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Dry forest bird communities in South America are often fragmented by intervening mountains and rainforests, generating high local endemism. The historical assembly of communities often results from dynamic processes linked to numerous population histories among co-distributed species. Nevertheless, species may diversify in the same way through time...
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... immaculatus. We included 9-14 individuals per population, all from vouchered specimens (Table S1, Supporting information). We also included one outgroup taxon that was sister to each pair (Tham- nophilus bridgesi; Melanopareia maximiliani; Campy- lorhynchus albobrunneus; Mimus saturninus; Arremon aurantiirostris; Saltator striatipectus from Panama). ...
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... collected thousands of loci and SNPs for six taxon (subspecies or species) pairs from 9-14 individuals per population that have distinct taxa in the Tumbes and Mara~ n on Valley of northwestern South America (Table S1, Supporting information). For convenience, we will refer to these taxon pairs by their generic names: Melanopareia, Thamnophilus, Campylorhynchus, Mimus, Arremon and Saltator. ...
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... multiplexed 136 sam- ples on two lanes of an Illumina HiSeq 2500. This pro- duced an average of 12 654 clusters per sample with a mean coverage depth of 199 (SD = 769) for all ingroup samples (except three that were omitted), where 46% of the clusters had a mean depth >59 (mean = (Table 1). We also col- lected data from one outgroup per taxon pair with the number of loci varying from 4 to 2770. ...
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... n = 5255; Saltator: n = 7186 (Table 1). STRUCTURE analysis indicated that the most likely number of clus- ters was two (K = 2) for each taxon pair except for Thamnophilus and Campylorhynchus, which were best explained by three clusters (K = 3; Table S2; Figs 2, S3, Supporting information; see Fig. S2, Supporting infor- mation for museum Accession nos for each individual). ...
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Citations
... Instead, it seems more plausible that non-homogeneous elevation along the Andes acts as a semi-permeable barrier that permits side-to-side dispersal (Smith et al., 2014;Rodriguez-Muñoz et al., 2022). Indeed, the northern and central Andes have five altitudinal depressions which likely have facilitated dispersal (Chapman, 1917(Chapman, , 1926 as suggested by ecological simulations (Cadena et al., 2016), paleontological data (Montes et al., 2021), and genetic evidence (Smith et al., 2014;Oswald et al., 2017). However, there are not many studies exploring the effect of these latitudinal depression using genomic approaches, even when they greatly improve the testing of phylogeographical hypotheses by facilitating the estimation of evolutionary parameters (McGaughran, 2015;Blanchet et al., 2017). ...
... However, there are not many studies exploring the effect of these latitudinal depression using genomic approaches, even when they greatly improve the testing of phylogeographical hypotheses by facilitating the estimation of evolutionary parameters (McGaughran, 2015;Blanchet et al., 2017). To date, only a single study explores the role of altitudinal depressions in connecting populations separated by the Andes using genomics (Oswald et al., 2017). This study found that a diversification model of isolation with asymmetric gene flow, at the Porculla Pass (central Andes), was common for six different pairs of bird species/subspecies with similar distributions. ...
... This suggests that dispersion through the Central Andes, rather than vicariance, is the most plausible hypothesis to explain our results. This hypothesis is further supported by reports of past and current dispersion of lowland species through the Central Andes, particularly at the Porculla pass, in birds and parasites (Cadena et al., 2016;Oswald et al., 2017;Van den Broeck et al., 2020). It is possible that some dispersal through the central Andes occurred in the recent past, as suggested by some individuals from Jaen nested within EA, that exhibited a low level (4.8%-9.5%) of shared ancestry with DP. ...
