Genomic tests of the species-pump hypothesis: Recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands

A historical stepping-stone path for an island-colonizing cactus across a submerged "bridge" archipelago

Here we use population genomic data (ddRAD-Seq) and ecological niche modeling to test biogeographic hypotheses for the divergence of the island-endemic cactus species Cereus insularis Hemsl. (Cereeae; Cactaceae) from its sister species C. fernambucensis Lem. The Cereus insularis grows in the Fernando de Noronha Islands (FNI), a Neotropical archipelago located 350 km off the Brazilian Atlantic Forest (BAF) coast. Phylogeographic reconstructions support a northward expansion by the common ancestor of C. insularis and C. fernambucensis along the mainland BAF coast, with C. insularis diverging from the widespread mainland taxon C. fernambucensis after colonizing FNI in the late Pleistocene. The morphologically distinct C. insularis is monophyletic and nested within C. fernambucensis, as expected from a progenitor-derivative speciation model. We tested alternative biogeographic and demographic hypotheses for the colonization of the FNI using Approximate Bayesian Computation. We found the greatest support for a stepping-stone path that emerged during periods of decreased sea level (the "bridge" hypothesis), in congruence with historical ecological niche modeling that shows highly suitable habitats on stepping-stone islands during glacial periods. The outlier analyses reveal signatures of selection in C. insularis, suggesting a putative role of adaptation driving rapid anagenic differentiation of this species in FNI.

Pleistocene diversification of unifoliolate-leaved Lupinus (Leguminosae: Papilionoideae) in Florida

The importance and prevalence of recent ice-age and post-glacial speciation and species diversification during the Pleistocene across many organismal groups and physiographic settings are well established. However, the extent to which Pleistocene diversification can be attributed to climatic oscillations and their effects on distribution ranges and population structure remains debatable. In this study, we use morphologic, geographic and genetic (RADseq) data to document Pleistocene speciation and intra-specific diversification of the unifoliolate-leaved clade of Florida Lupinus, a small group of species largely restricted to inland and coastal sand ridges across the Florida peninsula and panhandle. Phylogenetic and demographic analyses alongside morphological and geographic evidence suggest that recent speciation and intra-specific divergence within this clade were driven by a combination of non-adaptive allopatric divergence caused by edaphic niche conservatism and opportunities presented by the emergence of new post-glacial sand ridge habitats. These results highlight the central importance of even modest geographic isolation and short periods of allopatric divergence following range expansion in the emergence of new taxa and add to the growing evidence that Pleistocene climatic oscillations may contribute to rapid diversification in a myriad of physiographic settings. Furthermore, our results shed new light on long-standing taxonomic debate surrounding the number of species in the Florida unifoliate Lupinus clade providing support for recognition of five species and a set of intra-specific variants. The important conservation implications for the narrowly restricted, highly endangered species Lupinus aridorum, which we show to be genetically distinct from its sister species Lupinus westianus, are discussed.

Contrasting whole-genome and reduced representation sequencing for population demographic and adaptive inference: an alpine mammal case study

Genomes capture the adaptive and demographic history of a species, but the choice of sequencing strategy and sample size can impact such inferences. We compared whole genome and reduced representation sequencing approaches to study the population demographic and adaptive signals of the North American mountain goat (Oreamnos americanus). We applied the restriction site-associated DNA sequencing (RADseq) approach to 254 individuals and whole genome resequencing (WGS) approach to 35 individuals across the species range at mid-level coverage (9X) and to 5 individuals at high coverage (30X). We used ANGSD to estimate the genotype likelihoods and estimated the effective population size (Ne), population structure, and explicitly modelled the demographic history with δaδi and MSMC2. The data sets were overall concordant in supporting a glacial induced vicariance and extremely low Ne in mountain goats. We evaluated a set of climatic variables and geographic location as predictors of genetic diversity using redundancy analysis. A moderate proportion of total variance (36% for WGS and 21% for RADseq data sets) was explained by geography and climate variables; both data sets support a large impact of drift and some degree of local adaptation. The empirical similarities of WGS and RADseq presented herein reassuringly suggest that both approaches will recover large demographic and adaptive signals in a population; however, WGS offers several advantages over RADseq, such as inferring adaptive processes and calculating runs-of-homozygosity estimates. Considering the predicted climate-induced changes in alpine environments and the genetically depauperate mountain goat, the long-term adaptive capabilities of this enigmatic species are questionable.

Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods, sample size and population structure

The distribution of fitness effects (DFE) of new mutations has been of interest to evolutionary biologists since the concept of mutations arose. Modern population genomic data enable us to quantify the DFE empirically, but few studies have examined how data processing, sample size and cryptic population structure might affect the accuracy of DFE inference. We used simulated and empirical data (from Arabidopsis lyrata) to show the effects of missing data filtering, sample size, number of single nucleotide polymorphisms (SNPs) and population structure on the accuracy and variance of DFE estimates. Our analyses focus on three filtering methods-downsampling, imputation and subsampling-with sample sizes of 4-100 individuals. We show that (1) the choice of missing-data treatment directly affects the estimated DFE, with downsampling performing better than imputation and subsampling; (2) the estimated DFE is less reliable in small samples (<8 individuals), and becomes unpredictable with too few SNPs (<5000, the sum of 0- and 4-fold SNPs); and (3) population structure may skew the inferred DFE towards more strongly deleterious mutations. We suggest that future studies should consider downsampling for small data sets, and use samples larger than 4 (ideally larger than 8) individuals, with more than 5000 SNPs in order to improve the robustness of DFE inference and enable comparative analyses.

