River network rearrangements promote speciation in lowland Amazonian birds

Local adaptation has a role in reducing vulnerability to climate change in a widespread Amazonian forest lizard

The extant genetic variation within and among taxa reflects a long history of diversification and adaptive mechanisms in response to climate change and landscape alterations. However, the velocity of current anthropogenic changes poses an imminent threat to global biodiversity. Understanding how species and populations might respond to global climate change provides valuable information for conservation in the face of these impacts. Here, we use genomic data to observe candidate loci under climate selection and test for genetic vulnerability to climate change in a widespread Amazonian ombrophilous lizard population. We found nine populations across Amazonia with a considerable amount of admixture among them. Distinct approaches of genome-environment association analyses revealed 56 candidate single-nucleotide polymorphisms (SNPs) under climatic selection, showing an east-west gradient in the adaptive landscape and a signal of local climate adaptation across the species range. According to our results, signals of local adaptation indicate that the species may not respond equally throughout its range, with some populations facing higher extinction risks. Genomic offset analysis predicts the southern and central portions of Amazonia to have a higher vulnerability to future climate change. Our findings highlight the importance of considering spatially explicit contexts with a large sampling coverage to evaluate how local adaptation and climatic vulnerability affect Amazonian forest ectothermic fauna.

Rethinking spatial history: envisioning a mechanistic historical biogeography

Historical biogeography is the study of geographic distributions of taxa through space and time. Over the last 50 years, several methods have been proposed to reconstruct these histories. However, despite their particularities, conceptually they have been most often derived from the reconstruction of area relationships. Here we advocate that area cladograms lack explanatory power and that biogeography needs to move towards a more mechanistic approach. We discuss the ontological problems related to areas of endemism and their validity as biogeographic units. Specifically, we propose that areas of endemism are not discrete historical entities and that area-based analyses are inappropriate for analytical biogeography. Instead, we suggest that biogeographic analyses should focus on those spatial-geographic elements that cause diversification, namely barriers. We discuss how barriers have more discrete boundaries in space and time than do areas of endemism, which allows the identification of homologous units and the recovery of vicariant events. Reconstructing the history of vicariant events results in a better understanding of spatial evolution within a biota because barrier formation is the relevant causal mechanism of diversification. We end by acknowledging the largely ignored views of Peter Hovenkamp and his conceptual contributions to developing a mechanistic biogeography.

Amazonian rivers are leaky barriers to gene flow in forest understory birds

Ever since Alfred Russel Wallace's nineteenth-century observation that related terrestrial species are often separated on opposing riverbanks, major Amazonian rivers have been recognized as key drivers of speciation. However, rivers are dynamic entities whose widths and courses may vary through time. It thus remains unknown how effective rivers are at reducing gene flow and promoting speciation over long timescales. We fit demographic models to genomic sequences to reconstruct the history of gene flow in three pairs of avian taxa fully separated by different Amazonian rivers, and whose geographic ranges do not make contact in headwater regions where rivers may cease to be barriers. Models with gene flow were best fit but still supported an initial period without any gene flow, which ranged from 187 000 to over 959 000 years, suggesting that rivers are capable of initiating speciation through long stretches of allopatric divergence. Allopatry was followed by either bursts or prolonged episodes of gene flow that retarded genomic differentiation but did not fully homogenize populations. Our results support Amazonian rivers as key barriers that promoted speciation and the build-up of species richness, but they also suggest that river barriers are often leaky, with genomic divergence accumulating slowly owing to episodes of substantial gene flow.

Floristic analyses of Shandong peninsula and adjacent areas indicate the barrier effect of the Yellow river on floristic diversity

The Shandong Peninsula, the largest peninsula in China, is situated at the estuary of the Yellow River and is bordered by both the Bohai Sea and the Yellow Sea. This region is renowned for its rich plant diversity. However, the historical origins of these plant species remain poorly understood. This study analyzed 2410 shared species from 865 genera and 161 families distributed across Shandong and its nine adjacent regions to investigate the floristic diversity of the Shandong Peninsula. These regions were considered as operational taxonomic units (OTUs), with the shared species serving as the basis for each OTU. Hierarchical cluster analyses were performed to assess their floristic similarity, employing the Bray-Curtis distance algorithm and the UPGMA clustering method. The results revealed that the ten regions were grouped into three clusters, delineated by the Yellow River. Notably, the floristic similarity of the Shandong Peninsula was found to be more closely aligned with regions south of the Yellow River, despite Shandong historical connection to Liaoning in the north. These findings underscore the barrier effect of the Yellow River and provide insights into the formation of biotic diversity patterns between northern and eastern China.

