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H N Poinar

Publications and source records attributed to H N Poinar.

16 recordsLinked to original sources
PubMed2004

Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes.

Analysis of mitochondrial DNA sequence variation has been used extensively to study the evolutionary relationships of individuals and populations, both within and across species. So ubiquitous and easily acquired are mtDNA data that it has been suggested that such data could serve as a taxonomic 'barcode' for an objective species classification scheme. However, there are technical pitfalls associated with the acquisition of mtDNA data. One problem is the presence of translocated pieces of mtDNA in the nuclear genome of many taxa that may be mistaken for authentic organellar mtDNA. We assessed the extent to which such 'numt' sequences may pose an overlooked problem in analyses of mtDNA from humans and apes. Using long-range polymerase chain reaction (PCR), we generated necessarily authentic mtDNA sequences for comparison with sequences obtained using typical methods for a segment of the mtDNA control region in humans, chimpanzees, bonobos, gorillas and orangutans. Results revealed that gorillas are notable for having such a variety of numt sequences bearing high similarity to authentic mtDNA that any analysis of mtDNA using standard approaches is rendered impossible. Studies on humans, chimpanzees, bonobos or orangutans are apparently less problematic. One implication is that explicit measures need to be taken to authenticate mtDNA sequences in newly studied taxa or when any irregularities arise. Furthermore, some taxa may not be amenable to analysis of mtDNA variation at all.

Animals↗
PubMed2001

A molecular analysis of dietary diversity for three archaic Native Americans.

DNA was extracted from three fecal samples, more than 2,000 years old, from Hinds Cave, Texas. Amplification of human mtDNA sequences showed their affiliation with contemporary Native Americans, while sequences from pronghorn antelope, bighorn sheep, and cottontail rabbit allowed these animals to be identified as part of the diet of these individuals. Furthermore, amplification of chloroplast DNA sequences identified eight different plants as dietary elements. These archaic humans consumed 2-4 different animal species and 4-8 different plant species during a short time period. The success rate for retrieval of DNA from paleofeces is in strong contrast to that from skeletal remains where the success rate is generally low. Thus, human paleofecal remains represent a source of ancient DNA that significantly complements and may in some cases be superior to that from skeletal tissue.

Animals↗
PubMed2001

Ancient DNA.

DNA that has been recovered from archaeological and palaeontological remains makes it possible to go back in time and study the genetic relationships of extinct organisms to their contemporary relatives. This provides a new perspective on the evolution of organisms and DNA sequences. However, the field is fraught with technical pitfalls and needs stringent criteria to ensure the reliability of results, particularly when human remains are studied.

Animals↗
PubMed2000

A molecular analysis of ground sloth diet through the last glaciation.

DNA was extracted from five coprolites, excavated in Gypsum Cave, Nevada and radiocarbon dated to approximately 11 000, 20 000 and 28 500 years BP. All coprolites contained mitochondrial DNA sequences identical to a DNA sequence determined from a bone of the extinct ground sloth Nothrotheriops shastensis. A 157-bp fragment of the chloroplast gene for the large subunit of the ribulosebisphosphate carboxylase (rbcL) was amplified from the boluses and several hundred clones were sequenced. In addition, the same DNA fragment was sequenced from 99 plant species that occur in the vicinity of Gypsum Cave today. When these were compared to the DNA sequences in GenBank, 69 were correctly (two incorrectly) assigned to taxonomic orders. The plant sequences from the five coprolites as well as from one previously studied coprolite were compared to rbcL sequences in GenBank and the contemporary plant species. Thirteen families or orders of plants that formed part of the diet of the Shasta ground sloth could be identified, showing that the ground sloth was feeding on trees as well as herbs and grasses. The plants in the boluses further indicate that the climate 11 000 years BP was dryer than 20 000 and 28 500 years BP. However, the sloths seem to have visited water sources more frequently at 11 000 BP than at earlier times.

Animals↗
PubMed1999

Protein preservation and DNA retrieval from ancient tissues.

