Molecular Biology and Evolution, doi:10.1093/molbev/msp183
Molecular evolution of GYPC: Evidence for recent structural innovation and positive selection in humans
Jason A. Wilder et al.
Abstract
GYPC encodes two erythrocyte surface sialoglycoproteins in humans, glycophorin C and glycophorin D (GPC & GPD), via initiation of translation at two start codons on a single transcript. The malaria-causing parasite Plasmodium falciparum uses GPC as a means of invasion into the human red blood cell. Here we examine the molecular evolution of GYPC among the Hominoidea (Greater and Lesser Apes) and also the pattern of polymorphism at the locus in a global human sample. We find an excess of non-synonymous divergence among species that appears to be caused solely by accelerated evolution of GYPC in the human lineage. Moreover, we find that the ability of GYPC to encode both GPC and GPD is a uniquely human trait, caused by the evolution of the GPC start codon in the human lineage. The pattern of polymorphism among humans is consistent with a hitchhiking event at the locus, suggesting that positive natural selection affected GYPC in the relatively recent past. Because GPC is exploited by P. falciparum for invasion of the red blood cell, we hypothesize that selection for evasion of P. falciparum has caused accelerated evolution of GYPC in humans (relative to other primates), and that this positive selection has continued to act in the recent evolution of our species. These data suggest that malaria has played a powerful role in shaping molecules on the surface of the human red blood cell. In addition, our examination of GYPC reveals a novel mechanism of protein evolution: co-option of UTR sequence following the formation of a new start codon. In the case of human GYPC the ancestral protein (GPD) continues to be produced through leaky translation. Because leaky translation is a widespread phenomenon among genes and organisms, we suggest that co-option of UTR sequence may be an important source of protein innovation.
Link
August 17, 2009
August 16, 2009
72 thousand year old heat-treated tools from South Africa
Elsewhere:
Science doi:10.1126/science.1175028
Fire As an Engineering Tool of Early Modern Humans
Kyle S. Brown et al.
Abstract
The controlled use of fire was a breakthrough adaptation in human evolution. It first provided heat and light and later allowed the physical properties of materials to be manipulated for the production of ceramics and metals. The analysis of tools at multiple sites shows that the source stone materials were systematically manipulated with fire to improve their flaking properties. Heat treatment predominates among silcrete tools at ~72 thousand years ago (ka) and appears as early as 164 ka at Pinnacle Point, on the south coast of South Africa. Heat treatment demands a sophisticated knowledge of fire and an elevated cognitive ability and appears at roughly the same time as widespread evidence for symbolic behavior.
Link
Science doi:10.1126/science.1175028
Fire As an Engineering Tool of Early Modern Humans
Kyle S. Brown et al.
Abstract
The controlled use of fire was a breakthrough adaptation in human evolution. It first provided heat and light and later allowed the physical properties of materials to be manipulated for the production of ceramics and metals. The analysis of tools at multiple sites shows that the source stone materials were systematically manipulated with fire to improve their flaking properties. Heat treatment predominates among silcrete tools at ~72 thousand years ago (ka) and appears as early as 164 ka at Pinnacle Point, on the south coast of South Africa. Heat treatment demands a sophisticated knowledge of fire and an elevated cognitive ability and appears at roughly the same time as widespread evidence for symbolic behavior.
Link
August 14, 2009
Genome-wide STRs and American prehistory
American Journal of Physical Anthropology doi:10.1002/ajpa.21143
Hierarchical modeling of genome-wide Short Tandem Repeat (STR) markers infers native American prehistory
Cecil M. Lewis Jr.
Abstract
This study examines a genome-wide dataset of 678 Short Tandem Repeat loci characterized in 444 individuals representing 29 Native American populations as well as the Tundra Netsi and Yakut populations from Siberia. Using these data, the study tests four current hypotheses regarding the hierarchical distribution of neutral genetic variation in native South American populations: (1) the western region of South America harbors more variation than the eastern region of South America, (2) Central American and western South American populations cluster exclusively, (3) populations speaking the Chibchan-Paezan and Equatorial-Tucanoan language stock emerge as a group within an otherwise South American clade, (4) Chibchan-Paezan populations in Central America emerge together at the tips of the Chibchan-Paezan cluster. This study finds that hierarchical models with the best fit place Central American populations, and populations speaking the Chibchan-Paezan language stock, at a basal position or separated from the South American group, which is more consistent with a serial founder effect into South America than that previously described. Western (Andean) South America is found to harbor similar levels of variation as eastern (Equatorial-Tucanoan and Ge-Pano-Carib) South America, which is inconsistent with an initial west coast migration into South America. Moreover, in all relevant models, the estimates of genetic diversity within geographic regions suggest a major bottleneck or founder effect occurring within the North American subcontinent, before the peopling of Central and South America.
Link
Hierarchical modeling of genome-wide Short Tandem Repeat (STR) markers infers native American prehistory
Cecil M. Lewis Jr.
Abstract
This study examines a genome-wide dataset of 678 Short Tandem Repeat loci characterized in 444 individuals representing 29 Native American populations as well as the Tundra Netsi and Yakut populations from Siberia. Using these data, the study tests four current hypotheses regarding the hierarchical distribution of neutral genetic variation in native South American populations: (1) the western region of South America harbors more variation than the eastern region of South America, (2) Central American and western South American populations cluster exclusively, (3) populations speaking the Chibchan-Paezan and Equatorial-Tucanoan language stock emerge as a group within an otherwise South American clade, (4) Chibchan-Paezan populations in Central America emerge together at the tips of the Chibchan-Paezan cluster. This study finds that hierarchical models with the best fit place Central American populations, and populations speaking the Chibchan-Paezan language stock, at a basal position or separated from the South American group, which is more consistent with a serial founder effect into South America than that previously described. Western (Andean) South America is found to harbor similar levels of variation as eastern (Equatorial-Tucanoan and Ge-Pano-Carib) South America, which is inconsistent with an initial west coast migration into South America. Moreover, in all relevant models, the estimates of genetic diversity within geographic regions suggest a major bottleneck or founder effect occurring within the North American subcontinent, before the peopling of Central and South America.
Link
August 13, 2009
Artificial selection in dairy cattle
PLoS ONE 4(8): e6595. doi:10.1371/journal.pone.0006595
The Genome Response to Artificial Selection: A Case Study in Dairy Cattle
Laurence Flori et al.
