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BMC Evolutionary Biology

, 19:53 | Cite as

Contrasting patterns of molecular evolution in metazoan germ line genes

  • Carrie A. Whittle
  • Cassandra G. ExtavourEmail author
Open Access
Research article
Part of the following topical collections:
  1. Genome evolution and evolutionary systems biology

Abstract

Background

Germ lines are the cell lineages that give rise to the sperm and eggs in animals. The germ lines first arise from primordial germ cells (PGCs) during embryogenesis: these form from either a presumed derived mode of preformed germ plasm (inheritance) or from an ancestral mechanism of inductive cell-cell signalling (induction). Numerous genes involved in germ line specification and development have been identified and functionally studied. However, little is known about the molecular evolutionary dynamics of germ line genes in metazoan model systems.

Results

Here, we studied the molecular evolution of germ line genes within three metazoan model systems. These include the genus Drosophila (N=34 genes, inheritance), the fellow insect Apis (N=30, induction), and their more distant relative Caenorhabditis (N=23, inheritance). Using multiple species and established phylogenies in each genus, we report that germ line genes exhibited marked variation in the constraint on protein sequence divergence (dN/dS) and codon usage bias (CUB) within each genus. Importantly, we found that de novo lineage-specific inheritance (LSI) genes in Drosophila (osk, pgc) and in Caenorhabditis (pie-1, pgl-1), which are essential to germ plasm functions under the derived inheritance mode, displayed rapid protein sequence divergence relative to the other germ line genes within each respective genus. We show this may reflect the evolution of specialized germ plasm functions and/or low pleiotropy of LSI genes, features not shared with other germ line genes. In addition, we observed that the relative ranking of dN/dS and of CUB between genera were each more strongly correlated between Drosophila and Caenorhabditis, from different phyla, than between Drosophila and its insect relative Apis, suggesting taxonomic differences in how germ line genes have evolved.

Conclusions

Taken together, the present results advance our understanding of the evolution of animal germ line genes within three well-known metazoan models. Further, the findings provide insights to the molecular evolution of germ line genes with respect to LSI status, pleiotropy, adaptive evolution as well as PGC-specification mode.

Keywords

Germ line genes Primordial germ cells Protein divergence Codon usage Molecular evolution Metazoans Specification mode Drosophila Caenorhabditis Apis 

Background

Germ lines are the specialized cell lineage contained in the gonads of sexually reproducing animals that give rise to the sperm and eggs. The germ cell lineages are separate from the soma and are the only source of heritable genetic variation passed between generations, providing them with a crucial role in reproductive success, fitness and evolutionary biology. Extensive experimental and cytological research has focused on the discovery and functionality of germ line genes in animal models, which has led to the identification of a wide range of genes involved in germ line establishment and development [1, 2, 3, 4, 5]. At present however, much remains unknown about the molecular evolutionary dynamics of these germ line genes within metazoan model systems.

The germ lines first emerge in early embryogenesis with the formation of primordial germ cells (PGCs). The PGCs in some organisms arise from a presumed evolutionarily derived mode of maternally generated germ line determinants (inheritance), otherwise known as germ plasm (specialized cytoplasm containing proteins and RNAs), as has been observed in systems including flies (Drosophila), wasps (Nasonia), nematodes (Caenorhabditis), and frogs (Xenopus) [2, 4, 6, 7, 8, 9]. Alternatively, PGCs may emerge from an ancestral mechanism involving inductive cell-cell signalling pathways (induction) as has been supported by experimental embryological and functional genetic data in taxa such as crickets (Gryllus), mice (Mus), and salamanders (Ambystoma) [4, 5, 8, 9, 10, 11, 12]. Gene products involved in germ line specification and in various stages of germ line development have been identified using different model systems (e.g., [1, 2, 3, 4, 5, 13, 14, 15, 16]), allowing study of how those genes involved in core germ line functions have evolved.

A primary model for the study of germ line genes has been Drosophila. In Drosophila, PGC-specification depends on maternally provided germ plasm (inheritance), which is asymmetrically located in the posterior region of the oocyte cytoplasm [4, 17]. Genes essential to germ plasm formation and PGC specification in Drosophila include two genes believed to have originated only in insects, oskar (or osk) and pgc (polar granule component) [2, 4, 18, 19]. osk is involved in the recruitment of most other germ plasm components in D. melanogaster [2, 4]. pgc is involved in transcriptional repression in pole cells, and may be exclusive to Drosophila, as this gene has not been reported in other Dipteran insects or other animals to date [19, 20]. Together, these two genes, osk and pgc appear to be de novo genes [21] originating in specific insect lineages that may have facilitated the evolutionary transition to germ plasm and evolved crucial functions in early stages of germ line development, that is PGC specification [2, 4, 5, 17, 19].

Another central model for germ line gene research is the nematode C. elegans. In this taxon, similar to Drosophila, PGCs are specified under the inheritance mode, via localized molecular entities denoted in that system as P granules [3, 22]. Rather than presence alone, a sufficient concentration and specific conformation of P granules are required for them to act as germ line determinants [23, 24, 25]. P granules contain protein products of nematode-specific genes, including the RNA-binding pgl-1 (P-granule abnormality) (a partly redundant pgl-3 also plays a role; [26]), which helps keep P granule components localized and thus functional [4, 26]. meg-1 (maternal-effect germ cell defective), which has been linked to P-granule assembly and fertility [meg-2 has also been identified as putatively partly redundant; [27, 28]), may be specific to the species C. elegans, as it appears to display poor homology to any other animal proteins, including within the same genus [3, 27]. In addition, the Caenorhabditis gene pie-1 (pharyngeal and intestinal excess), is involved in transcriptional repression and maintaining germ cell fate [29], and shares functional (but not sequence) similarity to D. melanogaster pgc [1, 4, 19]. This gene is essential for PGC establishment and has only been reported in nematodes [4]. In this regard, whilst the inheritance mode (germ plasm) is shared between Drosophila and Caenorhabditis, the key upstream regulators appear to have arisen independently and in a lineage-restricted manner in these two model organisms [2, 3, 4, 19, 30], consistent with the proposed convergent evolution of this mechanism [7, 9].

An additional primary model of study of germ line genes including those involved in PGC-specification, this time using induction mode, or zygotic cell-cell signalling, is mouse [4, 5, 17]. Whilst much of the genetic programming remains to be understood, it has been established that in early embryogenesis ligands including BMPs (Bone Morphogenetic Proteins; particularly BMP2 and BMP4) and WNT3 are crucial for inducing signals that initiate PGC formation [4, 5]. Such signalling activates expression of the transcription factor Blimp-1 (B lymphocyte-induced maturation protein-1), needed for repression of somatic gene expression, epigenetic programming of the genome, and ultimately PGC formation [4, 5, 17, 31]. Recently, similar processes involving BMP and Blimp-1 signalling have been shown to be utilized in the induction of PGCs in a basally branching insect, the cricket Gryllus bimaculatus [10, 32] suggesting conservation of this signalling mechanism across these divergent taxa with the induction mode. Although the precise nature of the signalling pathways that may induce PGCs in other insects remains largely unknown, unlike in Drosophila, in some insects PGCs are first described as arising from among the mesoderm of the abdominal segments in the vicinity of the future primordial gonad [33]. This is the case, for example, in the honeybee Apis mellifera, where cells with the morphology and gene expression typical of animal PGCs are first detected late in embryogenesis in the abdominal segments that will house the primordial gonad [34, 35, 36, 37, 38]. Thus, we infer that BMP/Blimp-1 signalling to induce the germ line may likely be shared with other insect models that appear to specify PGCs via inductive-signalling [33] such as Apis.

