@article{scheible_stinson_breen_callahan_thomas_meiklejohn_2024, title={The development of non-destructive sampling methods of parchment skins for genetic species identification}, url={https://doi.org/10.1371/journal.pone.0299524}, DOI={10.1371/journal.pone.0299524}, abstractNote={Parchment, the skins of animals prepared for use as writing surfaces, offers a valuable source of genetic information. Many have clearly defined provenance, allowing for the genetic findings to be evaluated in temporal and spatial context. While these documents can yield evidence of the animal sources, the DNA contained within these aged skins is often damaged and fragmented. Previously, genetic studies targeting parchment have used destructive sampling techniques and so the development and validation of non-destructive sampling methods would expand opportunities and facilitate testing of more precious documents, especially those with historical significance. Here we present genetic data obtained by non-destructive sampling of eight parchments spanning the 15th century to the modern day. We define a workflow for enriching the mitochondrial genome (mtGenome), generating next-generation sequencing reads to permit species identification, and providing interpretation guidance. Using sample replication, comparisons to destructively sampled controls, and by establishing authentication criteria, we were able to confidently assign full/near full mtGenome sequences to 56.3% of non-destructively sampled parchments, each with greater than 90% of the mtGenome reference covered. Six of eight parchments passed all four established thresholds with at least one non-destructive sample, highlighting promise for future studies.}, journal={PLOS ONE}, author={Scheible, Melissa and Stinson, Timothy L. and Breen, Matthew and Callahan, Benjamin J. and Thomas, Rachael and Meiklejohn, Kelly A.}, editor={Shakoori, Abdul RaufEditor}, year={2024}, month={Mar} }
 @article{tiedge_meiklejohn_2023, title={Assessing three soil removal methods for environmental DNA analysis of mock forensic geology evidence}, volume={10}, ISSN={["1556-4029"]}, url={https://doi.org/10.1111/1556-4029.15399}, DOI={10.1111/1556-4029.15399}, abstractNote={Soil is useful in criminal investigations as it is highly variable and readily transferred. Forensic geologists use several different techniques to removal soil from evidence prior to the analysis of inorganic components. There has been recent interest from the forensic science community to analyze environmental deoxyribonucleic acid (eDNA) associated with soil to augment existing forensic analyses. Notably however, limited research has been conducted to compare commonly used soil removal methods for downstream eDNA analysis. In this study, three soil removal methods were assessed: picking/scraping, sonication, and swabbing. Three mock evidence types (t‐shirts, boot soles, and trowels) were sampled in triplicate with each removal method (n = 27). Soil samples underwent DNA isolation, quantification, and amplification of four genomic barcode regions: 16S for bacteria, ITS1 for fungi, ITS2 for plants, and COI for arthropods. Amplicons were prepared into libraries for DNA sequencing on an Illumina® MiniSeq. DNA concentrations were highest in picked/scraped samples and were statistically significant compared with swabbed and sonicated samples. Amplicon sequence variants (ASVs) were identified, and removal methods had no impact on the recovery of the total number of target ASVs. Additionally, when assessing each sample in multidimensional space, picked/scraped samples tended to cluster separately from swabbed and sonicated samples. The soil core used a reference in this study also clustered with the picked/scraped samples, indicating that these samples may be more reflective of the communities collected from soil cores. Based on these data, we identified that picking/scraping is an acceptable soil removal method for eDNA analysis.}, journal={JOURNAL OF FORENSIC SCIENCES}, author={Tiedge, Teresa M. and Meiklejohn, Kelly A.}, year={2023}, month={Oct} }
 @article{meiklejohn_scheible_boggs_dunn_ricke_2023, title={Using FastID to analyze complex SNP mixtures from indoor dust}, volume={4}, ISSN={["1556-4029"]}, url={https://doi.org/10.1111/1556-4029.15246}, DOI={10.1111/1556-4029.15246}, abstractNote={Forensically relevant single nucleotide polymorphisms (SNPs) can provide valuable supplemental information to short tandem repeats (STRs) for investigative leads, and genotyping can now be streamlined using massively parallel sequencing (MPS). Dust is an attractive evidence source, as it accumulates on undisturbed surfaces, often is overlooked by perpetrators, and contains sufficient human DNA for analysis. To assess whether SNPs genotyped from indoor dust using MPS could be used to detect known household occupants, 13 households were recruited and provided buccal samples from each occupant and dust from five predefined indoor locations. Thermo Fisher Scientific Precision ID Identity and Ancestry Panels were utilized for SNP genotyping, and sequencing was completed using Illumina® chemistry. FastID, a software developed to permit mixture analysis and identity searching, was used to assess whether known occupants could be detected from associated household dust samples. A modified “subtraction” method was also used in FastID to estimate the percentage of alleles in each dust sample contributed by known and unknown occupants. On average, 72% of autosomal SNPs were recovered from dust samples. When using FastID, (a) 93% of known occupants were detected in at least one indoor dust sample and could not be excluded as contributors to the mixture, and (b) non‐contributor alleles were detected in 54% of dust samples (29 ± 11 alleles per dust sample). Overall, this study highlights the potential of analyzing human DNA present in indoor dust to detect known household occupants, which could be valuable for investigative leads.}, journal={JOURNAL OF FORENSIC SCIENCES}, author={Meiklejohn, Kelly A. and Scheible, Melissa K. R. and Boggs, Laura M. and Dunn, Robert R. and Ricke, Darrell O.}, year={2023}, month={Apr} }
 @article{moore_scheible_robertson_meiklejohn_2022, title={Assessing the lysis of diverse pollen from bulk environmental samples for DNA metabarcoding}, volume={6}, url={https://doi.org/10.3897/mbmg.6.89753}, DOI={10.3897/mbmg.6.89753}, abstractNote={Pollen is ubiquitous year-round in bulk environmental samples and can provide useful information on previous and current plant communities. Characterization of pollen has traditionally been completed based on morphology, requiring significant time and expertise. DNA metabarcoding is a promising approach for characterizing pollen from bulk environmental samples, but accuracy hinges on successful lysis of pollen grains to free template DNA. In this study, we assessed the lysis of morphologically and taxonomically diverse pollen from one of the most common bulk environmental sample types for DNA metabarcoding, surface soil. To achieve this, a four species artificial pollen mixture was spiked into surface soils collected from Colorado, North Carolina, and Pennsylvania, and subsequently subjected to DNA extraction using both the PowerSoil and PowerSoil Pro Kits (Qiagen) with a heated incubation (either 65 °C or 90 °C). Amplification and Illumina sequencing of the internal transcribed spacer subunit 2 (ITS2) was completed in duplicate for each sample (total n, 76), and the resulting sequencing reads taxonomically identified using GenBank. The PowerSoil Pro Kit statistically outperformed the PowerSoil Kit for total DNA yield. When using either kit, incubation temperature (65 °C or 90 °C) used had no impact on the recovery of DNA, plant amplicon sequence variants (ASVs), or total plant ITS2 reads. This study highlighted that lysis of pollen in bulk environmental samples is feasible using commercially available kits, and downstream DNA metabarcoding can be used to accurately characterize pollen DNA from such sample types.}, journal={Metabarcoding and Metagenomics}, publisher={Pensoft Publishers}, author={Moore, Madison A. and Scheible, Melissa K.R. and Robertson, James B. and Meiklejohn, Kelly A.}, year={2022}, month={Sep} }
