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- Drivers of Cape Verde archipelagic endemism in keyhole limpetsPublication . Lopes Da Cunha, Regina; Assis, J.; Madeira, Celine; Seabra, Rui; Lima, Fernando P.; Lopes, Evandro P.; Williams, Suzanne T.; Castilho, RitaOceanic archipelagos are the ideal setting for investigating processes that shape species assemblages. Focusing on keyhole limpets, genera Fissurella and Diodora from Cape Verde Islands, we used an integrative approach combining molecular phylogenetics with ocean transport simulations to infer species distribution patterns and analyse connectivity. Dispersal simulations, using pelagic larval duration and ocean currents as proxies, showed a reduced level of connectivity despite short distances between some of the islands. It is suggested that dispersal and persistence driven by patterns of oceanic circulation favouring self-recruitment played a primary role in explaining contemporary species distributions. Mitochondrial and nuclear data revealed the existence of eight Cape Verde endemic lineages, seven within Fissurella, distributed across the archipelago, and one within Diodora restricted to Boavista. The estimated origins for endemic Fissurella and Diodora were 10.2 and 6.7 MY, respectively. Between 9.5 and 4.5 MY, an intense period of volcanism in Boavista might have affected Diodora, preventing its diversification. Having originated earlier, Fissurella might have had more opportunities to disperse to other islands and speciate before those events. Bayesian analyses showed increased diversification rates in Fissurella possibly promoted by low sea levels during Plio-Pleistocene, which further explain differences in species richness between both genera.
- Distinctive genetic signatures of two fairy shrimp species with overlapping ranges in Iberian temporary pondsPublication . Lopes Da Cunha, Regina; Sala, Jordi; Machado, Margarida; Boix, Dani; Madeira, Celine; Madeira, Pedro M.; Cristo, Margarida; Cancela Da Fonseca, Luís; Castilho, RitaTemporary lentic water bodies host biotic assemblages adapted to the transient nature of these freshwater habitats. Fairy shrimps (Crustacea, Branchiopoda, Anostraca) are one of the most important biological components of these unique environments and have a fossil record dating back to the Middle Jurassic (>150 million years). Some anostracan species show a geographically restricted distribution, whereas others are widely dispersed. We aimed to investigate the relationship between different geographic extents and patterns of genetic structure in species of Anostraca. Following this objective, we selected two species with contrasting ranges but overlapping geographic distributions and similar life-history traits in the study area. We analysed additional information that, from an ecological (e.g. egg-bank, niche breadth, and pond connectivity) and evolutionary (e.g. crown-group age of each species) perspective, may explain the obtained phylogeographic patterns. Between 2005 and 2018, we sampled two species of fairy shrimps (309 specimens of Branchipus cortesi and 264 specimens of Tanymastix stagnalis) from 53 temporary ponds of Portugal. We added five other locations from Spain and France to include other European locations for T. stagnalis. Additionally, we also sampled Branchipus schaefferi from two temporary water bodies (Spain and Morocco) to include in the dating analysis. Reconstructed phylogenies based on mitochondrial sequence data indicate the existence of deeply divergent clades with an unequivocal phylogeographic structure in T. stagnalis and shallower divergences in B. cortesi with a less clear geographic correspondence. We found evidence of frequent local and rare long-distance dispersal events in both species and limited intermediate dispersal, which was more common in B. cortesi. A Bayesian dating analysis using the Branchiopoda fossil record estimated the age of the most recent common ancestors of T. stagnalis and B. cortesi at 32.4 and 12.8 million years, respectively. Haplotype accumulation curves indicated that only a portion of the genetic composition of the species was sampled on each hydroperiod and showed the existence of large, genetically diverse egg banks that remain in the soil. These egg banks represent a genetic reservoir that guarantees the survival of the species because active populations from different hydroperiods may be genetically different and adapt to a changing environment. We hypothesise that the contrasting phylogeographic patterns displayed by the two fairy shrimp species may result from: (1) the earlier age of the most recent common ancestor of T. stagnalis, as older species have more time to accumulate mutations and, thus, are expected to exhibit higher genetic differentiation among populations; (2) slight differences in adult behaviour, life-history traits and cyst morphologies of T. stagnalis and B. cortesi favouring different animal dispersal vectors with distinct dispersal abilities. Therefore, phylogeographic patterns may be explained by both evolutionary and ecological processes, which operate in different time scales.
