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Publications of Elaine E. Guevara    :chronological  alphabetical  combined listing:

%% Journal Articles   
   Author = {Guevara, EE and Lawler, RR and Staes, N and White, CM and Sherwood, CC and Ely, JJ and Hopkins, WD and Bradley, BJ},
   Title = {Age-associated epigenetic change in chimpanzees and
   Journal = {Philosophical Transactions of the Royal Society of London.
             Series B, Biological Sciences},
   Volume = {375},
   Number = {1811},
   Pages = {20190616},
   Year = {2020},
   Month = {November},
   url = {http://dx.doi.org/10.1098/rstb.2019.0616},
   Abstract = {Methylation levels have been shown to change with age at
             sites across the human genome. Change at some of these sites
             is so consistent across individuals that it can be used as
             an 'epigenetic clock' to predict an individual's
             chronological age to within a few years. Here, we examined
             how the pattern of epigenetic ageing in chimpanzees compares
             with humans. We profiled genome-wide blood methylation
             levels by microarray for 113 samples from 83 chimpanzees
             aged 1-58 years (26 chimpanzees were sampled at multiple
             ages during their lifespan). Many sites (greater than 65
             000) showed significant change in methylation with age and
             around one-third (32%) of these overlap with sites showing
             significant age-related change in humans. At over 80% of
             sites showing age-related change in both species,
             chimpanzees displayed a significantly faster rate of
             age-related change in methylation than humans. We also built
             a chimpanzee-specific epigenetic clock that predicted age in
             our test dataset with a median absolute deviation from known
             age of only 2.4 years. However, our chimpanzee clock showed
             little overlap with previously constructed human clocks.
             Methylation at CpGs comprising our chimpanzee clock showed
             moderate heritability. Although the use of a human
             microarray for profiling chimpanzees biases our results
             towards regions with shared genomic sequence between the
             species, nevertheless, our results indicate that there is
             considerable conservation in epigenetic ageing between
             chimpanzees and humans, but also substantial divergence in
             both rate and genomic distribution of ageing-associated
             sites. This article is part of the theme issue 'Evolution of
             the primate ageing process'.},
   Doi = {10.1098/rstb.2019.0616},
   Key = {fds352546}

   Author = {Singh, SV and Staes, N and Guevara, EE and Schapiro, SJ and Ely, JJ and Hopkins, WD and Sherwood, CC and Bradley, BJ},
   Title = {Evolution of ASPM coding variation in apes and associations
             with brain structure in chimpanzees.},
   Journal = {Genes, Brain, and Behavior},
   Volume = {18},
   Number = {7},
   Pages = {e12582},
   Year = {2019},
   Month = {September},
   url = {http://dx.doi.org/10.1111/gbb.12582},
   Abstract = {Studying genetic mechanisms underlying primate brain
             morphology can provide insight into the evolution of human
             brain structure and cognition. In humans, loss-of-function
             mutations in the gene coding for ASPM (Abnormal Spindle
             Microtubule Assembly) have been associated with primary
             microcephaly, which is defined by a significantly reduced
             brain volume, intellectual disability and delayed
             development. However, less is known about the effects of
             common ASPM variation in humans and other primates. In this
             study, we characterized the degree of coding variation at
             ASPM in a large sample of chimpanzees (N = 241), and
             examined potential associations between genotype and various
             measures of brain morphology. We identified and genotyped
             five non-synonymous polymorphisms in exons 3 (V588G), 18
             (Q2772K, K2796E, C2811Y) and 27 (I3427V). Using T1-weighted
             magnetic resonance imaging of brains, we measured total
             brain volume, cerebral gray and white matter volume,
             cerebral ventricular volume, and cortical surface area in
             the same chimpanzees. We found a potential association
             between ASPM V588G genotype and cerebral ventricular volume
             but not with the other measures. Additionally, we found that
             chimpanzee, bonobo, and human lineages each independently
             show a signature of accelerated ASPM protein evolution.
             Overall, our results suggest the potential effects of ASPM
             variation on cerebral cortical development, and emphasize
             the need for further functional studies. These results are
             the first evidence suggesting ASPM variation might play a
             role in shaping natural variation in brain structure in
             nonhuman primates.},
   Doi = {10.1111/gbb.12582},
   Key = {fds346144}

