RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

May combine two claims.

Standard methods for estimating the strength and extent of purifying or positive selection from molecular sequence data are not suitable for detecting relaxed selection because they lack power and can mistake an increase in the intensity of positive selection for relaxation of both purifying and positive selection.

“Standard methods for estimating the strength and extent of purifying or positive selection from molecular sequence data are not suitable for detecting relaxed selection, because they lack power and can mistake an increase in the intensity of positive selection for relaxation of both purifying and positive selection.”

• Also stated in: § Introduction · plain

  “However, this test can be misleading because estimates of ! can be increased by processes such as intensification of positive selection when selective pressures vary both along branches and sites (Murrell et al. 2012).”

• cites Murrell et al. 2012 sourcePartly supported

  Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  Experimental — accuracy not yet measured

Classified as probably not a substantial claim.

The most obvious approach to look for evidence of relaxed selection has been to identify loss of trait or pseudogenization.

“The most obvious approach has been to identify loss of trait or pseudogenization (e.g., Dainat et al. [2012]).”

• cites Dainat et al. [2012] sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Relaxed selection has been implicated as both a driver of speciation and a precursor to extinction.

“Relaxed selection has also been implicated as both a driver of speciation (Templeton 2008) and a precursor to extinction (Moran 1996).”

• cites Templeton 2008 sourceNot checked — no full text of the source
• cites Moran 1996 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

Variation in the ! distribution across the phylogeny can be studied using the BS-REL model.

“Such variation across the phylogeny can be studied using the BS-REL model (Kosakovsky Pond et al. 2011).”

• cites Kosakovsky Pond et al. 2011 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

The introduction of branch-site models addressed evolutionary rate variation not only over sites but also over branches.

“The introduction of branch-site models addressed evolutionary rate variation not only over sites but also over branches (Yang and Nielsen 2002).”

• cites Yang and Nielsen 2002 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Random effects and mixed effects branch-site models allow detection of individual branches on which only a subset of sites are under positive selection or, conversely, individual sites which are under positive selection on only a subset of branches.

“Our random effects (Kosakovsky Pond et al. 2011) and mixed effects (Murrell et al. 2012) branch-site models allow detection of individual branches on which only a subset of sites are under positive selection or, conversely, individual sites which are under positive selection on only a subset of branches.”

• cites Kosakovsky Pond et al. 2011 sourcePartly supported

  Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  Experimental — accuracy not yet measured
• cites Murrell et al. 2012 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

An ! distribution can be thought of as an evolutionary fingerprint characterizing the evolutionary pattern of the gene, where a small subset of sites can have very large ! values even when the majority of sites evolved under strong purifying selection.

“An !distribution can be thought of as an evolutionary fingerprint characterizing the evolutionary pattern of the gene, where a small subset of sites can have very large !values even when the majority of sites evolved under strong purifying selection (Kosakovsky Pond, Scheffler, et al. 2010).”

• cites Kosakovsky Pond, Scheffler, et al. 2010 sourceCould not verify

  Split into 2 atoms — 0 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 2 unverifiable. Expand the claim to see per-atom verdicts.

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing).

The introduction of site-to-site rate variation allowed detection of individual sites evolving under positive selection by classifying sites into different rate categories and estimating a separate ! value specifically for the sites in the positive selection category.

“The introduction of site-to-site rate variation allowed detection of individual sites evolving under positive selection, by classifying sites into different rate categories and estimating a separate !value specifically for the sites in the positive selection category (Nielsen and Yang 1998).”

• cites Nielsen and Yang 1998 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

The first codon models estimated parameters representing an averaged nonsynonymous-synonymous rate ratio.

“The first codon models estimated parameters representing an averaged nonsynonymous-synonymous rate ratio.”

• cites Goldman and Yang 1994 sourceNot checked — no full text of the source
• cites Muse and Gaut 1994 sourcePartly supported

  The Probabilistic Model for Codon Evolution section says the model’s parameters determine synonymous and nonsynonymous substitution rates. But Parameter Interpretation describes the estimated parameters as products of instantaneous rates and time, not as an averaged nonsynonymous-to-synonymous rate ratio; its averaging over codons concerns expected substitution counts. (LLM, conf=0.82)

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing).

It became conventional to think in terms of the distribution of ! values over sites instead of a single gene-wide !.

“Therefore, it became conventional to think in terms of the distribution of !values over sites instead of a single gene-wide !(Yang et al. 2000).”

