Current Diversity Patterns Research Articles

Connecting Amazonian historical biogeography and local assemblages of understorey birds: Recurrent guild proportionality within areas of endemism

AbstractAimCurrent diversity patterns in local communities result from historical and contemporary events that operate at distinct spatial and temporal scales. However, the contribution of local and large‐scale processes in structuring species diversity remain a contentious topic in ecology. We investigated diversity patterns (species richness, composition and number of captures) of understorey bird assemblages in Amazonian unflooded (terra firme) forests. We sought to understand whether understorey bird assemblages in distinct areas of endemism show distinct patterns of diversity, and whether species replacements among areas of endemism occur while the proportion of species within guilds remains stable.LocationAmazonia.TaxonUnderstorey birds.MethodsTo investigate diversity patterns, we compiled studies that mist‐netted birds at 11 regions across seven Amazonian areas of endemism. We used coverage‐based rarefaction curves, non‐metric multidimensional scaling (NMDS) and created a heatmap based on the proportion of captures in each area of endemism to access patterns of richness, composition and captures of understorey birds, respectively. The relative variance (RVgp index) was calculated to investigate the existence of guild proportionality within each area of endemism.ResultsBird assemblages diverged across the seven areas of endemism, in terms of species richness, composition and captures. However, the proportion of species and individuals within guilds was similar among areas of endemism, indicating that species replacements across areas of endemism occur while maintaining the same ecological functions. Guild proportionality suggests that interspecific competition and resource availability are more important than environmental heterogeneity in structuring understorey bird assemblages.Main conclusionsThe similar proportion of species within guilds suggest that interspecific competition and resource availability are more important than environmental heterogeneity in structuring local assemblages, possibly via a process of limiting similarity in morphological and functional traits. The observed congruent structure in understorey bird assemblages across areas of endemism shows that coupled historical and ecological processes, operating at local to large scales, have led to current patterns of diversity and composition in Amazonian bird communities.

Disturbance History Explains Current Compositional and Diversity Patterns of Primary Picea Abies Forest Vegetation

Disturbance History Explains Current Compositional and Diversity Patterns of Primary Picea Abies Forest Vegetation

Direct and indirect effects of geographic and environmental factors on ant beta diversity across Amazon basin.

Understanding the direct and indirect effects of niche and neutral processes in structuring species diversity is particularly challenging because environmental factors are often geographically structured. Here, we used Structural Equation Modeling to quantify direct and indirect effects of geographic distance, the Amazon River's opposite margins, and environmental differences in temperature, precipitation, and vegetation density (Normalized Difference Vegetation Index-NDVI) on ant beta diversity (Jaccard's dissimilarity) across Amazon basin. We used a comprehensive survey of ground-dwelling ant species from 126 plots distributed across eight sampling sites along a broad environmental gradient. We found that geographic distance and NDVI differences were the major direct predictors of ant composition dissimilarity. The major indirect effect was that of temperature through NDVI, whereas precipitation neither had direct or indirect detectable effects on beta diversity. Thus, ant compositional dissimilarity seems to be mainly driven by a combination of isolation by distance (through dispersal limitation) and selection imposed by vegetation density, and indirectly, by temperature. Our results suggest that neutral and niche processes have been similarly crucial in driving the current beta diversity patterns of Amazonian ground-dwelling ants.

Genomic differentiation with gene flow in a widespread Amazonian floodplain‐specialist bird species

