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  • 1
    In: The American Journal of Human Genetics, Elsevier BV, Vol. 107, No. 2 ( 2020-08), p. 265-277
    Type of Medium: Online Resource
    ISSN: 0002-9297
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    Language: English
    Publisher: Elsevier BV
    Publication Date: 2020
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    SSG: 12
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  • 2
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 381, No. 6657 ( 2023-08-04)
    Abstract: Genetic analysis of historical individuals has the potential to help restore knowledge of people whose stories were omitted from written records. During the late 18th and early 19th centuries, Catoctin Furnace in Maryland relied on a workforce of enslaved individuals to operate the iron furnace and carry out domestic and agricultural tasks. Despite the role that Catoctin Furnace played in early US history (including supplying munitions during the Revolutionary War), relatively little is known about the African Americans who labored there or their descendants compared with the furnace’s later, predominantly white workforce. RATIONALE We produced genome-wide data for 27 individuals buried in the Catoctin Furnace African American Cemetery and compared them to ~9.3 million consenting research participants genotyped by 23andMe, Inc., to address the following questions: (i) How were the Catoctin individuals related to each other? (ii) What were the sources of their African and European ancestry? (iii) Where in the US do their genetic relatives live today, including their direct descendants? (iv) What can their genomes reveal about their health? RESULTS We identified five genetic families, consisting of biological mothers, children, and siblings, among the Catoctin individuals. In most cases, biological family members were buried in close proximity. All but one of the Catoctin individuals had primarily African ancestry, with variable amounts of European ancestry. To learn more about their ancestry, we developed an approach to detect identical-by-descent segments of the genome shared between the Catoctin individuals and 23andMe research participants. Identical-by-descent segments of DNA are shared by two or more people because they have been inherited from a recent common ancestor. We identified 41,799 close and distant relatives of the Catoctin individuals among 23andMe research participants. Within Africa, we found the highest rates of genetic sharing between Catoctin individuals and research participants who self-identified as belonging to the Wolof or Kongo ethnolinguistic groups. Within Europe, we observed the highest rates of genetic sharing with research participants that have ties to Great Britain and Ireland. Within the US, participants from the South showed elevated rates of sharing, largely reflecting distant connections to 23andMe research participants with sub-Saharan African ancestry (possibly tracing back to shared common ancestors in Africa). When we considered genetic relatives who share the most identical DNA with the Catoctin individuals, we observed the highest rates of sharing in Maryland, suggesting that at least some descendants stayed in the region after the furnace’s transition away from enslaved and paid African American labor. Finally, we found that some of the Catoctin individuals carried risk factors for sickle cell anemia and glucose-6-phosphate dehydrogenase deficiency, genetic diseases that are common in African Americans today. CONCLUSION These results demonstrate the power of joint analysis of DNA from historical individuals and the extremely large datasets generated through direct-to-consumer ancestry testing, and they serve as a model for obtaining direct insights into the genome-wide genetic ancestry of enslaved people in the historical US. Genetic connections to individuals from Catoctin Furnace African American Cemetery in Maryland. A timeline highlighting major events in the history of Catoctin Furnace and the birth years of research participants in the 23andMe cohort, presented alongside maps showing the proportion of 23andMe research participants associated with geographic coordinates in the US, sub-Saharan Africa, and Europe who share genetic connections to the Catoctin individuals.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2023
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    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
    SSG: 11
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  • 3
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    Online Resource
    Elsevier BV ; 2017
    In:  Molecular Phylogenetics and Evolution Vol. 112 ( 2017-07), p. 88-95
    In: Molecular Phylogenetics and Evolution, Elsevier BV, Vol. 112 ( 2017-07), p. 88-95
    Type of Medium: Online Resource
    ISSN: 1055-7903
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2017
    detail.hit.zdb_id: 1471402-4
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Wiley ; 2016
    In:  Methods in Ecology and Evolution Vol. 7, No. 3 ( 2016-03), p. 380-383
    In: Methods in Ecology and Evolution, Wiley, Vol. 7, No. 3 ( 2016-03), p. 380-383
    Abstract: Floristic Quality Assessments ( FQA s) are measurements of a natural area's ecological integrity based on their plant species composition. Widely used by government agencies and conservation organizations to monitor and assess natural areas, FQA data bases have been developed for much of the United States and beyond. Here, we present the Universal FQA Calculator ( http://universalFQA.org ), a free, open‐source web‐based FQA Calculator. The calculator offers 30 FQA data bases (with more being added regularly) from across the United States and Canada and has been used to calculate thousands of assessments. The Universal FQA Calculator's growing repository for site inventory and transect data is accessible via a REST API and represents a valuable resource for data on the occurrence and abundance of plant species. We describe the features and implementation of the Universal FQA Calculator, provide a summary of its increasing usage and discuss the benefits of cloud‐based storage of ecological assessment data.
