Pub Date : 2018-09-20DOI: 10.1142/9789813272620_0012
E. Willerslev, A. Cooper
In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.
{"title":"Ancient DNA.","authors":"E. Willerslev, A. Cooper","doi":"10.1142/9789813272620_0012","DOIUrl":"https://doi.org/10.1142/9789813272620_0012","url":null,"abstract":"In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.","PeriodicalId":88647,"journal":{"name":"Proceedings. Colloquium in Biological Sciences","volume":"9 1","pages":"3-16"},"PeriodicalIF":0.0,"publicationDate":"2018-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89814251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-11-17DOI: 10.6084/m9.figshare.4236365.v1
S. Barve, A. Dhondt, V. Mathur, Z. Cheviron
Hypobaric hypoxia at high elevation represents an important physiological stressor for montane organisms, but optimal physiological strategies to cope with hypoxia may vary among species with different life histories. Montane birds exhibit a range of migration patterns; elevational migrants breed at high elevations but winter at low elevations or migrate further south, while high-elevation residents inhabit the same elevation throughout the year. Optimal physiological strategies to cope with hypoxia might therefore differ between species that exhibit these two migratory patterns, because they differ in the amount time spent at high elevation. We examined physiological parameters associated with blood-oxygen transport (haemoglobin concentration and haematocrit, i.e. the proportion of red blood cells in blood) in nine species of elevational migrants and six species of high-elevation residents that were sampled along a 2200 m (1000-3200 m) elevational gradient. Haemoglobin concentration increased with elevation within species regardless of migratory strategy, but it was only significantly correlated with haematocrit in elevational migrants. Surprisingly, haemoglobin concentration was not correlated with haematocrit in high-elevation residents, and these species exhibited higher mean cellular haemoglobin concentration than elevational migrants. Thus, alternative physiological strategies to regulate haemoglobin concentration and blood O2 carrying capacity appear to differ among birds with different annual elevational movement patterns.
{"title":"Life-history characteristics influence physiological strategies to cope with hypoxia in Himalayan birds.","authors":"S. Barve, A. Dhondt, V. Mathur, Z. Cheviron","doi":"10.6084/m9.figshare.4236365.v1","DOIUrl":"https://doi.org/10.6084/m9.figshare.4236365.v1","url":null,"abstract":"Hypobaric hypoxia at high elevation represents an important physiological stressor for montane organisms, but optimal physiological strategies to cope with hypoxia may vary among species with different life histories. Montane birds exhibit a range of migration patterns; elevational migrants breed at high elevations but winter at low elevations or migrate further south, while high-elevation residents inhabit the same elevation throughout the year. Optimal physiological strategies to cope with hypoxia might therefore differ between species that exhibit these two migratory patterns, because they differ in the amount time spent at high elevation. We examined physiological parameters associated with blood-oxygen transport (haemoglobin concentration and haematocrit, i.e. the proportion of red blood cells in blood) in nine species of elevational migrants and six species of high-elevation residents that were sampled along a 2200 m (1000-3200 m) elevational gradient. Haemoglobin concentration increased with elevation within species regardless of migratory strategy, but it was only significantly correlated with haematocrit in elevational migrants. Surprisingly, haemoglobin concentration was not correlated with haematocrit in high-elevation residents, and these species exhibited higher mean cellular haemoglobin concentration than elevational migrants. Thus, alternative physiological strategies to regulate haemoglobin concentration and blood O2 carrying capacity appear to differ among birds with different annual elevational movement patterns.","PeriodicalId":88647,"journal":{"name":"Proceedings. Colloquium in Biological Sciences","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79972744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-11-08DOI: 10.6084/M9.FIGSHARE.C.3571617.V1
A. Pigot, Tom P. Bregman, C. Sheard, Benjamin G. Daly, R. Etienne, J. Tobias
Quantifying the role of biodiversity in ecosystems not only requires understanding the links between species and the ecological functions and services they provide, but also how these factors relate to measurable indices, such as functional traits and phylogenetic diversity. However, these relationships remain poorly understood, especially for heterotrophic organisms within complex ecological networks. Here, we assemble data on avian traits across a global sample of mutualistic plant-frugivore networks to critically assess how the functional roles of frugivores are associated with their intrinsic traits, as well as their evolutionary and functional distinctiveness. We find strong evidence for niche complementarity, with phenotypically and phylogenetically distinct birds interacting with more unique sets of plants. However, interaction strengths-the number of plant species dependent on a frugivore-were unrelated to evolutionary or functional distinctiveness, largely because distinct frugivores tend to be locally rare, and thus have fewer connections across the network. Instead, interaction strengths were better predicted by intrinsic traits, including body size, gape width and dietary specialization. Our analysis provides general support for the use of traits in quantifying species ecological functions, but also highlights the need to go beyond simple metrics of functional or phylogenetic diversity to consider the multiple pathways through which traits may determine ecological processes.