• cites Yang et al. 2000 sourcePartly supported

  The Theory section models site-to-site variation in the dN/dS ratio using a statistical distribution, and the Results compare those models with a one-ratio model. This supports the conceptual contrast in the claim, but the paper does not establish that thinking in distributions became conventional across the field. (LLM, conf=0.82)

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing).

Branch-level resolution vastly increased the detectable instances of positive selection.

“This development vastly increased the detectable instances of positive selection (Murrell et al. 2012).”

• cites Murrell et al. 2012 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Traces of relaxed selection have been documented in bacterial endosymbionts, including fixation of deleterious alleles and overall elevated rates of nonsynonymous and radical amino acid replacements.

“Accordingly, traces of relaxed selection have been documented in bacterial endosymbionts, including fixation of deleterious alleles (e.g., loss of DNA replication proofreading enzymes) and overall elevated rates of nonsynonymous and radical amino acid replacements (Wernegreen 2011).”

• cites Wernegreen 2011 sourcePartly supported

  The Introduction (page unavailable) reports genome-wide rate acceleration concentrated at nonsynonymous sites, and the Discussion reports elevated radical replacements and evidence consistent with fixation of slightly deleterious mutations. The copy does not document the cited example of lost DNA-replication proofreading enzymes. The Discussion also says relaxed selection may contribute but is unlikely to explain the genome-wide pattern on its own; it favors genetic drift and linkage. (LLM, conf=0.84)

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing).

Insects can also carry facultative (secondary) endosymbionts whose fitness effects on their hosts can be variable and complex.

“Insects can also carry facultative (secondary) endosymbionts whose fitness effects on their hosts can be variable and complex (Oliver et al. 2006(Oliver et al. , 2009;;Degnan et al. 2009;Burke et al. 2010).”

• cites Oliver et al. 2006 sourceSupported
• cites Oliver et al. 2009 sourceSupported
• cites Degnan et al. 2009 sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

Many insect species have obligate (primary) bacterial endosymbionts that perform crucial metabolic processes for the host.

“Many insect species have obligate (primary) bacterial endosymbionts that perform crucial metabolic processes for the host (Moran and Baumann 2000;McCutcheon et al. 2009;Vogel and Moran 2011).”

• cites Moran and Baumann 2000 sourceNot checked — no full text of the source
• cites McCutcheon et al. 2009 sourceSupported
• cites Vogel and Moran 2011 sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

Borna disease viruses may have integrated into mammalian genomes over 65 Ma.

“Borna disease viruses may have integrated into mammalian genomes over 65 Ma (Horie et al. 2013).”

• cites Horie et al. 2013 sourcePartly supported

  The ‘Paleovirology of bornaviruses’ section says that bornavirus-like elements in several mammalian genomes appear to have been established approximately 65 Ma, and that bornavirus infection in mammals may go back to 65 Ma. It does not establish integration over 65 Ma ago. (LLM, conf=0.85)

  Experimental — accuracy not yet measured

Classified as probably not a substantial claim.

Tucker et al. (2013) examined the genomes of sexual and asexual D. pulex lineages and found evidence for more recent transitions to asexuality, on the order of decades.

“Recently, Tucker et al. (2013) examined the genomes of sexual and asexual D. pulex lineages and found evidence for more recent transitions to asexuality, on the order of decades.”

• cites Tucker et al. (2013) sourceSupported

May combine two claims.

Asexual animal species are rare and typically do not persist for long periods of time.

“however, asexual animal species are rare and typically do not persist for long periods of time (Barton 2009).”

• cites Barton 2009 sourcePartly supported

  The paper states that asexual species have a “relatively short life,” supporting the persistence part of the claim (section and page not provided in our copy). Its introduction says sexual reproduction dominates eukaryotic biology, but does not specifically establish that asexual animal species are rare. (LLM, conf=0.83)

  Experimental — accuracy not yet measured

May combine two claims.

RELAX correctly identified intensified selection along test branches in 100/100 replicates, with a mean selection intensity parameter k of 3.79.

“RELAX, by avoiding the unrealistic single-!assumption, correctly identified intensified selection along test branches in 100/100 replicates, with a mean selection intensity parameter (k) of 3.79.”

May combine two claims.

In endosymbionts, !T,1 representing the strongest purifying selection shifted up by an order of magnitude; !T,2 representing weakly purifying selection shifted from 0.3 to 1.0; and !T,3 representing positive selection shifted down by an order of magnitude.