Abstract
Dairy cattle breeds have been subjected over the last fifty years to intense artificial selection towards improvement of milk production traits. In this study, we performed a whole genome scan for differentiation using 42,486 SNPs in the three major French dairy cattle breeds (Holstein, Normande and Montbéliarde) to identify the main physiological pathways and regions which were affected by this selection. After analyzing the population structure, we estimated FST within and across the three breeds for each SNP under a pure drift model. We further considered two different strategies to evaluate the effect of selection at the genome level. First, smoothing FST values over each chromosome with a local variable bandwidth kernel estimator allowed identifying 13 highly significant regions subjected to strong and/or recent positive selection. Some of them contained genes within which causal variants with strong effect on milk production traits (GHR) or coloration (MC1R) have already been reported. To go further in the interpretation of the observed signatures of selection we subsequently concentrated on the annotation of differentiated genes defined according to the FST value of SNPs localized close or within them. To that end we performed a comprehensive network analysis which suggested a central role of somatotropic and gonadotropic axes in the response to selection. Altogether, these observations shed light on the antagonism, at the genome level, between milk production and reproduction traits in highly producing dairy cows.
Link
The Genome Response to Artificial Selection: A Case Study in Dairy Cattle
Laurence Flori et al.
Abstract
Dairy cattle breeds have been subjected over the last fifty years to intense artificial selection towards improvement of milk production traits. In this study, we performed a whole genome scan for differentiation using 42,486 SNPs in the three major French dairy cattle breeds (Holstein, Normande and Montbéliarde) to identify the main physiological pathways and regions which were affected by this selection. After analyzing the population structure, we estimated FST within and across the three breeds for each SNP under a pure drift model. We further considered two different strategies to evaluate the effect of selection at the genome level. First, smoothing FST values over each chromosome with a local variable bandwidth kernel estimator allowed identifying 13 highly significant regions subjected to strong and/or recent positive selection. Some of them contained genes within which causal variants with strong effect on milk production traits (GHR) or coloration (MC1R) have already been reported. To go further in the interpretation of the observed signatures of selection we subsequently concentrated on the annotation of differentiated genes defined according to the FST value of SNPs localized close or within them. To that end we performed a comprehensive network analysis which suggested a central role of somatotropic and gonadotropic axes in the response to selection. Altogether, these observations shed light on the antagonism, at the genome level, between milk production and reproduction traits in highly producing dairy cows.
Link
August 12, 2009
Ethnicity inference from DNA in Madrid terrorist attacks
In case there was any lingering doubt about the utility of inferring ancestry from DNA:
PLoS ONE 4(8): e6583. doi:10.1371/journal.pone.0006583
Ancestry Analysis in the 11-M Madrid Bomb Attack Investigation
Christopher Phillips et al.
Abstract
The 11-M Madrid commuter train bombings of 2004 constituted the second biggest terrorist attack to occur in Europe after Lockerbie, while the subsequent investigation became the most complex and wide-ranging forensic case in Spain. Standard short tandem repeat (STR) profiling of 600 exhibits left certain key incriminatory samples unmatched to any of the apprehended suspects. A judicial order to perform analyses of unmatched samples to differentiate European and North African ancestry became a critical part of the investigation and was instigated to help refine the search for further suspects. Although mitochondrial DNA (mtDNA) and Y-chromosome markers routinely demonstrate informative geographic differentiation, the populations compared in this analysis were known to show a proportion of shared mtDNA and Y haplotypes as a result of recent gene-flow across the western Mediterranean, while any two loci can be unrepresentative of the ancestry of an individual as a whole. We based our principal analysis on a validated 34plex autosomal ancestry-informative-marker single nucleotide polymorphism (AIM-SNP) assay to make an assignment of ancestry for DNA from seven unmatched case samples including a handprint from a bag containing undetonated explosives together with personal items recovered from various locations in Madrid associated with the suspects. To assess marker informativeness before genotyping, we predicted the probable classification success for the 34plex assay with standard error estimators for a naïve Bayesian classifier using Moroccan and Spanish training sets (each n = 48). Once misclassification error was found to be sufficiently low, genotyping yielded seven near-complete profiles (33 of 34 AIM-SNPs) that in four cases gave probabilities providing a clear assignment of ancestry. One of the suspects predicted to be North African by AIM-SNP analysis of DNA from a toothbrush was identified late in the investigation as Algerian in origin. The results achieved illustrate the benefit of adding specialized marker sets to provide enhanced scope and power to an already highly effective system of DNA analysis for forensic identification.
Link
PLoS ONE 4(8): e6583. doi:10.1371/journal.pone.0006583
Ancestry Analysis in the 11-M Madrid Bomb Attack Investigation
Christopher Phillips et al.
Abstract
The 11-M Madrid commuter train bombings of 2004 constituted the second biggest terrorist attack to occur in Europe after Lockerbie, while the subsequent investigation became the most complex and wide-ranging forensic case in Spain. Standard short tandem repeat (STR) profiling of 600 exhibits left certain key incriminatory samples unmatched to any of the apprehended suspects. A judicial order to perform analyses of unmatched samples to differentiate European and North African ancestry became a critical part of the investigation and was instigated to help refine the search for further suspects. Although mitochondrial DNA (mtDNA) and Y-chromosome markers routinely demonstrate informative geographic differentiation, the populations compared in this analysis were known to show a proportion of shared mtDNA and Y haplotypes as a result of recent gene-flow across the western Mediterranean, while any two loci can be unrepresentative of the ancestry of an individual as a whole. We based our principal analysis on a validated 34plex autosomal ancestry-informative-marker single nucleotide polymorphism (AIM-SNP) assay to make an assignment of ancestry for DNA from seven unmatched case samples including a handprint from a bag containing undetonated explosives together with personal items recovered from various locations in Madrid associated with the suspects. To assess marker informativeness before genotyping, we predicted the probable classification success for the 34plex assay with standard error estimators for a naïve Bayesian classifier using Moroccan and Spanish training sets (each n = 48). Once misclassification error was found to be sufficiently low, genotyping yielded seven near-complete profiles (33 of 34 AIM-SNPs) that in four cases gave probabilities providing a clear assignment of ancestry. One of the suspects predicted to be North African by AIM-SNP analysis of DNA from a toothbrush was identified late in the investigation as Algerian in origin. The results achieved illustrate the benefit of adding specialized marker sets to provide enhanced scope and power to an already highly effective system of DNA analysis for forensic identification.
Link
August 11, 2009
Finally, an updated look at Y-chromosomes of Jewish priests (Hammer et al. 2009)
We had expected an update on the early Cohen Modal Haplotype work for a few years now. That work had established the distinctiveness of the Cohen Y-chromosome gene pool relative to that of other Jews, which suggested common founders to the Jewish priesthood, but did not provide sufficient phylogenetic resolution: the genetic signature of the Cohens was a 6-marker haplotype that could be found in both haplogroups J1 and J2 and in non-Jewish populations at substantial frequency.
Thus, it became necessary to find a more stringent characterization of Cohen Y-chromosomes that would represent true founder effects in that population. The new paper seems to identify at least two such lineages, one in J-P58, which is a subset of J1, and one in J2a-M410*, and estimates that they were founded 3.2 and 4.2 thousand years ago.
