Pleistocene speciation in Amazonian birds

Zoogeographical studies on distribution centers and population structure of Amazonian birds, lizards, and butterflies suggest that many subspecies and species originated from small isolated populations during several periods of ecologic-geographical separation. Repeated climatic fluctuations during the Quaternary leading to vast changes in the vegetation cover of tropical South America have been postulated by earth scientists and support the above biological interpretation. Numerous zones of secondary contact of Neotropical birds indicate the former existence of ecological barriers in Amazonia that have since disappeared. These contact zones are clustered in several well defined areas indicating that here entire faunas overlapped and partly fused, e.g. in northcentral Amazonia, in south-central Amazonia, in upper Amazonia south of the Rio Marañón, as well as in portions of the forest region west of the Andes. The ecological instability of the South American tropics during the Quaternary determined important aspects of the evolution of the Amazonian vertebrate faunas. Forests survived arid climatic periods probably in restricted areas which served as refugia for the Amazonian forest faunas. Using indirect evidence derived from inequalities of rainfall and from avian distribution patterns I reconstructed the probable geographic location of fifteen tentatively postulated forest refugia or groups of refugia in the lowlands of Middle and South America. Differentiation of isolated populations took place in these forest refugia due to varying selection pressure, chance and "plasticity" of systematic units following the model of geographic speciation. Large Amazonian rivers modified or occasionally limited the dispersal of forest birds from the forest refugia in reexpanding forests, especially in species inhabiting the dark forest interior. The range limit of several ecologically incompatible allies stabilized along broad river courses which, in these cases, constitute partial barriers to dispersal. In this way ecological competition is avoided. However, numerous component species of Amazonian superspecies are in direct contact and exclude one another geographically in uniform forests as a result of ecological competition. Nonforest faunas advanced into Amazonia during periods of forest reduction, repeatedly establishing contact between the savanna faunas north and south of the Amazonian forest during the pleistocene and post-Pleistocene. About 2400 years ago, readvancing forests led to the isolation of nonforest animal populations on savanna enclaves in the dry transverse zone of lower Amazonia. The present complexity of the Amazonian bird fauna is fairly "recent" in origin. This suggestion probably applies generally to the faunas of the Neotropical Region

Climatic forcing of evolution in Amazonia during the Cenozoic: On the refuge theory of biotic differentiation

Climatic-vegetational fluctuations due to astronomical Milankovitch cycles caused global changes in the distribution of tropical forests and nonforest vegetation during the Cenozoic (Tertiary-Quaternary) and before. Forest and nonforest biomes on the continents changed continuously in distribution during the geological past, breaking up into isolated blocks and again expanding and coalescing under the varying dry to humid climatic conditions. However, plant and animal communities disrupted and species changed their distributions individualistically during the various climatic phases. Field data indicating vegetational changes in Amazonia exist for the Quaternary; The refuge theory postulates that extensive patches of humid rainforests persisted during dry periods of the Tertiary and Quaternary, especially near areas of surface relief in peripheral portions of Amazonia, where many extant species and subspecies of plants and animals probably originated. The humid 'refugia' may have been separated by various types of savanna and dry forests as well as other intermediate vegetation types of seasonally dry climates. The number and size of refugia during different dry periods remain unknown. Biogeographic evidence for the former existence of forest refugia include areas of endemism and sharply defined contact zones between species and subspecies of Amazonian forest birds and other animals which represent zones of conspicuous biogeographic discontinuity in a continuous forest environment. Alternative models of barrier formation in Amazonia leading to allopatric speciation include the river hypothesis, river-refuge hypothesis; canopy-density hypothesis, disturbance-vicariance hypothesis, museum hypothesis and various paleogeography hypotheses, some aspects of which may be applicable to certain periods in the evolution of the biota

Impulsos climáticos da evolução na Amazônia durante o Cenozóico: sobre a teoria dos Refúgios da diferenciação biótica

