The geographical pattern of speciation and floral diversification in the neotropics: the tribe sinningieae (gesneriaceae) as a case study

The geographical pattern of speciation and the relationship between floral variation and species ranges were investigated in the tribe Sinningieae (Gesneriaceae), which is found mainly in the Atlantic forests of Brazil. Geographical distribution data recorded on a grid system of 0.5 x 0.5 degree intervals and a near-complete species-level phylogenetic tree of Sinningieae inferred from a simultaneous analysis of seven DNA regions were used to address the role of geographical isolation in speciation. Geographical range overlaps between sister lineages were measured across all nodes in the phylogenetic tree and analyzed in relation to relative ages estimated from branch lengths. Although there are several cases of species sympatry in Sinningieae, patterns of sympatry between sister taxa support the predominance of allopatric speciation. The pattern of sympatry between sister taxa is consistent with range shifts following allopatric speciation, except in one clade, in which the overlapping distribution of recent sister species indicates speciation within a restricted geographical area and involving changes in pollinators and habitats. The relationship between floral divergence and regional sympatry was also examined by analyzing floral contrasts, phenological overlap, and the degree of sympatry between sister clades. Morphological contrast between flowers is not increased in sympatry and phenological divergence is more apparent between allopatric clades than between sympatric clades. Therefore, our results failed to indicate a tendency for sympatric taxa to minimize morphological and phenological overlap (geographic exclusion and/or character displacement hypotheses). Instead, they point toward adaptation in phenology to local conditions and buildup of sympatries at random with respect to flower morphology. Additional studies at a lower geographical scale are needed to identify truely coexisting species and the components of their reproductive isolation.     

The geography of mammalian speciation: mixed signals from phylogenies and range maps

The importance of geographic isolation in speciation has been debated since the 19th century. Since the beginning of the 20th century, the consensus has been that most speciation involves divergence in allopatry. This consensus was based largely on decades of observations by naturalists and verbal arguments against speciation without isolation. Recent attempts to quantify the importance of allopatric versus sympatric speciation using comparative methods called "age-range correlation" (ARC) suggest that allopatric speciation is more common than sympatric speciation. However, very few taxa have been studied and there are concerns about the adequacy of the methods. We propose methodological improvements including changes in the way overlap between clades is quantified and Monte Carlo methods to test the null hypothesis of no relationship between phylogenetic relatedness and geographic range overlap. We analyze 14 clades of mammals, chosen because of the availability of data and the consensus among mammalogists that speciation is routinely allopatric. Although data from a few clades clearly indicate allopatric speciation, divergence with gene flow is plausible in others and many results are inconclusive. The relative rarity of significant correlations between phylogenetic distance and range overlap may have three distinct causes: (1) post-speciation range changes, (2) relative rarity of range overlap, and (3) a mixture of geographic modes of speciation. Our results support skepticism about ARC's power for inferring the biogeography of speciation. Yet, even if few clades provide clear signals, meta-analytic approaches such as ARC may set bounds on the prevalence of alternative modes of speciation.     

DOES NICHE CONSERVATISM PROMOTE SPECIATION? A CASE STUDY IN NORTH AMERICAN SALAMANDERS

Recent speciation research has generally focused on how lineages that originate in allopatry evolve intrinsic reproductive isolation, or how ecological divergence promotes nonallopatric speciation. However, the ecological basis of allopatric isolation, which underlies the most common geographic mode of speciation, remains poorly understood and largely unstudied. Here, we explore the ecological and evolutionary factors that promote speciation in Desmognathus and Plethodon salamanders from temperate eastern North America. Based on published molecular phylogenetic estimates and the degree of geographic range overlap among extant species, we find strong evidence for a role for geographic isolation in speciation. We then examine the relationship between climatic variation and speciation in 16 sister-taxon pairs using geographic information system maps of climatic variables, new methods for modeling species' potential geographic distributions, and data on geographic patterns of genetic variation. In contrast to recent studies in tropical montane regions, we found no evidence for parapatric speciation along climatic gradients. Instead, many montane sister taxa in the Appalachian Highlands inhabit similar climatic niches and seemingly are allopatric because they are unable to tolerate the climatic conditions in the intervening lowlands. This temporal and spatial-ecological pattern suggests that niche conservatism, rather than niche divergence, plays the primary role in promoting allopatric speciation and montane endemism in this species-rich group of vertebrates. Our results demonstrate that even the relatively subtle climatic differences between montane and lowland habitats in eastern North America may play a key role in the origin of new species.     

