| 1. |
- Dapporto, Leonardo, et al.
(author)
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Identifying zones of phenetic compression in West Mediterranean butterflies (Satyrinae) : refugia, invasion and hybridization
- 2012
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In: Diversity & distributions. - : Wiley. - 1366-9516 .- 1472-4642. ; 18:11, s. 1066-1076
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Journal article (peer-reviewed)abstract
- Aim Distinct insular populations are generally considered important units for conservation. In islandmainland situations, unidirectional introgressive gene flow from the most abundant, typically continental, populations into the smaller island populations can erase native insular genetic units. As an indication of threat, the concept of phenetic slope is developed, a measure proportional to differentiation and to geographical proximity. Location The Western Mediterranean, including the following islands: Sardinia, Sicily, Corsica, Balearics, circum-Italian, circum-Sicilian and circum-Sardo-Corsican archipelagos. Eastern Europe is included for comparison. Methods Geometric morphometrics was applied to 2392 male genitalia of seven butterfly species groups. Geographic Information System techniques were used to depict the pattern in the distribution of morphotypes. The slope of variation in genital shape was computed to highlight geographical areas showing abrupt morphological changes. Correlation analyses were performed between the mean slope values across sea straits separating islands and nearest sources and ecological traits of the species that underlie their colonization and migration capacity. Results Phenetic slope analysis has revealed that the strait of Messina and the northern Tyrrhenian Sea support particularly contrasting populations. In these areas, mean slopes for species also correlated with certain ecological traits of the species. Sardinia emerges as the most stable refugium for ancestral mediterranean populations. Main conclusions There is strong support for the hypothesis that Italy has experienced invasion by populations from Eastern Europe with postglacial expansion of these populations across Italy. However, propagules are impeded from invading islands by the expanse of sea straits. Even so, sea straits are not invariably barriers. Our results suggest that wind direction in combination with habitat occupancy may have maintained ancestral insular populations in key locations distinguished by phenetic compression. We conclude that native insular populations acting as barriers to introgression in the areas showing particularly steep phenetic slopes deserve attention in conservation programmes.
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| 2. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Dapporto, Leonardo, et al.
(author)
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Biogeography of western Mediterranean butterflies : combining turnover and nestedness components of faunal dissimilarity
- 2014
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In: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 41:9, s. 1639-1650
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Journal article (peer-reviewed)abstract
- Aim Unpartitioned dissimilarity indices such as the Sorensen index (beta(sor)) tend to categorize areas according to species number. The use of turnover indices, such as the Simpson index (beta(simp)), may lead to the loss of important information represented by the nestedness component (beta(nest)). Recent studies have suggested the importance of integrating nestedness and turnover information. We evaluated this proposition by comparing biogeographical patterns obtained by unpartitioned (beta(sor)) and partitioned indices (beta(simp) and beta(nest)) on presence data of western Mediterranean butterflies. Location Western Mediterranean. Methods We assessed the regionalization of 81 mainland and island faunas according to partitioned and unpartitioned dissimilarity by using cluster analyses with the unweighted pair-group method using arithmetic averages (UPGMA) combined with non-metric multidimensional scaling (NMDS). We also carried out dissimilarity interpolation for beta(sor), beta(simp), beta(nest) and the beta(nest)/beta(sor) ratio, to identify geographical patterns of variation in faunal dissimilarity. Results When the unpartitioned bsor index was used, the clustering of sites allowed a clear distinction between insular and mainland species assemblages. Most islands were grouped together, irrespective of their mainland source, because of the dominant effect of their shared low richness. bsimp was the most effective index for clustering islands with their respective mainland source. bsimp clustered mainland sites into broader regions than clusters obtained using bsor. A comparison of regionalization and interpolation provided complementary information and revealed that, in different regions, the patterns highlighted by bsor could largely be determined either by nestedness or turnover. Main conclusions Partitioned and unpartitioned indices convey complementary information, and are able to reveal the influence of historical and ecological processes in structuring species assemblages. When the effect of nestedness is strong, the exclusive use of turnover indices can generate geographically coherent groupings, but can also result in the loss of important information. Indeed, various factors, such as colonization-extinction events, climatic parameters and the peninsular effect, may determine dissimilarity patterns expressed by the nestedness component.
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| 4. |
- Dapporto, Leonardo, et al.
