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

Out of Amazonia: late-Holocene climate change and the Tupi–Guarani trans-continental expansion

The late Holocene expansion of the Tupi-Guarani languages from southern Amazonia to SE South America constitutes one of the largest expansions of any linguistic family in the world, spanning ~ 4000 km between latitudes 0°S and 35°S at about 2500 yr B.P. However, the underlying reasons for this expansion are a matter of debate. Here, we compare continental-scale palaeoecological, palaeoclimate, and archaeological datasets, to examine the role of climate change in facilitating the expansion of this forestfarming culture. Because this expansion lies within the path of the South American Low-Level Jet, the key mechanism for moisture transport across lowland South America, we were able to explore the relationship between climate change, forest expansion, and the Tupi-Guarani. Our data synthesis shows broad synchrony between late Holocene increasing precipitation and southerly expansion of both tropical forest and Guarani archaeological sites – the southernmost branch of the Tupi-Guarani. We conclude that climate change likely facilitated the agricultural expansion of the Guarani forest-farming culture by increasing the area of forested landscape that they could exploit, showing a prime example of ecological opportunism

From little things, big things grow: trends and fads in 110 years of Australian ornithology

Publishing histories can reveal changes in ornithological effort, focus or direction through time. This study presents a bibliometric content analysis of Emu (1901–2011) which revealed 115 trends (long-term changes in publication over time) and 18 fads (temporary increases in publication activity) from the classification of 9,039 articles using 128 codes organised into eight categories (author gender, author affiliation, article type, subject, main focus, main method, geographical scale and geographical location). Across 110 years, private authorship declined, while publications involving universities and multiple institutions increased; from 1960, female authorship increased. Over time, question-driven studies and incidental observations increased and decreased in frequency, respectively. Single species and ‘taxonomic group’ subjects increased while studies of birds at specific places decreased. The focus of articles shifted from species distribution and activities of the host organisation to breeding, foraging and other biological/ecological topics. Site- and Australian-continental-scales slightly decreased over time; non-Australian studies increased from the 1970s. A wide variety of fads occurred (e.g. articles on bird distribution, 1942–1951, and using museum specimens, 1906–1913) though the occurrence of fads decreased over time. Changes over time are correlated with technological, theoretical, social and institutional changes, and suggest ornithological priorities, like those of other scientific disciplines, are temporally labil

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