The rise and fall of the Refugial Hypothesis of Amazonian speciation: a paleoecological perspective

Population Genetic Structure and Diversity of Cryptic Species of the Plant Genus Macrocarpaea (Gentianaceae) from the Tropical Andes

The Pleistocene climatic oscillations (PCO) that provoked several cycles of glacial-interglacial periods are thought to have profoundly affected species distribution, richness and diversity around the world. While the effect of the PCO on population dynamics at temperate latitudes is well known, considerable questions remain about its impact on the biodiversity of neotropical mountains. Here, we use amplified fragment length polymorphism molecular markers (AFLPs) to investigate the phylogeography and genetic structure of 13 plant species belonging to the gentian genus Macrocarpaea (Gentianaceae) in the tropical Andes. These woody herbs, shrubs or small trees show complex and potentially reticulated relationships, including cryptic species. We show that populations of M. xerantifulva in the dry system of the Rio Marañón in northern Peru have lower levels of genetic diversity compared to other sampled species. We suggest that this is due to a recent demographic bottleneck resulting from the contraction of the montane wet forests into refugia because of the expansion of the dry system into the valley during the glacial cycles of the PCO. This may imply that the ecosystems of different valleys of the Andes might have responded differently to the PCO.

Genomic methods reveal independent demographic histories despite strong morphological conservatism in fish species

Human overexploitation of natural resources has placed conservation and management as one of the most pressing challenges in modern societies, especially in regards to highly vulnerable marine ecosystems. In this context, cryptic species are particularly challenging to conserve because they are hard to distinguish based on morphology alone, and thus it is often unclear how many species coexist in sympatry, what are their phylogenetic relationships and their demographic history. We answer these questions using morphologically similar species of the genus Mugil that are sympatric in the largest coastal Marine Protected Area in the Tropical Southwestern Atlantic marine province. Using a sub-representation of the genome, we show that individuals are assigned to five highly differentiated genetic clusters that are coincident with five mitochondrial lineages, but discordant with morphological information, supporting the existence of five species with conserved morphology in this region. A lack of admixed individuals is consistent with strong genetic isolation between sympatric species, but the most likely species tree suggests that in one case speciation has occurred in the presence of interspecific gene flow. Patterns of genetic diversity within species suggest that effective population sizes differ up to two-fold, probably reflecting differences in the magnitude of population expansions since species formation. Together, our results show that strong morphologic conservatism in marine environments can lead to species that are difficult to distinguish morphologically but that are characterized by an independent evolutionary history, and thus that deserve species-specific management strategies.

Phylogeographic model selection using convolutional neural networks

The discipline of phylogeography has evolved rapidly in terms of the analytical toolkit used to analyse large genomic data sets. Despite substantial advances, analytical tools that could potentially address the challenges posed by increased model complexity have not been fully explored. For example, deep learning techniques are underutilized for phylogeographic model selection. In non-model organisms, the lack of information about their ecology and evolution can lead to uncertainty about which demographic models are appropriate. Here, we assess the utility of convolutional neural networks (CNNs) for assessing demographic models in South American lizards in the genus Norops. Three demographic scenarios (constant, expansion, and bottleneck) were considered for each of four inferred population-level lineages, and we found that the overall model accuracy was higher than 98% for all lineages. We then evaluated a set of 26 models that accounted for evolutionary relationships, gene flow, and changes in effective population size among the four lineages, identifying a single model with an estimated overall accuracy of 87% when using CNNs. The inferred demography of the lizard system suggests that gene flow between non-sister populations and changes in effective population sizes through time, probably in response to Pleistocene climatic oscillations, have shaped genetic diversity in this system. Approximate Bayesian computation (ABC) was applied to provide a comparison to the performance of CNNs. ABC was unable to identify a single model among the larger set of 26 models in the subsequent analysis. Our results demonstrate that CNNs can be easily and usefully incorporated into the phylogeographer's toolkit.