Influence of the geography of speciation on current patterns of coral reef fish biodiversity across the Indo‐Pacific

The role of speciation processes in shaping current biodiversity patterns represents a major scientific question for ecologists and biogeographers. Hence, numerous methods have been developed to determine the geography of speciation based on co‐occurrence between sister‐species. Most of these methods rely on the correlation between divergence time and several metrics based on the geographic ranges of sister‐taxa (i.e. overlap, asymmetry). The relationship between divergence time and these metrics has scarcely been examined in a spatial context beyond regression curves. Mapping this relationship across spatial grids, however, may unravel how speciation processes have shaped current biodiversity patterns through space and time. This can be particularly relevant for coral reef fishes of the Indo‐Pacific since the origin of the exceptional concentration of biodiversity in the Indo‐Australian Archipelago (IAA) has been actively debated, with several alternative hypotheses involving species diversification and dispersal. We reconstructed the phylogenetic relationships between three species‐rich families of coral reef fish (Chaetodontidae, Labridae, Pomacentridae) and calculated co‐occurrence metrics between closely related lineages of those families. We demonstrated that repeated biogeographic processes can be identified in present‐day species distribution by projecting co‐occurrence metrics between related lineages in a geographical context. Our study also evidence that sister‐species do not co‐occur randomly across the Indo‐Pacific, but tend to overlap their range within the IAA. We identified the imprint of two important biogeographic processes that caused this pattern in 48% of the sister‐taxa considered: speciation events within the IAA and repeated divergence between the Indian and Pacific Ocean, with subsequent secondary contact in the IAA.     

Sympatric speciation in birds is rare: insights from range data and simulations

Sympatric speciation is now accepted as theoretically plausible and a likely explanation for divergence in a handful of taxa, but its contribution to large-scale patterns of speciation remains contentious. A major problem is that it is difficult to differentiate between alternate scenarios of geographic speciation when species ranges have shifted substantially in the past. Previous studies have searched for a signal of the geographic mode of speciation by testing for a correlation between time since speciation and range overlap. Here we use simulations to show that the proportion of species showing zero or complete range overlap are more reliable indicators of the geography of speciation than is the correlation between time since speciation and overlap. We then apply these findings to the distributions of 291 pairs of avian sister species. Although 49% of pairs show some overlap in their ranges, our simulations show that this is not surprising under allopatric models of speciation. More revealingly, less than 2% show complete range overlap. Our simulations demonstrate that the observed patterns are most consistent with a model in which allopatric speciation is dominant but in which sympatric speciation is also present and contributes 5% of speciation events.     

The relative importance of geography and ecology in species diversification: evidence from a tropical marine intertidal snail (Nerita)

Aim In this study, I examined the relative contributions of geography and ecology to species diversification within the genus Nerita, a prominent clade of marine snails that is widely distributed across the tropics and intertidal habitats. Specifically, I tested whether geographical patterns of speciation correspond primarily to allopatric or sympatric models, and whether habitat transitions have played a major role in species diversification. Location Indo‐West Pacific, eastern Pacific, Atlantic, tropical marine intertidal. Methods I used a previously reconstructed molecular phylogeny of Nerita as a framework to assess the relative importance of geographical and ecological factors in species diversification. To evaluate whether recently diverged clades exhibit patterns consistent with allopatric or sympatric speciation, I mapped the geo‐graphical distribution of each species onto the species‐level phylogeny, and examined the relationship between range overlap and time since divergence using age–range correlation analyses. To determine the relative contribution of habitat transitions to divergence, I traced shifts in intertidal substrate affinity and vertical zonation across the phylogeny using parsimony, and implemented randomization tests to evaluate the resulting patterns of ecological change. Results Within the majority of Nerita clades examined, age–range correlation analysis yielded a low intercept and a positive slope, similar to that expected under allopatric speciation. Approximately 75% of sister species pairs have maintained allopatric distributions; whereas more distantly related sister taxa often exhibited complete or nearly complete geographical overlap. In contrast, only 19% of sister species occupy distinct habitats. For both substrate and zonation, habitat transitions failed to concentrate towards either the tips or the root of the phylogeny. Instead, habitat shifts have occurred throughout the history of Nerita, with a general transition from the lower and mid‐littoral towards the upper and supra‐littoral zones, and multiple independent shifts from hard (rock) to softer substrates (mangrove, mud and sand). Main conclusions Both geography and ecology appear to have influenced diversification in Nerita, but to different extents. Geography seems to play a principal role, with allopatric speciation driving the majority of Nerita divergences. Habitat transitions appear insignificant in shaping the early and recent history of speciation, and promoting successive diversification in Nerita; however, shifts may have been important for respective divergences (i.e. those that correspond to the transitions) and enhancing diversity throughout the clade.     