Biogeography of the Sunda Shelf revisited: Insights from Macaranga section Pruinosae (Euphorbiaceae)

The Southeast Asian region of Sundaland is among the world’s major biodiversity hotspots. The region’s biodiversity coupled with its complex and dynamic geographic and climatic histories makes it an ideal region to study the various factors that determine the diversification and distribution patterns of tropical biota. Here we investigate the biogeographic patterns in the partly myrmecophytic Macaranga section Pruinosae to reveal some of the factors that play a role in determining the distribution of biota in Sundaland. We used single nucleotide polymorphisms (SNP) data derived from GBS, a next generation sequencing technique, in maximum likelihood and cluster analyses to determine phylogenetic relationships and population structures within this taxonomic section. Bayesian inference based on secondary calibration points and ancestral area reconstruction analyses were performed to infer spatial–temporal origins of the major lineages in the section. The results from these analyses were further substantiated using nuclear microsatellite data obtained from a broader sample set of two widely distributed species within the section: Macaranga gigantea and Macaranga pruinosa. Phylogenetic and cluster analyses reveal four well-defined, discrete species groups within section Pruinosae, all of which but one originated in Borneo with the crown node dated at 3.58 mya. Biogeographic patterns within the species reveal a biogeographic barrier between east and west Sundaland besides bringing to light the role played by various geological factors, especially the Crocker Range, on Borneo. Patterns also reveal a biogeographic barrier between the Bangka/Belitung islands and Sumatra for ant-free, swamp-adapted species. This study provides evidence that geographic barriers, edaphic conditions, and ecological adaptations are tightly linked and that their mutual interaction determines the diversification and distribution of species.

Genomic evidence of speciation by fusion in a recent radiation of grasshoppers

Postdivergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (i.e., adaptive introgression) to the formation of new species (i.e., hybrid speciation). Although neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the dual feeding regime (based on both scrub legumes and gramineous herbs) of the taxonomically controversial grasshopper Chorthippus saulcyi algoaldensis resulted from hybridization between the sister taxa C. binotatus (that exclusively feeds on scrub legumes) and C. saulcyi (that only feeds on gramineous herbs). Genetic clustering analyses and inferences from coalescent-based demographic simulations confirm that C. s. algoaldensis represents an independently evolving lineage and support the ancient hybrid origin of this taxon (about 1.4 Ma), which sheds light on its uncertain phylogenetic position and might explain its broader trophic niche. We propose a Pleistocene hybrid speciation model where range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate their long-term persistence through geographic isolation from parental forms in topographically complex landscapes.

Diverge and Conquer: Phylogenomics of southern Wallacean forest skinks (Genus: Sphenomorphus) and their colonization of the Lesser Sunda Archipelago

The archipelagos of Wallacea extend between the Sunda and Sahul Shelves, serving as a semipermeable two-way filter influencing faunal exchange between Asia and Australo-Papua. Forest skinks (Genus Sphenomorphus) are widespread throughout southern Wallacea and exhibit complex clinal, ontogenetic, sexual, and seasonal morphological variation, rendering species delimitation difficult. We screened a mitochondrial marker for 245 Sphenomorphus specimens from this area to inform the selection of 104 samples from which we used targeted sequence capture to generate a dataset of 1154 nuclear genes (∼1.8 Mb) plus complete mitochondrial genomes. Phylogenomic analyses recovered many deeply divergent lineages, three pairs of which are now sympatric, that began to diversify in the late Miocene shortly after the oldest islands are thought to have become emergent. We infer a complex and nonstepping-stone pattern of island colonization, with the group having originated in the Sunda Arc islands before using Sumba as a springboard for colonization of the Banda Arcs. Estimates of population structure and gene flow across the region suggest total isolation except between two Pleistocene Aggregate Island Complexes that become episodically land-bridged during glacial maxima. These historical processes have resulted in at least 11 Sphenomorphus species in the region, nine of which require formal description. This fine-scale geographic partitioning of undescribed species highlights the importance of utilizing comprehensive genomic studies for defining biodiversity hotspots to be considered for conservation protection.

Inferring the demographic history of the North American firefly Photinus pyralis

The firefly Photinus pyralis inhabits a wide range of latitudinal and ecological niches, with populations living from temperate to tropical habitats. Despite its broad distribution, its demographic history is unknown. In this study, we modelled and inferred different demographic scenarios for North American populations of P. pyralis, which were collected from Texas to New Jersey. We used a combination of ABC techniques (for multi-population/colonization analyses) and likelihood inference (dadi, StairwayPlot2, PoMo) for single-population demographic inference, which proved useful with our RAD data. We uncovered that the most ancestral North American population lays in Texas, which further colonized the Central region of the US and more recently the North Eastern coast. Our study confidently rejects a demographic scenario where the North Eastern populations colonized more southern populations until reaching Texas. To estimate the age of divergence between of P. pyralis, which provides deeper insights into the history of the entire species, we assembled a multi-locus phylogenetic data covering the genus Photinus. We uncovered that the phylogenetic node leading to P. pyralis lies at the end of the Miocene. Importantly, modelling the demographic history of North American P. pyralis serves as a null model of nucleotide diversity patterns in a widespread native insect species, which will serve in future studies for the detection of adaptation events in this firefly species, as well as a comparison for future studies of other North American insect taxa.

Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains

The Eastern Arc Mountains in Tanzania represent a hotspot for biological diversity of global importance. The level of endemism is high, and Eastern Arc biodiversity has been studied extensively in vertebrates and invertebrates, including millipedes. However, millipede evolution is vastly understudied at the molecular level. Therefore, we used next-generation ‘shotgun’ sequencing to obtain mitochondrial genome sequences of 26 museum specimens, representing six genera and 12 millipede species found across the Eastern Arc Mountains. Bayesian and maximum likelihood methods yielded consistent topologies with high node support, confirming a high level of congruence between molecular and morphological analyses. The only exception was a Tropostreptus sigmatospinus individual from Zanzibar, which was placed outside an otherwise monophyletic group consisting of mainland individuals of the same assumed species. For two species with a distribution across several mountain blocks (Tropostreptus sigmatospinus and Tropostreptus hamatus), each mountain population represents a distinct monophyletic lineage. In contrast, we also observe that distinct species exist sympatrically in the same montane forests, indicative of older speciation events that are not defined by current forest distribution. Our results are important for understanding speciation mechanisms in montane rain forests and highlight that ethanol-preserved invertebrates exhibit a tremendous potential for genomic analyses.

