Speciation in Hawaiian angiosperm lineages: cause, consequence, and mode

The biota of Hawaiian Islands is derived entirely from long distance dispersal, often followed by in situ speciation. Species descended from each colonist constitute monophyletic lineages that have diverged to varying degrees under similar spatial and temporal constraints. We partitioned the Hawaiian angiosperm flora into lineages and assessed morphological, ecological, and biogeographic characteristics to examine their relationships to variation in species number (S). Lineages with external bird dispersal (through adhesion) were significantly more species-rich than those with abiotic dispersal, but only weakly more species-rich than lineages with internal bird dispersal (involving fleshy fruits). Pollination mode and growth form (woody vs. herbaceous) had no significant effect on S, in contrast to studies of angiosperm families. S relates positively to the geographic and ecological range size of whole lineages, but negatively to local abundance and mean range sizes of constituent species. Species-rich lineages represent a large proportion of major adaptive shifts, although this appears to be an artifact of having more species. Examination of 52 sister species pairs in numerous lineages provides evidence for allopatric (including peripheral isolates) and parapatric (ecological) modes, with 15 cases of each. Although postspeciational dispersal may obscure these modes in many of the remaining cases, instances of sympatric and hybrid speciation are also discussed. Because speciation is both a consequence and a cause of ecological and biogeographic traits, speciation mode may be integral to relationships between traits. We discuss the role of speciation in shaping the regional species pool.     

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.     

Repeated vicariance of Eurasian songbird lineages since the Late Miocene

Aim The evolution of avian speciation patterns across much of Eurasia is under‐explored. Excepting phylogeographic patterns of single species, or speciation involving the Himalayas, there has been no attempt to understand the evolution of avian distributional patterns across the rest of the continent. Within many genera there is a pattern of (presumed) sister species occurring in adjacent areas (western, eastern or southern Eurasia), yet this pattern cannot be explained by existing biogeographic barriers. My aim was to examine the possible role of climate‐driven vicariance events in generating avian distributions. Location Eurasia. Methods I constructed a molecular phylogeny of Phoenicurus redstarts, and assembled phylogenetic data from published studies of seven other Eurasian bird genera. On each phylogeny, I assessed the distributional patterns of species and clades relative to refugial areas in western, eastern and southern Eurasia. I also estimated the timing of lineage divergences via a molecular clock, to determine whether distributional patterns can be explained by well‐defined periods of climate change in Eurasia that are recorded from dated sediments in the Chinese Loess Plateau. Results Species relationships in a well‐supported phylogeny of Phoenicurus show a pattern of distributions consistent with repeated speciation in major refugial areas, where one lineage is isolated in a single area of Eurasia relative to its sister lineage. This same pattern is evident in Eurasian Turdus thrushes, and six additional avian genera distributed across Eurasia. Molecular clock dating indicates that divergences within each genus are the result of multiple rounds of speciation in refugia through time, during major climate‐driven episodes of vicariance. Main conclusions Analyses revealed substantial evidence supporting a repeated, non‐random pattern of speciation within and across eight songbird lineages since the Late Miocene. The pattern of speciation supports a model of isolation in refugia during major episodes of vicariance, specifically periods of either intensified desertification of Central Asia or Eurasian glacial cycles. The densely sampled clades used here preclude inter‐continental dispersal as an alternative explanation for distributions. The signature of climate‐driven vicariance across epochs is, given the absence of extant biogeographic barriers, a suitable hypothesis to explain major lineage divergences in widely distributed Eurasian songbird lineages.     

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.     

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.     

Placing the Floridian marine genetic disjunction into a regional evolutionary context using the scorched mussel, Brachidontes exustus, species complex

