Giant tortoise genomes provide insights into longevity and age-related disease.

Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George-the iconic last member of Chelonoidis abingdonii-and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations.

Genetic divergence between two phenotypically distinct bottlenose dolphin ecotypes suggests separate evolutionary trajectories.

Due to their worldwide distribution and occupancy of different types of environments, bottlenose dolphins display considerable morphological variation. Despite limited understanding about the taxonomic identity of such forms and connectivity among them at global scale, coastal (or inshore) and offshore (or oceanic) ecotypes have been widely recognized in several ocean regions. In the Southwest Atlantic Ocean (SWA), however, there are scarce records of bottlenose dolphins differing in external morphology according to habitat preferences that resemble the coastal-offshore pattern observed elsewhere. The main aim of this study was to analyze the genetic variability, and test for population structure between coastal (n = 127) and offshore (n = 45) bottlenose dolphins sampled in the SWA to assess whether their external morphological distinction is consistent with genetic differentiation. We used a combination of mtDNA control region sequences and microsatellite genotypes to infer population structure and levels of genetic diversity. Our results from both molecular marker types were congruent and revealed strong levels of structuring (microsatellites FST = 0.385, p < .001; mtDNA FST =  0.183, p < .001; ΦST = 0.385, p < .001) and much lower genetic diversity in the coastal than the offshore ecotype, supporting patterns found in previous studies elsewhere. Despite the opportunity for gene flow in potential "contact zones", we found minimal current and historical connectivity between ecotypes, suggesting they are following discrete evolutionary trajectories. Based on our molecular findings, which seem to be consistent with morphological differentiations recently described for bottlenose dolphins in our study area, we recommend recognizing the offshore bottlenose dolphin ecotype as an additional Evolutionarily Significant Unit (ESU) in the SWA. Implications of these results for the conservation of bottlenose dolphins in SWA are also discussed.

Analysis of propagule pressure and genetic diversity in the invasibility of a freshwater apex predator: the peacock bass (genus Cichla)

An important step in invasive biology is to assess biological variables that could be used to predict invasion success. The study of genetics, evolution, and interactions of invasive and native species in invaded ranges provides a unique opportunity to study processes in population genetics and the capability of a species' range expansion. Here, we used information from microsatellite DNA markers to test if genetic variation relates to propagule pressure in the successful invasion of an apex predator (the Amazonian cichlid Cichla) into Southeastern Brazilian River systems. Invasive populations of Cichla have negatively impacted many freshwater communities in Southeastern Brazil since the 1960s. Reduction of genetic variation was observed in all invasive populations for both Cichla kelberi (CK) and Cichla piquiti (CP). For instance, heterozygosity was lower in the invasive range when compared to native populations from the Amazon basin (CP HE = 0.179/0.44; CK HE = 0.258/0.536 respectively). Therefore, despite the successful invasion of Cichla in southeast Brazil, low genetic diversity was observed in the introduced populations. We suggest that a combination of factors, such as Cichla's reproductive and feeding strategies, the "evolutionary trap" effect and the biotic resistance hypothesis, overcome their depauperete genetic diversity, being key aspects in this apex predator invasion. Uma importante etapa na biologia da invasão é acessar variáveis biológicas que podem predizer o sucesso de invasão. O estudo da genética, evolução e interações entre invasores e espécies nativas no ambiente invadido pode prover uma oportunidade única para o estudo dos processos em genética de populações e a capacidade de uma espécie ampliar seu habitat. Nesse trabalho, nos utilizamos dados de marcadores de DNA microssatélites para testar se a variação genética é relacionada a pressão de propágulo na invasão bem sucedida do predador de topo (o ciclídeo Amazônico Cichla) nos rios do Sudeste Brasileiro. Populações invasoras de Cichla vem impactando negativamente diversas comunidades de água doce no Sudeste brasileiro deste 1960. A redução da variação genética foi observada em todas populações invasoras, tanto para Cichla kelberi (CK) como Cichla piquiti (CP). Por exemplo, a heterozigose foi menor no ambiente invadido quando comparada com as populações nativas da bacia Amazônica (CP HE = 0.179/0.44; CK HE = 0.258/0.536 respectivamente). Assim, apesar do sucesso da invasão de Cichla no sudoeste do Brasil, baixa diversidade genética foi observada nas populações introduzidas. Nós sugerimos que uma combinação de fatores, como as estratégias reprodutivas de Cichla, o efeito de "armadilha evolutiva" e a hipótese de resistências biótica superam o efeito que a diversidade genética depauperada exerce, sendo aspectos-chave na invasão desse predador de topo de cadeia.

