Rapid progression of human socio-economic activities has altered the structure and function of na... more Rapid progression of human socio-economic activities has altered the structure and function of natural landscapes. Species that rely on multiple, complementary habitat types (i.e., landscape complementation) to complete their life cycle may be especially at risk. However, such landscape complementation has received little attention in the context of landscape connectivity modeling. A previous study on flower longhorn beetles (Cerambycidae: Lepturinae) integrated landscape complementation into a continuous habitat suitability ‘surface’, which was then used to quantify landscape connectivity between pairs of sampling sites using gradient-surface metrics. This connectivity model was validated with molecular genetic data collected for the banded longhorn beetle (Typocerus v. velutinus) in Indiana, United States. However, this approach has not been compared to alternative models in a landscape genetics context. Here, we used a discrete land use/land cover map to calculate landscape metrics related to landscape complementation based on a patch mosaic model (PMM) as an alternative to the previously published, continuous habitat suitability model (HSM). We evaluated the HSM surface with gradient surface metrics (GSM) and with two resistance-based models (RBM) based on least cost path (LCP) and commute distance (CD), in addition to an isolation-by-distance (IBD) model based on Euclidean distance. We compared the ability of these competing models of connectivity to explain pairwise genetic distances (RST) previously calculated from ten microsatellite genotypes of 454 beetles collected from 17 sites across Indiana, United States. Model selection with maximum likelihood population effects (MLPE) models found that GSM were most effective at explaining pairwise genetic distances as a proxy for gene flow across the landscape, followed by the landscape metrics calculated from the PMM, whereas the LCP model performed worse than both the CD and the isolation by distance model. We argue that the analysis of a continuous HSM with GSM might perform better because of their combined ability to effectively represent and quantify the continuous degree of landscape complementation (i.e., availability of complementary habitats in vicinity) found at and in-between sites, on which these beetles depend. Our findings may inform future studies that seek to model habitat connectivity in complex heterogeneous landscapes as natural habitats continue to become more fragmented in the Anthropocene.
Illegal hunting is a major threat to the elephants of Africa, with more elephants killed by poach... more Illegal hunting is a major threat to the elephants of Africa, with more elephants killed by poachers than die from natural causes. DNA from tusks has been used to infer the source populations for confiscated ivory, relying on nuclear genetic markers. However, mitochondrial DNA (mtDNA) sequences can also provide information on the geographic origins of elephants due to female elephant philopatry. Here, we introduce the Loxodonta Localizer (LL; www.loxodontalocalizer.org), an interactive software tool that uses a database of mtDNA sequences compiled from previously published studies to provide information on the potential provenance of confiscated ivory. A 316 bp control region sequence, which can be readily generated from DNA extracted from ivory, is used as a query. The software generates a listing of haplotypes reported among 1917 African elephants in 24 range countries, sorted in order of similarity to the query sequence. The African locations from which haplotype sequences have b...
Sex identification of ancient animal biological remains can benefit our understanding of historic... more Sex identification of ancient animal biological remains can benefit our understanding of historical population structure, demography and social behavior. Traditional methods for sex identification (e.g. osteological and morphometric comparisons) may be ineffective when animal remains are not well preserved, when sex distinguishing characteristics have not yet developed, or where organisms do not exhibit sex-associated phenotypic dimorphisms. Here we adapt a method developed for human sex determination so that it can be used to identify the sex of ancient and modern animal taxa. The method identifies sex by calculating the ratio of DNA reads aligning to the X chromosome to DNA reads aligning to autosomes (termed the Rx ratio). We tested the accuracy of this method using low coverage genomes from 15 modern elephants (Loxodonta africana) for which sex was known. We then applied this method to ancient elephant ivory samples for which sex was unknown, and describe how this method can be ...
Sex identification of ancient animal biological remains can benefit our understanding of historic... more Sex identification of ancient animal biological remains can benefit our understanding of historical population structure, demography and social behavior. Traditional methods for sex identification (e.g. osteological and morphometric comparisons) may be ineffective when animal remains are not well preserved, when sex distinguishing characteristics have not yet developed, or where organisms do not exhibit sex-associated phenotypic dimorphisms. Here we adapt a method developed for human sex determination so that it can be used to identify the sex of ancient and modern animal taxa. The method identifies sex by calculating the ratio of DNA reads aligning to the X chromosome to DNA reads aligning to autosomes (termed the Rx ratio). We tested the accuracy of this method using low coverage genomes from 15 modern elephants (Loxodonta africana) for which sex was known. We then applied this method to ancient elephant ivory samples for which sex was unknown, and describe how this method can be ...