{"title":"Quantifying species contributions to ecosystem processes: a global assessment of functional trait and phylogenetic metrics across avian seed-dispersal networks.","authors":"A. Pigot, Tom P. Bregman, C. Sheard, Benjamin G. Daly, R. Etienne, J. Tobias","doi":"10.6084/M9.FIGSHARE.C.3571617.V1","DOIUrl":"https://doi.org/10.6084/M9.FIGSHARE.C.3571617.V1","url":null,"abstract":"Quantifying the role of biodiversity in ecosystems not only requires understanding the links between species and the ecological functions and services they provide, but also how these factors relate to measurable indices, such as functional traits and phylogenetic diversity. However, these relationships remain poorly understood, especially for heterotrophic organisms within complex ecological networks. Here, we assemble data on avian traits across a global sample of mutualistic plant-frugivore networks to critically assess how the functional roles of frugivores are associated with their intrinsic traits, as well as their evolutionary and functional distinctiveness. We find strong evidence for niche complementarity, with phenotypically and phylogenetically distinct birds interacting with more unique sets of plants. However, interaction strengths-the number of plant species dependent on a frugivore-were unrelated to evolutionary or functional distinctiveness, largely because distinct frugivores tend to be locally rare, and thus have fewer connections across the network. Instead, interaction strengths were better predicted by intrinsic traits, including body size, gape width and dietary specialization. Our analysis provides general support for the use of traits in quantifying species ecological functions, but also highlights the need to go beyond simple metrics of functional or phylogenetic diversity to consider the multiple pathways through which traits may determine ecological processes.","PeriodicalId":88647,"journal":{"name":"Proceedings. Colloquium in Biological Sciences","volume":"84 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80777707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-10-12DOI: 10.6084/M9.FIGSHARE.C.3500439.V1
Long Wang, Yanchun Zhang, Chao Qin, Dacheng Tian, Sihai Yang, L. Hurst
Mutation rates and recombination rates vary between species and between regions within a genome. What are the determinants of these forms of variation? Prior evidence has suggested that the recombination might be mutagenic with an excess of new mutations in the vicinity of recombination break points. As it is conjectured that domesticated taxa have higher recombination rates than wild ones, we expect domesticated taxa to have raised mutation rates. Here, we use parent-offspring sequencing in domesticated and wild peach to ask (i) whether recombination is mutagenic, and (ii) whether domesticated peach has a higher recombination rate than wild peach. We find no evidence that domesticated peach has an increased recombination rate, nor an increased mutation rate near recombination events. If recombination is mutagenic in this taxa, the effect is too weak to be detected by our analysis. While an absence of recombination-associated mutation might explain an absence of a recombination-heterozygozity correlation in peach, we caution against such an interpretation.
