Alvarez-Fuster A, Juan C, Petitpierre E. 1991. Genome size in Tribolium flour-beetles: inter- and intraspecific variation. Genetical Research 58: 1-5.
These authors measured genome size in nine species of tenebrionid beetles in the tribe Ulomini; all but one of which are members of the genus Tribolium. Tribolium castaneum was and remains an exceptionally well-studied beetle, but genome size information was lacking, and few studies of insects had sought information about intraspecific variation in a comprehensive manner prior to this study.
Genome size was estimated by Feulgen densitometry measures of spermatids. Twenty spermatid nuclei from each of 10 individuals (five individuals of Alphitobius diaperinus) per species were measured, with spermatids of Dermestes maculatus used as a standard. For reasons not clear to me, detailed comparisons between D. maculatus and T. castaneum were carried out prior to studies of the other species. The procedure for isolation, fixation, and staining nuclei is similar to what we currently use but has some differences. Fixation was carried out for only 10 minutes in 10% formalin, rather than > 12 hours in MFA, hydrolysis lasted only 45 minutes (rather than 120) but used 5N-HCl as we use, and staining was for two hours (like what we do), but details of the chemical preparation of the stain are not given, though the cited Juan & Petitpierre (1989) may provide more information.
Statistical analysis included measures derived from Gold & Amemiya (1987) of within and between taxa comparisons. Nested ANOVA was also used to support an argument about the significance of intraspecific variation.
The discussion section includes an argument that large and uniform sampling as carried here provides a “solid base from which to analyze the pattern of distribution of genome sizes both inter- and intraspecifically.” Later discussion includes an odd argument that one species, T. brevicornis, with the largest genome size measured here, may be ancestral to the other species (including, presumably, the one species in another genus) and that genome evolution has proceeded by reduction and associated specialization of the type proposed by e.g. Hinegardner (1976).
Within each species, two to four significantly different groups of genome sizes were found, with the exception of one species (T. destructor), which did not show such structure. This, plus the nested ANOVA that indicated significant variation due to between-individuals-within-species comparisons, is taken as evidence in favour of (biologically) significant intraspecific variation in these beetles. The authors acknowledge that such intraspecific variation is surprising, but their arguments for evolutionary trends are not well constructed, so I do not know what to make of this intraspecific variation.
Showing posts with label Cited in Books On My Reading List. Show all posts
Showing posts with label Cited in Books On My Reading List. Show all posts
Wednesday, June 4, 2008
Saturday, April 12, 2008
Stevens 1989
Stevens GC. 1989. The latitudinal gradient in geographical range: how so many species coexist in the tropics. The American Naturalist 133: 240-256.
This paper is an essay that provides an overview of the evidence suggesting a relationship between Rapoport’s rule (larger species geographic ranges at higher latitudes) and the global latitude biodiversity gradient. Both phenomena show coincident exceptions of taxa, indicating a common underlying cause. This is also the paper that coins the term “Rapoport’s rule”.
The original explanatory mechanism for Rapoport’s rule invokes the range of temperatures or other climatic conditions experienced by individuals during their lifetimes at different latitudes. High latitude locations have wider annual ranges of temperature, for example a spruce tree in an Alaskan forest may experience lows below -50°C and highs above 30°C in a single year, while no tropical sites below mountain tops experience that range. Within the geographic range of a species in the tropics, such ranges of environmental variation may occur, but few or no individuals would experience the full range. In addition, bands of climate (such as between annual mean temperatures) that lie along mountain slopes are narrower in the tropics, providing less space for meso-habitat adapted populations to establish and persist, such that population sizes are smaller and long term persistence and local adaptation are less likely.
Narrower tolerances for abiotic conditions in the tropics results in smaller geographic ranges and higher diversities because areas of diversity measurement will encompass a larger number of distinct climate zones than comparable measurements made in temperate or polar latitudes. Further increasing diversity estimates is a predicted strong-in-the-tropics “rescue effect” (Brown and Kodric-Brown, 1977) that produces sink populations in areas a species is poorly adapted to, maintained by immigration from nearby populations in more suitable habitats.
I find these arguments convincing, but some of the exceptions described here are problematic. One key exception that Stevens (1989) mentions more than once is the hymenopteran family Ichneumonidae. Ichneumonid species richness peaks at temperate, not tropical latitudes (Owen & Owen, 1974). Stevens (1989) explains this exception to the general latitude-diversity pattern by invoking the summer-only activity pattern of these parasitoid wasps. Stevens (1989) claims that because they are inactive during all but the warmest part of the year, ichneumonids “… in sense, live in the tropics, no matter what latitude they call home.” I see two critical problems with this argument as applied to Ichneumonidae as an informative exception to Rapoport’s rule and the latitude-diversity pattern. First, many other organisms, plants and animals and presumably other kingdoms and phyla, show severely reduced winter activity in temperate regions. Why do they not similarly show exceptional species-richness patterns? Second, “inactive” is not a synonym with “immune to environmental factors”. Overwintering in places that have winter (i.e. distinctly lower temperatures in one season compared to other times of the year) requires adaptations, sometimes extreme adaptations. The large body of literature concerning overwintering strategies of animals, and the various adaptations that constitute “freeze-tolerant” and “freeze-resistant” forms, comes readily to mind. Overwintering ichneumonids must survive the conditions of winter, even if they do not move around or show high metabolic rates during winter. As a further consideration, another section of this paper clarifies that Rapoport’s rule does not describe a pattern of increased species numbers per genus, it describes changes in the geographical distribution of functional groups of organisms, and includes the example of willows. Willows do not have higher diversity in the tropics; they are absent from tropical regions. But, willows are not an exception to either pattern because they are replaced by several other genera of morphologically and ecologically similar plants at lower latitudes. Why does Stevens (1989) not apply this functional-group replacement criterion to the example of the Ichneumonidae? There are other families of parasitoids, surely one or more of those taxa have high tropical diversity.
This paper is an essay that provides an overview of the evidence suggesting a relationship between Rapoport’s rule (larger species geographic ranges at higher latitudes) and the global latitude biodiversity gradient. Both phenomena show coincident exceptions of taxa, indicating a common underlying cause. This is also the paper that coins the term “Rapoport’s rule”.