A snapshot of progenitor-derivative speciation in Iberodes (Boraginaceae)

Traditional classification of speciation modes has focused on physical barriers to gene flow. Allopatric speciation with complete reproductive isolation is viewed as the most common mechanism of speciation. Parapatry and sympatry, by contrast, entail speciation in the face of ongoing gene flow, making them more difficult to detect. The genus Iberodes (Boraginaceae, NW Europe) comprises five species with contrasting morphological traits, habitats, and species distributions. Based on the predominance of narrow and geographically distant endemic species, we hypothesized that geographic barriers were responsible for most speciation events in Iberodes. We undertook an integrative study including: (i) phylogenomics through restriction-site associated DNA sequencing, (ii) genetic structure analyses, (iii) demographic modeling, (iv) morphometrics, and (v) climatic niche modeling and niche overlap analysis. Results revealed a history of recurrent progenitor-derivative speciation manifested by a paraphyletic pattern of nested species differentiation. Budding speciation mediated by ecological differentiation is suggested for the coastal lineage, deriving from the inland widespread I. linifolia during Late Pliocene. Meanwhile, geographic isolation followed by niche shifts are suggested for the more recent differentiation of the coastland taxa. Our work provides a model for distinguishing speciation via ecological differentiation of peripheral, narrowly endemic I. kuzinskyanae and I. littoralis from a widespread extant ancestor, I. linifolia. Ultimately, our results illustrate a case of Pliocene speciation in the probable absence of geographic barriers and get away from the traditional cladistic perspective of speciation as producing two species from an extinct ancestor, thus reminding us that phylogenetic trees tell only part of the story.

Geographical isolation versus dispersal: Relictual alpine grasshoppers support a model of interglacial diversification with limited hybridization

Alpine biotas are paradigmatic of the countervailing roles of geographical isolation and dispersal during diversification. In temperate regions, repeated distributional shifts driven by Pleistocene climatic oscillations produced both recurrent pulses of population fragmentation and opportunities for gene flow during range expansions. Here, we test whether a model of divergence in isolation vs. with gene flow is more likely in the diversification of flightless alpine grasshoppers of the genus Podisma from the Iberian Peninsula. The answer to this question can also provide key insights about the pace of evolution. Specifically, if the data fit a divergence in isolation model, this suggests rapid evolution of reproductive isolation. Genomic data confirm a Pleistocene origin of the species complex, and multiple analytical approaches revealed limited asymmetric historical hybridization between two taxa. Genomic-based demographic reconstructions, spatial patterns of genetic structure and range shifts inferred from palaeodistribution modelling suggest severe range contraction accompanied by declines in effective population sizes during interglacials (i.e., contemporary populations confined to sky islands are relicts) and expansions during the coldest stages of the Pleistocene in each taxon. Although limited hybridization during secondary contact leads to phylogenetic uncertainty if gene flow is not accommodated when estimating evolutionary relationships, all species exhibit strong genetic cohesiveness. Our study lends support to the notion that the accumulation of incipient differences during periods of isolation were sufficient to lead to lineage persistence, but also that the demographic changes, dispersal constraints and spatial distribution of the sky islands themselves mediated species diversification in temperate alpine biotas.

Genomic data support multiple introductions and explosive demographic expansions in a highly invasive aquatic insect

The study of the genetic makeup and demographic fate of alien species is essential to understand their capacity to recover from founder effects, adapt to new environmental conditions and, ultimately, become invasive and potentially damaging. Here, we employ genomic data to gain insights into key demographic processes that might help to explain the extraordinarily successful invasion of the Western Mediterranean region by the North American boatman Trichocorixa verticalis (Hemiptera: Corixidae). Our analyses revealed the genetic distinctiveness of populations from the main areas comprising the invasive range and coalescent-based simulations supported that they originated from independent introductions events probably involving different source populations. Testing of alternative demographic models indicated that all populations experienced a strong bottleneck followed by a recent and instantaneous demographic expansion that restored a large portion (>30%) of their ancestral effective population sizes shortly after introductions took place (<60 years ago). Considerable genetic admixture of some populations suggest that hypothetical barriers to dispersal (i.e., land and sea water) are permeable to gene flow and/or that they originated from introductions involving multiple lineages. This study demonstrates the repeated arrival of propagules with different origins and short time lags between arrival and establishment, emphasizing the extraordinary capacity of the species to recover from founder effects and genetically admix in invaded areas. This can explain the demonstrated capacity of this aquatic insect to spread and outcompete native species once it colonizes new suitable regions. Future genomic analyses of native range populations could help to infer the genetic makeup of introduced populations and track invasion routes.

Diversification, disparification and hybridization in the desert shrubs Encelia

There are multiple hypotheses for the spectacular plant diversity found in deserts. We explore how different factors, including the roles of ecological opportunity and selection, promote diversification and disparification in Encelia, a lineage of woody plants in the deserts of the Americas. Using a nearly complete species-level phylogeny based on double-digest restriction-aided sequencing along with a broad set of phenotypic traits, we estimate divergence times and diversification rates, identify instances of hybridization, quantify trait disparity and assess phenotypic divergence across environmental gradients. We show that Encelia originated and diversified recently (mid-Pleistocene) and rapidly, with rates comparable to notable adaptive radiations in plants. Encelia probably originated in the hot deserts of North America, with subsequent diversification across steep environmental gradients. We uncover multiple instances of gene flow between species. The radiation of Encelia is characterized by fast rates of phenotypic evolution, trait lability and extreme disparity across environments and between species pairs with overlapping geographic ranges. Encelia exemplifies how interspecific gene flow in combination with high trait lability can enable exceptionally fast diversification and disparification across steep environmental gradients.