(author)
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Comparing population patterns for genetic and morphological markers with uneven sample sizes. An example for the butterfly Maniola jurtina
- 2014
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In: Methods in Ecology and Evolution. - 2041-210X. ; 5:8, s. 834-843
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Journal article (peer-reviewed)abstract
- 1. Integrating genetic and/or phenotypic traits at population level is considered a fundamental approach in the study of evolutionary processes, systematics, biogeography and conservation. But combining the two types of data remain a complex task, mostly due to the high, and sometimes different, sample sizes required for reliable assessments of community traits. Data availability has been increasing in recent years, thanks to online resources, but it is uncommon that different types of markers are available for any given specimen. 2. We provide new R functions aimed at directly correlating traits at population level, even if data sets only overlap partially. The new functions are based on a modified Procrustes algorithm that minimizes differences between bidimensional ordinations of two different markers, based on a subsample of specimens for which both characters are known. To test the new functions, we used a molecular and morphological data set comprising Mediterranean specimens of the butterfly Maniola jurtina. 3. By using this method, we have been able to maximize similarities between genotypic and phenotypic configurations obtained after principal coordinate analysis for the model species and evaluated their degree of correlation at both individual and population level. The new recluster. procrustes function retained the information of the relative importance of different morphological variables in determining the observed ordinations and preserved it in the transformed configurations. This allowed calculating the best combination of morphological variables mirroring genetic relationships among specimens and populations. Finally, it was possible to analyse the modality and variance of the phenotypic characters correlated with the genetic structure among populations. 4. The genetic and phenotypic markers displayed high overall correlation in the study area except in the contact zone, where discrepancies for particular populations were detected. Interestingly, such discrepancies were spatially structured, with southern populations displaying typical western morphotype and eastern haplotypes, while the opposite occurred in the northern populations. The methodology here described can be applied to any number and type of traits for which bidimensional configurations can be obtained, and opens new possibilities for datamining and formeta-analyses combining existing data sets in biogeography, systematics and ecology.
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| 5. |
- Dinca, Vlad, et al.
(author)
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Dispersal, fragmentation, and isolation shape the phylogeography of the European lineages of Polyommatus (Agrodiaetus) ripartii (Lepidoptera: Lycaenidae) :
- 2013
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In: Biological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4066 .- 1095-8312. ; 109:4, s. 817-829
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Journal article (peer-reviewed)abstract
- Polyommatus ripartii is a biogeographically and taxonomically poorly understood species of butterfly with a scattered distribution in Europe. Recently, it has been shown that this species includes several European endemic and localized taxa (galloi, exuberans, agenjoi) that were previously considered species and even protected, a result that poses further questions about the processes that led to its current distribution. We analysed mitochondrial DNA and the morphology of P.ripartii specimens to study the phylogeography of European populations. Three genetically differentiated but apparently synmorphic lineages occur in Europe that could be considered evolutionarily significant units for conservation. Their strongly fragmented and counterintuitive distribution seems to be the result of multiple range expansions and contractions along Pleistocene climatic oscillations. Remarkably, based on the 79 specimens studied, these genetic lineages do not seem to extensively coexist in the distributional mosaic, a phenomenon most evident in the Iberian Peninsula. One of the important gaps in the European distribution of P.ripartii is reduced by the discovery of new Croatian populations, which also facilitate a better understanding of the biogeography of the species.
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| 6. |
- Fiz-Palacios, Omar, et al.
(author)
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The uneven phylogeny and biogeography of Erodium (Geraniaceae) : radiations in the Mediterranean and recent recurrent intercontinental colonization
- 2010
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In: Annals of Botany. - : Oxford University Press (OUP). - 0305-7364 .- 1095-8290. ; 106:6, s. 871-884
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Journal article (peer-reviewed)abstract
- Background and Aims: The genus Erodium is a common feature of Mediterranean-type climates throughout the world, but the Mediterranean Basin has significantly higher diversity than other areas. The aim here is to reveal the biogeographical history of the genus and the causes behind the evolution of the uneven distribution. Methods Seventy-eight new nrITS sequences were incorporated with existing plastid data to explore the phylogenetic relationships and biogeography of Erodium using several reconstruction methods. Divergence times for major clades were calculated and contrasted with other previously published information. Furthermore, topological and temporal diversification rate shift analyses were employed using these data. Key Results Phylogenetic relationships among species are widely congruent with previous plastid reconstructions, which refute the classical taxonomical classification. Biogeographical reconstructions point to Asia as the ancestral area of Erodium, arising approx. 18 MYA. Four incidences of intercontinental dispersal from the Mediterranean Basin to similar climates are demonstrated. Increases in diversification were present in two independent Erodium lineages concurrently. Two bursts of diversification (3 MYA and 0·69 MYA) were detected only in the Mediterranean flora.Conclusions Two lineages diverged early in the evolution of the genus Erodium: (1) subgenus Erodium plus subgenus Barbata subsection Absinthioidea and (2) the remainder of subgenus Barbata. Dispersal across major water bodies, although uncommon, has had a major influence on the distribution of this genus and is likely to have played as significant role as in other, more easily dispersed, genera. Establishment of Mediterranean climates has facilitated the spread of the genus and been crucial in its diversification. Two, independent, rapid radiations in response to the onset of drought and glacial climate change indicate putative adaptive radiations in the genus.