The original explanatory mechanism for Rapoport’s rule invokes the range of temperatures or other climatic conditions experienced by individuals during their lifetimes at different latitudes. High latitude locations have wider annual ranges of temperature, for example a spruce tree in an Alaskan forest may experience lows below -50°C and highs above 30°C in a single year, while no tropical sites below mountain tops experience that range. Within the geographic range of a species in the tropics, such ranges of environmental variation may occur, but few or no individuals would experience the full range. In addition, bands of climate (such as between annual mean temperatures) that lie along mountain slopes are narrower in the tropics, providing less space for meso-habitat adapted populations to establish and persist, such that population sizes are smaller and long term persistence and local adaptation are less likely.
Narrower tolerances for abiotic conditions in the tropics results in smaller geographic ranges and higher diversities because areas of diversity measurement will encompass a larger number of distinct climate zones than comparable measurements made in temperate or polar latitudes. Further increasing diversity estimates is a predicted strong-in-the-tropics “rescue effect” (Brown and Kodric-Brown, 1977) that produces sink populations in areas a species is poorly adapted to, maintained by immigration from nearby populations in more suitable habitats.
I find these arguments convincing, but some of the exceptions described here are problematic. One key exception that Stevens (1989) mentions more than once is the hymenopteran family Ichneumonidae. Ichneumonid species richness peaks at temperate, not tropical latitudes (Owen & Owen, 1974). Stevens (1989) explains this exception to the general latitude-diversity pattern by invoking the summer-only activity pattern of these parasitoid wasps. Stevens (1989) claims that because they are inactive during all but the warmest part of the year, ichneumonids “… in sense, live in the tropics, no matter what latitude they call home.” I see two critical problems with this argument as applied to Ichneumonidae as an informative exception to Rapoport’s rule and the latitude-diversity pattern. First, many other organisms, plants and animals and presumably other kingdoms and phyla, show severely reduced winter activity in temperate regions. Why do they not similarly show exceptional species-richness patterns? Second, “inactive” is not a synonym with “immune to environmental factors”. Overwintering in places that have winter (i.e. distinctly lower temperatures in one season compared to other times of the year) requires adaptations, sometimes extreme adaptations. The large body of literature concerning overwintering strategies of animals, and the various adaptations that constitute “freeze-tolerant” and “freeze-resistant” forms, comes readily to mind. Overwintering ichneumonids must survive the conditions of winter, even if they do not move around or show high metabolic rates during winter. As a further consideration, another section of this paper clarifies that Rapoport’s rule does not describe a pattern of increased species numbers per genus, it describes changes in the geographical distribution of functional groups of organisms, and includes the example of willows. Willows do not have higher diversity in the tropics; they are absent from tropical regions. But, willows are not an exception to either pattern because they are replaced by several other genera of morphologically and ecologically similar plants at lower latitudes. Why does Stevens (1989) not apply this functional-group replacement criterion to the example of the Ichneumonidae? There are other families of parasitoids, surely one or more of those taxa have high tropical diversity.
Wednesday, March 19, 2008
Burch and Huber 1966
Burch JB, Huber JM. 1966. Polyploidy in mollusks. Malacologia 5: 41-43.
These authors present a very brief summary of examples of polyploidy discovered to date among molluscs. The conditions promoting or presumed necessary for polyploidy in animals are first presented; of chief importance is the ability to physiologically and developmentally tolerate increased chromosome numbers and the ability to either self-fertilize or reproduce parthenogenically.
Among known selfing-capable hermaphroditic molluscs, the family Lymnaeidae has no examples of polyploids among the 40 species studied. There are unconfirmed reports of polyploidy in other families, including the land snails Succineidae and the freshwater clams Sphaeriidae (see also the much more recent Lee and O Foighil, 2002). The authors suggest that most of the observed variation in molluscan chromosome numbers can be attributed to aneuploidy, an hypothesis I find unlikely in light of more recent understanding of genome organization, especially the role of chromosome fissions, fusions, and translocations in structuring genomes.
These authors present a very brief summary of examples of polyploidy discovered to date among molluscs. The conditions promoting or presumed necessary for polyploidy in animals are first presented; of chief importance is the ability to physiologically and developmentally tolerate increased chromosome numbers and the ability to either self-fertilize or reproduce parthenogenically.
Among known selfing-capable hermaphroditic molluscs, the family Lymnaeidae has no examples of polyploids among the 40 species studied. There are unconfirmed reports of polyploidy in other families, including the land snails Succineidae and the freshwater clams Sphaeriidae (see also the much more recent Lee and O Foighil, 2002). The authors suggest that most of the observed variation in molluscan chromosome numbers can be attributed to aneuploidy, an hypothesis I find unlikely in light of more recent understanding of genome organization, especially the role of chromosome fissions, fusions, and translocations in structuring genomes.
Monday, March 17, 2008
Oren 2004
Oren A. 2004. Prokaryote diversity and taxonomy: current status and future challenges. Philosophical Trans. of the Royal Society of London B 359: 623-638.
This author provides an overview of the current understanding of prokaryote diversity and taxonomy, and discusses recent developments and expected future challenges. The prokaryotes include two of the three Domains of life (Bacteria and Archaea), and their importance in global ecosystems includes astronomical numbers of cells and perhaps as much Carbon as all plants.
Species concepts in Prokaryotes are difficult, and tend to be pragmatic rather than based solidly in theory. Current concepts favour the use of DNA-DNA reassociation, with a 70% similarity cut-off for species identification, combined with 16s rDNA sequences and chemo-phenotypic markers. Higher taxonomic levels are based entirely on subjective decisions, as no clear guidelines for delineating genera, families, orders et cetera exist. However, the problem of horizontal gene transmission is mostly ignorable because species concepts are based on whole-genome properties, not the properties of individual genes. Additionally, a kind of taxonomic “do-over” in 1980 erased the problem of synonyms, by publishing a list of 100% of the known described prokaryotic species, with one name each.
Official recognition of a prokaryotic species is based on depositing viable cultures in two countries, which makes it impossible to officially recognize any species that cannot be cultured. The vast majority of predicted “candidatus” species cannot currently be cultured, though some interesting breakthroughs with marine pelagic forms have recently been made.
