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.
Monday, January 28, 2008
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.
Friday, January 18, 2008
Watanabe et al. 1999
Watanabe K, Yahara T, Denda T, Kosuge K. 1999. Chromosomal evolution in the genus Brachyscome (Asteraceae, Astereae): Statistical tests regarding correlation between changes in karyotype and habit using phylogenetic information. Journal of Plant Research 112: 145-161.
These authors used most of the described species in a large genus of Australasian flowering shrubs to test hypotheses regarding chromosome evolution and life-history. Brachyscome contains about 80 species; these authors examined 73, plus 8 other species in related genera. The genus includes a wide range of karyotypes, from 2n=4 up to 2n=36, with a mode of 2n=18. The species are distributed across a strong environmental gradient, from high-raingfall coasts and mountains to variable and semi-arid areas in central Australia. Lower chromosome numbers have been previously reported for species occuring in dryer areas, though there is a strong phylogenetic signal associated with those data.
The authors state in the Introduction that the main purpose of this study was to find “some evolutionary trends” in karyotypes and to test the correlations between changes in chromosome number, karyotype, and life-history habit using independent contrasts and a phylogenetic tree. They did this by asking three main questions:
1. Has the reduction in chromosome number occurred in correlation with the evolution of annuality?
2. Has the reduction in total chromosome length occurred in correlation with the reduction in chromosome number?
3. Have karyotypic asymmetry and length heterogeneity increased in correlation with the reduction in chromosome number?
Their phylogenetic tree was based on Denda et al. (in press), who used 47 taxa in this genus and the matK sequence. They resolved polytomies with morphological, anatomical, and cytological data, being careful not to make any assumptions about the directionality of chromosome evolution to “avoid a circular argument”.
Their main finding was that reductions in chromosome number and total chromosome length (i.e. genome size) were indeed associated with a shift from wet habitats to drier and more variable habitats, and strongly associated with a shift from perennial to annual life-history. These data support the existing hypothesis that annual life-history contributes to selection for smaller genomes.
An interesting section in the Discussion maintains that even if smaller genomes are selected for in annuals, it is still necessary to explain why large genomes would be maintained in perennials, in which it would also seem advantageous to have small genomes and rapid growth and early reproduction. The hypothesis proposed here involves population size: perennials (at least in this genus) have much larger effective population sizes than annuals, apparently due to the ephemeral and variable nature of the more xeric habitats typical of annual species. The neutral or mildly advantageous translocations involved in chromosome reduction and loss would not be as likely to become fixed in the larger effective populations of perennial species.
The model of chromosome reduction used in this paper involves translocation of chromosome segments, followed by loss of the centromere on the donor chromosome and associated loss of remaining segments. They found clear evidence supporting a history of large translocations in this genus, which is also consistent with a model of genome dynamics characterized by frequent small increases in genome size by proliferation of transposable elements and larger, rarer losses by translocation and centromere loss.
These authors used most of the described species in a large genus of Australasian flowering shrubs to test hypotheses regarding chromosome evolution and life-history. Brachyscome contains about 80 species; these authors examined 73, plus 8 other species in related genera. The genus includes a wide range of karyotypes, from 2n=4 up to 2n=36, with a mode of 2n=18. The species are distributed across a strong environmental gradient, from high-raingfall coasts and mountains to variable and semi-arid areas in central Australia. Lower chromosome numbers have been previously reported for species occuring in dryer areas, though there is a strong phylogenetic signal associated with those data.
The authors state in the Introduction that the main purpose of this study was to find “some evolutionary trends” in karyotypes and to test the correlations between changes in chromosome number, karyotype, and life-history habit using independent contrasts and a phylogenetic tree. They did this by asking three main questions:
1. Has the reduction in chromosome number occurred in correlation with the evolution of annuality?
2. Has the reduction in total chromosome length occurred in correlation with the reduction in chromosome number?
3. Have karyotypic asymmetry and length heterogeneity increased in correlation with the reduction in chromosome number?
Their phylogenetic tree was based on Denda et al. (in press), who used 47 taxa in this genus and the matK sequence. They resolved polytomies with morphological, anatomical, and cytological data, being careful not to make any assumptions about the directionality of chromosome evolution to “avoid a circular argument”.