AbstractAimEcological, climatic and palaeogeographical processes drive biological diversification. However, the evolutionary outcomes of those mechanisms are complex and difficult to discriminate. Here, we test how alternative drivers affected connectivity along the Amazonian floodplains generating current patterns of population structure and diversity within the Striped Woodcreeper, a widespread bird species tied to forests seasonally flooded by Amazonian rivers.LocationAmazonian floodplains.TaxonXiphorhynchus obsoletus (Aves, Furnariidae).MethodsWe sequenced 2213 loci of ultraconserved elements (UCEs) and 20 exons to investigate patterns of genetic structure and connectivity across the Striped Woodcreeper distribution, using a set of spatially explicit methods. Population genetics statistics were calculated for each sampled drainage and within each identified cluster. We tested alternative evolutionary scenarios and estimated past and current demographic parameters implementing a simulation‐based framework.ResultsThree genetic clusters with high admixture proportions were identified. These clusters are distributed in the western, central and eastern parts of the Amazon Basin and are not correlated with different river water types representing ecological gradients along the floodplains. Instead, migration rates indicate two putative historical barriers along the main channel of the Amazonas‐Solimões River. Demographic model tests suggest a process of sequential differentiation, partitioned across the Amazon Basin, with stable population sizes and continuous gene flow.Main conclusionOur results support the hypothesis that late Quaternary changes in connectivity between the eastern and western Amazonian drainages were responsible for driving genetic differentiation in the Striped Woodcreeper. Genomic differentiation occurred in the presence of long‐term gene flow throughout the X. obsoletus distribution, suggesting some degree of continuous historical connectivity across Amazonian floodplains. Compared to previous studies, our results suggest that although connectivity among populations of Amazonian bird species specialized in floodplain habitats varies in response to the same abiotic mechanisms, species‐specific differences in habitat use may be a strong predictor of population divergence.

Phylogenetic diversity of ferns reveals different patterns of niche conservatism and habitat filtering between epiphytic and terrestrial assemblages

Much attention has been directed to understanding species richness patterns, but adding an evolutionary perspective allows us to also consider the historical processes determining current diversity patterns. We analyzed phylogenetic patterns of fern species assemblages in 868 plots along a wide range of elevational (0-4000 m) and latitudinal (0°-23°N) gradients in the Neotropics to allow a deeper understanding of evolutionary processes underlying current patterns of diversity and community assembly. Overall, we found that phylogenetic mean pairwise distance (sMPD) and mean nearest taxon distance (sMNTD) decreased with increasing latitude and elevation, but that these geographical factors per se were weak explanatory variables. Incorporating environmental variables strongly enhanced the power of the predictive model, indicating that fern assemblages are phylogenetically more diverse under wet and warm to cool conditions at low latitudes and elevations. Further, whereas epiphytic fern assemblages were strongly influenced by climatic factors, this was not the case for terrestrial ones, suggesting that edaphic conditions and vegetation structure may have a stronger influence on the evolution and diversification of terrestrial ferns. We conclude that fern assemblages are strongly influenced by phylogenetic niche conservatism and environmental filtering. This has also been found for angiosperms, but the direction of the environment-phylogenetic relationship is often opposed in the two groups, suggesting that the older age of many fern lineages includes historical signals that are not evident in the more recent angiosperm radiation.

Divergence and hybridization in sea turtles: Inferences from genome data show evidence of ancient gene flow between species.

Reconstructing past events of hybridization and population size changes are required to understand speciation mechanisms and current patterns of genetic diversity, and ultimately contribute to species' conservation. Sea turtles are ancient species currently facing anthropogenic threats including climate change, fisheries, and illegal hunting. Five of the seven extant sea turtle species are known to currently hybridize, especially along the Brazilian coast where some populations can have ~32%–42% of hybrids. Although frequently observed today, it is not clear what role hybridization plays in the evolutionary diversification of this group of reptiles. In this study, we generated whole genome resequencing data of the five globally distributed sea turtle species to estimate a calibrated phylogeny and the population size dynamics, and to understand the role of hybridization in shaping the genomes of these ancient species. Our results reveal discordant species divergence dates between mitochondrial and nuclear genomes, with a high frequency of conflicting trees throughout the nuclear genome suggesting that some sea turtle species frequently hybridized in the past. The reconstruction of the species' demography showed a general decline in effective population sizes with no signs of recovery, except for the leatherback sea turtle. Furthermore, we discuss the influence of reference bias in our estimates. We show long‐lasting ancestral gene flow events within Chelonioidea that continued for millions of years after initial divergence. Speciation with gene flow is a common pattern in marine species, and it raises questions whether current hybridization events should be considered as a part of these species' evolutionary history or a conservation issue.

