Papers by Gisella Caccone
Comments on the proposed conservation of usage of Testudo gigantea Schweigger, 1812 (currently Geochelone (Aldabrachelys) gigantea; Reptilia, Testudines) 15
Ecology and Evolution, 2015
Long-term population history can influence the genetic effects of recent bottlenecks. Therefore, ... more Long-term population history can influence the genetic effects of recent bottlenecks. Therefore, for threatened or endangered species, an understanding of the past is relevant when formulating conservation strategies. Levels of variation at neutral markers have been useful for estimating local effective population sizes (N e) and inferring whether population sizes increased or decreased over time. Furthermore, analyses of genotypic, allelic frequency, and phylogenetic information can potentially be used to separate historical from recent demographic changes. For 15 populations of Gal apagos giant tortoises (Chelonoidis sp.), we used 12 microsatellite loci and DNA sequences from the mitochondrial control region and a nuclear intron, to reconstruct demographic history on shallow (past~100 generations,~2500 years) and deep (pre-Holocene, >10 thousand years ago) timescales. At the deep timescale, three populations showed strong signals of growth, but with different magnitudes and timing, indicating different underlying causes. Furthermore, estimated historical N e of populations across the archipelago showed no correlation with island age or size, underscoring the complexity of predicting demographic history a priori. At the shallow timescale, all populations carried some signature of a genetic bottleneck, and for 12 populations, point estimates of contemporary N e were very small (i.e., < 50). On the basis of the comparison of these genetic estimates with published census size data, N e generally represented~0.16 of the census size. However, the variance in this ratio across populations was considerable. Overall, our data suggest that idiosyncratic and geographically localized forces shaped the demographic history of tortoise populations. Furthermore, from a conservation perspective, the separation of demographic events occurring on shallow versus deep timescales permits the identification of naturally rare versus newly rare populations; this distinction should facilitate prioritization of management action.
Parasites & Vectors, 2011
Background: Glossina fuscipes, a riverine species of tsetse, is the major vector of human African... more Background: Glossina fuscipes, a riverine species of tsetse, is the major vector of human African trypanosomiasis (HAT) in sub-Saharan Africa. Understanding the population dynamics, and specifically the temporal stability, of G. fuscipes will be important for informing vector control activities. We evaluated genetic changes over time in seven populations of the subspecies G. f. fuscipes distributed across southeastern Uganda, including a zone of contact between two historically isolated lineages. A total of 667 tsetse flies were genotyped at 16 microsatellite loci and at one mitochondrial locus. Results: Results of an AMOVA indicated that time of sampling did not explain a significant proportion of the variance in allele frequencies observed across all samples. Estimates of differentiation between samples from a single population ranged from approximately 0 to 0.019, using Jost's D EST. Effective population size estimates using momentum-based and likelihood methods were generally large. We observed significant change in mitochondrial haplotype frequencies in just one population, located along the zone of contact. The change in haplotypes was not accompanied by changes in microsatellite frequencies, raising the possibility of asymmetric mating compatibility in this zone. Conclusion: Our results suggest that populations of G. f. fuscipes were stable over the 8-12 generations studied. Future studies should aim to reconcile these data with observed seasonal fluctuations in the apparent density of tsetse.
Proceedings of the Royal Society of London. Series B: Biological Sciences, 2004
As natural populations of endangered species dwindle to precarious levels, remaining members are ... more As natural populations of endangered species dwindle to precarious levels, remaining members are sometimes brought into captivity, allowed to breed and their offspring returned to the natural habitat. One goal of such repatriation programmes is to retain as much of the genetic variation of the species as possible. A taxon of giant Galápagos tortoises on the island of Españ ola has been the subject of a captive breedingrepatriation programme for 33 years. Core breeders, consisting of 12 females and three males, have produced more than 1200 offspring that have been released on Españ ola where in situ reproduction has recently been observed. Using microsatellite DNA markers, we have determined the maternity and paternity of 132 repatriated offspring. Contributions of the breeders are highly skewed. This has led to a further loss of genetic variation that is detrimental to the long-term survival of the population. Modifications to the breeding programme could alleviate this problem.
