Contrasting geographic structure in evolutionarily divergent Lake Tanganyika catfishes

Geographic isolation is suggested to be among the most important processes in the generation of cichlid fish diversity in East Africa's Great Lakes, both through isolation by distance and fluctuating connectivity caused by changing lake levels. However, even broad scale phylogeographic patterns are currently unknown in many non‐cichlid littoral taxa from these systems. To begin to address this, we generated restriction‐site‐associated DNA sequence (RADseq) data to investigate phylogeographic structure throughout Lake Tanganyika (LT) in two broadly sympatric rocky shore catfish species from independent evolutionary radiations with differing behaviors: the mouthbrooding claroteine, Lophiobagrus cyclurus, and the brood‐parasite mochokid, Synodontis multipunctatus. Our results indicated contrasting patterns between these species, with strong lake‐wide phylogeographic signal in L. cyclurus including a deep divergence between the northern and southern lake basins. Further structuring of these populations was observed across a heterogeneous habitat over much smaller distances. Strong population growth was observed in L. cyclurus sampled from shallow shorelines, suggesting population growth associated with the colonization of new habitats following lake‐level rises. Conversely, S. multipunctatus, which occupies a broader depth range, showed little phylogeographic structure and lower rates of population growth. Our findings suggest that isolation by distance and/or habitat barriers may play a role in the divergence of non‐cichlid fishes in LT, but this effect varies by species.     

Has past climate change affected cold‐specialized species differentially through space and time?

Quaternary climate change has been strongly linked to distributional shifts and recent species diversification. Montane species, in particular, have experienced enhanced isolation and rapid genetic divergence during glacial fluctuations, and these processes have resulted in a disproportionate number of neo‐endemic species forming in high‐elevation habitats. In temperate montane environments, a general model of alpine population history is well supported, where cold‐specialized species track favourable climate conditions downslope during glacial episodes and upslope during warmer interglacial periods, which leads to a climate‐driven population or species diversification pump. However, it remains unclear how geography mediates distributional changes and whether certain episodes of glacial history have differentially impacted rates of diversification. We address these questions by examining phylogenomic data in a North American clade of flightless, cold‐specialized insects, the ice crawlers (Insecta: Grylloblattodea: Grylloblattidae: Grylloblatta). These low‐vagility organisms have the potential to reveal highly localized refugia and patterns of spatial recolonization, as well as a longer history of in situ diversification. Using continuous phylogeographic analysis of species groups, we show that all species tend to retreat to nearby low‐elevation habitats across western North America during episodes of glaciation, but species at high latitude exhibit larger distributional shifts. Lineage diversification was examined over the course of the Neogene and Quaternary periods, with statistical analysis supporting a direct association between climate variation and diversification rate. Major increases in lineage diversification appear to be correlated with warm and dry periods, rather than with extreme glacial events. Finally, we identify substantial cryptic diversity among ice crawlers, leading to high endemism across their range. This diversity provides new insights into highly localized glacial refugia for cold‐specialized species across western North America.     

Extending ecological niche models to the past 120 000 years corroborates the lack of strong phylogeographic structure in the Crested Drongo (Dicrurus forficatus forficatus) on Madagascar

We conduct a phylogeographic study of the Crested Drongo (Dicrurus forficatus forficatus), a broadly distributed bird species on Madagascar. We first determined the demographic and spatial pattern inferred from mitochondrial and nuclear data, and then compared these results with predictions from a present to 0.120‐Myr‐old reconstruction of the spatial dynamics of the range of D. f. forficatus on Madagascar, enabling putative areas of stability (lineage persistence) to be detected. Weak genetic structure along an east–west pattern and comparatively low genetic diversity were recovered, with strong evidence of population expansion found at all ten loci sampled. The palaeoclimatic distribution models over the past 0.120 Myr suggest the presence of extensive areas of suitable climate in the east and west for the species since its colonization of Madagascar, a result in strong concordance with the spatial and genetic signal derived from our multilocus data set. © 2013 The Linnean Society of London     

Isolation in habitat refugia promotes rapid diversification in a montane tropical salamander

Aim Our goal was to reconstruct the phylogenetic history and historical demography of highly divergent populations of the endemic plethodontid salamander Pseudoeurycea leprosa, to elucidate the timing and mechanisms of divergence in the Trans‐Volcanic Belt of Mexico. Location The Trans‐Volcanic Belt (TVB) of central Mexico, including the states of Mexico, Morelos, Puebla, Tlaxcala and Veracruz. Methods We sequenced the cytochrome b mitochondrial DNA gene for 281 individuals from 26 populations and nine mountain ranges in the TVB, and used Bayesian phylogenetic reconstruction and Markov chain Monte Carlo coalescent methods to infer historical demographic parameters and divergences among populations in each mountain system. Results We found deep genetic divergences between eastern and central TVB mountain systems despite their recent volcanic origin. Populations of P. leprosa show a pattern of refugial populations in the north‐eastern and eastern limits of the species’ distribution, and genetic evidence of rapid population expansion in mountain ranges of the central TVB. The oldest divergences among populations date to c. 3.8 Ma, and the most recent divergences in the central TVB are Pleistocene in age (c. 0.7 Ma). Main conclusions Given the timing and order of population diversification in P. leprosa, we conclude that early isolation in multiple habitat refuges in north‐eastern and eastern mountain ranges played an important role in structuring population diversity in the TVB, followed by population expansion and genetic divergence of the central range populations. The dynamic climatic and volcanic changes in this landscape generally coincide with the history of intra‐specific diversification in P. leprosa. Climate‐driven changes in habitat distribution in an actively changing volcanic landscape have shaped divergences in the TVB and very likely contributed to the high levels of speciation and endemism in this biodiverse region.     