I will comment on this further when I get a hold of the paper and supplementary material.
UPDATE: The authors use the evolutionary mutation rate, and thus the presented ages are overestimated significantly. However, there are reasons to doubt the germline-rate estimate of about 1,000 years for the J1 lineage:
Pinpointing Jewish priestly founders to specific individuals, including Biblical ones, is not easy, as the Y-STR technology does not allow for anything resembling accurate age estimation. However, the paper is a welcome new study of a much-discussed topic, and adds significantly to our understanding.
UPDATE II: On the other hand, the J-P58* haplogroup was found in 325 of 2,099 non-Jews surveyed, but the extended Cohen Modal Haplotype (eCMH) in none (Table S2). If the eCMH founder lived 3+ kya, it would be strange indeed if he left no non-Jewish descendants, as it would imply zero conversion from that lineage to other religions. The lack of non-Jewish eCMHs does support the "Jewishness" of this lineage, but on the other hand, makes a very old age more difficult to accept.
My guess is that the eCMH founder lived in Roman times. This would simultaneously allow enough time to explain the lineage's geographical and demographic growth, while also explaining its limited penetration to non-Jewish populations.
Human Genetics doi:10.1007/s00439-009-0727-5
Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood
Michael F. Hammer et al.
Abstract
It has been known for over a decade that a majority of men who self report as members of the Jewish priesthood (Cohanim) carry a characteristic Y chromosome haplotype termed the Cohen Modal Haplotype (CMH). The CMH has since been used to trace putative Jewish ancestral origins of various populations. However, the limited number of binary and STR Y chromosome markers used previously did not provide the phylogenetic resolution needed to infer the number of independent paternal lineages that are encompassed within the Cohanim or their coalescence times. Accordingly, we have genotyped 75 binary markers and 12 Y-STRs in a sample of 215 Cohanim from diverse Jewish communities, 1,575 Jewish men from across the range of the Jewish Diaspora, and 2,099 non-Jewish men from the Near East, Europe, Central Asia, and India. While Cohanim from diverse backgrounds carry a total of 21 Y chromosome haplogroups, 5 haplogroups account for 79.5% of Cohanim Y chromosomes. The most frequent Cohanim lineage (46.1%) is marked by the recently reported P58 T->C mutation, which is prevalent in the Near East. Based on genotypes at 12 Y-STRs, we identify an extended CMH on the J-P58* background that predominates in both Ashkenazi and non-Ashkenazi Cohanim and is remarkably absent in non-Jews. The estimated divergence time of this lineage based on 17 STRs is 3,190 ± 1,090 years. Notably, the second most frequent Cohanim lineage (J-M410*, 14.4%) contains an extended modal haplotype that is also limited to Ashkenazi and non-Ashkenazi Cohanim and is estimated to be 4.2 ± 1.3 ky old. These results support the hypothesis of a common origin of the CMH in the Near East well before the dispersion of the Jewish people into separate communities, and indicate that the majority of contemporary Jewish priests descend from a limited number of paternal lineages.
Electronic supplementary material The online version of this article (doi:10.1007/s00439-009-0727-5) contains supplementary material, which is available to authorized users.
Link
Thus, it became necessary to find a more stringent characterization of Cohen Y-chromosomes that would represent true founder effects in that population. The new paper seems to identify at least two such lineages, one in J-P58, which is a subset of J1, and one in J2a-M410*, and estimates that they were founded 3.2 and 4.2 thousand years ago.
I will comment on this further when I get a hold of the paper and supplementary material.
UPDATE: The authors use the evolutionary mutation rate, and thus the presented ages are overestimated significantly. However, there are reasons to doubt the germline-rate estimate of about 1,000 years for the J1 lineage:
- Demographic plausibility of growth to encompass nearly a third the Cohanim in about 1,000 years. I am not sure what the demic size of Cohanim is, but going from 1 individual to the current population size would require a consistent high growth over many generations. This seems implausible, unless there is indeed historical evidence for such a Cohen founder's descendants extraordinary success.
- The presence of the founding lineage in both Ashkenazim and Sephardim may suggest a common ancestor before the separation of these two populations.
Pinpointing Jewish priestly founders to specific individuals, including Biblical ones, is not easy, as the Y-STR technology does not allow for anything resembling accurate age estimation. However, the paper is a welcome new study of a much-discussed topic, and adds significantly to our understanding.
UPDATE II: On the other hand, the J-P58* haplogroup was found in 325 of 2,099 non-Jews surveyed, but the extended Cohen Modal Haplotype (eCMH) in none (Table S2). If the eCMH founder lived 3+ kya, it would be strange indeed if he left no non-Jewish descendants, as it would imply zero conversion from that lineage to other religions. The lack of non-Jewish eCMHs does support the "Jewishness" of this lineage, but on the other hand, makes a very old age more difficult to accept.
My guess is that the eCMH founder lived in Roman times. This would simultaneously allow enough time to explain the lineage's geographical and demographic growth, while also explaining its limited penetration to non-Jewish populations.
Human Genetics doi:10.1007/s00439-009-0727-5
Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood
Michael F. Hammer et al.
Abstract
It has been known for over a decade that a majority of men who self report as members of the Jewish priesthood (Cohanim) carry a characteristic Y chromosome haplotype termed the Cohen Modal Haplotype (CMH). The CMH has since been used to trace putative Jewish ancestral origins of various populations. However, the limited number of binary and STR Y chromosome markers used previously did not provide the phylogenetic resolution needed to infer the number of independent paternal lineages that are encompassed within the Cohanim or their coalescence times. Accordingly, we have genotyped 75 binary markers and 12 Y-STRs in a sample of 215 Cohanim from diverse Jewish communities, 1,575 Jewish men from across the range of the Jewish Diaspora, and 2,099 non-Jewish men from the Near East, Europe, Central Asia, and India. While Cohanim from diverse backgrounds carry a total of 21 Y chromosome haplogroups, 5 haplogroups account for 79.5% of Cohanim Y chromosomes. The most frequent Cohanim lineage (46.1%) is marked by the recently reported P58 T->C mutation, which is prevalent in the Near East. Based on genotypes at 12 Y-STRs, we identify an extended CMH on the J-P58* background that predominates in both Ashkenazi and non-Ashkenazi Cohanim and is remarkably absent in non-Jews. The estimated divergence time of this lineage based on 17 STRs is 3,190 ± 1,090 years. Notably, the second most frequent Cohanim lineage (J-M410*, 14.4%) contains an extended modal haplotype that is also limited to Ashkenazi and non-Ashkenazi Cohanim and is estimated to be 4.2 ± 1.3 ky old. These results support the hypothesis of a common origin of the CMH in the Near East well before the dispersion of the Jewish people into separate communities, and indicate that the majority of contemporary Jewish priests descend from a limited number of paternal lineages.
