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The 20th century commercial whaling industry severely reduced populations of great whales throughout the Southern Hemisphere. The effect of this exploitation on genetic diversity and population structure remains largely undescribed. Here, we compare pre- and post-whaling diversity of mitochondrial DNA (mtDNA) control region sequences for 3 great whales in the South Atlantic, such as the blue, humpback, and fin whale. Pre-whaling diversity is described from mtDNA extracted from bones collected near abandoned whaling stations, primarily from the South Atlantic island of South Georgia. These bones are known to represent the first stage of 20th century whaling and thus pre-whaling diversity of these populations. Post-whaling diversity is described from previously published studies reporting large-scale sampling of living whales in the Southern Hemisphere. Despite relatively high levels of surviving genetic diversity in the post-whaling populations, we found evidence of a probable loss of mtDNA lineages in all 3 species. This is evidenced by the detection of a large number of haplotypes found in the pre-whaling samples that are not present in the post-whaling samples. A rarefaction analysis further supports a loss of haplotypes in the South Atlantic humpback and Antarctic blue whale populations. The bones from former whaling stations in the South Atlantic represent a remarkable molecular archive for further investigation of the decline and ongoing recovery in the great whales of the Southern Hemisphere. [ABSTRACT FROM AUTHOR]

Morphological stasis is generally associated with relative constancy in ecological pressures throughout time, producing strong stabilizing selection that retains similar shared morphology. Although climate and vegetation are commonly the main key factors driving diversity and phenotypic diversification in terrestrial vertebrates, fossorial organisms have their morphology mostly defined by their fossorial lifestyle. Among these secretive fossorial organisms, blind snakes of the South American genus Amerotyphlops are considered poorly studied when compared to other taxa. Here, we evaluate the cryptic diversity of Amerotyphlops using phylogenetic and multivariate approaches. We based our phylogenetic analysis on a molecular dataset composed of 12 gene fragments (eight nuclear and four mitochondrial) for 109 species of Typhlopidae. The multivariate analysis was implemented using 36 morphological variables for 377 specimens of Amerotyphlops. Additionally, we contrast our phylogenetic result with the morphological variation found in cranial, external and hemipenial traits. Our phylogenetic results recovered with strong support the following monophyletic groups within Amerotyphlops : (1) a clade formed by A. tasymicris and A. minuisquamus ; (2) a clade composed of A. reticulatus ; (3) a north-eastern Brazilian clade including A. yonenagae , A. arenensis , A. paucisquamus and A. amoipira ; and (4) a clade composed of A. brongersmianus and a complex of cryptic species. Based on these results we describe four new species of Amerotyphlops from north-eastern and south-eastern Brazil, which can be distinguished from the morphologically similar species, A. brongersmianus and A. arenensis. [ABSTRACT FROM AUTHOR]

Population genetic structure results from the interaction between historical events, current ecological conditions and life traits. The genetic structure and gene flow between populations are important to species dynamics, mainly for rare and endangered species that are more vulnerable to landscape changes and fragmentation. Here we evaluated the genetic diversity, population structure and gene exchange in Petunia bonjardinensis , P. reitzii and P. saxicola , three rare species endemic to subtropical highland grasslands in southern South America. We analysed the genetic diversity and structure considering historical events, such as founder effect and climate changes, and biological traits of each species. We also estimated the conservation status for these three species. We collected samples from all adult individuals and occurrence sites that could be found at the same flowering season and genotyped them for 13 nuclear microsatellite markers. Our results indicate that rarity is probably historical for these species, given that we found no genetic evidence for recent bottlenecks. Petunia bonjardinensis , with the largest occurrence area and population sizes, displayed the higher diversity indices. The other two showed lower genetic diversity and are geographically most restricted. Gene exchange among these species was low, although they share some ancestral genetic polymorphism. Historical migration, founder effects and Pleistocene climate cycles ae the main factors explaining genetic diversity, and this was also influenced by reproductive biology and recent habitat loss, whereas the landscape influences the structure. Based on IUCN criteria, the three species are endangered, and the main risk for their survival is probably anthropic activity in the occurrence area. We recommend an urgent programme for the preservation of these species in situ and ex situ. [ABSTRACT FROM AUTHOR]