Many germ line genes, including specification genes, appear to play multiple roles in germ line development and/or across animal models [1, 3, 4, 13, 14, 15, 16]. The gene vasa, an ATP-dependent RNA helicase, is a universal marker of germ lines [1, 39] (although in some animals it plays somatic roles (reviewed by [40]). The products of vasa are essential components of Drosophila germ plasm [18, 41, 42], localize to C. elegans P granules (the vasa ortholog glh-1 is essential for fertility; glh-2-4 may be nonessential; [43, 44]), and become upregulated in mouse and cricket PGCs following their induction (vasa mouse ortholog is mvh: 10, 32, [45, 46]), consistent with a ubiquitous role in germ lines across these divergent systems. In addition, nanos (or nos) and pumilio (pum) encode interacting RNA-binding proteins which have each been linked to germ plasm and PGCs in Drosophila and been associated with early germ line development across metazoans (reviewed by [1, 4, 47]). In sum, current data suggest that while certain germ line genes are particularly involved in either the inheritance and induction modes [1, 2, 3, 4, 5], many germ line genes play various roles across modes and/or throughout germ line development [1, 3, 4, 13, 14, 15, 16].

At present, investigations into the molecular evolution of germ line genes remain uncommon, and the few studies available have largely focused on putative genetic regulators in the germ line stem cells of Drosophila. For instance, a recent study in Drosophila examined 366 genes identified from RNAi screening as involved in adult self-renewing female germ line stem cells [48]. That study suggested those genes were increased targets of short-term selective sweeps, but not typically of recurrent long-term (interspecies) positive selection based on dN/dS [48]. Separate assessments have reported that certain genes expressed in adult germ lines including stem cells (e.g. pum, stone-wall (stwl)) have evolved adaptively and/or in response to Wolbachia infection in Drosophila [49, 50, 51]. In terms of the investigation of germ line genes involved in PGC specification [19, 52], a study of the osk gene in Drosophila has shown that dN/dS varies among segments of this protein and shows some signs of positive selection. However, these signs were reported for only one of the 18 species studied (D. virilis), and the signal was not consistent across various approaches even in that lineage [52]. Given the limited data on the molecular evolution of germ line genes further study is warranted in metazoan models.

In the present study, we investigate the molecular evolution of genes with experimental or cytological evidence of involvement in germ line specification and/or development, broadly referred to herein as germ line genes, in metazoan models. Specifically, we examine 34 genes in our main target and reference genus Drosophila (Phylum Arthropoda, Order Diptera), as well as 23 genes in the divergent genus Caenorhabditis (Phylum Nematoda, Order Rhabditida). These genera represent two cases of independently evolved inheritance mode of PGC-specification, and each contains lineage-specific inheritance (LSI) genes, essential to germ plasm functionality (osk, pgc for Drosophila and pie-1 and pgl-1 for Caenorhabditis). We also study 30 genes in a second insect genus, Apis (Phylum Arthropoda, Order Hymenoptera), a taxon likely to use the induction mode. Collectively, the results provide insights into the molecular evolutionary dynamics of germ line genes within each of three distinct metazoan model genera. Most notably, the data show that germ line genes exhibit wide variation in constraint on protein sequence evolution and codon usage within each genus. Further, the LSI genes, which are essential to germ line function and found only in certain lineages, consistently exhibit a striking history of rapid protein sequence evolution relative to other germ line genes in each respective genus. We show this pattern may be explained by adaptive evolution and/or low pleiotropy.

Results and Discussion

We assessed the molecular evolution of 34 germ line genes across six species of the melanogaster group in our main target and reference genus Drosophila (D melanogaster, D. erecta, D. sechellia, D. simulans, D. yakuba, and an outgroup species D. ananassae (Additional file 1: Table S1 and Figure S1). The gene list included 34 genes with known experimental or cytological evidence of functionality in early germ line development, including PGC specification, and is provided in Table 1. For our study, the genes for Drosophila were grouped into four categories as follows: 1) the LSI genes osk and pgc, which are directly involved in germ plasm function, and found only in certain insects, including Drosophila [2, 19]; 2) genes involved in regulating PGC-specification under the inheritance mode (“Inheritance”, N=13) in Drosophila (and other organisms) studied to date; 3) orthologs to genes found to be involved in inductive signalling mode in mice or other models (“Induction”, N=15); and 4) genes involved in germ line formation regardless of mode (“Inh/Ind”, N=4) (Table 1). In addition to studying these 34 germ line genes in Drosophila, we examined identifiable orthologs (see Methods) to this gene set in Caenorhabditis (for categories 2-4; four species studied, Tables S1 and S2), as well as two Caenorhabditis LSI genes (pie-1 and pgl-1; N=23 genes total, Additional file 1: Table S2, see Methods), and orthologs found in the fellow insect genus Apis (N=30 genes; four species studied; Additional file 1: Table S3), which likely exhibits induction.
Table 1

The 34 germ line genes studied in Drosophila. For this study, genes have been classified based on known roles in PGC-specification in established models. However, many genes (excluding LSI genes) have been reported to play roles in both germ line specification and at some stage(s) of germ line development or maintenance across model systems and specification modes [1, 3, 4, 13, 14, 15, 16].

Gene

Gene Name

FlyBase ID

Length (codons)

Established PGC or Germ Line Role in Animal Models

References

Category 1: Lineage-Specific Inheritance (LSI) (N=2)

osk

oskar

FBgn0003015

607

Assembly of germ plasm components

[2, 4, 18]

pgc

polar granule component

FBgn0016053

72

Localized to germ plasm; transcriptional repression in pole cells (DM)

[19, 20]

Category 2: Inheritance (N=13)

armi

armitage

FBgn0041164

1189

osk functionality and mRNA translocation (DM)

[125]

bru-1

bruno 1

FBgn0000114

811

osk regulation: binding mRNA, translocation (DM)

[126]

capu

cappuccino

FBgn0000256

1362

Interacts with spir; Localization of osk mRNA, VASA and STAUFF to germ plasm, oocyte polarity (DM)

[127, 128]

cup

cup

FBgn0000392

1118

Osk regulation, with bruno (DM)

[129]

cycB

cyclin B

FBgn0000405

531

Cell cycle; mRNA localized to germ plasm (DM)

[20, 130]

gcl

germ cell less

FBgn0005695

570

Localized to germ plasm; required for PGC specification (DM)

[20]

mago

mago nashi

FBgn0002736

148

Required for PGC specification; localization of osk mRNA and STAUF to posterior pole of oocyte (DM)

[131]

orb

oo18 RNA-binding protein

FBgn0004882

916

Localized to germ plasm; osk regulation, oocyte polarity (DM)

[20, 132]

psq

pipsqueak

FBgn0263102

1124

Required for germ plasm formation

[133]

spir

spire

FBgn0003475

1021

Products are component of germ plasm (DM), interacts with capu

[127, 128]

stau

staufen

FBgn0003520

1027

Localization to germ plasm, PGC specification

[1, 127, 134]

tud

tudor

FBgn0003891

2516

Component of germ plasm, germ cell formation (DM)

[1, 135]

vls

valois

FBgn0003978

368

Component of germ plasm, involved in assembly (DM)

[136]

Category 3: Induction (N=15)

Blimp-1

Blimp-1

FBgn0035625

1217

BMP signalling pathway for PGC specification, represses somatic expression (MM, GB)

[4, 5, 10, 17, 31, 137, 138]

bnl

branchless

FBgn0014135

771

FGF protein; mitogen for PGCs (MM)

[139, 140]

btl

breathless

FBgn0005592

1053

FGFR (FGF receptor), linked to PGCs (MM)

[140]

byn

brachyury

FBgn0011723

698

Activation of BLIMP-1; essential for PGC specification (MM)

[141]

dpp

decapentaplegic (BMP 2/4-ortholog)

FBgn0000490

589

BMP2/4 ortholog; involved in BMP-BLIMP1 signalling for PGC specification (MM, GB)

[5, 10, 32, 137]

gbb

glass bottom boat

FBgn0024234

456

BMP5/7/8 ortholog; involved in PGC specification (MM, GB)

[5, 32, 142]

mad

mothers against dpp

FBgn0011648

526

Ortholog to MM smad and GB mad genes; PGC specification (MM,GB)

[5, 142, 143]

med

medea

FBgn0011655

772

Ortholog to MM smad4; PGC induction (MM,GB)

[5, 142]

punt

punt

FBgn0003169

521

BMP receptor; putative ortholog in MM Bmpr2 (note; or Acvr2); associated with PGCs in GB