Electronic supplementary material The online version of this article (doi:10.1007/s00439-009-0727-5) contains supplementary material, which is available to authorized users.
Link
August 10, 2009
Y-STRs in HGDP-CEPH panel
This is very useful for those trying to discover associations between Y-SNPs (which are typed by microarrays such as those used by deCodeMe and 23andMe) and Y-STRs (studied here). Empirical mutation rates for many previously unstudied markers will also aid genetic genealogists who are pretty much the only ones who routinely type a large number of markers.
Forensic Sci Int Genet. 2009 Sep;3(4):205-13. Epub 2009 Feb 23.
Improving global and regional resolution of male lineage differentiation by simple single-copy Y-chromosomal short tandem repeat polymorphisms.
Vermeulen M, Wollstein A, van der Gaag K, Lao O, Xue Y, Wang Q, Roewer L, Knoblauch H, Tyler-Smith C, de Knijff P, Kayser M.
We analyzed 67 short tandem repeat polymorphisms from the non-recombining part of the Y-chromosome (Y-STRs), including 49 rarely studied simple single-copy (ss)Y-STRs and 18 widely used Y-STRs, in 590 males from 51 populations belonging to 8 worldwide regions (HGDP-CEPH panel). Although autosomal DNA profiling provided no evidence for close relationship, we found 18 Y-STR haplotypes (defined by 67 Y-STRs) that were shared by two to five men in 13 worldwide populations, revealing high and widespread levels of cryptic male relatedness. Maximal (95.9%) haplotype resolution was achieved with the best 25 out of 67 Y-STRs in the global dataset, and with the best 3-16 markers in regional datasets (89.6-100% resolution). From the 49 rarely studied ssY-STRs, the 25 most informative markers were sufficient to reach the highest possible male lineage differentiation in the global (92.2% resolution), and 3-15 markers in the regional datasets (85.4-100%). Considerably lower haplotype resolutions were obtained with the three commonly used Y-STR sets (Minimal Haplotype, PowerPlex Y, and AmpFlSTR Yfiler. Six ssY-STRs (DYS481, DYS533, DYS549, DYS570, DYS576 and DYS643) were most informative to supplement the existing Y-STR kits for increasing haplotype resolution, or - together with additional ssY-STRs - as a new set for maximizing male lineage differentiation. Mutation rates of the 49 ssY-STRs were estimated from 403 meiotic transfers in deep-rooted pedigrees, and ranged from approximately 4.8 x 10(-4) for 31 ssY-STRs with no mutations observed to 1.3 x 10(-2) and 1.5 x 10(-2) for DYS570 and DYS576, respectively, the latter representing the highest mutation rates reported for human Y-STRs so far. Our findings thus demonstrate that ssY-STRs are useful for maximizing global and regional resolution of male lineages, either as a new set, or when added to commonly used Y-STR sets, and support their application to forensic, genealogical and anthropological studies.
Link
Forensic Sci Int Genet. 2009 Sep;3(4):205-13. Epub 2009 Feb 23.
Improving global and regional resolution of male lineage differentiation by simple single-copy Y-chromosomal short tandem repeat polymorphisms.
Vermeulen M, Wollstein A, van der Gaag K, Lao O, Xue Y, Wang Q, Roewer L, Knoblauch H, Tyler-Smith C, de Knijff P, Kayser M.
We analyzed 67 short tandem repeat polymorphisms from the non-recombining part of the Y-chromosome (Y-STRs), including 49 rarely studied simple single-copy (ss)Y-STRs and 18 widely used Y-STRs, in 590 males from 51 populations belonging to 8 worldwide regions (HGDP-CEPH panel). Although autosomal DNA profiling provided no evidence for close relationship, we found 18 Y-STR haplotypes (defined by 67 Y-STRs) that were shared by two to five men in 13 worldwide populations, revealing high and widespread levels of cryptic male relatedness. Maximal (95.9%) haplotype resolution was achieved with the best 25 out of 67 Y-STRs in the global dataset, and with the best 3-16 markers in regional datasets (89.6-100% resolution). From the 49 rarely studied ssY-STRs, the 25 most informative markers were sufficient to reach the highest possible male lineage differentiation in the global (92.2% resolution), and 3-15 markers in the regional datasets (85.4-100%). Considerably lower haplotype resolutions were obtained with the three commonly used Y-STR sets (Minimal Haplotype, PowerPlex Y, and AmpFlSTR Yfiler. Six ssY-STRs (DYS481, DYS533, DYS549, DYS570, DYS576 and DYS643) were most informative to supplement the existing Y-STR kits for increasing haplotype resolution, or - together with additional ssY-STRs - as a new set for maximizing male lineage differentiation. Mutation rates of the 49 ssY-STRs were estimated from 403 meiotic transfers in deep-rooted pedigrees, and ranged from approximately 4.8 x 10(-4) for 31 ssY-STRs with no mutations observed to 1.3 x 10(-2) and 1.5 x 10(-2) for DYS570 and DYS576, respectively, the latter representing the highest mutation rates reported for human Y-STRs so far. Our findings thus demonstrate that ssY-STRs are useful for maximizing global and regional resolution of male lineages, either as a new set, or when added to commonly used Y-STR sets, and support their application to forensic, genealogical and anthropological studies.
Link
August 09, 2009
Genetic diversity of European cattle breeds
Mol Ecol. 2009 Jul 31. [Epub ahead of print]
Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size.
Medugorac I, Medugorac A, Russ I, Veit-Kensch CE, Taberlet P, Luntz B, Mix HM, Förster M.
In times of rapid global and unforeseeable environmental changes, there is an urgent need for a sustainable cattle breeding policy, based on a global view. Most of the indigenous breeds are specialized in a particular habitat or production system but are rapidly disappearing. Thus, they represent an important resource to meet present and future breeding objectives. Based on 105 microsatellites, we obtained thorough information on genetic diversity and population structure of 16 cattle breeds that cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the North-West of Europe. Breeds under strict artificial selection and indigenous breeds under traditional breeding schemes were included. The overall results showed that the genetic diversity is widespread in Busa breeds in the Anatolian and Balkan areas, when compared with the alpine and north-western European breeds. Our results reflect long-term evolutionary and short-term breeding events very well. The regular pattern of allele frequency distribution in the entire cattle population studied clearly suggests conservation of rare alleles by conservation of preferably unselected traditional breeds with large effective population sizes. From a global and long-term conservation genetics point of view, the native and highly variable breeds closer to the domestication centre could serve as valuable sources of genes for future needs, not only for cattle but also for other farm animals.
Link
Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size.
Medugorac I, Medugorac A, Russ I, Veit-Kensch CE, Taberlet P, Luntz B, Mix HM, Förster M.
