Beyond Refugia: New Insights on Quaternary Climate Variation and the Evolution of Biotic Diversity in Tropical South America

Ecotones as Windows into Organismal-to-Biome Scale Responses across Neotropical Forests

Tropical forests are incredibly diverse in structure and function. Despite, or perhaps because of, this diversity, tropical biologists often conduct research exclusively in one or perhaps a few forest types. Rarely do we study the ecotone-the interstitial region between forest types. Ecotones are hyper-diverse, dynamic systems that control the flow of energy and organisms between adjacent ecosystems, with their locations determined by species' physiological limits. In this review, we describe how studying ecotones can provide key indicators for monitoring the state of Neotropical forests from organisms to ecosystems. We first describe how ecotones have been studied in the past and summarize our current understanding of tropical ecotones. Next, we provide three example lines of research focusing on the ecological and evolutionary dynamics of the ecotone between tropical dry forests and desert; between tropical dry and rainforests; and between Cerrado and Atlantic rainforests, with the latter being a particularly well-studied ecotone. Lastly, we outline methods and tools for studying ecotones that combine remote sensing, new statistical techniques, and field-based forest dynamics plot data, among others, for understanding these important systems.

Diversity and biogeography of South American mud turtles elucidated by multilocus DNA sequencing (Testudines: Kinosternidae)

Kinosternon is the most speciose genus of extant turtles, with 22 currently recognized species, distributed across large parts of the Americas. Most species have small distributions, but K. leucostomum and K. scorpioides range from Mexico to South America. Previous studies have found discordance between mitochondrial and nuclear phylogenies in some kinosternid groups, with the current taxonomy following the nuclear-based results. Herein, based on extended molecular, geographic, and taxonomic sampling, we explore the phylogeographic structure and taxonomic limits for K. leucostomum and the K. scorpioides group and present a fossil-calibrated nuclear time tree for Kinosternon. Our results reveal contrasting differentiation patterns for the K. scorpioides group and K. leucostomum, despite overlapping distributions. Kinosternon leucostomum shows only shallow geographic divergence, whereas the K. scorpioides group is polyphyletic with up to 10 distinct taxa, some of them undescribed. We support the elevation of K. s. albogulare and K. s. cruentatum to species level. Given the deep divergence within the genus Kinosternon, we propose the recognition of three subgenera, Kinosternon, Cryptochelys and Thyrosternum, and the abandonment of the group-based classification, at least for the K. leucostomum and K. scorpioides groups. Our results show an initial split in Kinosternon that gave rise to two main radiations, one Nearctic and one mainly Neotropical. Most speciation events in Kinosternon occurred during the Quaternary and we hypothesize that they were mediated by both climatic and geological events. Additionally, our data imply that at least three South American colonizations occurred, two in the K. leucostomum group, and one in the K. scorpioides group. Additionally, we hypothesize that discordance between mitochondrial and nuclear phylogenetic signal is due to mitochondrial capture from an extinct kinosternine lineage.

Whole genomes show contrasting trends of population size changes and genomic diversity for an Amazonian endemic passerine over the late quaternary

The "Amazon tipping point" is a global change scenario resulting in replacement of upland terra-firme forests by large-scale "savannization" of mostly southern and eastern Amazon. Reduced rainfall accompanying the Last Glacial Maximum (LGM) has been proposed to have acted as such a tipping point in the past, with the prediction that terra-firme inhabiting species should have experienced reductions in population size as drier habitats expanded. Here, we use whole-genomes of an Amazonian endemic organism (Scale-backed antbirds - Willisornis spp.) sampled from nine populations across the region to test this historical demography scenario. Populations from southeastern Amazonia and close to the Amazon-Cerrado ecotone exhibited a wide range of demographic patterns, while most of those from northern and western Amazonia experienced uniform expansions between 400 kya and 80-60 kya, with gradual declines toward 20 kya. Southeastern populations of Willisornis were the last to diversify and showed smaller heterozygosity and higher runs of homozygosity values than western and northern populations. These patterns support historical population declines throughout the Amazon that affected more strongly lineages in the southern and eastern areas, where historical "tipping point" conditions existed due to the widespread replacement of humid forest by drier and open vegetation during the LGM.