The retrieval of DNA from fossils remains controversial. To substantiate claims of DNA recovery, one needs additional information on the preservation of other molecules within the same sample. Flash pyrolysis with GC and MS was used to assess the quality of protein preservation in 11 archaeological and paleontological remains, some of which have yielded ancient DNA sequences authenticated via a number of criteria and some of which have consistently failed to yield any meaningful DNA. Several samples, including the Neanderthal-type specimen from which DNA sequences were recently reported, yielded abundant pyrolysis products assigned to 2,5-diketopiperazines of proline-containing dipeptides. The relative amounts of these products provide a good index of the amount of peptide hydrolysis and DNA preservation. Of these samples, four stem from arctic or subarctic regions, emphasizing the importance of cooler temperatures for the preservation of macromolecules. Flash pyrolysis with GC and MS offers a rapid and effective method for assessing fossils for the possibility of DNA preservation.

Amino Acids↗
PubMed1999

DNA from fossils: the past and the future.

The recovery of DNA from archaeological and palaeontological remains has intrigued scientists for many years. The DNA molecule is a relatively weak molecule compared with other biomacromolecules in tissues, but the sequence of its bases holds insights into questions that cannot be resolved by standard palaeontological methods. Recent advances in the field, such as the recovery of DNA sequences from coprolites found in the southwestern USA, as well as from the Neanderthal-type specimen, have shed new light on populations that are now extinct. A better understanding of how DNA is preserved in fossils, as well as the use of novel agents that can release the DNA from archaeological and palaeontological materials, will likely lead to new successes in the field. The analysis of ancient DNA may provide new clues about human evolution and answer questions, for example, relating to the diversity of the Neanderthals and the mammoths.

DNA↗
PubMed1998

Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis.

DNA from excrements can be amplified by means of the polymerase chain reaction. However, this has not been possible with ancient feces. Cross-links between reducing sugars and amino groups were shown to exist in a Pleistocene coprolite from Gypsum Cave, Nevada. A chemical agent, N-phenacylthiazolium bromide, that cleaves such cross-links made it possible to amplify DNA sequences. Analyses of these DNA sequences showed that the coprolite is derived from an extinct sloth, presumably the Shasta ground sloth Nothrotheriops shastensis. Plant DNA sequences from seven groups of plants were identified in the coprolite. The plant assemblage that formed part of the sloth's diet exists today at elevations about 800 meters higher than the cave.

Animals↗
PubMed1996

Amino acid racemization and the preservation of ancient DNA.

The extent of racemization of aspartic acid, alanine, and leucine provides criteria for assessing whether ancient tissue samples contain endogenous DNA. In samples in which the D/L ratio of aspartic acid exceeds 0.08, ancient DNA sequences could not be retrieved. Paleontological finds from which DNA sequences purportedly millions of years old have been reported show extensive racemization, and the amino acids present are mainly contaminates. An exception is the amino acids in some insects preserved in amber.

Alanine↗
PubMed1996

Digital photogrammetric quantification of surface area and volume on scanning electron micrographs of frozen hydrated lung tissue.

A digital video plotter (DVP, Leica), the personal computer equivalent of an analytical plotter, was used to measure the coordinates of points chosen from stereo pair images of the surface of frozen hydrated lung imaged at magnifications of 2000 and 5000 X with a low-temperature scanning electron microscope (SEM). Rat lung tissue was frozen in vivo with a liquid nitrogen cryoprobe under carefully controlled physiologic conditions. At slow freezing rates, water in the aqueous layer at the surface of the lung segregates into ice crystals (dendrites) which branch in the plane of the surface. Coordinates of points on dendrite surfaces were measured by the DVP and passed to TERRAMODEL (Plus III Software, a land modeling program) where they were used to generate a three-dimensional model, from which surface area and planimetric area of the lung surface were calculated. Additional measurements were made at the top and bottom of the ice structures and a Basic language program was written to calculate the volume of ice on the lung surface. Digital photogrammetry coupled with low-temperature SEM of frozen samples allows measurement of water and water-containing microstructures ubiquitous in biology.

Animals↗
PubMed1994

Amino acid racemization in amber-entombed insects: implications for DNA preservation.