In times of rapid global and unforeseeable environmental changes, there is an urgent need for a sustainable cattle breeding policy, based on a global view. Most of the indigenous breeds are specialized in a particular habitat or production system but are rapidly disappearing. Thus, they represent an important resource to meet present and future breeding objectives. Based on 105 microsatellites, we obtained thorough information on genetic diversity and population structure of 16 cattle breeds that cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the North-West of Europe. Breeds under strict artificial selection and indigenous breeds under traditional breeding schemes were included. The overall results showed that the genetic diversity is widespread in Busa breeds in the Anatolian and Balkan areas, when compared with the alpine and north-western European breeds. Our results reflect long-term evolutionary and short-term breeding events very well. The regular pattern of allele frequency distribution in the entire cattle population studied clearly suggests conservation of rare alleles by conservation of preferably unselected traditional breeds with large effective population sizes. From a global and long-term conservation genetics point of view, the native and highly variable breeds closer to the domestication centre could serve as valuable sources of genes for future needs, not only for cattle but also for other farm animals.
Link
August 08, 2009
Expansion of mtDNA haplogroup R8 in India
PLoS ONE 4(8): e6545. doi:10.1371/journal.pone.0006545Deep Rooting In-Situ Expansion of mtDNA Haplogroup R8 in South Asia
Kumarasamy Thangaraj et al.
Abstract
Background
The phylogeny of the indigenous Indian-specific mitochondrial DNA (mtDNA) haplogroups have been determined and refined in previous reports. Similar to mtDNA superhaplogroups M and N, a profusion of reports are also available for superhaplogroup R. However, there is a dearth of information on South Asian subhaplogroups in particular, including R8. Therefore, we ought to access the genealogy and pre-historic expansion of haplogroup R8 which is considered one of the autochthonous lineages of South Asia.
Methodology/Principal Findings
Upon screening the mtDNA of 5,836 individuals belonging to 104 distinct ethnic populations of the Indian subcontinent, we found 54 individuals with the HVS-I motif that defines the R8 haplogroup. Complete mtDNA sequencing of these 54 individuals revealed two deep-rooted subclades: R8a and R8b. Furthermore, these subclades split into several fine subclades. An isofrequency contour map detected the highest frequency of R8 in the state of Orissa. Spearman's rank correlation analysis suggests significant correlation of R8 occurrence with geography.
Conclusions/Significance
The coalescent age of newly-characterized subclades of R8, R8a (15.4±7.2 Kya) and R8b (25.7±10.2 Kya) indicates that the initial maternal colonization of this haplogroup occurred during the middle and upper Paleolithic period, roughly around 40 to 45 Kya. These results signify that the southern part of Orissa currently inhabited by Munda speakers is likely the origin of these autochthonous maternal deep-rooted haplogroups. Our high-resolution study on the genesis of R8 haplogroup provides ample evidence of its deep-rooted ancestry among the Orissa (Austro-Asiatic) tribes.
Link
August 07, 2009
Y chromosome haplogroups from Tunisia and Morocco
As expected, the populations are dominated by haplogroups E (especially E-M81) and J1-M267. It used to be thought that J1 in North Africa represented the genetic impact of Arabs, and later of possible Neolithic origin. While it is true that the expansion of the Arabs would have brought some J1 into North Africa, the discovery of J1 in pre-Arab expansion Canary Islands makes it likely that this lineage has a complex history, and it would be useful to discover additional markers to distinguish between various population movements into the West.
Forensic Science International: Genetics Supplement Series
Volume 1, Issue 1, August 2008, Pages 235-236
doi:10.1016/j.fsigss.2007.10.173
Y-chromosome markers distribution in Northern Africa: High-resolution SNP and STR analysis in Tunisia and Morocco populations
Valerio Onofri et al.
Abstract
At the beginning of 2006 more than 301,000 immigrants resident in Italy resulted to come from Tunisia and Morocco, 66% of which are male subjects; in addition, it is estimated that some other thousand are clandestine. Our data show that there is an increasing involvement of Tunisian and Moroccan individuals in paternity testing and in individual identification cases. For these reasons, the aim of this work was to enrich forensic Y-chromosome databases with Northern Africa data to better know markers frequency and their distribution across these populations (in YHRD there are 246 Tunisian samples and 0 Moroccans, access date to www.yhrd.org: August 2007). 103 Tunisian and Moroccan healthy male donors were typed by 17 microsatellites extended haplotype and 41 Y-SNPs. A high-resolution level database was created, including both haplotype and haplogroup for each sample. This study confirmed that precious informations might come both from Y-SNPs haplogroup distribution besides Y-STRs data.
Link
Forensic Science International: Genetics Supplement Series
Volume 1, Issue 1, August 2008, Pages 235-236
doi:10.1016/j.fsigss.2007.10.173
Y-chromosome markers distribution in Northern Africa: High-resolution SNP and STR analysis in Tunisia and Morocco populations
Valerio Onofri et al.
Abstract
At the beginning of 2006 more than 301,000 immigrants resident in Italy resulted to come from Tunisia and Morocco, 66% of which are male subjects; in addition, it is estimated that some other thousand are clandestine. Our data show that there is an increasing involvement of Tunisian and Moroccan individuals in paternity testing and in individual identification cases. For these reasons, the aim of this work was to enrich forensic Y-chromosome databases with Northern Africa data to better know markers frequency and their distribution across these populations (in YHRD there are 246 Tunisian samples and 0 Moroccans, access date to www.yhrd.org: August 2007). 103 Tunisian and Moroccan healthy male donors were typed by 17 microsatellites extended haplotype and 41 Y-SNPs. A high-resolution level database was created, including both haplotype and haplogroup for each sample. This study confirmed that precious informations might come both from Y-SNPs haplogroup distribution besides Y-STRs data.
Link
August 06, 2009
Dog domestication history reconsidered
There are several important lessons from this new study:
One generally does not speak of humans as "domesticated" or "wild", but, nonetheless, humans vary greatly in the way they reproduce. In some cases, choice of marriage partner is a complex long-term process of selection from alternatives, while in others it is a shorter more "natural" one. It would be a great idea to study the social correlates of human genetic diversity, rather than assume that all humans are at a similar level of self-domestication and thus differences between them are simply the product of their respective antiquity.
PNAS doi:10.1073/pnas.0902129106
Complex population structure in African village dogs and its implications for inferring dog domestication history
Adam R. Boyko et al.