Current patterns of plant diversity and phylogenetic structure on the Kunlun Mountains

Large-scale patterns of biodiversity and the underlying mechanisms that regulate these patterns are central topics in biogeography and macroecology. The Qinghai-Tibet Plateau serves as a natural laboratory for studying these issues. However, most previous studies have focused on the entire Qinghai-Tibet Plateau, leaving independent physical geographic subunits in the region less well understood. We studied the current plant diversity of the Kunlun Mountains, an independent physical geographic subunit located in northwestern China on the northern edge of the Qinghai-Tibet Plateau. We integrated measures of species distribution, geological history, and phylogeography, and analyzed the taxonomic richness, phylogenetic diversity, and community phylogenetic structure of the current plant diversity in the area. The distribution patterns of 1911 seed plants showed that species were distributed mainly in the eastern regions of the Kunlun Mountains. The taxonomic richness, phylogenetic diversity, and genera richness showed that the eastern regions of the Kunlun Mountains should be the priority area of biodiversity conservation, particularly the southeastern regions. The proportion of Chinese endemic species inhabiting the Kunlun Mountains and their floristic similarity may indicate that the current patterns of species diversity were favored via species colonization. The Hengduan Mountains, a biodiversity hotspot, is likely the largest source of species colonization of the Kunlun Mountains after the Quaternary. The net relatedness index indicated that 20 of the 28 communities examined were phylogenetically dispersed, while the remaining communities were phylogenetically clustered. The nearest taxon index indicated that 27 of the 28 communities were phylogenetically clustered. These results suggest that species colonization and habitat filtering may have contributed to the current plant diversity of the Kunlun Mountains via ecological and evolutionary processes, and habitat filtering may play an important role in this ecological process.

Habitat heterogeneity, temperature, and primary productivity drive elevational gradients in avian species diversity.

AimAnticipating and mitigating the impacts of climate change on species diversity in montane ecosystems requires a mechanistic understanding of drivers of current patterns of diversity. We documented the shape of elevational gradients in avian species richness in North America and tested a suite of a priori predictions for each of five mechanistic hypotheses to explain those patterns.LocationUnited StatesMethodsWe used predicted occupancy maps generated from species distribution models for each of 646 breeding birds to document elevational patterns in avian species richness across the six largest U.S. mountain ranges. We used spatially explicit biotic and abiotic data to test five mechanistic hypotheses proposed to explain geographic variation in species richness.ResultsElevational gradients in avian species richness followed a consistent pattern of low elevation plateau‐mid‐elevation peak (as per McCain, 2009). We found support for three of the five hypotheses to explain the underlying cause of this pattern: the habitat heterogeneity, temperature, and primary productivity hypotheses.Main ConclusionsSpecies richness typically decreases with elevation, but the primary cause and precise shape of the relationship remain topics of debate. We used a novel approach to study the richness‐elevation relationship and our results are unique in that they show a consistent relationship between species richness and elevation among 6 mountain ranges, and universal support for three hypotheses proposed to explain the underlying cause of the observed relationship. Taken together, these results suggest that elevational variation in food availability may be the ecological process that best explains elevational gradients in avian species richness in North America. Although much attention has focused on the role of abiotic factors, particularly temperature, in limiting species’ ranges, our results offer compelling evidence that other processes also influence (and may better explain) elevational gradients in species richness.

Plant Biogeography and Vegetation Patterns of the Mediterranean Islands

With about 11,100 islands and islets of which ca. 250 are regularly inhabited by human, the Mediterranean Sea represents one of the regions of the world with the most islands and archipelagos. These numerous islands represent a significant component of the Mediterranean biodiversity, notably with the presence of range-restricted species and peculiar vegetation types. The aim of this review is to provide a balanced view of this highly diverse phytoecological heritage, but also taking into account the medium sized islands and the smaller ones that have not been highlighted so far. Mediterranean islands constitute both a museum for ancient lineages (paleoendemic taxa) and cradle for recent plant diversification. The complex historical biogeography (paleogeographical events of the Neogene, Messinian salinity crisis, climatic and eustatic changes of the Pleistocene, influence of glacial events) has profoundly influenced the current patterns of plant diversity. These insular landscapes were also precociously impacted by prehistoric man, possibly by Neanderthals. Among the 157 large Mediterranean islands (i.e. with a surface area exceeding 10 km2), 49 have a surface greater than 100 km2. The main patterns and dynamics of vegetation on the largests islands (Balearic Islands, Corsica, Sardinia, Sicily, Croatian islands, Greek islands, Crete, Cyprus) are summarized. Then, the specific ecosystem functioning (disturbance, plant-animal interactions) and vegetation structures of the small Mediterranean islands (i.e. a surface area less than 10 km2 or 1000 ha), are highlighted by evoking successively the small rocky islands, the volcanic ones, and the sandy and flat islands. Owing to their uniqueness and fragility, Mediterranean islands urgently need some integrated and ambitious conservation planning, aiming at the long-term preservation of their outstanding biotic and cultural heritage.