 @article{scheible_timpano_boggs_meiklejohn_2021, title={An alternate workflow for preparing Precision ID Ancestry and Identity Panel libraries for Illumina sequencing}, volume={135}, ISSN={["1437-1596"]}, url={https://doi.org/10.1007/s00414-021-02549-4}, DOI={10.1007/s00414-021-02549-4}, abstractNote={Single nucleotide polymorphisms (SNPs) are well-established for forensic applications. Although they are not compatible with existing criminal databases, they offer some advantages over short tandem repeat (STR) markers including smaller amplicons, no stutter artifacts, and biogeographic ancestry and phenotype predictions. The Precision ID NGS System, a commercial workflow by Thermo Fisher Scientific, offers a streamlined solution for genotyping forensically relevant SNPs using next-generation sequencing. The Precision ID Ancestry and Identity Panels combined target 289 SNPs, and their sensitivity, reproducibility, and accuracy have been evaluated by the forensic community. The aim of this study was to develop an alternative workflow to genotype these SNP panels using Illumina chemistry. Commercial genomic DNAs (gDNAs) (n, 3) were amplified using three uracil-tolerant polymerase master mixes. Resulting amplicons were prepared into libraries using the KAPA Hyper Prep Kit (KAPA Biosystems) and sequenced via Illumina's MiniSeq. Reads were analyzed using a published analysis pipeline to compile final genotypes with read depth information. Phusion U Multiplex PCR Master Mix (Thermo Fisher Scientific) statistically outperformed the other master mixes tested (P <0.0001), with respect to the number of SNPs genotyped. To ensure a workflow using Phusion U would be compatible across diverse samples, we optimized PCR cycle number using the same commercial gDNAs (n, 3), reference buccal swabs (n, 3), and environmental (household dust) samples (n, 6). Using the developed workflow, 93.9% of all SNPs were successfully genotyped across sample types. Implementation of the developed workflow should be straightforward for forensic laboratories and suitable for processing reference and casework samples.}, number={5}, journal={INTERNATIONAL JOURNAL OF LEGAL MEDICINE}, publisher={Springer Science and Business Media LLC}, author={Scheible, Melissa K. R. and Timpano, Emma K. and Boggs, Laura M. and Meiklejohn, Kelly A.}, year={2021}, month={Sep}, pages={1717–1726} }
 @article{damaso_ashe_meiklejohn_kavlick_robertson_2021, title={Comparison of polymerases used for amplification of mitochondrial DNA from challenging hairs and hairs of various treatments}, volume={52}, ISSN={["1878-0326"]}, DOI={10.1016/j.fsigen.2021.102484}, abstractNote={Forensic DNA analysis of hair evidence typically involves the amplification and sequencing of the control region (CR) of the mitochondrial genome (mtgenome). In compromised hair samples, such as shed hairs, the number of mtgenome copies could be low; thus, it is imperative that the polymerase used in PCR is efficient to ensure maximum amplification. Considering this, the first phase of this study compared the yields obtained from 12 polymerases (sourced from a range of commercial companies) when amplifying the CR, hypervariable (HV) region II (HV2), and hypervariable subregion II-B (HV2B). This initial assessment was performed using mitochondrial DNA (mtDNA) extracted from 2 cm of hair adjacent to the root from three donors of different self-reported ancestries and hair color/texture. PrimeSTAR HS and KAPA HiFi HotStart consistently generated significantly higher amplicon yields (p < 0.05, ~5-fold increase) for most regions than AmpliTaq Gold DNA polymerase (the polymerase validated for use in most forensic laboratories). The second phase of this project was focused on assessing the broad utility of these top two performing polymerases for amplifying two regions of the mtgenome (CR and HV2B) from hair samples representing diverse self-reported ancestral origins (European, Latin American, African American, Asian, and Native American), characteristics/treatments (bleached, dyed, and chemically straightened), and anatomical origins (e.g., head and pubic region) (n = 41). These regions were chosen as they are the most challenging to amplify and sequence in compromised hair samples due to length (i.e., the CR is ~1.2 kb) and repeat structure (i.e., the polycytosine stretch within HV2B). The results indicated that regardless of sample type, PrimeSTAR HS and KAPA HiFi HotStart polymerases outperformed (p < 0.05) AmpliTaq Gold DNA polymerase (averaging 11- and 8-fold increased yields, respectively). The results from this study highlight that enhanced commercially available polymerases appear to significantly improve the amplification of mtDNA from challenging hair samples.}, journal={FORENSIC SCIENCE INTERNATIONAL-GENETICS}, author={Damaso, Natalie and Ashe, Emily C. and Meiklejohn, Kelly A. and Kavlick, Mark F. and Robertson, James M.}, year={2021}, month={May} }
 @article{meiklejohn_burnham-curtis_straughan_giles_moore_2021, title={Current methods, future directions and considerations of DNA-based taxonomic identification in wildlife forensics}, volume={1}, url={https://doi.org/10.1016/j.fsiae.2021.100030}, DOI={10.1016/j.fsiae.2021.100030}, abstractNote={Wildlife forensic analyses are frequently concerned with taxonomic identification, and very often employ amplification and Sanger sequencing of informative regions of the genome to achieve this. The materials submitted to wildlife forensic laboratories for taxonomic identification span a wide scope, from plant and animal parts in trade to assemblages of incidental biota at crime scenes. As these analyses take place within the context of legal proceedings, the wildlife forensic community is subject to unique requirements and considerations. These requirements and considerations are quite different from those of human forensic DNA, and have driven standardization in this field. While there has been extensive debate over appropriate DNA-based methods for taxonomic identification of a wide variety of biota in research settings, there has been little discussion on the issues associated with this approach in the high scrutiny environment of forensic science. This review outlines: key procedural and biological factors that may impact the accuracy of interpretation and reporting taxonomic identifications; resulting conventions employed by the wildlife forensics community; and implications for the use of emergent DNA sequencing technologies in taxonomic identification of wildlife in casework.}, journal={Forensic Science International: Animals and Environments}, publisher={Elsevier BV}, author={Meiklejohn, Kelly A. and Burnham-Curtis, Mary K. and Straughan, Dyan J. and Giles, Jenny and Moore, M. Katherine}, year={2021}, month={Nov}, pages={100030} }
 @article{cooley_meiklejohn_damaso_robertson_dawson cruz_2021, title={Performance Comparison of Massively Parallel Sequencing (MPS) Instruments Using Single-Nucleotide Polymorphism (SNP) Panels for Ancestry}, volume={26}, ISSN={["2472-6311"]}, DOI={10.1177/2472630320954180}, abstractNote={Thermo Fisher Scientific released the Precision ID Ancestry Panel, a 165-single-nucleotide polymorphism (SNP) panel for ancestry prediction that was initially compatible with the manufacturer’s massively parallel sequencer, the Ion Torrent Personal Genome Machine (PGM). The semiautomated workflow using the panel with the PGM involved several time-consuming manual steps across three instruments, including making templating solutions and loading sequencing chips. In 2014, the manufacturer released the Ion Chef robot, followed by the Ion S5 massively parallel sequencer in late 2015. The robot performs the templating with reagent cartridges and loads the chips, thus creating a fully automated workflow across two instruments. The objective of the work reported here is to compare the performance of two massively parallel sequencing systems and ascertain if the change in the workflow produces different ancestry predictions. For performance comparison of the two systems, forensic-type samples (n = 16) were used to make libraries. Libraries were templated either with the Ion OneTouch 2 system (for the PGM) or on the Ion Chef robot (for the S5). Sequencing results indicated that the ion sphere particle performance metrics were similar for the two systems. The total coverages per SNP and SNP quality were both higher for the S5 system. Ancestry predictions were concordant for the mock forensic-type samples sequenced on both massively parallel sequencing systems. The results indicated that automating the workflow with the Ion Chef system reduced the labor involved and increased the sequencing quality.}, number={1}, journal={SLAS TECHNOLOGY}, author={Cooley, Ashley M. and Meiklejohn, Kelly A. and Damaso, Natalie and Robertson, James M. and Dawson Cruz, Tracey}, year={2021}, month={Feb}, pages={103–112} }