Abstract
High genetic diversity of East Asian village dogs has recently been used to argue for an East Asian origin of the domestic dog. However, global village dog genetic diversity and the extent to which semiferal village dogs represent distinct, indigenous populations instead of admixtures of various dog breeds has not been quantified. Understanding these issues is critical to properly reconstructing the timing, number, and locations of dog domestication. To address these questions, we sampled 318 village dogs from 7 regions in Egypt, Uganda, and Namibia, measuring genetic diversity >680 bp of the mitochondrial D-loop, 300 SNPs, and 89 microsatellite markers. We also analyzed breed dogs, including putatively African breeds (Afghan hounds, Basenjis, Pharaoh hounds, Rhodesian ridgebacks, and Salukis), Puerto Rican street dogs, and mixed breed dogs from the United States. Village dogs from most African regions appear genetically distinct from non-native breed and mixed-breed dogs, although some individuals cluster genetically with Puerto Rican dogs or United States breed mixes instead of with neighboring village dogs. Thus, African village dogs are a mosaic of indigenous dogs descended from early migrants to Africa, and non-native, breed-admixed individuals. Among putatively African breeds, Pharaoh hounds, and Rhodesian ridgebacks clustered with non-native rather than indigenous African dogs, suggesting they have predominantly non-African origins. Surprisingly, we find similar mtDNA haplotype diversity in African and East Asian village dogs, potentially calling into question the hypothesis of an East Asian origin for dog domestication.
Link
- We are back to square one when it comes to the origin of domestic dogs, as the discovery of similar genetic diversity in African and Asian dogs casts doubt on the Asian origin theory
- In general, making inferences of gene flow based on diversity measures is very sensitive to sampling.
- Greater genetic diversity may be the result of either greater antiquity or admixture; if an extra-terrestrial scientist, knowing nothing about human history, studied the genetic diversity of humans, he would probably conclude that they originated in the Americas, if he overlooked the possibility that the highly diverse population of the New World is the result of very recent admixture and settlement.
- Domestication resulting from artificial selection leads to loss of genetic diversity. Thus, differences in genetic diversity may be due to differences in the intensity of domestication-related changes, rather than due to differences in antiquity.
One generally does not speak of humans as "domesticated" or "wild", but, nonetheless, humans vary greatly in the way they reproduce. In some cases, choice of marriage partner is a complex long-term process of selection from alternatives, while in others it is a shorter more "natural" one. It would be a great idea to study the social correlates of human genetic diversity, rather than assume that all humans are at a similar level of self-domestication and thus differences between them are simply the product of their respective antiquity.
PNAS doi:10.1073/pnas.0902129106
Complex population structure in African village dogs and its implications for inferring dog domestication history
Adam R. Boyko et al.
Abstract
High genetic diversity of East Asian village dogs has recently been used to argue for an East Asian origin of the domestic dog. However, global village dog genetic diversity and the extent to which semiferal village dogs represent distinct, indigenous populations instead of admixtures of various dog breeds has not been quantified. Understanding these issues is critical to properly reconstructing the timing, number, and locations of dog domestication. To address these questions, we sampled 318 village dogs from 7 regions in Egypt, Uganda, and Namibia, measuring genetic diversity >680 bp of the mitochondrial D-loop, 300 SNPs, and 89 microsatellite markers. We also analyzed breed dogs, including putatively African breeds (Afghan hounds, Basenjis, Pharaoh hounds, Rhodesian ridgebacks, and Salukis), Puerto Rican street dogs, and mixed breed dogs from the United States. Village dogs from most African regions appear genetically distinct from non-native breed and mixed-breed dogs, although some individuals cluster genetically with Puerto Rican dogs or United States breed mixes instead of with neighboring village dogs. Thus, African village dogs are a mosaic of indigenous dogs descended from early migrants to Africa, and non-native, breed-admixed individuals. Among putatively African breeds, Pharaoh hounds, and Rhodesian ridgebacks clustered with non-native rather than indigenous African dogs, suggesting they have predominantly non-African origins. Surprisingly, we find similar mtDNA haplotype diversity in African and East Asian village dogs, potentially calling into question the hypothesis of an East Asian origin for dog domestication.
Link
August 05, 2009
ADMIXTURE, a new program for model-based estimation of ancestry in unrelated individuals (Alexander et al. 2009)
The improvement in speed is very important, as STRUCTURE runs very slowly for large number of markers/individuals. The authors write:
We are thus hesitant to make a definitive statement regarding the speed of admixture versus structure. Let us simply state that in the experiments we have run on a 2.8GHz Intel Xeon computer on datasets with around 1,000 individuals and 10,000 markers, we have found that point estimation with admixture typically took on the order of minutes, while point estimation with structure took on the order of hours.The paper includes free supplementary material (pdf).
UPDATE (Aug 9): Link to ADMIXTURE software.
Genome Research doi:10.1101/gr.094052.109
Fast model-based estimation of ancestry in unrelated individuals
David H. Alexander et al.
Abstract
Population stratification has long been recognized as a confounding factor in genetic association studies. Estimated ancestries, derived from multi-locus genotype data, can be used to perform a statistical correction for population stratification. One popular technique for estimation of ancestry is the model-based approach embodied by the widely applied program structure. Another approach, implemented in the program EIGENSTRAT, relies on Principal Component Analysis rather than model-based estimation and does not directly deliver admixture fractions. EIGENSTRAT has gained in popularity in part owing to its remarkable speed in comparison to structure. We present a new algorithm and a program, ADMIXTURE, for model-based estimation of ancestry in unrelated individuals. ADMIXTURE adopts the likelihood model embedded in structure. However, ADMIXTURE runs considerably faster, solving problems in minutes that take structure hours. In many of our experiments, we have found that ADMIXTURE is almost as fast as EIGENSTRAT. The runtime improvements of ADMIXTURE rely on a fast block relaxation scheme using sequential quadratic programming for block updates, coupled with a novel quasi-Newton acceleration of convergence. Our algorithm also runs faster and with greater accuracy than the implementation of an Expectation-Maximization (EM) algorithm incorporated in the program FRAPPE. Our simulations show that ADMIXTURE's maximum likelihood estimates of the underlying admixture coefficients and ancestral allele frequencies are as accurate as structure's Bayesian estimates. On real-world data sets, ADMIXTURE's estimates are directly comparable to those from structure and EIGENSTRAT. Taken together, our results show that ADMIXTURE's computational speed opens up the possibility of using a much larger set of markers in model-based ancestry estimation and that its estimates are suitable for use in correcting for population stratification in association studies.
Link
Genome Research doi:10.1101/gr.094052.109
Fast model-based estimation of ancestry in unrelated individuals
David H. Alexander et al.
