Combining the analyses of introgressive hybridisation and linkage mapping to investigate the genetic architecture of population divergence in the lake whitefish (Coregonus clupeaformis, Mitchill)

Adaptation and reproductive isolation, the engines of biological diversity, are still elusive when discussing the genetic bases of speciation. Namely, the number of genes and magnitude of selection acting positively or negatively on genomic traits implicated in speciation is contentious. Here, we describe the first steps of an ongoing research program aimed at understanding the genetic bases of population divergence and reproductive isolation in the lake whitefish (Coregonus clupeaformis). A preliminary linkage map originating from a hybrid cross between dwarf and normal ecotypes is presented, whereby some of the segregating AFLP markers were found to be conserved among natural populations. Maximum-likelihood was used to estimate hybrid indices from non-diagnostic markers at 998 AFLP loci. This allowed identification of the most likely candidate loci that have been under the influence of selection during the natural hybridisation of whitefish originating from different glacial races. As some of these loci could be identified on the linkage map, the possibility that selection of traits in natural populations may eventually be correlated to specific chromosomal regions was demonstrated. The future prospects and potential of these approaches to elucidate the genetic bases of adaptation and reproductive isolation among sympatric ecotypes of lake whitefish is discussed.

Petrology and geochemistry of the Bandas del Sur Formation, Las Canadas Edifice, Tenerife (Canary Islands)

The Bandas del Sur Formation preserves a Quaternary extra-caldera record of central phonolitic explosive volcanism of the Las Canadas volcano at Tenerife. Volcanic rocks are bimodal in composition, being predominantly phonolitic pyroclastic deposits, several eruptions of which resulted in summit caldera collapse, alkali basaltic lavas erupted from many fissures around the flanks. For the pyroclastic deposits, there is a broad range of pumice glass compositions from phonotephrite to phonolite. The phonolite pyroclastic deposits are also characterized by a diverse, 7-8-phase phenocryst assemblage (alkali feldspar + biotite + sodian diopside + titanomagnetite + ilmenite + nosean-hauyne + titanite + apatite) with alkali feldspar dominant, in contrast to interbedded phonolite lavas that typically have lower phenocryst contents and lack hydrous phases. Petrological and geochemical data are consistent with fractional crystallization (involving the observed phenocryst assemblages) as the dominant process in the development of phonolite magmas. New stratigraphically constrained data indicate that petrological and geochemical differences exist between pyroclastic deposits of the last two explosive cycles of phonolitic volcanism. Cycle 2 (0.85-0.57 Ma) pyroclastic fall deposits commonly show a cryptic compositional zonation indicating that several eruptions tapped chemically, and probably thermally stratified magma systems. Evidence for magma mixing is most widespread in the pyroclastic deposits of Cycle 3 (0.37-0.17 Ma), which includes the presence of reversely and normally zoned phenocrysts, quenched mafic glass blebs in pumice, banded pumice, and bimodal to polymodal phenocryst compositional populations. Syn-eruptive mixing events involved mostly phonolite and tephriphonolite magmas, whereas a pre-eruptive mixing event involving basaltic magma is recorded in several banded pumice-bearing ignimbrites of Cycle 3. The periodic addition and mixing of basaltic magma ultimately may have triggered several eruptions. Recharge and underplating by basaltic magma is interpreted to have elevated sulphur contents (occurring as an exsolved gas phase) in the capping phonolitic magma reservoir. This promoted nosean-hauyne crystallization over nepheline, elevated SO3 contents in apatite, and possibly resulted in large, climatologically important SO2 emissions.