“Specifically, !T;1 , representing the strongest purifying selection, shifted up by an order of magnitude; !T;2 , representing weakly purifying selection shifted from 0.3 to 1.0; and !T;3 , representing positive selection, shifted down by an order of magnitude.”

May combine two claims.

Relative to free-living bacteria, there was sufficient signal to detect relaxation in both primary endosymbionts (k = 0.28; P < 0.0001) and secondary endosymbionts (k = 0.61; P < 0.0001) independently.

“Relative to free-living bacteria, there was sufficient signal to detect relaxation in both primary endosymbionts (k = 0.28; P-value < 0.0001) and secondary endosymbionts (k = 0.61; Pvalue < 0.0001) independently.”

May combine two claims.

The backbone of the phylogeny is under intense selection (k_b > 1), as are terminal branches leading to free-living -proteobacteria, whereas the endosymbiont lineages tend to be more relaxed (k_b < 1).

“The backbone of the phylogeny is under intense selection (k b 41 shown as red in fig.6), as are terminal branches leading to free-living -proteobacteria, whereas the endosymbiont lineages tend to be more relaxed (k b < 1 shown as blue/purple in fig.6).”

May combine two claims.

RELAX is well behaved on simulated data and has power to detect relaxed selection via simulation and in four biological systems predicted to exhibit changes in the intensity of selection on a subset of branches.

“We demonstrated that RELAX is well behaved on simulated data and established its power to detect relaxed selection via simulation and in four biological systems predicted to exhibit changes in the intensity of selection on a subset of branches.”

May combine two claims.

We inferred 78% of the sites evolved under an omega of 0.82, with the remaining 22% evolving under omega = 1.2.

“We inferred 78% of the sites evolved under an ! of 0.82, with the remaining 22% evolving under !¼ 1:2.”

Classified as probably not a substantial claim. May combine two claims.

A higher ! within a group is interpreted as evidence for relaxation of selective constraints, as those constraints tend to reduce the rate of nonsynonymous substitutions relative to that of synonymous substitutions, thereby keeping ! values low.

“A higher !within a group is interpreted as evidence for relaxation of selective constraints, as those constraints tend to reduce the rate of nonsynonymous substitutions relative to that of synonymous substitutions, thereby keeping !values low.”

May combine two claims.

Identifying loss of trait or pseudogenization detects the terminal effects of relaxation but is not capable of detecting subtler changes in the intensity of selection that may not drive a gene to obsolescence or cause a loss of function.

“This approach detects the terminal effects of relaxation, but it is not capable of detecting subtler changes in the intensity of selection that may not drive a gene to obsolescence or cause a loss of function.”

May combine two claims.

RELAX's validity is established via simulations, and it can distinguish between increased positive selection and a relaxation of selective strength.

“We establish the validity of our test via simulations and show that it can distinguish between increased positive selection and a relaxation of selective strength.”

Probably not a substantial claim: may not pass S4 (based).

When rate variation over time is not modeled, ! values for specific sites or site categories represent time-averages over all branches in the phylogeny.

“When rate variation over time is not modeled, !values for specific sites or site categories represent time-averages over all branches in the phylogeny.”

May combine two claims.

In branch-site models with multiple ! categories represented by different proportions of sites, relaxation can cause the ! values inferred for the selection categories to move toward 1 and/or the proportions of sites belonging to the different categories to change in such a way that more sites are assigned to categories with ! values closer to 1.

“In the context of branch-site models with multiple !categories represented by different proportions of sites, this trend can have two different effects: The ! values inferred for the selection categories can move toward 1 (fig.1) and/or the proportions of sites belonging to the different categories can Detecting Relaxed Selection .doi:10.1093/molbev/msu400MBE change in such a way that more sites”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Gene-wide average ! values were typically below 1 because most sites in protein-coding genes are strongly conserved.

“Such gene-wide average !values were typically below 1, because most sites in protein-coding genes are strongly conserved.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Site-to-site rate variation led to the detection of sites for which ! is well above 1, even in genes where the average ! value estimated across all sites is below 1.

“This approach led to the detection of sites for which ! is well above 1, even in genes where the average !value estimated across all sites is below 1.”

May combine two claims.

When the introduction of k produces a statistically significant improvement in model fit, selection on test branches is intensified (k > 1) or relaxed (k < 1) compared with background branches.

“When the introduction of k produces a statistically significant improvement in model fit, we conclude that selection on test branches is intensified (k 4 1) or relaxed (k < 1) compared with background branches.”