Multiple-scale processes shape the population genetics of Tehuelche scallop, Aequipecten tehuelchus, in Northern Patagonia

The population genetic structure and oceanographic boundaries to gene flow are relevant for understanding biological connectivity in marine environments. However, the relative contribution of historical (e.g., sea-level change) and recent (e.g., fisheries) processes in shaping current patterns of genetic structure and diversity are commonly unknown. This study focuses in the population genetics of the commercially harvested Tehuelche scallop, Aequipecten tehuelchus. This species presents three morphotypes; tehuelchus, madrynensis, and a non-common variant felipponei, which are meristically differentiated by the number of ribs. The genetic structure of the two main morphotypes (tehuelchus and madrynensis) was studied using microsatellite loci in seven locations of the Argentine coast. Historic demography analyses revealed a trend of population expansion after the last glacial period. Two genetic groups were detected that correspond to morphotypes distributed northward (tehuelchus) and southward (madrynensis) of the Peninsula Valdés tidal front. On the other hand, the lack of genetic differentiation among locations with fishery activity in the northern cluster indicates that the commercially exploited demes may belong to a single genetic stock. As this stock is distributed in waters under federal and provincial jurisdictions, the findings highlight the need to integrate management of the species across political boundaries.

Historical and Current Diversity Patterns of Mediterranean Marine Species

The Mediterranean is a sea which, despite its peculiar geomorphological history and ecological–oceanographic features, still receives less attention than it ought to [...]

Evolutionary analyses of the major variant surface antigen-encoding genes reveal population structure of Plasmodium falciparum within and between continents.

Malaria remains a major public health problem in many countries. Unlike influenza and HIV, where diversity in immunodominant surface antigens is understood geographically to inform disease surveillance, relatively little is known about the global population structure of PfEMP1, the major variant surface antigen of the malaria parasite Plasmodium falciparum. The complexity of the var multigene family that encodes PfEMP1 and that diversifies by recombination, has so far precluded its use in malaria surveillance. Recent studies have demonstrated that cost-effective deep sequencing of the region of var genes encoding the PfEMP1 DBLα domain and subsequent classification of within host sequences at 96% identity to define unique DBLα types, can reveal structure and strain dynamics within countries. However, to date there has not been a comprehensive comparison of these DBLα types between countries. By leveraging a bioinformatic approach (jumping hidden Markov model) designed specifically for the analysis of recombination within var genes and applying it to a dataset of DBLα types from 10 countries, we are able to describe population structure of DBLα types at the global scale. The sensitivity of the approach allows for the comparison of the global dataset to ape samples of Plasmodium Laverania species. Our analyses show that the evolution of the parasite population emerging out of Africa underlies current patterns of DBLα type diversity. Most importantly, we can distinguish geographic population structure within Africa between Gabon and Ghana in West Africa and Uganda in East Africa. Our evolutionary findings have translational implications in the context of globalization. Firstly, DBLα type diversity can provide a simple diagnostic framework for geographic surveillance of the rapidly evolving transmission dynamics of P. falciparum. It can also inform efforts to understand the presence or absence of global, regional and local population immunity to major surface antigen variants. Additionally, we identify a number of highly conserved DBLα types that are present globally that may be of biological significance and warrant further characterization.