    Type of Medium: Online Resource
    ISSN: 2041-210X , 2041-210X
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 2528492-7
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  • 5
    Online Resource
    Online Resource
    Wiley ; 2021
    In:  American Journal of Botany Vol. 108, No. 10 ( 2021-10), p. 2015-2037
    In: American Journal of Botany, Wiley, Vol. 108, No. 10 ( 2021-10), p. 2015-2037
    Abstract: Expanded phylogenetic analyses of the Hawaiian silversword alliance ( Argyroxiphium , Dubautia , Wilkesia ; Compositae) were undertaken to assess evolutionary and biogeographic informativeness of cytonuclear discordance and any biases in evolutionary directionality of ecological transitions within this prominent example of adaptive radiation. Methods Samples spanning the geographic and ecological distributions of all recognized taxa were included in phylogenetic and biogeographic analyses of nuclear ribosomal DNA (nrDNA) and cpDNA sequences. Bayesian model testing approaches were used to model ecological evolution and the evolution of nuclear chromosomal arrangements while accounting for phylogenetic uncertainty. Results Cytonuclear discordance detected previously appears to reflect chloroplast capture, at least in part, with nrDNA trees being largely congruent with nuclear chromosomal structural data and fine‐scale taxonomy. Comparison of biogeographic histories estimated from the posterior distributions of nrDNA and cpDNA trees, including inferred chloroplast‐capture events, provides additional resolution of dispersal history, including a back‐dispersal to Maui Nui from Hawai‘i. A newly resolved major nrDNA clade of endemic Kaua‘i taxa that mostly were described as new‐to‐science since the 1980s strengthens the earlier hypothesis that diversification on Kaua‘i has not waned since the island began to decline in area through subsidence and erosion. Bias in habitat shifts was estimated, with transitions from dry‐to‐mesic or ‐wet and from wet‐to‐mesic or ‐bog habitats dominating diversification of the silversword alliance from a dry‐adapted tarweed ancestor. Conclusions The habitat‐transition biases estimated here may indicate more limited pathways of ecological evolution than proposed previously for an adaptive radiation involving such major ecological shifts.
    Type of Medium: Online Resource
    ISSN: 0002-9122 , 1537-2197
    URL: Issue
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    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2053581-8
    SSG: 12
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  • 6
    In: BMC Biology, Springer Science and Business Media LLC, Vol. 15, No. 1 ( 2017-12)
    Type of Medium: Online Resource
    ISSN: 1741-7007
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 2133020-7
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  • 7
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2020
    In:  Systematic Biology Vol. 69, No. 4 ( 2020-07-01), p. 774-794
    In: Systematic Biology, Oxford University Press (OUP), Vol. 69, No. 4 ( 2020-07-01), p. 774-794
    Abstract: Species selection, the effect of heritable traits in generating between-lineage diversification rate differences, provides a valuable conceptual framework for understanding the relationship between traits, diversification, and phylogenetic tree shape. An important challenge, however, is that the nature of real diversification landscapes—curves or surfaces which describe the propensity of species-level lineages to diversify as a function of one or more traits—remains poorly understood. Here, we present a novel, time-stratified extension of the QuaSSE model in which speciation/extinction rate is specified as a static or temporally shifting Gaussian or skewed-Gaussian function of the diversification trait. We then use simulations to show that the generally imbalanced nature of real phylogenetic trees, as well as their generally greater than expected frequency of deep branching events, are typical outcomes when diversification is treated as a dynamic, trait-dependent process. Focusing on four basic models (Gaussian-speciation with and without background extinction; skewed-speciation; Gaussian-extinction), we also show that particular features of the species selection regime produce distinct tree shape signatures and that, consequently, a combination of tree shape metrics has the potential to reveal the species selection regime under which a particular lineage diversified. We evaluate this idea empirically by comparing the phylogenetic trees of plant lineages diversifying within climatically and geologically stable environments of the Greater Cape Floristic Region, with those of lineages diversifying in environments that have experienced major change through the Late Miocene-Pliocene. Consistent with our expectations, the trees of lineages diversifying in a dynamic context are less balanced, show a greater concentration of branching events close to the present, and display stronger diversification rate-trait correlations. We suggest that species selection plays an important role in shaping phylogenetic trees but recognize the need for an explicit probabilistic framework within which to assess the likelihoods of alternative diversification scenarios as explanations of a particular tree shape. [Cape flora; diversification landscape; environmental change; gamma statistic; species selection; time-stratified QuaSSE model; trait-dependent diversification; tree imbalance.]