Testing the relationship between morphological and molecular rates of change along phylogenies

Molecular evolution has been considered to be essentially a stochastic process, little influenced by the pace of phenotypic change. This assumption was challenged by a study that demonstrated an association between rates of morphological and molecular change estimated for total-evidence phylogenies, a finding that led some researchers to challenge molecular date estimates of major evolutionary radiations. Here we show that Omland's (1997) result is probably due to methodological bias, particularly phylogenetic nonindependence, rather than being indicative of an underlying evolutionary phenomenon. We apply three new methods specifically designed to overcome phylogenetic bias to 13 published phylogenetic datasets for vertebrate taxa, each of which includes both morphological characters and DNA sequence data. We find no evidence of an association between rates of molecular and morphological rates of change.

Phylogeography of the pipefish, Urocampus carinirostris, suggests secondary intergradation of ancient lineages

We assayed the pattern of mitoehondrial DNA evolution in the live bearing, seagrass specialist pipefish, Urocampus carinirostris, in eastern Australia. These life history attributes were predicted to result in strong phylogeographic structure in U. carinirostris. Phylogenetic analysis of cytochrome b sequences detected two monophyletic mtDNA clades that differed by 8.69% sequence divergence - a large level of intraspecific divergence for a marine fish. The geographical distribution of clades was non-random and resembled clinal secondary intergradation over a 130-km stretch of coastline. Contrary to phylogeographic predictions, this large phylogeographic break does not occur across a traditionally recognised biogeographic boundary. Analyses of historical demography suggested that individuals belonging to the most widespread clade underwent a population expansion from a small refuge population during the Pleistocene.

Distribution and evolution of the Anopheles punctulatus group (Diptera : Culicidae) in Australia and Papua New Guinea

The members of the Anopheles punctulatus group are major vectors of malaria and Bancroftian filariasis in the southwest Pacific region. The group is comprised of 12 cryptic species that require DNA-based tools for species identification. From 1984 to 1998 surveys were carried out in northern Australia, Papua New Guinea and on islands in the southwest Pacific to determine the distribution of the A. punctulatus group. The results of these surveys have now been completed and have generated distribution data from more than 1500 localities through this region. Within this region several climatic and geographical barriers were identified that restricted species distribution and gene flow between geographic populations. This information was further assessed in light of a molecular phylogeny derived from the ssrDNA (18S). Subsequently, hypotheses have been generated on the evolution and distribution of the group so that future field and laboratory studies may be approached more systematically. This study suggested that the ability for widespread dispersal was found to have appeared independently in species that show niche-specific habitat preference (Anopheles farauti s.s. and A. punctulatus) and conversely in species that showed diversity in their larval habitat (Anopheles farauti 2). Adaptation to the monsoonal climate of northern Australia and southwest Papua New Guinea was found to have appeared independently in A. farauti s.s., A. farauti 2 and Anopheles farauti 3. Shared or synapomorphic characters were identified as saltwater tolerance (A. farauti s.s. and Anopheles farauti 7) and elevational affinities above 1500 m (Anopheles farauti 5, Anopheles farauti 6 and A. farauti 2). (C) 2002 Australian Society for Parasitology Inc. Published by Elsevier Science Ltd. All rights reserved.

Revisiting the question of limited genetic variation within Schistosoma japonicum

Recent electrophoretic data have indicated that Schistosoma japonicum in mainland China may be a species complex, with the existence of a cryptic species being predicted from the analysis of schistosome populations from Sichuan province. To investigate the Sichuan form of S. japonicum, 4.9 kbp of mitochondrial DNA from each of three samples of the parasite from China (two from Sichuan and one from Hunan) and one from Sorsogon in the Philippines were amplified, sequenced and characterized. The sequence data were compared with those from the related South-east Asian species of S. mekongi (Khong Island, Laos) and S. malayensis (Baling, Malaysia) and that from S. japonicum from Anhui (China). At both the nucleotide and amino-acid levels, the variation among the five S. japonicum samples was limited ( < 1%). This was consistent with the conclusions drawn from previous molecular studies, in which minimal variation among S. japonicum populations was also detected. In contrast, S. mekongi and S. malayensis, species recognized as separate but closely related, differ from each other by about 10%, and each differs by 25%-26% from S. japonicum. Phylogenetic trees provided a graphic representation of these differences, showing all S. japonicum sequences to be very tightly clustered and distant from S. mekongi and S. malayensis, the last two being clearly distinct from each other. The results thus indicate no significant intraspecific genetic variation among S. japonicum samples collected from different geographical areas and do not support the idea of a distinct form in Sichuan.