Permanent genetic resources added to Molecular Ecology Resources Database 1 February 2013-31 March 2013.

This article documents the addition of 142 microsatellite marker loci to the Molecular Ecology Resources database. Loci were developed for the following species: Agriophyllum squarrosum, Amazilia cyanocephala, Batillaria attramentaria, Fungal strain CTeY1 (Ascomycota), Gadopsis marmoratus, Juniperus phoenicea subsp. turbinata, Liriomyza sativae, Lupinus polyphyllus, Metschnikowia reukaufii, Puccinia striiformis and Xylocopa grisescens. These loci were cross-tested on the following species: Amazilia beryllina, Amazilia candida, Amazilia rutila, Amazilia tzacatl, Amazilia violiceps, Amazilia yucatanensis, Campylopterus curvipennis, Cynanthus sordidus, Hylocharis leucotis, Juniperus brevifolia, Juniperus cedrus, Juniperus osteosperma, Juniperus oxycedrus, Juniperus thurifera, Liriomyza bryoniae, Liriomyza chinensis, Liriomyza huidobrensis and Liriomyza trifolii.

Species tree of a recent radiation: the subfamily Delphininae (Cetacea, Mammalia).

Lineages undergoing rapid radiations provide exceptional opportunities for studying speciation and adaptation, but also represent a challenge for molecular systematics because retention of ancestral polymorphisms and the occurrence of hybridization can obscure relationships among lineages. Dolphins in the subfamily Delphininae are one such case. Non-monophyly, rapid speciation events, and discordance between morphological and molecular characters have made the inference of phylogenetic relationships within this subfamily very difficult. Here we approach this problem by applying multiple methods intended to estimate species trees using a multi-gene dataset for the Delphininae (Sousa, Sotalia, Stenella, Tursiops, Delphinus and Lagenodelphis). Incongruent gene trees obtained indicate that incomplete lineage sorting and possibly hybridization are confounding the inference of species history in this group. Nonetheless, using coalescent-based methods, we have been able to extract an underlying species-tree signal from divergent histories of independent genes. This is the first time a molecular study provides support for such relationships. This study further illustrates how methods of species-tree inference can be very sensitive both to the characteristics of the dataset and the evolutionary processes affecting the evolution of the group under study.

The use of carcasses for the analysis of cetacean population genetic structure: a comparative study in two dolphin species.

Advances in molecular techniques have enabled the study of genetic diversity and population structure in many different contexts. Studies that assess the genetic structure of cetacean populations often use biopsy samples from free-ranging individuals and tissue samples from stranded animals or individuals that became entangled in fishery or aquaculture equipment. This leads to the question of how representative the location of a stranded or entangled animal is with respect to its natural range, and whether similar results would be obtained when comparing carcass samples with samples from free-ranging individuals in studies of population structure. Here we use tissue samples from carcasses of dolphins that stranded or died as a result of bycatch in South Australia to investigate spatial population structure in two species: coastal bottlenose (Tursiops sp.) and short-beaked common dolphins (Delphinus delphis). We compare these results with those previously obtained from biopsy sampled free-ranging dolphins in the same area to test whether carcass samples yield similar patterns of genetic variability and population structure. Data from dolphin carcasses were gathered using seven microsatellite markers and a fragment of the mitochondrial DNA control region. Analyses based on carcass samples alone failed to detect genetic structure in Tursiops sp., a species previously shown to exhibit restricted dispersal and moderate genetic differentiation across a small spatial scale in this region. However, genetic structure was correctly inferred in D. delphis, a species previously shown to have reduced genetic structure over a similar geographic area. We propose that in the absence of corroborating data, and when population structure is assessed over relatively small spatial scales, the sole use of carcasses may lead to an underestimate of genetic differentiation. This can lead to a failure in identifying management units for conservation. Therefore, this risk should be carefully assessed when planning population genetic studies of cetaceans.