Evidence for gene flow and trait reversal during radiation of Mexican Goodeid fish

Understanding the phylogeographic history of a group and identifying the factors contributing to speciation is an important challenge in evolutionary biology. The Goodeinae are a group of live-bearing fishes endemic to Mexico. Here, we develop genomic resources for species within the Goodeinae and use phylogenomic approaches to characterise their evolutionary history. We sequenced, assembled and annotated the genomes of four Goodeinae species, including Ataeniobius toweri, the only matrotrophic live-bearing fish without a trophotaenia in the group. We estimated timings of species divergence and examined the extent and timing of introgression between the species to assess if this may have occurred during an early radiation, or in more recent episodes of secondary contact. We used branch-site models to detect genome-wide positive selection across Goodeinae, and we specifically asked whether this differs in A. toweri, where loss of placental viviparity has recently occurred. We found evidence of gene flow between geographically isolated species, suggesting vicariant speciation was supplemented by limited post-speciation gene flow, and gene flow may explain previous uncertainties about Goodeid phylogeny. Genes under positive selection in the group are likely to be associated with the switch to live-bearing. Overall, our studies suggest that both volcanism-driven vicariance and changes in reproductive mode influenced radiation in the Goodeinae.

An ecohydrological approach to assess water provisioning and supporting ecosystem services in the Budhabalanga River Basin, India

Rivers are vital and complex natural systems that provide a wide range of ecosystem services. This study presents a methodology for assessing the riverine provisioning and supporting ecosystem services, whose applicability has been demonstrated over the Budhabalanga River Basin of India. The Soil and Water Assessment Tool (SWAT) is used to generate streamflow time series at various ungauged sites, and then the streamflow is characterized for the evaluation of provisioning services. Further, the diversity and abundance of macroinvertebrates, along with the Lotic-invertebrate Index for Flow Evaluation (LIFE), is used to study the riverine supporting ecosystem services. The streams show intermittent behavior and strong seasonality for low flows, which limits the water availability, particularly during pre-monsoon season. The Baseflow Index (BFI) is greater than 0.6, indicating that groundwater contributes more than 60% of the total streamflow. Interestingly, despite the high BFI, the streams did not conform to the prevailing opinion that a greater baseflow contribution results in a later commencement of the low-flow period in the hydrological year. Furthermore, the study depicts significant variations in the diversity and abundance of the macroinvertebrates across the various sampling sites. However, the LIFE score across the sites remained consistent within a narrow range, i.e., 8 to 9, suggesting a steady supply of supporting ecosystem services. The results of the study can help the policymakers towards an informed decision making and the simplistic methodology proposed in this study can be replicated in other river basins for identifying vulnerable watersheds and prioritizing management actions.

Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)

Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of 4 populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered 2 primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z-chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) genetrees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification. [Amazonia; biogeography; demographic modeling; gene flow; gene tree; genome architecture; geogenomics; introgression; linked selection; neural network; phylogenomic; phylogeography; reproductive isolation; speciation; species tree.].

The role of biogeographical barriers on the historical dynamics of passerine birds with a circum-Amazonian distribution