Along the speciation continuum: Quantifying intrinsic and extrinsic isolating barriers across five million years of evolutionary divergence in California jewelflowers

Understanding the relative roles of intrinsic and extrinsic reproductive barriers, and their interplay within the geographic context of diverging taxa, remains an outstanding challenge in the study of speciation. We conducted a comparative analysis of reproductive isolation in California Jewelflowers (Streptanthus, s.l., Brassicaceae) by quantifying potential barriers to gene flow at multiple life history stages in 39 species pairs spanning five million years of evolutionary divergence. We quantified nine potential pre‐ and postzygotic barriers and explored patterns of reproductive isolation in relation to genetic distance. Intrinsic postzygotic isolation was initially weak, increased at intermediate genetic distances, and reached a threshold characterized by complete genetic incompatibility. Climatic niche differences were strong at shallow genetic distances, and species pairs with overlapping ranges showed slight but appreciable phenological isolation, highlighting the potential for ecological barriers to contribute to speciation. Geographic analyses suggest that speciation is not regionally allopatric in the California Jewelflowers, as recently diverged taxa occur in relatively close proximity and display substantial range overlap. Young pairs are characterized by incomplete intrinsic postzygotic isolation, suggesting that extrinsic barriers or fine‐scale spatial segregation are more important early in the divergence process than genetic incompatibilities.     

Ecological divergence and speciation between lemur (Eulemur) sister species in Madagascar

Understanding ecological niche evolution over evolutionary timescales is crucial to elucidating the biogeographic history of organisms. Here, we used, for the first time, climate‐based ecological niche models (ENMs) to test hypotheses about ecological divergence and speciation processes between sister species pairs of lemurs (genus Eulemur) in Madagascar. We produced ENMs for eight species, all of which had significant validation support. Among the four sister species pairs, we found nonequivalent niches between sisters, varying degrees of niche overlap in ecological and geographic space, and support for multiple divergence processes. Specifically, three sister‐pair comparisons supported the null model that niches are no more divergent than the available background region. These findings are consistent with an allopatric speciation model, and for two sister pairs (E. collaris–E. cinereiceps and E. rufus–E. rufifrons), a riverine barrier has been previously proposed for driving allopatric speciation. However, for the fourth sister pair E. flavifrons–E. macaco, we found support for significant niche divergence, and consistent with their parapatric distribution on an ecotone and the lack of obvious geographic barriers, these findings most strongly support a parapatric model of speciation. These analyses thus suggest that various speciation processes have led to diversification among closely related Eulemur species.     

Genetic divergence and speciation in lowland and montane peruvian poison frogs

Amazonia is famous for high biodiversity, and the highlands of the transition zone between the Andes and the lowlands of the Amazon basin show particularly high species diversity. Hypotheses proposed to explain the high levels of diversity in the highlands include repeated parapatric speciation across ecological gradients spanning the transition zone, repeated allopatric speciation across geographic barriers between the highlands and lowlands, divergence across geographic barriers within the transition zone, and simple lineage accumulation over long periods of time. In this study, we investigated patterns of divergence in frogs of the genus Epipedobates (family Dendrobatidae) using phylogenetic and biogeographic analyses of divergence in mitochondrial DNA (1778 aligned positions from genes encoding cyt b, 12S and 16S rRNA for 60 Epipedobates and 11 outgroup specimens) and coloration (measured for 18 specimens representing nine species in Epipedobates). The majority of phenotypic and species diversity in the poison frog genus Epipedobates occurs in the transition zone, although two morphologically conserved members of the genus are distributed across the lowlands of the Amazon basin. Phylogenetic analysis reveals that there is a single highland clade derived from an ancestral colonization event in northern Peru by a population of lowland ancestry. Epipedobates trivittatus, a widespread Amazonian species, is a member of the highland clade that reinvaded the lowlands. Comparative analyses of divergence in coloration and mtDNA reveals that divergence in coloration among populations and species in the highlands has been accelerated relative to the lowlands. This suggests a role for selection in the divergence of coloration among populations and species.     