 @article{scheible_straughan_burnham-curtis_meiklejohn_2021, title={Using hybridization capture to obtain mitochondrial genomes from forensically relevant North American canids: Assessing sequence variation for species identification}, volume={1}, url={https://doi.org/10.1016/j.fsiae.2021.100018}, DOI={10.1016/j.fsiae.2021.100018}, abstractNote={The majority of DNA casework processed by forensic laboratories focuses on human samples, but material from canids (dogs, wolves, coyotes) can also be encountered. Undomesticated canids can be the center of forensic investigations in the U.S. since some species are endangered. As many wolf species are similar morphologically, identification in the field by wildlife officers is not always straight-forward, making molecular based-approaches ideal. While some published methods using mitochondrial DNA targets can discriminate among Canis species, they are either not compatible with highly degraded samples or cannot differentiate closely related sub-species. Although some U.S. laboratories regularly perform veterinary/wildlife casework including canid identifications, their validated methods and reference genetic databases are not publicly available. We aimed to assess the utility of alternative regions in the mitochondrial genome for discriminating among canid species, including the complete genome. To achieve this, we utilized a commercial hybridization capture panel composed of biotinylated RNA “baits” designed for the domestic dog to enrich canid mitochondrial genomes for next-generation sequencing. We used this panel to successfully sequence complete mitochondrial genomes for 51 samples, representing four U.S. forensically relevant canids (coyote, wolf, Mexican wolf, dog). While the complete mitochondrial genome permitted discrimination, we also assessed previously published mitochondrial DNA targets (n, 5) for resolution and identified four alternate ∼200 bp fragments from ND1, ND5, COI and CYTB genes that could help resolve canids. The utility of these alternate regions should be assessed in future studies using forensic-type samples representing canids from diverse geographic areas, prior to casework implementation.}, journal={Forensic Science International: Animals and Environments}, publisher={Elsevier BV}, author={Scheible, Melissa K.R. and Straughan, Dyan J. and Burnham-Curtis, Mary K. and Meiklejohn, Kelly A.}, year={2021}, month={Nov}, pages={100018} }
 @article{timpano_scheible_meiklejohn_2020, title={Optimization of the second internal transcribed spacer (ITS2) for characterizing land plants from soil}, volume={15}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0231436}, DOI={10.1371/journal.pone.0231436}, abstractNote={Molecular-based taxonomy, specifically DNA barcoding, has streamlined organism identification. For land plants, the recommended 2-locus barcode of rbcL and matK is not suitable for all groups, thus the second subunit of the nuclear internal transcribed spacer (ITS2) has received attention as a possible alternative. To date, evaluations of ITS2 have mostly been limited in scope to specific plant orders/families and single source material. Prior to using ITS2 to routinely characterize land plants present in environmental samples (i.e., DNA metabarcoding), a wet lab protocol optimized for bulk sample types is needed. To address this gap, in this study we determined the broad recoverability across land plants when using published ITS2 primer pairs, and subsequently optimized the PCR reaction constituents and cycling conditions for the best two performing primer pairs (ITS2F/ITSp4 and ITSp3/ITSu4). Using these conditions, both primer pairs were used to characterize land plants present in 17 diverse soils collected from across the US. The resulting PCR amplicons were prepared into libraries and pooled for sequencing on an Illumina® MiniSeq. Our existing bioinformatics workflow was used to process raw sequencing data and taxonomically assign unique ITS2 plant sequences by comparison to GenBank. Given strict quality criteria were imposed on sequences for inclusion in data analysis, only 43.6% and 7.5% of sequences from ITS2F/ITSp4 and ITSp3/ITSu4 respectively remained for taxonomic comparisons; ~7–11% of sequences originated from fungal co-amplification. The number of orders and families recovered did differ between primer pairs, with ITS2F/ITSp4 consistently outperforming ITSp3/ITSu4 by >15%. Primer pair bias was observed in the recovery of certain taxonomic groups; ITS2F/ITSp4 preferentially recovered flowering plants and grasses, whereas ITSp3/ITSu4 recovered more moss taxa. To maximize data recovery and reduce potential bias, we advocate that studies using ITS2 to characterize land plants from environmental samples such as soil use a multiple primer pair approach.}, number={4}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Timpano, Emma K. and Scheible, Melissa K. R. and Meiklejohn, Kelly A.}, editor={Kalendar, RuslanEditor}, year={2020}, month={Apr} }
 @article{sequence-based autosomal str characterization in four us populations using powerseq™ auto/y system_2020, url={http://dx.doi.org/10.1016/j.fsigen.2020.102311}, DOI={10.1016/j.fsigen.2020.102311}, abstractNote={The forensic science community is poised to utilize modern advances in massively parallel sequencing (MPS) technologies to better characterize biological samples with higher resolution. A critical component towards the advancement of forensic DNA analysis with these technologies is a comprehensive understanding of the diversity and population distribution of sequence-based short tandem repeat (STR) alleles. Here we analyzed 786 samples of individuals from different population groups, including four of the mostly commonly encountered in forensic casework in the USA. DNA samples were amplified with the PowerSeq™ Auto/Y System Prototype Kit (Promega Corp.), and sequencing was performed on an Illumina® MiSeq instrument. Sequence data were analyzed using a bioinformatics processing tool, Altius. For additional data analysis and profile comparison, capillary electrophoresis (CE) size-based STR genotypes were generated for a subset of individuals, and where possible, also with a second commercially available MPS STR assay. Autosomal STR loci were analyzed and frequencies were calculated based on sequence composition. Also, population genetics studies were performed, with Hardy–Weinberg equilibrium, polymorphic information content (PIC), and observed and expected heterozygosity all assessed. Overall, sequence-based allelic variants of the repeat region were observed in 20 out of 22 different STR loci commonly used in forensic DNA genotyping, with the highest number of sequence variation observed at locus D12S391. The highest increase in allelic diversity and in PIC through sequence-based genotyping was observed at loci D3S1358 and D8S1179. Such detailed sequence analysis, as the one performed in the present study, is important to help understand the diversity of sequence-based STR alleles across different populations and to demonstrate how such allelic variation can improve statistics used for forensic casework.}, journal={Forensic Science International: Genetics}, year={2020}, month={Jun} }