Geographic barriers, such as mountain ranges, impede genetic exchange among populations, promoting diversification and speciation. The effectiveness of these barriers in limiting gene flow varies between lineages due to each species’ unique dispersal modes and capacities. Our understanding of how the Andes orogeny contributes to species diversification comes from well-studied vertebrates and a few insects, neglecting organisms unable to fly or walk long distances. Additionally, although the Andean altitude is usually assumed to be the driver of diversification, it is not often formally tested. This limits our understanding of how landscape changes, particularly altitude, influence population structure. Some arachnids, such as the colorful spider Gasteracantha cancriformis have been hypothesized to disperse long distances via ballooning (i.e., using their silk to interact with the wind). Still, we do not know how the environment and geography shape its genetic diversity. To address this question, we sampled thousands of loci across the distribution of this spider and implemented population genetics, phylogenetic, and landscape genetic analyses. We identified two genetically distinct groups structured by the Central Andes and a third less structured group in the northern Andes that shares ancestry with the previous two. This structure is largely explained by the elevation along the Andes, which decreases in some regions, facilitating cross-Andean dispersal and gene flow. Our findings support that elevation in the Andes plays a major role in structuring populations in South America, but the strength of this barrier can be defeated by organisms with long-distance dispersal modes together with altitudinal depressions
... Andes have five altitudinal depressions which likely have facilitated dispersal (Chapman, 1917(Chapman, , 1926 as suggested by ecological simulations (Cadena et al., 2016), paleontological data (Montes et al., 2021), and genetic evidence (Dick et al., 2007;Oswald et al., 2017;Rymer et al., 2013;Smith et al., 2014). However, there are not many studies exploring the effect of these latitudinal depressions using genomic approaches, even when they greatly improve the testing of phylogeographical hypotheses by facilitating the estimation of evolutionary parameters (Blanchet et al., 2017;McGaughran, 2015). ...
... However, there are not many studies exploring the effect of these latitudinal depressions using genomic approaches, even when they greatly improve the testing of phylogeographical hypotheses by facilitating the estimation of evolutionary parameters (Blanchet et al., 2017;McGaughran, 2015). To date, only a single study explores the role of altitudinal depressions in connecting populations separated by the Andes using genomics (Oswald et al., 2017). This study found that a diversification model of isolation with asymmetric gene flow, at the Porculla Pass (Río Marañon Valley in the Central Andes), was common for six different pairs of bird species/subspecies with similar distributions. ...
... This hypothesis is further supported by reports of past and current (Cadena et al., 2016;Oswald et al., 2017;Van den Broeck et al., 2020). It is possible that some dispersal through the Central Andes occurred in the recent past, as suggested by some individuals from Jaen nested within EA, that exhibited a low level (4.8%-9.5%) of shared ancestry with DP. ...
Geographical barriers like mountain ranges impede genetic exchange among populations, promoting diversification. The effectiveness of these barriers in limiting gene flow varies between lineages due to each species' dispersal modes and capacities. Our understanding of how the Andes orogeny contributes to species diversification comes from well‐studied vertebrates and a few arthropods and plants, neglecting organisms unable to fly or walk long distances. Some arachnids, such as Gasteracantha cancriformis , have been hypothesized to disperse long distances via ballooning (i.e. using their silk to interact with the wind). Yet, we do not know how the environment and geography shape its genetic diversity. Therefore, we tested whether the Andes contributed to the diversification of G. cancriformis acting as an absolute or semi‐permeable barrier to genetic connectivity between populations of this spider at opposite sides of the mountain range. We sampled thousands of loci across the distribution of the species and implemented population genetics, phylogenetic, and landscape genetic analyses. We identified two genetically distinct groups structured by the Central Andes, and a third less structured group in the Northern Andes that shares ancestry with the previous two. This structure is largely explained by the altitude along the Andes, which decreases in some regions, possibly facilitating cross‐Andean dispersal and gene flow. Our findings support that altitude in the Andes plays a major role in structuring populations in South America, but the strength of this barrier can be overcome by organisms with long‐distance dispersal modes together with altitudinal depressions.
... We found evidence of asynchronous divergences for the Andes- (Bocalini et al., 2021(Bocalini et al., , 2023Kopuchian et al., 2020;Lavinia et al., 2019;Leaché et al., 2020;Oswald et al., 2017), suggesting that this phenomenon is a common scenario across codistributed taxa. Our results for the Andes-Atlantic Forest split contradict the premise that closely related codistributed lineages should have similar responses to the same factors (Papadopoulou & Knowles, 2016). ...
Common distributional patterns have provided the foundations of our knowledge of Neotropical biogeography. A distinctive pattern is the "circum-Amazonian distribu-tion", 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 phylogeo-graphical 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 inter-connectedness 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.
