Positive selection in the adhesion domain of Mus sperm Adam genes through gene duplications and function-driven gene complex formations.

BACKGROUND: Sperm and testes-expressed Adam genes have been shown to undergo bouts of positive selection in mammals. Despite the pervasiveness of positive selection signals, it is unclear what has driven such selective bouts. The fact that only sperm surface Adam genes show signals of positive selection within their adhesion domain has led to speculation that selection might be driven by species-specific adaptations to fertilization or sperm competition. Alternatively, duplications and neofunctionalization of Adam sperm surface genes, particularly as it is now understood in rodents, might have contributed to an acceleration of evolutionary rates and possibly adaptive diversification.
RESULTS: Here we sequenced and conducted tests of selection within the adhesion domain of sixteen known sperm-surface Adam genes among five species of the Mus genus. We find evidence of positive selection associated with all six Adam genes known to interact to form functional complexes on Mus sperm. A subset of these complex-forming sperm genes also displayed accelerated branch evolution with Adam5 evolving under positive selection. In contrast to our previous findings in primates, selective bouts within Mus sperm Adams showed no associations to proxies of sperm competition. Expanded phylogenetic analysis including sequence data from other placental mammals allowed us to uncover ancient and recent episodes of adaptive evolution.
CONCLUSIONS: The prevailing signals of rapid divergence and positive selection detected within the adhesion domain of interacting sperm Adams is driven by duplications and potential neofunctionalizations that are in some cases ancient (Adams 2, 3 and 5) or more recent (Adams 1b, 4b and 6).

Background

The majority of protein coding genes analyzed through molecular evolutionary studies have been found to evolve under purifying selection, but genes that function in perception, immunity and reproduction are often fast-evolving exceptions to this rule [1-3]. Reproductive genes, such as those that code for species-specific fertilization proteins, male accessory gland proteins, and sperm proteins have been shown to exhibit rapid evolution in taxa as diverse as invertebrates, mammals and plants [4-9].

The ADAM (A Disintegrin And Metalloprotease) gene family contains at least 35 members in mammals, with more than half known to be testes-expressed. The analysis of ADAM family evolution among mammals has found faster divergence of genes expressed in testes with evidence of positive selection at codon sites within the adhesion domain of sperm surface genes [10-13]. This localization of adaptive selection in Adam genes led us to hypothesize an important role in sperm-egg interactions with positive selection possibly driven by sexual selection. Thus far, very few studies have successfully linked bouts of positive selection at sperm surface genes to differences in mating systems, testes masses or other proxies of sexual selection [14].

Sexual selection is likely to have driven positive selection within the adhesion domain of sperm Adam genes in rodents. In the Mus genus, sperm competition favours larger numbers of sperm and has resulted in marked differences in relative testes size between different species, with Mus spicilegus having the largest relative testes mass (RTM) and relative testes weight (RTW) [15-17]. Moreover, knockout mice for ADAM2 and ADAM3 show drastic decreases in sperm aggregation, a trait that has been suggested to confer sperm with competitive advantages [18-20].

Alternatively, localized signals of positive selection within the adhesion domain of Adam genes could result from species-specific adaptations to fertilization. There are sixteen Adam sperm surface genes in mice, with twelve known to be localized on mature sperm and three (Adams 1, 2 and 3) being directly linked to sperm migration and sperm-egg adhesion and fusion. ADAM3 knockouts appear to have the most severe effect on reproductive fitness, resulting in infertile males due to deficiencies in sperm-zona pellucida (ZP) interactions, and more importantly, sperm migration into the oviduct [21-23]. ADAM2 knockouts also significantly affect reproductive success. In vivo, ADAM2 null mice have a fertility rate 50 times lower than the wild-type. This drop in fertility once again does not appear to be the result of a single process, but is instead a combination of deficiencies in sperm-egg fusion, sperm-egg binding, sperm-ZP binding and sperm migration [24]. ADAM1a knockouts result in sperm unable to migrate to the egg; in vivo the knockout produces an infertile phenotype but in vitro, sperm are able to fertilize eggs. ADAM1b knockouts appear to produce normal sperm but affect the levels of ADAM2 on mature sperm [25,26]. Interestingly, six of the sperm surface genes (Adams 1 to 6) assemble into functional complexes. Currently, there is evidence for three sperm-specific complexes (ADAM2-ADAM3-ADAM4, ADAM2-ADAM3-ADAM5, and ADAM2-ADAM3-ADAM6), two testes-specific complexes (ADAM1a-ADAM2, and ADAM2-ADAM3), and one complex common to both (ADAM1b-ADAM2) [27]. All complexes require at least ADAM2 and/or ADAM3, if not both, and their interactions appear to be central for a variety of sperm functional adaptations to fertility in mice.

