pages tagged speciation

Nat Commun. 2018 Nov 30;9(1):5114. doi:10.1038/s41467-018-07641-9

Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S.

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.

Less than 0.2% of the genome pairs had an average nucleotide identity between 83% and 95%.

Ohta N, Kaplan N, Ng JT, Gravez BJ, Christiaen L.

G3 (Bethesda). 2020 Aug 5;10(8):2697-2711. doi:10.1534/g3.120.401427

Asymmetric Fitness of Second-Generation Interspecific Hybrids Between Ciona robusta and Ciona intestinalis.

Comprehensive introduction on intestinalis-robusta taxonomic situation. Conclusions weakened by the the absence of homotypic F2 C. intestinalis animals caused by the failure of C. intestinalis to reproduce in the culture system. The viability and fertility hybrids born from intestinalis oocytes or robusta (sperm) x intestinalis (oocytes) oocytes is reduced.

“Wild-type Ciona robusta (C. intestinalis type A) and Ciona intestinalis (C. intestinalis type adults were collected in San Diego (CA) and Woods Hole (MA)”. “Sea water (Bio-Actif Salt, Tropic Marin) was controlled by bio-balls (Biomate, Lifegard Aquatics) seeded with bacteria (BioDigest, Prodibio)”. “We obtained hundreds of swimming larvae from each cross [..] this contrasts with previous studies, which suggested that C. robusta oocytes were largely refractory to fertilization by C. intestinalis sperm”. “there were no significant differences in the survival rate between F1 RxI and IxR hybrids”. “By 50 dpf, half of the C. robusta individuals were producing sperm, whereas that proportion dropped significantly for the other groups of animals.”

”For both RxI and IxR hybrids, the majority of animals had [orange pigment organ] at the tip of the sperm duct, in agreement with a previous report (Sato et al. 2014), thus indicating that [orange pigment organ] formation is a dominant trait.”

”C. intestinalis has yellow and orange pigmentation around the tip of siphons that is lacking in C. robusta [...] the majority of RxI and IxR hybrids displayed a bright red pigmentation at the rim of oral and atrial siphons, also consistent with a previous report (Sato et al. 2014). The observation that siphon pigmentation displays an overdominant phenotype in hybrids is consistent with its lack of reliability for taxonomic purposes.“

“the sperm of F1 RxI hybrid appeared less potent to fertilize C. robusta eggs than that of F1 IxR hybrids, which is reminiscent of previously reported difficulties in using C. robusta eggs in interspecific fertilizations.” “Both BC1 (RxI)xR and (IxR)xR hybrids had lower survival rates than F2 C. robusta animals, while an ANOVA did not show significant differences in survival rate on 28 and 50 dpf between (RxI)xR and (IxR)xR hybrids.”

“We obtained sperm from 7 and 10 individuals, and eggs from 7 and 11 F1 RxI and IxR mature animals, respectively, and used them for within-type fertilizations. Fertilization rates were significantly higher for IxR hybrids than for RxI hybrids”

“Finally, F2 IxR hybrids grew and matured to produce sperm and eggs (Table 5 and Supplemental table S3). The sperm and eggs could fertilize each other to produce F3 IxR hybrids, which survived at least 28 dpf, after which we stopped observations.”

“simple quantitative traits, such as body size, showed an increased variability in F2 hybrids as expected for polygenic traits following allele segregation.”

Berná L, Alvarez-Valin F, D'Onofrio G.

Comp Funct Genomics. 2009;2009:875901. doi:10.1155/2009/875901

How fast is the sessile ciona?

“Tajima’s test results [...] for the great majority of the alignments, Ciona genes evolve faster than those of all vertebrate groups[...].” “On the average, Ciona evolves 50% faster than all vertebrates, with the exception of O. anatinus and M. domestica.” “The divergence between C. intestinalis and C. savignyi was reestimated and found to took place ~184 (±15) My ago.”

Wolf M, Chen S, Song J, Ankenbrand M, Müller T.

PLoS One. 2013 Jun 24;8(6):e66726. doi:10.1371/journal.pone.0066726

Compensatory base changes in ITS2 secondary structures correlate with the biological species concept despite intragenomic variability in ITS2 sequences--a proof of concept.