Morphometrics Parallel Genetics in a Newly Discovered and Endangered Taxon of Galápagos Tortoise
PLoS ONE, 2009
Parasites & Vectors, 2012
Background: Glossina fuscipes fuscipes is the primary vector of trypanosomiasis in humans and liv... more Background: Glossina fuscipes fuscipes is the primary vector of trypanosomiasis in humans and livestock in Uganda. The Lake Victoria basin has been targeted for tsetse eradication using a rolling carpet initiative, from west to east, with four operational blocks (3 in Uganda and 1 in Kenya), under a Pan-African Tsetse and Trypanosomiasis Eradication Campaign (PATTEC). We screened tsetse flies from the three Ugandan PATTEC blocks for genetic diversity at 15 microsatellite loci from continental and offshore populations to provide empirical data to support this initiative. Methods: We collected tsetse samples from 11 sites across the Lake Victoria basin in Uganda. We performed genetic analyses on 409 of the collected tsetse flies and added data collected for 278 individuals in a previous study. The flies were screened across 15 microsatellite loci and the resulting data were used to assess the temporal stability of populations, to analyze patterns of genetic exchange and structuring, to estimate dispersal rates and evaluate the sex bias in dispersal, as well as to estimate demographic parameters (N E and N C). Results: We found that tsetse populations in this region were stable over 4-16 generations and belong to 4 genetic clusters. Two genetic clusters (1 and 2) corresponded approximately to PATTEC blocks 1 and 2, while the other two (3 and 4) fell within PATTEC block 3. Island populations grouped into the same genetic clusters as neighboring mainland sites, suggesting presence of gene flow between these sites. There was no evidence of the stretch of water separating islands from the mainland forming a significant barrier to dispersal. Dispersal rates ranged from 2.5 km per generation in cluster 1 to 14 km per generation in clusters 3 and 4. We found evidence of male-biased dispersal. Few breeders are successfully dispersing over large distances. Effective population size estimates were low (33-310 individuals), while census size estimates ranged from 1200 (cluster 1) to 4100 (clusters 3 and 4). We present here a novel technique that adapts an existing census size estimation method to sampling without replacement, the scheme used in sampling tsetse flies. Conclusion: Our study suggests that different control strategies should be implemented for the three PATTEC blocks and that, given the high potential for re-invasion from island sites, mainland and offshore sites in each block should be targeted at the same time.
Genetics, 2005
Volcanic islands represent excellent models with which to study the effect of vicariance on colon... more Volcanic islands represent excellent models with which to study the effect of vicariance on colonization and dispersal, particularly when the evolution of genetic diversity mirrors the sequence of geological events that led to island formation. Phylogeographic inference, however, can be particularly challenging for recent dispersal events within islands, where the antagonistic effects of land bridge formation and vicariance can affect movements of organisms with limited dispersal ability. We investigated levels of genetic divergence and recovered signatures of dispersal events for 631 Galápagos giant tortoises across the volcanoes of Sierra Negra and Cerro Azul on the island of Isabela. These volcanoes are among the most recent formations in the Galápagos (<0.7 million years), and previous studies based on genetic and morphological data could not recover a consistent pattern of lineage sorting. We integrated nested clade analysis of mitochondrial DNA control region sequences, t...
Evolution, 2002
We examined the phylogeography and history of giant Galápagos tortoise populations based on mitoc... more We examined the phylogeography and history of giant Galápagos tortoise populations based on mitochondrial DNA sequence data from 161 individuals from 21 sampling sites representing the 11 currently recognized extant taxa. Molecular clock and geological considerations indicate a founding of the monophyletic Galápagos lineage around 2-3 million years ago, which would allow for all the diversification to have occurred on extant islands. Founding events generally occurred from geologically older to younger islands with some islands colonized more than once. Six of the 11 named taxa can be associated with monophyletic maternal lineages. One, Geochelone porteri on Santa Cruz Island, consists of two distinct populations connected by the deepest node in the archipelago-wide phylogeny, whereas tortoises in northwest Santa Cruz are closely related to those on adjacent Pinzó n Island. Volcan Wolf, the northernmost volcano of Isabela Island, consists of both a unique set of maternal lineages and recent migrants from other islands, indicating multiple colonizations possibly due to human transport or multiple colonization and partial elimination through competition. These genetic findings are consistent with the mixed morphology of tortoises on this volcano. No clear genetic differentiation between two taxa on the two southernmost volcanoes of Isabela was evident. Extinction of crucial populations by human activities confounds whether domed versus saddleback carapaces of different populations are mono-or polyphyletic. Our findings revealed a complex phylogeography and history for this tortoise radiation within an insular environment and have implications for efforts to conserve these endangered biological treasures.