{"title":"Mutation rate analysis via parent-progeny sequencing of the perennial peach. II. No evidence for recombination-associated mutation.","authors":"Long Wang, Yanchun Zhang, Chao Qin, Dacheng Tian, Sihai Yang, L. Hurst","doi":"10.6084/M9.FIGSHARE.C.3500439.V1","DOIUrl":"https://doi.org/10.6084/M9.FIGSHARE.C.3500439.V1","url":null,"abstract":"Mutation rates and recombination rates vary between species and between regions within a genome. What are the determinants of these forms of variation? Prior evidence has suggested that the recombination might be mutagenic with an excess of new mutations in the vicinity of recombination break points. As it is conjectured that domesticated taxa have higher recombination rates than wild ones, we expect domesticated taxa to have raised mutation rates. Here, we use parent-offspring sequencing in domesticated and wild peach to ask (i) whether recombination is mutagenic, and (ii) whether domesticated peach has a higher recombination rate than wild peach. We find no evidence that domesticated peach has an increased recombination rate, nor an increased mutation rate near recombination events. If recombination is mutagenic in this taxa, the effect is too weak to be detected by our analysis. While an absence of recombination-associated mutation might explain an absence of a recombination-heterozygozity correlation in peach, we caution against such an interpretation.","PeriodicalId":88647,"journal":{"name":"Proceedings. Colloquium in Biological Sciences","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90789383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The major histocompatibility complex (MHC) is a dense region of immune genes with high levels of polymorphism, which are arranged in haplotype blocks. Traditional models of balancing selection (i.e. overdominance and negative frequency dependence) were developed to study the population genetics of single genes. However, the MHC is a multigene family surrounded by linked (non-neutral) polymorphisms, and not all of its features are well explained by these models. For example, (i) the high levels of polymorphism in small populations, (ii) the unexpectedly large genetic differentiation between populations, (iii) the shape of the allelic genealogy associated with trans-species evolution, and (iv) the close associations between particular MHC (human leucocyte antigen, HLA) haplotypes and the approximately 100 pathologies in humans. Here, I propose a new model of MHC evolution named Associative Balancing Complex evolution that can explain these phenomena. The model proposes that recessive deleterious mutations accumulate as a 'sheltered load' nearby MHC genes. These mutations can accumulate because (i) they are rarely expressed as homozygotes given the high MHC gene diversity and (ii) purifying selection is inefficient with low recombination rates (cf. Muller's ratchet). Once fixed, these mutations add to balancing selection and further reinforce linkage through epistatic selection against recombinants.
{"title":"A new theory of MHC evolution: beyond selection on the immune genes.","authors":"C. van Oosterhout","doi":"10.1098/rspb.2008.1299","DOIUrl":"https://doi.org/10.1098/rspb.2008.1299","url":null,"abstract":"The major histocompatibility complex (MHC) is a dense region of immune genes with high levels of polymorphism, which are arranged in haplotype blocks. Traditional models of balancing selection (i.e. overdominance and negative frequency dependence) were developed to study the population genetics of single genes. However, the MHC is a multigene family surrounded by linked (non-neutral) polymorphisms, and not all of its features are well explained by these models. For example, (i) the high levels of polymorphism in small populations, (ii) the unexpectedly large genetic differentiation between populations, (iii) the shape of the allelic genealogy associated with trans-species evolution, and (iv) the close associations between particular MHC (human leucocyte antigen, HLA) haplotypes and the approximately 100 pathologies in humans. Here, I propose a new model of MHC evolution named Associative Balancing Complex evolution that can explain these phenomena. The model proposes that recessive deleterious mutations accumulate as a 'sheltered load' nearby MHC genes. These mutations can accumulate because (i) they are rarely expressed as homozygotes given the high MHC gene diversity and (ii) purifying selection is inefficient with low recombination rates (cf. Muller's ratchet). Once fixed, these mutations add to balancing selection and further reinforce linkage through epistatic selection against recombinants.","PeriodicalId":88647,"journal":{"name":"Proceedings. Colloquium in Biological Sciences","volume":"235 1","pages":"657-65"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76566656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
D. Leopold, G. Rhodes, Kai-Markus Müller, L. Jeffery