Impact of Pleistocene Eustatic Fluctuations on Evolutionary Dynamics in Southeast Asian Biodiversity Hotspots

Pleistocene Climatic Fluctuations (PCF) are frequently highlighted as important evolutionary engines that triggered cycles of biome expansion and contraction. While there is ample evidence of the impact of PCF on biodiversity of continental biomes, the consequences in insular systems depend on the geology of the islands and the ecology of the taxa inhabiting them. The idiosyncratic aspects of insular systems are exemplified by the islands of the Sunda Shelf in Southeast Asia (Sundaland), where PCF-induced eustatic fluctuations had complex interactions with the geology of the region, resulting in high species diversity and endemism. Emergent land in Southeast Asia varied drastically with sea level fluctuations during the Pleistocene. Climate-induced fluctuations in sea level caused temporary connections between insular and continental biodiversity hotspots in Southeast Asia. These exposed lands likely had freshwater drainage systems that extended between modern islands: the Paleoriver Hypothesis. Built upon the assumption that aquatic organisms are among the most suitable models to trace ancient river boundaries and fluctuations of landmass coverage, the present study aims to examine the evolutionary consequences of PCF on the dispersal of freshwater biodiversity in Southeast Asia. Time-calibrated phylogenies of DNA-delimited species were inferred for six species-rich freshwater fish genera in Southeast Asia (Clarias, Channa, Glyptothorax, Hemirhamphodon, Dermogenys, Nomorhamphus). The results highlight rampant cryptic diversity and the temporal localization of most speciation events during the Pleistocene, with 88% of speciation events occurring during this period. Diversification analyses indicate that sea level-dependent diversification models poorly account for species proliferation patterns for all clades excepting Channa. Ancestral area estimations point to Borneo as the most likely origin for most lineages, with two waves of dispersal to Sumatra and Java during the last 5 Myr. Speciation events are more frequently associated with boundaries of the paleoriver watersheds, with 60%, than islands boundaries, with 40%. In total, one-third of speciation events are inferred to have occured within paleorivers on a single island, suggesting that habitat heterogeneity and factors other than allopatry between islands substantially affected diversification of Sundaland fishes. Our results suggest that species proliferation in Sundaland is not wholly reliant on Pleistocene sea-level fluctuations isolating populations on different islands.

An escape-to-radiate model for explaining the high plant diversity and endemism in campos rupestres†

With extraordinary levels of plant diversity and endemism, the Brazilian campos rupestres across the Espinhaço Range have a species/area ratio 40 times higher than the lowland Amazon. Although diversification drivers in campos rupestres remain a matter of debate, the Pleistocene refugium hypothesis (PRH) is often adopted as the most plausible explanation for their high diversity. The PRH has two main postulates: highland interglacial refugia and a species pump mechanism catalysed by climatic changes. We critically assessed studies on campos rupestres diversification at different evolutionary levels and conclude that most of them are affected by sampling biases, unrealistic assumptions or inaccurate results that do not support the PRH. By modelling the palaeo-range of campos rupestres based on the distribution of 1123 species of vascular plants endemic to the Espinhaço Range and using climate and edaphic variables, we projected a virtually constant suitable area for campos rupestres across the last glacial cycle. We challenge the great importance placed on Pleistocene climatic oscillations in campos rupestres plant diversification and offer an alternative explanation named escape-to-radiate model, which emphasizes niche shifts. Under this biogeographic model of diversification, the long-term fragmentation of campos rupestres combined with recurrent extinctions after genetic drift and sporadic events of adaptive radiation may provide an explanation for the current diversity and endemism in the Espinhaço Range. We conclude that long-term diversification dynamics in campos rupestres are mainly driven by selection, while most endemic diversity is ephemeral, extremely fragile and mainly driven by drift.

Dispersal barriers and opportunities drive multiple levels of phylogeographic concordance in the Southern Alps of New Zealand

Phylogeographic concordance, or the sharing of phylogeographic patterns among codistributed species, suggests similar responses to topography or climatic history. While the orientation and timing of breaks between lineages are routinely compared, spatial dynamics within regions occupied by individual lineages provide a second opportunity for comparing responses to past events. In environments with complex topography and glacial history, such as New Zealand's South Island, geographically nested comparisons can identify the processes leading to phylogeographic concordance between and within regional genomic clusters. Here, we used single nucleotide polymorphisms (obtained via ddRADseq) for two codistributed forest beetle species, Agyrtodes labralis (Leiodidae) and Brachynopus scutellaris (Staphylinidae), to evaluate the role of climate change and topography in shaping phylogeographic concordance at two, nested spatial scales: do species diverge over the same geographic barriers, with similar divergence times? And within regions delimited by these breaks, do species share similar spatial dynamics of directional expansion or isolation-by-distance? We found greater congruence of phylogeographic breaks between regions divided by the strongest dispersal barriers (i.e., the Southern Alps). However, these shared breaks were not indicative of shared spatial dynamics within the regions they delimit, and the most similar spatial dynamics between species occurred within regions with the strongest gradients in historical climatic stability. Our results indicate that lack of concordance as traditionally detected by lineage turnover does not rule out the possibility of shared histories, and variation in the presence and type of concordance may provide insights into the different processes shaping phylogeographic patterns across geologically dynamic regions.