One final consideration is that while the inclusion of a wide range of species in prior phylogenetic studies of Adam genes has served to resolve some aspects of the history of the gene family, the use of very distant species makes the proper identification of selective pressures more difficult [12,28,29]. This is because bouts of selection can be localized to specific clades or even branches within the phylogeny, causing a failure to detect a signal of selection when a wide range of species are included in the analysis [12,30]. Similarly, analyses utilizing wide ranges of ancient paralogs that cluster within a phylogenetic clade can fail to detect positive selection that is gene-specific [29].

Here we present novel sequence data for all sperm-expressed members of the ADAM family in Mus. Sequences were utilized to conduct tests of selection within the adhesion domain of sixteen known sperm surface genes among five species of the Mus genus. We find evidence of positive selection associated with all six sperm surface Adam genes involved in interacting complexes within the Mus phylogeny, and see accelerated branch evolution for some. The selective bouts showed no associations to proxies of sperm competition. We expanded the phylogenetic analysis to include species within the Glires clade and from the superorder Laurasiatheria and found positive selection across groups (ancient) for Adams 2, 3 and 5 and more recent localized bouts of selection for Adams 1b, 4b and 6 in Mus/Glires.

Methods

DNA samples and sequencing

Genomic DNA was obtained from the Jackson Laboratory (http://www.jax.org) for M. musculus musculus, M. m. domesticus, M. spretus, M. spicilegus and M. caroli (Strain Names: SKIVE/Ei, LEWES/Ei, SPRET/Ei, PANCEVO/Ei and Mus caroli/Ei respectively). Primers were designed for the adhesion domain of all known Mus sperm Adams (1a, 1b, 2, 3, 4a, 4b, 5, 6a, 6b, 7, 18, 24, 26a, 26b, 30 and 32) using Primer3 (http://frodo.wi.mit.edu/) and published M. m. domesticus sequence data (Additional file 1: Table S1). The adhesion domain was identified for each gene using The Motif Scan Server’s Prosite options (http://myhits.isb-sib.ch/cgi-bin/motif_scan). Polymerase chain reaction (PCR) amplification of adhesion domain exons was carried out with Phusion High-Fidelity DNA Polymerase (Thermo Scientific) in 12.5 and 25.0 μl reactions using the following general conditions: initial denaturation for 30 s (98°C) was followed by 35 cycles of denaturation for 10 s (98°C), annealing for 30 s (temperature gradient), and extension for 9 s (72°C). A final extension step was carried out for 5 min (72°C). Optimization of most primer pairs resulted in a species-specific temperature gradient for the annealing step that ranged from 55-70°C (see Additional file 1: Table S2 for optimized primer conditions).

Optimized PCR products were Sanger sequenced at the SickKids TCAG DNA Sequencing Facilities in Toronto, Canada. Products were sequenced using both the forward and reverse primers and a consensus sequence for each species was constructed using ClustalW in Mega 5.2 with visual inspection and manual adjustments [31,32]. For some Adam genes, M. spretus sequences were retrieved from the SNP database (http://www.sanger.ac.uk/cgi-bin/modelorgs/mousegenomes/snps.pl). All our sequence data has been deposited in Genbank under accession numbers KF144343 to KF144410.

Phylogenetic reconstruction

The Basic Local Alignment Search Tool (BLAST) at NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi) was used to query sequence data against the mouse genome to ensure that primers had correctly isolated targeted Adam exons. To further enhance confidence in Mus species sequencing data, and to confirm orthology among different Adam genes, we included our sequences within a larger mammalian phylogeny. We collected Adam gene sequence data for 98 additional mammals from NCBI and Ensembl (See Additional file 1: Table S1 for accession numbers) and aligned the adhesion domain using ClustalW in Mega5.2. The ProtTest 2.4 Server was utilized to determine the best model of protein evolution for phylogenetic reconstruction [33]. The phylogeny was built in Mega 5.2 using Maximum Likelihood and the reliability of the tree branching was assessed using 1,000 bootstrap replicates [34]. This alignment and phylogeny has been deposited to treeBASE as indicated in the Availability of supporting data section.