- Invasion genetics of the mummichog (Fundulus heteroclitus): recent anthropogenic introduction in IberiaPublication . Morim, Teófilo; Bigg, Grant R.; Madeira, Pedro M.; Palma, Jorge; Duvernell, David D.; Gisbert, Enric; Lopes Da Cunha, Regina; Castilho, RitaHuman activities such as trade and transport have increased considerably in the last decades, greatly facilitating the introduction and spread of non-native species at a global level. In the Iberian Peninsula, Fundulus heteroclitus, a small euryhaline coastal fish with short dispersal, was found for the first time in the mid-1970s. Since then, F. heteroclitus has undergone range expansions, colonizing the southern region of Portugal, southwestern coast of Spain and the Ebro Delta in the Mediterranean Sea. Cytochrome b sequences were used to elucidate the species invasion pathway in Iberia. Three Iberian locations (Faro, Cádiz and Ebro Delta) and 13 other locations along the native range of F. heteroclitus in North America were sampled. Results revealed a single haplotype, common to all invasive populations, which can be traced to the northern region of the species' native range. We posit that the origin of the founder individuals is between New York and Nova Scotia. Additionally, the lack of genetic structure within Iberia is consistent with a recent invasion scenario and a strong founder effect. We suggest the most probable introduction vector is associated with the aquarium trade. We further discuss the hypothesis of a second human-mediated introduction responsible for the establishment of individuals in the Ebro Delta supported by the absence of adequate muddy habitats linking Cádiz and the Ebro Delta. Although the species has a high tolerance to salinity and temperature, ecological niche modelling indicates that benthic habitat constraints prevent along-shore colonisation suggesting that such expansions would need to be aided by human release.
- Different diversity-dependent declines in speciation rate unbalances species richness in terrestrial slugsPublication . Lopes Da Cunha, Regina; Patrao, Claudia; Castilho, RitaTwo genera of terrestrial slugs (Arion and Geomalacus) display a striking disproportion in species richness in the Iberian Peninsula. While there are 17 Iberian endemic species in Arion, morphological criteria only recognize four species within Geomalacus. Sequence data were used to test whether these differences could result from: (1) cryptic diversity within Geomalacus; (2) an earlier origin for Arion (older clades are expected to accumulate more species); (3) distinct patterns of diversification rates (higher initial speciation rates in Arion), and (4) some combination of the above factors (e.g., an older clade with higher speciation rates). Species delimitation tests based on mitochondrial and nuclear data revealed eight cryptic lineages within Geomalacus that lessened the asymmetry; nevertheless, the disparity required further investigation. No meaningful differences in crown group ages of each recovered clade were found. Regardless the different premises of the two equally plausible diversification models (similar initial speciation rates vs. higher initial speciation rates in Geomalacus), both coincide on diversity-dependent diversification for the two groups but weaker rate declines in Arion best explains the observed asymmetry in species richness. Also, the broader environmental tolerance combined with a faster dispersal and wider distribution may have represented an evolutionary advantage for Arion.
- Asymmetrical dispersal and putative isolation-by-distance of an intertidal blenniid across the Atlantic-Mediterranean dividePublication . Castilho, Rita; Lopes Da Cunha, Regina; Faria, Claudia; Velasco, Eva M.; Robalo, Joana I.Transition zones are of high evolutionary interest because unique patterns of spatial variation are often retained. Here, we investigated the phylogeography of the peacock blenny, Salaria pavo, a small marine intertidal fish that inhabits rocky habitats of the Mediterranean and the adjacent Atlantic Ocean. We screened 170 individuals using mitochondrial and nuclear sequence data from eight locations. Four models of genetic structure were tested: panmixia, isolation-by-distance, secondary contact and phylogeographic break. Results indicated clear asymmetric migration from the Mediterranean to the Atlantic but only marginally supported the isolation-by-distance model. Additionally, the species displays an imprint of demographic expansion compatible with the last glacial maximum. Although the existence of a refugium in the Mediterranean cannot be discarded, the ancestral lineage most likely originated in the Atlantic, where most of the genetic diversity occurs.