Prokaryotic diversity can be sampled in nature using mass sequencing of 16s rDNA. This approach leads to the above estimate of huge numbers of uncultured species, but because 16s rDNA is not fully congruent with whole-genome measures of species identification, cannot be used on its own to identify species. The inability of researchers to cultivate more than a few percent of predicted species is known as the “Great Plate Count Anomaly” (Staley and Konopka, 1985). Extreme estimates for total global prokaryotic species diversity run to billions, based on both soil samples and the observation that prokaryote species numbers probably climb steadily over time because they have enormous populations, ready dispersal, rapid reproduction, and excellent survival of adverse conditions. Thus, in prokaryotes speciation is probably easy and extinction is probably hard.
Little is know about prokaryotic biogeography, and questions of endemicity have hardly been asked. However, no species has yet been identified from both the Arctic and Antarctic, suggesting a possibility of endemicity at that scale.
Until recently, it was apparently widely thought that while we knew little about species, we knew a great deal about the contributions of prokaryotes to global nutrient cycles. Recent novel discoveries of widepread and important biogeochemical processes indicates this is not so. It has been suggested that all thermodynamically favourable chemical reactions may be exploited by some organism, somewhere on Earth.
No prokaryote is considered “endangered”, but a few species are on lists for eradiction, such as the causative agent of leprosy. Other species are probably realistically endangered, as they are obligate symbionts of (for example) endangered species of animals and plants.
The author concludes with a call for better understanding of the issues facing microbiologists today, especially the vast, unexplored numbers of species, and the generally poor funding situation for microbiological research. Ongoing developments in molecular technologies suggest great promise for future work.
This author provides an overview of the current understanding of prokaryote diversity and taxonomy, and discusses recent developments and expected future challenges. The prokaryotes include two of the three Domains of life (Bacteria and Archaea), and their importance in global ecosystems includes astronomical numbers of cells and perhaps as much Carbon as all plants.
Species concepts in Prokaryotes are difficult, and tend to be pragmatic rather than based solidly in theory. Current concepts favour the use of DNA-DNA reassociation, with a 70% similarity cut-off for species identification, combined with 16s rDNA sequences and chemo-phenotypic markers. Higher taxonomic levels are based entirely on subjective decisions, as no clear guidelines for delineating genera, families, orders et cetera exist. However, the problem of horizontal gene transmission is mostly ignorable because species concepts are based on whole-genome properties, not the properties of individual genes. Additionally, a kind of taxonomic “do-over” in 1980 erased the problem of synonyms, by publishing a list of 100% of the known described prokaryotic species, with one name each.
Official recognition of a prokaryotic species is based on depositing viable cultures in two countries, which makes it impossible to officially recognize any species that cannot be cultured. The vast majority of predicted “candidatus” species cannot currently be cultured, though some interesting breakthroughs with marine pelagic forms have recently been made.
Prokaryotic diversity can be sampled in nature using mass sequencing of 16s rDNA. This approach leads to the above estimate of huge numbers of uncultured species, but because 16s rDNA is not fully congruent with whole-genome measures of species identification, cannot be used on its own to identify species. The inability of researchers to cultivate more than a few percent of predicted species is known as the “Great Plate Count Anomaly” (Staley and Konopka, 1985). Extreme estimates for total global prokaryotic species diversity run to billions, based on both soil samples and the observation that prokaryote species numbers probably climb steadily over time because they have enormous populations, ready dispersal, rapid reproduction, and excellent survival of adverse conditions. Thus, in prokaryotes speciation is probably easy and extinction is probably hard.
Little is know about prokaryotic biogeography, and questions of endemicity have hardly been asked. However, no species has yet been identified from both the Arctic and Antarctic, suggesting a possibility of endemicity at that scale.
Until recently, it was apparently widely thought that while we knew little about species, we knew a great deal about the contributions of prokaryotes to global nutrient cycles. Recent novel discoveries of widepread and important biogeochemical processes indicates this is not so. It has been suggested that all thermodynamically favourable chemical reactions may be exploited by some organism, somewhere on Earth.
No prokaryote is considered “endangered”, but a few species are on lists for eradiction, such as the causative agent of leprosy. Other species are probably realistically endangered, as they are obligate symbionts of (for example) endangered species of animals and plants.
The author concludes with a call for better understanding of the issues facing microbiologists today, especially the vast, unexplored numbers of species, and the generally poor funding situation for microbiological research. Ongoing developments in molecular technologies suggest great promise for future work.
Lee and Ó Foighil 2002
Lee T, Ó Foighil D. 2002. 6-Phosphogluconate dehydrogenase (PGD) allele phylogeny is incongruent with a recent origin of polyploidization in some North American Sphaeriidae (Mollusca, Bivalvia). Molecular Phylogenetics and Evolution 25: 112-124.
These authors produced a phylogeny for seven species in three genera in the freshwater clam family Sphaeriidae. These clams have high and variable chromosome numbers, with previous studies suggesting a majority of species polyploid up to 13n (e.g. Lee, 1999). The earliest fossils from the family are found in Cretaceous freshwater deposits, with some genera appearing in the Miocene.
Allopolyploids, derived by hybridization between relatively interfertile (segmental allopolyploidy) or nearly intersterile (genomic allopolyploidy) cause reticulations in phylogenies. Phylogenies based on mtDNA (as exist for this family: Cooley and Ó Foighil, 2000) will not capture such reticulations because of the uniparental inheritance of mtDNA. Nuclear markers, on the other hand, may show a wide range of fates after a duplication event, including gene silencing, homogenization, or independent evolution and differentiation. This variation makes some nuclear markers difficult to analyze in the context of ancient polyploidy.
These authors chose to construct a phylogeny based on a single nuclear gene, using c-DNA to examine only expressed alleles. They found many alleles for this gene in two major clades in the three genera examined. Clade A was widespread and common, while Clade B was not found at all in several species and had fewer alleles in fewer individuals where it was found. Why this imbalance should appear is difficult to state with great certainty. The authors suggest the most likely explanation is that more Clade B alleles have been lost through psuedogenization and / or recombination, though they also acknowledge the possibility, considered by them less likely, that their primer set was biased towards amplification of Clade A alleles. This is considered less likely because some B alleles were detected, such that any bias must be considerably less than 100% effective.