Phylogenetic branch and site tests of selection

Alignments were analyzed using different models within the codeml program of PAML v. 4.7 using an unrooted Mus phylogeny [35]. The likelihoods of the one ratio model, with ω estimated or fixed at 1.0, and that of the free-ratio model were compared. We also used the two-ratio and the branch-site models to test for differential evolutionary rates and selection linked to proxies of sexual selection. The tests were done by flagging the ancestral branch and the branches leading to the two species with larger relative testes measurements (M. spicilegus and M. spretus). Two measures of testes size are commonly used in the literature, relative testes weight (RTW) and relative testes mass (RTM). Depending on the scale used, there is a 4 to 5-fold difference in relative testes size for the Mus species examined in this work. M. spicilegus boasts the largest values (RTW = 0.030, RTM = 1.682) followed by M. spretus (RTW = 0.017, RWM = 1.072). The remaining species utilized in this study have the following values: M. m. musculus (RTW = 0.006, RTM = 0.411), M. m. domesticus (RTW = 0.008, RTM = 0.506) and M. caroli (RTW =0.007, RTM = 0.434) [15-17].

The likelihoods of the site models M8 and M8a were calculated to identify, within the Mus phylogeny, genes and sites that had experienced positive selection. These models allow ω to vary among codon sites; model M8 assumes that positive selection might occur and ω values can exceed 1 while the null model, M8a, fixes ω at 1. For genes showing evidence of positive selection within the Mus genus, the M8-M8a tests of selection were conducted for species of the Glires clade (Rodentia and Lagomorpha) and the superorder Laurasiatheria. This approach was used to determine whether bouts of positive selection were restricted to Mus and/or Glires or more ancestrally shared with other placental mammals. The Bayes Empirical Bayes (BEB) method was conducted in conjunction with model M8 to identify specific amino acid sites experiencing bouts of adaptive evolution [36].

Additional tests of selection and functional divergence

Tests of site-specific functional divergence were conducted on complex-forming paralogous Mus sperm Adams (1a/1b, 4a/4b, 6a/6b) using the GU99 method within DIVERGE v. 1.04 [37,38]. This analysis identifies gene pairs evolving under functional divergence, where one duplicate is highly conserved while the other evolves in a highly variable manner [39]. TreeSAAP v. 3.2, a program that examines amino acid substitution by measuring selection’s effect on 31 different amino acid properties, was utilized within the expanded phylogenies (Glires and Laurasiatheria) to identify sites of positive selection for Adams 1, 2, 3, 4 and 5 [40]. These two analyses provide amino acid sites believed to be positively selected or integral for functional divergence. Sites identified through TreeSAAP were utilized to validate or reject those from the PAML BEB results, while DIVERGE assessed if amino acids identified as evolving under positive selection by BEB in PAML contributed to functional divergence between paralogous Adam genes.

Results

Our phylogenetic reconstruction supported the overall orthology of mammalian Adam genes used in this study (Figure 1 and Additional file 1: Table S3). The nested branch models of evolution showed that in most cases a model that allows for different ω estimates per tree branch was not necessarily a better fit to the data than a model assuming a single estimated ω for all branches in the Mus tree (Additional file 1: Table S4). For Adams 1a, 4a, 6a, 6b, 7 and 30, an average branch ω significantly lower than one (purifying selection) was a better fit to the data than an average branch ω of one. Adam4b also showed a significant result in support of purifying selection at a 10% level of significance (FDR corrected P < 0.1), whereas Adam5 was found to be evolving under positive selection throughout the phylogeny (Table 1 and Additional file 1: Table S4). Those Adams not listed above had average branch ω values non-significantly different from one, indicating rapid branch evolution due to relaxed selection (Table 1). It is noteworthy that several genes (Adams 1b, 2, 3, 4 and 5) that interact to form functional complexes on mature mouse sperm are among the relaxed/positively selected genes with large average ω branch values (Table 1).