Gene flow via seed or pollen dispersal is fundamental for establishing population diversity and structure of plants, especially in naturally fragmented environments. Petunia exserta (Solanaceae) is endemic to small shelters in rocky towers in the Brazilian Pampa grassland, an ancient and isolated region. The landscape is a long-term fragmented habitat, and ecological conditions inside the shelters constitute an inhospitable environment for other Petunia spp. which usually inhabit open and sunny grasslands. We aimed to evaluate the mating system and gene flow impact on genetic diversity and population structure in P. exserta throughout its geographical range. We used eight microsatellite markers to employ fine-scale genetic structure and paternity analyses in 15 populations, including 361 adults and 244 progeny. Our results showed that P. exserta has low genetic diversity and a homozygous excess compared with its congeners. We identified four genetic clusters that did not reflect the spatial population distribution and a strong genetic structure at the first spatial distance. Pollen and seed dispersal mainly occurred at short distances, and the species has a mixed mating system with high selfing levels. We did not observe recent population reduction, and most population clusters showed a small effective population size. The landscape micro-habitat features contribute to pollen flow that occurs mainly inside shelters through geitonogamy or biparental inbreeding. The self-compatible status of P. exserta and related lineages could be important in the colonization of a new environment for the genus. [ABSTRACT FROM AUTHOR]

The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here, we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 and 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be nonmonophyletic, with California (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Zalophus wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family. [Hybridization; ILS; phylogenomics; Pleistocene; Pliocene; monophyly.] [ABSTRACT FROM AUTHOR]

The Brazilian Atlantic Forest (BAF) is one of the most impacted biomes in the world, and in this region, there are several examples of the effects of Pleistocene climate changes among the species found there. Athenaea fasciculata (Solanaceae) is a forest component distributed mainly throughout the BAF extension. Here, we investigated the genetic diversity and population structure of A. fasciculata based on plastid and nuclear markers, aiming to better understand the impact of Pleistocene climate changes on BAF vegetation. We used population genetics, demographic methods and ecological niche modelling coupled to an evolutionary approach to describe the species distribution across time. The phylogeographic analysis of A. fasciculata indicated that Pleistocene climate changes played an important role in its evolution. The species is structured in two groups of populations that emerged from different refugia and were under different climate influences, supporting previously proposed connections between the Atlantic and Amazon Forests, the two most important Neotropical rainforests. [ABSTRACT FROM AUTHOR]

Plant hybridization is frequently observed in nature and considered an important driver of angiosperm diversity. Species are thought to arise through the accumulation of morphological and genetic differences that promote their evolutionary independence, even in the presence of hybridization. Natural hybrid zones yield an excellent system to study the outcomes of hybridization in terms of species diversity. Two recently diverged species, Petunia axillaris and P. exserta , show floral differentiation attributed to attraction of varying pollinators. Previous studies suggested natural hybridization between these species to explain morphological floral polymorphisms found among individuals of P. exserta. Here, we analyse genetic and morphological diversity in plants from the contact zone between these species and from isolated populations of each species to evaluate natural hybridization and its consequences. We found that the species' integrity is maintained despite interspecific hybridization and introgression that drove the origin of a new lineage in P. exserta in the contact zones. [ABSTRACT FROM AUTHOR]

We assessed the level of genetic variability and population structure of the common bottlenose dolphin (Tursiops truncatus) in the tropical and subtropical portions of the southwestern Atlantic Ocean and compared the results with previous morphological findings. We analyzed 109 samples of common bottlenose dolphins that were sequenced for control region mtDNA and genotyped for seven polymorphic microsatellite loci. The results suggested that the species in this region can be separated in two major biological units, northern and southern, with an area of parapatry at southern Brazil. The northern unit seems to occur in a wide range of depths, including offshore waters, is consistent with the canonical morphology of T. truncatus, and can be divided into three management units: 1) Saint Paul's Rocks, 2) north and northeast of Brazil, and 3) Campos and Santos Basins (that extend at least to southernmost Brazil). The southern unit is coastal, occurring exclusively in very shallow waters (< 10 m) and estuaries, and is consistent with the previously described (putative) Tursiops gephyreus. Nevertheless, a formal decision on the taxonomic status of T. gephyreus should wait for a more geographically comprehensive and data-integrative study. O objetivo deste estudo foi avaliar o nível de variabilidade genética e a estrutura populacional do golfinho-nariz-de-garrafa (Tursiops truncatus) das porções tropical e subtropical do Oceano Atlântico Sul Ocidental e comparar os resultados com análises morfológicas prévias. Para tanto, analisamos 109 amostras de golfinhos-nariz-de-garrafa, as quais foram sequenciadas para a região controle do DNAmt e genotipadas para sete loci de microssatélites polimórficos. Os resultados sugerem que a espécie nessa região pode ser separada em duas grandes unidades biológicas, norte e sul, com uma área de parapatria no sul do Brasil. A unidade norte parece ocorrer em uma faixa de profundidade ampla, incluindo águas oceânicas. Esta unidade é consistente com a morfologia canônica de T. truncatus e pode ser dividida em três unidades de manejo: i) Arquipélago de São Pedro e São Paulo; ii) Norte e Nordeste do Brasil; iii) Bacia de Campos e Santos (que se estende pelo menos até o extremo sul do Brasil). A unidade sul é costeira, ocorrendo exclusivamente em águas muito rasas (< 10 m) e estuários. Esta unidade é consistente com descrições anteriores para Tursiops gephyreus (putativo). Entretanto, uma decisão formal sobre o status taxonômico de T. gephyreus deve aguardar estudos mais integrativos e geograficamente abrangentes. [ABSTRACT FROM AUTHOR]