[32, 142, 144]; orthology match in FlyBase.org

sax

saxophone

FBgn0003317

583

BMP receptor; putative mammalian ortholog Bmpr1a/b (note: or Acvr) involved PGC specification in birds

[142]; orthology match in FlyBase.org

smox

smad on X

FBgn0025800

487

Orthologs are smad2/3 in MM, which are transcriptional regulators needed for inductive PGC specification

[5]; orthology from FlyBase.org

sog

short gastrulation

FBgn0003463

1039

MM ortholog CHRD involved in BMP/CHRD signalling pathway, which relates to PGCs; Regulates DPP (DM)

[145, 146]; Orthology from FlyBase.org

tkv

thick veins

FBgn0003716

576

BMP receptor; mammalian ortholog (Bmpr1a/b) involved PGC specification in birds, GB

[142]; orthology match in FlyBase.org

wg

wingless

FBgn0284084

469

Ortholog to MM wnt genes; essential for PGC specification

[5, 147]

wit

wishful thinking

FBgn0024179

914

BMP receptor; putative ortholog to MM Bmpr2 (similar to punt), GB-punt is linked to PGCs in GB

[32, 144]; orthology match in FlyBase.org

Category 4: Inh/Ind (N=4)

nos

nanos

FBgn0002962

402

Germ plasm component (DM), regulates mRNA, associated with PGCs in MM; common germ cell across metazoans

[1, 4, 17, 20, 148]

piwi

P-element induced wimpy testis

FBgn0004872

844

Component of germ plasm (DM); germ line essential across metazoans (DM, MM)

[1, 149]

pum

pumilio

FBgn0003165

1534

Regulate mRNA in PGCs (DM), conserved germ cell role in humans

[1, 150]

vasa

vasa

FBgn0283442

662

mRNA and protein localizes to germ plasm (DM, zebrafish, C. elegans), PGCS in Xenopus and MM

[1, 149, 151, 152]

NOTE: Gene identifiers are from the reference species D. melanogaster. Genes were placed in one of four categories based on their role in PGC-specification. Experimental or cytological evidence linking genes to lineage-specific inheritance (LSI), to Inheritance or Induction modes, or Inh/Ind are shown. This gene list was used as a reference to identify orthologs in five other Drosophila species from the melanogaster group, and in C. elegans and A. mellifera using reciprocal BLASTX. Length is for the full CDS per gene. Species abbreviations in cited evidence are Drosophila melanogaster (DM), Gryllus bimaculatus (GB), or Mus musculus (MM).

Molecular evolution in each genus was analyzed fully independently (using within-genus alignments), allowing us to evaluate how these genes evolve in each taxon (cf. [53, 54]). We determined dN/dS, dN and dS for each phylogeny using the free-ratio model (M1) in PAML [55], a model which allows all species branches to have independent values, and using the one-ratio model (M0) which estimates a phylogeny-wide value for each parameter [55, 56, 57]. Typically, dN/dS values >1, =1 and <1 indicate positive selection, neutral evolution and purifying selection, respectively [55]. However, even when <1, elevated values of dN/dS are indicative of greater rates of protein sequence evolution and reduced constraint. Thus, dN/dS provides a means to assess the relative constraint among genes involved in specific developmental processes [58]. The distributions of dN/dS, dN and dS for all genes studied in each of the three genera are shown in box plots in Additional file 1: Figure S2 and S3 (values for free-ratio model per branch are shown, see also Tables S4-S6). As indicated therein, dN and dS were unsaturated for all species branches in Drosophila, Caenorhabditis and Apis with values <<1 (Additional file 1: Figure S3A-F). The only species branch among all genera nearing saturation for dS was in the outgroup of Drosophila, D. ananassae, which had a median value of 1.158, and 25th and 75th percentiles values of 0.989 and 1.705, remaining in a suitable range for analysis [53, 59]. To study dN/dS of each gene per genus, we determined Mean dN/ Mean dS (\( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \)) across all terminal species branches per phylogeny from the free-ratio model. Values obtained using this approach were strongly correlated to the model M0 dN/dS values within each genus (Spearman’s ranked correlation R=0.95, 0.99 and 0.99 for genes studied in Drosophila, Caenorhabditis and in Apis respectively, P<2X10-7). We present results for \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) throughout, as this provides a phylogeny wide measure of dN/dS, while allowing us to determine branch-specific values of dN and dS (Additional file 1: Figure S2 and S3).

Summary of Molecular Evolution of Germ Line Genes in Each Genus

We first summarize the patterns of \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) and codon usage bias across germ line genes examined within each genus. The \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) for each germ line gene across all six species branches in the Drosophila phylogeny and the four species in each of Caenorhabditis and Apis are reported in Tables 2, 3 and 4 (mean dN and mean dS values are provided in Additional file 1: Tables S4-S6). We found that \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) varied extensively among genes within each genus. As an example, across all 34 germ line genes studied in Drosophila the \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) values ranged from a high of 0.1573 in the LSI gene osk to a low of 0.0001 (Table 2) in mago nashi (mago). Similar patterns were observed in the genus Caenorhabditis, with \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) values ranging from a high of 0.1619 for the LSI gene pie-1 to a low of 0.0081 for mag-1, the ortholog to Drosophila mago. For Apis, values varied from 0.0001 to 0.1393, for the ortholog to mago (tied with mad and nos) and piwi respectively. Together, these patterns show there has been marked variation in selective pressures on germ line genes in each of the three genera, and that these germ line genes are not a homogenous group sharing similar selective profiles.
Table 2

\( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) and mENC’ across the phylogeny of six species of the reference model Drosophila

Gene

\( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \)

Mean mENC'

SE

Alignment Length (codons)

Lineage-specific Inheritance N=2

osk

0.1573

52.18

0.29

580

pgc

0.0933

37.25

0.66

71

Inheritance N=13

capu

0.1189

54.26

0.35

1007

orb

0.1102

54.09

0.25

789

stau

0.0885

53.59

0.19

990

cup

0.0878

54.23

0.55

1048

vls

0.0810

51.02

0.44

367

armi

0.0773

54.28

0.44

888

spir

0.0751

54.34

0.17

1001

tud

0.0716

53.77

0.38

1446

cycB

0.0692

50.23

0.41

509

gcl

0.0392

55.13

0.20

568

bru-1

0.0369

51.39

0.19

723

psq

0.0297

49.71

0.27

469

mago

0.0001

42.29

0.72

147

Induction N=15

bnl

0.1303

53.17

0.43

494

btl

0.0935

53.99

0.63

1040

wg

0.0833

47.48

0.95

261

tkv

0.0734

50.42

0.32

561

byn

0.0575

49.71

0.23

651

Blimp-1

0.0572

51.06

0.44

1110

dpp

0.0517

51.64

0.24

430

wit

0.0462

53.52

0.39

897

med

0.0422

52.47

0.57

759

sax

0.0402

50.88

0.80

565

sog

0.0305

49.45

0.48

919

gbb

0.0303

49.58

0.72

451

mad

0.0248

49.75

0.54

510

punt

0.0232

52.42

0.31

433

smox

0.0135

50.54

0.17

468

Inh/Ind N=4

nos

0.1145

50.51

0.38

389

vasa

0.0545

50.59

0.70

572

piwi

0.0446

54.91

0.76

711

pum

0.0320

50.53

0.38

798

NOTE. Results are shown for each of the 34 genes under study a measured using codeml in PAML [55]. Genes are classified based on their role in PGC specification and ranked by \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) within each group. The mean dN and mean dS values are provided in Table S4. SE=standard error for mENC’.