Rapid speciation and ecological divergence into North American alpine habitats: the Nippononebria (Coleoptera: Carabidae) species complex

The climate-driven species pump hypothesis has been supported in a number of phylogeographic studies of alpine species. Climate-driven shifts in distribution, coupled with rapid demographic change, have led to strong genetic drift and lineage diversification. Although the species pump has been linked to rapid speciation in a number of studies, few studies have demonstrated that ecological divergence accompanies rapid speciation. Here we examine genetic, morphological and physiological variation in members of the ground beetle taxon Nippononebria, to test three competing hypotheses of evolutionary diversification: isolation and incomplete lineage sorting (no speciation), recent speciation without ecological divergence, or recent speciation with ecological divergence into alpine habitats. Genetic data are consistent with recent divergence, with major lineages forming in the last million years. A species tree analysis, in conjunction with morphological divergence in male reproductive traits, support the formation of three recognized Nippononebria taxa. Furthermore, both morphological and physiological traits demonstrate ecological divergence in alpine lineages, with convergent shifts in body shape and thermal tolerance breadth. This provides strong evidence that the climate-driven species pump can generate ecological novelty, though it is argued that spatial scale may be a key determinant of broader patterns of macroevolution in alpine communities.

Genetic differentiation through dispersal and isolation in two freshwater fish species from coastal basins of Northeastern Brazil

Abstract The coastal basins in Northeastern Brazil used in this study make up two different ecoregions for freshwater fishes (Amazonas estuary and coastal drainages, and Parnaiba) and two areas of endemism for Characiformes (Maranhão and Parnaíba), and exhibits a diversified yet poorly explored freshwater fish fauna. The population structure and biogeography of two migratory freshwater fish species that are commercially exploited from Maranhão and Parnaíba regions were herein analyzed. Molecular sequence data and statistical analyses were used to estimate haplotypes networks and lineage divergence times and correlated with hydrographic history of drainage and paleodrainages of the region. A total of 171 sequences was produced for both species, Schizodon dissimilis (coI, n = 70) and Prochilodus lacustris (D-loop, n = 101). All analyses identified the presence of three genetically delimited groups of S. dissimilis and six groups of P. lacustris. The lineage time analyses indicate diversification among these species within the past 1 million year. The results indicate the influence of geodispersal in the formation of the ichthyofauna in the studied area through headwater stream capture events and reticulated connections between the mouths of rivers along the coastal plain due to eustatic sea level fluctuations.

The paradox behind the pattern of rapid adaptive radiation: how can the speciation process sustain itself through an early burst?

Rapid adaptive radiation poses a distinct question apart from speciation and adaptation: what happens after one speciation event? That is, how are some lineages able to continue speciating through a rapid burst? This question connects global macroevolutionary patterns to microevolutionary processes. Here we review major features of rapid radiations in nature and their mismatch with theoretical models and what is currently known about speciation mechanisms. Rapid radiations occur on three major diversification axes - species richness, phenotypic disparity, and ecological diversity - with exceptional outliers on each axis. The paradox is that the hallmark early stage of adaptive radiation, a rapid burst of speciation and niche diversification, is contradicted by most existing speciation models which instead predict continuously decelerating speciation rates and niche subdivision through time. Furthermore, while speciation mechanisms such as magic traits, phenotype matching, and physical linkage of co-adapted alleles promote speciation, it is often not discussed how these mechanisms could promote multiple speciation events in rapid succession. Additional mechanisms beyond ecological opportunity are needed to understand how rapid radiations occur. We review the evidence for five emerging theories: 1) the 'transporter' hypothesis: introgression and the ancient origins of adaptive alleles, 2) the 'signal complexity' hypothesis: the dimensionality of sexual traits, 3) the connectivity of fitness landscapes, 4) 'diversity begets diversity', and 5) flexible stem/'plasticity first'. We propose new questions and predictions to guide future work on the mechanisms underlying the rare origins of rapid radiation.

Gradual Distance Dispersal Shapes the Genetic Structure in an Alpine Grasshopper

The location of the high mountains of southern Europe has been crucial in the phylogeography of most European species, but how extrinsic (topography of sky islands) and intrinsic features (dispersal dynamics) have interacted to shape the genetic structure in alpine restricted species is still poorly known. Here we investigated the mechanisms explaining the colonisation of Cantabrian sky islands in an endemic flightless grasshopper. We scrutinised the maternal genetic variability and haplotype structure, and we evaluated the fitting of two migration models to understand the extant genetic structure in these populations: Long-distance dispersal (LDD) and gradual distance dispersal (GDD). We found that GDD fits the real data better than the LDD model, with an onset of the expansion matching postglacial expansions after the retreat of the ice sheets. Our findings suggest a scenario with small carrying capacity, migration rates, and population growth rates, being compatible with a slow dispersal process. The gradual expansion process along the Cantabrian sky islands found here seems to be conditioned by the suitability of habitats and the presence of alpine corridors. Our findings shed light on our understanding about how organisms which have adapted to live in alpine habitats with limited dispersal abilities have faced new and suitable environmental conditions.

The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago

A primary goal of biogeography is to understand how large-scale environmental processes, like climate change, affect diversification. One often-invoked but seldom tested process is the "species-pump" model, in which repeated bouts of cospeciation are driven by oscillating climate-induced habitat connectivity cycles. For example, over the past three million years, the landscape of the Philippine Islands has repeatedly coalesced and fragmented due to sea-level changes associated with glacial cycles. This repeated climate-driven vicariance has been proposed as a model of speciation across evolutionary lineages codistributed throughout the islands. This model predicts speciation times that are temporally clustered around the times when interglacial rises in sea level fragmented the islands. To test this prediction, we collected comparative genomic data from 16 pairs of insular gecko populations. We analyze these data in a full-likelihood, Bayesian model-choice framework to test for shared divergence times among the pairs. Our results provide support against the species-pump model prediction in favor of an alternative interpretation, namely that each pair of gecko populations diverged independently. These results suggest the repeated bouts of climate-driven landscape fragmentation have not been an important mechanism of speciation for gekkonid lizards across the Philippine Archipelago.

