Although sexual reproduction is ubiquitous throughout nature, the molecular machinery behind it has been repeatedly disrupted during evolution, leading to the emergence of asexual lineages in all eukaryotic phyla. Despite intensive research, little is known about what causes the switch from sexual reproduction to asexuality. Interspecific hybridization is one of the candidate explanations but the reasons for the apparent association between hybridization and asexuality remain unclear.
In this study we combined cross-breeding experiments with population genetic and phylogenomic approaches to reveal the history of speciation and asexuality evolution in European spined loaches (Cobitis). Contemporary species readily hybridize in hybrid zones, but produce infertile males and fertile but clonally reproducing females that cannot mediate introgressions. However, our analysis of exome data indicates that intensive gene flow between species has occurred in the past. Crossings among species with various genetic distances showed that, while distantly related species produced asexual females and sterile males, closely related species produce sexually reproducing hybrids of both sexes. Our results suggest that hybridization leads to sexual hybrids at the initial stages of speciation, but as the species diverge further, the gradual accumulation of reproductive incompatibilities between species could distort their gametogenesis towards asexuality. Interestingly, comparative analysis of published data revealed that hybrid asexuality generally evolves at lower genetic divergences than hybrid sterility or inviability. Given that hybrid asexuality effectively restricts gene flow, it may establish a primary reproductive barrier earlier during diversification than other ‘classical’ forms of postzygotic incompatibilities. Hybrid asexuality may thus indirectly contribute to the speciation process.
RNAseq_1
G736HC302.RL5.sff.gz
RNAseq_2
G736HC302.RL8.sff.gz
RNAseq_3
IFMUJ8101.RL4.sff.gz
RNAseq_4
IFMUJ8101.RL5.sff.gz
RNAseq_5
IFMUJ8102.RL6.sff.gz
RNAseq_6
IFMUJ8102.RL10.sff.gz
RNAseq_7
IGASIBU01.RL5.sff.gz
SeqCap_1.zip
To extract the contents of netrimovane_SeqCap.zip, first concatenate the parts 001 through 020 -- On a Unix or Linux machine, you may use the "cat" command as $ cat netrimovane* > netrimovane_SeqCap.zip -- On a Windows machine, you may use the copy command, or a software such as HJSplit.
netrimovane_SeqCap.zip.001
SeqCap_2.zip
netrimovane_SeqCap.zip.002
SeqCap_3.zip
netrimovane_SeqCap.zip.003
SeqCap_4.zip
netrimovane_SeqCap.zip.004
SeqCap_5.zip
netrimovane_SeqCap.zip.005
SeqCap_6.zip
netrimovane_SeqCap.zip.006
SeqCap_7.zip
netrimovane_SeqCap.zip.007
SeqCap_8.zip
netrimovane_SeqCap.zip.008
SeqCap_9.zip
netrimovane_SeqCap.zip.009
SeqCap_10.zip
netrimovane_SeqCap.zip.010
SeqCap_11.zip
netrimovane_SeqCap.zip.011
SeqCap_12.zip
netrimovane_SeqCap.zip.012
SeqCap_13.zip
netrimovane_SeqCap.zip.013
SeqCap_14.zip
netrimovane_SeqCap.zip.014
SeqCap_15.zip
netrimovane_SeqCap.zip.015
SeqCap_16.zip
netrimovane_SeqCap.zip.016
SeqCap_17.zip
netrimovane_SeqCap.zip.017
SeqCap_18.zip
netrimovane_SeqCap.zip.018
SeqCap_19.zip
netrimovane_SeqCap.zip.019
SeqCap_20.zip
netrimovane_SeqCap.zip.020
Four reference samples for exome capture and SNP calling_1.zip
To extract the contents of 'Four reference samples for exome capture and SNP calling_1.zip', first concatenate the parts 001 through 006 -- On a Unix or Linux machine, you may use the "cat" command as $ cat Four* > Four_reference_samples_for_exome_capture_and_SNP_calling.zip -- On a Windows machine, you may use the copy command, or a software such as HJSplit.
Four reference samples for exome capture and SNP calling.zip.001
Four reference samples for exome capture and SNP calling_2.zip
Four reference samples for exome capture and SNP calling.zip.002
Four reference samples for exome capture and SNP calling_3.zip
Four reference samples for exome capture and SNP calling.zip.003
Four reference samples for exome capture and SNP calling_4.zip
Four reference samples for exome capture and SNP calling.zip.004
Four reference samples for exome capture and SNP calling_5.zip
Four reference samples for exome capture and SNP calling.zip.005
Four reference samples for exome capture and SNP calling_6.zip
Four reference samples for exome capture and SNP calling.zip.006
README_Description of original rna-seq and exome capture sequence data files
Table S1. Locality information from the Danube River hybrid zone
Table S1.docx
Appendix S2. SNP dataset
Every contig is represented by 18 lines, with two lines per individual in standard fasta format. Header line of each sequence contains: sampleID_genotype_contigID. Individuals' genotypes are indicated by letters as follows: LL, C. paludica; PP, C. pontica; EE, C. elongatoides; TT, C. taenia; NN, C. tanaitica. Variant positions are expressed using IUPAC notation and invariant positions are excluded.
Appendix S2.txt
Table S3. Summary of the coalescent models
Table S3.docx
Appendix S4. Summary of genetic divergences of fish species producing asexual hybrids
Appendix S4.docx
Table S5. Microsatellite allelic profiles of parents and their progeny within crossing experiments
Table S5.xlsx
Table S6. Oocyte analysis
For each female we indicate her biotype, origin, allozyme profile and the number of analyzed eggs.
Table S6.xlsx
Table S7. Microsatellite markers and cytochrome b gene haplotypes
This Table lists the alleles found in each sampled individual (specified by a respective ID number) on the basis of eight microsatellite markers. The cytochrome b gene haplotype is also specified.
Table S7.xlsx
Table S8. Summary statistics of microsatellite DNA analysis for three taxa based on eight loci
Table S8.xlsx
Table S9. SNP statistics
Summary statistics for within-species and between-species genetic distances.
Table S9.xlsx