Phylogenetics and biogeography of the two‐wing flyingfish (Exocoetidae: Exocoetus)

Two‐wing flyingfish (Exocoetus spp.) are widely distributed, epipelagic, mid‐trophic organisms that feed on zooplankton and are preyed upon by numerous predators (e.g., tunas, dolphinfish, tropical seabirds), yet an understanding of their speciation and systematics is lacking. As a model of epipelagic fish speciation and to investigate mechanisms that increase biodiversity, we studied the phylogeny and biogeography of Exocoetus, a highly abundant holoepipelagic fish taxon of the tropical open ocean. Morphological and molecular data were used to evaluate the phylogenetic relationships, species boundaries, and biogeographic patterns of the five putative Exocoetus species. We show that the most widespread species (E. volitans) is sister to all other species, and we find no evidence for cryptic species in this taxon. Sister relationship between E. monocirrhus (Indo‐Pacific) and E. obtusirostris (Atlantic) indicates the Isthmus of Panama and/or Benguela Barrier may have played a role in their divergence via allopatric speciation. The sister species E. peruvianus and E. gibbosus are found in different regions of the Pacific Ocean; however, our molecular results do not show a clear distinction between these species, indicating recent divergence or ongoing gene flow. Overall, our phylogeny reveals that the most spatially restricted species are more recently derived, suggesting that allopatric barriers may drive speciation, but subsequent dispersal and range expansion may affect the distributions of species.     

Speciation and diversity on tropical rocky shores: a global phylogeny of snails of the genus Echinolittorina

A phylogenetic approach to the origin and maintenance of species diversity ideally requires the sampling of all species within a clade, confirmation that they are evolutionarily distinct entities, and knowledge of their geographical distributions. In the marine tropics such studies have mostly been of fish and reef-associated organisms, usually with high dispersal. In contrast, snails of the genus Echinolittorina (Littorinidae) are restricted to rocky shores, have a four-week pelagic development (and recorded dispersal up to 1400 km), and show different evolutionary patterns. We present a complete molecular phylogeny of Echinolittorina, derived from Bayesian analysis of sequences from nuclear 28S rRNA and mitochondrial 12S rRNA and COI genes (nodal support indicated by posterior probabilities, maximum likelihood, and neighbor-joining bootstrap). This consists of 59 evolutionarily significant units (ESUs), including all 50 known taxonomic species. The 26 ESUs found in the Indo-West Pacific region form a single clade, whereas the eastern Pacific and Atlantic species are basal. The earliest fossil occurred in the Tethys during the middle Eocene and we suggest that the Indo-West Pacific clade has been isolated since closure of the Tethyan seaway in the early Miocene. The geographical distributions of all species (based on more than 3700 locality records) appear to be circumscribed by barriers of low temperature, unsuitable sedimentary habitat, stretches of open water exceeding about 1400 km, and differences in oceanographic conditions on the continuum between oceanic and continental. The geographical ranges of sister species show little or no overlap, indicating that the speciation mode is predominantly allopatric. Furthermore, range expansion following speciation appears to have been limited, because a high degree of allopatry is maintained through three to five branching points of the phylogeny. This may be explained by infrequent long-distance colonization, habitat specialization on the oceanic/continental gradient, and perhaps by interspecific competition. In the eastern Pacific plus Atlantic we identify five cases of divergence on either side of the Isthmus of Panama, but our estimates of their ages pre-date the emergence of the Isthmus. There are three examples of sister relationships between species in the western Atlantic and eastern Atlantic, all resulting from dispersal to the east. Within the Indo-West Pacific, we find no geographical pattern of speciation events; narrowly endemic species of recent origin are present in both peripheral and central parts of the region. Evidence from estimated divergence times of sister species, and from a plot of the number of lineages over time, suggest that there has been no acceleration of diversification during the glacio-eustatic cycles of the Plio-Pleistocene. In comparison with reefal organisms, species of Echinolittorina on rocky shores may be less susceptible to extinction or isolation during sea-level fluctuations. The species richness of Echinolittorina in the classical biogeographic provinces conforms to the common pattern of highest diversity (11 species) in the central "East Indies Triangle" of the Indo-West Pacific, with a subsidiary focus in the eastern Pacific and western Atlantic, and lowest diversity in the eastern Atlantic. The diversity focus in the East Indies Triangle is produced by a mosaic of restricted allopatric species and overlap of a few widespread ones, and is the result of habitat specialization rather than historical vicariance. This study emphasizes the plurality of biogeographic histories and speciation patterns in the marine tropics.     