The Brazilian Atlantic Rainforest is one of the most diverse and threatened ecoregions on the planet and displays high levels of endemism. Despite several population analyses and phylogeographical studies, the origins of its species richness and the evolutionary processes that gave rise to this diversification remain poorly understood, especially at the southern edge of the Atlantic Forest. Passiflora actinia is an indigenous species from the southern Atlantic Forest and, as such, was influenced by climatic changes during the Pleistocene. In this study, we investigated the effects of past climate changes on the genetic diversity of P. actinia, using nuclear and plastid markers. We subsequently suggest strategies for the preservation of this species in particular and the whole ecoregion in general. We employed phylogeographical methods and combined these results with past, present and future ensemble niche models. Genetic variability in P. actinia was similar to that of other species with similar geographical distributions, and geographical structuring was not observed based on either type of genetic marker. Diversification in P. actinia was dated to the Pleistocene, suggesting that climate changes could have influenced the distribution of genetic diversity in this species. Our results predicted that suitable P. actinia habitat will persist in the highlands but will be reduced in the lowlands, especially with higher greenhouse gas concentrations. Conservation efforts should focus on populations with unique genetic units and populations from areas with greater climatic instability. Habitat loss due to deforestation in the Atlantic Forest constitutes a major risk to this species, especially to small populations or those with low diversity indices. [ABSTRACT FROM AUTHOR]

* Background and Aims The evolution of selfing is one of the most common transitions in flowering plants, and this change in mating pattern has important systematic and ecological consequences because it often initiates reproductive isolation and speciation. Petunia axillaris (Solanaceae) includes three allopatric subspecies widely distributed in temperate South America that present different degrees of self-compatibity and incompatibility. One of these subspecies is co-distributed with P. exserta in a restricted area and presents a complex, not well-understood mating system. Artificial crossing experiments suggest a complex system of mating in this sympatric area. The main aims of this study were to estimate the pollen dispersal distance and to evaluate the breeding structure of P. axillaris subsp. axillaris, a hawkmoth-pollinated taxon from this sympatric zone. * Methods Pollen dispersal distance was compared with nearest-neighbours distance, and the differentiation in the pollen pool among mother plants was estimated. In addition, the correlation between genetic differentiation and spatial distance among plants was tested. All adult individuals (252) within a space of 2800 m² and 15 open-pollinated progeny (285 seedlings) were analysed. Genetic analyses were based on 12 polymorphic microsatellite loci. * Key Results A high proportion of self-pollination was found, indicating a mixed-mating system. The maximum pollen dispersal distance was 1013 m, but most pollination events (96 %) occurred at a distance of 0m, predominantly in an inbreeding system. Both parents among sampled individuals could be identified in 60-85 % of the progeny. * Conclusions The results show that most pollen dispersal in the hawkmoth-pollinated P. axillaris subsp. axillaris occurs within populations and there is a high proportion of inbreeding. This mating system appears to favour species integrity in a secondary contact zone with the congener species P. exserta. [ABSTRACT FROM AUTHOR]