A recent shark radiation: molecular phylogeny, biogeography and speciation of wobbegong sharks (family: Orectolobidae).

The elasmobranch fish are an ancient, evolutionarily successful, but under-researched vertebrate group, particularly in regard to their recent evolutionary history. Their lineage has survived four mass extinction events and most present day taxa are thought to be derived from Mesozoic forms. Here we present a molecular phylogenetic analysis of the family Orectolobidae that provides evidence for recent events of diversification in this shark group. Species interrelationships in Orectolobidae were reconstructed based on four mitochondrial and nuclear genes. In line with previous morphological work, our results do not support current taxonomic arrangements in Orectolobidae and indicate that a taxonomic revision of the family is warranted. We propose that the onset of diversification of orectolobid sharks is of Miocene age and occurred within the Indo-Australian region. Surprisingly, we also find evidence for a recent ( approximately last 2 million years) and rapid radiation of wobbegong sharks. Allopatric speciation followed by range expansion seems like the general most likely explanation to account for wobbegong relationships and distributions. We suggest that the evolution of this shark group was mostly influenced by two temporal scenarios of diversification. The oldest relates to major geological changes in the Indo-West Pacific associated with the Miocene collision of the Indo-Australian and Eurasian plates. The most recent scenario was influenced by changes in oceanography and the emergence of biogeographic barriers related to Pleistocene glacial cycles in Australian waters.

Genetic characterization of native and introduced populations of the neotropical cichlid genus Cichla in Brazil

A molecular phylogenetic analysis based on mitochondrial 16S ribosomal DNA and Control Region sequences from native and introduced populations was undertaken, in order to characterize the introduction of Cichla (peacock bass or tucunaré) species in Brazil. Mitochondrial DNA haplotypes found in introduced fish from Minas Gerais state (southeastern Brazil) clustered only with those from native species of the Tocantins River (Cichla piquiti and C. kelberi), thereby suggesting a single or, at most, few translocation acts in this area, even though with fish from the same source-population. Our study contributes to an understanding of the introduction of Cichla in regions of Brazil outside the Amazon basin, and adds phylogenetic data to the recently describe Cichla species, endemic from the Tocantins-Araguaia basin.

A rapid fish radiation associated with the last sea-level changes in southern Brazil: the silverside Odontesthes perugiae complex.

Coastal freshwater fishes provide valuable models for studying the role of the last glaciations in promoting speciation. To date, the great majority of studies are of Northern Hemisphere taxa, and reflect the influence of vicariant events during, or prior to, the Pleistocene. Microsatellite markers and mitochondrial DNA sequences were used to investigate patterns of population divergence and evolutionary relationships in a freshwater group of silverside fishes (Odontesthes perugiae complex), endemic to the recently formed coastal plain of southern Brazil. Lacustrine morphotypes showed concordant patterns of genetic and morphological divergence consistent with the geographical history of the coastal plain. The results support the proposal of a silverside radiation chronologically shaped by the sea-level changes of the Pleistocene and Holocene. The radiating lineage comprises a minimum of three allopatric and two sympatric lacustrine species. Four species displayed extremely high levels of genetic variation and some of the most rapid speciation rates reported in fishes. These features were related to a marine-estuarine origin of the radiation. To the best of our knowledge, this study represents the first molecular phylogeographic survey of a coastal radiation in South America.