Abstract
Population stratification has long been recognized as a confounding factor in genetic association studies. Estimated ancestries, derived from multi-locus genotype data, can be used to perform a statistical correction for population stratification. One popular technique for estimation of ancestry is the model-based approach embodied by the widely applied program structure. Another approach, implemented in the program EIGENSTRAT, relies on Principal Component Analysis rather than model-based estimation and does not directly deliver admixture fractions. EIGENSTRAT has gained in popularity in part owing to its remarkable speed in comparison to structure. We present a new algorithm and a program, ADMIXTURE, for model-based estimation of ancestry in unrelated individuals. ADMIXTURE adopts the likelihood model embedded in structure. However, ADMIXTURE runs considerably faster, solving problems in minutes that take structure hours. In many of our experiments, we have found that ADMIXTURE is almost as fast as EIGENSTRAT. The runtime improvements of ADMIXTURE rely on a fast block relaxation scheme using sequential quadratic programming for block updates, coupled with a novel quasi-Newton acceleration of convergence. Our algorithm also runs faster and with greater accuracy than the implementation of an Expectation-Maximization (EM) algorithm incorporated in the program FRAPPE. Our simulations show that ADMIXTURE's maximum likelihood estimates of the underlying admixture coefficients and ancestral allele frequencies are as accurate as structure's Bayesian estimates. On real-world data sets, ADMIXTURE's estimates are directly comparable to those from structure and EIGENSTRAT. Taken together, our results show that ADMIXTURE's computational speed opens up the possibility of using a much larger set of markers in model-based ancestry estimation and that its estimates are suitable for use in correcting for population stratification in association studies.
Link
August 04, 2009
Ancient Y chromosomes from the Canary Islands
On the aboriginal remains (ABO):Aboriginal remains were clearly pre-conquest for all the analyzed islands: Tenerife (2210 ± 60 to 1720 ± 60 BP), Gomera (1743 ± 40 to 1493 ± 40 BP), Hierro (1740 ± 50 to 970 ± 50 BP) and Gran Canaria (1410 ± 60 to 750 ± 60 BP) [33].It is clear that the aboriginal population was dominated by haplogroups E-M81, E-M78, J-M267. In the historical period (a few centuries ago) new haplogroups make their appearance (e.g., R1a) and a massive increase in the frequency of R1b is observed.
UPDATE (Aug 5):
There are several interesting observations one could make based on these results:
- The idea of European-descended fair-haired Guanches has taken a hit, as the aboriginal population looks largely like North African Berbers in terms of their Y-chromosomes. No real need to invoke mythical "Nordic" tribes as some have attempted to do.
- The common view about the dispersal of J-haplogroup in the West has been of early Neolithic dispersal of J2 agriculturalists, followed by J1 dispersal of Arabs, Jews, etc. This paper pretty much destroys that picture.
- The two most conspicuous "missing" haplogroups in the clearly pre-Indo-European population of the Canary Islands are J2 and R1a,.
BMC Evolutionary Biology 2009, 9:181 doi:10.1186/1471-2148-9-181
Demographic history of Canary Islands male gene-pool: replacement of native lineages by European
Rosa Fregel et al.
Abstract (provisional)
Background
The origin and prevalence of the prehispanic settlers of the Canary Islands has attracted great multidisciplinary interest. However, direct ancient DNA genetic studies on indigenous and historical 17th-18th century remains, using mitochondrial DNA as a female marker, have only recently been possible. In the present work, the analysis of Y-chromosome polymorphisms in the same samples, has shed light on the way the European colonization affected male and female Canary Island indigenous genetic pools, from the conquest to present-day times.
Results
Autochthonous (E-M81) and prominent (E-M78 and J-M267) Berber Y-chromosome lineages were detected in the indigenous remains, confirming a North West African origin for their ancestors which confirms previous mitochondrial DNA results. However, in contrast with their female lineages, which have survived in the present-day population since the conquest with only a moderate decline, the male indigenous lineages have dropped constantly being substituted by European lineages. Male and female sub-Saharan African genetic inputs were also detected in the Canary population, but their frequencies were higher during the 17th-18th centuries than today.
Conclusions
The European colonization of the Canary Islands introduced a strong sex-biased change in the indigenous population in such a way that indigenous female lineages survived in the extant population in a significantly higher proportion than their male counterparts.
Link (provisional pdf)
August 03, 2009
Strong men and tender women in Bronze Age Serbia
Journal of Anthropological Archaeology doi:10.1016/j.jaa.2009.06.001
Physical activity and social status in Early Bronze Age society: The Mokrin necropolis
Marko Porčić and Sofija Stefanović
Abstract
This paper investigates the social structure of an Early Bronze Age society whose members were buried at the necropolis of Mokrin (Serbia, Southeastern Europe), by comparative analysis of musculo-skeletal markers (MSM) of activity and social status as induced on the basis of grave contents. The main objective of the analysis is to determine whether quantitative and qualitative differences in activity are related to social status. Besides using an overall measure of activity, we attempted to isolate different qualitative aspects (facets) of activity through factor analysis of MSM scores. No correlation between social status and overall labor intensity was found. However, there are clues that social status and a single facet of activity are related. Positive correlation between vertical status and the intensity of use of upper arm and shoulder muscles was found among male individuals, while negative correlation between the aforementioned variables was found among the females. The general conclusion based on the results of this study is that there is no simple correlation between the overall labor intensity and social status.
Link
Physical activity and social status in Early Bronze Age society: The Mokrin necropolis
Marko Porčić and Sofija Stefanović
Abstract
This paper investigates the social structure of an Early Bronze Age society whose members were buried at the necropolis of Mokrin (Serbia, Southeastern Europe), by comparative analysis of musculo-skeletal markers (MSM) of activity and social status as induced on the basis of grave contents. The main objective of the analysis is to determine whether quantitative and qualitative differences in activity are related to social status. Besides using an overall measure of activity, we attempted to isolate different qualitative aspects (facets) of activity through factor analysis of MSM scores. No correlation between social status and overall labor intensity was found. However, there are clues that social status and a single facet of activity are related. Positive correlation between vertical status and the intensity of use of upper arm and shoulder muscles was found among male individuals, while negative correlation between the aforementioned variables was found among the females. The general conclusion based on the results of this study is that there is no simple correlation between the overall labor intensity and social status.
Link
August 02, 2009
Genetic composition of Brazilian population (Lins et al. 2009)
American Journal of Human Biology doi:10.1002/ajhb.20976
Genetic composition of Brazilian population samples based on a set of twenty-eight ancestry informative SNPs
Tulio C. Lins et al.
Abstract
Ancestry informative SNPs can be useful to estimate individual and population biogeographical ancestry. Brazilian population is characterized by a genetic background of three parental populations (European, African, and Brazilian Native Amerindians) with a wide degree and diverse patterns of admixture. In this work we analyzed the information content of 28 ancestry-informative SNPs into multiplexed panels using three parental population sources (African, Amerindian, and European) to infer the genetic admixture in an urban sample of the five Brazilian geopolitical regions. The SNPs assigned apart the parental populations from each other and thus can be applied for ancestry estimation in a three hybrid admixed population. Data was used to infer genetic ancestry in Brazilians with an admixture model. Pairwise estimates of Fst among the five Brazilian geopolitical regions suggested little genetic differentiation only between the South and the remaining regions. Estimates of ancestry results are consistent with the heterogeneous genetic profile of Brazilian population, with a major contribution of European ancestry (0.771) followed by African (0.143) and Amerindian contributions (0.085). The described multiplexed SNP panels can be useful tool for bioanthropological studies but it can be mainly valuable to control for spurious results in genetic association studies in admixed populations.