The CBC Species Concept

Paula Villa Martín, Aleš Buček, Thomas Bourguignon and Simone Pigolotti

Science Advances 15 Jul 2020 Vol. 6, no. 29, eaaz9037 doi:10.1126/sciadv.aaz9037

Ocean currents promote rare species diversity in protists

The model runs backwards in time and merge individuals in species if they can be traced to a common geographical origin. Ocean currents increase species diversity by limiting mixture.

Hu Y, Thapa A, Fan H, Ma T, Wu Q, Ma S, Zhang D, Wang B, Li M, Yan L, Wei F.

Sci Adv. 2020 Feb 26;6(9):eaax5751. doi:10.1126/sciadv.aax5751

Genomic evidence for two phylogenetic species and long-term population bottlenecks in red pandas.

“Data from 65 whole genomes, 49 Y-chromosomes, and 49 mitochondrial genomes provide the first comprehensive genetic evidence for species divergence in red pandas, demonstrating substantial inter-species genetic divergence for all three markers and correcting species-distribution boundaries.”

Russo CA, Takezaki N, Nei M.

Mol Biol Evol. 1995 May;12(3):391-404 doi:10.1093/oxfordjournals.molbev.a040214

Molecular phylogeny and divergence times of drosophilid species.

Study of Adh genes, nuclear 18S rRNA and mitochondrial DNA suggests that D. mel and D. pseudoobscura diverged 24.9 +/- 2.88 My ago, based on the assumption that D. picticornis and D. silvestris diverged 5.1 My ago.

Beckenbach AT, Wei YW, Liu H.

Mol Biol Evol. 1993 May;10(3):619-34 doi:10.1093/oxfordjournals.molbev.a040034

Relationships in the Drosophila obscura species group, inferred from mitochondrial cytochrome oxidase II sequences.

Analysis of Cox2 sequences of Drosophila species is most compatible with a speciation of D. melanogaster and D. pseudoobscura ~35 My ago. Sequence divergence between D. mel. and members of the D. obscura species group is in average of 11.4 %.

Yang Y, Servedio MR, Richards-Zawacki CL.

Nature. 2019 Oct;574(7776):99-102. doi:10.1038/s41586-019-1599-z

Imprinting sets the stage for speciation.

Oophaga pumilio tadpoles learn congeneric coat color from their mother.

Ichikawa K, Tomioka S, Suzuki Y, Nakamura R, Doi K, Yoshimura J, Kumagai M, Inoue Y, Uchida Y, Irie N, Takeda H, Morishita S.

Nat Commun. 2017 Nov 28;8(1):1833. doi:10.1038/s41467-017-01982-7

Centromere evolution and CpG methylation during vertebrate speciation.

Comparison of centromere sequences between interfertile medaka strains that separated 18~25 My ago. Also, within a species, homologous pairs of centromeres (derived from the same ancestral pre-teleost (350 My ago) chromosome) were conserved, and acrocentric ones were shown to evolve slower.

Brunetti, R. , Gissi, C. , Pennati, R. , Caicci, F. , Gasparini, F. and Manni, L.

J Zoolog Syst Evol Res, 2015, 53: 186-193. doi:10.1111/jzs.12101

Morphological evidence that the molecularly determined Ciona intestinalis type A and type B are different species: Ciona robusta and Ciona intestinalis.

Discriminates C. robusta from C. intestinalis by the presence of tubercular prominences in the tunic.

Mitogenomics reveals two cryptic species in Ciona intestinalis.

Trends Genet. 2007 Sep;23(9):419-22 doi:10.1016/j.tig.2007.07.001

Iannelli F, Pesole G, Sordino P, Gissi C.

Mitochondrial gene order differs between C. robusta and C. intestinalis.

Mol Biol Evol. 2013 Jul;30(7):1574-87. doi:10.1093/molbev/mst066

Roux C, Tsagkogeorga G, Bierne N, Galtier N.

Crossing the species barrier: genomic hotspots of introgression between two highly divergent Ciona intestinalis species.

Speciation during the Pliocene (≈ 3.8 Ma) and then recent introgression 15,000 years ago.

Bouchemousse S, Liautard-Haag C, Bierne N, Viard F.

Mol Ecol. 2016 Nov;25(21):5527-5542. doi:10.1111/mec.13854

Distinguishing contemporary hybridization from past introgression with postgenomic ancestry-informative SNPs in strongly differentiated Ciona species.

The only hybrids detected are F1 and have a C. int mitochondrial haplotype.