... Por otra parte, los bosques húmedos y los parches de bosque estacionalmente secos de la vertiente Atlántica se concentraron en un mismo clúster. La disimilitud en la composición de especies de plantas y animales entre diferentes áreas ocupadas por bosques secos ha sido previamente documentada (Banda et al., 2016;Oswald et al., 2017; Ríos-Muñoz y Navarro-Sigüenza, 2012) y se ha sugerido que se debe a una compleja historia evolutiva y eventos de diferenciación que han ocurrido de forma independiente en los parches formados por estas comunidades. Nuestro trabajo corrobora estos hallazgos y además indica que, en el caso de la comparación entre los bosques secos de México, la disimilitud no solo se debe a los procesos de divergencia evolutiva que han caracterizado la historia biogeográfica del Pacífico, sino también a un efecto de la colonización de los parches distribuidos en el Golfo de México por taxones presentes en los bosques húmedos aledaños. ...
Presentamos un análisis de la diversidad y de los patrones biogeográficos de 260 especies de aves residentes de los bosques tropicales de México, realizado a partir de datos históricos (recolectados entre el siglo XVIII y 2007) y registros de presencia de la última década (2013-2023). Realizamos comparaciones del número y cambio de composición de especies, considerando las matrices de distribución “histórica” y “actual”, y un análisis de parsimonia de endemismos. De acuerdo con los datos históricos, la mayor riqueza de especies se localiza en la vertiente del Golfo de México y la península de Yucatán, mientras que los bosques estacionalmente secos de la costa del Pacífico y la Cuenca del Balsas presentaron los valores más altos de especies endémicas. Sin embargo, los datos recopilados en la última década muestran una disminución significativa del número de especies en todas las áreas analizadas. La estimación de la diversidad beta indicó valores elevados de cambio en la composición de especies para las matrices evaluadas. La hipótesis biogeográfica obtenida indica la existencia de 2 grandes grupos: i) vertiente pacífica de México y la Cuenca del Balsas y ii) norte de la provincia Veracruzana, el norte del Istmo de Tehuantepec y la península de Yucatán.
... fossoria) is predicted to exhibit stronger sexual isolation due to the lower fitness of hybrids (Fig. S3). Despite asymmetric migration and asymmetric RI being commonly found across different study systems (Bolnick et al. 2008;Lowry et al. 2008a;Oswald et al. 2017) and the understanding that migration rate is important with respect to reinforcement (Servedio and Noor 2003), few studies have formally described the relationship between asymmetry in migration and asymmetry in the evolution of RI (but see Yukilevich 2012; Suni and Hopkins 2018). ...
Ecology and geography can play important roles in the evolution of reproductive isolation across the speciation continuum, but few studies address both at the later stages of speciation. This notable gap in knowledge arises from the fact that traditional ecological speciation studies have predominantly focused on the role of ecology in initiating the speciation process, while many studies exploring the effect of geography (e.g., reinforcement) concentrate on species pairs that lack divergent ecological characteristics. We simultaneously examine the strength of habitat isolation and sexual isolation among three closely related species of Belonocnema gall-forming wasps on two species of live oaks, Quercus virginiana and Q. geminata, that experience divergent selection from their host plants and variable rates of migration due to their geographic context. We find that the strength of both habitat isolation and sexual isolation is lowest among allopatric species pairs with the same host plant association, followed by allopatric species with different host plant associations, and highest between sympatric species with different host-plant associations. This pattern suggests that divergent selection due to different host use interacts with geography in the evolution of habitat isolation and sexual isolation during the later stages of speciation of Belonocnema wasps.
... in which the divergence times do not always match the origin of the geographical barrier, and there are some signatures of past or ongoing gene flow [2][3][4]. This suggests that the dispersal abilities of each taxon are a determining factor of its demographic history. ...
... Crossing the Andes is a plausible hypothesis because its elevation varies throughout its range. In fact, there is palaeontologic [7] and genetic evidence [3] that described five altitudinal depressions [8], which likely facilitated dispersal of taxa. ...