 @article{kidd_pakstis_donnelly_bulbul_cherni_gurkan_kang_li_yun_paschou_et al._2020, title={The distinctive geographic patterns of common pigmentation variants at the OCA2 gene}, volume={10}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-020-72262-6}, abstractNote={Abstract Oculocutaneous Albinism type 2 ( OCA2 ) is a gene of great interest because of genetic variation affecting normal pigmentation variation in humans. The diverse geographic patterns for variant frequencies at OCA2 have been evident but have not been systematically investigated, especially outside of Europe. Here we examine population genetic variation in and near the OCA2 gene from a worldwide perspective. The very different patterns of genetic variation found across world regions suggest strong selection effects may have been at work over time. For example, analyses involving the variants that affect pigmentation of the iris argue that the derived allele of the rs1800407 single nucleotide polymorphism, which produces a hypomorphic protein, may have contributed to the previously demonstrated positive selection in Europe for the enhancer variant responsible for light eye color. More study is needed on the relationships of the genetic variation at OCA2 to variation in pigmentation in areas beyond Europe.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Kidd, Kenneth K. and Pakstis, Andrew J. and Donnelly, Michael P. and Bulbul, Ozlem and Cherni, Lotfi and Gurkan, Cemal and Kang, Longli and Li, Hui and Yun, Libing and Paschou, Peristera and et al.}, year={2020}, month={Sep} }
 @article{meiklejohn_damaso_robertson_2019, title={Assessment of BOLD and GenBank - Their accuracy and reliability for the identification of biological materials}, volume={14}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0217084}, DOI={10.1371/journal.pone.0217084}, abstractNote={Taxonomic identification of biological materials can be achieved through DNA barcoding, where an unknown “barcode” sequence is compared to a reference database. In many disciplines, obtaining accurate taxonomic identifications can be imperative (e.g., evolutionary biology, food regulatory compliance, forensics). The Barcode of Life DataSystems (BOLD) and GenBank are the main public repositories of DNA barcode sequences. In this study, an assessment of the accuracy and reliability of sequences in these databases was performed. To achieve this, 1) curated reference materials for plants, macro-fungi and insects were obtained from national collections, 2) relevant barcode sequences (rbcL, matK, trnH-psbA, ITS and COI) from these reference samples were generated and used for searching against both databases, and 3) optimal search parameters were determined that ensure the best match to the known species in either database. While GenBank outperformed BOLD for species-level identification of insect taxa (53% and 35%, respectively), both databases performed comparably for plants and macro-fungi (~81% and ~57%, respectively). Results illustrated that using a multi-locus barcode approach increased identification success. This study outlines the utility of the BLAST search tool in GenBank and the BOLD identification engine for taxonomic identifications and identifies some precautions needed when using public sequence repositories in applied scientific disciplines.}, number={6}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Meiklejohn, Kelly A. and Damaso, Natalie and Robertson, James M.}, editor={Fugmann, Sebastian D.Editor}, year={2019}, month={Jun} }
 @article{boggs_scheible_machado_meiklejohn_2019, title={Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation?}, volume={10}, ISSN={2073-4425}, url={http://dx.doi.org/10.3390/genes10060431}, DOI={10.3390/genes10060431}, abstractNote={In forensic geology casework, sample size typically limits routine characterization of material using bulk approaches. To address this, DNA-based characterization of biological taxa has received attention, as the taxa present can be useful for sample-to-sample comparisons and source attribution. In our initial work, low biodiversity was captured when DNA barcodes were Sanger-sequenced from plant and insect fragments isolated from 10 forensic-type surface soils. Considering some forensic laboratories now have access to massively parallel sequencing platforms, we assessed whether biological taxa present in the same surface soils could be better characterized using DNA metabarcoding. To achieve this, plant and animal barcodes were amplified and sequenced on an Illumina® MiniSeq for three different DNA sample types (n = 50): individual fragments used in our initial study, and 250 and 100 mg of bulk soil (from the 10 sites used in the initial study). A total of 572 unique target barcode sequences passed quality filtering and were used in downstream statistical analyses: 54, 321, and 285 for individual fragments, 100 mg, and 250 mg bulk soil samples, respectively. Plant barcodes permitted some spatial separation of sample sites in non-metric multidimensional scaling plots; better separation was obtained for samples prepared from bulk soil. This study confirmed that bulk soil DNA metabarcoding is a better approach for characterizing biological taxa present in surface soils, which could supplement traditional geologic examinations.}, number={6}, journal={Genes}, publisher={MDPI AG}, author={Boggs, Laura M. and Scheible, Melissa K. R. and Machado, Gustavo and Meiklejohn, Kelly A.}, year={2019}, month={Jun}, pages={431} }
 @article{meiklejohn_jackson_stern_robertson_2018, title={A protocol for obtaining DNA barcodes from plant and insect fragments isolated from forensic-type soils}, volume={132}, ISSN={0937-9827 1437-1596}, url={http://dx.doi.org/10.1007/s00414-018-1772-1}, DOI={10.1007/s00414-018-1772-1}, abstractNote={Soil is often collected from a suspect’s tire, vehicle, or shoes during a criminal investigation and subsequently submitted to a forensic laboratory for analysis. Plant and insect material recovered in such samples is rarely analyzed, as morphological identification is difficult. In this study, DNA barcoding was used for taxonomic identifications by targeting the gene regions known to permit discrimination in plants [maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL)] and insects [cytochrome oxidase subunit I (COI)]. A DNA barcode protocol suitable for processing forensic-type biological fragments was developed and its utility broadly tested with forensic-type fragments (e.g., seeds, leaves, bark, head, legs; n, 213) isolated from soils collected within Virginia, USA (n, 11). Difficulties with PCR inhibitors in plant extracts and obtaining clean Sanger sequence data from insect amplicons were encountered during protocol development; however, the final protocol produced sequences specific to the expected locus and taxa. The overall quantity and quality of DNA extracted from the 213 forensic-type biological fragments was low (< 15 ng/μL). For plant fragments, only the rbcL sequence data was deemed reliable; thus, taxonomic identifications were limited to the family level. The majority of insect sequences matched COI in both GenBank and Barcode of Life DataSystems; however, they were identified as an undescribed environmental contaminant. Although limited taxonomic information was gleaned from the forensic-type fragments processed in this study, the new protocol shows promise for obtaining reliable and specific identifications through DNA barcoding, which could ultimately enhance the information gleaned from soil examinations.}, number={6}, journal={International Journal of Legal Medicine}, publisher={Springer Nature}, author={Meiklejohn, Kelly A. and Jackson, Megan L. and Stern, Libby A. and Robertson, James M.}, year={2018}, month={Feb}, pages={1515–1526} }
 @article{vlachos_meiklejohn_robertson_2018, title={An automated independent workflow for the analysis of massively parallel sequence data from forensic SNP assays}, volume={39}, ISSN={["1522-2683"]}, DOI={10.1002/elps.201800085}, abstractNote={Illumina and Thermo Fisher Scientific have developed assays that permit the sequencing of forensically relevant single nucleotide polymorphisms (SNPs), along with software to determine the associated genotypes. Currently there is no method to either independently confirm the genotypes determined using the manufacturer's software, or to compare genotypes and quality metrics among samples processed using both platforms. This paper outlines an automated workflow developed in CLC Genomics Workbench that permits accurate, fast and independent analysis of SNP sequence data from either platform. To facilitate the straightforward comparison of genotypes generated from both the manufacturer's software and the independent CLC analysis, a Python script was written. Data for a total of 323 forensically relevant ancestry, identity and phenotypic SNPs can be analyzed, and the resulting genotypes, coverage, quality flags and major allele frequencies are easily compared across samples and platforms.}, number={21}, journal={ELECTROPHORESIS}, author={Vlachos, Nicholas T. and Meiklejohn, Kelly A. and Robertson, James M.}, year={2018}, month={Nov}, pages={2752–2756} }