Environment and pathogens shape local and regional adaptations to climate change in the chocolate tree, Theobroma cacao L

Predicting the potential fate of a species in the face of climate change requires knowing the distribution of molecular adaptations across the geographic range of the species. In this work, we analysed 79 genomes of Theobroma cacao, an Amazonian tree known for the fruit from which chocolate is produced, to evaluate how local and regional molecular signatures of adaptation are distributed across the natural range of the species. We implemented novel techniques that incorporate summary statistics from multiple selection scans to infer selective sweeps. The majority of the molecular adaptations in the genome are not shared among populations. We show that ~71.5% of genes under selection also show significant associations with changes in environmental variables. Our results support the interpretation that these genes contribute to local adaptation of the populations in response to abiotic factors. We also found strong patterns of molecular adaptation in a diverse array of disease resistance genes (6.5% of selective sweeps), suggesting that differential adaptation to pathogens also contributes significantly to local adaptations. Our results are consistent with the interpretation that local selective pressures are more important than regional selective pressures in explaining adaptation across the range of a species.

Contrasting Trends of Population Size Change for Two Eurasian Owlet Species—Athene brama and Glaucidium radiatum From South Asia Over the Late Quaternary

Climatic oscillations over the Quaternary have had a lasting impact on species’ distribution, evolutionary history, and genetic composition. Many species show dramatic population size changes coinciding with the last glacial period. However, the extent and direction of change vary across biogeographic regions, species-habitat associations, and species traits. Here we use genomic data to assess population size changes over the late Quaternary using the Pairwise Sequential Markovian Coalescent (PSMC) approach in two Eurasian Owlet species—the Spotted Owlet, Athene brama, and the Jungle Owlet, Glaucidium radiatum. While Spotted Owlets are typically associated with open habitats, Jungle Owlets are found in deciduous forests and scrublands. We find that the effective population size for the Spotted Owlet increased after the Interglacial period till the Last Glacial Maxima and subsequently declined toward the Mid-Holocene. On the other hand, effective population size estimates for the Jungle Owlet increased gradually throughout this period. These observations are in line with climatic niche model-based predictions for range size change for both species from a previous study and suggest that habitat associations at the local scale are important in determining responses to past climatic and vegetational changes. The Spotted Owlet result also aligns well with the expectation of open habitat expansion during the arid Glacial Maxima, whereas for the Jungle Owlet the contrasting expectation does not hold. Therefore, assessing the impacts of glacial history on population trajectories of multiple species with different habitat associations is necessary to understand the impacts of past climate on South Asian taxa.

Glassfrogs of Ecuador: Diversity, Evolution, and Conservation

Glassfrogs (family: Centrolenidae) represent a fantastic radiation (~150 described species) of Neotropical anurans that originated in South America and dispersed into Central America. In this study, we review the systematics of Ecuadorian glassfrogs, providing species accounts of all 60 species, including three new species described herein. For all Ecuadorian species, we provide new information on the evolution, morphology, biology, conservation, and distribution. We present a new molecular phylogeny for Centrolenidae and address cryptic diversity within the family. We employ a candidate species system and designate 24 putative new species that require further study to determine their species status. We find that, in some cases, currently recognized species lack justification; specifically, we place Centrolene gemmata and Centrolene scirtetes under the synonymy of Centrolene lynchi; C. guanacarum and C. bacata under the synonymy of Centrolene sanchezi; Cochranella phryxa under the synonymy of Cochranella resplendens; and Hyalinobatrachium ruedai under the synonymy of Hyalinobatrachium munozorum. We also find that diversification patterns are mostly congruent with allopatric speciation, facilitated by barriers to gene flow (e.g., valleys, mountains, linearity of the Andes), and that niche conservatism is a dominant feature in the family. Conservation threats are diverse, but habitat destruction and climate change are of particular concern. The most imperiled glassfrogs in Ecuador are Centrolene buckleyi, C. charapita, C. geckoidea, C. medemi, C. pipilata, Cochranella mache, Nymphargus balionotus, N. manduriacu, N. megacheirus, and N. sucre, all of which are considered Critically Endangered. Lastly, we identify priority areas for glassfrog conservation in Ecuador.