Figure 1

Sperm molecular phylogeny supporting sequence orthology. The WAG model of protein evolution with G, the gamma distribution shape parameter, and I, invariant sites, was selected for the phylogenetic reconstruction. The model was selected based on its likelihood and AIC (akaike information criterion) value (Additional file 1: Table S3).

Table 1

Branch and site tests of selection in

Gene	l	n	2Δℓ M0N0	ω	Branch	2Δℓ	p1; ω (M8)	Site
			(ω vs ω = 1.0)		Selection	(M8-M8a)		Selection
Adam1a	321	5	9.78	0.16	Purifying	0		Purifying
Adam1b	321	5	0.03	0.91	Relaxed	3.89	0.07; 9.10	Positive
Adam1	321	10	63.11	0.21	Purifying	1.94		Purifying
Adam2	333	5	0.2	0.78	Relaxed	9.77	0.11; 12.87	Positive
Adam3	339	5	0.04	0.89	Relaxed	4.08	0.13; 8.92	Positive
Adam4a	327	5	6.18	0.22	Purifying	0		Purifying
Adam4b	327	5	3.25	4.69	Purifying	15.36	0.04; 38.74	Positive
Adam4	327	10	0.8	1.39	Relaxed	49.84	0.07; 23.54	Positive
Adam5	273	5	4.36	3.78	Positive	24.38	0.20; 30.03	Positive
Adam6a	327	5	9.75	0.21	Purifying	2.02		Purifying
Adam6b	327	5	9.74	0.17	Purifying	0.65		Purifying
Adam6	327	10	11.67	0.32	Purifying	8.15	0.08; 5.69	Positive
Adam7	267	5	11.03	0.15	Purifying	0		Purifying
Adam18	339	5	1.96	0.46	Relaxed	2.21		Purifying
Adam24	330	5	0.06	1.15	Relaxed	7.64	0.06; 19.11	Positive
Adam26a	327	4	0.07	0.87	Relaxed	1.53		Purifying
Adam26b	327	4	1.35	0.5	Relaxed	0.11		Purifying
Adam26	327	7	0.24	0.78	Relaxed	4.03	0.29; 3.63	Positive
Adam30	327	5	7.95	0.14	Purifying	0		Purifying
Adam32	285	5	1.91	0.46	Relaxed	0.01		Purifying

n = number of species included; l = length of adhesion domain analyzed (bp); 2Δℓ = the difference in likelihood estimates from different models of selection; ω= dN/dS per codon for sites under positive selection; p1 = proportion of codon sites under positive selection. Test statistics (2Δℓ) are bolded (FDR corrected P < 0.05) or underlined (FDR corrected P < 0.10) to denote statistical significance.

While there was evidence of an overall constancy of ω ratios across all branches in the Mus phylogeny, it is possible that localized bouts of sexual selection within branches might have been lost in such a test. Therefore we tested branches leading to species with larger testes, as a proxy of sperm competition, by estimating the likelihood of a model with estimated ω along the foreground and background branches against a model with the foreground branch ω fixed at 1.0. Down the M. spicilegus and M. spretus foreground lineages, an estimated ω < 1.0 was only a better model for Adams 4a and 7. Results from the branch-site model within PAML also indicated that codon sites specific to M. spicilegus and/or M. spretus were not evolving more quickly under the influence of sexual selective pressures. Thus, we found evidence of purifying selection for two Adam genes and no indication of sexual selection at the branch ancestral to the species with largest RTW and RTM or at the branch leading to M. spicilegus or M. spretus individually using two separate tests (Additional file 1: Tables S4 and S5).

Despite the apparent constancy of evolutionary rates within branches of the Mus phylogeny, it is possible that some codon sites might have been influenced by bouts of positive selection. Likelihood ratio tests comparing PAML’s site models (M8 and M8a) were conducted on each of the 16 known Mus sperm Adams (as listed in the Methods section). The results indicate that positive selection has driven the evolution of codon sites within Adams 2, 4b, 5 and 24 (FDR corrected P < 0.05), with Adams 1b, 3 and 26 also showing evidence of positive selection (FDR corrected P < 0.1) (Table 1). When paralogous gene pairs were examined together, positive selection was also found to influence the evolution of Adams 4, 6 and 26 (Table 1). We used DIVERGE analysis on Adams 1, 4 and 6 to assess the potential role of positively selected sites on functional divergence between gene paralogs. For Adam1, seven out of nine positively selected sites were supported as contributors to functional divergence between Adams 1a and 1b (Additional file 2: Figure S1). Nine out of eleven positively selected sites were supported as contributors to functional divergence between Adams 4a and 4b (Additional file 2: Figure S2). Adams 6a and 6b did not show positive selection by themselves but they did when analyzed together (Table 1). None of the positively selected sites detected using PAML were found to contribute to functional divergence between these paralogs (Additional file 2: Figure S3).