 @article{meiklejohn_robertson_2017, title={Evaluation of the Precision ID Identity Panel for the Ion Torrent™ PGM™ sequencer}, volume={31}, ISSN={1872-4973}, url={http://dx.doi.org/10.1016/j.fsigen.2017.08.009}, DOI={10.1016/j.fsigen.2017.08.009}, abstractNote={In cases where only a partial or incomplete STR profile is obtained from a sample, information contained in single nucleotide polymorphisms (SNPs) can prove informative for human identification. Thermo Fisher Scientific, which developed the high throughput Ion Torrent™ PGM™ sequencer, released the Precision ID Identity Panel, a multiplex SNP panel for human identity. We evaluated the reproducibility and sensitivity of this multiplex, which contains primers for the amplification of 90 autosomal SNPs and 34 Y-clade SNPs. The manufacturer’s protocol was tested using five commercially available pure native DNAs and six forensic type samples at a range of DNA input amounts (0.2–1.0 ng; n, 90). In addition to analyzing the data using the manufacturer’s software, HID SNP Genotyper (v4.3.1), we also used CLC Genomics Workbench (Qiagen). Although library yields and templating of ion sphere particles (ISPs) were low, downstream sequencing was still successful. Across all samples, only 1.5% of all possible quality control (QC) flags were raised by both the plugin QC filter and CLC; 85% of those flags were raised as the SNP had a major allele frequency outside the thresholds specified by the manufacturer. For the remaining SNPs, coverage of >1500 X and >780 X was obtained for autosomal and Y-clade SNPs respectively, and 100% congruence among genotype calls from both analysis programs was observed. Our results demonstrate that it is possible to obtain reliable and reproducible genotypes using the Precision ID Identity Panel, when using low quantities (≥0.2 ng) of either pure native DNA or forensic type DNA samples.}, journal={Forensic Science International: Genetics}, publisher={Elsevier BV}, author={Meiklejohn, Kelly A. and Robertson, James M.}, year={2017}, month={Nov}, pages={48–56} }
 @article{harper_meiklejohn_merritt_walker_fisher_robertson_2017, title={Isolation of Mitochondrial DNA from Single, Short Hairs without Roots Using Pressure Cycling Technology}, volume={23}, ISSN={2472-6303 2472-6311}, url={http://dx.doi.org/10.1177/2472630317732073}, DOI={10.1177/2472630317732073}, abstractNote={Hairs are commonly submitted as evidence to forensic laboratories, but standard nuclear DNA analysis is not always possible. Mitochondria (mt) provide another source of genetic material; however, manual isolation is laborious. In a proof-of-concept study, we assessed pressure cycling technology (PCT; an automated approach that subjects samples to varying cycles of high and low pressure) for extracting mtDNA from single, short hairs without roots. Using three microscopically similar donors, we determined the ideal PCT conditions and compared those yields to those obtained using the traditional manual micro-tissue grinder method. Higher yields were recovered from grinder extracts, but yields from PCT extracts exceeded the requirements for forensic analysis, with the DNA quality confirmed through sequencing. Automated extraction of mtDNA from hairs without roots using PCT could be useful for forensic laboratories processing numerous samples.}, number={1}, journal={SLAS TECHNOLOGY: Translating Life Sciences Innovation}, publisher={SAGE Publications}, author={Harper, Kathryn A. and Meiklejohn, Kelly A. and Merritt, Richard T. and Walker, Jessica and Fisher, Constance L. and Robertson, James M.}, year={2017}, month={Oct}, pages={97–105} }
 @article{meiklejohn_wallman_pape_2017, title={Sarcophaga maxima
 sp. nov. (Diptera: Sarcophagidae: Sarcophaginae), a new Australian flesh fly recognised by morphology and DNA barcoding}, volume={57}, ISSN={2052-174X}, url={http://dx.doi.org/10.1111/aen.12272}, DOI={10.1111/aen.12272}, abstractNote={A new species, Sarcophaga (Sarcorohdendorfia) maxima sp. nov., supported by both morphological and DNA barcoding data, is described from Queensland and New South Wales, Australia. The major morphological features of the new species are listed, and the male terminalia are documented with both photography and scanning electron microscopy. Sarcophaga alcicornis Hardy, 1932 is transferred from subgenus Lioproctia Enderlein to Sarcorohdendorfia Baranov.}, number={1}, journal={Austral Entomology}, publisher={Wiley}, author={Meiklejohn, Kelly A and Wallman, James F and Pape, Thomas}, year={2017}, month={Feb}, pages={17–24} }
 @article{meiklejohn_faircloth_glenn_kimball_braun_2016, title={Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods}, volume={65}, ISSN={1063-5157 1076-836X}, url={http://dx.doi.org/10.1093/sysbio/syw014}, DOI={10.1093/sysbio/syw014}, abstractNote={Rapid evolutionary radiations are expected to require large amounts of sequence data to resolve. To resolve these types of relationships many systematists believe that it will be necessary to collect data by next-generation sequencing (NGS) and use multispecies coalescent ("species tree") methods. Ultraconserved element (UCE) sequence capture is becoming a popular method to leverage the high throughput of NGS to address problems in vertebrate phylogenetics. Here we examine the performance of UCE data for gallopheasants (true pheasants and allies), a clade that underwent a rapid radiation 10-15 Ma. Relationships among gallopheasant genera have been difficult to establish. We used this rapid radiation to assess the performance of species tree methods, using ∼600 kilobases of DNA sequence data from ∼1500 UCEs. We also integrated information from traditional markers (nuclear intron data from 15 loci and three mitochondrial gene regions). Species tree methods exhibited troubling behavior. Two methods [Maximum Pseudolikelihood for Estimating Species Trees (MP-EST) and Accurate Species TRee ALgorithm (ASTRAL)] appeared to perform optimally when the set of input gene trees was limited to the most variable UCEs, though ASTRAL appeared to be more robust than MP-EST to input trees generated using less variable UCEs. In contrast, the rooted triplet consensus method implemented in Triplec performed better when the largest set of input gene trees was used. We also found that all three species tree methods exhibited a surprising degree of dependence on the program used to estimate input gene trees, suggesting that the details of likelihood calculations (e.g., numerical optimization) are important for loci with limited phylogenetic information. As an alternative to summary species tree methods we explored the performance of SuperMatrix Rooted Triple - Maximum Likelihood (SMRT-ML), a concatenation method that is consistent even when gene trees exhibit topological differences due to the multispecies coalescent. We found that SMRT-ML performed well for UCE data. Our results suggest that UCE data have excellent prospects for the resolution of difficult evolutionary radiations, though specific attention may need to be given to the details of the methods used to estimate species trees.}, number={4}, journal={Systematic Biology}, publisher={Oxford University Press (OUP)}, author={Meiklejohn, Kelly A. and Faircloth, Brant C. and Glenn, Travis C. and Kimball, Rebecca T. and Braun, Edward L.}, year={2016}, month={Feb}, pages={612–627} }