On the Causes of Rapid Diversification in the Páramos: Isolation by Ecology and Genomic Divergence in Espeletia

How diversity arises and what is the relative role of allopatric and ecological divergence are among the most persistent questions in evolution and ecology. Here, we assessed whether ecological divergence has enhanced the diversification of the Neotropical alpine plant complex Espeletia, also known as frailejones. This genus has one of the highest diversification rates ever reported and is distributed in the world's fastest evolving biodiversity hotspot, the Páramo (Neotropical alpine grasslands at elevations of c. 2800-4700 m). Our goal was to determine whether ecology plays a role in divergence within the Espeletia complex by quantifying genome-wide patterns of ecological divergence. We characterized 162 samples of the three most common and contrasting ecotypes (distinct morphotypes occupying particular habitats) co-occurring in six localities in the northern Andes using Genotyping by Sequencing. Contrasting ecotypes were caulescent cloud forest populations, caulescent populations from wind-sheltered and well-irrigated depressions and acaulescent populations from wind-exposed drier slopes. We found high polymorphism with a total of 1,273 single nucleotide polymorphisms (SNPs) that defined the relationships among nine genetic clusters. We quantified allelic associations of these markers with localities and habitats using 18 different general and mixed-effects statistical models that accounted for phylogenetic distance. Despite that these models always yielded more SNPs associated with the localities, markers associated with the habitat types were recovered too. We found strong evidence for isolation-by-distance (IBD) across populations despite rampant gene flow, as expected for plant groups with limited seed dispersal. Contrasts between populations of different habitat types showed that an isolation-by-environment (IBE) trend emerged and masked the IBD signal. Maximum likelihood estimation of the number of migrants per generation (Nem) among ecotypes confirmed the IBE pattern. This result illustrates the importance of mountains' environmental variation at a local scale in generating rapid morphological radiations and maintaining multiple adaptations in a fast-evolving ecosystem like the Páramo.

Flowing into the unknown: inferred paleodrainages for studying the ichthyofauna of Brazilian coastal rivers

ABSTRACT The eastern coastal basins of Brazil are a series of small and isolated rivers that drain directly into the Atlantic Ocean. During the Pleistocene, sea-level retreat caused by glaciations exposed the continental shelf, resulting in enlarged paleodrainages that connected rivers that are isolated today. Using Geographic Information System (GIS), we infer the distribution of these paleodrainages, and their properties for the east Brazilian coast. Specifically, using elevation/bathymetric data for the largest sea-level retreats during the Pleistocene, the paleodrainages, their area and the number of contemporary basins connected by each palaeodrainage, was inferred. For the 145 inferred paleodrainages, total paleodrainage area is strongly correlated with the contemporary area encompassed by each paleodrainage, as well as with the number of contemporary basins encompassed by a paleodrainage. Differences in the continental shelf exposure along the coast affected the degree of past connectivity among contemporary rivers. With our results freely available, we discuss how paleodrainages have tremendous utility in biological studies, especially in regions with limited geologic data. With respect to the diverse ichthyofauna of the Brazilian coast, and its high endemism, we highlight how the inferred paleodrainages provide a backdrop to test hypotheses about the effect of past riverine connectivity on diversity patterns.

Pleistocene glacial cycles drive isolation, gene flow and speciation in the high-elevation Andes

Mountain ranges are amongst the most species-rich habitats, with many large and rapid evolutionary radiations. The tempo and mode of diversification in these systems are key unanswered questions in evolutionary biology. Here we study the Andean Lupinus radiation to understand the processes driving very rapid diversification in montane systems. We use genomic and transcriptomic data of multiple species and populations, and apply phylogenomic and demographic analyses to test whether diversification proceeded without interspecific gene flow - as expected if Andean orogeny and geographic isolation were the main drivers of diversification - or if diversification was accompanied by gene flow, in which case other processes were probably involved. We uncover several episodes of gene flow between species, including very recent events likely to have been prompted by changes in habitat connectivity during Pleistocene glacial cycles. Furthermore, we find that gene flow between species was heterogeneously distributed across the genome. We argue that exceptionally fast diversification of Andean Lupinus was partly a result of Late Pleistocene glacial cycles, with associated cycles of expansion and contraction driving geographic isolation or secondary contact of species. Furthermore, heterogeneous gene flow across the genome suggests a role for selection and ecological speciation in rapid diversification in this system.

Pleistocene land bridges act as semipermeable agents of avian gene flow in Wallacea

Cyclical periods of global cooling have been important drivers of biotic differentiation throughout the Quaternary. Ice age-induced sea level fluctuations can lead to changing patterns of land connections, both facilitating and disrupting gene flow. In this study, we test if species with differing life histories are differentially affected by Quaternary land connections. We used genome-wide SNPs in combination with mitochondrial gene sequences to analyse levels of divergence and gene flow between two songbird complexes across two Wallacean islands that have been repeatedly connected during glaciations. Although the two bird complexes are similar in ecological attributes, the forest and edge-inhabiting golden whistler Pachycephala pectoralis is comparatively flexible in its diet and niche requirements as compared to the henna-tailed jungle-flycatcher Cyornis colonus, which is largely restricted to the forest interior. Using population-genomic and coalescent approaches, we estimated levels of gene flow, population differentiation and divergence time between the two island populations. We observed higher levels of differentiation, an approximately two to four times deeper divergence time and near-zero levels of gene flow between the two island populations of the more forest-dependent henna-tailed jungle-flycatcher as compared to the more generalist golden whistler. Our results suggest that Quaternary land bridges act as semipermeable agents of gene flow in Wallacea, allowing only certain taxa to connect between islands while others remain isolated. Quaternary land bridges do not accommodate all terrestrial species equally, differing in suitability according to life history and species biology. More generalist species are likely to use Quaternary land connections as a conduit for gene flow between islands whereas island populations of more specialist species may continue to be reproductively isolated even during periods of Quaternary land bridges.