Expanded phylogenies for Glires (including our Mus sequences) and Laurasiatheria, were produced for all complex-forming sperm Adams to examine whether the signals of positive selection identified for Mus were clade specific, shared with Rodentia and Lagomorpha (Glires), or ancient and shared with other placental mammals (Laurasiatheria). PAML analyses suggested that Adams 2, 3 and 5 displayed site-specific evidence of positive selection throughout the Glires and Laurasitheria, indicating that these signals are not Mus-specific. In contrast to these results, clade-specific bouts of selection appear to be present for Adams 1, 4 and 6. Positive selection of Adam1 in Mus is restricted to Adam1b (Table 1), a pattern mirrored by the paralogs in Glires, with no evidence of positive selection within Laurasiatheria (Table 2). There were not enough sequences available for Adams 4 and 6 to run the analysis outside Glires, but a signal of positive selection was found for Adam4b but not Adam4a in Mus (Table 1), so the situation could be similar to what was seen for Adam1. Adam6 was only positively selected when both paralogs (6a and 6b) were pooled together in the analysis (Table 1), and the signal was lost when other species of Glires were included, suggesting that positive selection is localized in Mus. The majority of positively selected sites detected by PAML’s BEB analysis within Glires and Laurasiatheria were validated using TreeSAAP (Table 2).

Table 2

Sperm site selection for expanded species groups showing clade localization of selective bouts

Gene	Group	n	p1; ω (M8)	2Δℓ (M8-M8a)	BEB sites (P > 95%)	TreeSAAP sites (BEB)
Adam1a	Glires	9		1.51
Adam1b	Glires	9	0.24; 1.93	4.56	2	30 (2)
Adam1	Glires	18	0.16; 2.05	10.89	4	59 (4)
	Laurasiatheria	6		2.44
Adam2	Glires	9	0.02; 21.73	11.34	2	38 (2)
	Laurasiatheria	7	0.33; 2.54	22.71	16	55 (15)
Adam3	Glires	9	0.03; 8.44	5.07	1	27 (1)
	Laurasiatheria	8	0.13; 2.64	10.05	1	48 (1)
Adam4	Glires	12	0.31; 3.98	24.71	11	20 (9)
	Laurasiatheria	2	Not Run
Adam5	Glires	8	0.05; 21.51	23.32	4	20 (3)
	Laurasiatheria	8	0.16; 3.55	24.09	9	37 (9)
Adam6	Glires	13		0.6
	Laurasiatheria	3	Not Run

n, 2Δℓ, ω, and p1 are utilized as in Table 1. BEB Sites are the number of sites identified as being under positive selection using model M8 in PAML and a posterior probability threshold higher than 95%. TreeSAAP Sites are the number of positively selected sites as identified by TreeSAAP with the number of sites shared with PAML in brackets. Significance of the 2Δℓ test statistics is depicted as in Table 1.

Discussion

The lack of evidence of linkages between proxies of sexual selection and adaptive evolution in Mus is in contrast to prior evidence we have found of sexual selection in primates for Adam2 and Adam18 [12]. This result highlights the importance of testing selection within specific groups or clades before making generalizations about sexual selection, as selective bouts can be lineage-specific and thus lost in phylogenetic analysis that include widely diverged species [41]. In fact, based on evidence on the potential role of sperm aggregation in sperm competition, it is possible that sexual selection might drive the evolution of some sperm Adam genes in different genera such as Apodemus (common wood mouse) and Peromyscus (deer mice) [18,19]. The different results observed between Adam genes in primates [12] and species of the Mus genus could also be explained if any relationship between proxies of sperm competition and positive selection is driven by transitions from monandry to polyandry.

