scholarly journals Population genomic analysis of the speckled dace species complex (Rhinichthys osculus) identifies three species-level lineages in California

2021 ◽  
Author(s):  
Yingxin Su ◽  
Peter B. Moyle ◽  
Matthew A. Campbell ◽  
Amanda J. Finger ◽  
Sean M. O’Rourke ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Principal Component ◽  
Single Species ◽  
Death Valley ◽  
Conservation Strategies ◽  
Geologic History ◽  
Santa Ana ◽  
Long Valley ◽  
Rhinichthys Osculus ◽  
Speckled Dace

The speckled dace ( Rhinichthys osculus ) is small cyprinid fish that is widespread in the Western USA. Currently treated as a single species, speckled dace consists of multiple evolutionary lineages that can be recognized as species and subspecies throughout its range. Recognition of taxonomic distinctiveness of speckled dace populations is important for developing conservation strategies. In this study, we collected samples of speckled dace from 38 locations in the American West, with a focus on California. We used RAD sequencing to extract thousands of SNPs across the genome from samples to identify genetic differences among seven California populations informally recognized as speckled dace subspecies: Amargosa, Owens, Long Valley, Lahontan, Klamath, Sacramento, and Santa Ana speckled dace. We performed principal component analysis, admixture analysis, estimated pairwise Fst, and constructed a phylogeny to explore taxonomic relationships among these groups and test if these subspecies warrant formal recognition. Our analyses show that the seven subspecies fit into three major lineages equivalent to species: western (Sacramento-Klamath), Santa Ana, and Lahontan speckled dace. Death Valley speckled dace were determined to be two lineages (Amargosa and Long Valley) within Lahontan speckled dace. Western and Lahontan speckled dace lineages had branches that can be designated as subspecies. These designations fit well with the geologic history of the region which has promoted long isolation of populations. This study highlights the importance of genetic analysis for conservation and management of freshwater fishes.

scholarly journals Defining Relictual Biodiversity: Conservation Units in Speckled Dace (Cyprinidae: Rhinichthys osculus) of the Greater Death Valley Ecosystem

2020 ◽  
Author(s):  
Steven M. Mussmann ◽  
Marlis R. Douglas ◽  
David D. Oakey ◽  
Michael E. Douglas
Keyword(s):  
Mojave Desert ◽  
Death Valley ◽  
Hybrid Population ◽  
Conservation Units ◽  
Strong Argument ◽  
Multispecies Coalescent ◽  
Proactive Management ◽  
Outlier Loci ◽  
Rhinichthys Osculus ◽  
Speckled Dace

AbstractThe tips in the tree of life serve as foci for conservation and management, yet clear delimitations are masked by inherent variance at the species-population interface. Analyses using thousands of nuclear loci can potentially sort inconsistencies, yet standard categories applied to this parsing are themselves potentially conflicting and/or subjective [e.g., DPS (distinct population segments); DUs (Diagnosable Units-Canada); MUs (management units); SSP (subspecies); Evolutionarily Significant Units (ESUs)]. One potential solution for consistent categorization is to create a comparative framework by accumulating statistical results from independent studies and evaluating congruence among data sets. Our study illustrates this approach in speckled dace (Cyprinidae: Rhinichthys osculus) endemic to two basins (Owens and Amargosa) in the Death Valley ecosystem (DVE). These fish persist in the Mojave Desert as isolated Pleistocene-relicts and are of conservation concern, but lack formal taxonomic descriptions/designations. Double-digest RAD (ddRAD) methods identified 14,355 SNP loci across 10 populations (N=140). Species delimitation analyses [multispecies coalescent (MSC) and unsupervised machine learning (UML)] delineated four putative ESUs. FST outlier loci (N=106) were juxtaposed to uncover the potential for localized adaptations. We detected one hybrid population that resulted from upstream reconnection of habitat following contemporary pluvial periods, whereas remaining populations represent relics of ancient tectonism within geographically-isolated springs and groundwater-fed streams. Our study offers three salient conclusions: A blueprint for a multi-faceted delimitation of conservation units; a proposed mechanism by which criteria for intraspecific biodiversity can be potentially standardized; and a strong argument for the proactive management of critically-endangered DVE fishes.