Estimation of contemporary effective population size and population declines using RAD sequence data

Large genomic data sets generated with restriction site-associated DNA sequencing (RADseq), in combination with demographic inference methods, are improving our ability to gain insights into the population history of species. We used a simulation approach to examine the potential for RADseq data sets to accurately estimate effective population size (N _e) over the course of stable and declining population trends, and we compare the ability of two methods of analysis to accurately distinguish stable from steadily declining populations over a contemporary time scale (20 generations). Using a linkage disequilibrium-based analysis, individual sampling (i.e., n ≥ 30) had the greatest effect on N _e estimation and the detection of population size declines, with declines reliably detected across scenarios ~10 generations after they began. Coalescent-based inference required fewer sampled individuals (i.e., n = 15), and instead was most influenced by the size of the SNP data set, with 25,000-50,000 SNPs required for accurate detection of population trends and at least 20 generations after decline began. The number of samples available and targeted number of RADseq loci are important criteria when choosing between these methods. Neither method suffered any apparent bias due to the effects of allele dropout typical of RAD data. With an understanding of the limitations and biases of these approaches, researchers can make more informed decisions when designing their sampling and analyses. Overall, our results reveal that demographic inference using RADseq data can be successfully applied to infer recent population size change and may be an important tool for population monitoring and conservation biology.

Genomic signatures of paleodrainages in a freshwater fish along the southeastern coast of Brazil: genetic structure reflects past riverine properties

Past shifts in connectivity in riverine environments (for example, sea-level changes) and the properties of current drainages can act as drivers of genetic structure and demographic processes in riverine population of fishes. However, it is unclear whether the same river properties that structure variation on recent timescales will also leave similar genomic signatures that reflect paleodrainage properties. By characterizing genetic structure in a freshwater fish species (Hollandichthys multifasciatus) from a system of basins along the Atlantic coast of Brazil we test for the effects of paleodrainages caused by sea-level changes during the Pleistocene. Given that the paleodrainage properties differ along the Brazilian coast, we also evaluate whether estimated genetic diversity within paleodrainages can be explained by past riverine properties (i.e., area and number of rivers in a paleodrainage). Our results demonstrate that genetic structure between populations is not just highly concordant with paleodrainages, but that differences in the genetic diversity among paleodrainages correspond to the joint effect of differences in the area encompassed by, and the number of rivers, within a paleodrainage. Our findings extend the influence of current riverine properties on genetic diversity to those associated with past paleodrainage properties. We discuss how these findings may explain the inconsistent support for paleodrainages in structuring divergence from different global regions and the importance of taking into account past conditions for understanding the high species diversity of freshwater fish that we currently observe in the world, and especially in the Neotropics.

Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species

Understanding the demography of species over recent history (e.g. <100 years) is critical in studies of ecology and evolution, but records of population history are rarely available. Surveying genetic variation is a potential alternative to census-based estimates of population size, and can yield insight into the demography of a population. However, to assess the performance of genetic methods, it is important to compare their estimates of population history to known demography. Here, we leveraged the exceptional resources from a wetland with 37 years of amphibian mark-recapture data to study the utility of genetically based demographic inference on salamander species with documented population declines (Ambystoma talpoideum) and expansions (A. opacum), patterns that have been shown to be correlated with changes in wetland hydroperiod. We generated ddRAD data from two temporally sampled populations of A. opacum (1993, 2013) and A. talpoideum (1984, 2011) and used coalescent-based demographic inference to compare alternate evolutionary models. For both species, demographic model inference supported population size changes that corroborated mark-recapture data. Parameter estimation in A. talpoideum was robust to our variations in analytical approach, while estimates for A. opacum were highly inconsistent, tempering our confidence in detecting a demographic trend in this species. Overall, our robust results in A. talpoideum suggest that genome-based demographic inference has utility on an ecological scale, but researchers should also be cognizant that these methods may not work in all systems and evolutionary scenarios. Demographic inference may be an important tool for population monitoring and conservation management planning.

Contrasting support for alternative models of genomic variation based on microhabitat preference: species-specific effects of climate change in alpine sedges

Deterministic processes may uniquely affect codistributed species' phylogeographic patterns such that discordant genetic variation among taxa is predicted. Yet, explicitly testing expectations of genomic discordance in a statistical framework remains challenging. Here, we construct spatially and temporally dynamic models to investigate the hypothesized effect of microhabitat preferences on the permeability of glaciated regions to gene flow in two closely related montane species. Utilizing environmental niche models from the Last Glacial Maximum and the present to inform demographic models of changes in habitat suitability over time, we evaluate the relative probabilities of two alternative models using approximate Bayesian computation (ABC) in which glaciated regions are either (i) permeable or (ii) a barrier to gene flow. Results based on the fit of the empirical data to data sets simulated using a spatially explicit coalescent under alternative models indicate that genomic data are consistent with predictions about the hypothesized role of microhabitat in generating discordant patterns of genetic variation among the taxa. Specifically, a model in which glaciated areas acted as a barrier was much more probable based on patterns of genomic variation in Carex nova, a wet-adapted species. However, in the dry-adapted Carex chalciolepis, the permeable model was more probable, although the difference in the support of the models was small. This work highlights how statistical inferences can be used to distinguish deterministic processes that are expected to result in discordant genomic patterns among species, including species-specific responses to climate change.