... Unexpectedly, we found that Dry Pacific (Western Perú and Ecuador; DP) was more closely related to the Eastern side of the Andes (EA) rather than the Western side of the Andes (WA; excluding the Dry Pacific populations), which is counterintuitive since dispersal along the Pacific coast would presumably be easier than crossing the Andes. However, this pattern has also been documented in birds distributed in dry tropical forests at both sides of the Central Andes [3,38,39]. Interestingly, there is a humidity transition right on the Equator that is leading to a biome shift [43], which may be contributing to maintaining the DP and WA lineages apart. Even so, we observed some shared haplotypes between these lineages, suggesting that the barrier that separates them, whatever it is, is permeable. ...
Species with large distributions provide unique opportunities to test how geography has influenced biotic diversification. In this work, we aimed to explore the effect of geographic barriers on the distribution of the phenotypic and genetic variation of a spider species that is widespread in continental and insular America. We obtained an alignment of the mitochondrial locus Cytochrome Oxidase I (COI) for 408 individuals across the geographic range of Gasteracantha cancriformis. We used phylogenetics, population genetics, and morphology to explore the genetic and phenotypic variation of this species. We found five genetically differentiated and geographically structured populations. Three of them are distributed in continental America, separated by the Andes mountains, and two are in the Caribbean and Galapagos Islands. Some of these geographic clades shared haplotypes between them, which may be a consequence of dispersal. We detected at least 20 phenotypes of G. cancriformis, some of which were exclusive to a geographic region, while others occurred in multiple regions. We did not observe well-defined morphological differences across male genitalia. This evidence suggests that G. cancriformis is a widespread species with high phenotypic variation that should be explored in more depth.
... . In contrast, when communities have species that vary in dispersal ability, niche breadth, or population history, differentiation and diversification may be asynchronous across taxa based on those species' intrinsic characteristics (e.g., Naka & Brumfield, 2018;Oswald et al., 2017;Papadopoulou et al., 2009). ...
Taxon‐specific characteristics and extrinsic climatic and geological forces may both shape population differentiation and speciation. In geographically and taxonomically focused investigations, differentiation may occur synchronously as species respond to the same external conditions. Conversely, when evolution is investigated in taxa with largely varying traits, population differentiation and speciation is complex and shaped by interactions of Earth’s template and species‐specific traits. As such, it is important to characterize evolutionary histories broadly across the tree of life, especially in geographic regions that are exceptionally diverse and under pressures from human activities such as in biodiversity hotspots. Here, using whole‐genome sequencing data, we characterize genomic variation in populations of six Ethiopian Highlands forest bird species separated by a lowland biogeographic barrier, the Great Rift Valley (GRV). In all six species, populations on either side of the GRV exhibited significant but varying levels of genetic differentiation. Species’ dispersal ability was negatively correlated with levels of population differentiation. Isolation with migration models indicated varied patterns of population differentiation and connectivity among populations of the focal species. We found that demographic histories—estimated for each individual—varied by both species and population but were consistent between individuals of the same species and sampling region. We found that genomic diversity varied by half an order of magnitude across species, and that this variation could largely be explained by the harmonic mean of effective population size over the past 200,000 years. Overall, we found that even in highly dispersive species like birds, the GRV acts as a substantial biogeographic barrier.
... In speciation scenarios dominated by geologic or climatic change, entire communities may differentiate in pulses synchronous with the changes in the Earth's template (e.g., Barber & Klicka, 2010;Musher et al., 2019;O'Connell et al., 2018). In contrast, when communities have species that vary in dispersal ability, niche breadth, or population history, diversification may be asynchronous across taxa based on those species' intrinsic characteristics (e.g., Naka & Brumfield, 2018;Oswald et al., 2017;Papadopoulou et al., 2009). ...