scholarly journals Defining relictual biodiversity: Conservation units in speckled dace (Leuciscidae: Rhinichthys osculus ) of the Greater Death Valley ecosystem

2020 ◽  
Vol 10 (19) ◽  
pp. 10798-10817 ◽  
Author(s):  
Steven M. Mussmann ◽  
Marlis R. Douglas ◽  
David D. Oakey ◽  
Michael E. Douglas
Keyword(s):  
Biodiversity Conservation ◽  
Death Valley ◽  
Conservation Units ◽  
Rhinichthys Osculus ◽  
Speckled Dace

scholarly journals Phenotypic Characterisation for Growth and Nut Characteristics Revealed the Extent of Genetic Diversity in Wild Macadamia Germplasm

Agriculture ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 680
Author(s):  
Thuy T. P. Mai ◽  
Craig M. Hardner ◽  
Mobashwer M. Alam ◽  
Robert J. Henry ◽  
Bruce L. Topp
Keyword(s):  
Genetic Diversity ◽  
Growth Traits ◽  
Principal Component ◽  
Conservation Strategies ◽  
Wild Germplasm ◽  
Phenotypic Characterisation ◽  
Wide Range ◽  
Genetic And Environmental Factors ◽  
Positive Correlations ◽  
Wild Accessions

Macadamia is a recently domesticated Australian native nut crop, and a large proportion of its wild germplasm is unexploited. Aiming to explore the existing diversity, 247 wild accessions from four species and inter-specific hybrids were phenotyped. A wide range of variation was found in growth and nut traits. Broad-sense heritability of traits were moderate (0.43–0.64), which suggested that both genetic and environmental factors are equally important for the variability of the traits. Correlations among the growth traits were significantly positive (0.49–0.76). There were significant positive correlations among the nut traits except for kernel recovery. The association between kernel recovery and shell thickness was highly significant and negative. Principal component analysis of the traits separated representative species groups. Accessions from Macadamia integrifolia Maiden and Betche, M. tetraphylla L.A.S. Johnson, and admixtures were clustered into one group and those of M. ternifolia F. Muell were separated into another group. In both M. integrifolia and M. tetraphylla groups, variation within site was greater than across sites, which suggested that the conservation strategies should concentrate on increased sampling within sites to capture wide genetic diversity. This study provides a background on the utilisation of wild germplasm as a genetic resource to be used in breeding programs and the direction for gene pool conservation.

scholarly journals Co-occurring cryptic species pose challenges for conservation: a case study of the African dwarf crocodile (Osteolaemusspp.) in Cameroon

Oryx ◽  
2014 ◽  
Vol 49 (4) ◽  
pp. 584-590 ◽  
Author(s):  
Nicole L. Smolensky
Keyword(s):  
Cryptic Species ◽  
Conservation Status ◽  
Taxonomic Revision ◽  
Single Species ◽  
Conservation Strategies ◽  
Encounter Rates ◽  
Distribution Maps ◽  
Species Complexes ◽  
Threatened Taxa ◽  
Population Structures

AbstractThe conservation status of threatened taxa may be obfuscated by the detection of cryptic species complexes, in both vertebrate and invertebrate species. African dwarf crocodiles (Osteolaemusspp.) are hunted throughout their range but their conservation status is unknown. Few population assessments have been carried out and there has been a taxonomic revision of the number of species in the genus. The similar morphologies ofOsteolaemus tetraspisandOsteolaemus osbornipose a challenge for conservation in Cameroon, where they are still managed as a single species. Nocturnal spotlight surveys were conducted in three regions during August–November 2010 and December 2011–February 2012 to provide population assessments ofO. tetraspisandO. osborniand raise awareness of the two species in Cameroon. The mean encounter rates ofO. tetraspisandO. osborniwere 1.02 ± SD 1.34 (65 individuals in 39 surveys) and 0.61 ± SD 0.38 (three in four surveys) crocodiles per km, respectively. TheO. tetraspispopulation comprised juveniles predominantly and had a male-biased sex ratio. The fewO. osbornidetected comprised both adults and juveniles. Both species are threatened in Cameroon, based on low encounter rates, young population structures and the threats of habitat loss and hunting pressure. This study provides distribution maps and serves as a baseline to quantify population trends and inform conservation strategies.

scholarly journals A phylogenetic community approach for studying termite communities in a West African savannah

