Anabela Cardoso | Universidade do Minho (original) (raw)

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Papers by Anabela Cardoso

Abdominal Imaging, 1981

A prospective study of 33 patients with cholestatic jaundice was performed with combined use of e... more A prospective study of 33 patients with cholestatic jaundice was performed with combined use of endoscopic retrograde cholangiopancreatography (ERCP), percutaneous transhepatic cholangiography (PTC), ultrasonography, and liver biopsy. A higher rate of success with PTC in 25 cases of extrahepatic cholestasis was offset by the better score of ERCP in 8 cases of intrahepatic cholestasis and its wider diagnostic scope. The procedures were complementary in 10 cases. Ultrasonic imaging of intrahepatic bile ducts proved useful for selecting the first cholangiographic technique. Liver biopsy established etiology in intrahepatic cholestasis. Our combined approach allowed us to develop through objective criteria a diagnostic flow chart of cholestasis.

Systematic Biology, 2004

The genus Cicindela (Coleoptera: Cicindelidae) is a species-rich cosmopolitan group of tiger beet... more The genus Cicindela (Coleoptera: Cicindelidae) is a species-rich cosmopolitan group of tiger beetles useful for comparing clade diversification worldwide. Knowledge about relationships of major groups is important for this analysis but basal nodes in Cicindela have been difficult to resolve with standard mtDNA markers. Here we developed the Mp20 gene, a single-copy nuclear marker coding for a muscle-associated protein in insects, for phylogenetic analysis of basal groups of Cicindela. Nearly full-length sequences were obtained for 51 cicindelids, including major taxonomic groups from all continents. Sequences of Mp20 were between 1.2 and 1.7 kb and spanning three introns. Phylogenetic signal of exon and intron sequences was compared with that from four gene regions of mtDNA (COI, COIII, Cytb, 16S rRNA; 2.4 kb total). Because introns differed in length, sequence alignment was conducted using various procedures of phenetic and parsimony-based character coding of indels to assess their phylogenetic information content, but major nodes were recovered consistently. Mp20 sequences contributed two thirds of the total support of the combined analysis, with most signal from the introns. We found major clades of Cicindela to be geographically largely coincident with continental regions, confined to Australasia, the Holarctic, the Indian subcontinent, Africa, and South and Central America. Clock estimates using various maximum-likelihood (ML) branch length calculations resulted in roughly similar divergence times whether Mp20 exon, introns, or mtDNA were used, and they were not greatly affected by different procedures for coding and optimizing indel characters. Based on existing clock calibrations in Cicindela, basal splits of continental lineages occurred in the mid-Miocene, placing the radiation of basal groups of Cicindela to a period when their open-vegetation habitats expanded globally.

Molecular Ecology, 2009

Current taxon assignments at the species level are frequently discordant with DNA-based analyses.... more Current taxon assignments at the species level are frequently discordant with DNA-based analyses. Recent studies on tiger beetles in the Cicindela hybrida complex identified discordance between mtDNA patterns and the entities currently defined by the taxonomic literature. To test the accuracy of morphologically delimited groups, five named taxa (species) from 24 representative sampling sites across Europe were scored for 41 external morphological characters. Three of the named taxa were ‘diagnosable’, that is, defined by between one and three characters unique to each group. Newly sequenced ITS1 and existing mitochondrial cox1 markers established 20 and 22 different haplotypes, respectively, but only cox1 produced (four) diagnosable units. Phylogenetic analysis and statistical parsimony networks showed poor congruence of character variation with the taxonomic entities (and each other). Variation in morphological characters was therefore tested directly for association with DNA-based nesting groups at various hierarchical levels using permutational contingency analysis. Significant statistical associations of 11 (of 13 variable) morphological characters were observed with nesting groups from ITS1 and mitochondrial DNA markers, predominantly at the 4-step level. The analysis demonstrates the need for formal tests of congruence with morphological variation at the level of individual characters, a step that is omitted from recent studies of ‘integrative taxonomy’. In addition, statistical correlation of particular morphological characters with DNA-based nesting groups can identify the lowest hierarchical level at which various character sets show congruence, as a means to define evolutionarily separated entities supported by diverse data sources.