Table 3

\( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) and mENC’ across the phylogeny of four species of Caenorhabditis

CE Gene

DM Gene

\( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \)

Mean mENC'

SE

Lineage-specific Inheritance N=2

pie-1

-

0.1619

46.13

0.42

pgl-1

-

0.1553

50.29

0.45

Inheritance N=8

cyb-2

cycB

0.1127

45.01

0.68

cpb-3

orb

0.0833

51.56

1.40

gcl-1

gcl

0.0719

52.78

0.58

ifet-1

cup

0.0570

51.68

0.58

stau-1

stau

0.0499

52.63

0.80

par-1

par-1

0.0433

51.35

0.46

etr-1

bru-1

0.0386

50.54

1.52

mag-1

mago

0.0081

38.41

1.79

Induction N=10

dbl-1

dpp

0.0963

51.18

0.80

let-756

bnl

0.0748

49.36

1.09

sma-6

sax

0.0675

50.00

1.30

egl-15

btl

0.0639

52.74

0.37

blmp-1

Blimp-1

0.0575

52.56

0.41

sma-4

med

0.0548

52.34

0.67

tig-2

gbb

0.0522

50.24

1.15

crm-1

sog

0.0395

47.73

0.45

cwn-1

wg

0.0264

49.69

0.42

sma-2

mad

0.0128

46.30

0.78

Inh/Ind N=3

glh-1

vasa

0.0761

43.98

1.48

puf-8

pum

0.0753

50.79

0.92

prg-1

piwi

0.0642

46.13

1.81

NOTE. Values are shown for each of the 23 genes under study as measured using codeml in PAML [55]. Genes are ranked from highest to lowest \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) values within each category. CE Caenorhabditis elegans, DM D. melanogaster. The inheritance gene par-1 was included for Caenorhabditis (see Methods). SE standard error for mENC’.

Table 4

\( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) and mENC’ across the phylogeny of four species of Apis

Gene

\( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \)

Mean mENC'

SE

Inheritance N=13

armi

0.1011

54.66

0.13

tud

0.0792

56.67

0.27

cycB

0.0774

53.24

0.07

vls

0.0673

51.78

0.34

spir

0.0564

56.22

0.05

bru-1

0.0560

53.13

0.15

stau

0.0395

51.24

0.10

gcl

0.0326

53.42

0.27

capu

0.0238

53.39

0.53

orb

0.0192

55.04

0.13

psq

0.0173

54.07

0.32

par-1

0.0067

54.84

0.25

mago

0.0001

46.43

0.39

Induction N=13

dpp

0.1342

52.24

0.14

sax

0.1163

51.80

0.24

wg

0.0854

48.68

0.48

sog

0.0627

55.22

0.21

wit

0.0462

55.48

0.15

Blimp-1

0.0375

49.42

0.72

gbb

0.0363

46.37

0.40

punt

0.0335

52.73

0.39

byn

0.0324

53.20

0.25

med

0.0133

52.72

0.26

tkv

0.0116

53.91

0.09

smox

0.0080

52.44

0.36

mad

0.0001

51.63

0.29

Inh/Ind N=4

piwi

0.1393

54.72

0.39

vasa

0.1155

53.33

0.31

pum

0.0038

53.84

0.29

nos

0.0001

38.89

0.96

NOTE. Values are from codeml in PAML [55]. Genes are listed using the ortholog name from D. melanogaster. The inheritance gene par-1 was included for Apis (see Methods). SE standard error for mENC

In addition to \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \), we measured codon usage bias (CUB) for each of the germ line genes within each genus. The effective number of codons (ENC) determines the deviation from equal usage of all codons in a gene, wherein values range from 20 to 61 (number of codons in the genetic code), and lower values indicate greater codon usage bias [60]. We used the modified ENC’ measure (mENC’), which accounts for abundance of rare amino acids and for nucleotide content (mutational biases) of the genes under study [61, 62]. Preferential usage of codons is thought to usually (but not always) result from weak but persistent selection pressures that promote efficient and accurate transcription and/or translation, as has been reported in studies of Drosophila, Caenorhabditis and Apis [63, 64, 65, 66, 67, 68].

The results showed that of all 34 germ line genes studied in Drosophila, the highest and lowest CUB were observed in the two LSI genes, pgc and osk respectively (mENC’=37.25±0.66 and 52.18±0.29 respectively, values are means and standard errors across species, Table 2). This result reveals marked differences in the degree of codon usage bias of the two LSI genes. In turn, 25 of the remaining 32 studied genes exhibited mENC’ values that were >50, implying comparatively low CUB, with respect to pgc. For the genus Caenorhabditis, among the 23 germ line genes studied in that genus, the CUB was highest for mag-1 (mENC’=38.41±1.79) and lowest for gcl-1 (52.78±0.58), with intermediate values observed for its two LSI genes (Table 3). The broadest range of CUB was observed within the genus Apis where mENC’ values ranged from 38.89±0.96 to 56.67±0.27 (Table 4), suggesting a propensity for greater variation in CUB of germ line genes in that taxon.

In sum, it is evident that germ line genes exhibit wide variation in selective pressures on protein sequence divergence and in codon usage bias within each of the three genera under study here (see the below section “Relative Ranking of dN/dS and CUB Between Genera” for details on how dN/dS and CUB compared between genera). In this regard, the germ line genes are not a homogenous group exhibiting a similar range of \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) values or common CUB profiles. Sex and reproductive gene proteins are thought to often evolve rapidly, particularly those involving gametogenesis and sperm and eggs [69, 70]. However, our results showed that a subset of germ line genes had \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) <0.05, which suggests very high purifying selection (Tables 2, 3 and 4), and thus that pattern may not broadly apply to genes involved in germ line specification or development (see also, [50, 51]). Nonetheless, certain germ line genes studied here, such as the LSI genes, exhibited comparatively rapid evolution, suggesting they may be particularly significant to the evolutionary changes of the molecular mechanisms regulating germ lines in each genus.

Rapid Evolution of LSI Genes in Drosophila and in Caenorhabditis

Accelerated Divergence of LSI Genes in Drosophila

The LSI germ line genes are of particular interest as they may be crucial to enhancing our understanding the evolution of germ plasm in animals, since they appear to be de novo genes that have arisen and developed specialized germ line functions within only certain animal lineages. Our results show that the proteins of LSI genes are among the most rapidly evolving of the 34 germ line genes under study in Drosophila. Specifically, the finding that the highest \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) in Drosophila was observed for the LSI gene osk (0.1573, Table 2) suggests it may have experienced the least constraint among all the studied germ line genes in this genus. The osk gene is involved in germ plasm assembly and has only been reported to date in Drosophila and certain insects [1, 2, 4]. Osk proteins are essential for recruitment of molecules to germ plasm (e.g. via direct interactions with Vasa and Staufen proteins) and have RNA-binding functions to nos and its own mRNA [18, 42, 71, 72]. The \( \overline{\mathrm{dS}} \) value for osk was intermediate (0.2779), near the median of values across all germ line genes (0.2580; Additional file 1: Table S4). However, its \( \overline{\mathrm{dN}} \) value (0.0437) was the highest observed across all studied genes (Additional file 1: Table S4), affirming that its elevated \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) value is due to accelerated protein sequence divergence. Such high nonsynonymous changes, if not adaptive, would be apt to often be deleterious in a gene essential for fecundity and fitness [73], and thus would be unlikely to be fixed. In this regard, the high \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) in osk appears potentially to be the result of episodic adaptive evolution. That is, changes in amino acids of protein sequences may have been retained due to positive selection, via a selective advantage of the phenotypes associated with these protein sequence changes [55, 74, 75, 76]. Analysis of positive selection using sites analysis in PAML (see Methods, [55]), which we used to test for positive selection at specific codon sites in each gene across all six Drosophila species, did not show positive selection within this LSI gene (Table 5). This is similar to results reported in a prior assessment of the gene osk within the melanogaster group [52] (the previously reported sites under putative positive selection were reported from a branch site test for D. virilis, a species outside of the melanogaster group and thus not studied herein [52]). However, positive selection analyses (in specific branch-sites or sites) can be highly conservative [56, 76, 77], and often lack sensitivity to detect functional changes [78]. In this regard, positive selection cannot be excluded by the absence of statistically significant sites tests.
Table 5

Results from sites analysis of positive selection (M7 versus M8) in Drosophila, Caenorhabditis and Apis

Gene

Role

 

P

Sites (BEB Probabilities)

Drosophila

byn

Induction

 

**

29 S**

capu

Inheritance

 