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.

Humid and cold forest connections in South America between the eastern Andes and the southern Atlantic coast during the LGM

The presence of Andean plant genera in moist forests of the Brazilian Atlantic Coast has been historically hypothesized as the result of cross-continental migrations starting at the eastern Andean flanks. Here we test hypotheses of former connections between the Atlantic and Andean forests by examining distribution patterns of selected cool and moist-adapted plant arboreal taxa present in 54 South American pollen records of the Last Glacial Maximum (LGM), ca. 19-23 cal ka, known to occur in both plant domains. Pollen taxa studied include Araucaria, Drimys, Hedyosmum, Ilex, Myrsine, Podocarpus, Symplocos, Weinmannia, Myrtaceae, Ericaceae and Arecaceae. Past connectivity patterns between these two neotropical regions as well as individual ecological niches during the LGM were explored by cluster analysis of fossil assemblages and modern plant distributions. Additionally, we examined the ecological niche of 137 plant species with shared distributions between the Andes and coastal Brazil. Our results revealed five complex connectivity patterns for South American vegetation linking Andean, Amazonian and Atlantic Forests and one disjunction distribution in southern Chile. This study also provides a better understanding of vegetation cover on the large and shallow South American continental shelf that was exposed due to a global sea level drop.

Implications of headwater contact zones for the riverine barrier hypothesis: a case study of the Blue-capped Manakin (Lepidothrix coronata)

Rivers frequently delimit the geographic ranges of species in the Amazon Basin. These rivers also define the boundaries between genetic clusters within many species, yet river boundaries have been documented to break down in headwater regions where rivers are narrower. To explore the evolutionary implications of headwater contact zones in Amazonia, we examined genetic variation in the Blue-capped Manakin (Lepidothrix coronata), a species previously shown to contain several genetically and phenotypically distinct populations across the western Amazon Basin. We collected restriction site-associated DNA sequence data (RADcap) for 706 individuals and found that spatial patterns of genetic structure indicate several rivers, particularly the Amazon and Ucayali, are dispersal barriers for L. coronata. We also found evidence that genetic connectivity is elevated across several headwater regions, highlighting the importance of headwater gene flow for models of Amazonian diversification. The headwater region of the Ucayali River provided a notable exception to findings of headwater gene flow by harboring non-admixed populations of L. coronata on opposite sides of a < 1-km-wide river channel with a known dynamic history, suggesting that additional prezygotic barriers may be limiting gene flow in this region.

Biogeography and environmental preferences of Butia yatay (Mart.) Becc

During the Quaternary, Chaco Phytogeographic Domain (Chaco) flora in subtropical South America experienced temperature and humidity fluctuations, primarily driven by wind dynamics, leading to significant shifts in species distribution. The palm Butia yatay is endemic to the Chaco and thrives in areas characterized by a warm-rainy climate and mostly restricted to sandy soils. To investigate the current geographic distribution of suitable habitat for B. yatay while assessing the significance of soil variables, we employed two distinct algorithms in species distribution modeling (SDM). We also determined whether the distribution of B. yatay has changed since the Pleistocene and whether these changes align with previously proposed Pleistocene refugia. In the present SDMs, we considered two separate sets of predictors, one set with bioclimatic variables only and the other set with bioclimatic topographic and soil variables. Additionally, we reconstructed the historical geographic distribution of suitable habitats using bioclimatic data. Our results suggested that the primary determinants of B. yatay's current distribution include precipitation and temperature of the driest month and soil cation exchange capacity. Incorporating soil variables affected the estimated size and range of suitable areas. Projections into the past indicated similar suitable habitat distributions during interglacial periods compared with the present. During the Last Glacial Maximum, climatically suitable habitat may have shifted northward, partially overlapping with previously suggested Pleistocene refugia located between the Paraná and Uruguay Rivers. These findings indicate the main factors driving the distribution and ecology of B. yatay and enhance understanding of subtropical flora shifts during the Quaternary. The approach also may prove valuable for other studies within the Chaco.