Overall, while the family-level tree does provide evidence of an allopolyploidization event predating the divergence of the three genera, at least some of the more recently-derived lineages experienced duplication events not reflected in this phylogeny. Further examination of the alleles of this gene in more members of this ecologically important family are required to elucidate the history of genomic and genetic events.
One outgroup species came from Cuba, and was preserved and shipped in a solution containing “TRI Reagent (Molecular Research Center)”. This reagent was also used in RNA extraction procedures for all species. I am unfamiliar with this reagent, though its possible use as a tissue preservative that appears to preserve chromatin as well as RNA is very interesting.
These authors produced a phylogeny for seven species in three genera in the freshwater clam family Sphaeriidae. These clams have high and variable chromosome numbers, with previous studies suggesting a majority of species polyploid up to 13n (e.g. Lee, 1999). The earliest fossils from the family are found in Cretaceous freshwater deposits, with some genera appearing in the Miocene.
Allopolyploids, derived by hybridization between relatively interfertile (segmental allopolyploidy) or nearly intersterile (genomic allopolyploidy) cause reticulations in phylogenies. Phylogenies based on mtDNA (as exist for this family: Cooley and Ó Foighil, 2000) will not capture such reticulations because of the uniparental inheritance of mtDNA. Nuclear markers, on the other hand, may show a wide range of fates after a duplication event, including gene silencing, homogenization, or independent evolution and differentiation. This variation makes some nuclear markers difficult to analyze in the context of ancient polyploidy.
These authors chose to construct a phylogeny based on a single nuclear gene, using c-DNA to examine only expressed alleles. They found many alleles for this gene in two major clades in the three genera examined. Clade A was widespread and common, while Clade B was not found at all in several species and had fewer alleles in fewer individuals where it was found. Why this imbalance should appear is difficult to state with great certainty. The authors suggest the most likely explanation is that more Clade B alleles have been lost through psuedogenization and / or recombination, though they also acknowledge the possibility, considered by them less likely, that their primer set was biased towards amplification of Clade A alleles. This is considered less likely because some B alleles were detected, such that any bias must be considerably less than 100% effective.
Overall, while the family-level tree does provide evidence of an allopolyploidization event predating the divergence of the three genera, at least some of the more recently-derived lineages experienced duplication events not reflected in this phylogeny. Further examination of the alleles of this gene in more members of this ecologically important family are required to elucidate the history of genomic and genetic events.
One outgroup species came from Cuba, and was preserved and shipped in a solution containing “TRI Reagent (Molecular Research Center)”. This reagent was also used in RNA extraction procedures for all species. I am unfamiliar with this reagent, though its possible use as a tissue preservative that appears to preserve chromatin as well as RNA is very interesting.
Friday, March 14, 2008
Selker 1997
Selker EU. 1997. Epigenetic phenomena in filamentous fung: useful paradigms or repeat-induced confusion? Trends in Genetics 13: 296-301.
This author reviews point mutations, methylation, and other mechanisms of gene silencing in two common model fungi, Neurospora and Ascobolus. Repeat induced point mutation (RIP) acts in Neurospora, and causes GC to AT transitions in both copies of duplicate genes, and a low level of CpG methylation in both copies. Methylation induced meiotically (MIP) acts in Ascobolus, and causes methylation without point mutation, again in both copies of duplicate genes. Both processes detect larger sequences and tandem duplications more reliably.
Methylation reduces gene expression by interfering with transcription elongation, not transcription initiation as previously suggested.
There are two components to methylation: de novo methylation of previously unmethylated sites, and maintenance of methylation through DNA replication. Maintenance may be carried out primarily by a system that preferentially methylates hemimethylated CpG sites, as are generated during DNA replication, but other mechanisms must also occur to account for a set of observations other maintenance patterns. The mechanism of de novo methylation was apparently not understood in 1997; I do not know if that situation has changed.
The author describes the phenomenon termed “quelling”, in which transformed DNA in some fungi causes gene silencing of homologous genes; I suspect this is one of the observations that led to the discovery of RNA interference (RNAi), as the author describes further evidence that quelling is caused by some factor that diffuses from the nucleus to the cytoplasm.
The author also describes transvection, in which loci that do not occur in allelic positions on chromosomes have reduced expression. I do not know how widespread this phenomenon is, or if a mechanism has been proposed since 1997.All of these epigenetic processes are considered to function in cells as defenses against transposable elements, as they all would reduce expression (and, in the case of RIP, inheritance) of actively-transposing sequences. RIP and MIP act on very large duplications, up to the scale of chromosome rearrangements; thus they preserve chromosome structure at a range of scales.
This author reviews point mutations, methylation, and other mechanisms of gene silencing in two common model fungi, Neurospora and Ascobolus. Repeat induced point mutation (RIP) acts in Neurospora, and causes GC to AT transitions in both copies of duplicate genes, and a low level of CpG methylation in both copies. Methylation induced meiotically (MIP) acts in Ascobolus, and causes methylation without point mutation, again in both copies of duplicate genes. Both processes detect larger sequences and tandem duplications more reliably.
Methylation reduces gene expression by interfering with transcription elongation, not transcription initiation as previously suggested.
There are two components to methylation: de novo methylation of previously unmethylated sites, and maintenance of methylation through DNA replication. Maintenance may be carried out primarily by a system that preferentially methylates hemimethylated CpG sites, as are generated during DNA replication, but other mechanisms must also occur to account for a set of observations other maintenance patterns. The mechanism of de novo methylation was apparently not understood in 1997; I do not know if that situation has changed.
The author describes the phenomenon termed “quelling”, in which transformed DNA in some fungi causes gene silencing of homologous genes; I suspect this is one of the observations that led to the discovery of RNA interference (RNAi), as the author describes further evidence that quelling is caused by some factor that diffuses from the nucleus to the cytoplasm.
The author also describes transvection, in which loci that do not occur in allelic positions on chromosomes have reduced expression. I do not know how widespread this phenomenon is, or if a mechanism has been proposed since 1997.All of these epigenetic processes are considered to function in cells as defenses against transposable elements, as they all would reduce expression (and, in the case of RIP, inheritance) of actively-transposing sequences. RIP and MIP act on very large duplications, up to the scale of chromosome rearrangements; thus they preserve chromosome structure at a range of scales.