   Author = {Webster, T and Guevara, E and Lawler, R and Bradley,
   Title = {Successful exome capture and sequencing in lemurs using
             human baits},
   Year = {2018},
   Month = {December},
   url = {http://dx.doi.org/10.1101/490839},
   Abstract = {ABSTRACT Objectives We assessed the efficacy of exome
             capture in lemurs using commercially available human baits.
             Materials and Methods We used two human kits (Nimblegen
             SeqCap EZ Exome Probes v2.0; IDT xGen Exome Research Panel
             v1.0) to capture and sequence the exomes of wild
             Verreaux’s sifakas ( Propithecus verreauxi, n = 8), a
             lemur species distantly related to humans. For comparison,
             we also captured exomes of a primate species more closely
             related to humans ( Macaca mulatta, n= 4). We mapped reads
             to both the human reference assembly and the most closely
             related reference for each species before calling variants.
             We used measures of mapping quality and read coverage to
             compare capture success. Results We observed high and
             comparable mapping qualities for both species when mapped to
             their respective nearest-relative reference genomes. When
             investigating breadth of coverage, we found greater capture
             success in macaques than sifakas using both nearest-relative
             and human assemblies. Exome capture in sifakas was still
             highly successful with more than 90% of annotated coding
             sequence in the sifaka reference genome captured, and 80%
             sequenced to a depth greater than 7x using Nimblegen baits.
             However, this success depended on probe design: the use of
             IDT probes resulted in substantially less callable sequence
             at low-to-moderate depths. Discussion Overall, we
             demonstrate successful exome capture in lemurs using human
             baits, though success differed between kits tested. These
             results indicate that exome capture is an effective and
             economical genomic method of broad utility to evolutionary
             primatologists working across the entire primate
   Doi = {10.1101/490839},
   Key = {fds346145}

   Author = {Guevara, EE and Lawler, RR},
   Title = {Epigenetic Clocks.},
   Journal = {Evolutionary Anthropology},
   Volume = {27},
   Number = {6},
   Pages = {256-260},
   Year = {2018},
   Month = {November},
   url = {http://dx.doi.org/10.1002/evan.21745},
   Abstract = {Recent research has revealed clock-like patterns of
             epigenetic change across the life span in humans. Models
             describing these epigenetic changes have been dubbed
             "epigenetic clocks," and they can not only predict
             chronological age but also reveal biological age, which
             measures physiological homeostasis and deterioration over
             the life span. Comparative studies of the epigenetic clocks
             of different primate species are likely to provide insights
             into the evolution of life history schedules, as well as
             shed light on the physiological and genetic bases of aging
             and aging-related diseases. Chronological age estimation
             using clock-based calculators may also offer biological
             anthropologists a useful tool for applying to forensic and
             demographic studies.},
   Doi = {10.1002/evan.21745},
   Key = {fds346146}

   Author = {Guevara, EE and Frankel, DC and Ranaivonasy, J and Richard, AF and Ratsirarson, J and Lawler, RR and Bradley, BJ},
   Title = {A simple, economical protocol for DNA extraction and
             amplification where there is no lab},
   Journal = {Conservation Genetics Resources},
   Volume = {10},
   Number = {1},
   Pages = {119-125},
   Year = {2018},
   Month = {March},
   url = {http://dx.doi.org/10.1007/s12686-017-0758-5},
   Abstract = {© 2017, Springer Science+Business Media Dordrecht. Genetic
             analyses are well suited to address many research questions
             in the study of wild populations, yet species of interest
             often have distributions that are geographically distant
             from molecular laboratories, necessitating potentially
             lengthy transport of biological specimens. Performing basic
             genetic analyses on site would avoid the project delays and
             risks of sample quality decline associated with transport,
             as well as allow original specimens to remain in the country
             of origin. Further, diagnostic genetic assays performed in
             the field could provide real-time information allowing for
             more nimble adjustments to research plans and use of
             resources. To this end, we developed protocols for reliably
             performing front-end genetics bench work in the field,
             without the requirements of electricity or permanent
             shelter. We validated these protocols on buccal swabs
             collected during routine capturing of sifaka lemurs
             (Propithecus verreauxi) at Bezà Mahafaly Special Reserve in
             Southwest Madagascar and faecal samples collected from
             captive sifakas (P. coquereli) at the Duke Lemur Center. Our
             basic protocol pipeline involves a chelating resin based DNA
             extraction followed by whole genome amplification or
             polymerase chain reaction using reagents stored at ambient
             temperature and portable, compact equipment powered by a
             lightweight solar panel. We achieved a high success rate
             (CloseSPigtSPi80%) in downstream procedures, demonstrating
             the promise of such protocols for performing basic genetic
             analyses in a broad range of field situations.},
   Doi = {10.1007/s12686-017-0758-5},
   Key = {fds346308}

