserving species by using their levels of genetic diversity, usually measured as neutral genome-wide diversity, as a barometer for evaluating population health and extinction risk. A fundamental assumption is that higher levels of genetic diversity lead to an increase in fitness and long-term survival of a species. Here, we argue against the perceived importance of neutral genetic diversity for the conservation of wild populations and species. We demonstrate that no simple general relationship exists between neutral genetic diversity and the risk of species extinction. Instead, a better understanding of the properties of functional genetic diversity, demographic history, and ecological relationships is necessary for developing and implementing effective conservation genetic strategies.
Developing fast, cost-effective assessments of wild animal abundance is an important goal for many researchers, and environmental DNA (eDNA) holds much promise for this purpose. However, the ...quantitative relationship between species abundance and the amount of DNA present in the environment is likely to vary substantially among taxa and with ecological context. Here, we report a strong quantitative relationship between eDNA concentration and the abundance of spawning sockeye salmon in a small stream in Alaska, USA, where we took temporally- and spatially-replicated samples during the spawning period. This high-resolution dataset suggests that (1) eDNA concentrations vary significantly day-to-day, and likely within hours, in the context of the dynamic biological event of a salmon spawning season; (2) eDNA, as detected by species-specific quantitative PCR probes, seems to be conserved over short distances (tens of meters) in running water, but degrade quickly over larger scales (ca. 1.5 km); and (3) factors other than the mere presence of live, individual fish — such as location within the stream, live/dead ratio, and water temperature — can affect the eDNA-biomass correlation in space or time. A multivariate model incorporating both biotic and abiotic variables accounted for over 75% of the eDNA variance observed, suggesting that where a system is well-characterized, it may be possible to predict species' abundance from eDNA surveys, although we underscore that species- and system-specific variables are likely to limit the generality of any given quantitative model. Nevertheless, these findings provide an important step toward quantitative applications of eDNA in conservation and management.
•We measured salmon DNA in water samples collected daily during the spawning season•This environmental DNA (eDNA) closely tracked the rise and fall of salmon numbers in the creek•Concentrations of eDNA changed over fine spatial and temporal scales•A statistical model including fish and environmental variables accounted for >75% of the variance in recovered salmon eDNA•Both dead and live fish shed DNA into the water, but model results suggest that the shedding rate is much greater after death
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Alleles that introgress between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it ...has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments.
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