Leitch and Bennett 1997
Leitch IJ, Bennett MD. 1997. Polyploidy in angiosperms. Trends in Plant Science 2: 470-476.
These authors reviewed the occurrence and patterns of polyploidy in angiosperms. The majority of “higher plants” apparently have polyploid ancestry, some quite recently reverted to diploid. Most polyploid plants appear to be allopolyploids, derived by hybridization. Allopolyploidy presents the possibility of multiple origins of hybrid polyploid taxa, which has been identified in a few species.
The evolution of duplicated genes is discussed, with an interesting section on homology-dependent gene silencing. This is a phenomenon possibly mediated by repeat-induced changes to chromatin structure, in which some copies within a gene family are silenced or their expression altered.
These authors reviewed the occurrence and patterns of polyploidy in angiosperms. The majority of “higher plants” apparently have polyploid ancestry, some quite recently reverted to diploid. Most polyploid plants appear to be allopolyploids, derived by hybridization. Allopolyploidy presents the possibility of multiple origins of hybrid polyploid taxa, which has been identified in a few species.
The evolution of duplicated genes is discussed, with an interesting section on homology-dependent gene silencing. This is a phenomenon possibly mediated by repeat-induced changes to chromatin structure, in which some copies within a gene family are silenced or their expression altered.
Friday, February 29, 2008
Olmo 2003
This author synthesized data from several different sources including his own previous work to examine possible correlations between genome size, developmental rate, and metabolism predicted by nucleotypic theory. The nucleotype effect is defined here as the variations in genome size that are the result of selective pressures for morphological and functional characteristics of cell and organism that favour adaptations to given environments or lifestyles.
Reptiles are phenotypically intermediate in many ways between anamniotes (amphibians) and homeothermic amniotes (birds and mammals). The range of genome sizes of reptiles is similar to the range in mammals, reptile DNA-methylation patterns are similar to birds and mammals, and reptile AT-content patterns (isochores) are similar to those of amphibians. Many reptiles are capable of generating significant endogenous heat, and can maintain body temperatures above ambient for “fairly long periods”; in other words, there is not a strict division between pure endothermy and pure poikilothermy, as the middle ground is occupied by various reptiles. Given the paraphyletic status of the class Reptilia, these intermediates are not surprising.
The paucity of data for all three parameters for each species led to an analysis at higher taxonomic scales, including family, suborder, and order. Several correlations emerged at these higher scales: metabolic rate was not significantly correlated with genome size at the species level, but was significant at the order level. However, this correlation, as illustrated in figure 3, appears to be largely driven by one order, the Tuatara or Sphenodon. Similarly, the correlation between metabolic rate and genome size for 9 families of lizards (for which consistent data were available from a single study of metabolism) appears to be driven by the single family with the largest genome size; all other data points appear in figure 5 to be approximately on 5 pg genome size, with considerable variation in metabolic rate among those 5 pg families.
The discussion section includes a long consideration of the models of genome size evolution of Hartl and Petrov (various references these authors, between about 2000 and 2002). Under their model of variations in “indel spectra” with mass of noncoding DNA (nc-DNA), a runaway process of increasing genome size may occur, and may have occurred in chelonians (turtles); this may explain the generally larger genomes of chelonians compared to squamates. A role for recombination frequency and the transition areas between R (gene rich isochores) and G (gene poor isochores) bands is also described; chelonians appear to have more suitable sites for TE insertion than do either squamates or homeotherms.
This author reiterates the point that the nucleotypic effect provides thresholds, between which phenotypes such as genome size may vary independently of other phenotypes. Thus, some differences between taxa may be driven more by other, unexamined factors than by genome size or (e.g.) metabolic rate per se; large-scale comparisons are most useful for revealing the role of the nucleotypic effect in genomic evolution.
Thursday, February 28, 2008
Deiana et al. 1999
These authors report genome sizes for 12 species of decapods within one monophyletic lineage, plus one additional species considered as an outgroup. Decapod genome sizes cover a broad range, from about 1.3 to 22.6 pg, with a mode of about 2 or 3 pg, based on a previous study (Lécher et al., 1995). This study used flow cytometry, using Propidium Iodide (PI) for genome size estimation and DAPI for AT-content. Species identification was simplified by the use of primarily commercially-derived species, though non-Mediterranean species were identified by reference to Holthius (1991).
The tissue used in flow cytometry was either gill or antennal gland; both tissues provided low-variability cells. All samples were coprepared with European Eel (Anguilla anguilla) red blood cells. Samples were run with PI first, then washed and fixed with 70% ethanol and stained with DAPI; in all cases a count of at least 2500 cells was obtained.
Friday, February 22, 2008
Salemaa 1984
Salemaa H. 1984. Polyploidy in the evolution of the glacial relict Pontoporeia spp. (Amphipoda, Crustacea). Hereditas 100: 53-60.
This author examined the karyotypes of two closely related species of amphipods found in the Baltic sea and other locations in northern Europe. One species is considered to have descended from the other, speciating about 100 000 years ago during a glacial maximum. The more recent species is tetraploid, but shows normal meiosis and evidence of crossing-over. The two species occur in sympatry, despite apparent ecological congruence.
The tetraploid species shows several differences from the diploid that may or may not relate to its increased chromosome number. They use greater habitat diversity, including a microhabitat difference that exposes them to increased predation from fish. The tetraploids show higher but more variable productivity in some locations where both species are found. Population density of the tetraploids varies greatly; some locations included up to 10 000 individuals per square meter of muddy benthos. The life history of the tetraploid includes more, smaller eggs (contrary to my expectations) and may be better at seasonal synchronization for breeding, based on improved visual sensitivity that allows deeper-dwelling populations to react to season variation in light levels.
All of these differences may have evolved after the speciation event that split this lineage. In particular, greater DNA content per cell should, all else being equal, lead to larger cells including embryos. The opposite difference suggests adaptations of life history to either unmeasured different environmental factors or to the larger cell nuclei of the tetraploids.
This is the first report of a dioecious tetraploid amphipod; no sex chromosomes were detected, removing the obstacle to polyploidy inherent in chromosomal sex determination.