Link
Genetic composition of Brazilian population samples based on a set of twenty-eight ancestry informative SNPs
Tulio C. Lins et al.
Abstract
Ancestry informative SNPs can be useful to estimate individual and population biogeographical ancestry. Brazilian population is characterized by a genetic background of three parental populations (European, African, and Brazilian Native Amerindians) with a wide degree and diverse patterns of admixture. In this work we analyzed the information content of 28 ancestry-informative SNPs into multiplexed panels using three parental population sources (African, Amerindian, and European) to infer the genetic admixture in an urban sample of the five Brazilian geopolitical regions. The SNPs assigned apart the parental populations from each other and thus can be applied for ancestry estimation in a three hybrid admixed population. Data was used to infer genetic ancestry in Brazilians with an admixture model. Pairwise estimates of Fst among the five Brazilian geopolitical regions suggested little genetic differentiation only between the South and the remaining regions. Estimates of ancestry results are consistent with the heterogeneous genetic profile of Brazilian population, with a major contribution of European ancestry (0.771) followed by African (0.143) and Amerindian contributions (0.085). The described multiplexed SNP panels can be useful tool for bioanthropological studies but it can be mainly valuable to control for spurious results in genetic association studies in admixed populations.
Link
August 01, 2009
The shape of dogs' heads and their performance
A nice study establishing a relationship between dogs' abilities and (i) their modus operandi (independent/co-operating in proximity with humans), or (ii) their head shape (brachycephalic vs. dolichocephalic).
It would be interesting to do similar studies in humans. I seriously doubt that a proposal for the study of the human cephalic index, or cranial shape, with any type of human ability would have a high chance of getting funded.
It is true that a lot of nonsense on the topic was published by statistically naive anthropologists of past decades, but this is no reason to refrain from it forever.
We can now do 3D scans of human heads, we have the fast computers and sophisticated statistical methods to analyze large quantities of anthropometric data. It's a shame that timidity is keeping anthropologists from exploring the plethora of opportunities for exciting research in the area of anthropometry-psychology interactions.
Behav Brain Funct. 2009 Jul 24;5(1):31.
Effects of selection for cooperation and attention in dogs.
Gacsi M, McGreevy P, Kara E, Miklosi A.
ABSTRACT: BACKGROUND: It has been suggested that the functional similarities in the socio-cognitive behaviour of dogs and humans emerged as a consequence of comparable environmental selection pressures. Here we use a novel approach to account for the facilitating effect of domestication in dogs and reveal that selection for two factors under genetic influence (visual cooperation and focused attention) may have led independently to increased comprehension of human communicational cues. METHOD: In Study 1, we observed the performance of three groups of dogs in utilizing the human pointing gesture in a two-way object choice test. We compared breeds selected to work while visually separated from human partners (N=30, 21 breeds, clustered as independent worker group), with those selected to work in close cooperation and continuous visual contact with human partners (N=30, 22 breeds, clustered as cooperative worker group), and with a group of mongrels (N=30). Secondly, it has been reported that, in dogs, selective breeding to produce an abnormal shortening of the skull is associated with a more pronounced area centralis (location of greatest visual acuity). In Study 2, breeds with high cephalic index and more frontally placed eyes (brachycephalic breeds, N=25, 14 breeds) were compared with breeds with low cephalic index and laterally placed eyes (dolichocephalic breeds, N=25, 14 breeds). RESULTS: In Study 1, cooperative workers were significantly more successful in utilizing the human pointing gesture than both the independent workers and the mongrels. In study 2, we found that brachycephalic dogs performed significantly better than dolichocephalic breeds. DISCUSSION: After controlling for environmental factors, we have provided evidence that at least two independent phenotypic traits with certain genetic variability affect the ability of dogs to rely on human visual cues. This finding should caution researchers against making simple generalizations about the effects of domestication and on dog-wolf differences in the utilization of human visual signals.
Link
It would be interesting to do similar studies in humans. I seriously doubt that a proposal for the study of the human cephalic index, or cranial shape, with any type of human ability would have a high chance of getting funded.
It is true that a lot of nonsense on the topic was published by statistically naive anthropologists of past decades, but this is no reason to refrain from it forever.
We can now do 3D scans of human heads, we have the fast computers and sophisticated statistical methods to analyze large quantities of anthropometric data. It's a shame that timidity is keeping anthropologists from exploring the plethora of opportunities for exciting research in the area of anthropometry-psychology interactions.
Behav Brain Funct. 2009 Jul 24;5(1):31.
Effects of selection for cooperation and attention in dogs.
Gacsi M, McGreevy P, Kara E, Miklosi A.
ABSTRACT: BACKGROUND: It has been suggested that the functional similarities in the socio-cognitive behaviour of dogs and humans emerged as a consequence of comparable environmental selection pressures. Here we use a novel approach to account for the facilitating effect of domestication in dogs and reveal that selection for two factors under genetic influence (visual cooperation and focused attention) may have led independently to increased comprehension of human communicational cues. METHOD: In Study 1, we observed the performance of three groups of dogs in utilizing the human pointing gesture in a two-way object choice test. We compared breeds selected to work while visually separated from human partners (N=30, 21 breeds, clustered as independent worker group), with those selected to work in close cooperation and continuous visual contact with human partners (N=30, 22 breeds, clustered as cooperative worker group), and with a group of mongrels (N=30). Secondly, it has been reported that, in dogs, selective breeding to produce an abnormal shortening of the skull is associated with a more pronounced area centralis (location of greatest visual acuity). In Study 2, breeds with high cephalic index and more frontally placed eyes (brachycephalic breeds, N=25, 14 breeds) were compared with breeds with low cephalic index and laterally placed eyes (dolichocephalic breeds, N=25, 14 breeds). RESULTS: In Study 1, cooperative workers were significantly more successful in utilizing the human pointing gesture than both the independent workers and the mongrels. In study 2, we found that brachycephalic dogs performed significantly better than dolichocephalic breeds. DISCUSSION: After controlling for environmental factors, we have provided evidence that at least two independent phenotypic traits with certain genetic variability affect the ability of dogs to rely on human visual cues. This finding should caution researchers against making simple generalizations about the effects of domestication and on dog-wolf differences in the utilization of human visual signals.
Link
Subscribe to:
Posts (Atom)