**

252 P**, 253H**, 437 T*

Caenorhabditis

cpb-3

Inheritance

 

**

423 N*

let-756

Induction

 

**

231 S*

par-1

Inheritance

 

**

468 A**, 625 N*, 647 Q*, 701 G**, 704 T**,705V*

Apis

bru-1

Inheritance

 

**

337 T*, 339 A*, 341 A*

cycB

Inheritance

 

**

4 G**, 5 L**

dpp

Induction

 

*

80 S*, 81 T*, 86 Q**, 87 L *

med

Induction

 

**

-

orb

Inheritance

 

**

-

piwi

Inh/Ind

 

**

153 H**,318 T** ,320 A **

psq

Inheritance

 

**

-

pum

Inh/Ind

 

**

306 Y*

stau

Inheritance

 

**

-

wit

Induction

 

**

329 I*

NOTE: Analysis was conducted in PAML [55]. Only those genes at or near statistical significance are shown. ** P<0.05 for 2X∆lnL *P=0.062. BEB probabilities for specific sites are indicated as ** P≥0.95 (**) and *0.95≥P>0.9

Here, based on several lines of evidence we propose that adaptive evolution may have contributed towards the observed rapid protein sequence evolution of osk, as compared to all other 33 Drosophila germ line genes studied herein (Table 2). First, experimental findings have shown that functionality of osk has evolved rapidly, namely based on an inability of the gene in one Drosophila species (D. virilis) to rescue loss of function mutations in D. melanogaster [79], although these two species shared a last common ancestor > 55 My [80]. Second, some functional binding regions within the gene have been shown to have at least two-fold higher dN/dS than other segments [52], which may be deemed consistent with non-random, and thus putatively adaptive, changes. Third, relaxed selection appears unlikely to explain the relatively fast evolution of osk given that this lineage-restricted de novo gene has evolved crucial functions, involving high protein and RNA interactivity, in the germ plasm and during PGC-specification [2, 4, 18, 42, 71, 72]. These functions may act as constraints that limit relaxed purifying selection. Given that osk evolved before the advent of germ plasm in insects [81], such that the ancestral role of osk was unlikely to have been be a germ plasm role, we can infer that the evolution of essential roles in germ plasm must have been due to changes that arose following its origin approximately 300 Mya [79, 81], and such episodic changes may have been ongoing in the ~44 Mya history of the melanogaster group of Drosophila studied here [80]. Fourth, adaptive changes linked to germ line functions may have been facilitated by the low expression breadth observed for osk across development (as shown in the below section, “Expression breadth and pleiotropy in Drosophila”). Low pleiotropy appears characteristic of functional de novo genes [21, 82, 83], and while this might sometimes cause relaxed selection, it can also allow adaptive protein changes with minimal interference from functions in other tissues [84]. Collectively, these four lines of evidence suggest that the rapid divergence of osk observed here is at least partly the result of a history of episodic adaptive evolution within the Drosophila genus.

The other Drosophila LSI gene, pgc, also evolved relatively rapidly compared with all 34 Drosophila genes studied (\( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) = 0.0933, ranked 7th of 34 genes). pgc encodes a small protein (72 codons in D. melanogaster, Table 1) that is involved in transcriptional silencing in PGCs by preventing phosphorylation of RNA PolII and by inhibiting recruitment of the positive transcription elongation factor b (P-TEFb) to transcription sites. The suppression of expression is crucial for preventing germ cells from differentiating into somatic cells, and thus for sustaining the germ line [19]. Our alignment for six species is nearly identical to that produced by Hanyu-Nakamura et al. [19] who studied functionality of this protein in Drosophila (including more divergent taxa) and suggested that it is highly conserved. Our findings showing \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) of 0.0933, which is <<1, concurs with conservation, but nonetheless, indicates that with respect to other genes involved in germ line development, this protein evolves notably rapidly. We note that we examined the dN/dS of all orthologous protein-coding genes in the Drosophila clade studied here using the data provided by the flyDIVaS resource [57], and found that pgc, like osk, was above the average observed across the genome (see Additional file 1: Text file S1). As pgc is believed to be restricted to Drosophila and is not found in other metazoans, including within fellow Dipteran insects [19], its de novo status as a germ plasm regulator, similar to osk, appears to be a factor potentially shaping its fast divergence as compared to most other germ line genes.

With respect to codon usage, as described earlier the mENC’ value was extremely low for pgc in Drosophila (37.25±0.66, Table 2), in fact lowest among all 34 genes studied in this insect and was comparatively higher in osk (52.18±0.29; Mann Whitney U-test P<0.002), suggesting CUB is under greater selective constraint in pgc. This is also supported by higher GC3s in pgc than osk (mean values of 0.712±0.015 and 0.652±0.010 respectively, MWU-test P=0.004, Additional file 1: Table S7), indicating greater use of optimal codons, which have been shown to typically end in G and C in these Drosophila taxa [66, 85]. Thus, the greater CUB in the former gene might reflect a crucial role of efficient translation of this gene, potentially due to high translation rates during PGC formation. Alternatively, it might also be connected to the exceptionally short CDS length of pgc, which comprises the shortest CDS under study (Table 1), a feature which has been proposed to be linked to elevated selection coefficients on codon usage [86] and to be associated with greater CUB [63, 66].

Accelerated Divergence of LSI genes in Caenorhabditis

With respect to the nematode genus Caenorhabditis, we studied two LSI genes, pie-1 and pgl-1, each of which showed markedly elevated \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) among the 23 germ line genes under investigation in this genus (Table 3). For instance, as shown in Table 3, pie-1 and pgl-1 in Caenorhabditis had the two highest \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) values of all 23 germ line genes under study (0.1619 and 0.1553). This suggests that, similar to the situation in Drosophila, genes specifically involved in germ plasm, and that arose independently within a lineage, have experienced accelerated divergence as compared to other germ line genes. pie-1 and pgl-1 products are localized to the P granules and essential to fertility, have not been reported in other metazoans and are thought to be specific to Caenorhabditis [3, 4, 22, 29, 87, 88]. PIE-1 is crucial to germ line establishment as it represses mRNA transcription in germ line blastomeres and prevents differentiation into somatic cells by inhibiting activity of P-TEFb, which ultimately impedes phosphorylation of RNA PolII and prevents transcription elongation [19, 87, 89]. In this regard, pie-1 shares functionality (but not sequence homology) with the rapidly evolving Drosophila gene pgc (Tables 2 and 3) [19]. Remarkably, our data here shows that pie-1 and pgc, which are de novo genes with convergent functions that have arisen independently in Caenorhabditis and in Drosophila respectively [4, 19], each diverge rapidly as compared to other germ line genes in their associated taxonomic group (Tables 2 and 3).

The relatively rapidly diverging Caenorhabditis LSI gene pgl-1 is essential in the P granule assembly pathway [3, 88, 90]. Its protein contains RGG-binding motifs (which are linked to genes involved in transcription, translation, splicing) similar to those found in the protein product of vasa (glh-1 in Caenorhabditis) [3, 22]. The P granule pathway presumably involves the localization of pgl-1 products to the P granules by glh-1, as mutants of the latter gene contain PGL proteins dispersed throughout the cytoplasm [3]. We found that glh-1 had a \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) of 0.0761, which is about half the value of pgl-1 (0.1553). This suggests that pgl-1 has evolved at a much faster rate than its localization protein, whilst presumably not interfering negatively with their interaction. While pgl-1 is part of a gene family with other members pgl-2 and pgl-3 that may have arisen from gene duplication, the other paralogs are, unlike pgl-1, not essential to P granules or PGCs, as pgl-2 and pgl-3 loss of function mutants do not exhibit obvious defects in germ line development on their own [3, 90]. pgl-3, however can be partially redundant to pgl-1 under cold temperatures [3, 90]. Thus, the rapid evolution of pgl-1 might partly result from some redundancy (or relaxed selection) of function under specific conditions. However, the fact that the other LSI genes studied in Drosophila and in Caenorhabditis do not have apparent paralogs, and each evolve relatively fast among the germ line genes (Tables 1 and 2), suggests that accelerated protein divergence is a common feature of the lineage-restricted germ plasm genes, rather than being an artefact due to the existence of a partially redundant paralog of pgl-1.