AS FLUTUAÇÕES climático-vegetacionais causadas pelos ciclos astronômicos de Milan-kovitch provocaram mudanças globais na distribuição de florestas tropicais e demais vegetações não-florestais antes e durante o Cenozóico (Terciário-Quaternário). Os biomas continentais de florestas e vegetações não-florestais mudaram continuamente sua distribuição durante o seu passado geológico, fragmentando-se em blocos isolados, expandindo-se e juntando-se novamente sob condições climáticas alternadas entre secas e úmidas. Entretanto, durante as diversas fases climáticas, comunidades de plantas e animais fragmentaram-se e as espécies mudaram suas distribuições de maneira individual. Existem, para o Quaternário, dados de campo indicando mudanças na vegetação da Amazônia. A teoria dos Refúgios postula a persistência de grandes manchas de florestas tropicais úmidas durante os períodos secos do Terciário e do Quaternário, especialmente aquelas localizadas próximo de superfícies rebaixadas, sobretudo nas porções periféricas da Amazônia. Essas áreas são, provavelmente, a origem de muitas espécies e subespécies de plantas e animais existentes hoje em dia. Os "refúgios" úmidos podem ter sido separados por vários tipos de savana e florestas secas, como também por outros tipos de vegetação intermediária de climas sazonalmente secos. A quantidade e o tamanho dos refúgios durante os diferentes períodos de seca continuam desconhecidos. Indícios biogeográficos da existência de refúgios florestais anteriores incluem áreas de endemismo e zonas de contato entre espécies e subespécies de pássaros e outros animais da floresta amazônica nitidamente definidos. Essas áreas representam zonas de distinta descontinuidade biogeográfica num ambiente florestal contínuo. Modelos alternativos para a formação de barreiras na Amazônia que conduzem à especiação alopátrica incluem as seguintes hipóteses: do Rio, dos Refúgios do Rio, da Densidade do Dossel, da Perturbação da Vicariânia, do Museu e várias hipóteses paleogeográficas, das quais alguns aspectos poderiam ser aplicáveis a certos períodos na evolução da biota

Testing main Amazonian rivers as barriers across time and space within widespread taxa

AimPresent Amazonian diversity patterns can result from many different mechanisms and, consequently, the factors contributing to divergence across regions and/or taxa may differ. Nevertheless, the riverâ barrier hypothesis is still widely invoked as a causal process in divergence of Amazonian species. Here we use modelâ based phylogeographic analyses to test the extent to which major Amazonian rivers act similarly as barriers across time and space in two broadly distributed Amazonian taxa.LocalAmazon rain forest.TaxonThe lizard Gonatodes humeralis (Sphaerodactylidae) and the tree frog Dendropsophus leucophyllatus (Hylidae).MethodsWe obtained RADseq data for samples distributed across main river barriers, representing main Areas of Endemism previously proposed for the region. We conduct modelâ based phylogeographic and genetic differentiation analyses across each population pair.ResultsMeasures of genetic differentiation (based on FST calculated from genomic data) show that all rivers are associated with significant genetic differentiation. Parameters estimated under investigated divergence models showed that divergence times for populations separated by each of the 11 bordering rivers were all fairly recent. The degree of differentiation consistently varied between taxa and among rivers, which is not an artifact of any corresponding difference in the genetic diversities of the respective taxa, or to amounts of migration based on analyses of the siteâ frequency spectrum.Main conclusionsTaken together, our results support a dispersal (rather than vicariance) history, without strong evidence of congruence between these species and rivers. However, once a species crossed a river, populations separated by each and every river have remained isolatedâ in this sense, rivers act similarly as barriers to any further gene flow. This result suggests differing degrees of persistence and gives rise to the seeming contradiction that the divergence process indeed varies across time, space and species, even though major Amazonian rivers have acted as secondary barriers to gene flow in the focal taxa.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152608/1/jbi13676_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152608/2/jbi13676.pd