Systematic Biology, 2006

Cataloging the very large number of undescribed species of insects could be greatly accelerated b... more Cataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia. Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique ("diagnostic") characters. The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees. Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes. Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units). Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects. The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group.

Systematic Biology, 2005

Species-level phylogenetic studies require fast-evolving nucleotide positions to resolve relation... more Species-level phylogenetic studies require fast-evolving nucleotide positions to resolve relationships among close relatives, but these sites may be highly homoplastic and perhaps uninformative or even misleading deeper in the tree. Here we describe a species-level analysis of tiger beetles in the genus Cicindela (Coleoptera: Cicindelidae ) for 132 terminal taxa and 1897 nucleotide positions from three regions of mtDNA, comprising 75% coverage of species occurring in North America. Evenly weighted parsimony analysis recovered four major clades representing radiations confined to North and Central America. Relationships near the tips were well supported but signal was contradictory at deeper nodes. Two major categories (3rd positions and all others) can be distinguished in likelihood analysis of character variation, of which only the fast-changing 3rd position characters were affected by saturation. However, their downweighting under a variety of criteria did not improve the tree topology at basal nodes. There was weak conflict between 3rd and non-3rd position characters deep in the tree, but support levels declined towards the root for all categories, even on trees that were reconstructed from 3rd and non-3rd positions separately. Statistical analysis of parsimony-based character transitions along branches showed a largely homogeneous distribution of change along the root-to-tip axis. The comparison of character transitions among the four major portions of the tree revealed deviations from stochastic distribution for the non-3rd positions, but not for 3rd positions. Hence, variability of functionally constrained non-3rd positions differs between clades and may be dependent on the character states at other sites, consistent with the covarion model of molecular evolution. The results suggest that some properties of 3rd positions are less problematic for phylogenetic reconstruction than other categories despite their high total homoplasy. In densely sampled data sets of closely related species, the disadvantages of weighting schemes according to homoplasy levels outweigh the benefits, showing the difficulty of devising meaningful weighting schemes that are applicable universally throughout the tree.

Molecular Ecology, 2005

Species delimitation is complicated where morphological variation is continuous or poorly subdivi... more Species delimitation is complicated where morphological variation is continuous or poorly subdivided, but for taxonomic convenience it is common practice to separate and name geographical groups to capture this variation. DNA-based approaches may be used to test if these groups in fact represent historically divided, discrete species entities. The Cicindela hybrida complex (Coleoptera: Cicindelidae) is an assemblage of up to seven morphologically recognized species and 15 subspecies with wide distribution in the Palaearctic region. We sequenced a discontinuous segment of 1899 bp of mtDNA including three regions (coxI, rrnL+trnL2+nad1, cob) for a total of 99 specimens from 36 sampling localities across Europe, revealing 48 haplotypes. Four major clades could be identified corresponding to geographical groups from central Iberia, Ukraine, central Europe, and a band from the Atlantic Iberian coast to northern Europe. Taking into account further subdivisions within these clades, four of the six named species included in the analysis were recognizable by applying various procedures for species delimitation. Age estimates from calibrated molecular clocks date the diversification of the hybrida group within the past 2 million years (Myr), and the separation of the northern clade within 0.4 Myr. Nested clade analysis revealed the rapid range expansion of the northern group consistent with postglacial dispersal, but we did not find support for specific source population(s) in the postulated southern refugia. The evolutionary framework based on mtDNA sequences is shown to identify species entities as discrete clusters of closely related sequences and provides an objective system for delineating and recognizing hierarchically structured groups. In the case of the C. hybrida complex, these groups largely coincided with those established from morphology. The study adds further support to the utility of mtDNA-based sequence profiles (the ‘DNA taxonomy’) as a rapid and objective synthesis of evolutionary diversity and as reference system for communication.