The well-documented Floridian Gulf/Atlantic marine genetic disjunction provides an influential example of presumed vicariant cladogenesis along a continental coastline for major elements of a diverse nearshore fauna. However, it is unclear if this disjunction represents a local anomaly for regionally distributed morphospecies, or if it is merely one of many such cryptic phylogenetic splits that underlay their assumed genetic cohesiveness. We aimed to place the previously characterized scorched mussel Gulf/Atlantic genetic disjunction into a regional phylogenetic perspective by incorporating genotypes of nominal conspecifics sampled throughout the Caribbean Basin as well as those of eastern Pacific potential geminate species. Our results show it to be one of multiple latent regional genetic disjunctions, involving five cryptic Caribbean species, that appear to be the product of a long history of regional cladogenesis. Disjunctions involving three stem lineages clearly predate formation of the Isthmus of Panama and of the Caribbean Sea, although four of the five cryptic species have within-basin sister relationships. Surprisingly, the Atlantic clade was also found to be widespread in the southern Caribbean, and ancestral demography calculations through time for Atlantic coast-specific genotypes are consistent with a northward range extension after the last glacial maximum. Our new data seriously undermine the hypothesis of a Floridian vicariant genesis and imply that the scorched mussel Gulf/Atlantic disjunction represents a case of geographic and temporal pseudocongruence. All five Caribbean Basin cryptic species exhibited an intriguing pattern of predominantly allopatric distribution characterized by distinct geographic areas of ecological dominance, often adjoining those of sister taxa. This pattern of distribution is consistent with allopatric speciation origins, coupled with restricted postspeciation range extensions. Several lines of indirect evidence favor the hypothesis that the predominantly allopatric distributions are maintained over evolutionary time scales, primarily by postrecruitment ecological filters rather than by oceanographic barriers to larval-mediated gene flow.     

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.     

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.     

Out of the Andes: patterns of diversification in clearwing butterflies

Global biodiversity peaks in the tropical forests of the Andes, a striking geological feature that has likely been instrumental in generating biodiversity by providing opportunities for both vicariant and ecological speciation. However, the role of these mountains in the diversification of insects, which dominate biodiversity, has been poorly explored using phylogenetic methods. Here we study the role of the Andes in the evolution of a diverse Neotropical insect group, the clearwing butterflies. We used dated species-level phylogenies to investigate the time course of speciation and to infer ancestral elevation ranges for two diverse genera. We show that both genera likely originated at middle elevations in the Andes in the Middle Miocene, contrasting with most published results in vertebrates that point to a lowland origin. Although we detected a signature of vicariance caused by the uplift of the Andes at the Miocene–Pliocene boundary, most sister species were parapatric without any obvious vicariant barrier. Combined with an overall decelerating speciation rate, these results suggest an important role for ecological speciation and adaptive radiation, rather than simple vicariance.     

Phylogenetic perspectives on reef fish functional traits

Functional traits have been fundamental to the evolution and diversification of entire fish lineages on coral reefs. Yet their relationship with the processes promoting speciation, extinction and the filtering of local species pools remains unclear. We review the current literature exploring the evolution of diet, body size, water column use and geographic range size in reef‐associated fishes. Using published and new data, we mapped functional traits on to published phylogenetic trees to uncover evolutionary patterns that have led to the current functional diversity of fishes on coral reefs. When examining reconstructed patterns for diet and feeding mode, we found examples of independent transitions to planktivory across different reef fish families. Such transitions and associated morphological alterations may represent cases in which ecological opportunity for the exploitation of different resources drives speciation and adaptation. In terms of body size, reconstructions showed that both large and small sizes appear multiple times within clades of mid‐sized fishes and that extreme body sizes have arisen mostly in the last 10 million years (Myr). The reconstruction of range size revealed many cases of disparate range sizes among sister species. Such range size disparity highlights potential vicariant processes through isolation in peripheral locations. When accounting for peripheral speciation processes in sister pairs, we found a significant relationship between labrid range size and lineage age. The diversity and evolution of traits within lineages is influenced by trait–environment interactions as well as by species and trait–trait interactions, where the presence of a given trait may trigger the development of related traits or behaviours. Our effort to assess the evolution of functional diversity across reef fish clades adds to the burgeoning research focusing on the evolutionary and ecological roles of functional traits. We argue that the combination of a phylogenetic and a functional approach will improve the understanding of the mechanisms of species assembly in extraordinarily rich coral reef communities.     

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.     

A comparative analysis of island floras challenges taxonomy‐based biogeographical models of speciation

Speciation on islands, and particularly the divergence of species in situ, has long been debated. Here, we present one of the first, complete assessments of the geographic modes of speciation for the flora of a small oceanic island. Cocos Island (Costa Rica) is pristine; it is located 550 km off the Pacific coast of Central America. It harbors 189 native plant species, 33 of which are endemic. Using phylogenetic data from insular and mainland congeneric species, we show that all of the endemic species are derived from independent colonization events rather than in situ speciation. This is in sharp contrast to the results of a study carried out in a comparable system, Lord Howe Island (Australia), where as much as 8.2% of the plant species were the product of sympatric speciation. Differences in physiography and age between the islands may be responsible for the contrasting patterns of speciation observed. Importantly, comparing phylogenetic assessments of the modes of speciation with taxonomy‐based measures shows that widely used island biogeography approaches overestimate rates of in situ speciation.     