- Rising the persian gulf black-lip pearl oyster to the species level: fragmented habitat and chaotic genetic patchiness in Pinctada persicaPublication . Ranjbar, Mohammad Sharif; Zolgharnien, Hossein; Yavari, Vahid; Archangi, Bita; Salari, Mohammad Ali; ARNAUD-HAOND, Sophie; Lopes Da Cunha, ReginaMarine organisms with long pelagic larval stages are expected to exhibit low genetic differentiation due to their potential to disperse over large distances. Growing body of evidence, however, suggests that marine populations can differentiate over small spatial scales. Here we focused on black-lip pearl oysters from the Persian Gulf that are thought to belong to the Pinctada margaritifera complex given their morphological affinities. This species complex includes seven lineages that show a wide distribution ranging from the Persian Gulf (Pinctada margaritifera persica) and Indian Ocean (P. m. zanzibarensis) to the French Polynesia (P. m. cumingii) and Hawai'i (P. m. galtsoffi). Despite the long pelagic larval phase of P. m. persica, this lineage is absent from continental locations and can only be found on a few islands of the Persian Gulf. Mitochondrial COI-based analyses indicated that P. m. persica belongs to a clearly divergent ESU and groups with specimens from Mauritius (P. m. zanzibarensis). Microsatellite data, used here to assess the spatial scale of realized dispersal of Persian Gulf black-lip pearl oysters, revealed significant genetic structure among islands distant of only a few dozen kilometres. The scantiness of suitable habitats most likely restricted the distribution of this lineage originating the observed chaotic genetic patchiness. The hatchery-based enhancement performed in one of the sampled islands may also have affected population genetic structure. The long-term accumulation of genetic differences likely resulted from the allopatric divergence between P. m. persica and the neighbouring Indian Ocean black-lip pearl oysters.
- Wider sampling reveals a non-sister relationship for geographically contiguous lineages of a marine musselPublication . Lopes Da Cunha, Regina; Nicastro, Katy; Costa, Joana; McQuaid, Christopher D.; Serrao, Ester A.; Zardi, GerardoThe accuracy of phylogenetic inference can be significantly improved by the addition of more taxa and by increasing the spatial coverage of sampling. In previous studies, the brown mussel Perna perna showed a sister-lineage relationship between eastern and western individuals contiguously distributed along the South African coastline. We used mitochondrial (COI) and nuclear (ITS) sequence data to further analyze phylogeographic patterns within P.perna. Significant expansion of the geographical coverage revealed an unexpected pattern. The western South African lineage shared the most recent common ancestor (MRCA) with specimens from Angola, Venezuela, and Namibia, whereas eastern South African specimens and Mozambique grouped together, indicating a non-sister relationship for the two South African lineages. Two plausible biogeographic scenarios to explain their origin were both supported by the hypotheses-testing analysis. One includes an Indo-Pacific origin for P.perna, dispersal into the Mediterranean and Atlantic through the Tethys seaway, followed by recent secondary contact after southward expansion of the western and eastern South African lineages. The other scenario (Out of South Africa) suggests an ancient vicariant divergence of the two lineages followed by their northward expansion. Nevertheless, the Out of South Africa hypothesis would require a more ancient divergence between the two lineages. Instead, our estimates indicated that they diverged very recently (310 kyr), providing a better support for an Indo-Pacific origin of the two South African lineages. The arrival of the MRCA of P.perna in Brazil was estimated at 10 [0-40] kyr. Thus, the hypothesis of a recent introduction in Brazil through hull fouling in wooden vessels involved in the transatlantic itineraries of the slave trade did not receive strong support, but given the range for this estimate, it could not be discarded. Wider geographic sampling of marine organisms shows that lineages with contiguous distributions need not share a common ancestry.