Mitochondrial DNA variation in roe deer (Capreolus capreolus) from Italy: Evidence of admixture in one of the lastC. c. italicuspure populations from central‐southern Italy
Italian Journal of Zoology, 2009
PLoS Neglected Tropical Diseases, 2010
Invasive, exotic plant pathogens pose a major threat to native and agricultural ecosystems. Phyto... more Invasive, exotic plant pathogens pose a major threat to native and agricultural ecosystems. Phytophthora × cambivora is an invasive, destructive pathogen of forest and fruit trees causing severe damage worldwide to chestnuts (Castanea), apricots, peaches, plums, almonds and cherries (Prunus), apples (Malus), oaks (Quercus), and beech (Fagus). It was one of the first damaging invasive Phytophthora species to be introduced to Europe and North America, although its origin is unknown. We determined its population genetic history in Europe, North and South America, Australia and East Asia (mainly Japan) using genotyping-by-sequencing. Populations in Europe and Australia appear clonal, those in North America are highly clonal yet show some degree of sexual reproduction, and those in East Asia are partially sexual. Two clonal lineages, each of opposite mating type, and a hybrid lineage derived from these two lineages, dominated the populations in Europe and were predominantly found on fagaceous forest hosts (Castanea, Quercus, Fagus). Isolates from fruit trees (Prunus and Malus) belonged to a separate lineage found in Australia, North America, Europe and East Asia, indicating the disease on fruit trees could be caused by a distinct lineage of P. × cambivora, which may potentially be a separate sister species and has likely been moved with live plants. The highest genetic diversity was found in Japan, suggesting that East Asia is the centre of origin of the pathogen. Further surveys in unsampled, temperate regions of East Asia are needed to more precisely identify the location and range of the centre of diversity.
Conservation Genetics Resources, 2011
Mauritia flexuosa L.f. (Arecaceae) is a New World tropical palm that generally grows in isolated ... more Mauritia flexuosa L.f. (Arecaceae) is a New World tropical palm that generally grows in isolated swamps along meandering rivers and is in danger of fragmentation through unsustainable harvest practices. To explore gene flow among populations of M. flexuosa in Amazonia, we developed 13 novel, polymorphic microsatellite loci for M. flexuosa. Further studies will employ these loci to investigate the impacts of artisanal gold mining and wild-harvest on gene flow among populations of M. flexuosa. Keywords Mauritia flexuosa Á Amazonia Á Microsatellite Á Arecaceae Mauritia flexuosa L.f. (Arecaceae) is a dioecious, diploid palm (Röser et al. 1997) covering millions of hectares in Amazonia in monodominant stands (Peters et al. 1989). M. flexuosa populations are naturally isolated from one another as they generally dominate swamps along meandering rivers that originated as ox-bow lakes (Kalliola et al. 1991). The fruit of M. flexuosa has a high wild harvest potential, but harvesters often fell females for easier access to the fruit (Holm et al. 2008). This harvesting strategy, combined with artisanal gold mining that often occurs along meandering rivers in Amazonia in both Peru and Brazil, could restrict gene flow in naturally fragmented
Conservation Genetics, 2013
Studies of small-scale spatial genetic structure are crucial to the implementation of successful ... more Studies of small-scale spatial genetic structure are crucial to the implementation of successful conservation and management plans as they enhance our capacity to predict a population's ability to respond to changing environments. This is especially true in the tropics, where high rates of fragmentation and land-use change create potential barriers to genetic exchanges. We examined the genetic diversity of wild populations of the economically important palm, Mauritia flexuosa (Arecaceae) in and around the Aripo Savannas Scientific Reserve on the island of Trinidad. In a small collection area of roughly 10 km 2 we found both spatial and inter-generational, or temporal, genetic differentiation and high levels of nearest-neighbor mating. We suggest that these spatial and temporal genetic patterns reflect recent and drastic anthropogenic changes to the landscape of the study sites, which we hypothesize have created barriers to gene flow through animal-mediated seed dispersal and pollination.