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| 7. |
- Sanudo-Restrepo, Claudia P., et al.
(author)
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Biogeography and systematics of Aricia butterflies (Lepidoptera, Lycaenidae)
- 2013
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In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 66:1, s. 369-379
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Journal article (peer-reviewed)abstract
- Butterflies of the Aricia species group represent a paradigm of unresolved taxonomy, both at the genus and species levels. We studied phylogenetic relationships, biogeography, and systematics based on genetic - nuclear and mitochondrial - and morphometric - external (wings) and internal (genitalia) data. We show that Aricia is a monophyletic genus comprising the taxa Pseudoaricia, Ultraaricia and Umpria, which are here considered junior synonyms of Aricia. The taxa allous, inhonora, issekutzi, mandzhuriana, myrmecias and transalaica, which have often been raised to species rank, are shown to probably represent subspecies or synonyms. We show that montensis is likely a good species that is sister to all A. artaxerxes populations across the Palearctic region. The species A. anteros and A. morronensis are shown to display deep intraspecific divergences and they may harbor cryptic species. We also discovered that A. cramera and A. agestis exhibit a pattern of mutual exclusion on islands, and a parapatric distribution in mainland with a narrow contact zone where potential hybrids were detected. The lack of a prezygotic barrier that prevents their coexistence could explain this phenomenon. This study will hopefully contribute to the stability of the systematics of Aricia, a group with potential for the study of the link between speciation and biogeography.
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| 8. |
- Talavera, Gerard, et al.
(author)
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Factors affecting species delimitations with the GMYC model : insights from a butterfly survey
- 2013
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In: Methods in Ecology and Evolution. - 2041-210X. ; 4:12, s. 1101-1110
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Journal article (peer-reviewed)abstract
- The generalized mixed Yule-coalescent (GMYC) model has become one of the most popular approaches for species delimitation based on single-locus data, and it is widely used in biodiversity assessments and phylogenetic community ecology. We here examine an array of factors affecting GMYC resolution (tree reconstruction method, taxon sampling coverage/taxon richness and geographic sampling intensity/geographic scale). We test GMYC performance based on empirical data (DNA barcoding of the Romanian butterflies) on a solid taxonomic framework (i.e. all species are thought to be described and can be determined with independent sources of evidence). The data set is comprehensive (176 species), and intensely and homogeneously sampled (1303 samples representing the main populations of butterflies in this country). Taxonomy was assessed based on morphology, including linear and geometric morphometry when needed. The number of GMYC entities obtained constantly exceeds the total number of morphospecies in the data set. We show that c.80% of the species studied are recognized as entities by GMYC. Interestingly, we show that this percentage is practically the maximum that a single-threshold method can provide for this data set. Thus, the c.20% of failures are attributable to intrinsic properties of the COI polymorphism: overlap in inter- and intraspecific divergences and non-monophyly of the species likely because of introgression or lack of independent lineage sorting. Our results demonstrate that this method is remarkably stable under a wide array of circumstances, including most phylogenetic reconstruction methods, high singleton presence (up to 95%), taxon richness (above five species) and the presence of gaps in intraspecific sampling coverage (removal of intermediate haplotypes). Hence, the method is useful to designate an optimal divergence threshold in an objective manner and to pinpoint potential cryptic species that are worth being studied in detail. However, the existence of a substantial percentage of species wrongly delimited indicates that GMYC cannot be used as sufficient evidence for evaluating the specific status of particular cases without additional data. Finally, we provide a set of guidelines to maximize efficiency in GMYC analyses and discuss the range of studies that can take advantage of the method.
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