Abdominal Imaging, 1981

A prospective study of 33 patients with cholestatic jaundice was performed with combined use of e... more A prospective study of 33 patients with cholestatic jaundice was performed with combined use of endoscopic retrograde cholangiopancreatography (ERCP), percutaneous transhepatic cholangiography (PTC), ultrasonography, and liver biopsy. A higher rate of success with PTC in 25 cases of extrahepatic cholestasis was offset by the better score of ERCP in 8 cases of intrahepatic cholestasis and its wider diagnostic scope. The procedures were complementary in 10 cases. Ultrasonic imaging of intrahepatic bile ducts proved useful for selecting the first cholangiographic technique. Liver biopsy established etiology in intrahepatic cholestasis. Our combined approach allowed us to develop through objective criteria a diagnostic flow chart of cholestasis.

Systematic Biology, 2004

The genus Cicindela (Coleoptera: Cicindelidae) is a species-rich cosmopolitan group of tiger beet... more The genus Cicindela (Coleoptera: Cicindelidae) is a species-rich cosmopolitan group of tiger beetles useful for comparing clade diversification worldwide. Knowledge about relationships of major groups is important for this analysis but basal nodes in Cicindela have been difficult to resolve with standard mtDNA markers. Here we developed the Mp20 gene, a single-copy nuclear marker coding for a muscle-associated protein in insects, for phylogenetic analysis of basal groups of Cicindela. Nearly full-length sequences were obtained for 51 cicindelids, including major taxonomic groups from all continents. Sequences of Mp20 were between 1.2 and 1.7 kb and spanning three introns. Phylogenetic signal of exon and intron sequences was compared with that from four gene regions of mtDNA (COI, COIII, Cytb, 16S rRNA; 2.4 kb total). Because introns differed in length, sequence alignment was conducted using various procedures of phenetic and parsimony-based character coding of indels to assess their phylogenetic information content, but major nodes were recovered consistently. Mp20 sequences contributed two thirds of the total support of the combined analysis, with most signal from the introns. We found major clades of Cicindela to be geographically largely coincident with continental regions, confined to Australasia, the Holarctic, the Indian subcontinent, Africa, and South and Central America. Clock estimates using various maximum-likelihood (ML) branch length calculations resulted in roughly similar divergence times whether Mp20 exon, introns, or mtDNA were used, and they were not greatly affected by different procedures for coding and optimizing indel characters. Based on existing clock calibrations in Cicindela, basal splits of continental lineages occurred in the mid-Miocene, placing the radiation of basal groups of Cicindela to a period when their open-vegetation habitats expanded globally.

Molecular Ecology, 2009

Current taxon assignments at the species level are frequently discordant with DNA-based analyses.... more Current taxon assignments at the species level are frequently discordant with DNA-based analyses. Recent studies on tiger beetles in the Cicindela hybrida complex identified discordance between mtDNA patterns and the entities currently defined by the taxonomic literature. To test the accuracy of morphologically delimited groups, five named taxa (species) from 24 representative sampling sites across Europe were scored for 41 external morphological characters. Three of the named taxa were ‘diagnosable’, that is, defined by between one and three characters unique to each group. Newly sequenced ITS1 and existing mitochondrial cox1 markers established 20 and 22 different haplotypes, respectively, but only cox1 produced (four) diagnosable units. Phylogenetic analysis and statistical parsimony networks showed poor congruence of character variation with the taxonomic entities (and each other). Variation in morphological characters was therefore tested directly for association with DNA-based nesting groups at various hierarchical levels using permutational contingency analysis. Significant statistical associations of 11 (of 13 variable) morphological characters were observed with nesting groups from ITS1 and mitochondrial DNA markers, predominantly at the 4-step level. The analysis demonstrates the need for formal tests of congruence with morphological variation at the level of individual characters, a step that is omitted from recent studies of ‘integrative taxonomy’. In addition, statistical correlation of particular morphological characters with DNA-based nesting groups can identify the lowest hierarchical level at which various character sets show congruence, as a means to define evolutionarily separated entities supported by diverse data sources.