Testing the role of climate in speciation: New methods and applications to squamate reptiles (lizards and snakes)

Climate may play important roles in speciation, such as causing the range fragmentation that underlies allopatric speciation (through niche conservatism) or driving divergence of parapatric populations along climatic gradients (through niche divergence). Here, we developed new methods to test the frequency of climate niche conservatism and divergence in speciation, and applied it to species pairs of squamate reptiles (lizards and snakes). We used a large‐scale phylogeny to identify 242 sister species pairs for analysis. From these, we selected all terrestrial allopatric pairs with sufficient occurrence records (n = 49 pairs) and inferred whether each originated via climatic niche conservatism or climatic niche divergence. Among the 242 pairs, allopatric pairs were most common (41.3%), rather than parapatric (19.4%), partially sympatric (17.7%), or fully sympatric species pairs (21.5%). Among the 49 selected allopatric pairs, most appeared to have originated via climatic niche divergence (61–76%, depending on the details of the methods). Surprisingly, we found greater climatic niche divergence between allopatric sister species than between parapatric pairs, even after correcting for geographic distance. We also found that niche divergence did not increase with time, further implicating niche divergence in driving lineage splitting. Overall, our results suggest that climatic niche divergence may often play an important role in allopatric speciation, and the methodology developed here can be used to address the generality of these findings in other organisms.     

Pliocene forest dynamics as a primary driver of African bird speciation

Aim Montane tropics are areas of high endemism, and mechanisms driving this endemism have been receiving increasing attention at a global scale. A general trend is that climatic factors do not explain the species richness of species with small to medium‐sized geographic ranges, suggesting that geological and evolutionary processes must be considered. On the African continent, several hypotheses including both refugial and geographic uplift models have been advanced to explain avian speciation and diversity in the lowland forest and montane regions of central and eastern Africa; montane regions in particular are recognized as hotspots of vertebrate endemism. Here, we examine the possible role of these models in driving speciation in a clade of African forest robins. Location Africa. Methods We constructed the first robustly supported molecular phylogenetic hypothesis of forest robins. On this phylogeny, we reconstructed habitat‐based distributions and geographic distributions relative to the Albertine Rift. We also estimated the timing of lineage divergences via a molecular clock. Results Robust estimates of phylogenetic relationships and clock‐based divergences reject Miocene tectonic uplift and Pleistocene forest refugia as primary drivers of speciation in forest robins. Instead, our data suggest that most forest robin speciation took place in the Late Pliocene, from 3.2 to 2.2 Ma. Distributional patterns are complex, with the Albertine Rift region serving as a general east–west break across the group. Montane distributions are inferred to have evolved four times. Main conclusions Phylogenetic divergence dates coincide with a single period of lowland forest retraction in the late Pliocene, suggesting that most montane speciation resulted from the rapid isolation of populations in montane areas, rather than montane areas themselves being drivers of speciation. This conclusion provides additional evidence that Pliocene climate change was a major driver of speciation in broadly distributed African animal lineages. We further show that lowland forest robins are no older than their montane relatives, suggesting that lowland areas are not museums which house ‘ancient’ taxa; rather, for forest robins, montane areas should be viewed as living museums of a late Pliocene diversification event. A forest refugial pattern is operating in Africa, but it is not constrained to the Pleistocene.     