While the karyotype is strongly suggestive of a polyploid recent ancestor followed by some centric fusions (the chromosome number is not exactly double), the illustrations of karyotype do not appear to show longer total chromatin. Genome size, as opposed to karyotype, is not reported here for either species; a doubling of cellular DNA contents would be more convincing to me for an argument of recent polyploidy.
This author examined the karyotypes of two closely related species of amphipods found in the Baltic sea and other locations in northern Europe. One species is considered to have descended from the other, speciating about 100 000 years ago during a glacial maximum. The more recent species is tetraploid, but shows normal meiosis and evidence of crossing-over. The two species occur in sympatry, despite apparent ecological congruence.
The tetraploid species shows several differences from the diploid that may or may not relate to its increased chromosome number. They use greater habitat diversity, including a microhabitat difference that exposes them to increased predation from fish. The tetraploids show higher but more variable productivity in some locations where both species are found. Population density of the tetraploids varies greatly; some locations included up to 10 000 individuals per square meter of muddy benthos. The life history of the tetraploid includes more, smaller eggs (contrary to my expectations) and may be better at seasonal synchronization for breeding, based on improved visual sensitivity that allows deeper-dwelling populations to react to season variation in light levels.
All of these differences may have evolved after the speciation event that split this lineage. In particular, greater DNA content per cell should, all else being equal, lead to larger cells including embryos. The opposite difference suggests adaptations of life history to either unmeasured different environmental factors or to the larger cell nuclei of the tetraploids.
This is the first report of a dioecious tetraploid amphipod; no sex chromosomes were detected, removing the obstacle to polyploidy inherent in chromosomal sex determination.
While the karyotype is strongly suggestive of a polyploid recent ancestor followed by some centric fusions (the chromosome number is not exactly double), the illustrations of karyotype do not appear to show longer total chromatin. Genome size, as opposed to karyotype, is not reported here for either species; a doubling of cellular DNA contents would be more convincing to me for an argument of recent polyploidy.
Monday, January 28, 2008
Steinemann and Steinemann 1998
Steinemann M, Steinemann S. 1998. Enigma of Y chromosome degeneration: Neo-Y and Neo-X chromosomes of Drosophila miranda a model for sex chromosome evolution. Genetica 102/103: 409-420.
These authors examined the Neo-Y chromosome and its meiotic-pairing partner X2 in Drosophila miranda, a species in the Drosophila psuedoobscura species subgroup, about 25 million years removed from D. melanogaster.
These sex chromosomes are unique to D. miranda, and represent an early stage in the evolution of degenerate Y chromosomes. Two major changes distinguish degenerate Y chromosomes from X chromosomes: loss of functional genes by psuedogenization and conversion of euchromatin to heterochromatin.
Muller’s ratchet and the accumulation of point mutations on a non-recombining Y chromosome can account for the first difference, but does not explain the heterochromatinization of the Neo-Y chromosome. A block of repeats homologous to telomere sequences was found in the interior region of the Neo-Y, suggesting an end-to-end chromosome fusion event as the origin of the Neo-Y. These authors examined a region of the Neo-Y associated with a clustered family of genes. On the Neo-Y but not on the X2 they found a “massive accumulation of transposable elements” in this region, associated with the silencing of two of the genes in the examined family.
Finally, the authors suggest that transposable elements are directly involved in the formation of heterochromatin, though the mechanism by which this occurs is not described. The high level of TE insertion in the Neo-Y of D. miranda is strong evidence for chromosome degeneration as in Y chromosomes driven at least partly by the activities of TEs.
These authors examined the Neo-Y chromosome and its meiotic-pairing partner X2 in Drosophila miranda, a species in the Drosophila psuedoobscura species subgroup, about 25 million years removed from D. melanogaster.
These sex chromosomes are unique to D. miranda, and represent an early stage in the evolution of degenerate Y chromosomes. Two major changes distinguish degenerate Y chromosomes from X chromosomes: loss of functional genes by psuedogenization and conversion of euchromatin to heterochromatin.
Muller’s ratchet and the accumulation of point mutations on a non-recombining Y chromosome can account for the first difference, but does not explain the heterochromatinization of the Neo-Y chromosome. A block of repeats homologous to telomere sequences was found in the interior region of the Neo-Y, suggesting an end-to-end chromosome fusion event as the origin of the Neo-Y. These authors examined a region of the Neo-Y associated with a clustered family of genes. On the Neo-Y but not on the X2 they found a “massive accumulation of transposable elements” in this region, associated with the silencing of two of the genes in the examined family.
Finally, the authors suggest that transposable elements are directly involved in the formation of heterochromatin, though the mechanism by which this occurs is not described. The high level of TE insertion in the Neo-Y of D. miranda is strong evidence for chromosome degeneration as in Y chromosomes driven at least partly by the activities of TEs.
Wednesday, January 23, 2008
Blumenstiel et al. 2002
Blumenstiel JP, Hartl Dl, Lozovsky ER. 2002. Patterns of insertion and deletion in contrasting chromatin domains. Molecular Biology and Evolution 19: 2211-2225.
These authors examined “dead-on-arrival” (DOA) transposable elements (TEs) in the genome of Drosophila melanogaster. They divided the genome into three categories for their analysis: heterochromatin, euchromatin of low recombination frequency, and euchromatin of high recombination frequency. They also calculated local rates of DNA gain or loss by small indels.
TEs were more abundant in heterochromatin than in either type of euchromatin, and more abundant in low-recombination euchromatin than in high-recombination euchromatin. Young TEs (more recent insertions) were more evenly distributed while older “mature” TEs were heavily biased towards heterochromatin. The average rate of DNA loss over the entire genome examined was 5.6 bp per nucleotide substition, a rate of spontaneous DNA loss much faster than found in mammals (Petrov and Hartl, 1998).
The authors propose four potential mechanisms to explain the observed distribution of TEs. The first two, that TEs insert preferentially in heterochromatin and that the rate of spontaneous deletion is lowest in heterochromatin, are each rejected. The examined TEs do not insert preferentially anywhere in the genome, as evidenced by the even distribution of the youngest TEs. Spontaneous deletion rates calculated in this study did not vary across regions of the genome, and were insensitive to local recombination rates. Small deletions in TEs should be favoured (and commonly detected) if the deletion rate varies in such an adaptive manner.
