Evolution / Phylogeography
Back to Water: Signature of Adaptive Evolution in Cetacean Mitochondrial tRNAs
Autori: Montelli S, Peruffo A, Patarnello T, Cozzi B, Negrisolo E
Riferimenti: PLoS One. (2016) Jun 23; 11(6): e0158129
Summary: The mitochondrion is the power plant of the eukaryotic cell, and tRNAs are the fundamental components of its translational machinery. In the present paper, the evolution of mitochondrial tRNAs was investigated in the Cetacea, a clade of Cetartiodactyla that retuned to water and thus had to adapt its metabolism to a different medium than that of its mainland ancestors. Our analysis focussed on identifying the factors that influenced the evolution of Cetacea tRNA double-helix elements, which play a pivotal role in the formation of the secondary and tertiary structures of each tRNA and consequently manipulate the whole translation machinery of the mitochondrion. Our analyses showed that the substitution pathways in the stems of different tRNAs were influenced by various factors, determining a molecular evolution that was unique to each of the 22 tRNAs. Our data suggested that the composition, AT-skew, and GC-skew of the tRNA stems were the main factors influencing the substitution process. In particular, the range of variation and the fluctuation of these parameters affected the fate of single tRNAs. Strong heterogeneity was observed among the different species of Cetacea. Finally, it appears that the evolution of mitochondrial tRNAs was also shaped by the environments in which the Cetacean taxa differentiated. This latter effect was particularly evident in toothed whales that either live in freshwater or are deep divers.
Link: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158129
Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish
Autori: Pauletto M, Manouzaki T, Ferraresso S, Babbucci M, Tsakogiannis A, Louro B, Vitulo N, Viet HQ, Carraro R, Bertotto D, Franch R, Maroso F, Aslam LM, Simionati B, Malacrida G, Cestaro A, Sarropoulou E, Mylonas CC, Power D, Patarnello T, Canario A, Tsigenoploulos C, Bargelloni L
Riferimenti: Communications Biology volume 1 (2018) Article number: 119
Summary: Sexual dimorphism is a fascinating subject in evolutionary biology and mostly results from sex-biased expression of genes, which have been shown to evolve faster in gonochoristic species. We report here genome and sex-specific transcriptome sequencing of Sparus aurata, a sequential hermaphrodite fish. Evolutionary comparative analysis reveals that sex-biased genes in S. aurata are similar in number and function, but evolved following strikingly divergent patterns compared with gonochoristic species, showing overall slower rates because of stronger functional constraints. Fast evolution is observed only for highly ovary-biased genes due to female-specific patterns of selection that are related to the peculiar reproduction mode of S. aurata, first maturing as male, then as female. To our knowledge, these findings represent the first genome-wide analysis on sex-biased loci in a hermaphrodite vertebrate species, demonstrating how having two sexes in the same individual profoundly affects the fate of a large set of evolutionarily relevant genes.
Assemblages of micronektonic fishes and invertebrates in a gradient of regional warming along the Western Antarctic Peninsula
Autori: Parker ML, Fraser WR, Ashford, J, Patarnello T, Zane L, Torres JJ
Riferimenti: JOURNAL OF MARINE SYSTEMS, vol. 152: 18-41, 2015. DOI: 10.1016/j.jmarsys.2015.07.005
Summary: Micronektonic fishes and invertebrates were sampled with 32 midwater trawls at nine sites along the Western Antarctic Peninsula (WAP) in the austral fall (March–April) of 2010. Study sites were located within four hypothesized hydrographic regions: near Joinville Island in Region I, at Croker Passage, near Anvers Island, and near Renaud Island in Region II, within Marguerite Bay and the Marguerite Trough in Region III, and near Charcot Island in Region IV. A total of 62 taxa representing 12 taxonomic groups of pelagic invertebrates and 9 families of fish were captured, but assemblages were dominated by only a few species. The most numerically abundant taxa were the euphausiids, Thysanoessa macrura, Euphausia superba, and E. crystallorophias, combining to contribute nearly 79% of the total catch. Biomass dominants included E. superba, which contributed more than 44% of the total catch, the notothenioid Pleuragramma antarctica, and the salp, Salpa thompsoni. A comparison of total catches among sites revealed that the largest volumetric abundances and biomasses were captured at the Marguerite Bay site.