With respect to CUB, pie-1 exhibited greater bias (mean mENC’ 46.13±0.42) than pgl-1 (50.29±0.45; MWU test P=0.029), suggesting enhanced selection on CUB in the former gene, perhaps reflecting a higher translation rate. However, similar to pgc from Drosophila, the short CDS of pie-1 might contribute to its high CUB. Short CDS not only generally exhibit high CUB, but sometimes also low dN/dS (and/or dN), trends perhaps mediated by protein-protein interactions and/or elevated expression levels [63, 86, 91, 92]. Whilst pie-1 is markedly shorter than pgl-1 (note the average lengths per gene across species were 351±8,9 and 770±4.8 codons, a nearly two-fold difference; the conservative alignment lengths had nearly three-fold difference) consistent with elevated CUB, the \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) values were very similar between genes (Table 3), thus suggesting while length might influence the relative CUB, it is unlinked to their amino acid divergence in Caenorhabditis. Alternatively, it is possible that adaptive evolution at specific amino acid sites has occurred more frequently for pgl-1, leading to selective sweeps at linked sites containing slightly deleterious non-optimal codon mutations [93], which over the long-term can reduce CUB [93, 94]. Although positive selection was not found in the four Caenorhabditis species studied here for these two genes using sites analysis (Table 5), further studies including even more species, as data becomes available, will allow greater power of these tests and fuller discernment of the role of positive selection in these genes.

In our assessment, we also wished to examine the Caenorhabditis LSI gene meg-1, which is a P-granule component required for germ line development [27], but found that identification of meg-1 orthologs for all four species was ambiguous. The best matches to the C. elegans meg-1 had an e-value of 5.0X10-5 for C. brenneri, 6.0X10-4 for C. briggsae and 0.053 for C. remanei, and were largely unalignable across most of the sequence. We therefore excluded this gene from analysis herein. The lack of clearly identifiable orthologs is suggestive of rapid divergence or potential gene loss in nematodes, or might indicate that this de novo gene occurs solely in a single species, C. elegans [27]. While meg-1 is an LSI gene, multiple copies (meg-1-4) have been reported in C. elegans with partial overlap in function [28], and this might explain potential rapid sequence evolution and/or gene losses in some species of this genus.

Summary of Findings on LSI Genes

Taken together, the collective results from LSI genes from Drosophila and Caenorhabditis (osk, pgc, pie-1 and the pgl-1) suggest all these de novo genes evolve rapidly as compared to other studied germ line genes. As these four genes appear not to have originated from a gene duplication due to the absence of ancestral orthologs [whilst pgl has multiple paralogs in Caenorhabditis, pgl genes appear limited to nematode genomes; 3], we speculate that these LSI protein-coding genes might have arisen at least partially from noncoding regions [95, 96, 97, 98] or horizontal gene transfer [21, 99]. In fact, recent evidence has supported a putative role of horizontal gene transfer in the origin of osk [100]. De novo genes have been previously linked to expression in sexual organs, including germ lines [21, 95, 96]. Nonetheless, whilst it appears these LSI genes have not arisen from duplication, we can neither formally exclude nor directly test the hypothesis that they originally arose from a duplication and evolved so rapidly that the orthologs cannot be identified [21].

Regardless of the precise origin, these four de novo genes have not degenerated into pseudogenes or been loss from the genome due to lack or loss of function, as frequently occurs for orphan genes [101], but rather play a crucial role in PGC specification and thus fertility. A plausible explanation for their existence and evolution of novel functionalities is their involvement in lineage-specific adaptive processes [102], potentially accompanied by phenotypic novelties, as is thought to occur for de novo genes that become functional [98, 102, 103]. For LSI genes, the adaptations would involve their crucial roles in germ plasm, which is believed to be a novelty in the context of nematodes and insects [7]. This notion is further consistent with recent findings in Drosophila that surviving (not lost from the genome) de novo genes exhibit functionalities specific to a narrow developmental phase or tissue type [82]: germ plasm and the PGCs are limited to the stages involving the egg or early embryo. It can be speculated that adaptive amino acid changes in LSI genes might have been historically mediated by sexual selection, as the pre-formed germ plasm could conceivably indirectly influence sperm-egg fertilization success (and thus, sexual antagonism), from natural selection on germ plasm due to its effect on zygotic or embryonic fitness, and/or from cell-lineage selection among the precursors to PGCs or among PGCs, each of which could accelerate protein sequence divergence [30].

We speculate that a history that includes episodic adaptive evolution in the emergence of functions in the de novo LSI genes may have potentially continued after the establishment of their primitive germ plasm roles and extended to within the intra-genus level. This notion appears consistent with multiple lines of evidence for osk (Table 2) [52, 79], and could account for elevated \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) observed for all four of the LSI genes studied here (Tables 2 and 3). Nonetheless, we do not exclude a role of neutral functional or non-functional amino acid changes in the rapid divergence of LSI genes relative to other germ line genes, which appears consistent with the absence of detection of positive selection in Table 5; however, such tests can be highly conservative [77] and be prone to substantial inaccuracies [104, 105] (see Additional file 1: Text file S2), and thus cannot reliably exclude positive selection. At present, much remains to be unknown about the evolution of de novo functional genes, including about the roles of adaptive and neutral changes in those genes that that form essential roles in genetic networks [21, 97, 98], such as has occurred for the LSI genes involved in germ plasm.

Expression Breadth and Pleiotropy in Drosophila

Protein sequence evolution may be influenced by pleiotropy, where the greater a gene’s involvement in multiple functions or tissues, the more indispensable it may be to fitness, and thus more likely to exhibit stringent purifying selection [83, 84, 106]. In turn, those genes with reduced pleiotropy may be more dispensable and evolve faster due to relaxed selective pressures (neutral changes), and/or due to adaptive functional changes unimpeded by pleiotropic constraints [84, 107]. Expression breadth across developmental stages and tissues provides a proxy for the pleiotropy of a gene [83, 84, 106]. Further, data from Drosophila suggests that young de novo gene products which exhibit functional roles may often have those roles restricted to one or a few developmental stages, and thus may be specialized for specific developmental processes [82]. We thus determined expression breadth across developmental stages/tissues with expression using the large-scale transcriptome data available for our main target and reference taxon Drosophila, from its most well studied model species, D. melanogaster [48, 108, 109]. For each of the 34 Drosophila germ line genes in Table 2, we measured expression breadth across 30 developmental stages (spanning from 0-2 hour embryos, larvae, pupae, to adult males and females, described in Additional file 1: Table S8).

As shown in Fig. 1a, we found that the majority of germ line genes in Table 2 (N=22 of 34) were expressed ubiquitously at a level of >0 RPKM in all the disparate stages (expression breadth=100%; N=28 had values of >95%), indicating high pleiotropy in these germ line genes. The LSI genes osk and pgc had the lowest values, with a breadth of 63.3 and 46.7% respectively. Using a higher cutoff of >5 RPKM to define specificity (Fig. 1b), we observed even more variation in expression breadth; most genes had values between 40-100%, but remarkably low breadth was observed for Inh/Ind genes such as vasa and piwi and again for the two LSI genes, which had values of 20% (Fig. 1b). With respect to \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}}, \), we observed a negative correlation between expression breadth and \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) using both criteria of >0 RPKM and >5 RPKM (Spearman R=-0.612, P=1.3X10-4 and R=-0.565, P=5.4X10-4 respectively, (Fig. 1c and d) consistent with higher protein divergence in narrowly expressed genes. In contrast, no correlation was observed between \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) and the average expression level across developmental stages (P=0.926). mENC’ was uncorrelated to expression breadth (P=0.498). Together, these data suggest that most of the germ line genes under study exhibit broad expression, or high pleiotropy. In turn, low expression breadth may substantially contribute towards the accelerated evolution of the LSI genes.
Fig. 1.