Vascular Epiphyte Assemblages on Isolated Trees along an Elevational Gradient in Southwest Panama

Ongoing destruction of tropical forests makes isolated pasture trees potentially important for the persistence of original forest dwellers such as many vascular epiphytes. We studied epiphyte assemblages on 100 isolated trees at ten pasture sites in southwest Panama along an elevational gradient ranging from 140 to 1240 m a.s.l. We analysed epiphyte species composition (richness, similarity) and registered climate and host trait variables of potential influence on their occurrence. We found a total of 5876 epiphyte individuals belonging to 148 species. Epiphyte abundance, species richness and diversity all varied about 4-fold among the 10 sites, with a high similarity of epiphyte assemblages among sites. Two sites at 870 and 1050 m a.s.l. did not fit into the overall elevational trend of increased abundance, species richness and diversity. However, all three measures were significantly correlated with humidity as the independent variable. This highlights that a gradient in humidity, and not elevation as such, is responsible for the typical elevational changes in epiphyte assemblages, so that special local conditions may lead to deviations from expected patterns. Our documentation of current elevational diversity patterns also provides a baseline for the study of long-term changes in epiphyte assemblages in anthropogenically modified landscapes.

Global biogeography and diversification of a group of brown seaweeds (Phaeophyceae) driven by clade‐specific evolutionary processes

AbstractAimHistorical processes that shaped current diversity patterns of seaweeds remain poorly understood. Using Dictyotales, a globally distributed order of brown seaweeds as a model, we test if historical biogeographical and diversification patterns are comparable across clades. Dictyotales contain some 22 genera, three of which, Dictyota, Lobophora and Padina, are exceptionally diverse. Specifically, we test whether the evolutionary processes that shaped the latitudinal diversity patterns in these clades are in line with the tropical conservatism, out‐of‐the‐tropics or diversification rate hypotheses.LocationGlobal coastal benthic marine environments.TaxonDictyotales (Phaeophyceae).MethodsSpecies diversity was inferred using DNA‐based species delineation, addressing cryptic diversity and circumventing taxonomic problems. A six‐gene time‐calibrated phylogeny, distribution data of 3,755 specimens and probabilistic modelling of geographical range evolution were used to infer historical biogeographical patterns. The phylogeny was tested against different trait‐dependent models to compare diversification rates for different geographical units as well as different thermal affinities.ResultsOur results indicate that Dictyotales originated in the Middle Jurassic and reach a current peak of species diversity in the Central Indo‐Pacific. Ancestral range estimation points to a southern hemisphere origin of Dictyotales corresponding to the tropical southern Tethys Sea. Our results demonstrate that diversification rates were generally higher in tropical regions, but increased diversification rates in different clades are driven by different processes. Our results suggest that three major clades underwent a major diversification burst in the early Cenozoic, with Dictyota and Padina expanding their distribution into temperate regions while Lobophora retained a predominantly tropical niche.Main conclusionsOur results are consistent with both the tropical conservatism hypothesis, in which clades originate and remain in the tropics (Lobophora), and the out‐of‐the‐tropics scenario, where taxa originate and expand towards the temperate regions while preserving their presence in the tropics (Dictyota, Padina).

Pleistocene glacial cycles as drivers of allopatric differentiation in Arctic shorebirds

AbstractAimSpatio‐temporal changes have likely caused range fragmentation and population isolation, which could have given rise to the observed current intraspecific differentiation in some species. Here, we test several hypotheses on the potential effect of Pleistocene glacial cycles in the diversification of Arctic shorebird species, comparing between different scenarios of fragmentation of the breeding distribution during glacial and interglacial periods.LocationGlobal.TaxonArctic migratory shorebirds.MethodsWe performed species distribution models (SDMs) to explore the changes in the breeding and non‐breeding ranges of 69 species between the last glacial maximum (c. 21,000 years ago) and the present. We also included independent evidence from the fossil record and estimations on the potential extension of the tundra during glacial periods to validate the results from the SDMs. We assigned each species to one of four potential scenarios based on fragmentation and potential recolonization patterns of their breeding ranges during glaciations.ResultsOur findings show that most of the species with subspecies experienced fragmentation of their ranges during the glacial, the interglacial or both periods. Meanwhile, the majority of the monotypic species maintained their ranges as a continuum. Moreover, the impacts of glacial cycles in the distribution were not homogeneous across the Arctic, and some regions were more prone to the fragmentation of breeding ranges than others.Main conclusionsOur work suggests that Pleistocene climatic cycles drove the diversification of Arctic shorebirds by creating allopatric breeding distributions. While the fragmentation of the breeding ranges occurred mainly during glacial periods, interglacials also played a part in maintaining or establishing newly isolated breeding populations for many species. Furthermore, species' distribution changes varied between different regions and habitats, which determined current shorebird diversity patterns.