Common distributional patterns have provided the foundations of our knowledge of Neotropical biogeography. A distinctive pattern is the "circum-Amazonian distribution", which surrounds Amazonia across the forested lowlands south and east of the basin, the Andean foothills, the Venezuelan Coastal Range, and the Tepuis. The underlying evolutionary and biogeographical mechanisms responsible for this widespread pattern of avian distribution have yet to be elucidated. Here, we test the effects of biogeographical barriers in four species in the passerine family Thamnophilidae by performing comparative demographic analyses of genome-scale data. Specifically, we used flanking regions of ultraconserved regions to estimate population historical parameters and genealogical trees and tested demographic models reflecting contrasting biogeographical scenarios explaining the circum-Amazonian distribution. We found that taxa with circum-Amazonian distribution have at least two main phylogeographical clusters: (1) Andes, often extending into Central America and the Tepuis; and (2) the remaining of their distribution. These clusters are connected through corridors along the Chaco-Cerrado and southeastern Amazonia, allowing gene flow between Andean and eastern South American populations. Demographic histories are consistent with Pleistocene climatic fluctuations having a strong influence on the diversification history of circum-Amazonian taxa, Refugia played a crucial role, enabling both phenotypic and genetic differentiation, yet maintaining substantial interconnectedness to keep considerable levels of gene flow during different dry/cool and warm/humid periods. Additionally, steep environmental gradients appear to play a critical role in maintaining both genetic and phenotypic structure.

Habitat specialization predicts demographic response and vulnerability of floodplain birds in Amazonia

The annual flooding cycle of Amazonian rivers sustains the largest floodplains on Earth, which harbour a unique bird community. Recent studies suggest that habitat specialization drove different patterns of population structure and gene flow in floodplain birds. However, the lack of a direct estimate of habitat affinity prevents a proper test of its effects on population histories. In this work, we used occurrence data, satellite images and genomic data (ultra-conserved elements) from 24 bird species specialized on a variety of seasonally flooded environments to classify habitat affinities and test its influence on evolutionary histories of Amazonian floodplain birds. We demonstrate that birds with higher specialization in river islands and dynamic environments have gone through more recent demographic expansion and currently have less genetic diversity than floodplain generalist birds. Our results indicate that there is an intrinsic relationship between habitat affinity and environmental dynamics, influencing patterns of population structure, demographic history and genetic diversity. Within the floodplains, historical landscape changes have had more severe impacts on island specialists, making them more vulnerable to current and future anthropogenic changes, as those imposed by hydroelectric dams in the Amazon Basin.

Microgeographic speciation in a complex of Anatolian bush crickets facilitated by fast evolution of reproductive isolation

Identifying the drivers of microgeographic speciation (i.e., speciation over small, local geographic scales) is key to understand the origin of speciose groups. Here, we use genomic data to infer the demographic processes underlying diversification in Poecilimon luschani (Orthoptera: Tettigoniidae), a species complex belonging to the most diverse genus of bush crickets from the Mediterranean region (>170 taxa) that comprises three recognized subspecies with small allopatric distributions in the topographically complex Teke Peninsula, southwestern Anatolia. Phylogenomic reconstructions that include all other taxa within the species group confirmed that subspecies of P. luschani originated from a common ancestor during the Pleistocene, supporting recent (<1 Ma) diversification within a small geographical area (ca. 120 × 80 km). Genetic clustering analyses corroborated the distinctiveness of each subspecies and the cohesiveness of their respective populations, with abrupt genetic discontinuities coinciding with contemporary range boundaries. Indeed, our analyses uncovered the presence of two sympatric cryptic sister lineages that diverged <300 ka ago and do not admix despite being co-distributed. Collectively, these results support that all lineages within the complex represent independently evolving entities corresponding to full-fledged species. Statistical evaluation of alternative models of speciation strongly supports a scenario of divergence in isolation followed by a period of limited gene flow during the last glacial period, when all lineages experienced marked expansions according to demographic reconstructions. Our study exemplifies how localized allopatric divergence and fast evolution of reproductive isolation can promote microgeographic speciation and explain the high rates of endemism characterizing biodiversity hotspots.

Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow

Understanding the factors that govern variation in genetic structure across species is key to the study of speciation and population genetics. Genetic structure has been linked to several aspects of life history, such as foraging strategy, habitat association, migration distance, and dispersal ability, all of which might influence dispersal and gene flow. Comparative studies of population genetic data from species with differing life histories provide opportunities to tease apart the role of dispersal in shaping gene flow and population genetic structure. Here, we examine population genetic data from sets of bird species specialized on a series of Amazonian habitat types hypothesized to filter for species with dramatically different dispersal abilities: stable upland forest, dynamic floodplain forest, and highly dynamic riverine islands. Using genome-wide markers, we show that habitat type has a significant effect on population genetic structure, with species in upland forest, floodplain forest, and riverine islands exhibiting progressively lower levels of structure. Although morphological traits used as proxies for individual-level dispersal ability did not explain this pattern, population genetic measures of gene flow are elevated in species from more dynamic riverine habitats. Our results suggest that the habitat in which a species occurs drives the degree of population genetic structuring via its impact on long-term fluctuations in levels of gene flow, with species in highly dynamic habitats having particularly elevated gene flow. These differences in genetic variation across taxa specialized in distinct habitats may lead to disparate responses to environmental change or habitat-specific diversification dynamics over evolutionary time scales.

Biogeographical events, not cospeciation, might be the main drivers in the historical association between Noctiliostrebla species (Streblidae) and their bulldog bat hosts

The genus Noctiliostrebla Wenzel (Diptera: Streblidae) stands out for its high degree of specificity exhibited in relation to bat species of the genus Noctilio Linnaeus and provides an exciting system for understanding the history behind host–parasite associations. Here, we present a phylogeny of Noctiliostrebla based on an analysis of DNA sequences and morphological characters, along with cophylogenetic and biogeographical analyses. Our results strongly support the monophyly of Noctiliostrebla, but with uncertainties within the genus. With a low frequency of cospeciation events explaining the associations between hosts and parasites, cophylogenetic analyses did not show an overall congruence between the host and parasite phylogenies. Indeed, two parallel histories were recovered in the host–parasite associations, which might indicate that niche segregation is determined evolutionarily, facilitating the coexistence of parasites and promoting diversification. Biogeographical analysis showed a strong spatial congruence between disjunct distributions of Noctiliostrebla and major river basins in South America and with areas of higher elevation, which might be associated with the glacial periods throughout the Pliocene and Pleistocene. Overall, our findings suggest an agreement with the expectations of the ‘Stockholm paradigm’ framework, in which biogeographical events and ecological factors act as important components to explain the associations, instead of cospeciation events.

Riverine Barriers as Obstacles to Dispersal in Amazonian Birds

Amazonian rivers represent known barriers for avian dispersal, reducing gene flow and enhancing differentiation. Despite the importance of rivers in the avian evolutionary process, we have made only minor advances in understanding the limitations imposed by rivers on flying birds. To fill that gap, we conducted dispersal-challenge experiments over water, assessing the flying capabilities of 84 tropical bird species of 22 different avian families. We mist-netted and released 484 birds from a stationary boat on the Rio Branco, northern Amazonia, at increasing distances from the shore, including 249 individuals at 100; 219 at 200; 8 at 300; and 5 at 400 m. A successful trial was represented by a bird reaching the riverbank, whereas a failure would refer to birds not reaching the shore and landing on the water, when they were rescued by our team. Our main goal was to understand if the outcome in the experiments could be predicted by (i) phylogenetic constraints, (ii) morphology (body mass and wing shape), (iii) flight speed, (iv) ecological preferences (stratum, habitat, and river-island specialization), and (v) psychological reluctance to fly. Nearly two thirds of the individuals (332) were successful in reaching the riverbank, whereas 152 failed. We found significant differences among lineages. Whereas seven avian families succeeded in all of the trials, two families (antbirds and wrens) were particularly bad dispersers (&lt;40% success). The hand-wing index (HWI) was the single most powerful predictor of trial success. Flying speed was also a significant predictor of success. Overall, ecological attributes had a low explanatory power. Only forest stratum preference had a significant, although weak, effect on dispersal ability: canopy- and ground-dwellers performed better than understory birds. However, we found no effect of habitat preference or river-island specialization on dispersal ability. Our speed estimates for 64 bird species are among the first produced for the tropics and suggest slower flying speeds than those reported from temperate migratory birds. Although birds showed behavioral differences when presented with the opportunity to fly away from the boat, we found no evidence that their reluctance to fly could predict the outcome in the experiments. This represents the first experimental study evaluating the riverine effect through dispersal ability of Amazonian birds, providing important insights to better understand dispersal limitations provided by riverine barriers.