Discrepancies between genetic and ecological divergence patterns suggest a complex biogeographic history in a Neotropical genus

Phylogenetic patterns and the underlying speciation processes can be deduced from morphological, functional, and ecological patterns of species similarity and divergence. In some cases, though, species retain multiple similarities and remain almost indistinguishable; in other cases, evolutionary convergence can make such patterns misleading; very often in such cases, the "true" picture only emerges from carefully built molecular phylogenies, which may come with major surprises. In addition, closely related species may experience gene flow after divergence, thus potentially blurring species delimitation. By means of advanced inferential methods, we studied molecular divergence between species of the Virola genus (Myristicaceae): widespread Virola michelii and recently described, endemic V. kwatae, using widespread V. surinamensis as a more distantly related outgroup with different ecology and morphology-although with overlapping range. Contrary to expectations, we found that the latter, and not V. michelii, was sister to V. kwatae. Therefore, V. kwatae probably diverged from V. surinamensis through a recent morphological and ecological shift, which brought it close to distantly related V. michelii. Through the modeling of the divergence process, we inferred that gene flow between V. surinamensis and V. kwatae stopped soon after their divergence and resumed later, in a classical secondary contact event which did not erase their ecological and morphological differences. While we cannot exclude that initial divergence occurred in allopatry, current species distribution and the absence of geographical barriers make complete isolation during speciation unlikely. We tentatively conclude that (a) it is possible that divergence occurred in allopatry/parapatry and (b) secondary contact did not suppress divergence.

What has become of the refugia hypothesis to explain biological diversity in Amazonia?

The spatial distribution of biodiversity and related processes is the core of Biogeography. Amazonia is the world's most diverse rainforest and the primary source of diversity to several Neotropical regions. The origins of such diversity continue to be an unresolved question in evolutionary biology. Among many competing hypotheses to explain the evolution of the Amazonian biodiversity, one stands out as the most influential: the refugia hypothesis by Jürgen Haffer. Here, we provide a chronological overview on how the refugia hypothesis evolved over the decades and how the criticism from different fields affected its acceptance. We conclude that the refugia hypothesis alone cannot explain the diversification of the complex Amazonian diversity, and perhaps it was not the most important diversification mechanism. However, the debate provoked by refugia has produced a great amount of knowledge on Amazonian climatic, geological, and evolutionary processes, as well as on species distributions, movements, and history.

Deep divergence of Red-crowned Ant Tanager (Habia rubica: Cardinalidae), a multilocus phylogenetic analysis with emphasis in Mesoamerica

Many neotropical species have a complex history of diversification as a result of the influence of geographical, ecological, climatic, and geological factors that determine the distribution of populations within a lineage. Phylogeography identifies such populations, determines their geographic distributions, and quantifies the degree of genetic divergence. In this work we explored the genetic structure of Habia rubica populations, a polytypic taxon with 17 subspecies described, in order to obtain hypotheses about their evolutionary history and processes of diversification. We undertook multilocus analyses using sequences of five molecular markers (ND2, ACOI-I9, MUSK, FGB-I5 and ODC), and sampling from across the species’ distribution range, an area encompassing from Central Mexico throughout much of South America. With these data, we obtained a robust phylogenetic hypothesis, a species delimitation analysis, and estimates of divergence times for these lineages. The phylogenetic hypothesis of concatenated molecular markers shows that H. rubica can be divided in three main clades: the first includes Mexican Pacific coast populations, the second is formed by population from east of Mexico to Panama and the third comprises the South American populations. Within these clades we recognize seven principal phylogroups whose limits have a clear correspondence with important geographical discontinuities including the Isthmus of Tehuantepec in southern Mexico, the Talamanca Cordillera, and the Isthmus of Panama in North America. In South America, we observed a marked separation of two phylogroups that include the populations that inhabit mesic forests in western and central South America (Amazon Forest) and those inhabiting the seasonal forest from the eastern and northern regions of the South America (Atlantic Forest). These areas are separated by an intervening dry vegetation “diagonal” (Chaco, Cerrado and Caatinga). The geographic and genetic structure of these phylogroups describes a history of diversification more active and complex in the northern distribution of this species, producing at least seven well-supported lineages that could be considered species.