Probably not a substantial claim: may not pass S3 (load-bearing).

The change from phylogeny-level resolution to branch-level resolution yielded higher branch-specific ! values than phylogeny-wide ! values.

“The change from phylogeny-level resolution to branch-level resolution yielded higher branch-specific !values than phylogeny-wide !values, mirroring the effect obtained when site-to-site rate variation was introduced.”

May combine two claims.

When selection is relaxed, ! values smaller than 1 increase toward 1, whereas ! values above 1 decrease.

“When selection is relaxed, the smaller !values increase toward 1, whereas !values above 1 decrease.”

May combine two claims.

RELAX's performance is validated using simulations as well as four biological examples where relaxation would be expected according to evolutionary theory.

“We validate the performance of RELAX using simulations as well as four biological examples where relaxation would be expected according to evolutionary theory: 1) endosymbiosis in -proteobacteria, 2) color vision genes in bats, 3) viral endogenization in bornaviruses, and 4) asexual reproduction in crustaceans.”

May combine two claims.

If the null model is rejected by the LRT, selection on the test branches is intensified (k > 1) or relaxed (k < 1) compared with the reference branches.

“If the null model is rejected by the LRT, it indicates that selection on the test branches is intensified (k 4 1) or relaxed (k < 1) compared with the reference branches.”

Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based).

The simulated scenarios capture only a tiny fraction of the breadth under which selection may actually operate.

“Importantly, these simulated scenarios capture only a tiny fraction of the breadth under which selection may actually operate.”

Classified as probably not a substantial claim.

Three sets of simulations were performed to assess the validity of RELAX.

“Three sets of simulations were performed to assess the validity of RELAX.”

Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

In empirical data sets, the signal for relaxed selection is expected to be driven primarily by sites evolving under purifying rather than positive selection, which are by far the majority.

“In empirical data sets, we expect the signal for relaxed selection to be driven primarily by sites evolving under purifying rather than positive selection, which are by far the majority.”

Classified as probably not a substantial claim.

The robustness of RELAX to the effect of increasing only the selection intensity of positive selection in a subset of branches (model misspecification) was investigated.

“We also investigated the robustness of RELAX to the effect of increasing only the selection intensity of positive selection in a subset of branches (i.e., model misspecification).”

May combine two claims.

High ! values have a flat likelihood surface, making larger empirical estimates for this parameter unreliable.

“We enforced this constraint due to the flat likelihood surface associated with high !values, which makes the larger empirical estimate for this parameter unreliable.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Natural selection is less efficient in this setting, and Muller's Ratchet can lead to the accumulation of slightly deleterious mutations.

“Natural selection is less efficient in this setting, and Muller's Ratchet can lead to the accumulation of slightly deleterious mutations (Muller 1964).”

• cites Muller 1964 sourceNot checked — no full text of the source

May combine two claims.

Obligate endosymbionts have arisen multiple times among the -proteobacteria and are passed vertically from mother to child, thereby introducing convergent features in the bacterial genomes: gene loss, smaller genomes, lower GC content, and reduced thermal stability of proteins.

“These obligate endosymbionts have arisen multiple times among the -proteobacteria (Husn ık et al. 2011) and are passed vertically from mother to child, thereby introducing convergent features in the bacterial genomes: gene loss, smaller genomes, lower GC content, and reduced thermal stability of proteins (Wernegreen 2002).”

• cites Husn ık et al. 2011Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

• cites Wernegreen 2002 sourceNot checked — no full text of the source

Classified as probably not a substantial claim. May combine two claims.

Using the General Descriptive model to select partitions for formal RELAX hypothesis testing would amount to using the data twice and substantially bias the test result.

“Furthermore, the General Descriptive model should not be used to select partitions for formal RELAX hypothesis testing, because it would amount to using the data twice and substantially bias the test result.”

May combine two claims.

Phylogenetic inference that does not account for variable substitution rates arising from skewed GC content found in endosymbionts tends to force their lineages together in a phylogenetic tree, whereas nonhomogeneous models of molecular evolution suggest a larger number of independent origins of endosymbionts from free-living bacteria.

“Phylogenetic inference that does not account for variable substitution rates arising from skewed GC content found in endosymbionts tends to force their lineages together in a phylogenetic tree, whereas nonhomogeneous models of molecular evolution suggest a larger number of independent origins of endosymbionts from free-living bacteria (Husn ık et al. 2011).”