Subtribe Withaniinae ( Solanaceae) comprises seven genera and c. 40 species, with an almost cosmopolitan distribution. Athenaea and Aureliana are exclusively South American, with diversity centres in the Brazilian Atlantic Rainforest. The generic status of Athenaea and Aureliana was investigated using molecular phylogenetic analysis of five plastid regions ( ndh F gene, trn L intron and trn L-trn F, psa I-acc D and trn C-ycf6 intergenic spacers), nuclear internal transcribed spacers ( ITS) and morphometric analysis of the calyx. Divergence time estimates were also performed. Withaniinae was recovered as monophyletic. The diversification time estimated for Withaniinae was 6.3 Myr, and the estimated diversification time for the Athenaea and Aureliana clades was 2.3 Myr. Athenaea and Aureliana species formed a strongly supported clade. However, the genera were not monophyletic, and support for internal relationships was moderate to weak. The morphometric analysis of the increasing size of the fruit calyx that included all species of the genera showed a cline that did not allow us to conclude that the species could be separated into two genera. Because the accrescent calyx is the only morphological character that distinguishes them, we recognize Athenaea as a synonym of Aureliana and propose five new combinations . The list of accepted species is presented. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 00, 000-000. [ABSTRACT FROM AUTHOR]

Genetic diversity analyses, coupled with ecological niche modelling ( ENM) of species with a restricted distribution, may provide valuable information for understanding diversification patterns in endangered areas. We analyzed the genetic diversity of Recordia reitzii, a tree restricted to the threatened and highly fragmented Brazilian Atlantic forest, using three intergenic cpDNA spacers and ten microsatellite ( SSR) loci. To assess the historical processes that may have influenced the distribution of extant R. reitzii populations, the current potential distributions of R. reitzii and Recordia boliviana, a closely related species, were modelled and projected onto the Last Glacial Maximum ( LGM) and Last Interglacial ( LIG) periods. Niche divergence was quantified between these two. The cpDNA and SSR data showed a north-south pattern of the diversity distribution and structured populations, suggesting that gene flow is probably limited. According to our data, R. reitzii exhibits low genetic diversity, which may be a result of a founder or distribution-reduction effect, narrow distribution or small population size. The ecological niche models showed a wider palaeodistribution during the LIG and a retraction during the LGM for both species. Tests of niche divergence and conservatism indicated that bioclimatic factors might have influenced the diversification of these Recordia species. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176, 332-348. [ABSTRACT FROM AUTHOR]

In this study, we evaluated the genetic diversity of the Petunia integrifolia species group using a phylogeographical approach, and attempted to understand better its diversification and taxonomy. Plants from five morphological groups were collected, covering a large part of the geographical distribution of most of the species. Two major clades were found in the phylogenetic tree, and an additional lineage, corresponding to P. inflata, was found in the haplotype network obtained for plastid markers. All three lineages are clearly delimited geographically, but, with the exception of P. inflata, the morphological groups were not genetically distinct. Our results suggest that a population expansion after a size reduction resulted in the establishment of two distinct and allopatric groups c. 0.5 Mya, one group occurring in a geologically ancient area, and the other occurring in areas that were under the influence of a series of marine transgressions/regressions at the end of the Pleistocene. These two clades are evolutionarily significant units with significantly different allele frequencies in their nuclear genome and reciprocal monophyly in maternal, uniparentally inherited markers. All our results suggest that the morphology-based taxonomy in this group does not reflect its evolutionary history, and revision of its species limits should incorporate the distribution of the genetic diversity. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 199-213. [ABSTRACT FROM AUTHOR]

The Pampas in the southern Neotropics is a vast region with vegetation composed mainly of grasses, and it may be the least-studied ecosystem in southern South America. Contrary to what was thought until recently, this region is heterogeneous and harbours rich biodiversity and many endemic species; however, little is known about the current geographical distribution and evolution of its plants. Here, we present results from phylogeographical studies on two genera typical of open environments ( Petunia and Calibrachoa) that occur in both the Pampas and the high-altitude grasslands of southern Brazil. The rapid radiations of Petunia and Calibrachoa are examples of how strong selective pressures for different pollinators, coupled with adaptation to edaphic and climatic differences, may drive the diversification of plants in the Pampas. We also discuss factors that could have affected and driven the diversification and speciation of plants in this environment. Further studies, including some focusing on other taxa, are required to characterize the diversification of plant species in this region more accurately. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ••, ••-••. [ABSTRACT FROM AUTHOR]