Their main finding was that reductions in chromosome number and total chromosome length (i.e. genome size) were indeed associated with a shift from wet habitats to drier and more variable habitats, and strongly associated with a shift from perennial to annual life-history. These data support the existing hypothesis that annual life-history contributes to selection for smaller genomes.
An interesting section in the Discussion maintains that even if smaller genomes are selected for in annuals, it is still necessary to explain why large genomes would be maintained in perennials, in which it would also seem advantageous to have small genomes and rapid growth and early reproduction. The hypothesis proposed here involves population size: perennials (at least in this genus) have much larger effective population sizes than annuals, apparently due to the ephemeral and variable nature of the more xeric habitats typical of annual species. The neutral or mildly advantageous translocations involved in chromosome reduction and loss would not be as likely to become fixed in the larger effective populations of perennial species.
The model of chromosome reduction used in this paper involves translocation of chromosome segments, followed by loss of the centromere on the donor chromosome and associated loss of remaining segments. They found clear evidence supporting a history of large translocations in this genus, which is also consistent with a model of genome dynamics characterized by frequent small increases in genome size by proliferation of transposable elements and larger, rarer losses by translocation and centromere loss.
Thursday, January 17, 2008
Matlock and Dornfeld 1981
Matlock DB, Dornfeld EJ. 1981. Somatic polyploidy in the marine isopod Idothea wasnesenskii. Comparative Biochemistry and Physiology 69A: 777-781.
These authors examined polyploid somatic tissues in an intertidal isopod with a fun name, using a combination of Feuglen cytophotometry (DNA contents) and Autoradiography (DNA synthesis). They were able to examine three tissues (hepatic cecum, midgut, testis sheath) in adult, juvenile, and “emerger” isopods, except testis tissue in emergers.
Endopolyploidy was found to start first in hepatic cecum, as emergers had very few polyploid cells in their midguts. The pattern of cell ploidy distribution varied between tissues: midgut and cecum cells showed a continuous series of larger cells up to 256C, while testis sheath cells did not exceed 32C, and were distributed discontinuously.
Four hypotheses regarding the intercell synchronisation and duration of DNA synthesis were proposed in the Discussion section, though none of the four could be conclusively rejected based on these data. However, the authors suggest that hypothesis 2, that DNA synthesis is confined to a definite S phase in each cell, but there is no synchrony between cells, is probably correct for the studied tissues in this species. Finally, the authors tentatively suggest that moulting hormones may play a role in stimulating DNA synthesis, a phenomenon that has been partly demonstrated in other contexts in arthropods.
These authors examined polyploid somatic tissues in an intertidal isopod with a fun name, using a combination of Feuglen cytophotometry (DNA contents) and Autoradiography (DNA synthesis). They were able to examine three tissues (hepatic cecum, midgut, testis sheath) in adult, juvenile, and “emerger” isopods, except testis tissue in emergers.
Endopolyploidy was found to start first in hepatic cecum, as emergers had very few polyploid cells in their midguts. The pattern of cell ploidy distribution varied between tissues: midgut and cecum cells showed a continuous series of larger cells up to 256C, while testis sheath cells did not exceed 32C, and were distributed discontinuously.
Four hypotheses regarding the intercell synchronisation and duration of DNA synthesis were proposed in the Discussion section, though none of the four could be conclusively rejected based on these data. However, the authors suggest that hypothesis 2, that DNA synthesis is confined to a definite S phase in each cell, but there is no synchrony between cells, is probably correct for the studied tissues in this species. Finally, the authors tentatively suggest that moulting hormones may play a role in stimulating DNA synthesis, a phenomenon that has been partly demonstrated in other contexts in arthropods.
Subscribe to:
Posts (Atom)