The oldest known shipwreck in southern Africa was found in Namibia in 2008.1, 2, 3, 4 Forty tons ... more The oldest known shipwreck in southern Africa was found in Namibia in 2008.1, 2, 3, 4 Forty tons of cargo, including gold and silver coins, helped identify the ship as the Bom Jesus, a Portuguese nau (trading vessel) lost in 1533 while headed to India.4, 5, 6 The cargo included >100 elephant tusks,7 which we examined using paleogenomic and stable isotope analyses. Nuclear DNA identified the ivory source as African forest (Loxodonta cyclotis) rather than savanna (Loxodonta africana) elephants. Mitochondrial sequences traced them to West and not Central Africa and from ≥17 herds with distinct haplotypes. Four of the haplotypes are known from modern populations; others were potentially lost to subsequent hunting of elephants for ivory. Stable isotope analyses (δ13C and δ15N) indicated that the elephants were not from deep rainforests but from savanna and mixed habitats. Such habitats surround the Guinean forest block of West Africa8 and accord with the locations of major historic Portuguese trading ports.9,10 West African forest elephants currently range into savanna habitats;11, 12, 13 our findings suggest that this was not consequent to regional decimation of savanna elephants for their ivory in the 19th and 20th centuries. During the time of the Bom Jesus, ivory was a central driver in the formation of maritime trading systems connecting Europe, Africa, and Asia. Our integration of paleogenomic, archeological, and historical methods to analyze the Bom Jesus ivory provides a framework for examining vast collections of archaeological ivories around the world, in shipwrecks and other contexts.
Sex estimation of skeletons is fundamental to many archaeological studies. currently, three appro... more Sex estimation of skeletons is fundamental to many archaeological studies. currently, three approaches are available to estimate sex-osteology, genomics, or proteomics, but little is known about the relative reliability of these methods in applied settings. We present matching osteological, shotgun-genomic, and proteomic data to estimate the sex of 55 individuals, each with an independent radiocarbon date between 2,440 and 100 cal BP, from two ancestral Ohlone sites in Central California. Sex estimation was possible in 100% of this burial sample using proteomics, in 91% using genomics, and in 51% using osteology. Agreement between the methods was high, however conflicts did occur. Genomic sex estimates were 100% consistent with proteomic and osteological estimates when DNA reads were above 100,000 total sequences. However, more than half the samples had DNA read numbers below this threshold, producing high rates of conflict with osteological and proteomic data where nine out of twenty conditional DNA sex estimates conflicted with proteomics. While the DNA signal decreased by an order of magnitude in the older burial samples, there was no decrease in proteomic signal. We conclude that proteomics provides an important complement to osteological and shotgun-genomic sex estimation. Biological sex plays an important role in the human experience, correlating to lifespan, reproduction, and a wide range of other biological factors 1-5. Sex and gender are also fundamental in structuring an array of cultural behaviors, including residence patterns, kinship, economic roles, and identity construction and expression 6-9. How sex interacts with gender and these particular issues is not static and can vary in detail across societies and over time 10-12. It is not surprising that sex is one of the most basic and important measures in bioarchaeological and forensic analyses. Typically, osteological features are used to estimate sex of skeletal remains, and the most widely used marker is the morphology of the os coxae 13-16. However, appropriate markers are not always sufficiently expressed or preserved to estimate sex using morphological criteria 17. A lack of sexually-dimorphic markers is especially acute for skeletons of infants and children who have not undergone puberty. Mortuary practices, such as cremation or secondary burial in charnel houses, can also can impose limitations on the utility of osteological sex estimates 18. The advent of DNA sequencing made it possible to use skeletal remains to estimate the sex of very young individuals ; it also expanded sex estimations for fragmentary, pathological, and degraded skeletal materials 19-21. More recently, development of massively parallel DNA sequencing greatly improved genome coverage in archaeological samples 22-25. In addition to providing detailed genetic information, this allows biological sex to be estimated from shotgun sequencing data 25-27. These approaches were an improvement over earlier PCR-based marker open