The expression breadth (percentage of 30 developmental stages expressed) for the 34 Drosophila genes under study and its relationship to protein divergence. a breadth of expression across developmental stages at a level >0 RPKM; b breadth of expression at a level >5 RPKM; c \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) versus expression breadth (RPKM>0); d \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) versus expression breadth (RPKM>5). The 30 tissues and stages are provided in Table S8. For A-B, genes are listed on the X-axis in the same order as presented in Table 2, from highest to lowest \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) within each of the four categories of genes. Gene names associated with each dN/dS point are provided in Table 2.

As an example, the extraordinarily low expression breadth for the LSI genes osk and pgc, using both the criteria of >0 RPKM (Fig. 1a and c) and >5 RPKM (Fig. 1b and d), indicates high specialization and limited pleiotropy of those genes, consistent with their specialized functions in germ plasm. For both genes, the only stages with relatively high expression (for instance, using a cut-off of >15 RPPM) were adult females (42 to 372 RPKM) and 0-4 hour embryos (17 to 270 RPKM), consistent with their PGC specification roles in female sexual cells and young embryos. This observed pattern concurs with the notion that young de novo genes exhibit expression limited to one or a few developmental stages as they acquire new functions in an organism [21, 82]. Further, such de novo genes may become essential if they integrate into existing networks [21], as appears to be the case for osk and pgc where these genes have assumed an upstream regulatory role in the pathway of PGC-specification and germ line development [4, 17]. Moreover, their low pleiotropy may facilitate evolution of new functions by permitting adaptive evolution largely unimpeded by co-functionality in other tissues [84], and/or may contribute towards divergence via drift (see above section “Rapid evolution of LSI genes in Drosophila and in Caenorhabditis”). Further consideration of the putative role of pleiotropy with respect to the \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) of specific germ line genes is provided in Additional file 1: Text File S3.

Relative Ranking of dN/dS and CUB Between Genera

After considering the evolution of LSI genes, we next asked whether the germ line genes studied here shared parallels in their patterns of molecular evolution across genera. For this, we assessed whether the relative ranking of \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) and of mENC’ were similar between our reference model Drosophila and Caenorhabditis and Apis. By examining the relative ranking of dN/dS and of CUB, between genera using Spearman’s Ranked R (not absolute values), this controls for taxon-specific factors, and allows us to assess if the relative dN/dS and CUB within this group of germ line genes has been retained across genera.

As shown in Fig. 2, for the Drosophila genes having orthologs identified in Caenorhabditis, we found \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) was positively correlated between genera (pooled across all categories, excluding the LSI genes, Spearman’s rank correlation R=0.44, P=0.05, N=20, Fig. 2a). However, the correlation was not statistically significant for the orthologs between Drosophila versus Apis (P=0.215, Fig 2b; note, nor for those common to Caenorhabditis vs. Apis (P=0.112)). Reducing the Drosophila-Apis ortholog gene list (which was larger than for the distant nematodes, Fig. 2, Tables 3 and 4) to those also found in Caenorhabditis, also did not yield a correlation between Drosophila and Apis (P=0.181). Thus, this indicates that the germ line gene sets share greater similarity in the relative protein divergence between Drosophila and its distant relative Caenorhabditis (from different phyla) than between the two insects. The values of \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) in Drosophila, Caenorhabditis and Apis were in a largely similar range across all the three genera examined here (Tables 2, 3 and 4, Fig. 2). Thus in that context the magnitude of \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}\ } \) did not appear to vary among taxa, but rather the relative dN/dS among genes simply appeared more conserved between Drosophila and Caenorhabditis than either was to Apis. Previous reports have shown that Drosophila and Caenorhabditis, despite being from different phyla, share striking parallels in gene expression profiles and networks across developmental stages [108]. In this regard, our present data suggest these divergent systems also share similar relative protein divergence patterns of their germ line genes. One obvious similarity between these organisms with respect to germ lines that speculatively could contribute towards this latter pattern is the use of the inheritance mode in both models. However, further study in more genera would be needed to ascertain whether specification mode plays any role in these shared patterns.
Fig. 2.

Correlations in \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) and in mENC’ between Drosophila and Caenorhabditis and Drosophila and Apis. a The \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) values for Caenorhabditis versus those from Drosophila; b the \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) values for Apis versus those from Drosophila; c mENC’ for Caenorhabditis versus Drosophila; d mENC’ for Apis versus Drosophila. Spearman’s ranked R and P values are shown across all genes for the between genus orthologs (pooled across categories). The lineage-specific inheritance (LSI) genes in Drosophila and in Caenorhabditis genes are shown on the X and Y axis respectively in A and C and were not included in the calculation of between genus correlations. The gene names associated with each value of \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) and mENC’ shown are provided in Tables 2, 3, and 4.

In terms of CUB, we report a strong positive correlation between mean mENC’ of genes in Drosophila and their orthologs in Caenorhabditis (R=0.83, P=2X10-7) and also a significant positive correlation between Drosophila and Apis (R=0.45, P=0.011) (Fig. 2c and d). This suggests the relative CUB in each germ line gene set has been largely retained across these disparate organisms, particularly between the flies and nematodes. We note that the mENC’ levels were fairly high for many germ line genes (values >50 for genes), indicating that these germ line genes as a group do not exhibit exceptionally strong codon bias. Nonetheless, the correlation in CUB values between genera shows that the relative degree of bias tends to be largely conserved across these three divergent animal models. As CUB is believed to often promote translational efficiency of highly translated genes [63], we speculate that germ line genes might have retained their relative translation rates across divergent models.

While the nucleotide composition in germ line genes differed among taxa, including a GC bias in Drosophila (GC content across all germ line genes=0.561±0.006) and AT biases in Caenorhabditis and Apis (GC content=0.450±0.020 and 0.405±0.002) (Additional file 1: Table S7), nucleotide content has been accounted for using mENC’ [61, 62], and thus Fig. 2 c and d suggests that the relative selective pressure on CUB, despite different types of background nucleotides or optimal codons in these three genera [54, 56, 64, 66, 67, 85, 110] is at least partly retained across orthologous gene sets. The relevancy of correcting for background composition [61] was demonstrated by the fact that traditional ENC showed no correlation between taxa (Drosophila and Caenorhabditis P=0.392, Drosophila and Apis P= 0.116, Additional file 1: Figure S4).

Protein Sequence Divergence and the Transition to Inheritance Mode

As a final note, we briefly mention here that a prior hypothesis in the literature had suggested that the transition from induction to inheritance mode results in a release of selective constraint, and accelerated evolution of proteins that is detectable at the genome-wide level [111]. We previously assessed that hypothesis using methods adhering to established principles of molecular evolution, and found some examples disagreeing with its predictions on protein sequence evolution [30, 54]. We had noted that the hypothesis may apply to smaller subsets of genes such as germ line genes, or PGC-specification genes [30, 54]. We thus compared dN/dS of Drosophila and Apis, which are each from the class Insecta, and have inheritance and induction mode respectively. We did not observe evidence consistent with accelerated evolution (or release of constraint) on proteins of germ line genes of Drosophila as compared to Apis (Tables 2 and 4, Fig. 2). For instance, dN/dS was not statistically significantly higher for Drosophila than for Apis using Mann-Whitney (Ranked) U test of all germ line genes with orthologs between these genera (P=0.320), or for the subset of genes with known roles under “Induction” mode (P=0.720). If the PGC-specification hypothesis, as it pertains to protein sequence evolution [111], indeed applied to germ line genes then a tendency towards higher dN/dS would be expected in flies after a transition to inheritance, which is not what we observed. Nonetheless, as this pattern is solely from two genera, we consider it alone anecdotal rather than conclusive or generalizable. Further study across more germ line genes and taxon groups, including even more closely related genera, would be valuable for rigorous testing of any such general relationship.