DNA Barcode Detects High Genetic Structure within Neotropical Bird Species

BACKGROUND: Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna. METHODS AND FINDINGS: Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520) of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N = 21) or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N = 20). Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism. CONCLUSIONS: The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent geological periods

Wide but not impermeable: Testing the riverine barrier hypothesis for an Amazonian plant species

Fundação de Ampara Pesquisa do Estado de São Paulo (FAPESP), Grant/AwardNumber: 2013/12633-8; 2015/07141-4,2012/50260-6; Conselho Nacional de Desenvolvimento Científico e Tecnológico(CNPq), Grant/Award Number: 307781/2013-5; National Science Foundation,Grant/Award Number: FESD 1338694, DEB1240869Wallace’s riverine barrier hypothesis postulates that large rivers, such as the Amazon and its tributaries, reduce or prevent gene flow between populations on opposite banks, leading to allopatry and areas of species endemism occupying interfluvial regions. Several studies have shown that two major tributaries, Rio Branco and RioNegro, are important barriers to gene flow for birds, amphibians and primates. No botanical studies have considered the potential role of the Rio Branco as a barrier,while a single botanical study has evaluated the Rio Negro as a barrier. We studied an Amazon shrub, Amphirrhox longifolia (A. St.-Hil.) Spreng (Violaceae), as a model totest the riverine barrier hypothesis. Twenty-six populations of A. longifolia were sampled on both banks of the Rio Branco and Rio Negro in the core Amazon Basin.Double-digest RADseq was used to identify 8,010 unlinked SNP markers from thenuclear genome of 156 individuals. Data relating to population structure support the hypothesis that the Rio Negro acted as a significant genetic barrier for A. longi-folia. On the other hand, no genetic differentiation was detected among populations spanning the narrower Rio Branco, which is a tributary of the Rio Negro. This study shows that the strength of riverine barriers for Amazon plants is dependent on the width of the river separating populations and species-specific dispersal traits. Future studies of plants with contrasting life history traits will further improve our under-standing of the landscape genetics and allopatric speciation history of Amazon plant diversity.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136763/1/Nazareno_et_al-2017-Molecular_Ecology.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136763/4/Nazareno2017b.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136763/5/Nazareno2017b.pdfDescription of Nazareno_et_al-2017-Molecular_Ecology.pdf : Main articleDescription of Nazareno2017b.pdf : Main articleDescription of Nazareno2017b.pdf : Main articl

Occurrence Patterns of Afrotropical Ticks (Acari: Ixodidae) in the Climate Space Are Not Correlated with Their Taxonomic Relationships

Foci of tick species occur at large spatial scales. They are intrinsically difficult to detect because the effect of geographical factors affecting conceptual influence of climate gradients. Here we use a large dataset of occurrences of ticks in the Afrotropical region to outline the main associations of those tick species with the climate space. Using a principal components reduction of monthly temperature and rainfall values over the Afrotropical region, we describe and compare the climate spaces of ticks in a gridded climate space. The dendrogram of distances among taxa according to occurrences in the climate niche is used to draw functional groups, or clusters of species with similar occurrences in the climate space, as different from morphologically derived (taxonomical) groups. We aim to further define the drivers of species richness and endemism at such a grid as well as niche similarities (climate space overlap) among species. Groups of species, as defined from morphological traits alone, are uncorrelated with functional clusters. Taxonomically related species occur separately in the climate gradients. Species belonging to the same functional group share more niche among them than with species in other functional groups. However, niche equivalency is also low for species within the same taxonomic cluster. Thus, taxa evolving from the same lineage tend to maximize the occupancy of the climate space and avoid overlaps with other species of the same taxonomic group. Richness values are drawn across the gradient of seasonal variation of temperature, higher values observed in a portion of the climate space with low thermal seasonality. Richness and endemism values are weakly correlated with mean values of temperature and rainfall. The most parsimonious explanation for the different taxonomic groups that exhibit common patterns of climate space subdivision is that they have a shared biogeographic history acting over a group of ancestrally co-distributed organisms