    Type of Medium: Online Resource
    ISSN: 1063-5157 , 1076-836X
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    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1482572-7
    detail.hit.zdb_id: 1123455-6
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Elsevier BV ; 2021
    In:  The American Journal of Human Genetics Vol. 108, No. 11 ( 2021-11), p. 2052-2070
    In: The American Journal of Human Genetics, Elsevier BV, Vol. 108, No. 11 ( 2021-11), p. 2052-2070
    Type of Medium: Online Resource
    ISSN: 0002-9297
    RVK:
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2021
    detail.hit.zdb_id: 1473813-2
    SSG: 12
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  • 9
    In: Journal of Systematics and Evolution, Wiley, Vol. 58, No. 6 ( 2020-11), p. 853-880
    Abstract: Rock daisies (Perityleae; Compositae) are a diverse clade of seven genera and ca. 84 minimum‐rank taxa that mostly occur as narrow endemics on sheer rock cliffs throughout the southwest United States and northern Mexico. Taxonomy of Perityleae has traditionally been based on morphology and cytogenetics. To test taxonomic hypotheses and utility of characters emphasized in past treatments, we present the first densely sampled molecular phylogenies of Perityleae and reconstruct trait and chromosome evolution. We inferred phylogenetic trees from whole chloroplast genomes, nuclear ribosomal cistrons, and hundreds of low‐copy nuclear genes using genome skimming and target capture. Discordance between sources of molecular data suggests an underappreciated history of hybridization in Perityleae. Phylogenies support the monophyly of subtribe Peritylinae, a distinctive group possessing a four‐lobed disc corolla; however, all of the phylogenetic trees generated in this study reject the monophyly of the most species‐rich genus, Perityle , as well as its sections: Perityle sect. Perityle, Perityle sect. Laphamia , and Perityle sect. Pappothrix . Using reversible jump MCMC, our results suggest that morphological characters traditionally used to classify members of Perityleae have evolved multiple times within the group. A base chromosome number x  = 9 gave rise to higher base numbers in subtribe Peritylinae ( x  = 12, 13, 16, 17, 18, and 19) through polyploidization, followed by ascending or descending dysploidy. Most taxa constitute a monophyletic lineage with a base chromosome number of x  = 17, with multiple neo‐polyploidization events. These results demonstrate the advantages and obstacles of next‐generation sequencing approaches in synantherology while laying the foundation for taxonomic revision and comparative study of the evolutionary ecology of Perityleae.
    Type of Medium: Online Resource
    ISSN: 1674-4918 , 1759-6831
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
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    SSG: 6,25
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    Wiley ; 2023
    In:  Methods in Ecology and Evolution Vol. 14, No. 5 ( 2023-05), p. 1230-1244
    In: Methods in Ecology and Evolution, Wiley, Vol. 14, No. 5 ( 2023-05), p. 1230-1244
    Abstract: Organisms such as allopolyploids and F1 hybrids contain multiple distinct subgenomes, each potentially with its own evolutionary history. These organisms present a challenge for multilocus phylogenetic inference and other analyses since it is not apparent which gene copies from different loci are from the same subgenome and thus share an evolutionary history. Here we introduce homologizer, a flexible Bayesian approach that uses a phylogenetic framework to infer the phasing of gene copies across loci into their respective subgenomes. Through the use of simulation tests, we demonstrate that homologizer is robust to a wide range of factors, such as incomplete lineage sorting and the phylogenetic informativeness of loci. Furthermore, we establish the utility of homologizer on real data, by analysing a multilocus dataset consisting of nine diploids and 19 tetraploids from the fern family Cystopteridaceae. Finally, we describe how homologizer may potentially be used beyond its core phasing functionality to identify non‐homologous sequences, such as hidden paralogs or contaminants.
    Type of Medium: Online Resource
    ISSN: 2041-210X , 2041-210X
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2528492-7
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