BMC Evolutionary Biology, 2009
Background: Marine iguanas (Amblyrhynchus cristatus) inhabit the coastlines of large and small is... more Background: Marine iguanas (Amblyrhynchus cristatus) inhabit the coastlines of large and small islands throughout the Galápagos archipelago, providing a rich system to study the spatial and temporal factors influencing the phylogeographic distribution and population structure of a species. Here, we analyze the microevolution of marine iguanas using the complete mitochondrial control region (CR) as well as 13 microsatellite loci representing more than 1200 individuals from 13 islands. Results: CR data show that marine iguanas occupy three general clades: one that is widely distributed across the northern archipelago, and likely spread from east to west by way of the South Equatorial current, a second that is found mostly on the older eastern and central islands, and a third that is limited to the younger northern and western islands. Generally, the CR haplotype distribution pattern supports the colonization of the archipelago from the older, eastern islands to the younger, western islands. However, there are also signatures of recurrent, historical gene flow between islands after population establishment. Bayesian cluster analysis of microsatellite genotypes indicates the existence of twenty distinct genetic clusters generally following a onecluster-per-island pattern. However, two well-differentiated clusters were found on the easternmost island of San Cristóbal, while nine distinct and highly intermixed clusters were found on youngest, westernmost islands of Isabela and Fernandina. High mtDNA and microsatellite
BMC Ecology, 2007
Background: Giant Galápagos tortoises on the island of Española have been the focus of an intensi... more Background: Giant Galápagos tortoises on the island of Española have been the focus of an intensive captive breeding-repatriation programme for over 35 years that saved the taxon from extinction. However, analysis of 118 samples from released individuals indicated that the bias sex ratio and large variance in reproductive success among the 15 breeders has severely reduced the effective population size (N e). Results: We report here that an analysis of an additional 473 captive-bred tortoises released back to the island reveals an individual (E1465) that exhibits nuclear microsatellite alleles not found in any of the 15 breeders. Statistical analyses incorporating genotypes of 304 field-sampled individuals from all populations on the major islands indicate that E1465 is most probably a hybrid between an Española female tortoise and a male from the island of Pinzón, likely present on Española due to human transport. Conclusion: Removal of E1465 as well as its father and possible (half-)siblings is warranted to prevent further contamination within this taxon of particular conservation significance. Despite this detected single contamination, it is highly noteworthy to emphasize the success of this repatriation program conducted over nearly 40 years and involving release of over 2000 captive-bred tortoises that now reproduce in situ. The incorporation of molecular genetic analysis of the program is providing guidance that will aid in monitoring the genetic integrity of this ambitious effort to restore a unique linage of a spectacular animal.
Animal Conservation, 2007
Ex situ conservation strategies may be substantially informed by genetic data, and yet only recen... more Ex situ conservation strategies may be substantially informed by genetic data, and yet only recently have such approaches been used to facilitate captive population management of endangered species. The Gal´apagos tortoise Geochelone nigra is an endangered species that has benefited greatly from the application of molecular and population genetic data, but remains vulnerable throughout its range. The geographic and evolutionary origins of 98 tortoises in private collections and zoos on three continents were identified using mitochondrial DNA (mtDNA) control region sequences and multi-locus microsatellite genotype data relative to a large database of representative samplings from all extant populations, including historical population allele frequency data for the Geochelone nigra abingdoni taxon on Pinta by way of museum specimens. All but six individuals had mtDNA haplotypes previously sampled, with the novel haplotypes identified as most closely related to robust populations on the islands of Santa Cruz and Isabela. Multi-locus genotypic assignments corroborated the results obtained from the mtDNA analyses, with 83.7% of individuals consistently assigned to the same locality by both datasets. Overall, the majority of captive unknowns sampled were assigned to the La Caseta Geochelone nigra porteri population, with no fewer than six individuals of hybrid origin detected. Although a purported Pinta individual was revealed to be of Pinz´on ancestry, the two females currently housed with Lonesome George exhibited haplotypic and genotypic signatures that indicate that they are among the most appropriate matches for captive breeding. More generally, molecular approaches continue to represent important tools for assessing conservation value, minimizing hybridization and guiding management programs for preserving the distinctiveness of G. nigra taxa in captivity.
Journal of Medical Entomology, 2008
In the malaria vector Anopheles gambiae Giles sensu stricto, two molecular forms denoted M and S ... more In the malaria vector Anopheles gambiae Giles sensu stricto, two molecular forms denoted M and S are considered units of incipient speciation within this species. Very low hybrid frequencies and signiÞcant genetic differentiation have been found in sympatric M-and S-form populations. We studied the molecular form composition and the degree of genetic differentiation at 15 microsatellites in two samples of An. gambiae collected in two consecutive years from Bissau, Guinea Bissau. High frequencies of M/S hybrids (19 Ð24%) were found in this area. Coincidently, very low levels of genetic differentiation were detected between forms when analysis involved microsatellites mapped at chromosome-3 (mean F st , 0.000 Ð 0.002). The single exception was the X-linked AGXH678, for which high differentiation was measured (F st , 0.158 Ð 0.301). This locus maps near the centromere of chromosome X, a low recombination region in which selection is likely to promote divergence between M and S forms. These results strongly suggest that the degree of isolation between M and S forms, considered the units of incipient speciation within An. gambiae, is not homogenous throughout the species distribution range.