Genetic and Historical Colonization Analyses of an Endemic Savanna Tree, Qualea grandiflora, Reveal Ancient Connections Between Amazonian Savannas and Cerrado Core

The evolutionary processes underlying the high diversity and endemism in the Cerrado, the most extensive Neotropical savanna, remain unclear, including the factors promoting the presence and evolution of savanna enclaves in the Amazon forest. In this study, we investigated the effects of past climate changes on genetic diversity, dynamics of species range and the historical connections between the savanna enclaves and Cerrado core for Qualea grandiflora, a tree species widely distributed in the biome. Totally, 40 populations distributed in the Cerrado core and Amazon savannas were analyzed using chloroplast and nuclear DNA sequences. We used phylogeographic, coalescent and ecological niche modeling approaches. Genetic data revealed a phylogeographic structure shaped by Pleistocene climatic oscillations. An eastern-western split in the Cerrado core was observed. The central portion of the Cerrado core harbored most of the sampled diversity for cpDNA. Ecological niche models predicted the presence of a large historical refuge in this region and multiple small refuges in peripheral areas. Relaxed Random Walk (RRW) models indicated the ancestral population in the north-western border of the central portion of the Cerrado core and cyclical dynamics of colonization related to Pleistocene climatic oscillations. Central and western ancient connections between Cerrado core and Amazonian savannas were observed. No evidence of connections among the Amazonian savannas was detected. Our study highlights the importance of Pleistocene climatic oscillations for structuring the genetic diversity of Q. grandiflora and complex evolutionary history of ecotonal areas in the Cerrado. Our results do not support the recent replacement of a large area in the Amazon forest by savanna vegetation. The Amazonian savannas appear to be fragmented and isolated from each other, evolving independently a long ago.

Tropical rainforests that persisted: inferences from the Quaternary demographic history of eight tree species in the Guiana shield

How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rainfall and temperature changes during and/or immediately after the last glacial maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil records in Neotropical forests prevents a direct reconstruction of such processes. To describe community-level historical trends in forest composition, we turned therefore to inferential methods based on the reconstruction of past demographic changes. In particular, we modelled the history of rainforests in the eastern Guiana Shield over a timescale of several thousand generations, through the application of approximate Bayesian computation and maximum-likelihood methods to diversity data at nuclear and chloroplast loci in eight species or subspecies of rainforest trees. Depending on the species and on the method applied, we detected population contraction, expansion or stability, with a general trend in favour of stability or expansion, with changes presumably having occurred during or after the LGM. These findings suggest that Guiana Shield rainforests have globally persisted, while expanding, through the Quaternary, but that different species have experienced different demographic events, with a trend towards the increase in frequency of light-demanding, disturbance-associated species.

A Skull Might Lie: Modeling Ancestral Ranges and Diet from Genes and Shape of Tree Squirrels

Tropical forests of Central and South America represent hotspots of biological diversity. Tree squirrels of the tribe Sciurini are an excellent model system for the study of tropical biodiversity as these squirrels disperse exceptional distances, and after colonizing the tropics of the Central and South America, they have diversified rapidly. Here, we compare signals from DNA sequences with morphological signals using pictures of skulls and computational simulations. Phylogenetic analyses reveal step-wise geographic divergence across the Northern Hemisphere. In Central and South America, tree squirrels form two separate clades, which split from a common ancestor. Simulations of ancestral distributions show western Amazonia as the epicenter of speciation in South America. This finding suggests that wet tropical forests on the foothills of Andes possibly served as refugia of squirrel diversification during Pleistocene climatic oscillations. Comparison of phylogeny and morphology reveals one major discrepancy: Microsciurus species are a single clade morphologically but are polyphyletic genetically. Modeling of morphology-diet relationships shows that the only group of species with a direct link between skull shape and diet are the bark-gleaning insectivorous species of Microsciurus. This finding suggests that the current designation of Microsciurus as a genus is based on convergent ecologically driven changes in morphology.

Pleistocene niche stability and lineage diversification in the subtropical spider Araneus omnicolor (Araneidae)

