Multi-locus species tree of the chub genus Squalius (Leuciscinae: Cyprinidae) from western Iberia: new insights into its evolutionary history

Waap, Silke; Amaral, Ana Rita; Gomes, Bruno; Coelho, M. M.

doi:10.1007/s10709-011-9602-0

Cited by 15 publications

(29 citation statements)

References 30 publications

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“…In four genes (cry1ba, per1a, per3 and bmal2) the best topology for the inferred gene tree is congruent with the species tree with two main clusters: i) S. aradensis and S. torgalensis; ii) S. pyrenaicus and S. carolitertii [25,26]. This could indicate that these genes evolved neutrally during speciation.…”

Section: Evidence Of Adaptive Convergence From Phylogenetic Trees Andmentioning

confidence: 63%

“…Mira and Arade, respectively). Based on phylogenies of nuclear and mitochondrial markers, the species tree of these species is well known, comprising two main groups: (i) S. carolitertii and S. pyrenaicus; and (ii) S. torgalensis and S. aradensis [25,26]. In Western Iberian Peninsula there is a transition between two contrasting climate types ( Fig.…”

Section: Backgroungmentioning

confidence: 99%

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Adaptation and convergence in circadian-related genes in Iberian freshwater fish

Moreno

Jesus

Sousa³

et al. 2020

Preprint

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BackgroundThe circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of transcription-translation feedback loops, involving genes that activate (bmal and clock – positive loop) and repress expression (cryptochrome (cry) and period (per) – negative loop). This is regulated by daily alternations of light but can also be affected by temperature. Fish, as ectothermic, depend on the environmental temperature and thus are good models to study its integration within the circadian system. Here, we studied the molecular evolution of circadian genes in four Squalius freshwater fish species, distributed across Western Iberian rivers affected by two climatic types with different environmental conditions (e.g. light and temperature). S. carolitertii and S. pyrenaicus inhabit the colder northern region under Atlantic climate type, while S. torgalensis, S. aradensis and some populations of S. pyrenaicus inhabit the warmer southern region affected by summer droughts, under Mediterranean climate type. ResultsWe identified 16 circadian-core genes in the Squalius species using a comparative transcriptomics approach. We detected evidence of positive selection in nine of these genes using methods based on dN/dS. Positive selection was mainly found in cry and per genes of the negative loop of the cycle, with 11 putatively adaptive substitutions mostly located on protein domains. Evidence for positive selection is predominant in southern populations affected by the Mediterranean climate type. By predicting protein features we found that changes at sites under positive selection can impact protein thermostability by changing their aliphatic index and isoelectric point. Additionally, in nine genes, the phylogenetic clustering of species that belong to different clades but inhabit southern basins with similar environmental conditions indicated evolutionary convergence.ConclusionsOur results support that temperature may be a strong selective pressure driving the evolution of genes involved in the circadian system. By integrating sequence-based functional protein prediction with dN/dS-based methods to detect selection we also uncovered adaptive convergence in the southern populations, probably related to their similar thermal conditions.

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Section: Evidence Of Adaptive Convergence From Phylogenetic Trees Andmentioning

confidence: 63%

Section: Backgroungmentioning

confidence: 99%

Adaptation and convergence in circadian-related genes in Iberian freshwater fish

Moreno

Jesus

Sousa³

et al. 2020

Preprint

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“…Actually, putative river captures between the Tejo and Mondego have already been suggested in other studies to explain occasional genetic exchanges between the northern Squalius carolitertii and the southern S. pyrenaicus (Brito et al ., ; Sousa‐Santos et al ., ). Furthermore, recent data (Waap et al ., ; T. Jesus, C. Fernandes & M. M. Coelho, unpublished data) have reinforced this hypothesis by showing that, at the nuclear level, S. pyrenaicus from Tejo is phylogenetically more closely related to S. carolitertii than to other populations of S. pyrenaicus .…”

Section: Discussionmentioning

confidence: 83%

Assessing inter-drainage connections: patterns of genetic diversity in an Iberian cyprinid fish