Several recent demonstrations using visual adaptation have revealed high-level aftereffects for complex patterns including faces. While traditional aftereffects involve perceptual distortion of simple attributes such as orientation or colour that are processed early in the visual cortical hierarchy, face adaptation affects perceived identity and expression, which are thought to be products of higher-order processing. And, unlike most simple aftereffects, those involving faces are robust to changes in scale, position and orientation between the adapting and test stimuli. These differences raise the question of how closely related face aftereffects are to traditional ones. Little is known about the build-up and decay of the face aftereffect, and the similarity of these dynamic processes to traditional aftereffects might provide insight into this relationship. We examined the effect of varying the duration of both the adapting and test stimuli on the magnitude of perceived distortions in face identity. We found that, just as with traditional aftereffects, the identity aftereffect grew logarithmically stronger as a function of adaptation time and exponentially weaker as a function of test duration. Even the subtle aspects of these dynamics, such as the power-law relationship between the adapting and test durations, closely resembled that of other aftereffects. These results were obtained with two different sets of face stimuli that differed greatly in their low-level properties. We postulate that the mechanisms governing these shared dynamics may be dissociable from the responses of feature-selective neurons in the early visual cortex.
{"title":"The dynamics of visual adaptation to faces.","authors":"D. Leopold, G. Rhodes, Kai-Markus Müller, L. Jeffery","doi":"10.1167/5.8.830","DOIUrl":"https://doi.org/10.1167/5.8.830","url":null,"abstract":"Several recent demonstrations using visual adaptation have revealed high-level aftereffects for complex patterns including faces. While traditional aftereffects involve perceptual distortion of simple attributes such as orientation or colour that are processed early in the visual cortical hierarchy, face adaptation affects perceived identity and expression, which are thought to be products of higher-order processing. And, unlike most simple aftereffects, those involving faces are robust to changes in scale, position and orientation between the adapting and test stimuli. These differences raise the question of how closely related face aftereffects are to traditional ones. Little is known about the build-up and decay of the face aftereffect, and the similarity of these dynamic processes to traditional aftereffects might provide insight into this relationship. We examined the effect of varying the duration of both the adapting and test stimuli on the magnitude of perceived distortions in face identity. We found that, just as with traditional aftereffects, the identity aftereffect grew logarithmically stronger as a function of adaptation time and exponentially weaker as a function of test duration. Even the subtle aspects of these dynamics, such as the power-law relationship between the adapting and test durations, closely resembled that of other aftereffects. These results were obtained with two different sets of face stimuli that differed greatly in their low-level properties. We postulate that the mechanisms governing these shared dynamics may be dissociable from the responses of feature-selective neurons in the early visual cortex.","PeriodicalId":88647,"journal":{"name":"Proceedings. Colloquium in Biological Sciences","volume":"29 1","pages":"897-904"},"PeriodicalIF":0.0,"publicationDate":"2005-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90018041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The philosophy of a biologist.","authors":"A L STRAND","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":88647,"journal":{"name":"Proceedings. Colloquium in Biological Sciences","volume":" ","pages":"25-9"},"PeriodicalIF":0.0,"publicationDate":"1945-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28821724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Science in Russia.","authors":"F A GILFILLAN","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":88647,"journal":{"name":"Proceedings. Colloquium in Biological Sciences","volume":" ","pages":"11-3"},"PeriodicalIF":0.0,"publicationDate":"1945-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28821711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Cytogenetics.","authors":"F H SMITH","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":88647,"journal":{"name":"Proceedings. Colloquium in Biological Sciences","volume":" ","pages":"37-40"},"PeriodicalIF":0.0,"publicationDate":"1945-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28821726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genetics and geographic distribution.","authors":"R R HUESTIS","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":88647,"journal":{"name":"Proceedings. Colloquium in Biological Sciences","volume":" ","pages":"45-9"},"PeriodicalIF":0.0,"publicationDate":"1945-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28821728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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