2015 ◽  
Vol 11 (10) ◽  
pp. 20150625 ◽  
Author(s):  
Barbara Hausberger ◽  
Judith Korb
Keyword(s):  
Environmental Filtering ◽  
Single Species ◽  
Insect Species ◽  
Conservation Strategies ◽  
Closely Related Species ◽  
Community Processes ◽  
Community Approach ◽  
Macrotermes Bellicosus ◽  
Single Insect ◽  
West African Savannah

Termites play fundamental roles in tropical ecosystems, and mound-building species in particular are crucial in enhancing species diversity, from plants to mammals. However, it is still unclear which factors govern the occurrence and assembly of termite communities. A phylogenetic community approach and null models of species assembly were used to examine structuring processes associated with termite community assembly in a pristine savannah. Overall, we did not find evidence for a strong influence of interspecific competition or environmental filtering in structuring these communities. However, the presence of a single species, the mound-building termite Macrotermes bellicosus , left a strong signal on structuring and led to clustered communities of more closely related species. Hence, this species changes the assembly rules for a whole community. Our results show the fundamental importance of a single insect species for community processes, suggesting that more attention to insect species is warranted when developing conservation strategies.

Identification of actionable BRAF mutations and their genomic associations in advanced prostate cancer.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e17597-e17597
Author(s):  
Giordano Fabricio Cittolin Santos ◽  
Malshundria Prophet ◽  
Theodore Stewart Gourdin ◽  
Leylah Drusbosky ◽  
Elisa Marie Ledet ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Genomic Analysis ◽  
Principal Component ◽  
Mek Inhibitor ◽  
Circulating Tumor Dna ◽  
Specific Gene ◽  
Missense Mutations ◽  
Genomic Profile ◽  
Braf Mutations ◽  
The Difference

e17597 Background: Circulating tumor DNA (ctDNA) can be used to identify mutations and amplifications in patients with prostate cancer (PC). Identification of actionable mutations in BRAF may allow the use of targeted therapeutics not typically used in prostate cancer. Methods: We analyzed a ctDNA-based genomic profile database (Guardant Health) with 2274 unique advanced-stage patients, and a tissue-based genomic database (TCGA) with 3178 unique patients (73% locoregional, 27% metastatic). We compared the frequency and types of BRAF anomalies found in those datasets. We calculated the odds ratio of observing other genetic anomalies based on the BRAF mutation and amplification status. Finally, we utilized Principal Component Analysis (PCA) to study the utility of BRAF as a discriminator in identifying genetic subtypes of PC. Results: BRAF missense mutations in PC were found in 3.34% of the 2274 patients in the ctDNA cohort and in 1.1% of the 3178 patients in the TCGA cohort. Variants of Uncertain Significance (VUS) mutations were more commonly identified by ctDNA (53.8% of all mutations) vs TCGA (16.1% of all mutations). Biologically-significant mutations of all classes (I, II, III) were found in both datasets. BRAF mutations were mainly non-V600E and most mutations were clonal. Significant mutations common to both the ctDNA and TCGA cohorts include K601E, G469A, D594G, V600E, G466E, G446R, Q257K, I300V and R271H. Mutations unique to either ctDNA or TCGA datasets were found as well. BRAF mutations are highly associated with additional mutations in CDKN2A, TERT, and KRAS, as well as amplifications of CCNE1, KRAS, CDK6 (p < 0.01). BRAF amplifications are highly associated with multiple other gene amplifications, and with AR mutations (p < 0.01). Tumors with BRAF mutations and with BRAF amplifications are genetically distinct, and PCA indicates that BRAF status accounts for a significant amount of the difference. We described two patients that were treated with MEK targeted therapy with treatment response. Conclusions: 1. The use of ctDNA-based genomic analysis identified BRAF anomalies with a higher frequency than tissue-based techniques, but this is mostly due to higher numbers of VUS mutants found with ctDNA. Biologically significant BRAF mutations are mostly clonal and non-V600E mutations. 2. BRAF mutations and amplifications are associated with other specific gene anomalies. 3. ctDNA is a useful tool for identifying the genomic profile of PC in the clinical setting. 4. PC subjects with BRAF mutations identified by ctDNA may respond to MEK inhibitor therapy.