Exotic vs endemic biocontrol agents: Would the real stratiolaelaps miles (Berlese) (Acari : Mesostigmata : Laelapidae), please stand up?

The ability of introduced organisms to invade undisturbed native habitats is a major concern in conservation biology and has resulted in a re-evaluation of the introduction of exotic biocontrol agents, especially of generalist predators. One such agent is Stratiolaelaps miles (Berlese), a predatory mite described from Italy, known from throughout the Holarctic, and apparently accidentally introduced to other areas of the world, including Australia. Initial investigations revealed that putative S. miles could be found in both disturbed and relatively pristine habitats in Queensland, Australia. However, analysis of the mitochondrial DNA of five populations showed most to be highly divergent genetically. Subsequent morphological analysis established two species groups: the lamington-group from cool-temperate to subtropical rainforests in Eastern Australia and the more eurytopic miles-group with a cosmopolitan distribution. We describe two new species from each of these complexes (Stratiolaelaps womersleyi, Stratiolaelaps lamington; Stratiolaelaps marilyn, Stratiolaelaps lorna, respectively), and resurrect Stratiolaelaps scimitus (Womersley), a species which often appears to have been confused with S. miles. Additionally, the large genetic distances among morphologically homogenous species in the miles-group suggest that the apparently cosmopolitan S. miles may be composed of a suite of cryptic species of potentially varying utility in biological control. (C) 2002 Elsevier Science (USA). All rights reserved.

Geographic range size, life history and rates of diversification in Australian mammals

What causes species richness to vary among different groups of organisms? Two hypotheses are that large geographical ranges and fast life history either reduce extinction rates or raise speciation rates, elevating a clade's rate of diversification. Here we present a comparative analysis of these hypotheses using data on the phylogenetic relationships, geographical ranges and life history of the terrestrial mammal fauna of Australia. By comparing species richness patterns to null models, we show that species are distributed nonrandomly among genera. Using sister-clade comparisons to control for clade age, we then find that faster diversification is significantly associated with larger geographical ranges and larger litters, but there is no evidence for an effect of body size or age at first breeding on diversification rates. We believe the most likely explanation for these patterns is that larger litters and geographical ranges increase diversification rates because they buffer species from extinction. We also discuss the possibility that positive effects of litter size and range size on diversification rates result from elevated speciation rates.

Species richness in agamid lizards: chance, body size, sexual selection or ecology?

Why does species richness vary so greatly across lineages? Traditionally, variation in species richness has been attributed to deterministic processes, although it is equally plausible that it may result from purely stochastic processes. We show that, based on the best available phylogenetic hypothesis, the pattern of cladogenesis among agamid lizards is not consistent with a random model, with some lineages having more species, and others fewer species, than expected by chance. We then use phylogenetic comparative methods to test six types of deterministic explanation for variation in species richness: body size, life history, sexual selection, ecological generalism, range size and latitude. Of eight variables we tested, only sexual size dimorphism and sexual dichromatism predicted species richness. Increases in species richness are associated with increases in sexual dichromatism but reductions in sexual size dimorphism. Consistent with recent comparative studies, we find no evidence that species richness is associated with small body size or high fecundity. Equally, we find no evidence that species richness covaries with ecological generalism, latitude or range size.