The influence of Quaternary climate oscillations on the diversification of the South American fauna is being increasingly explored. However, most of these studies have focused on taxa that are endemic to tropical environments, and relatively few have treated organisms restricted to subtropical biomes. Here we used an integrative phylogeographical framework to investigate the effects of these climate events on the ecological niche and genetic patterns of the subtropical orb-weaver spider Araneus omnicolor (Araneidae). We analyzed the mitochondrial (Cytochrome Oxidase I, COI) and nuclear (Internal Transcribed Subunit II, ITS2) DNA of 130 individuals throughout the species' range, and generated distribution models in three different climate scenarios [present, Last Glacial Maximum (LGM), and Last Interglacial Maximum (LIG)]. Additionally, we used an Approximate Bayesian Computation (ABC) approach to compare possible demographic scenarios and select the hypothesis that better explains the genetic patterns of A. omnicolor. We obtained high haplotype diversity but low nucleotide variation among sequences. The population structure and demographic analyses showed discrepancies between markers, suggesting male-biased dispersal in the species. The time-calibrated COI phylogenetic inference showed a recent diversification of lineages (Middle/Late Pleistocene), while the paleoclimate modeling indicated niche stability since ~120 Kya. The ABC results agreed with the niche models, supporting a panmictic population as the most likely historical scenario for the species. These results indicate that A. omnicolor experienced no niche or population reductions during the Late Pleistocene, despite the intense landscape modifications that occurred in the subtropical region, and that other factors beside LGM and LIG climate oscillations might have contributed to the demographic history of this species. This pattern may be related to the high dispersal ability and wide environmental tolerance of A. omnicolor, highlighting the need for more phylogeographical studies with invertebrates and other generalist taxa, in order to understand the effects of Quaternary climate changes on Neotropical biodiversity.

Phylogeny and biogeography of the New World siskins and goldfinches: rapid, recent diversification in the Central Andes

Time-calibrated molecular phylogenies can help us to understand the origins of the diverse and unique Andean avifauna. Previous studies have shown that the tempo of diversification differed between the Andes and adjacent lowland regions of South America. Andean taxa were found to have speciated more recently and to have avoided the decelerated diversification that is typical of Neotropical lowland clades. The South American siskins, a Pleistocene finch radiation, may typify this Andean pattern. We investigated the phylogenetic biogeography of all the New World siskins and goldfinches in new detail. To understand the specific role of the Andes in siskin diversification, we asked: (1) Was diversification faster in Andean siskin lineages relative to non-Andean ones? (2) Did siskin lineages move into and out of the Andes at different rates? We found that siskin lineages in the Andes had higher diversification rates and higher outward dispersal rates than siskin lineages outside the Andes. We conclude that páramo expansion and contraction in response to Pleistocene climatic cycles caused accelerated diversification and outward dispersal in Andean siskins. The younger average age of bird species in the Andes compared to lowland South America may be attributable to bursts of recent diversification in siskins and several other vagile, open-habitat clades.

Latitudinal gradients in climatic-niche evolution accelerate trait evolution at high latitudes

Despite the importance of divergent selection to the speed of evolution, it remains poorly understood if divergent selection is more prevalent in the tropics (where species richness is highest), or at high latitudes (where paleoclimate change has been most intense). We tested whether the rate of climatic-niche evolution - one proxy for divergent selection - varies with latitude for 111 pairs of bird species. Using Brownian motion and Ornsetin-Ulhenbeck models, we show that evolutionary rates along two important axes of the climatic-niche - temperature and seasonality - have been faster at higher latitudes. We then tested whether divergence of the climatic-niche was associated with evolution in traits important in ecological differentiation (body mass) and reproductive isolation (song), and found that climatic divergence is associated with faster rates in both measures. These results highlight the importance of climate-mediated divergent selection pressures in driving evolutionary divergence and reproductive isolation at high latitudes.

Renewed diversification is associated with new ecological opportunity in the Neotropical turtle ants

Ecological opportunity, defined as access to new resources free from competitors, is thought to be a catalyst for the process of adaptive radiation. Much of what we know about ecological opportunity, and the larger process of adaptive radiation, is derived from vertebrate diversification on islands. Here, we examine lineage diversification in the turtle ants (Cephalotes), a species-rich group of ants that has diversified throughout the Neotropics. We show that crown group turtle ants originated during the Eocene (around 46 mya), coincident with global warming and the origin of many other clades. We also show a marked lineage-wide slowdown in diversification rates in the Miocene. Contrasting this overall pattern, a species group associated with the young and seasonally harsh Chacoan biogeographic region underwent a recent burst of diversification. Subsequent analyses also indicated that there is significant phylogenetic clustering within the Chacoan region and that speciation rates are highest there. Together, these findings suggest that recent ecological opportunity, from successful colonization of novel habitat, may have facilitated renewed turtle ant diversification. Our findings highlight a central role of ecological opportunity within a successful continental radiation.