 @article{persons_hosner_meiklejohn_braun_kimball_2016, title={Sorting out relationships among the grouse and ptarmigan using intron, mitochondrial, and ultra-conserved element sequences}, volume={98}, ISSN={1055-7903}, url={http://dx.doi.org/10.1016/j.ympev.2016.02.003}, DOI={10.1016/j.ympev.2016.02.003}, abstractNote={The Holarctic phasianid clade of the grouse and ptarmigan has received substantial attention in areas such as evolution of mating systems, display behavior, and population ecology related to their conservation and management as wild game species. There are multiple molecular phylogenetic studies that focus on grouse and ptarmigan. In spite of this, there is little consensus regarding historical relationships, particularly among genera, which has led to unstable and partial taxonomic revisions. We estimated the phylogeny of all currently recognized species using a combination of novel data from seven nuclear loci (largely intron sequences) and published data from one additional autosomal locus, two W-linked loci, and four mitochondrial regions. To explore relationships among genera and assess paraphyly of one genus more rigorously, we then added over 3000 ultra-conserved element (UCE) loci (over 1.7million bp) gathered using Illumina sequencing. The UCE topology agreed with that of the combined nuclear intron and previously published sequence data with 100% bootstrap support for all relationships. These data strongly support previous studies separating Bonasa from Tetrastes and Dendragapus from Falcipennis. However, the placement of Lagopus differed from previous studies, and we found no support for Falcipennis monophyly. Biogeographic analysis suggests that the ancestors of grouse and ptarmigan were distributed in the New World and subsequently underwent at least four dispersal events between the Old and New Worlds. Divergence time estimates from maternally-inherited and autosomal markers show stark differences across this clade, with divergence time estimates from maternally-inherited markers being nearly half that of the autosomal markers at some nodes, and nearly twice that at other nodes.}, journal={Molecular Phylogenetics and Evolution}, publisher={Elsevier BV}, author={Persons, Nicholas W. and Hosner, Peter A. and Meiklejohn, Kelly A. and Braun, Edward L. and Kimball, Rebecca T.}, year={2016}, month={May}, pages={123–132} }
 @article{pakstis_haigh_cherni_elgaaied_barton_evsanaa_togtokh_brissenden_roscoe_bulbul_et al._2015, title={52 additional reference population samples for the 55 AISNP panel}, volume={19}, ISSN={1872-4973}, url={http://dx.doi.org/10.1016/j.fsigen.2015.08.003}, DOI={10.1016/j.fsigen.2015.08.003}, abstractNote={Ancestry inference for a person using a panel of SNPs depends on the variation of frequencies of those SNPs around the world and the amount of reference data available for calculation/comparison. The Kidd Lab panel of 55 AISNPs has been incorporated in commercial kits by both Life Technologies and Illumina for massively parallel sequencing. Therefore, a larger set of reference populations will be useful for researchers using those kits. We have added reference population allele frequencies for 52 population samples to the 73 previously entered so that there are now allele frequencies publicly available in ALFRED and FROG-kb for a total of 125 population samples.}, journal={Forensic Science International: Genetics}, publisher={Elsevier BV}, author={Pakstis, Andrew J. and Haigh, Eva and Cherni, Lotfi and ElGaaied, Amel Ben Ammar and Barton, Alison and Evsanaa, Baigalmaa and Togtokh, Ariunaa and Brissenden, Jane and Roscoe, Janet and Bulbul, Ozlem and et al.}, year={2015}, month={Nov}, pages={269–271} }
 @article{dowton_meiklejohn_cameron_wallman_2014, title={A Preliminary Framework for DNA Barcoding, Incorporating the Multispecies Coalescent}, volume={63}, ISSN={1076-836X 1063-5157}, url={http://dx.doi.org/10.1093/sysbio/syu028}, DOI={10.1093/sysbio/syu028}, abstractNote={The capacity to identify an unknown organism using the DNA sequence from a single gene has many applications. These include the development of biodiversity inventories (Janzen et al. 2005), forensics (Meiklejohn et al. 2011), biosecurity (Armstrong and Ball 2005), and the identification of cryptic species (Smith et al. 2006). The popularity and widespread use (Teletchea 2010) of the DNA barcoding approach (Hebert et al. 2003), despite broad misgivings (e.g., Smith 2005; Will et al. 2005; Rubinoff et al. 2006), attest to this. However, one major shortcoming to the standard barcoding approach is that it assumes that gene trees and species trees are synonymous, an assumption that is known not to hold in many cases (Pamilo and Nei 1988; Funk and Omland 2003). Biological processes that violate this assumption include incomplete lineage sorting and interspecific hybridization (Funk and Omland 2003). Indeed, simulation studies indicate that the concatenation approach (in which these two processes are ignored) can lead to statistically inconsistent estimation of the species tree (Kubatko and Degnan 2007)...}, number={4}, journal={Systematic Biology}, publisher={Oxford University Press (OUP)}, author={Dowton, Mark and Meiklejohn, Kelly and Cameron, Stephen L. and Wallman, James}, year={2014}, month={Mar}, pages={639–644} }
 @article{robertson_dineen_scott_lucyshyn_saeed_murphy_schweighardt_meiklejohn_2014, title={Assessing PreCR™ repair enzymes for restoration of STR profiles from artificially degraded DNA for human identification}, volume={12}, ISSN={1872-4973}, url={http://dx.doi.org/10.1016/j.fsigen.2014.05.011}, DOI={10.1016/j.fsigen.2014.05.011}, abstractNote={Forensic scientists have used several approaches to obtain short tandem repeat (STR) profiles from compromised DNA samples, including supplementing the polymerase chain reaction (PCR) with enhancers and using procedures yielding reduced-length amplicons. For degraded DNA, the peak intensities of the alleles separated by electrophoresis generally decrease as the length of the allele increases. When the intensities of the alleles decrease below an established threshold, they are described as drop-outs, thus contributing to a partial STR profile. This work assesses the use of repair enzymes to improve the STR profiles from artificially degraded DNA. The commercial PreCR™ repair kit of DNA repair enzymes was tested on both purified DNA and native DNA in body fluids exposed to oxidizing agents, hydrolytic conditions, ultraviolet (UV) and ionizing radiation, and desiccation. The strategy was to restrict the level of DNA damage to that which yields partial STR profiles in order to test for allele restoration as opposed to simple allele enhancement. Two protocols were investigated for allele restoration: a sequential protocol using the manufacturer's repair procedure and a modified protocol reportedly designed for optimal STR analysis of forensic samples. Allele restoration was obtained with both protocols, but the peak height appeared to be higher for the modified protocol (determined by Mann–Kendall Trend Test). The success of the approach using the PreCR™ repair enzymes was sporadic; it led to allele restoration as well as allele drop-out. Additionally, allele restoration with the PreCR™ enzymes was compared with restoration by alternative, but commonly implemented approaches using Restorase™, PCRBoost™, bovine serum albumin (BSA) and the Minifiler™ STR system. The alternative methods were also successful in improving the STR profile, but their success also depended on the quality of the template encountered. Our results indicate the PreCR™ repair kit may be useful for restoring STR profiles from damaged DNA, but further work is required to develop a generalized approach.}, journal={Forensic Science International: Genetics}, publisher={Elsevier BV}, author={Robertson, James M. and Dineen, Shauna M. and Scott, Kristina A. and Lucyshyn, Jonathan and Saeed, Maria and Murphy, Devonie L. and Schweighardt, Andrew J. and Meiklejohn, Kelly A.}, year={2014}, month={Sep}, pages={168–180} }
 @article{meiklejohn_danielson_faircloth_glenn_braun_kimball_2014, title={Incongruence among different mitochondrial regions: A case study using complete mitogenomes}, volume={78}, ISSN={1055-7903}, url={http://dx.doi.org/10.1016/j.ympev.2014.06.003}, DOI={10.1016/j.ympev.2014.06.003}, abstractNote={Mitochondrial sequences have long been used to examine vertebrate phylogenetic relationships. The extensive use of mitochondrial data reflects the ease of obtaining mitochondrial sequences and its relatively rapid coalescence time. Mitochondrial genomes typically do not undergo recombination, so the entire mitogenome should have the same underlying gene tree. Thus, given appropriate analyses, conflict among estimates of phylogeny from different mitochondrial regions should not exist. However, estimates of phylogeny based upon different mitochondrial regions can exhibit incongruence. Conflict in phylogenetic signal among mitochondrial regions has been observed in galliform birds for the position of the Odontophoridae (New World quail). To explore this, we expanded sampling to 47 galliform mitogenomes, adding six new mitogenomes, which included representatives of two previously unsampled families. Analyses of complete mitogenomes recovered a well-supported topology that was congruent with expectations from multi-locus studies. However, when analyzing individual regions, we found conflicting positions for the Odontophoridae and several other relationships at multiple taxonomic levels. We tested multiple analytical strategies to reduce incongruence among regions, including partitioning by codon position, using mixture and codon-based models, RY coding, and excluding potentially misleading sites. No approach consistently reduced the conflict among mitochondrial regions at any taxonomic level. The biological attributes of both strongly misleading and non-misleading sites were essentially identical. Increasing taxa actually appeared to increase conflicting signal, even when taxa were selected to break up long branches. Collectively, our results indicate that analyzing mitochondrial data remains difficult, although analyzing complete mitogenomes resulted in a good estimate of the mitochondrial gene tree.}, journal={Molecular Phylogenetics and Evolution}, publisher={Elsevier BV}, author={Meiklejohn, Kelly A. and Danielson, Melany J. and Faircloth, Brant C. and Glenn, Travis C. and Braun, Edward L. and Kimball, Rebecca T.}, year={2014}, month={Sep}, pages={314–323} }