Rapid progression of human socio-economic activities has altered the structure and function of na... more Rapid progression of human socio-economic activities has altered the structure and function of natural landscapes. Species that rely on multiple, complementary habitat types (i.e., landscape complementation) to complete their life cycle may be especially at risk. However, such landscape complementation has received little attention in the context of landscape connectivity modeling. A previous study on flower longhorn beetles (Cerambycidae: Lepturinae) integrated landscape complementation into a continuous habitat suitability ‘surface’, which was then used to quantify landscape connectivity between pairs of sampling sites using gradient-surface metrics. This connectivity model was validated with molecular genetic data collected for the banded longhorn beetle (Typocerus v. velutinus) in Indiana, United States. However, this approach has not been compared to alternative models in a landscape genetics context. Here, we used a discrete land use/land cover map to calculate landscape metrics related to landscape complementation based on a patch mosaic model (PMM) as an alternative to the previously published, continuous habitat suitability model (HSM). We evaluated the HSM surface with gradient surface metrics (GSM) and with two resistance-based models (RBM) based on least cost path (LCP) and commute distance (CD), in addition to an isolation-by-distance (IBD) model based on Euclidean distance. We compared the ability of these competing models of connectivity to explain pairwise genetic distances (RST) previously calculated from ten microsatellite genotypes of 454 beetles collected from 17 sites across Indiana, United States. Model selection with maximum likelihood population effects (MLPE) models found that GSM were most effective at explaining pairwise genetic distances as a proxy for gene flow across the landscape, followed by the landscape metrics calculated from the PMM, whereas the LCP model performed worse than both the CD and the isolation by distance model. We argue that the analysis of a continuous HSM with GSM might perform better because of their combined ability to effectively represent and quantify the continuous degree of landscape complementation (i.e., availability of complementary habitats in vicinity) found at and in-between sites, on which these beetles depend. Our findings may inform future studies that seek to model habitat connectivity in complex heterogeneous landscapes as natural habitats continue to become more fragmented in the Anthropocene.
Illegal hunting is a major threat to the elephants of Africa, with more elephants killed by poach... more Illegal hunting is a major threat to the elephants of Africa, with more elephants killed by poachers than die from natural causes. DNA from tusks has been used to infer the source populations for confiscated ivory, relying on nuclear genetic markers. However, mitochondrial DNA (mtDNA) sequences can also provide information on the geographic origins of elephants due to female elephant philopatry. Here, we introduce the Loxodonta Localizer (LL; www.loxodontalocalizer.org), an interactive software tool that uses a database of mtDNA sequences compiled from previously published studies to provide information on the potential provenance of confiscated ivory. A 316 bp control region sequence, which can be readily generated from DNA extracted from ivory, is used as a query. The software generates a listing of haplotypes reported among 1917 African elephants in 24 range countries, sorted in order of similarity to the query sequence. The African locations from which haplotype sequences have b...
Sex identification of ancient animal biological remains can benefit our understanding of historic... more Sex identification of ancient animal biological remains can benefit our understanding of historical population structure, demography and social behavior. Traditional methods for sex identification (e.g. osteological and morphometric comparisons) may be ineffective when animal remains are not well preserved, when sex distinguishing characteristics have not yet developed, or where organisms do not exhibit sex-associated phenotypic dimorphisms. Here we adapt a method developed for human sex determination so that it can be used to identify the sex of ancient and modern animal taxa. The method identifies sex by calculating the ratio of DNA reads aligning to the X chromosome to DNA reads aligning to autosomes (termed the Rx ratio). We tested the accuracy of this method using low coverage genomes from 15 modern elephants (Loxodonta africana) for which sex was known. We then applied this method to ancient elephant ivory samples for which sex was unknown, and describe how this method can be ...
Sex identification of ancient animal biological remains can benefit our understanding of historic... more Sex identification of ancient animal biological remains can benefit our understanding of historical population structure, demography and social behavior. Traditional methods for sex identification (e.g. osteological and morphometric comparisons) may be ineffective when animal remains are not well preserved, when sex distinguishing characteristics have not yet developed, or where organisms do not exhibit sex-associated phenotypic dimorphisms. Here we adapt a method developed for human sex determination so that it can be used to identify the sex of ancient and modern animal taxa. The method identifies sex by calculating the ratio of DNA reads aligning to the X chromosome to DNA reads aligning to autosomes (termed the Rx ratio). We tested the accuracy of this method using low coverage genomes from 15 modern elephants (Loxodonta africana) for which sex was known. We then applied this method to ancient elephant ivory samples for which sex was unknown, and describe how this method can be ...