Hydraulic variability of tropical forests is largely independent of water availability

Tropical rainforest woody plants have been thought to have uniformly low resistance to hydraulic failure and to function near the edge of their hydraulic safety margin (HSM), making these ecosystems vulnerable to drought; however, this may not be the case. Using data collected at 30 tropical forest sites for three key traits associated with drought tolerance, we show that site-level hydraulic diversity of leaf turgor loss point, resistance to embolism (P50 ), and HSMs is high across tropical forests and largely independent of water availability. Species with high HSMs (>1 MPa) and low P50 values (< -2 MPa) are common across the wet and dry tropics. This high site-level hydraulic diversity, largely decoupled from water stress, could influence which species are favoured and become dominant under a drying climate. High hydraulic diversity could also make these ecosystems more resilient to variable rainfall regimes.

Geodiversity influences limnological conditions and freshwater ostracode species distributions across broad spatial scales in the northern Neotropics

Abstract. Geodiversity is recognized as one of the most important drivers of ecosystem characteristics and biodiversity globally. However, in the northern Neotropics, the contribution of highly diverse landscapes, environmental conditions, and geological history in structuring large-scale patterns of aquatic environments and aquatic species associations remains poorly understood. We evaluated the relationships among geodiversity, limnological conditions, and freshwater ostracodes from southern Mexico to Nicaragua. A cluster analysis (CA), based on geological, geochemical, mineralogical, and water-column physical and chemical characteristics of 76 aquatic ecosystems (karst, volcanic, tectonic) revealed two main limnological regions: (1) karst plateaus of the Yucatán Peninsula and northern Guatemala, and (2) volcanic terrains of the Guatemalan highlands, mid-elevation sites in El Salvador and Honduras, and the Nicaraguan lowlands. In addition, seven subregions were recognized, demonstrating a high heterogeneity of aquatic environments. Principal component analysis (PCA) identified water chemistry (ionic composition) and mineralogy as most influential for aquatic ecosystem classification. Multi-parametric analyses, based on biological data, revealed that ostracode species associations represent disjunct faunas. Five species associations, distributed according to limnological regions, were recognized. Structural equation modeling (SEM) revealed that geodiversity explains limnological patterns of the study area. Limnology further explained species composition, but not species richness. The influence of conductivity and elevation were individually evaluated in SEM and were statistically significant for ostracode species composition, though not for species richness. We conclude that geodiversity has a central influence on the limnological conditions of aquatic systems, which in turn influence ostracode species composition in lakes of the northern Neotropical region.

The dynamics of introgression across an avian radiation

Hybridization and resulting introgression can play both a destructive and a creative role in the evolution of diversity. Thus, characterizing when and where introgression is most likely to occur can help us understand the causes of diversification dynamics. Here, we examine the prevalence of and variation in introgression using phylogenomic data from a large (1300+ species), geographically widespread avian group, the suboscine birds. We first examine patterns of gene tree discordance across the geographic distribution of the entire clade. We then evaluate the signal of introgression in a subset of 206 species triads using Patterson's D‐statistic and test for associations between introgression signal and evolutionary, geographic, and environmental variables. We find that gene tree discordance varies across lineages and geographic regions. The signal of introgression is highest in cases where species occur in close geographic proximity and in regions with more dynamic climates since the Pleistocene. Our results highlight the potential of phylogenomic datasets for examining broad patterns of hybridization and suggest that the degree of introgression between diverging lineages might be predictable based on the setting in which they occur.