Cluster analysis of abundance data identified distinct multispecies assemblages at Joinville Island in Region I, Croker Passage in Region II, Marguerite Bay in Region III, and Charcot Island in Region IV. A fifth distinct assemblage included samples from sites near Anvers and Renaud Island in Region II, and from the Marguerite Trough in Region III. Assemblages at Joinville Island and Croker Passage were both dominated by E. superba and S. thompsoni, but hydrographic conditions at Joinville Island favored a neritic assemblage, underscored by substantial numbers of P. antarctica. The assemblage at Croker Passage was more oceanic in nature with major inputs from the myctophid, Electrona antarctica and the hyperiid amphipod, Themisto gaudichaudii. Marguerite Bay and Charcot Island were well-mixed assemblages with strong representation by both neritic and oceanic fauna. The mid-peninsula assemblage was oceanic in character, being overwhelmingly dominated by Thysanoessa macrura and T. gaudichaudii.
Pleuragramma antarctica were captured at five sites: Joinville Island, Croker Passage, Marguerite Bay, and the two sites near Charcot Island. They were completely absent at the two sites near Anvers Island, at Renaud Island, and in the Marguerite Trough. One fish was captured in Croker Passage. The majority of fish captured in Marguerite Bay were larger than 150 mm standard length (SL), with very few fish of smaller size present. If resident populations of Pleuragramma reproduce and recruit locally rather than being sustained by larval advection, those populations will be highly susceptible to local disappearance. This may be the causative factor behind the absence of Pleuragramma from the mid-peninsula region. Continued warming and subsequent sea ice reductions may not only cause Pleuragramma population collapses in the Marguerite Bay and Charcot Island regions, but may also change the character of the faunal assemblages along the WAP to those of an oceanic system.
Link: https://www.sciencedirect.com/science/article/pii/S0924796315001207
Phylogeography and demographic history of two widespread Indo-Pacific mudskippers (Gobiidae: Periophthalmus)
Autori: Polgar G, L. Zane, M. Babbucci, F. Barbisan, T. Patarnello, L. Rüber, C. Papetti
Riferimenti: MOLECULAR PHYLOGENETICS AND EVOLUTION, vol. 73, p. 161-176, ISSN: 1055-7903, doi: 10.1016/j.ympev.2014.01.014
Summary: This study provides a first description of the phylogeographic patterns and evolutionary history of two species of the mudskipper genus Periophthalmus. These amphibious gobies are distributed throughout the whole Indo-Pacific region and Atlantic coast of Africa, in peritidal habitats of soft-bottom coastal ecosystems. Three sequence datasets of two widely distributed species, Periophthalmus argentilineatus and P. kalolo, were obtained by amplifying and sequencing two mtDNA markers (D-loop and 16S rDNA) and the nDNA rag1 region. The three datasets were then used to perform phylogeographic, demographic and population genetic analyses. Our results indicate that tectonic events and past climatic oscillations strongly contributed to shape present genetic differentiation, phylogeographic and demographic patterns. We found support for the monophyly of P. kalolo, and only shallow genetic differentiation between East-African and Indo-Malayan populations of this species. However, our collections of the morphospecies P. argentilineatus include three molecularly distinct lineages, one of them more closely related to P. kalolo. The presence of Miocenic timings for the most recent common ancestors of some of these morphologically similar clades, suggests the presence of strong stabilising selection in mudskippers’ habitats. At population level, demographic analyses and palaeoecological records of mangrove ecosystems suggest that Pleistocene bottlenecks and expansion plus secondary contact events of the studied species were associated with recurrent sea transgressions during interglacials, and sea regressions or stable regimes during glacials, respectively.