   Author = {Staes, N and Sherwood, CC and Wright, K and de Manuel, M and Guevara,
             EE and Marques-Bonet, T and Krützen, M and Massiah, M and Hopkins, WD and Ely, JJ and Bradley, BJ},
   Title = {FOXP2 variation in great ape populations offers insight into
             the evolution of communication skills.},
   Journal = {Scientific Reports},
   Volume = {7},
   Number = {1},
   Pages = {16866},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1038/s41598-017-16844-x},
   Abstract = {The gene coding for the forkhead box protein P2 (FOXP2) is
             associated with human language disorders. Evolutionary
             changes in this gene are hypothesized to have contributed to
             the emergence of speech and language in the human lineage.
             Although FOXP2 is highly conserved across most mammals,
             humans differ at two functional amino acid substitutions
             from chimpanzees, bonobos and gorillas, with an additional
             fixed substitution found in orangutans. However, FOXP2 has
             been characterized in only a small number of apes and no
             publication to date has examined the degree of natural
             variation in large samples of unrelated great apes. Here, we
             analyzed the genetic variation in the FOXP2 coding sequence
             in 63 chimpanzees, 11 bonobos, 48 gorillas, 37 orangutans
             and 2 gibbons and observed undescribed variation in great
             apes. We identified two variable polyglutamine
             microsatellites in chimpanzees and orangutans and found
             three nonsynonymous single nucleotide polymorphisms, one in
             chimpanzees, one in gorillas and one in orangutans with
             derived allele frequencies of 0.01, 0.26 and 0.29,
             respectively. Structural and functional protein modeling
             indicate a biochemical effect of the substitution in
             orangutans, and because of its presence solely in the
             Sumatran orangutan species, the mutation may be associated
             with reported population differences in vocalizations.},
   Doi = {10.1038/s41598-017-16844-x},
   Key = {fds346147}

   Author = {Guevara, EE and Chen-Kraus, C and Jacobs, RL and Baden,
   Title = {Celebrating fifty years of research at the Duke Lemur
   Journal = {Evolutionary Anthropology},
   Volume = {26},
   Number = {2},
   Pages = {47-48},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1002/evan.21521},
   Doi = {10.1002/evan.21521},
   Key = {fds346148}

   Author = {Bradley, BJ and Snowdon, CT and McGrew, WC and Lawler, RR and Guevara,
             EE and McIntosh, A and O'Connor, T},
   Title = {Non-human primates avoid the detrimental effects of prenatal
             androgen exposure in mixed-sex litters: combined
             demographic, behavioral, and genetic analyses.},
   Journal = {American Journal of Primatology},
   Volume = {78},
   Number = {12},
   Pages = {1304-1315},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1002/ajp.22583},
   Abstract = {Producing single versus multiple births has important life
             history trade-offs, including the potential benefits and
             risks of sharing a common in utero environment. Sex hormones
             can diffuse through amniotic fluid and fetal membranes, and
             females with male littermates risk exposure to high levels
             of fetal testosterone, which are shown to have masculinizing
             effects and negative fitness consequences in many mammals.
             Whereas most primates give birth to single offspring,
             several New World monkey and strepsirrhine species regularly
             give birth to small litters. We examined whether neonatal
             testosterone exposure might be detrimental to females in
             mixed-sex litters by compiling data from long-term breeding
             records for seven primate species (Saguinus oedipus; Varecia
             variegata, Varecia rubra, Microcebus murinis, Mirza
             coquereli, Cheirogaleus medius, Galago moholi). Litter sex
             ratios did not differ from the expected 1:2:1 (MM:MF:FF for
             twins) and 1:2:2:1 (MMM:MMF:MFF:FFF for triplets). Measures
             of reproductive success, including female survivorship,
             offspring-survivorship, and inter-birth interval, did not
             differ between females born in mixed-sex versus all-female
             litters, indicating that litter-producing non-human
             primates, unlike humans and rodents, show no signs of
             detrimental effects from androgen exposure in mixed sex
             litters. Although we found no evidence for CYP19A1 gene
             duplications-a hypothesized mechanism for coping with
             androgen exposure-aromatase protein evolution shows patterns
             of convergence among litter-producing taxa. That some
             primates have effectively found a way to circumvent a major
             cost of multiple births has implications for understanding
             variation in litter size and life history strategies across
   Doi = {10.1002/ajp.22583},
   Key = {fds346149}