Historical climatic instability predicts the inverse latitudinal pattern in speciation rate of modern mammalian biota.

Evolutionary rate explanations for latitudinal diversity gradients predict faster speciation and diversification rates in richer, older and more stable tropical regions (climatic stability hypothesis). Numerous modern lineages have emerged in high latitudes, however, suggesting that climatic oscillations can drive population divergence, at least among extratropical species (glacial refugia hypothesis). This conflicting evidence suggests that geographical patterns of evolutionary rates are more complicated than previously thought. Here, we reconstructed the complex evolutionary dynamics of a comprehensive data set of modern mammals, both terrestrial and marine. We performed global and regional regression analyses to investigate how climatic instability could have indirectly influenced contemporary diversity gradients through its effects on evolutionary rates. In particular, we explored global and regional patterns of the relationships between species richness and assemblage-level evolutionary rates and between evolutionary rates and climatic instability. We found an inverse relationship between evolutionary rates and species richness, especially in the terrestrial domain. Additionally, climatic instability was strongly associated with the highest evolutionary rates at high terrestrial latitudes, supporting the glacial refugia hypothesis there. At low latitudes, evolutionary rates were unrelated to climatic stability. The inverse relationship between evolutionary rates and the modern latitudinal diversity gradient casts doubt on the idea that higher evolutionary rates in the tropics underlie the current diversity patterns of modern mammals. Alternatively, the longer time spans for diversity to accumulate in the older and more stable tropics (and not high diversification rates) may explain the latitudinal diversity gradient.

Historical legacies and contemporary processes shape beta diversity in Neotropical montane streams

AbstractAimContemporary dispersal constraints and environmental conditions are broadly recognized as significant drivers of beta diversity patterns. However, beta diversity patterns may also reflect the legacy of past climatic and geological events. In this study, we investigated the relative importance of historical and contemporary factors as drivers of taxonomic, functional and phylogenetic beta diversity in Neotropical stream communities.LocationThe Colombian Orinoco basin.TaxonDiatoms and insects.MethodsWe estimated taxonomic, phylogenetic and functional beta diversity using Baselga's (BAS) and Podani's (POD) frameworks. Following both frameworks, we further partitioned every biodiversity facet into turnover and nestedness or richness difference components. Then, we used generalized linear models (GLM) to relate each biodiversity facet with environmental, spatial and historical factors.ResultsWe found that both historical and contemporary factors affected current patterns of beta diversity. Historical factors and water pH and temperature had the strongest effect on beta diversity patterns, particularly for taxonomic and phylogenetic facets. GLM models performed better for insects than for diatoms in all three facets. Within communities, our analysis also revealed a partial congruence between BAS‐ and POD‐based results.Main conclusionsDue to their past geological history and contemporary environmental gradients, tropical montane streams are natural laboratories for disentangling the joint effects of ecological and biogeographical factors on biodiversity patterns. Our study reveals that present‐day distribution patterns cannot be fully explained without accounting for the effects of past geological and climatic events on mountain landscapes. In the Neotropics, montane geology sets the stage for speciation and landscape formation, with which ecological (e.g., dispersal limitation) and environmental factors interact to generate spatial variation in species turnover.