Aboim

Mesquita

Drago

et al. 2013

Biol J Linn Soc Lond

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The phylogeography of Iberian freshwater fish species strongly reflects the geomorphological history of Iberian water drainages and formation of mountain ranges. In particular, the Iberian Central Massif limits two ichthyogeographical districts based on fish distribution assemblages: the Northwest district, which comprises all river basins north of the Central massif, and the Central‐west district, which comprises the Tejo and Sado basins. Despite this scenario, the cyprinid Pseudochondrostoma polylepis occurs in both the Tejo and Mondego rivers (one either side of the Estrela Mountains, in the western end of the Central Massif). By analysing the population structure and demographic history of this straight‐mouth nase, based on both mtDNA and microsatellites, we have found evidence of a relatively recent common origin for both Mondego and Tejo populations. Shared haplotypes and lack of divergent lineages for mitochondrial marker, high levels of admixture and common ancestry at the nuclear level, together with signatures of asymmetrical gene flow from Tejo to Mondego suggest a Mondego colonization through a founder event with an origin in Tejo. We suggest that this colonization might have resulted from the occurrence of river connections/captures between Mondego and Tejo headwater tributaries in the recent past. With this study we reinforce that local‐scale geomorphological events and the adaptation/dispersal ability of a species to new environments can have a major impact on its demographic history, colonization processes, and ultimately its distribution. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 656–669.

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“…History of the gene families associated with the circadian system reflects the whole genome duplication events during evolution of teleost fish, including posterior gene losses described for the various gene families as well (Toloza-Villalobos et al 2015). Phylogenies were investigated individually for each protein to assess whether relationships between the studied species recovered the previously described species tree topology based on a multi-locus phylogenetic analysis with other nuclear markers (Waap et al 2011;Sousa-Santos et al 2019). The previously described species tree showed two main clusters: i) S. aradensis and S. torgalensis; ii) S. pyrenaicus from Tagus clustering with S. carolitertii (Waap et al 2011;Sousa-Santos et al 2019).…”

Section: Molecular Evolution and Positive Selection Within Squalius Cmentioning

confidence: 99%

“…Phylogenies were investigated individually for each protein to assess whether relationships between the studied species recovered the previously described species tree topology based on a multi-locus phylogenetic analysis with other nuclear markers (Waap et al 2011;Sousa-Santos et al 2019). The previously described species tree showed two main clusters: i) S. aradensis and S. torgalensis; ii) S. pyrenaicus from Tagus clustering with S. carolitertii (Waap et al 2011;Sousa-Santos et al 2019). Southern populations of S. pyrenaicus (Almargem and Guadiana) rendered paraphyletic to S.…”

Section: Molecular Evolution and Positive Selection Within Squalius Cmentioning

confidence: 99%

Adaptation and convergence in circadian-related genes in Iberian freshwater fish

Moreno

Sousa

Jesus

et al. 2019

Preprint

View full text Add to dashboard Cite

The circadian clock is a biological timing system that improves the inherent ability of organisms to deal with environmental fluctuations. It is regulated by daily alternations of light but can also be affected by temperature. Fish, as ectothermic, have an increased dependence on the environmental temperature and thus are good models to study the integration of temperature within the circadian system. Here, we studied four species of freshwater fish of Squalius genus, distributed across a latitudinal gradient in Portugal with variable conditions of light and temperature. We identified and characterised the expected sixteen genes belonging to four main gene families (Cryptochromes, Period, CLOCK and BMAL) involved in the circadian system. We conducted phylogenetic analysis and tested these genes for the presence of signatures of selection based on dN/dS that revealed the presence of mutations under positive selection in nine genes. Furthermore, we analysed functional features of the proteins and found that these mutations alter protein isoelectric point and aliphatic index. Additionally, in 50% of the genes we found a pattern of convergence uncovered by the phylogenetic clustering of S. aradensis and S. pyrenaicus from Almargem, which inhabit basins with similar environmental conditions. Although this clustering can be explained by incomplete lineage sorting, evidence of positive selection in one gene in the two species and similar functional features in seven proteins are consistent with convergence at protein level. Our results highlight the importance of integrating sequence-based functional protein characterisation with dN/dS-based methods when studying the molecular adaptation of species.

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Multi-locus species tree of the chub genus Squalius (Leuciscinae: Cyprinidae) from western Iberia: new insights into its evolutionary history

Cited by 15 publications

References 30 publications

Adaptation and convergence in circadian-related genes in Iberian freshwater fish

Adaptation and convergence in circadian-related genes in Iberian freshwater fish

Assessing inter-drainage connections: patterns of genetic diversity in an Iberian cyprinid fish

Adaptation and convergence in circadian-related genes in Iberian freshwater fish

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