• cites Husn ık et al. 2011Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

May combine two claims.

The pattern of stronger relaxation in primary than secondary endosymbionts was expected because primary endosymbionts likely experience tighter bottlenecks during vertical transmission and their genomes show greater evidence of extreme evolutionary features (e.g., gene loss and AT bias).

“This pattern was expected since primary endosymbionts likely experience tighter bottlenecks during vertical transmission and their genomes show greater evidence of extreme evolutionary features (e.g., gene loss and AT bias; McCutcheon and Moran 2012).”

• cites McCutcheon and Moran 2012 sourceNot checked — no full text of the source

May combine two claims.

RELAX determines the strength of evidence that k is different from 1 (reported as P-values) but not the sampling variances of the estimates.

“For all of the point estimates of k and ! reported below, it should be borne in mind that our statistical methodology allows us to determine the strength of evidence that k is different from 1 (reported as P-values) but not the sampling variances of the estimates.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Zhao, Rossiter, et al. (2009) inferred lineage-specific omega values and consistent patterns of purifying selection (omega ranging between 0.0 and 0.48).

“Zhao, Rossiter, et al. (2009) inferred lineage-specific !values and consistent patterns of purifying selection (! ranging between 0.0 and 0.48).”

• cites Zhao, Rossiter, et al. (2009)Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing).

The loss of vision in animals that reside in total darkness is a classic case of trait loss caused by relaxed selection.

“The loss of vision in animals that reside in total darkness (e.g., cave-dwelling fish) is a classic case of trait loss caused by relaxed selection (Darwin 1859).”

• cites Darwin 1859Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

May combine two claims.

The relaxation of selection in all echolocating species over tens of millions of years has not led to the formation of M/LWS1 pseudogenes in echolocating species, suggesting some functionality of this gene may have been retained.

“This relaxation of selection in all echolocating species, over tens of millions of years, has not led to the formation of M/LWS1 pseudogenes in the echolocating species, which suggests some functionality of this gene may have been retained.”

Probably not a substantial claim: may not pass S3 (load-bearing).

One would expect an excess of mildly deleterious mutations accumulating in mitochondrial genomes due to relaxed selection in asexual lineages.

“Therefore, one would expect an excess of mildly deleterious mutations accumulating in mitochondrial genomes due to relaxed selection in asexual lineages.”

• AssumptionRests on an assumption: After the transition to asexuality, there is no longer segregation between the nuclear and mitochondrial genomes, and the mitochondrial and nuclear genomes are in complete linkage disequilibrium.

Probably not a substantial claim: may not pass S3 (load-bearing).

This bias can be corrected by using nonhomogeneous nucleotide substitution models in phylogenetic inference.

“This bias can be corrected by using nonhomogeneous nucleotide substitution models in phylogenetic inference (Galtier andGouy 1995, 1998).”

• cites Galtier andGouy 1995, 1998Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S4 (based). May combine two claims.

A caveat of phylogenetic methods in general is that sequence data are uninformative regarding changes that happen at subbranch timescales and consequently that changes in selective pressure over short timescales are difficult to characterize.

“A caveat of phylogenetic methods in general is that sequence data are uninformative regarding changes that happen at subbranch timescales and consequently that changes in selective pressure over short timescales are difficult to characterize.”

May combine two claims.

Mitochondria are not part of the sexually reproducing genome, but they should experience the selective effects of a transition from sexuality to asexuality.

“Mitochondria are not part of the sexually reproducing genome, but they should experience the selective effects of a transition from sexuality to asexuality (Paland and Lynch 2006).”

• cites Paland and Lynch 2006 sourceNot checked — no full text of the source

Classified as probably not a substantial claim.

Sexual reproduction is costly from an evolutionary perspective.

“From an evolutionary perspective, sexual reproduction is costly (Maynard Smith 1978);”

• cites Maynard Smith 1978Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing).

These selective constraints likely arise from the necessity to encode genes for complex biological functions in compact genomes.

“These selective constraints likely arise from the necessity to encode genes for complex biological functions in compact genomes.”

Probably not a substantial claim: may not pass S3 (load-bearing).

The small deviation from neutrality may be driven by the components of these branches preceding viral endogenization.

“The small deviation from neutrality may be driven by the components of these branches preceding viral endogenization.”

• AssumptionRests on an assumption: If the endogenous viral elements were not subject to any level of purifying selection at the amino acid level, one would expect all the sites to evolve under an omega equal to 1.