The Southwestern Atlantic Ocean humpback whales wintering ground (breeding stock A) are distributed along the Brazilian coast (5–23°S), and their main mating and calving ground is in the Abrolhos Bank. We investigated genetic diversity, population structure, and relatedness of individuals sampled from the entire Southwest Atlantic humpback whale population. A total of 275 individuals sampled from 2 subregions (Abrolhos Bank, n = 229 and Praia do Forte, n = 46) were screened for 9 microsatellite loci. This population showed a high level of allelic diversity (A = 12.1) and a high mean observed heterozygosity (HO = 0.733). No signal of significant genetic bottleneck was detected in accordance with the mitochondrial DNA data. We find no evidence of temporal (between years) genetic structure as well as no genetic differentiation between whales from the 2 subregions of the Brazilian breeding ground. We observed that the proportion of males and females in this population was approximately 1:1, which differs from the male-biased sex ratio observed in other breeding grounds. The data obtained through this study provided no evidence of kinship associations within social groups. Finally, a female sampled off South Georgia Islands showed a putative parent–offspring relationship with a female off Abrolhos Bank, supporting the migratory link between these 2 areas. [ABSTRACT FROM PUBLISHER]

A total of 85 wild plants were collected in different areas of southern and south-eastern Brazil, and studied for nrDNA internal transcribed spacers (ITS). Thirty-two of them were also investigated for two other nuclear ( G3pdh and LEAFY), as well as eight plastid systems. Sixty-one ITS sequence types were identified, in a region of 412 bp, whereas 42 G3pdh haplotypes were found in a region of 1010 bp, and 23 LEAFY haplotypes in a region of 565 bp. GC content was higher in ITS (65%) than in the two other nuclear regions (40–42%), whereas nucleotide diversity was markedly higher in G3pdh than in the other two. No variability was found in the plastid systems. Most of the nuclear molecular diversity (56–86%) occurs at the intrapopulation level, and there is clear evidence of population expansion and little geographical structure. Historical information and field studies indicate that Passiflora alata is actively colonizing previously unoccupied areas in southern Brazil. High indices of intrapopulation variability were found in the region that is being colonized, similar to those found in areas where P. alata is native. Multiple introductions, as well the species’ genetic structure and human interference, may explain these findings. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 88, 611–630. [ABSTRACT FROM AUTHOR]

• Background and Aims Passiflora actinia and P. elegans, two markedly parapatric species, have their southern and northern distribution limits, respectively, in the most southern part of the Brazilian Atlantic Rain Forest. Despite the fact that they are classified in different taxonomic series, previous phylogenetic studies of this genus revealed a high genetic similarity between them. The aim of the present work was to analyse in more detail their geographical range in this region of overlap, to investigate intraspecific genetic variability and phylogeographic structure, and to search for possible hybrids.• Methods Eighty-two localities were searched for these species, and nuclear internal transcribed spacer (ITS) sequences were investigated for 32 individuals of P. actinia, 20 of P. elegans and one putative interspecific hybrid. Plastid trnL-trnF and psbA-trnH were examined for 12 plants of each species and the putative hybrid.• Key Results Both species showed a high level of intraspecific and intra-individual ITS variability. Network analysis revealed a north–south geographic gradient in their intra and interspecific relationships. Mismatch analyses suggested a recent population expansion of P. elegans. The plastid markers showed restricted variability but, together with the nuclear data, they contributed to the identification of an interspecific hybrid of intermediate morphology at the border of the distribution of these two species. Both genetic and morphological data indicate the absence of an extensive hybridization zone between these species.• Conclusions Gene flow between lineages is the possible cause for the presence of different ITS sequences within a given plant, the absence of homogenization being due to the high degree of vegetative reproduction in the two species. Differentiation of P. actinia into geographic groups and the origin of P. elegans may have been influenced by the Atlantic Forest migration towards southern Brazil. The genetic pattern of the interspecific hybrid indicates that plastid inheritance in these species is at least sometimes paternal. [ABSTRACT FROM AUTHOR]

Different genetic patterns have been demonstrated for narrowly distributed taxa, many of them linking rarity to evolutionary history. Quite a few species in young genera are endemics and have several populations that present low variability, sometimes attributed to geographical isolation or dispersion processes. Assessing the genetic diversity and structure of such species may be important for protecting them and understanding their diversification history. In this study, we used microsatellite markers and plastid sequences to characterize the levels of genetic variation and population structure of two endemic and restricted species that grow in isolated areas on the margin of the distribution of their respective genera. Plastid and nuclear diversities were very low and weakly structured in their populations. Evolutionary scenarios for both species are compatible with open-field expansions during the Pleistocene interglacial periods and genetic variability supports founder effects to explain diversification. At present, both species are suffering from habitat loss and changes in the environment can lead these species towards extinction. [ABSTRACT FROM AUTHOR]