Toward a paradigm shift in comparative phylogeography driven by trait-based hypotheses

For three decades, comparative phylogeography has conceptually and methodologically relied on the concordance criterion for providing insights into the historical/biogeographic processes driving population genetic structure and divergence. Here we discuss how this emphasis, and the corresponding lack of methods for extracting information about biotic/intrinsic contributions to patterns of genetic variation, may bias our general understanding of the factors driving genetic structure. Specifically, this emphasis has promoted a tendency to attribute discordant phylogeographic patterns to the idiosyncracies of history, as well as an adherence to generic null expectations of concordance with reduced predictive power. We advocate that it is time for a paradigm shift in comparative phylogeography, especially given the limited utility of the concordance criterion as genomic data provide ever-increasing levels of resolution. Instead of adhering to the concordance-discordance dichotomy, comparative phylogeography needs to emphasize the contribution of taxon-specific traits that will determine whether concordance is a meaningful criterion for evaluating hypotheses or may predict discordant phylogeographic structure. Through reference to some case studies we illustrate how refined hypotheses based on taxon-specific traits can provide improved predictive frameworks to forecast species responses to climatic change or biogeographic barriers while gaining unique insights about the taxa themselves and their interactions with their environment. We outline a potential avenue toward a synthetic comparative phylogeographic paradigm that includes addressing some important conceptual and methodological challenges related to study design and application of model-based approaches for evaluating support of trait-based hypotheses under the proposed paradigm.

Hierarchical genetic structure shaped by topography in a narrow-endemic montane grasshopper

BACKGROUND

Understanding the underlying processes shaping spatial patterns of genetic structure in free-ranging organisms is a central topic in evolutionary biology. Here, we aim to disentangle the relative importance of neutral (i.e. genetic drift) and local adaptation (i.e. ecological divergence) processes in the evolution of spatial genetic structure of the Morales grasshopper (Chorthippus saulcyi moralesi), a narrow-endemic taxon restricted to the Central Pyrenees. More specifically, we analysed range-wide patterns of genetic structure and tested whether they were shaped by geography (isolation-by-distance, IBD), topographic complexity and present and past habitat suitability models (isolation-by-resistance, IBR), and environmental dissimilarity (isolation-by-environment, IBE).

RESULTS

Different clustering analyses revealed a deep genetic structure that was best explained by IBR based on topographic complexity. Our analyses did not reveal a significant role of IBE, a fact that may be due to low environmental variation among populations and/or consequence of other ecological factors not considered in this study are involved in local adaptation processes. IBR scenarios informed by current and past climate distribution models did not show either a significant impact on genetic differentiation after controlling for the effects of topographic complexity, which may indicate that they are not capturing well microhabitat structure in the present or the genetic signal left by dispersal routes defined by habitat corridors in the past.

CONCLUSIONS

Overall, these results indicate that spatial patterns of genetic variation in our study system are primarily explained by neutral divergence and migration-drift equilibrium due to limited dispersal across abrupt reliefs, whereas environmental variation or spatial heterogeneity in habitat suitability associated with the complex topography of the region had no significant effect on genetic discontinuities after controlling for geography. Our study highlights the importance of considering a comprehensive suite of potential isolating mechanisms and analytical approaches in order to get robust inferences on the processes promoting genetic divergence of natural populations.

Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach

Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus Quercus). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation process, we (i) analysed inter- and intraspecific patterns of genetic differentiation and employed an approximate Bayesian computation (ABC) framework to evaluate different plausible scenarios of species divergence. In a second step, we (ii) linked the inferred divergence pathways with current and past species distribution models (SDMs) and (iii) tested for niche differentiation and phylogenetic niche conservatism across taxa. ABC analyses showed that the most plausible scenario is the one considering the divergence of two main lineages followed by a more recent pulse of speciation. Genotypic data in conjunction with SDMs and niche differentiation analyses support that different factors (geography vs. environment) and modes of speciation (parapatry, allopatry and maybe sympatry) have played a role in the divergence process within this complex. We found no significant relationship between genetic differentiation and niche overlap, which probably reflects niche lability and/or that multiple factors, have contributed to speciation. Our study shows that different mechanisms can drive divergence even among closely related taxa representing early stages of species formation and exemplifies the importance of adopting integrative approaches to get a better understanding of the speciation process.

Paternity analyses in wild-caught and laboratory-reared Caribbean cricket females reveal the influence of mating environment on post-copulatory sexual selection

Polyandry is ubiquitous in insects and provides the conditions necessary for male- and female-driven forms of post-copulatory sexual selection to arise. Populations of Amphiacusta sanctaecrucis exhibit significant divergence in portions of the male genitalia that are inserted directly into the female reproductive tract, suggesting that males may exercise some post-copulatory control over fertilization success. We examine the potential for male-male and male-female post-copulatory interactions to influence paternity in wild-caught females of A. sanctaecrucis and contrast our findings with those obtained from females reared in a high-density laboratory environment. We find that female A. sanctaecrucis exercise control by mating multiple times (females mount males), but that male-male post-copulatory interactions may influence paternity success. Moreover, post-copulatory interactions that affect reproductive success of males are not independent of mating environment: clutches of wild-caught females exhibit higher sire diversity and lower paternity skew than clutches of laboratory-reared females. There was no strong evidence for last male precedence in either case. Most attempts at disentangling the contributions of male-male and male-female interactions towards post-copulatory sexual selection have been undertaken in a laboratory setting and may not capture the full context in which they take place--such as the relationship between premating and post-mating interactions. Our results reinforce the importance of designing studies that can capture the multifaceted nature of sexual selection for elucidating the role of post-copulatory sexual selection in driving the evolution of male and female reproductive traits, especially when different components (e.g. precopulatory and post-copulatory interactions) do not exert independent effects on reproductive outcomes.