 @article{sun_meiklejohn_faircloth_glenn_braun_kimball_2014, title={The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach}, volume={281}, ISSN={0962-8452 1471-2954}, url={http://dx.doi.org/10.1098/rspb.2014.0823}, DOI={10.1098/rspb.2014.0823}, abstractNote={The most striking feature of peafowl (Pavo) is the males' elaborate train, which exhibits ocelli (ornamental eyespots) that are under sexual selection. Two additional genera within the Phasianidae (Polyplectron and Argusianus) exhibit ocelli, but the appearance and location of these ornamental eyespots exhibit substantial variation among these genera, raising the question of whether ocelli are homologous. Within Polyplectron, ocelli are ancestral, suggesting ocelli may have evolved even earlier, prior to the divergence among genera. However, it remains unclear whether Pavo, Polyplectron and Argusianus form a monophyletic clade in which ocelli evolved once. We estimated the phylogeny of the ocellated species using sequences from 1966 ultraconserved elements (UCEs) and three mitochondrial regions. The three ocellated genera did form a strongly supported clade, but each ocellated genus was sister to at least one genus without ocelli. Indeed, Polyplectron and Galloperdix, a genus not previously suggested to be related to any ocellated taxon, were sister genera. The close relationship between taxa with and without ocelli suggests multiple gains or losses. Independent gains, possibly reflecting a pre-existing bias for eye-like structures among females and/or the existence of a simple mutational pathway for the origin of ocelli, appears to be the most likely explanation.}, number={1790}, journal={Proceedings of the Royal Society B: Biological Sciences}, publisher={The Royal Society}, author={Sun, K. and Meiklejohn, K. A. and Faircloth, B. C. and Glenn, T. C. and Braun, E. L. and Kimball, R. T.}, year={2014}, month={Jul}, pages={20140823–20140823} }
 @article{meiklejohn_dowton_pape_wallman_2013, title={A key to the Australian Sarcophagidae (Diptera) with special emphasis on <i>Sarcophaga</i> (<i>sensu lato</i>)}, volume={3680}, ISSN={1175-5334 1175-5326}, url={http://dx.doi.org/10.11646/zootaxa.3680.1.11}, DOI={10.11646/zootaxa.3680.1.11}, abstractNote={The Australian Sarcophagidae (Diptera) currently comprise 84 species, classified into ten genera from the subfamilies Miltogramminae and Sarcophaginae. A key is provided to the Australian sarcophagids, allowing for separation into sub-families and genera, along with the identification of all species of Sarcophaga ( sensu lato ). A comprehensive database of illustrations and photographs of male terminalia, as well as updated biological information, is given for each species of Sarcophaga s.l.}, number={1}, journal={Zootaxa}, publisher={Magnolia Press}, author={Meiklejohn, Kelly A and Dowton, Mark and Pape, Thomas and Wallman, James F}, year={2013}, month={Jun}, pages={148} }
 @article{meiklejohn_wallman_dowton_2013, title={DNA Barcoding Identifies all Immature Life Stages of a Forensically Important Flesh Fly (Diptera: Sarcophagidae)}, volume={58}, ISSN={0022-1198}, url={http://dx.doi.org/10.1111/j.1556-4029.2012.02220.x}, DOI={10.1111/j.1556-4029.2012.02220.x}, abstractNote={Carrion‐breeding insects, such as flesh flies (Diptera: Sarcophagidae), can be used as evidence in forensic investigations. Despite their considerable forensic potential, their use has been limited because morphological species identification, at any life stage, is very challenging. This study investigated whether DNA could be extracted and cytochrome oxidase subunit I (COI) barcode sequences obtained for molecular identification of each immature life stage of the forensically important Australian flesh fly, Sarcophaga (Sarcorohdendorfia) impatiens (Walker). Genomic DNA extracts were prepared from all larval instars and puparia. Amplification of the barcoding region was successful from all extracts, but puparia amplicons were weak. All sequences were identified as S. impatiens with 99.95% confidence using the Barcoding of Life Database (BOLD). Importantly, crop removal was necessary to eliminate PCR inhibition for specimens from late second and early third instars. Similar results are expected for immatures of other carrion‐breeding species, enhancing the use of evidence from immature flies in forensic investigations.}, number={1}, journal={Journal of Forensic Sciences}, publisher={Wiley}, author={Meiklejohn, Kelly A. and Wallman, James F. and Dowton, Mark}, year={2013}, month={Jan}, pages={184–187} }
 @article{lu_lin_luo_blondel_meiklejohn_sun_feng_2013, title={Phylogeography of the Rickett’s big-footed bat, Myotis pilosus (Chiroptera: Vespertilionidae): a novel pattern of genetic structure of bats in China}, volume={13}, ISSN={1471-2148}, url={http://dx.doi.org/10.1186/1471-2148-13-241}, DOI={10.1186/1471-2148-13-241}, abstractNote={China is characterized by complex topographic structure and dramatic palaeoclimatic changes, making species biogeography studies particularly interesting. Previous researchers have also demonstrated multiple species experienced complex population histories, meanwhile multiple shelters existed in Chinese mainland. Despite this, species phylogeography is still largely unexplored. In the present study, we used a combination of microsatellites and mitochondrial DNA (mtDNA) to investigate the phylogeography of the east Asian fish-eating bat (Myotis pilosus). Phylogenetic analyses showed that M. pilosus comprised three main lineages: A, B and C, which corresponded to distinct geographic populations of the Yangtze Plain (YTP), Sichuan Basin (SCB) and North and South of China (NSC), respectively. The most recent common ancestor of M. pilosus was dated as 0.25 million years before present (BP). Population expansion events were inferred for populations of Clade C, North China Plain region, Clade B and YunGui Plateau region at 38,700, 15,900, 4,520 and 4,520 years BP, respectively. Conflicting results were obtained from mtDNA and microsatellite analyses; strong population genetic structure was obtained from mtDNA data but not microsatellite data. The microsatellite data indicated that genetic subdivision fits an isolation-by-distance (IBD) model, but the mtDNA data failed to support this model. Our results suggested that Pleistocene climatic oscillations might have had a profound influence on the demographic history of M. pilosus. Spatial genetic structures of maternal lineages that are different from those observed in other sympatric bats species may be as a result of interactions among special population history and local environmental factors. There are at least three possible refugia for M. pilosus during glacial episodes. Apparently contradictory genetic structure patterns of mtDNA and microsatellite could be explained by male-mediated gene flow among populations. This study also provides insights on the necessity of conservation of M. pilosus populations to conserve this genetic biodiversity, especially in the areas of YTP, SCB and NSC regions.}, number={1}, journal={BMC Evolutionary Biology}, publisher={Springer Nature}, author={Lu, Guanjun and Lin, Aiqing and Luo, Jinhong and Blondel, Dimitri V and Meiklejohn, Kelly A and Sun, Keping and Feng, Jiang}, year={2013}, pages={241} }