Journal of Heredity, 2011
Evolution of population structure on islands is the result of physical processes linked to volcan... more Evolution of population structure on islands is the result of physical processes linked to volcanism, orogenic events, changes in sea level, as well as habitat variation. We assessed patterns of genetic structure in the giant tortoise of the Aldabra atoll, where previous ecological studies suggested population subdivisions as a result of landscape discontinuity due to unsuitable habitat and island separation. Analysis of mitochondrial DNA (mtDNA) control region sequences and allelic variation at 8 microsatellite loci were conducted on tortoises sampled in 3 locations on the 2 major islands of Aldabra. We found no variation in mtDNA sequences. This pattern corroborated earlier work supporting the occurrence of a founding event during the last interglacial period and a further reduction in genetic variability during historical time. On the other hand, significant population structure recorded at nuclear loci suggested allopatric divergence possibly due to geographical barriers among islands and ecological partitions hindering tortoise movements within islands. This is the first attempt to study the population genetics of Aldabra tortoises, which are now at carrying capacity in an isolated terrestrial ecosystem where ecological factors appear to have a strong influence on population dynamics.
Journal of Heredity, 1997
We have used RAPD-PCR assays to Identify DNA polymorphisms In the European sea bass (Dlcentrarchu... more We have used RAPD-PCR assays to Identify DNA polymorphisms In the European sea bass (Dlcentrarchus labratf. We studied samples from eight Mediterranean localities and one Atlantic sample from Portugal. A sample from a congeneric species (D. punctatus) was Included for comparison. The study included 107 RAPD markers and 260 Individuals. Wlthln-population RAPD variation was high, but between-populatlon genetic differentiation was quite low. Mediterranean populations clustered along a northwest-southeast transect. This distribution may be related to past marine regressions, which have shaped the distribution of other fish species in the region. The pattern of genetic differentiation based on RAPD markers was compared to the patterns of genetic differentiation based on allozyme data on the same populations. Data were also compared to a mlcrosatellite survey on the same species. Merits and limits of the three techniques In detecting genetic differentiation are discussed. Through a comparison with a previous study in which hatchery samples were repeatedly subjected to acclimation to freshwater, It was possible to detect an ecological component to the pattern of RAPD differentiation in wild samples. We Identified a subset of RAPD bands that differed significantly In frequency between marine and lagoon samples. These same bands changed in frequency In the experimental samples after freshwater acclimation, with the acclimated samples resembling samples from lagoons. We suggest that markers are associated with genomlc regions involved In tolerance for varying salinity levels and that the acclimation experiments reflected the differential survival of genotypes naturally occurring in lagoons.
Journal of Evolutionary Biology, 1992
In this paper we attempt to investigate relationships between the amount of genetic divergence in... more In this paper we attempt to investigate relationships between the amount of genetic divergence in nuclear genes and the degree of morphological differentiation for different sets of characters in Dolichopoda cave crickets. Six populations representing five Dolichopoda species from Central and Southern Italy have been studied. The overall genetic divergence at nuclear genes was estimated both by single copy DNA-DNA hybridization and allozyme frequencies at 26 loci. Euclidean distances for two multivariate sets of morphometric variables: one describing body and appendage morphology, the other male epiphallus shape. Results showed a close agreement between the branching patterns of ATm values from DNA hybridization and Nei's allozyme distance values. On the other hand, patterns of morphological divergence revealed independent trends, although the branching pattern based on epiphallus morphology matched to some extent the phylogenies inferred from molecular data. The relative value of molecular and morphological characters as reliable phylogenetic tracers was evaluated in relation to their dependence on evolutionary factors. Implications of these findings on the calibration of molecular clocks are also discussed. The absolute rate of molecular change based on scDNA was estimated to be at least 0.98% divergence/my/lineage. This result is in agreement with calibrations attempted on other insects. Estimates of time of divergence based on allozymes (Nei's D) were highly consistent with the estimate from geological data.
Genetic variability and divergence between populations and species of Nesticus cave spiders
Genetica, 1981
Genetic variability and divergence at 21 enzyme loci were studied in and between Italian populati... more Genetic variability and divergence at 21 enzyme loci were studied in and between Italian populations of the cave spiders Nesticus eremita (13 populations), N. menozzii and N. sbordonii (one population each). The three species differ with respect to the degree of specialization to cave life, dispersion ability, isolation of populations, abundancy, extent of the distribution area, and range from the
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Papers by Gisella Caccone