The tempo of trait divergence in geographic isolation: Avian speciation across the Marañon Valley of Peru

Geographic isolation is considered essential to most speciation events, but our understanding of what controls the pace and degree of phenotypic divergence among allopatric populations remains poor. Why do some taxa exhibit phenotypic differentiation across barriers to dispersal, whereas others do not? To test factors controlling phenotypic divergence in allopatry, we employed a comparative phylogeographic approach consisting of replicates of ecologically similar Andean bird species isolated across a major biogeographic barrier, the Marañon Valley of Peru. Our study design leverages variation among codistributed taxa in their degree of plumage, morphometric, and vocal differentiation across the Marañon to examine the tempo of phenotypic evolution. We found that substantial plumage differences between populations required roughly two million years to evolve. In contrast, morphometric trait evolution showed greater idiosyncrasy and stasis. Our results demonstrate that despite a large degree of idiosyncrasy in the relationship between genetic and phenotypic divergence across taxa and environments, comparative studies within regions may reveal predictability in the pace of phenotypic divergence. Our results also suggest that social selection is important for driving differentiation of populations found in similar environments.     

The phylogenetic pattern of speciation and wing pattern change in neotropical Ithomia butterflies (Lepidoptera: nymphalidae)

Species level phylogenetic hypotheses can be used to explore patterns of divergence and speciation. In the tropics, speciation is commonly attributed to either vicariance, perhaps within climate-induced forest refugia, or ecological speciation caused by niche adaptation. Mimetic butterflies have been used to identify forest refugia as well as in studies of ecological speciation, so they are ideal for discriminating between these two models. The genus Ithomia contains 24 species of warningly colored mimetic butterflies found in South and Central America, and here we use a phylogenetic hypothesis based on seven genes for 23 species to investigate speciation in this group. The history of wing color pattern evolution in the genus was reconstructed using both parsimony and likelihood. The ancestral pattern for the group was almost certainly a transparent butterfly, and there is strong evidence for convergent evolution due to mimicry. A punctuationist model of pattern evolution was a significantly better fit to the data than a gradualist model, demonstrating that pattern changes above the species level were associated with cladogenesis and supporting a model of ecological speciation driven by mimicry adaptation. However, there was only one case of sister species unambiguously differing in pattern, suggesting that some recent speciation events have occurred without pattern shifts. The pattern of geographic overlap between clades over time shows that closely related species are mostly sympatric or, in one case, parapatric. This is consistent with modes of speciation with ongoing gene flow, although rapid range changes following allopatric speciation could give a similar pattern. Patterns of lineage accumulation through time differed significantly from that expected at random, and show that most of the extant species were present by the beginning of the Pleistocene at the latest. Hence Pleistocene refugia are unlikely to have played a major role in Ithomia diversification.     

Small body size increases the regional differentiation of populations of tropical mantellid frogs (Anura: Mantellidae)

The processes affecting species diversification may also exert an influence on patterns of genetic variability within species. We evaluated the contributions of five variables potentially influencing clade diversification (body size, reproductive mode, range size, microhabitat and skin texture) on mtDNA divergence and polymorphism among populations of 40 species of frogs (Mantellidae) from two rainforest communities in Madagascar. We report an inverse association between body size and nucleotide divergence between populations but find no influence of other variables on genetic variation. Body size explained ca. 11% of the variation in nucleotide divergence between populations and was coupled with high F_ST levels and an absence of haplotype sharing in small‐bodied and medium‐sized frogs. Low dispersal ability is likely the proximate mechanism producing higher population differentiation in small mantellids. The lack of genetic cohesion among populations establishes regional genetic fragmentation which in turn has the potential to accelerate rates of allopatric speciation in small frogs relative to large species. However, there is little evidence of increased speciation rates in these or other small‐bodied organisms. We reconcile these contradictory observations by suggesting that lower dispersal ability also curbs colonization of new areas, decelerating diversification in weak dispersers. Our results imply that the intermediate dispersal model also applies to amphibians and may explain inconsistent previous results on the correlation of body size and speciation rate.     

Rapid allopatric speciation in logperch darters (Percidae: Percina)