Female gametophyte and seed development in Musella lasiocarpa (Musaceae), a monotypic genus endemic to Southwestern China

2007 ◽  
Vol 85 (10) ◽  
pp. 964-975 ◽  
Author(s):  
Chun-Ying Xue ◽  
Hong Wang ◽  
De-Zhu Li
Keyword(s):  
Seed Development ◽  
Female Gametophyte ◽  
Wild Population ◽  
Embryo Sac ◽  
Single Species ◽  
Ex Situ ◽  
Southwestern China ◽  
Conservation Strategies ◽  
Female Sterility ◽  
Monotypic Genus

Musella is a monotypic genus composed of a single species, Musella lasiocarpa (Franch.) C.Y. Wu ex H.W. Li, endemic to Southwestern China. The genus status of Musella remains controversial. Musella had been placed first in Musa , then in Ensete , and back to Musa before its monotypic status was recognized. Musella was reported to be extinct in the wild and maintained through cultivation only via vegetative propagation through sprouting of rhizomes. In this study, female gametophyte and seed development of Musella are described to assess its systematic position and possible reasons why the wild population is now extinct. The ovules are anatropous, bitegmic, and crassinucellar. The micropyle is formed by both integuments. The megaspore mother cell undergoes meiotic division and forms a linear megaspore triad or more rarely, a T-shaped megaspore tetrad. The chalazal megaspore develops into a Polygonum type embryo sac. A nucellar pad forms, and a hypostase differentiates. Fertilization is porogamous. Endosperm formation is of the nuclear type. The zygote degenerates and so the process by which the embryo develops, if it does, remains unclear. An operculum, micropylar collar, and chalazal chamber form in mature seeds. The storage tissue is mainly endosperm containing large, compound starch grains and some perisperm. The seed coat has lignified exotestal cells, 25–30 cell layers of sclerotic mesotestal cells, and unspecialized endotesta cells; the tegment consists of two layers of longitudinally elongated cells. The seed is inviable. After comparison with the other Musaceae s. str. taxa using embryological and botanical features, we conclude that Musella should be a distinct genus. Female sterility in Musella may be the main reason why the wild population is extinct. Based on these findings, we propose conservation strategies for this endemic species, including habitat protection as well as ex-situ conservation.

Riverscape genetics identifies speckled dace (Rhinichthys osculus) cryptic diversity in the Klamath–Trinity Basin

2017 ◽  
Vol 19 (1) ◽  
pp. 111-127
Author(s):  
Jesse C. Wiesenfeld ◽  
Damon H. Goodman ◽  
Andrew P. Kinziger
Keyword(s):  
Cryptic Diversity ◽  
Rhinichthys Osculus ◽  
Speckled Dace

scholarly journals Projection in genomic analysis: A theoretical basis to rationalize tensor decomposition and principal component analysis as feature selection tools

2020 ◽  
Author(s):  
Y-h. Taguchi ◽  
Turki Turki
Keyword(s):  
Principal Component Analysis ◽  
Gene Selection ◽  
Statistical Tests ◽  
Projection Pursuit ◽  
Null Distribution ◽  
Genomic Analysis ◽  
Principal Component ◽  
Tensor Decomposition ◽  
Component Analysis ◽  
Singular Value

ABSTRACTIdentifying differentially expressed genes is difficult because of the small number of available samples compared with the large number of genes. Conventional gene selection methods employing statistical tests have the critical problem of heavy dependence of P-values on sample size. Although the recently proposed principal component analysis (PCA) and tensor decomposition (TD)-based unsupervised feature extraction (FE) has often outperformed these statistical test-based methods, the reason why they worked so well is unclear. In this study, we aim to understand this reason in the context of projection pursuit that was proposed a long time ago to solve the problem of dimensions; we can relate the space spanned by singular value vectors with that spanned by the optimal cluster centroids obtained from K-means. Thus, the success of PCA- and TD-based unsupervised FE can be understood by this equivalence. In addition to this, empirical threshold adjusted P-values of 0.01 assuming the null hypothesis that singular value vectors attributed to genes obey the Gaussian distribution empirically corresponds to threshold-adjusted P-values of 0.1 when the null distribution is generated by gene order shuffling. These findings thus rationalize the success of PCA- and TD-based unsupervised FE for the first time.

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