Taxon-specific characteristics and extrinsic climatic and geological forces may both shape population differentiation and speciation. In geographically and taxonomically focused investigations, differentiation may occur synchronously as species respond to the same external conditions. Conversely, when evolution is investigated in taxa with largely varying traits, population differentiation and speciation is complex and shaped by interactions of Earth’s template and species-specific traits. As such, it is important to characterize evolutionary histories broadly across the tree of life, especially in geographic regions that are exceptionally diverse and under pressures from human activities such as in biodiversity hotspots. Here, using whole-genome sequencing data, we characterize genomic variation in populations of six Ethiopian Highlands forest bird species separated by a lowland biogeographic barrier, the Great Rift Valley (GRV). In all six species, populations on either side of the GRV exhibited significant but varying levels of genetic differentiation. Species’ dispersal ability was negatively correlated with levels of population differentiation. Isolation with migration models indicated varied patterns of population differentiation and connectivity among populations of the focal species. We found that demographic histories—estimated for each individual—varied by both species and population but were consistent between individuals of the same species and sampling region. We found that genomic diversity varied by half an order of magnitude across species, and that this variation could largely be explained by the harmonic mean of effective population size over the past 200,000 years. Overall, we found that even in highly dispersive species like birds, the GRV acts as a substantial biogeographic barrier.
... Recent studies have suggested that dispersal limitation in the Andes, occurring after major uplift episodes, is an important driver of Neotropical bird distribution (Cadena et al., 2016;Oswald et al., 2017;Smith et al., 2014). Bird taxonomic and phylogenetic β-diversity was more similar within the northern and southern group of paramos identified in our spatial analyses then between these distinct groups. ...
Aim
The role of evolutionary history in shaping the patterns of species distributions is generally explored at coarse spatial extents. However, at small spatial extents, the combined effects of history and ecological processes on local diversity has received less attention. We test the relative importance of historical and ecological factors on the spatial distribution of bird taxonomic (TβD) and phylogenetic (PβD) β‐diversity on Paramo ecosystems.
Location
South‐western Colombia.
Taxon
Andean bird species.
Methods
Using point occurrence data for 175 bird species recorded in 11 Paramos, we calculated TβD and PβD. We used a lineage through time plot to evaluate the association between bird species richness and the time of Andean uplift and Quaternary climatic oscillations. To capture range dynamics associated with past climate oscillations, we delimited paramos using connectivity matrices based on four distance criteria (i.e. paramos connected at 20, 25, 35 and 55 km apart) to compute Moran's eigenvectors maps. Then, we evaluated the relative importance of altitude, past climatic oscillations, current climate and connectivity on the spatial distribution of avian TβD and PβD.
Results
Two‐thirds of the bird species in the paramos are recent and emerged after the late Miocene/early Pliocene. The average TβD was four times higher than the average PβD indicating that paramo assemblages harbour distinct, but closely related, species. We found that distribution of β‐diversity had a spatial structure resulting in two groups of paramos – one in the north of our study area containing four paramos and other in the south with seven paramos. This spatial structure together with past climate conditions explained the variation of both TβD and PβD.
Main conclusions
Our results are consistent with the hypothesis that patterns of β‐diversity reflect the complex history of Andean region including mountain uplift and climatic oscillations in the Pleistocene. We demonstrated that the integration of different facets of β‐diversity into a community ecology framework provides new insights about the historical and ecological factors responsible for generating the patterns of species distribution.
... (1,300); (1, 100)) (Gronau et al. 2011;Smith et al. 2014;Oswald et al. 2017;Bocalini et al. 2021) because we were interested in assessing how the choice of prior distributions affected estimates of divergence times and effective population sizes. Because we performed these three different analyses with two RAD datasets (6,000 and 10,000 loci), this resulted in a total of six G-PhoCS runs. ...
Secondary contact between species often results in the formation of a hybrid zone, with the eventual fates of the hybridizing species dependent on evolutionary and ecological forces. We examine this process in the Amazon Basin by conducting the first genomic and phenotypic characterization of the hybrid zone formed after secondary contact between two obligate army-ant-followers: the White-breasted Antbird (Rhegmatorhina hoffmannsi) and the Harlequin Antbird (R. berlepschi). We found a major geographic displacement (∼120 km) between the mitochondrial and nuclear clines, and we explore potential hypotheses for the displacement, including sampling error, genetic drift, and asymmetric cytonuclear incompatibilities. We cannot exclude roles for sampling error and genetic drift in contributing to the discordance; however, the data suggest expansion and unidirectional introgression of hoffmannsi into the distribution of berlepschi.
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