DNA depurination and amino acid racemization take place at similar rates in aqueous solution at neutral pH. This relationship suggests that amino acid racemization may be useful in accessing the extent of DNA chain breakage in ancient biological remains. To test this suggestion, we have investigated the amino acids in insects entombed in fossilized tree resins ranging in age from <100 years to 130 million years. The amino acids present in 40 to 130 million year old amber-entombed insects resemble those in a modern fly and are probably the most ancient, unaltered amino acids found so far on Earth. In comparison to other geochemical environments on the surface of the Earth, the amino acid racemization rate in amber insect inclusions is retarded by a factor of >10(4). These results suggest that in amber insect inclusions DNA depurination rates would also likely be retarded in comparison to aqueous solution measurements, and thus DNA fragments containing many hundreds of base pairs should be preserved. This conclusion is consistent with the reported successful retrieval of DNA sequences from amber-entombed organisms.

Amber↗
PubMed1994

Bacillus DNA in fossil bees: an ancient symbiosis?

We report here the isolation of DNA from abdominal tissue of four extinct stingless bees (Proplebeia dominicana) in Dominican amber, PCR amplification of a 546-bp fragment of the 16S rRNA gene from Bacillus spp., and their corresponding nucleotide sequences. These sequences were used in basic local alignment search tool searches of nonredundant nucleic acid data bases, and the highest scores were obtained with 16S rRNA sequences from Bacillus spp. Phylogenetic inference analysis by the maximum-likelihood method revealed close phylogenetic relationships of the four presumed ancient Bacillus sequences with Bacillus pumilus, B. firmus, B. subtilis, and B. circulans. These four extant Bacillus spp. are commonly isolated from abdominal tissue of stingless bees. The close phylogenetic association of the extracted DNA sequences with these bee colonizers suggests that a similar bee-Bacillus association existed in the extinct species P. dominicana.

Animals↗
PubMed1993

Amplification and sequencing of DNA from a 120-135-million-year-old weevil.

DNA has been successfully isolated from both fossilized plant and animal tissues. The oldest material, dated as 25-40 million years old (Tertiary), was obtained from amber-entombed bees and termites. Tissues from both these insects yielded DNA of good quality, which could be amplified by the polymerase chain reaction (PCR) and subsequently sequenced, including the genes encoding 18S ribosomal RNA and 16S rRNA. We report here the extraction of DNA from a 120-135-million-year-old weevil (Nemonychidae, Coleoptera) found in Lebanese amber, PCR amplification of segments of the 18S rRNA gene and the internal transcribed spacer, and the corresponding nucleotide sequences of their 315- and 226-base-pair fragments, respectively. These sequences were used for preliminary phylogenetic analysis of the nemonychid's sequence with three extant coleopterans: Lecontellus pinicola (Nemonychidae), Hypera brunneipennis (Curculionidae) and the mealworm Tenebrio molitor (Tenebrionidae), and two extant dipterans: the fruitfly Drosophila melanogaster (Drosophilidae) and mosquito Aedes albopictus (Culicidae) for the purpose of ascertaining the origin of the extracted and amplified DNA. The results revealed that the PCR-amplified material is that of the extinct nemonychid weevil. This represents the oldest fossil DNA ever extracted and sequenced, extending by 80 million years the age of any previously reported DNA.

Animals↗
PubMed1993

Rapid isolation of DNA from fossil and museum specimens suitable for PCR.

We describe a simple process for extraction of DNA from amber-entombed fossils and museum specimens that is suitable for enzymatic amplification by PCR. Five to ten milligrams of the macerated specimen were mixed in 300 microliters of silica matrix and shaken at 55 degrees C for 1 h in a sterile, screw-capped microcentrifuge tube. After incubation, the silica matrix was transferred to the upper chamber of a SpinFilter, centrifuged at maximum speed for 1 min and then washed twice with 500 microliters of wash solution and the DNA eluted with 50 microliters of TE buffer. The eluate was used as template for PCR, and the results were evaluated by electrophoresis and nucleotide sequence analysis. All samples tested yielded positive results, which were subsequently verified by sequence analysis. It appears, at least in our hands, that the procedure described here is a rapid and efficient way of obtaining small amounts of DNA for PCR in museum and fossilized specimens.

Animals↗