 @article{meiklejohn_wallman_pape_2013, title={Updates on the taxonomy and nomenclature of Australian <i>Sarcophaga</i> (<i>sensu lato</i>) (Diptera: Sarcophagidae), with descriptions of two new species}, volume={3680}, ISSN={1175-5334 1175-5326}, url={http://dx.doi.org/10.11646/zootaxa.3680.1.10}, DOI={10.11646/zootaxa.3680.1.10}, abstractNote={Two new species, Sarcophaga ( Sarcosolomonia ) collessi sp.nov. and Sarcophaga ( Sarcorohdendorfia ) clavus sp.nov. , both collected in Queensland, Australia, are described, and the following four new synonymies are proposed: Sarcophaga horti Blackith and Blackith, 1988 syn.nov. of Sarcophaga bancroftorum Johnston and Tiegs, 1921; Sarcophaga fergusoni-na Hardy, 1940 syn.nov. of Sarcophaga assimilis Macquart, 1851; Sarcophaga brevicornis Ho, 1934 syn.nov. of Sar-cophaga kohla Johnston and Hardy, 1923a; and Sarcophaga triplex Hardy, 1943 syn.nov. of Sarcophaga furcata Hardy, 1932.}, number={1}, journal={Zootaxa}, publisher={Magnolia Press}, author={Meiklejohn, Kelly A and Wallman, James F and Pape, Thomas}, year={2013}, month={Jun}, pages={139} }
 @article{meiklejohn_wallman_pape_cameron_dowton_2013, title={Utility of COI, CAD and morphological data for resolving relationships within the genus Sarcophaga (sensu lato) (Diptera: Sarcophagidae): A preliminary study}, volume={69}, ISSN={1055-7903}, url={http://dx.doi.org/10.1016/j.ympev.2013.04.034}, DOI={10.1016/j.ympev.2013.04.034}, abstractNote={Currently there are ≈ 3000 known species of Sarcophagidae (Diptera), which are classified into 173 genera in three subfamilies. Almost 25% of sarcophagids belong to the genus Sarcophaga (sensu lato) however little is known about the validity of, and relationships between the ≈ 150 (or more) subgenera of Sarcophaga s.l. In this preliminary study, we evaluated the usefulness of three sources of data for resolving relationships between 35 species from 14 Sarcophaga s.l. subgenera: the mitochondrial COI barcode region, ≈ 800 bp of the nuclear gene CAD, and 110 morphological characters. Bayesian, maximum likelihood (ML) and maximum parsimony (MP) analyses were performed on the combined dataset. Much of the tree was only supported by the Bayesian and ML analyses, with the MP tree poorly resolved. The genus Sarcophaga s.l. was resolved as monophyletic in both the Bayesian and ML analyses and strong support was obtained at the species-level. Notably, the only subgenus consistently resolved as monophyletic was Liopygia. The monophyly of and relationships between the remaining Sarcophaga s.l. subgenera sampled remain questionable. We suggest that future phylogenetic studies on the genus Sarcophaga s.l. use combined datasets for analyses. We also advocate the use of additional data and a range of inference strategies to assist with resolving relationships within Sarcophaga s.l.}, number={1}, journal={Molecular Phylogenetics and Evolution}, publisher={Elsevier BV}, author={Meiklejohn, Kelly A. and Wallman, James F. and Pape, Thomas and Cameron, Stephen L. and Dowton, Mark}, year={2013}, month={Oct}, pages={133–141} }
 @article{meiklejohn_wallman_cameron_dowton_2012, title={Comprehensive evaluation of DNA barcoding for the molecular species identification of forensically important Australian Sarcophagidae (Diptera)}, volume={26}, ISSN={1445-5226}, url={http://dx.doi.org/10.1071/is12008}, DOI={10.1071/is12008}, abstractNote={Abstract. Carrion-breeding Sarcophagidae (Diptera) can be used to estimate the post-mortem interval in forensic cases. Difficulties with accurate morphological identifications at any life stage and a lack of documented thermobiological profiles have limited their current usefulness. The molecular-based approach of DNA barcoding, which utilises a 648-bp fragment of the mitochondrial cytochrome oxidase subunit I gene, was evaluated in a pilot study for discrimination between 16 Australian sarcophagids. The current study comprehensively evaluated barcoding for a larger taxon set of 588 Australian sarcophagids. In total, 39 of the 84 known Australian species were represented by 580 specimens, which includes 92% of potentially forensically important species. A further eight specimens could not be identified, but were included nonetheless as six unidentifiable taxa. A neighbour-joining tree was generated and nucleotide sequence divergences were calculated. All species except Sarcophaga (Fergusonimyia) bancroftorum, known for high morphological variability, were resolved as monophyletic (99.2% of cases), with bootstrap support of 100. Excluding S. bancroftorum, the mean intraspecific and interspecific variation ranged from 1.12% and 2.81–11.23%, respectively, allowing for species discrimination. DNA barcoding was therefore validated as a suitable method for molecular identification of Australian Sarcophagidae, which will aid in the implementation of this fauna in forensic entomology.}, number={6}, journal={Invertebrate Systematics}, publisher={CSIRO Publishing}, author={Meiklejohn, Kelly A. and Wallman, James F. and Cameron, Stephen L. and Dowton, Mark}, year={2012}, pages={515} }
 @article{meiklejohn_dowton_wallman_2012, title={Notes on the Distribution of 31 Species of Sarcophagidae (Diptera) in Australia, Including new Records in Australia for Eight Species}, volume={136}, ISSN={0372-1426 2204-0293}, url={http://dx.doi.org/10.1080/03721426.2012.10887163}, DOI={10.1080/03721426.2012.10887163}, abstractNote={Abstract The Australian sarcophagidae (Diptera) are a neglected fauna, with no extensive work undertaken on this group since Lopes in the 1950s. Using locality information obtained from broad Australian taxon sampling and pinned museum specimens, we present new distributional information for 31 species known from Australia. In addition, we document the first Australian records of eight species: Amobia pelopei (rondani, 1859), Metopia sauteri (Townsend, 1933), Oxysarcodexia varia (Walker, 1836), Sarcophaga (Harpagophalla) kempi senior-White, 1924, Sarcophaga (Lioproctia) multicolor Johnston & Tiegs, 1922, Sarcophaga (Sarcosolomonia) crinita Parker, 1917, Sarcophaga (Sarcosolomonia) sumunensis (Lopes, 1967) and Sarcophaga simplex (Lopes, 1967; not assigned to a subgenus, Pape, 1996).}, number={1}, journal={Transactions of the Royal Society of South Australia}, publisher={Informa UK Limited}, author={MeikleJohn, Kelly A. and Dowton, Mark and Wallman, James F.}, year={2012}, month={Jan}, pages={56–64} }
 @article{meiklejohn_wallman_dowton_2009, title={DNA-based identification of forensically important Australian Sarcophagidae (Diptera)}, volume={125}, ISSN={0937-9827 1437-1596}, url={http://dx.doi.org/10.1007/s00414-009-0395-y}, DOI={10.1007/s00414-009-0395-y}, abstractNote={The utility of the forensically important Sarcophagidae (Diptera) for time since death estimates has been severely limited, as morphological identification is difficult and thermobiological histories are inadequately documented. A molecular identification method involving the sequencing of a 658-bp 'barcode' fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene from 85 specimens, representing 16 Australian species from varying populations, was evaluated. Nucleotide sequence divergences were calculated using the Kimura-two-parameter distance model and a neighbour-joining phylogenetic tree generated. All species were resolved as reciprocally monophyletic, except Sarcophaga dux. Intraspecific and interspecific variation ranged from 0.000% to 1.499% (SE = 0.044%) and 6.658% to 8.983% (SE = 0.653%), respectively. The COI 'barcode' sequence was found to be suitable for the molecular identification of the studied Australian Sarcophagidae: 96.5% of the examined specimens were assigned to the correct species. Given that the sarcophagid fauna is poorly described, it is feasible that the few incorrectly assigned specimens represent cryptic species. The results of this research will be instrumental for implementation of the Australian Sarcophagidae in forensic entomology.}, number={1}, journal={International Journal of Legal Medicine}, publisher={Springer Science and Business Media LLC}, author={Meiklejohn, Kelly A. and Wallman, James F. and Dowton, Mark}, year={2009}, month={Dec}, pages={27–32} }