The phylogenetic diversity and structure of the seasonally dry forests in the Neotropics

AbstractAimExceptions to the quasi‐ubiquitous latitudinal diversity gradient (LDG) have been poorly studied. A reverse LDG, when species richness (SR) increases away from the Equator, has been suggested for several taxa and entire biomes. The Neotropical seasonally dry tropical forests (SDTF) are a well‐known example of a reverse LDG that could be caused by the climatic stability of Pleistocene Refugia and dispersion from distinct source areas. Here, we test these predictions under a spatial and phylogenetic framework.LocationNeotropics.TaxonWoody plants.MethodsWe used a recent species‐level seed plant phylogeny and the DRYFLOR dataset to evaluate the geographic patterns of phylogenetic diversity (PD) and structure of woody plant assemblages associated with the Neotropical SDTFs. We conducted spatial regressions to test the effect of climatic instability since the Last Glacial Maximum (LGM) on assemblages’ residual PD (controlling for SR) and null model analysis to evaluate their phylogenetic structure using the Net Relatedness Index.ResultsPhylogenetic diversity of the Neotropical SDTFs increased away from the Equator, likely driven by SR. This pattern was not related to climatic instability since the LGM. Phylogenetic structure of SDTF assemblages showed considerable spatial patterning, with significant phylogenetic clustering in the Mesoamerica and Caatinga regions.Main conclusionThe reverse latitudinal SR gradient of the Neotropical SDTF assemblages is mirrored by their PD. Phylogenetic history seems to have influenced such patterns differently across the Neotropics with no relationship to climatic stability since the LGM, where particular SDTF nuclei previously suggested as Pleistocene refugia served as cradles and source areas for the current diversity pattern of the biome.

Comparative phylogeographic and demographic analyses reveal a congruent pattern of sister relationships between bird populations of the northern and south-central Atlantic Forest

The Pernambuco Center of Endemism (PCE) is the northernmost strip of the Atlantic Forest (AF). Biogeographic affinities among avifaunas in the PCE, the southern-central Atlantic Forest (SCAF), and Amazonia (AM) have not been studied comprehensively, and current patterns of genetic diversity in the PCE remain unclear. The interplay between species’ ecological attributes and historical processes, such as Pleistocene climate fluctuations or the appearance of rivers, may have affected population genetic structures in the PCE. Moreover, the role of past connections between the PCE and AM and the elevational distribution of species in assembling the PCE avifauna remain untested. Here, we investigated the biogeographic history of seven taxa endemic to the PCE within a comparative phylogeographic framework based on a mean of 3,618 independent single nucleotide polymorphisms (SNPs) extracted from flanking regions of ultraconserved elements (UCEs) and one mitochondrial gene. We found that PCE populations were more closely related to SCAF populations than they were to those in AM, regardless of their elevational range, with divergence times placed during the Mid-Pleistocene. These splits were consistent with a pattern of allopatric divergence with gene flow until the upper Pleistocene and no signal of rapid changes in population sizes. Our results support the existence of a Pleistocene refugium driving current genetic diversity in the PCE, thereby rejecting the role of the São Francisco River as a primary barrier for population divergence. Additionally, we found that connections with Amazonia also played a significant role in assembling the PCE avifauna through subsequent migration events.

Disproportionate extinction of South American mammals drove the asymmetry of the Great American Biotic Interchange

The interchange between the previously disconnected faunas of North and South America was a massive experiment in biological invasion. A major gap in our understanding of this invasion is why there was a drastic increase in the proportion of mammals of North American origin found in South America. Four nonmutually exclusive mechanisms may explain this asymmetry: 1) Higher dispersal rate of North American mammals toward the south, 2) higher origination of North American immigrants in South America, 3) higher extinction of mammals with South American origin, and 4) similar dispersal rate but a larger pool of native taxa in North versus South America. We test among these mechanisms by analyzing ∼20,000 fossil occurrences with Bayesian methods to infer dispersal and diversification rates and taxonomic selectivity of immigrants. We find no differences in the dispersal and origination rates of immigrants. In contrast, native South American mammals show higher extinction. We also find that two clades with North American origin (Carnivora and Artiodactyla) had significantly more immigrants in South America than other clades. Altogether, the asymmetry of the interchange was not due to higher origination of immigrants in South America as previously suggested, but resulted from higher extinction of native taxa in southern South America. These results from one of the greatest biological invasions highlight how biogeographic processes and biotic interactions can shape continental diversity.