   Author = {Guevara, EE and Veilleux, CC and Saltonstall, K and Caccone, A and Mundy, NI and Bradley, BJ},
   Title = {Potential arms race in the coevolution of primates and
             angiosperms: brazzein sweet proteins and gorilla taste
   Journal = {American Journal of Physical Anthropology},
   Volume = {161},
   Number = {1},
   Pages = {181-185},
   Year = {2016},
   Month = {September},
   url = {http://dx.doi.org/10.1002/ajpa.23046},
   Abstract = {We explored whether variation in the sweet taste receptor
             protein T1R3 in primates could contribute to differences in
             sweet taste repertoire among species, potentially reflecting
             coevolution with local plants. Specifically, we examined
             which primates are likely to be sweet "tasters" of brazzein,
             a protein found in the fruit of the African plant
             Pentadiplandra brazzeana that tastes intensely sweet to
             humans, but provides little energy. Sweet proteins like
             brazzein are thought to mimic the taste of sugars to entice
             seed dispersers. We examined the evolution of T1R3 and
             assessed whether primates are likely "deceived" by such
             biochemical mimicry.Using published and new sequence data
             for TAS1R3, we characterized 57 primates and other mammals
             at the two amino acid sites necessary to taste brazzein to
             determine which species are tasters. We further used
             dN/dS-based methods to look for statistical evidence of
             accelerated evolution in this protein across primate
             lineages.The taster genotype is shared across most
             catarrhines, suggesting that most African primates can be
             "tricked" into eating and dispersing P. brazzeana's seeds
             for little caloric gain. Western gorillas (Gorilla gorilla),
             however, exhibit derived mutations at the two
             brazzein-critical positions, and although fruit is a
             substantial portion of the western gorilla diet, they have
             not been observed to eat P. brazzeana. Our analyses of
             protein evolution found no signature of positive selection
             on TAS1R3 along the gorilla lineage.We propose that the
             gorilla-specific mutations at the TAS1R3 locus encoding T1R3
             could be a counter-adaptation to the false sweet signal of
   Doi = {10.1002/ajpa.23046},
   Key = {fds346150}

   Author = {Perlman, RF and Nishimura, AC and Mongle, CS and Kling, K and Guevara,
             EE and Arslanian, K},
   Title = {Life's a peach for anthropologists in atlanta.},
   Journal = {Evolutionary Anthropology},
   Volume = {25},
   Number = {3},
   Pages = {81-83},
   Year = {2016},
   Month = {May},
   url = {http://dx.doi.org/10.1002/evan.21493},
   Doi = {10.1002/evan.21493},
   Key = {fds346151}

   Author = {Perlman, RF and de Vries, D and Jacobs, RL and Holowka, NB and Pain, EL and Guevara, EE and Thompson, NE},
   Title = {The gateway to anthropology in St. Louis.},
   Journal = {Evolutionary Anthropology},
   Volume = {24},
   Number = {3},
   Pages = {101-103},
   Year = {2015},
   Month = {May},
   url = {http://dx.doi.org/10.1002/evan.21450},
   Doi = {10.1002/evan.21450},
   Key = {fds346152}

   Author = {Guevara, EE and Steiper, ME},
   Title = {Molecular phylogenetic analysis of the Papionina using
             concatenation and species tree methods.},
   Journal = {Journal of Human Evolution},
   Volume = {66},
   Pages = {18-28},
   Year = {2014},
   Month = {January},
   url = {http://dx.doi.org/10.1016/j.jhevol.2013.09.003},
   Abstract = {The Papionina is a geographically widespread subtribe of
             African cercopithecid monkeys whose evolutionary history is
             of particular interest to anthropologists. The phylogenetic
             relationships among arboreal mangabeys (Lophocebus), baboons
             (Papio), and geladas (Theropithecus) remain unresolved.
             Molecular phylogenetic analyses have revealed marked gene
             tree incongruence for these taxa, and several recent
             concatenated phylogenetic analyses of multilocus datasets
             have supported different phylogenetic hypotheses. To address
             this issue, we investigated the phylogeny of the
             Lophocebus + Papio + Theropithecus group using
             concatenation methods, as well as alternative methods that
             incorporate gene tree heterogeneity to estimate a 'species
             tree.' Our compiled DNA sequence dataset was ∼56 kb pairs
             long and included 57 independent partitions. All analyses of
             concatenated alignments strongly supported a
             Lophocebus + Papio clade and a basal position for
             Theropithecus. The Bayesian concordance analysis supported
             the same phylogeny. A coalescent-based Bayesian method
             resulted in a very poorly resolved species tree. The
             topological agreement between concatenation and the Bayesian
             concordance analysis offers considerable support for a
             Lophocebus + Papio clade as the dominant relationship
             across the genome. However, the results of the Bayesian
             concordance analysis indicate that almost half the genome
             has an alternative history. As such, our results offer a
             well-supported phylogenetic hypothesis for the
             Papio/Lophocebus/Theropithecus trichotomy, while at the same
             time providing evidence for a complex evolutionary history
             that likely includes hybridization among
   Doi = {10.1016/j.jhevol.2013.09.003},
   Key = {fds346153}

%% Papers Presented/Symposia/Abstracts   
   Author = {Guevara, EEG and Steiper, ME},
   Title = {Analysis of multi-locus sequence data indicates complex
             speciation in the evolutionary history of the
   Journal = {American Journal of Physical Anthropology},
   Volume = {150},
   Pages = {139-140},
   Publisher = {WILEY-BLACKWELL},
   Year = {2013},
   Month = {January},
   Key = {fds346154}

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