Testing the link between the latitudinal gradient in species richness and rates of molecular evolution

Numerous hypotheses have been proposed to explain latitudinal gradients in species richness, but all are subject to ongoing debate. Here we examine Rohde's (1978, 1992) hypothesis, which proposes that climatic conditions at low latitudes lead to elevated rates of speciation. This hypothesis predicts that rates of molecular evolution should increase towards lower latitudes, but this prediction has never been tested. We discuss potential links between rates of molecular evolution and latitudinal diversity gradients, and present the first test of latitudinal variation in rates of molecular evolution. Using 45 phylogenetically independent, latitudinally separated pairs of bird species and higher taxa, we compare rates of evolution of two mitochondrial genes and DNA-DNA hybridization distances. We find no support for an effect of latitude on rate of molecular evolution. This result casts doubt on the generality of a key component of Rohde's hypothesis linking climate and speciation.

A molecular phylogeny of the Australian skink genera Eulamprus, Gnypetoscincus and Nangura

Skinks from the genera Eulamprus, Gnypetoscincus and Nangura are a prominent component of the reptile fauna of the mesic forests of the east coast of Australia and have been the subject of numerous ecological studies. Highly conserved morphology and the retention of ancestral traits have limited our understanding of the relationships within and among these genera beyond an initial identification of species groups within Eulamprus. To address this deficit and to explore the relationships between Eulamprus and the monotypic genera Nangura and Gnypetoscincus, sections of two mitochondrial genes (ND4 and 16S rRNA) were sequenced and subjected to Bayesian phylogenetic analysis. This phylogenetic analysis supports recognition of the three species groups proposed for Eulamprus (murrayi, quoyii and tenuis) and indicates that this genus is paraphyletic, with Gnypetoscincus and Nangura being proximal to basal lineages of the tenuis group. To resolve these and broader problems of paraphyly, we suggest that each of the species groups from 'Eulamprus' should be recognised as a distinct genus. The phylogenetically and ecologically distinct water skinks of the quoyii group would be retained within Eulamprus and the diverse species of the tenuis group allocated to Concinnia. We suggest placing the monophyletic murrayi group, endemic to the rainforests of central eastern Australia, in a new genus ( yet to be formally described). The sequencing data also revealed the existence of a genetically divergent but morphologically cryptic lineage within E. murrayi and substantial diversity within E. quoyii. There is evidence for two major habitat shifts from rainforest towards drier habitats, one leading to the quoyii group and the second defining a clade of three species within the tenuis complex. These ecological transitions may represent adaptations to general drying across eastern Australia during the late Miocene - Pliocene. Each of the major areas of east coast tropical or subtropical rainforest contains multiple phylogenetically diverse endemic species, reflecting the long-term persistence and high conservation value of wet forest habitats in each area.

A global health problem caused by arsenic from natural sources

Arsenic is a carcinogen to both humans and animals. Arsenicals have been associated with cancers of the skin, lung, and bladder. Clinical manifestations of chronic arsenic poisoning include non-cancer end point of hyper- and hypo-pigmentation, keratosis, hypertension, cardiovascular diseases and diabetes. Epidemiological evidence indicates that arsenic concentration exceeding 50 mug l(-1) in the drinking water is not public health protective. The current WHO recommended guideline value for arsenic in drinking water is 10 mug l(-1), whereas many developing countries are still having a value of 50 mug 1(-1). It has been estimated that tens of millions of people are. at risk exposing to excessive levels of arsenic from both contaminated water and arsenic-bearing coal from natural sources. The global health implication and possible intervention strategies were also discussed in this review article. (C) 2003 Elsevier Ltd. All rights reserved.