THE EVOLUTION OF LOCAL ENDEMISM IN MADAGASCAR: WATERSHED VERSUS CLIMATIC GRADIENT HYPOTHESES EVALUATED BY NULL BIOGEOGRAPHIC MODELS

Substantial insular speciation has resulted in exceptionally high levels of endemism in Madagascar, creating locally restricted species' ranges that remain poorly understood. The contributions of alternative processes that could influence patterns of local endemism—including speciation by geographic isolation or adaptation to environmental gradients—are widely debated, both for Madagascar and elsewhere. A recently proposed hypothesis (the "watershed hypothesis") suggests that allopatric speciation driven by isolation in watersheds during Quaternary climate shifts provides a general explanation for patterns of local endemism across taxa in Madagascar. Here we tested coincidence between species' distributions and areas of endemism predicted by two contrasting biogeographic hypotheses: (1) the watershed hypothesis, and (2) an alternative hypothesis driven by climatic gradients (the "current climate hypothesis"). Statistical significance of coincidence was assessed by comparing against a null model. Surprisingly, we found that extant distributions of lemurs, geckos, and chameleons reveal species patterns that are significantly coincident with the watershed and current climate hypotheses. These results strongly support local endemism developing from multiple processes, even among closely related species. Our findings thus indicate that pluralistic approaches will offer the best option both for understanding processes that generate local endemism, and for incorporating endemism within conservation priority setting.     

Dynamics of speciation and diversification in a metapopulation

We develop a simple framework for modeling speciation and diversification as a continuous process of accumulation of genetic (or morphological) differences accompanied by species and subpopulation extinction and/or range expansion. This framework can be used to approach a number of questions such as species-area distribution, species-range size distribution, the rate of ecological turnover, asymmetries of range division between sister species, waiting time until speciation and extinction, the relationship between the geographic range size and the probability of speciation, the relationships between subpopulation-level parameters and metapopulation-level parameters, and the effects of taxonomic level on these rates, distributions, and parameters. We illustrate some of these applications using numerical simulations. We develop approximations describing the dependence of the number of different taxonomic units, their average range size, and the rate of their turnover on the system size, the rate of fixation of genetic (or morphological) changes in local demes, and the rate of local extinction and colonization.     

A protocol for temporal calibration of general area cladograms

Aim To describe a protocol for incorporating a temporal dimension into historical biogeographical analysis, while maintaining the essential independence of all datasets, involving the generation of general area cladograms. Location Global. Methods General area cladograms (GACs) are a reconstruction of the evolutionary history of a set of areas and unrelated clades within those areas. Nodes on a GAC correspond to speciation events in a group of taxa; general nodes are those at which multiple unrelated clades speciate. We undertake temporal calibration of GACs using molecular clock estimates of splitting events between extant taxa as well as first appearance data from the fossil record. We present two examples based on re‐analysis of previously published data: first, a temporally calibrated GAC generated from secondary Brooks parsimony analysis (BPA) of six extant bird clades from the south‐west of North America using molecular clock estimates of divergence times; and second, an analysis of African Neogene mammals based on a phylogenetic analysis for comparing trees (PACT) analysis. Results A hypothetical example demonstrates how temporal calibration reveals potentially critical information about the timing of both unique and general events, while also illustrating instances of incongruence between dates generated from molecular clock estimates and fossils. For the African Neogene mammal dataset, our analysis reveals that most mammal clades underwent geodispersal associated with the Neogene climatic optimum (c. 16 Ma) and vicariant speciation in central Africa correlated with increased aridity and cooler temperatures around 2.5 Ma. Main conclusions Temporally calibrated GACs are valuable tools for assessing whether coordinated patterns of speciation are associated with large‐scale climatic or tectonic phenomena.     

Marine radiations at small geographic scales: speciation in neotropical reef gobies (Elacatinus)