Two centuries of distribution data: detection of areas of endemism for the Brazilian angiosperms

Brazil has high levels of biodiversity and has received strong criticism for the increasing country-wide deforestation that threatens it. Although a significant percentage of land area in Brazil is protected, the areas are insufficient and unevenly distributed. Many studies have contributed to the biogeographical knowledge of Brazilian flora, but no endemicity analysis (EA) has been conducted including all endemic angiosperms. We investigated the spatial component, drawing on a huge and taxonomically diverse dataset based on 827 016 records collected over the last two centuries. We conducted an EA for 15 034 species from 173 families using an optimality criterion with 2° and 3° grid sizes, in order to search for distributional concordance, to identify the biogeographical units and discuss the implications for conservation. Six analyses were run for basal angiosperms, monocots and eudicots. The EA recovered 66 consensus areas (CAs). The concordance of CAs enabled the identification of five best-supported areas of endemism--three in the Atlantic and Parana Forest and two areas in the Cerrado province--supported by species of 120 families. The age of divergence for some genera that contributed significantly to the identification of areas recovered in the Cerrado coincides with the recent, <10 Ma, estimated age of that province. By contrast, the areas in the Atlantic and Parana Forest are supported by genera with earlier diversification >30 Ma, supporting an ancient origin. Most areas in the Atlantic Forest are partially superimposed with the limits of the protected areas, however, big gaps were identified in the Cerrado. Protecting Brazilian biomes was at the heart of Brazil's environmental policy. Regrettably, this scenario has radically changed based on misleading divergences in conservation policy. Areas of endemism are pivotal for biodiversity conservation due to the common evolutionary history shared by their endemic taxa. Thus, we hope that these congruent patterns of endemism support the establishment of biodiversity priorities.

The evolutionary history of vines in a neotropical biodiversity hotspot: Phylogenomics and biogeography of a large passion flower clade (Passiflora section Decaloba)

Because of their extraordinary flower and leaf morphology, passion flowers (Passifloraceae) have fascinated naturalists since their discovery. Within the large, diverse (600 species) genus Passiflora is an especially enigmatic and species-rich (120 spp.) subclade, Section Decaloba, which occurs in the Neotropics and has its center of diversity in Andean montane forests. A recent phylogenetic study of Passifloraceae showed that Section Decaloba was monophyletic, but was unable to resolve relationships within the clade, thus preventing inferences of evolutionary history and biogeography. The goal of this study was to elucidate the phylogeny and biogeography of Section Decaloba. We sampled 206 accessions representing 91 of the ~ 120 known species in section Decaloba and four outgroups, with samples derived predominantly from herbarium specimens. We generated DNA sequences using a high-throughput DNA sequencing technique called 2b-RAD, reconstructed the phylogeny, and conducted ancestral area reconstructions to infer the biogeographic history of the group. We recovered predominantly well-supported trees in which species were grouped into two main clades: 1) the Central American clade, within which the majority of nodes well supported and species were monophyletic and 2) the South American clade, a large clade that showed overall lower resolution and included several polyphyletic species and species complexes that need additional research. RASP analysis showed that section Decaloba originated in Central America around 10.4 Ma, and then dispersed to South America, the Greater Antilles, and the Bahamas. The South American clade diversified in the Northern Andes and then dispersed to the rest of South America, and Lesser Antilles. Results suggest that both long-distance dispersal and colonization of newly available habitats (i.e., in the Andes) likely promoted diversification of this clade. This study also illustrates how using herbarium specimens and a RAD-seq approach can produce phylogenies for broadly distributed, highly diverse, and poorly accessible groups of plants where field collections would be unfeasible.