Link: https://www.sciencedirect.com/science/article/pii/S105579031400027X
Genetic differentiation and phylogeography of Mediterranean-North Eastern Atlantic blue shark (Prionace glauca, L. 1758) using mitochondrial DNA: Panmixia or complex stock structure?
Autori: Leone A, Urso I, Damalas D, Martinsohn J, Zanzi A, Mariani S, Sperone E, Micarelli P, Garibaldi F, Megalofonou P, Bargelloni L, Franch R, Macias D, Prodöhl P, Fitzpatrick S, Stagioni M, Tinti F, Cariani A
Riferimenti: PeerJOpen AccessVolume 2017, Issue 12, 2017, Article number e4112
Summary: Background The blue shark (Prionace glauca, Linnaeus 1758) is one of the most abundant epipelagic shark inhabiting all the oceans except the poles, including the Mediterranean Sea, but its genetic structure has not been confirmed at basin and interoceanic distances. Past tagging programs in the Atlantic Ocean failed to find evidence of migration of blue sharks between the Mediterranean and the adjacent Atlantic, despite the extreme vagility of the species. Although the high rate of by-catch in the Mediterranean basin, to date no genetic study on Mediterranean blue shark was carried out, which constitutes a significant knowledge gap, considering that this population is classified as “Critically Endangered”, unlike its open-ocean counterpart.
Methods Blue shark phylogeography and demography in the Mediterranean Sea and North-Eastern Atlantic Ocean were inferred using two mitochondrial genes (Cytb and control region) amplified from 207 and 170 individuals respectively, collected from six localities across the Mediterranean and two from the North-Eastern Atlantic.
Results Although no obvious pattern of geographical differentiation was apparent from the haplotype network, Φst analyses indicated significant genetic structure among four geographical groups. Demographic analyses suggest that these populations have experienced a constant population expansion in the last 0.4–0.1 million of years.
Discussion The weak, but significant, differences in Mediterranean and adjacent North-eastern Atlantic blue sharks revealed a complex phylogeographic structure, which appears to reject the assumption of panmixia across the study area, but also supports a certain degree of population connectivity across the Strait of Gibraltar, despite the lack of evidence of migratory movements observed by tagging data. Analyses of spatial genetic structure in relation to sex-ratio and size could indicate some level of sex/stage biased migratory behaviour.
Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas
Autori: Paterno, M., Schiavina, M., Aglieri, G., Ben Souissi, J., Boscari, E., Casagrandi, R., Chassanite, A., Chiantore, M., Congiu, L., Guarnieri, G., Kruschel, C., Macic, V., Marino, I.A.M., Papetti, C., Patarnello, T., Zane, L Melià, P.
Riferimenti: Ecology and EvolutionOpen Access, Volume 7, Issue 8, April 2017, Pages 2463-2479
Summary: Connectivity between populations influences both their dynamics and the genetic structuring of species. In this study, we explored connectivity patterns of a marine species with long‐distance dispersal, the edible common sea urchin Paracentrotus lividus, focusing mainly on the Adriatic–Ionian basins (Central Mediterranean). We applied a multidisciplinary approach integrating population genomics, based on 1,122 single nucleotide polymorphisms (SNPs) obtained from 2b‐RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal. We detected genetic homogeneity among eight population samples collected in the focal Adriatic–Ionian area, whereas weak but significant differentiation was found with respect to two samples from the Western Mediterranean (France and Tunisia). This result was not affected by the few putative outlier loci identified in our dataset. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic–Ionian locations, supporting the hypothesis of connectivity of P. lividus populations in this area. A peculiar pattern emerged from the comparison of our results with those obtained from published P. lividus cytochrome b (cytb) sequences, the latter revealing genetic differentiation in the same geographic area despite a smaller sample size and a lower power to detect differences. The comparison with studies conducted using nuclear markers on other species with similar pelagic larval durations in the same Adriatic–Ionian locations indicates species‐specific differences in genetic connectivity patterns and warns against generalizing single‐species results to the entire community of rocky shore habitats.
Link: https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.2844