The oldest known shipwreck in southern Africa was found in Namibia in 2008.1, 2, 3, 4 Forty tons ... more The oldest known shipwreck in southern Africa was found in Namibia in 2008.1, 2, 3, 4 Forty tons of cargo, including gold and silver coins, helped identify the ship as the Bom Jesus, a Portuguese nau (trading vessel) lost in 1533 while headed to India.4, 5, 6 The cargo included >100 elephant tusks,7 which we examined using paleogenomic and stable isotope analyses. Nuclear DNA identified the ivory source as African forest (Loxodonta cyclotis) rather than savanna (Loxodonta africana) elephants. Mitochondrial sequences traced them to West and not Central Africa and from ≥17 herds with distinct haplotypes. Four of the haplotypes are known from modern populations; others were potentially lost to subsequent hunting of elephants for ivory. Stable isotope analyses (δ13C and δ15N) indicated that the elephants were not from deep rainforests but from savanna and mixed habitats. Such habitats surround the Guinean forest block of West Africa8 and accord with the locations of major historic Portuguese trading ports.9,10 West African forest elephants currently range into savanna habitats;11, 12, 13 our findings suggest that this was not consequent to regional decimation of savanna elephants for their ivory in the 19th and 20th centuries. During the time of the Bom Jesus, ivory was a central driver in the formation of maritime trading systems connecting Europe, Africa, and Asia. Our integration of paleogenomic, archeological, and historical methods to analyze the Bom Jesus ivory provides a framework for examining vast collections of archaeological ivories around the world, in shipwrecks and other contexts.
Sex estimation of skeletons is fundamental to many archaeological studies. currently, three appro... more Sex estimation of skeletons is fundamental to many archaeological studies. currently, three approaches are available to estimate sex-osteology, genomics, or proteomics, but little is known about the relative reliability of these methods in applied settings. We present matching osteological, shotgun-genomic, and proteomic data to estimate the sex of 55 individuals, each with an independent radiocarbon date between 2,440 and 100 cal BP, from two ancestral Ohlone sites in Central California. Sex estimation was possible in 100% of this burial sample using proteomics, in 91% using genomics, and in 51% using osteology. Agreement between the methods was high, however conflicts did occur. Genomic sex estimates were 100% consistent with proteomic and osteological estimates when DNA reads were above 100,000 total sequences. However, more than half the samples had DNA read numbers below this threshold, producing high rates of conflict with osteological and proteomic data where nine out of twenty conditional DNA sex estimates conflicted with proteomics. While the DNA signal decreased by an order of magnitude in the older burial samples, there was no decrease in proteomic signal. We conclude that proteomics provides an important complement to osteological and shotgun-genomic sex estimation. Biological sex plays an important role in the human experience, correlating to lifespan, reproduction, and a wide range of other biological factors 1-5. Sex and gender are also fundamental in structuring an array of cultural behaviors, including residence patterns, kinship, economic roles, and identity construction and expression 6-9. How sex interacts with gender and these particular issues is not static and can vary in detail across societies and over time 10-12. It is not surprising that sex is one of the most basic and important measures in bioarchaeological and forensic analyses. Typically, osteological features are used to estimate sex of skeletal remains, and the most widely used marker is the morphology of the os coxae 13-16. However, appropriate markers are not always sufficiently expressed or preserved to estimate sex using morphological criteria 17. A lack of sexually-dimorphic markers is especially acute for skeletons of infants and children who have not undergone puberty. Mortuary practices, such as cremation or secondary burial in charnel houses, can also can impose limitations on the utility of osteological sex estimates 18. The advent of DNA sequencing made it possible to use skeletal remains to estimate the sex of very young individuals ; it also expanded sex estimations for fragmentary, pathological, and degraded skeletal materials 19-21. More recently, development of massively parallel DNA sequencing greatly improved genome coverage in archaeological samples 22-25. In addition to providing detailed genetic information, this allows biological sex to be estimated from shotgun sequencing data 25-27. These approaches were an improvement over earlier PCR-based marker open
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Papers by Alida de Flamingh