Conclusions

Our results herein showed that germ line genes exhibit a wide range of \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}\ } \) values and CUB in each of three genera, Drosophila, Caenorhabditis, and Apis. Relative to other germ line genes, we found evidence that LSI genes in Drosophila (osk, pgc) and in Caenorhabditis (pie-1, pgl-1) have diverged especially rapidly, and we conclude this could be a common property of de novo germ plasm genes. Whilst adaptive evolution is a strong candidate to explain this fast divergence of LSI genes, particularly for osk which has several lines of evidence consistent with a history of positive selection in Drosophila, we do not exclude some role of relaxed purifying selection; both adaptive changes and relaxed selection may be facilitated by the narrow expression breadth and low pleiotropy of LSI genes, as found using data from Drosophila. Our findings further show that the relative ranking of \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}\ } \)and of CUB germ line genes in the reference Drosophila were each correlated to their orthologs in Caenorhabditis while only CUB was correlated to the orthologs from Apis. The molecular evolutionary patterns of germ line genes in the flies and nematodes may be similar to developmental expression profiles [108], wherein striking parallels were observed across these organisms, despite being from different phyla.

Future research should explore how LSI genes evolve within populations, including the study of their amino acid mutational spectra relative to other identified (non-germ line) de novo genes [82], and to experimentally assess shifts in in their functionality within or between genera (cf. [79]). Moreover, transcriptome data from the germ lines during early embryogenesis and germ line development in multiple species per genus may provide a means to assess how their gene expression has evolved between species, which may be as relevant to understanding divergence in their function as protein sequence changes. Furthering our understanding of the molecular evolution of germ line genes will be facilitated by expanding research to species from a wider range of genera, including the induction model systems mice, crickets and salamanders [5, 8, 10, 32, 112] and inheritance species such as wasps and frogs [2, 4, 6, 7, 8, 9]. Together, the present findings provide a framework for further study of the molecular evolution of germ line genes in metazoans.

Methods

Identification of Germ Line Genes for Analysis

A set of 34 genes with experimental and/or cytological evidence of involvement in PGC-specification under induction mode (N=13), inheritance mode (N=15), or both modes (N=4) as well as two LSI genes osk and pgc (Table 1), were selected for study in Drosophila. CDS from D. melanogaster (longest isoform per gene) were used as the reference CDS set for orthology searching as PGC-specification has been well-studied in that organism, its genome has been well annotated (www.flybase.org), and it is arguably the best annotated species in the genus [48]. For study within the genus, five additional species of Drosophila within the melanogaster group, D. erecta, D. sechellia, D. simulans, D. yakuba, were chosen, as well as a relative outgroup species D. ananassae (Additional file 1: Figure S1 and Table S1). All six species are closely related taxa and exhibit a range of dN/dS values (Additional file 1: Figure S2) and largely unsaturated dN and dS (Additional file 1: Figure S3), making them suitable for study of molecular evolution [48, 56]. The procedures used for identification of suitable orthologs for study between Drosophila and Caenorhabditis and Apis, as well for among the various species within each genus, are described in detail in Additional file 1: Text file S4.

Molecular Evolutionary Analysis

The CDS for each gene per genus were aligned by codons using MUSCLE [113] in MEGA [114] set at default parameters with the exception that the gap penalty was set to -1.9, which yielded more effective alignments (than the default of -2.9) across multiple-species. Regions with gaps were removed. It has been proposed that small segments in a gene with poor alignment or greater divergence might influence measures such as dN and dS, and detection of positive selection, and their removal improves such estimates despite loss of some sequence information [115, 116]. Thus, we used a dual approach of filtering using the program GBLOCKS [115] set at default parameters, which accordingly shortened divergent alignments, and inspection of protein alignments by eye, always retaining the start codon [117, 118], to remove residual divergent and putatively misaligned segments. Thus, all alignments and measures of substitution rates herein are considered conservative, and the latter applies specifically to the aligned regions per gene.

Protein sequence divergence per phylogenetic branch was measured using dN and dS under the free ratio model (M1) in codeml of PAML based on an unrooted tree for each genus [55]. Whilst some studies have used the M0 model in PAML to measure dN/dS in taxa including the melanogaster group in Drosophila, which determines a single dN/dS across all branches in the phylogeny [56], we allowed a separate dN/dS in each branch to include potential species-specific effects on dN/dS (Additional file 1: Figure S2) using the free-ratios model [55]. As noted in the Results and Discussion \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) (using M1 model) and M0 dN/dS were strongly correlated across genes within each genus (Spearman’s ranked R>0.95, P<2X10-7). The value of \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) was used instead of mean dN/dS across the branches as the latter can be biased towards extremely high values due to rare cases (branches) with extremely low dS and avoids exclusion of a branch (i.e., no dN/dS value) in cases when dN>0 and dS=0 [119]. The phylogeny for Drosophila was taken as that provided at FlyBase [109] and was unrooted for PAML. The unrooted Caenorhabditis four-species phylogeny was taken from [120] and for Apis from [121]. For the latter genus, which is less strongly resolved for (ingroup) positions of A.dorsata and A. cerena, alternate phylogenies were employed for the ingroup yielding highly similar results. We note that we did not detect orthologs of the germ line gene par-1 in all six Drosophila species, and thus we did not formally include it in the Drosophila gene set for study, but a three-species alignment was studied, and par-1 was examined in Caenorhabditis and Apis; the results are described in Additional file 1: Text File S5.

Positive selection was assessed using “sites” analysis in PAML across all species per genus [55]. For this we compared M7 versus M8. For those genes exhibiting positive selection using 2X∆lnlikelihood based on the Chi2 table, we obtained the BEB posterior probabilities identifying the sites with P>0.90.

Codon Usage Bias

The values of mENC’, which accounts for abundance of rare amino acids and for nucleotide content of the genes under study [61] was conducted using a program from Satapathy et al. [62]. Standard ENC [60], GC3 content at 3rd synonymous codon positions (GC3s) and GC content per CDS was determined in CodonW [122]. For consistency with \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \), all mENC’, ENC and GC values were determined using the aligned sequences per gene excluding gaps for each species.

Inter-Genus Contrasts

We compared the \( \overline{\mathrm{dN}} \)/\( \overline{\mathrm{dS}} \) values and the mENC’ values of orthologs present in each of the two genera per contrast (cf. [123]). As genes varied in sequence between genera and were aligned separately within each genus, under a conservative approach, we compared the relative ranking of germ line genes within each genus (using Spearman Rank Correlations) to assess any relationships between genera.

Pleiotropy

For analysis of pleiotropy in D. melanogaster, gene expression breadth was determined using the modENCODE transcriptome database as presented at FlyBase.org [109, 124] across 30 tissues and stages of development. These included twelve stages from embryos, six from larvae, six from pupae, and three for adult males and for adult females (shown in Additional file 1: Table S8). Breadth of expression was quantified as the number of developmental stages in which a gene was expressed [83, 106], and was converted into percentages of the 30 stages studied (Additional file 1: Table S8). Analysis was repeated for those using a cutoff of >5 RPKM.

Notes

Acknowledgements

The authors acknowledge members of the Extavour lab group at Harvard OEB Department for valuable comments on this project. Helpful comments by the two anonymous Reviewers are acknowledged.

Funding

This work was supported by funds from Harvard University and National Institutes of Health grant R01 HD073499-01 to CGE.

Availability of data and materials

All genomic sequence data under study were obtained from public databases and are described in Additional file 1: Table S1. Unique gene identifiers for our reference taxa in each genus D. melanogaster, C. elegans and A. mellifera are provided in Table 1 and Additional file 1: Tables S2 and S3 respectively. Alignments are available in Additional file 2.

Authors' contributions

CAW and CGE designed the study, analyzed data and wrote the manuscript. Both authors read and approved the final manuscript.

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary material

12862_2019_1363_MOESM1_ESM.pdf (540 kb)
Additional file 1: The file contains the supplementary Tables, Figures and Text which are denoted and Tables S1 to S8, Figures S1, S2,S3 and S4, and Text files S1,S2, S3, S4 and S5. (PDF 509 kb)
12862_2019_1363_MOESM2_ESM.zip (214 kb)
Additional file 2: Alignments. (ZIP 213 kb)

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Authors and Affiliations

  1. 1.Department of Organismic and Evolutionary BiologyHarvard University, 16 Divinity AvenueCambridgeUSA
  2. 2.Department of Molecular and Cellular BiologyHarvard University, 16 Divinity AvenueCambridgeUSA

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