Rivers, refuges and population divergence of fire-eye antbirds (Pyriglena) in the Amazon Basin

The identification of ecological and evolutionary mechanisms that might account for the elevated biotic diversity in tropical forests is a central theme in evolutionary biology. This issue is especially relevant in the Neotropical region, where biological diversity is the highest in the world, but where few studies have been conducted to test factors causing population differentiation and speciation. We used mtDNA sequence data to examine the genetic structure within white-backed fire-eye (Pyriglena leuconota) populations along the Tocantins River valley in the south-eastern Amazon Basin, and we confront the predictions of the river and the Pleistocene refuge hypotheses with patterns of genetic variation observed in these populations. We also investigated whether these patterns reflect the recently detected shift in the course of the Tocantins River. We sampled a total of 32 individuals east of, and 52 individuals west of, the Tocantins River. Coalescent simulations and phylogeographical and population genetics analytical approaches revealed that mtDNA variation observed for fire-eye populations provides little support for the hypothesis that populations were isolated in glacial forest refuges. Instead, our data strongly support a key prediction of the river hypothesis. Our study shows that the Tocantins River has probably been the historical barrier promoting population divergence in fire-eye antbirds. Our results have important implications for a better understanding of the importance of large Amazonian rivers in vertebrate diversification in the Neotropics.

The role of glacial cycles in promoting genetic diversity in the Neotropics: the case of cloud forests during the Last Glacial Maximum

The increasing aridity during the Last Glacial Maximum (LGM) has been proposed as a major factor affecting Neotropical species. The character and intensity of this change, however, remains the subject of ongoing debate. This review proposes an approach to test contrasting paleoecological hypotheses by way of their expected demographic and genetic effects on Neotropical cloud forest species. We reviewed 48 paleoecological records encompassing the LGM in the Neotropics. The records show contrasting evidence regarding the changes in precipitation during this period. Some regions remained fairly moist and others had a significantly reduced precipitation. Many paleoecological records within the same region show apparently conflicting evidence on precipitation and forest stability. From these data, we propose and outline two demographic/genetic scenarios for cloud forests species based on opposite precipitation regimes: the dry refugia and the moist forests hypotheses. We searched for studies dealing with the population genetic structure of cloud forest and other montane taxa and compared their results with the proposed models. To date, the few available molecular studies show insufficient genetic evidence on the predominance of glacial aridity in the Neotropics. In order to disentangle the climatic history of the Neotropics, the present study calls for a general multi-disciplinary approach to conduct future phylogeographic studies. Given the contradictory paleoecological information, population genetic data on Neotropical cloud forest species should be used to explicitly test the genetic consequences of competing paleoecological models.

Phylogeographical patterns shed light on evolutionary process in South America

The South American continent is composed of several biogeographical regions harbouring the highest biodiversity on the globe, encompassing five of the world's biodiversity 'hot spots'. Nonetheless, the patterns and processes responsible for shaping its astonishing species diversity are largely unknown. Here, we present a review of current South American phylogeographical knowledge based on published articles on this topic. An appraisal of the literature reveals emerging phylogeographical patterns in the biota of South America. The striking phylogeographical divergence observed among organism lineages in South American studies is suggestive of high levels of undocumented species diversity. The interplay between Pleistocene climatic oscillations and Pliocene/Miocene orogenic events has contributed to shaping the current diversity and distribution of modern lineages in both the tropical and temperate regions of South America. Although older divergence times were observed for a range of species, most herpetofauna underwent an intraspecific lineage split much earlier than other organisms. The geographical ranges of species associated with forest habitats were reduced mainly during glacial cycles, whereas species associated with open vegetation domains have shown variable responses to climatic oscillations. The results suggest a highly complex mosaic of phylogeographical patterns in South America. We suggest future research directions to promote a better understanding of the origin and maintenance of the South American biota.

Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in pleistocene refugia followed by human-influenced dispersal