Divergence, gene flow, and the origin of leapfrog geographic distributions: The history of colour pattern variation in Phyllobates poison-dart frogs

The geographic distribution of phenotypic variation among closely related populations is a valuable source of information about the evolutionary processes that generate and maintain biodiversity. Leapfrog distributions, in which phenotypically similar populations are disjunctly distributed and separated by one or more phenotypically distinct populations, represent geographic replicates for the existence of a phenotype, and are therefore especially informative. These geographic patterns have mostly been studied from phylogenetic perspectives to understand how common ancestry and divergent evolution drive their formation. Other processes, such as gene flow between populations, have not received as much attention. Here, we investigate the roles of divergence and gene flow between populations in the origin and maintenance of a leapfrog distribution in Phyllobates poison frogs. We found evidence for high levels of gene flow between neighbouring populations but not over long distances, indicating that gene flow between populations exhibiting the central phenotype may have a homogenizing effect that maintains their similarity, and that introgression between 'leapfroging' taxa has not played a prominent role as a driver of phenotypic diversity in Phyllobates. Although phylogenetic analyses suggest that the leapfrog distribution was formed through independent evolution of the peripheral (i.e. leapfrogging) populations, the elevated levels of gene flow between geographically close populations poise alternative scenarios, such as the history of phenotypic change becoming decoupled from genome-averaged patterns of divergence, which we cannot rule out. These results highlight the importance of incorporating gene flow between populations into the study of geographic variation in phenotypes, both as a driver of phenotypic diversity and as a confounding factor of phylogeographic inferences.

Evidence for the Pleistocene Arc Hypothesis from genome-wide SNPs in a Neotropical dry forest specialist, the Rufous-fronted Thornbird (Furnariidae: Phacellodomus rufifrons)

South American dry forests have a complex and poorly understood biogeographic history. Based on the fragmented distribution of many Neotropical dry forest species, it has been suggested that this biome was more widely distributed and contiguous under drier climate conditions in the Pleistocene. To test this scenario, known as the Pleistocene Arc Hypothesis, we studied the phylogeography of the Rufous-fronted Thornbird (Phacellodomus rufifrons), a widespread dry forest bird with a disjunct distribution closely matching that of the biome itself. We sequenced mtDNA and used ddRADseq to sample 7,167 genome-wide single-nucleotide polymorphisms from 74 P. rufifrons individuals across its range. We found low genetic differentiation over two prominent geographic breaks - particularly across a 1,000 km gap between populations in Bolivia and Northern Peru. Using demographic analyses of the joint site frequency spectrum, we found evidence of recent divergence without subsequent gene flow across those breaks. By contrast, parapatric morphologically distinct populations in northeastern Brazil show high genetic divergence with evidence of recent gene flow. These results, in combination with our paleoclimate species distribution modelling, support the idea that currently disjunct patches of dry forest were more connected in the recent past, probably during the Middle and Late Pleistocene. This notion fits the major predictions of the Pleistocene Arc Hypothesis and illustrates the importance of comprehensive genomic and geographic sampling for examining biogeographic and evolutionary questions in complex ecosystems like Neotropical dry forests.

Systematics of a Neotropical clade of dead-leaf-foraging antwrens (Aves: Thamnophilidae; Epinecrophylla)

The stipple-throated antwrens of the genus Epinecrophylla (Aves: Thamnophilidae) are represented by eight species primarily found in the lowlands of the Amazon Basin and the Guiana Shield. The genus has a long and convoluted taxonomic history, with many attempts made to address the taxonomy and systematics of the group. Here we employ massively parallel sequencing of thousands of ultraconserved elements (UCEs) to provide both the most comprehensive subspecies-level phylogeny of Epinecrophylla antwrens and the first population-level genetic analyses for most species in the genus. Most of our results are robust to a diversity of phylogenetic and population genetic methods, but we show that even with thousands of loci we are unable to fully resolve the relationships between some western Amazonian species in the haematonota group. We uncovered phylogenetic relationships between taxa and patterns of population structure that are discordant with both morphology and current taxonomy. For example, we found deep genetic breaks between taxa in the ornata group that are currently regarded as species, and in the haematonota and leucophthalma groups we found paraphyly at the species and subspecies levels, respectively. As has been found in many Amazonian taxa, our phylogenetic results show that the major river systems of the Amazon Basin appear to have an effect on the genetic structure and range limits within Epinecrophylla. Our population genetics analyses showed extensive admixture between some taxa despite their deep genetic divergence. We present a revised taxonomy for the group and suggest areas for further study.