Filogenia e evolução de roedores Echimyidae na Mata Atlântica

Os roedores Echimyidae tem distribuição Neotropical e são a família mais diversa de roedores Caviomorpha. Apesar da grande diversidade, pouco se sabe sobre a distribuição geográfica, história natural e evolução de vários grupos de equimídeos. O histórico taxonômico dessa família é confuso, sendo alguns grupos raramente coletados e, consequentemente, inferências sobre aspectos evolutivos e biológicos são pouco conclusivas e limitadas à análise de poucos exemplares. Filogenias moleculares não corroboram a classificação taxonômica para a família baseada em dados morfológicos, evidenciando a complexidade da história evolutiva desse grupo. Na Mata Atlântica são registrados cinco gêneros de Echimyidae: o rato-do-bambu, Kannabateomys; os arborícolas Phyllomys e Callistomys; o terrestre Trinomys, e o semi-fossorial Euryzygomatomys. O presente trabalho se baseou na utilização de sequências de DNA para abordar aspectos da evolução e filogenia de roedores equimídeos da Mata Atlântica em três níveis taxonômicos: família, gênero e espécie. O primeiro capítulo aborda a posição filogenética do gênero Callistomys dentro da família, utilizando sequências de 1 marcador mitocondrial (CitB) e 3 nucleares (GHR, RAG1 e vWF). Os resultados mostram que Callistomys forma um clado com o ratão-do-banhado (Myocastor), roedor semi-aquático das regiões abertas no cone sul da América do Sul e com o rato-de-espinho terrestre Proechimys com ocorrência na Amazônia. Esse clado é irmão de Thrichomys, um equimídeo terrestre que ocupa as áreas secas do centro da América do Sul. O agrupamento encontrado é inesperado, uma vez que seus membros apresentam aspectos morfológico, ecológicos e distribuição geográfica distintos e contrastantes. A filogenia resultante indica que Callistomys não é proximamente relacionado aos outros equimídeos arborícolas e sugere que o hábito arborícolas evoluiu mais de uma vez na família. O segundo capítulo investiga aspectos da filogenia, evolução e limites entre espécies de Phyllomys utilizando dois marcadores mitocondriais (CitB e COI) e três nucleares (GHR, RAG1 e vWF). Foram identificados três grupos principais de espécies: um com distribuição longitudinal pela porção central da Mata Atlântica (P. pattoni (P. mantiqueirensis, Phyllomys sp. 4)); e a partir daí dois outros grupos, um com distribuição na porção norte da Mata Atlântica (Phyllomys sp. 2 (P. blainvilii (P. brasiliensis, P. lamarum))); e outro na porção sul (Phyllomys sp. 3 ((Phyllomys sp. 1, P. lundi), (Phyllomys sp. 5 (P. dasythrix (P. nigrispinus (P. sulinus, Phyllomys sp. 6)))))). Foram identificadas duas linhagens independentes representando possíveis espécies novas, elevando o potencial número de espécies do gênero de 17 para 19. As filogenias associadas aos dados de distribuição geográfica sugerem que a diversificação e distribuição das espécies de Phyllomys foi influenciada pela ação conjunta de vários fatores como atividade neotectônica, gradientes altitudinais e latitudinais e mudanças climáticas que atuaram desde o Mioceno, marcando os primeiros eventos de diversificação do gênero até as especiações mais recentes, no Pleistoceno. O terceiro capítulo avalia a variação genética, distribuição geográfica e status taxonômico da espécie Euryzygomaotmys spinosus utilizando dois marcadores mitocondriais (CitB e D-loop). Os resultados mostraram que E.spinosus apresenta distribuição em áreas de Mata Atlântica e adjacências ao sul do Rio Doce, no Brasil, Paraguai e Argentina, incluindo um registro confirmado no Cerrado. A espécie ocupa habitats muito diversos e pode ser considerada generalista. As populações são geneticamente estruturadas ao longo da sua distribuição e os dados genéticos corroboram a taxonomia atual que considera apenas uma espécie, E. spinosus, para o gênero.

Perspectives and progress of ecology and conservation science in the Azores: the possible contribution of Artificial Intelligence

EPIA 2013 - XVI Portuguese Conference on Artificial Intelligence Angra do Heroísmo, Azores, Portugal, 9 – 12 September.

Investigação em ambientes marinhos naturalmente acidificados

Jornadas "Ciência nos Açores – que futuro?", Ponta Delgada, 7-8 de Junho de 2013.