The remaining explanatory mechanisms both involve selection, either relaxed selection against TEs in heterochromatin relative to in euchromatin, or positive selection on TEs in heterochromatin for some reason. This analysis suggested the relaxed selection hypothesis is more likely, though it is neutral with respect to the relative contributions to that selection of avoiding ectopic recombination and avoidance of interference with gene function.
The authors suggest that while they have no evidence that small deletions are favoured any more in one region than another, they claim to have some evidence that large deletions, greater than 400 bp, may be favoured. However, this statement is based on a difference in mean deletion sizes between regions that is not statistically significant; they seem to be claiming a trend that does not exist! Perhaps I misread that section of the Discussion.
These authors examined “dead-on-arrival” (DOA) transposable elements (TEs) in the genome of Drosophila melanogaster. They divided the genome into three categories for their analysis: heterochromatin, euchromatin of low recombination frequency, and euchromatin of high recombination frequency. They also calculated local rates of DNA gain or loss by small indels.
TEs were more abundant in heterochromatin than in either type of euchromatin, and more abundant in low-recombination euchromatin than in high-recombination euchromatin. Young TEs (more recent insertions) were more evenly distributed while older “mature” TEs were heavily biased towards heterochromatin. The average rate of DNA loss over the entire genome examined was 5.6 bp per nucleotide substition, a rate of spontaneous DNA loss much faster than found in mammals (Petrov and Hartl, 1998).
The authors propose four potential mechanisms to explain the observed distribution of TEs. The first two, that TEs insert preferentially in heterochromatin and that the rate of spontaneous deletion is lowest in heterochromatin, are each rejected. The examined TEs do not insert preferentially anywhere in the genome, as evidenced by the even distribution of the youngest TEs. Spontaneous deletion rates calculated in this study did not vary across regions of the genome, and were insensitive to local recombination rates. Small deletions in TEs should be favoured (and commonly detected) if the deletion rate varies in such an adaptive manner.
The remaining explanatory mechanisms both involve selection, either relaxed selection against TEs in heterochromatin relative to in euchromatin, or positive selection on TEs in heterochromatin for some reason. This analysis suggested the relaxed selection hypothesis is more likely, though it is neutral with respect to the relative contributions to that selection of avoiding ectopic recombination and avoidance of interference with gene function.
The authors suggest that while they have no evidence that small deletions are favoured any more in one region than another, they claim to have some evidence that large deletions, greater than 400 bp, may be favoured. However, this statement is based on a difference in mean deletion sizes between regions that is not statistically significant; they seem to be claiming a trend that does not exist! Perhaps I misread that section of the Discussion.
Tuesday, January 22, 2008
Nikaido et al. 2003
Nikaido M, Nishihara H, Hukumoto Y, Okada N. 2003. Ancient SINEs from African endemic mammals. Molecular Biology and Evolution 20: 522-527.
These authors discovered a family of Short Interspersed Nuclear Elements (SINEs) restricted to the genomes of Afrotherian mammals. Afrotheria is clade of mammals that originated in Africa during the 60 million years or so it was isolated from the other continents, from approximately 100 to 40 mya, and includes elephants, hyraxes, aardvarks and other mammals. The monophyly of the afrotherian clade is a recent hypothesis, which these authors sought to test by a molecular phylogenetic analysis.
SINEs are not expected to experience horizontal transmission, in contrast to some other retrotransposons, and endemic SINE families have been found in other mammal clades. For example, the Alu family of SINEs are only found in primates.
The main result of this study was the discovery of this family of SINEs and its restriction to animals included in the Afrotheria clade by previous authors based on other data. This result supports the monophyly hypothesis for Afrotheria, and thus helps to connect phylogeny with plate tectonics.
These authors discovered a family of Short Interspersed Nuclear Elements (SINEs) restricted to the genomes of Afrotherian mammals. Afrotheria is clade of mammals that originated in Africa during the 60 million years or so it was isolated from the other continents, from approximately 100 to 40 mya, and includes elephants, hyraxes, aardvarks and other mammals. The monophyly of the afrotherian clade is a recent hypothesis, which these authors sought to test by a molecular phylogenetic analysis.
SINEs are not expected to experience horizontal transmission, in contrast to some other retrotransposons, and endemic SINE families have been found in other mammal clades. For example, the Alu family of SINEs are only found in primates.
The main result of this study was the discovery of this family of SINEs and its restriction to animals included in the Afrotheria clade by previous authors based on other data. This result supports the monophyly hypothesis for Afrotheria, and thus helps to connect phylogeny with plate tectonics.
Monday, January 21, 2008
Palestis et al. 2004
Palestis BG, Burt A, Jones RN, Trivers R. 2004. B chromosomes are more frequent in mammals with acrocentric karyotypes: support for the theory of centromeric drive. Proceedings of the Royal Society of London B (Supplement) 271: S22-S24.
These authors tested the predictions of the theory of centromeric drive (apparently proposed by Pardo-Manuel de Villena and Sapienza, 2001) using a dataset of cytological and taxonomic information for mammals.
The theory of centromeric drive explains the distribution of B chromosomes among species by asymmetries during female meiosis. Female meiosis involves the production of only one gamete from a diploid progenitor cell, compared with the four gametes from one diploid progenitor in males. This unbalance in female meiosis offers an opportunity for selfish genetic elements like B chromosomes to achieve meiotic drive by exploiting differences in spindle capabilities between eggs and polar bodies.
A “strong” spindle in the egg compared with the polar body will capture more centromeres during meiotic division when there are odd numbers, as in the case of a centromeric fission or fusion translocation event that leads to meiotic pairing of one metacentric with two acrocentric chromosomes. This stronger spindle will also tend to capture the centromeres of any B chromosomes, as well. Conversely, if the polar body has the stronger spindle, B chromosomes will be lost from the population more often than chance.
This study found support for the theory of centromeric drive, in that most mammals with Bs had predominantly acrocentric A chromosomes, while acrocentrics were relatively rare among species without Bs. These data support both the proliferation of Bs in predominantly-acrocentric genomes and the typical failure of Bs to establish in predominantly-metacentric genomes.