Systematic Biology, 2006

Cataloging the very large number of undescribed species of insects could be greatly accelerated b... more Cataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia. Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique ("diagnostic") characters. The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees. Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes. Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units). Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects. The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group.

Systematic Biology, 2005

Species-level phylogenetic studies require fast-evolving nucleotide positions to resolve relation... more Species-level phylogenetic studies require fast-evolving nucleotide positions to resolve relationships among close relatives, but these sites may be highly homoplastic and perhaps uninformative or even misleading deeper in the tree. Here we describe a species-level analysis of tiger beetles in the genus Cicindela (Coleoptera: Cicindelidae ) for 132 terminal taxa and 1897 nucleotide positions from three regions of mtDNA, comprising 75% coverage of species occurring in North America. Evenly weighted parsimony analysis recovered four major clades representing radiations confined to North and Central America. Relationships near the tips were well supported but signal was contradictory at deeper nodes. Two major categories (3rd positions and all others) can be distinguished in likelihood analysis of character variation, of which only the fast-changing 3rd position characters were affected by saturation. However, their downweighting under a variety of criteria did not improve the tree topology at basal nodes. There was weak conflict between 3rd and non-3rd position characters deep in the tree, but support levels declined towards the root for all categories, even on trees that were reconstructed from 3rd and non-3rd positions separately. Statistical analysis of parsimony-based character transitions along branches showed a largely homogeneous distribution of change along the root-to-tip axis. The comparison of character transitions among the four major portions of the tree revealed deviations from stochastic distribution for the non-3rd positions, but not for 3rd positions. Hence, variability of functionally constrained non-3rd positions differs between clades and may be dependent on the character states at other sites, consistent with the covarion model of molecular evolution. The results suggest that some properties of 3rd positions are less problematic for phylogenetic reconstruction than other categories despite their high total homoplasy. In densely sampled data sets of closely related species, the disadvantages of weighting schemes according to homoplasy levels outweigh the benefits, showing the difficulty of devising meaningful weighting schemes that are applicable universally throughout the tree.

Molecular Ecology, 2005

Species delimitation is complicated where morphological variation is continuous or poorly subdivi... more Species delimitation is complicated where morphological variation is continuous or poorly subdivided, but for taxonomic convenience it is common practice to separate and name geographical groups to capture this variation. DNA-based approaches may be used to test if these groups in fact represent historically divided, discrete species entities. The Cicindela hybrida complex (Coleoptera: Cicindelidae) is an assemblage of up to seven morphologically recognized species and 15 subspecies with wide distribution in the Palaearctic region. We sequenced a discontinuous segment of 1899 bp of mtDNA including three regions (coxI, rrnL+trnL2+nad1, cob) for a total of 99 specimens from 36 sampling localities across Europe, revealing 48 haplotypes. Four major clades could be identified corresponding to geographical groups from central Iberia, Ukraine, central Europe, and a band from the Atlantic Iberian coast to northern Europe. Taking into account further subdivisions within these clades, four of the six named species included in the analysis were recognizable by applying various procedures for species delimitation. Age estimates from calibrated molecular clocks date the diversification of the hybrida group within the past 2 million years (Myr), and the separation of the northern clade within 0.4 Myr. Nested clade analysis revealed the rapid range expansion of the northern group consistent with postglacial dispersal, but we did not find support for specific source population(s) in the postulated southern refugia. The evolutionary framework based on mtDNA sequences is shown to identify species entities as discrete clusters of closely related sequences and provides an objective system for delineating and recognizing hierarchically structured groups. In the case of the C. hybrida complex, these groups largely coincided with those established from morphology. The study adds further support to the utility of mtDNA-based sequence profiles (the ‘DNA taxonomy’) as a rapid and objective synthesis of evolutionary diversity and as reference system for communication.