Studies of speciation in the marine environment have historically compared broad-scale distributions and estimated larval dispersal potential to infer the geographic barriers responsible for allopatric speciation. However, many marine clades show high species diversity in geographically restricted areas where barriers are not obvious and estimated dispersal potential should bring many sister taxa into contact. Genetic differentiation at small (separation < 1000 km) spatial scales could facilitate speciation by mechanisms other than the gradual accumulation of reproductive isolation during extended allopatry, such as ecological adaptation to local environmental conditions or the rapid evolution of genes tied to mate recognition, but the role of each of these possibilities has not been simultaneously explored for any species-rich marine taxon. Here, we develop a robust phylogenetic framework for 31 taxa from a species-rich group of Neotropical reef fishes (Gobiidae: Elacatinus) using 3230 bp from one mitochondrial and two nuclear gene regions. We use this framework to explore the contribution of large- and small-scale geographic isolation, ecological differentiation, and coloration toward the formation and maintenance of species. Although species of Elacatinus occur on both sides of the Isthmus of Panama, no sister species are separated by this barrier. Instead, our results indicate that sister taxa occur within oceans. Sister taxa usually differ by coloration, and more distantly related sympatric species frequently differ by resource use. This suggests that some combination of coloration and ecological differences may facilitate assortative mating at range boundaries or in sympatry. Overall, speciation in Elacatinus is consistent with a model of recurring adaptive radiations in stages taking place at small geographic scales.     

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.     

Origins of social parasitism: the importance of divergence ages in phylogenetic studies

Phylogenetic studies on insect social parasites have found very close host-parasite relationships, and these have often been interpreted as providing evidence for sympatric speciation. However, such phylogenetic inferences are problematic because events occurring after the origin of parasitism, such as extinction, host switching and subsequent speciation, or an incomplete sampling of taxa, could all confound the interpretation of phylogenetic relationships. Using a tribe of bees where social parasitism has repeatedly evolved over a wide time-scale, we show the problems associated with phylogenetic inference of sympatric speciation. Host-parasite relationships of more ancient species appear to support sympatric speciation, whereas in a case where parasitism has evolved very recently, sympatric speciation can be ruled out. However, in this latter case, a single extinction event would have lead to relationships that support sympatric speciation, indicating the importance of considering divergence ages when analysing the modes of social parasite evolution.     

Inferring speciation history in the Andes with reduced‐representation sequence data: an example in the bay‐backed antpittas (Aves; Grallariidae; Grallaria hypoleuca s. l.)

In the Andes, humid‐forest organisms frequently exhibit pronounced genetic structure and geographic variation in phenotype, often coincident with physical barriers to dispersal. However, phylogenetic relationships of clades have often been difficult to resolve due to short internodes. Consequently, even in taxa with well‐defined genetic structure, the temporal and geographic sequences of dispersal and vicariance events that led to this differentiation have remained opaque, hindering efforts to test the association between diversification and earth history and to understand the assembly of species‐rich communities on Andean slopes. Here, we use mitochondrial DNA and thousands of short‐read sequences generated with genotyping by sequencing (GBS) to examine the geographic history of speciation in a lineage of passerine birds found in the humid forest of the Andes, the ‘bay‐backed’ antpitta complex (Grallaria hypoleuca s. l). Mitochondrial DNA genealogies documented genetic structure among clade but were poorly resolved at nodes relevant for biogeographic inference. By contrast, relationships inferred from GBS loci were highly resolved and suggested a biogeographic history in which the ancestor originated in the northern Andes and dispersed south. Our results are consistent with a scenario of vicariant speciation wherein the range of a widespread ancestor was fragmented as a result of geologic or climatic change, rather than a stepping‐stone series of dispersal events across pre‐existing barriers. However, our study also highlights challenges of distinguishing dispersal‐mediated speciation from static vicariance. Our results further demonstrate the substantial evolutionary timescale over which the diverse biota of the Andes was assembled.     

Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences

Molecular phylogenetic analyses were conducted using the whole mitochondrial genome sequences of all 18 species/subspecies of the freshwater eels genus Anguilla to infer their phylogenetic relationships and to evaluate hypotheses about the possible dispersal routes of this genus. The Bayesian and maximum likelihood analyses using a total of 15,187 sites of mitochondrial DNA sequences suggested that A. mossambica was the most basal species of anguillid eel, and that the other species (except for A. borneensis) formed three geographic clades: Atlantic (two species), Oceania (three species), and Indo-Pacific (11 species). The present study clearly indicated a sister relationship between the Atlantic and Oceanian species, which now have distantly separated geographic distributions. This suggests that the previous hypotheses to estimate the dispersal route of anguillid eels into the Atlantic Ocean based on the current geographic distribution of species are unsupported by the present more complete analysis. Alternatively, the unique geographic distribution of the present day species in the genus Anguilla appears to have resulted from multiple dispersal events. Although the age of the beginning of speciation among anguillid eels was tentatively estimated as 20 million years ago using a calibration for bony fishes of 7.3x10(-4) substitutions/site/million years, it is possible that this divergence time was underestimated because of the ecological characteristics of these fishes. The results of the present study suggest that the hypotheses for the dispersal route and divergence time of the genus Anguilla should be reconsidered.