Results for the site model (M8 vs. M8a) indicate that positive selection has driven the evolution of codon sites within Adams 1b, 2, 3, 4b, 5, 6, 24 and 26. Six of these sperm surface genes (Adams 1–6) interact in forming functional complexes, and an interesting divide exists within these positively selected genes in Mus. As examined by Huxley-Jones and colleagues, Adams 2, 3 and 5 are closely related members of clade B [28]. They are all large, single-copy, multi-exon genes that display positive selection throughout the Glires clade and the superorder Laurasiatheria, indicating that these selective bouts are ancient and not Mus-specific. Adams 1, 4 and 6 belong to the more recently derived clade C [28]. They are all small, single-exon genes that are thought to have arisen through retrotransposition of spliced Adam mRNA into an ancestral genome [27]. In rodents, paralogous members of clade C are likely the result of even more recent tandem duplications, as they are situated adjacent to their duplicates on chromosomes 5 (Adam1) and 12 (Adams 4 and 6). In agreement with a recent origin, we found positive selection for clade C Adams within Mus affecting either a single member of the gene pair or when both paralogs were analyzed together. The pairing of purifying and positive selection seen for Adams 1a and 1b alongside differences in protein localization and function is in support of the classical model of neofunctionalization [25,26,42]. Adam 4 paralogs show the same pattern of purifying and positive selection, which is also strongly suggestive of neofunctionalization, but nothing is yet known about the duplicate functions or protein localization. The fact that most codon sites identified to be under positive selection in Adam1b and Adam4b in Mus are also found to contribute to functional divergence between paralogs provides further support to the hypothesis of neofunctionalization of both Adams 1 and 4. Adam1 showed no evidence of selection within Laurasiatheria and the Adam6 signal was lost when other species of Glires were included, suggesting that positive selection within these clade C Adams is specific to Mus. Interestingly, Adam6 showed no evidence of functional divergence between paralogs which might suggest a more recent duplication event or weaker selective pressures acting on this gene.

It is yet unclear what drives positive selection at Adams 24 and 26 (Table 1). Adam26 is another member of clade C, and although little is known about its function, the positive selection signal within its adhesion domain is similar to that of Adam6, thus likely driven by a relatively recent duplication event. Adam24 mice have been functionally assessed previously. They show a 50% drop in fertility with an increased number of sperm fusing to each egg, supporting the hypothesis that ADAM24 functions as an important sperm component to block polyspermy [43]. It is therefore possible that the adaptive evolution of Mus Adam24 might be linked to species-specific adaptation to trigger such blocks.

Conclusions

We have tested positive selection within the adhesion domain of all sperm-expressed members of the Mus Adam gene family and have identified an important role played by duplications and neofunctionalization. We also established that these bouts are not driven by selection linked to sperm competitive pressures. This stands in contrast to our previous findings in primates and highlights the importance of phylogenetically testing bouts of selection within specific species groups [12]. An expansion of the phylogenetic analysis beyond Mus highlights a dichotomy in the mode of evolution of the adhesion domain of sperm surface Adam genes driven by a combination of ancient (Adams 2, 3 and 5) and more recent (Adams 1b, 4b and 6) neofunctionalization of complex forming sperm proteins.

Availability of supporting data

The data set supporting the results of this article is available from the TreeBase repository, http://purl.org/phylo/treebase/phylows/study/TB2:S14416. Sequencing data supporting the results of this study is available from NCBI under the following accession numbers: KF144343 to KF144410.

Competing interests

Both authors declare that they have no competing interests.

Authors’ contributions

AC conceived of the study. PG carried out molecular genetic studies and bioinformatics. PG and AC analyzed the final dataset and wrote the manuscript. Both authors read and approved the final manuscript.

Additional file 1

Tables S1, S2, S3, S4 and S5. Accession numbers for species included in expanded phylogeny, primer conditions, ProtTest output, nested model (M0, M1, M2) likelihood ratio test results from PAML, and branch site model likelihood ratio results from PAML.

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Additional file 2

Figures S1, S2 and S3. Alignments of positively selected and functionally divergent sites as identified by Bayes Empirical Bayes in PAML and GU99 in Diverge for paralogous complex-forming Adam genes (1, 4, and 6).

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