Two alternative hypotheses for these data are presented, but no other evidence consistent with either acrocentric chromosomes being prone to generating Bs nor with other selection pressures on centromeres are described, apparently because such evidence has not been found. Additionally, although mammal Bs are poorly studied, two cases of strong female meiotic drive in rat Bs are known, associated with weak or absent drive in males, and two other species in which nothing is known about female meiotic drive but mitotic instability in males has been found do not contradict the theory of centromeric drive.
These authors tested the predictions of the theory of centromeric drive (apparently proposed by Pardo-Manuel de Villena and Sapienza, 2001) using a dataset of cytological and taxonomic information for mammals.
The theory of centromeric drive explains the distribution of B chromosomes among species by asymmetries during female meiosis. Female meiosis involves the production of only one gamete from a diploid progenitor cell, compared with the four gametes from one diploid progenitor in males. This unbalance in female meiosis offers an opportunity for selfish genetic elements like B chromosomes to achieve meiotic drive by exploiting differences in spindle capabilities between eggs and polar bodies.
A “strong” spindle in the egg compared with the polar body will capture more centromeres during meiotic division when there are odd numbers, as in the case of a centromeric fission or fusion translocation event that leads to meiotic pairing of one metacentric with two acrocentric chromosomes. This stronger spindle will also tend to capture the centromeres of any B chromosomes, as well. Conversely, if the polar body has the stronger spindle, B chromosomes will be lost from the population more often than chance.
This study found support for the theory of centromeric drive, in that most mammals with Bs had predominantly acrocentric A chromosomes, while acrocentrics were relatively rare among species without Bs. These data support both the proliferation of Bs in predominantly-acrocentric genomes and the typical failure of Bs to establish in predominantly-metacentric genomes.
Two alternative hypotheses for these data are presented, but no other evidence consistent with either acrocentric chromosomes being prone to generating Bs nor with other selection pressures on centromeres are described, apparently because such evidence has not been found. Additionally, although mammal Bs are poorly studied, two cases of strong female meiotic drive in rat Bs are known, associated with weak or absent drive in males, and two other species in which nothing is known about female meiotic drive but mitotic instability in males has been found do not contradict the theory of centromeric drive.
SanMiguel et al. 1998
SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. 1998. The paleontology of intergene retrotransposons of maize. Nature Genetics 20: 43-45.
These authors dated the insertions of 16 retrotransposons inserted in the 240kb region of the maize genome near the gene adh1. The retrotransposons in this region encompass approximately 160kb; three protein-coding genes have been described from this region.
The dating method was based on divergence of the Long Terminal Repeats (LTR) of this family of retrotransposons. The two repeats per retrotransposon would have been identical in sequence when the elements inserted, but have diverged by neutral substitution since that time. If a good estimate of neutral substitution is known, then the divergence in sequence between LTR can provide an estimate of time since insertion.
Many of the retrotransposons inserted into existing retrotransposons in a hierarchical manner, leading to a prediction that LTR divergences of retros-within-retros should be lower (i.e. more recent) than retrotransposons inserted directly into the maize genome. This prediction was correct for 10 of 11 examined retros-in-retros; in the eleventh, the divergences of the LTRs in the two retrotransposons were similar, suggesting similar dates of insertion. This is at least not inconsistent with the prediction.
When the authors compared the maize adh1 region to the orthologous region in sorghum, no retrotransposons were found in sorghum. These authors estimated divergence between the two plant species at 17.4 million years ago, consistent with a previously-published estimate of 16 mya. Thus, all 16 retrotransposon insertions most likely occurred in the last 16 million years or so. The dating based on LTR divergences suggest that almost all of these insertions occurred in the last 6 million years.
The authors discuss and are able to cautiously disregard several potential sources of error, such as gene converstion altering LTR sequences and RNA recombination among distantly-related transcripts.
Their main conclusion, which is well-supported by their data, is that the 240-kb region of the adh1 gene has experienced intense retrotransposon insertion activity over the last 6 million years, greatly increasing the size of this local region. From this, and from four published LTR retrotransposon sequences in other parts of the maize genome, they extrapolate that the maize genome doubled in size from 1200 Mb to 2400 Mb over roughly the same period, a conclusion I find consistent with their results but not particularly well-supported. They end with a request for greater study of this and related phenomena in plant genomes.
These authors dated the insertions of 16 retrotransposons inserted in the 240kb region of the maize genome near the gene adh1. The retrotransposons in this region encompass approximately 160kb; three protein-coding genes have been described from this region.
The dating method was based on divergence of the Long Terminal Repeats (LTR) of this family of retrotransposons. The two repeats per retrotransposon would have been identical in sequence when the elements inserted, but have diverged by neutral substitution since that time. If a good estimate of neutral substitution is known, then the divergence in sequence between LTR can provide an estimate of time since insertion.
Many of the retrotransposons inserted into existing retrotransposons in a hierarchical manner, leading to a prediction that LTR divergences of retros-within-retros should be lower (i.e. more recent) than retrotransposons inserted directly into the maize genome. This prediction was correct for 10 of 11 examined retros-in-retros; in the eleventh, the divergences of the LTRs in the two retrotransposons were similar, suggesting similar dates of insertion. This is at least not inconsistent with the prediction.
When the authors compared the maize adh1 region to the orthologous region in sorghum, no retrotransposons were found in sorghum. These authors estimated divergence between the two plant species at 17.4 million years ago, consistent with a previously-published estimate of 16 mya. Thus, all 16 retrotransposon insertions most likely occurred in the last 16 million years or so. The dating based on LTR divergences suggest that almost all of these insertions occurred in the last 6 million years.
The authors discuss and are able to cautiously disregard several potential sources of error, such as gene converstion altering LTR sequences and RNA recombination among distantly-related transcripts.
Their main conclusion, which is well-supported by their data, is that the 240-kb region of the adh1 gene has experienced intense retrotransposon insertion activity over the last 6 million years, greatly increasing the size of this local region. From this, and from four published LTR retrotransposon sequences in other parts of the maize genome, they extrapolate that the maize genome doubled in size from 1200 Mb to 2400 Mb over roughly the same period, a conclusion I find consistent with their results but not particularly well-supported. They end with a request for greater study of this and related phenomena in plant genomes.
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