Cacao (Theobroma cacao L.) is indigenous to the Amazon basin, but is generally believed to have been domesticated in Mesoamerica for the production of chocolate beverage. However, cacao’s distribution of genetic diversity in South America is also likely to reflect pre-Columbian human influences that were superimposed on natural processes of genetic differentiation. Here we present the results of a spatial analysis of the intra-specific diversity of cacao in Latin America, drawing on a dataset of 939 cacao trees genotypically characterized by means of 96 SSR markers. To assess continental diversity patterns we performed grid-based calculations of allelic richness, Shannon diversity and Nei gene diversity, and distinguished different spatially coherent genetic groups by means of cluster analysis. The highest levels of genetic diversity were observed in the Upper Amazon areas from southern Peru to the Ecuadorian Amazon and the border areas between Colombia, Peru and Brazil. On the assumption that the last glaciation (22,000–13,000 BP) had the greatest pre-human impact on the current distribution and diversity of cacao, we modeled the species’ Pleistocene niche suitability and overlaid this with present-day diversity maps. The results suggest that cacao was already widely distributed in the Western Amazon before the onset of glaciation. During glaciations, cacao populations were likely to have been restricted to several refugia where they probably underwent genetic differentiation, resulting in a number of genetic clusters which are representative for, or closest related to, the original wild cacao populations. The analyses also suggested that genetic differentiation and geographical distribution of a number of other clusters seem to have been significantly affected by processes of human management and accompanying genetic bottlenecks. We discuss the implications of these results for future germplasm collection and in situ, on farm and ex situ conservation of cacao.

Shrinking forests under warming: evidence of Podocarpus parlatorei (pino del cerro) from the subtropical Andes

Phylogeography in combination with ecological niche modeling (ENM) is a robust tool to analyze hypotheses on range shifts under changing climates particularly of taxa and areas with scant fossil records. We combined phylogeographic analysis and ENM techniques to study the effects of alternate cold and warm (i.e., glacial and interglacial) periods on the subtropical montane cold-tolerant conifer Podocarpus parlatorei from Yungas forests of the central Andes. Twenty-one populations, comprising 208 individuals, were analyzed by sequences of the trnL -trnF cpDNA region, and 78 sites were included in the ENM. Eight haplotypes were detected, most of which were widespread while 3 of them were exclusive of latitudinally marginal areas. Haplotype diversity was mostly even throughout the latitudinal range. Two distribution models based on 8 bioclimatic variables indicate a rather continuous distribution during cooling, while under warming remained within stable, yet increasingly fragmented, areas. Although no major range shifts are expected with warming, long-lasting persistence of cold-hardy taxa inhabiting subtropical mountains may include in situ and ex situ conservation actions particularly toward southern (colder) areas.

Pliocene diversification within the South American Forest falcons (Falconidae: Micrastur)

The Neotropics are one of the most species rich regions on Earth, with over 3150 species of birds. This unrivaled biodiversity has been attributed to higher proportions of mountain ranges, tropical rain forest or rain fall in the forest than in any other major biogeographic regions. Five primary hypotheses aim to explain processes of diversification within the Neotropics; (1) the Pleistocene refuge hypothesis, (2) the riverine barrier hypothesis, (3) the Miocene marine incursions hypothesis, (4) the ecological gradient hypothesis, and (5) the impact of the last Andean uplift serving as a barrier between eastern and western population Andean populations. We assessed these hypotheses to see which best explained the species richness of the forest-falcons (Micrastur), a poorly known lineage of birds that inhabit lowland and mid-elevation humid forest. Our analyses suggest all speciation events within the genus Micrastur probably occurred in the last 2.5-3.6 myrs, at or before the Pliocene/Pleistocene boundary, with the basal split within the genus being 7 myrs old. Hence our data allow us to formerly reject the classical Pleistocene refuge for Micrastur, Our divergence time estimates are younger that dates for the Miocene marine incursions, the riverine barrier and the Andean uplift hypotheses.

Speciation timing and neotropical biodiversity: the Tertiary-Quaternary debate in the light of molecular phylogenetic evidence

The evolutionary origin of extant species in the Neotropics, one of the most biodiverse regions of the world, has been widely debated. One hypothesis is that neotropical species emerged primarily during the Quaternary (the last approximately 2 million years), favoured by alternating glacial/interglacial climates. An opposite view proposes an older Tertiary origin linked primarily to palaeogeographical changes. Here, a thorough review of the available literature on DNA molecular dating shows that the Tertiary-Quaternary debate no longer makes sense. Indeed, the > 1400 neotropical species whose origin has been dated have appeared in a continual fashion since the late Eocene/early Oligocene (approximately 39 million years before present) to the Quaternary. Palaeogeographical mechanisms of speciation are relatively well accepted, but diversification processes linked to climate are still controversial. These results are important to unravel both the origin of present-day biodiversity patterns at both local and global scales and the genetic and environmental mechanisms involved, which are two crucial aspects for suitable biodiversity conservation strategies.