Theory predicts that clades diversifying via sympatric speciation will exhibit high diversification rates. However, the expected rate of diversification in clades characterized by allopatric speciation is less clear. Previous studies have documented significantly higher speciation rates in freshwater fish clades diversifying via sympatric versus allopatric modes, leading to suggestions that the geographic pattern of speciation can be inferred solely from knowledge of the diversification rate. We tested this prediction using an example from darters, a clade of approximately 200 species of freshwater fishes endemic to eastern North America. A resolved phylogeny was generated using mitochondrial DNA gene sequences for logperches, a monophyletic group of darters composed of 10 recognized species. Divergence times among logperch species were estimated using a fossil calibrated molecular clock in centrarchid fishes, and diversification rates in logperches were estimated using several methods. Speciation events in logperches are recent, extending from 4.20 +/- 1.06 million years ago (mya) to 0.42 +/- 0.22 mya, with most speciation events occurring in the Pleistocene. Diversification rates are high in logperches, at some nodes exceeding rates reported for well-studied adaptive radiations such as Hawaiian silverswords. The geographic pattern of speciation in logperches was investigated by examining the relationship between degree of sympatry and the absolute age of the contrast, with the result that diversification in logperches appears allopatric. The very high diversification rate observed in the logperch phylogeny is more similar to freshwater fish clades thought to represent examples of sympatric speciation than to clades representing allopatric speciation. These results demonstrate that the geographic mode of speciation for a clade cannot be inferred from the diversification rate. The empirical observation of high diversification rates in logperches demonstrates that allopatric speciation can occur rapidly.     

LATITUDINAL VARIATION IN SPECIATION MECHANISMS IN FROGS

Speciation often has a strong geographical and environmental component, but the ecological factors that potentially underlie allopatric and parapatric speciation remain understudied. Two ecological mechanisms by which speciation may occur on geographic scales are allopatric speciation through niche conservatism and parapatric or allopatric speciation through niche divergence. A previous study on salamanders found a strong latitudinal pattern in the prevalence of these mechanisms, with niche conservatism dominating in temperate regions and niche divergence dominating in the tropics, and related this pattern to Janzen's hypothesis of greater climatic zonation between different elevations in the tropics. Here, we test for latitudinal patterns in speciation in a related but more diverse group of amphibians, the anurans. Using data from up to 79 sister-species pairs, we test for latitudinal variation in elevational and climatic overlap between sister species, and evaluate the frequency of speciation via niche conservatism versus niche divergence in relation to latitude. In contrast to salamanders, we find no tendency for greater niche divergence in the tropics or for greater niche conservatism in temperate regions. Although our results support the idea of greater climatic zonation in tropical regions, they show that this climatic pattern does not lead to straightforward relationships between speciation, latitude, and niche evolution.     

Integrating phylogenetics and environmental niche models to explore speciation mechanisms in dendrobatid frogs

We developed an approach that combines distribution data, environmental geographic information system layers, environmental niche models, and phylogenetic information to investigate speciation processes. We used Ecuadorian frogs of the family Dendrobatidae to illustrate our methodology. For dendrobatids there are several cases for which there is significant environmental divergence for allopatric and parapatric lineages. The consistent pattern that many related taxa or nodes exist in distinct environmental space reinforces Lynch and Duellman's hypothesis that differential selection likely played an important role in species differentiation of frogs in the Andes. There is also some evidence that the Río Esmeraldas basin is a geographic barrier to species distributed in low to middle elevations on the western side of the Andes. Another useful aspect of this approach is that it can point to common environmental parameters that correlate with speciation. For dendrobatids, sister clades generally segregate along temperature/elevational and/or seasonality axes. The joint analysis of environmental and geographic data for this group of dendrobatid frogs has identified potentially important speciation mechanisms and specific sister lineages that warrant intensive study to test hypotheses generated in this investigation. Further, the method outlined in this paper will be increasingly useful as knowledge of distribution and phylogeny of tropical species increases.     

Assessing models of speciation under different biogeographic scenarios; an empirical study using multi‐locus and RNA‐seq analyses

Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus. These lineages offer a powerful system to study speciation, because different biogeographic patterns (physical vs. ecological segregation) are observed at opposing ends of their distributions. We use 82 samples collected from 38 sites, representing the entire species' distribution and generate sequence data for mtDNA and four nuclear loci. A multilocus phylogenetic analysis in *BEAST estimates the species tree. RNA‐seq data yield 20,126 synonymous variants from 7665 contigs from two individuals of each of the three lineages. Analyses of these data using the demographic inference package ?a?i serve to test the null hypothesis of no gene flow during divergence. The best‐fit demographic model for the three taxa is concordant with the *BEAST species tree, and the ?a?i analysis does not indicate gene flow among any of the three lineages during their divergence. These analyses suggest that divergence among the lineages occurred in the absence of gene flow and in this scenario the genetic signature of ecological isolation (parapatric model) cannot be differentiated from geographic isolation (allopatric model).