High levels of intraspecific genetic divergences revealed for Antarctic springtails: evidence for small‐scale isolation during Pleistocene glaciation

We examined levels of genetic variability within and among populations of three Antarctic springtail species (Arthropoda: Collembola) and tested the hypothesis that genetic divergences occur among glacially‐isolated habitats. The study was conducted in southern Victoria Land, Ross Dependency, Antarctica, and samples were collected from locations in the vicinity of the Mackay Glacier. We analyzed mtDNA (cytochrome c oxidase subunit I; COI) sequence variability for 97 individuals representing three species (Gomphiocephalus hodgsoni, N = 67; Cryptopygus nivicolus, N = 20; and Antarcticinella monoculata, N = 8). Haplotype diversity and genetic divergences were calculated and used to indicate population variability and also to infer divergence times of isolated populations using molecular clock estimates. Two of the three species showed high levels of genetic divergence. Gomphiocephalus hodgsoni, a widespread and common species, showed 7.6% sequence divergence on opposite sides of the Mackay Glacier. The more range restricted C. nivicolus showed 4.0% divergence among populations. The third species, A. monoculata, was found in only one location. Molecular clock estimates based on sequence divergences suggest that populations separated within the last 4 Mya. We conclude that habitat fragmentation resulting from Pliocene (5 Mya) and Pleistocene (2 Mya to 10 Kya) glaciations has promoted and maintained high levels of diversity among isolated springtail populations on relatively small spatial scales. The region surrounding the Mackay Glacier is likely to have provided refugia for springtail populations during glacial maxima and remains an area of high genetic and species diversity for Collembola within the Ross Sea region.     

Phylogeographic analysis of the nocturnal velvet ant genus Dilophotopsis (Hymenoptera: Mutillidae) provides insights into diversification in the Nearctic deserts

Understanding the history of diversification in the North American deserts has long been a goal of biogeographers and evolutionary biologists. Although it appears that a consensus is forming regarding the patterns of diversification in the Nearctic deserts in vertebrate taxa, little work has been done exploring the historical biogeography of widespread invertebrate taxa. Before a robust model of geobiotic change in the North American deserts can be proposed, it needs to be determined whether the same historical events affected vertebrate and invertebrate taxa in the same way. We explore the phylogeographic patterns in a widespread nocturnal wasp genus Dilophotopsis using two rDNA loci, the internal transcribed spacer regions 1 and 2 (ITS1 and ITS2). We use Bayesian phylogenetic analysis and haplotype network analysis to determine whether a consistent geographic pattern exists among species and populations within Dilophotopsis. We also used molecular dating techniques to estimate divergence dates of the major phylogenetic clades. Our analyses indicates that the species‐level divergences in Dilophotopsis occurred in the Neogene, and likely were driven by mountain building during the Miocene–Pliocene boundary (approximately 5 Mya) similar to the divergences in many vertebrate taxa. The population‐level divergences within species occurred during the Pleistocene (0.1–1.8 Mya). The present study shows that similar patterns of diversification exist in vertebrate and invertebrate taxa. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 360–375.     

Cryptic species and co‐diversification in sand scorpions from the Karakum and Kyzylkum deserts of Central Asia

Little is known about species diversification within the deserts of Central Asia. For example, the degree of lineage divergence and timing of population differentiation, as well as potential biogeographic barriers driving diversification, are nearly unknown. Here, we analysed a multi‐locus data set for a widespread sand scorpion (Mesobuthus gorelovi) to evaluate cryptic species diversity and phylogeographic patterns across the Karakum and Kyzylkum deserts. We also combined these data with previously published sequence data to test for a signal of co‐diversification. A consensus species delimitation approach indicated that the widespread M. gorelovi is likely composed of up to five distinct species that began to diversify at the Miocene–Pliocene boundary. We observed shared patterns of lineage divergence across the Amu Darya River region in three scorpion taxa and found support for a shared history of assemblage diversification across this biogeographic barrier. Thus, major river systems appear to facilitate diversification among desert scorpions.     

Evolutionary drivers of phylogeographical diversity in the highlands of Mexico: a case study of the Crotalus triseriatus species group of montane rattlesnakes

Aim To assess the genealogical relationships of widespread montane rattlesnakes in the Crotalus triseriatus species group and to clarify the role of Late Neogene mountain building and Pleistocene pine–oak forest fragmentation in driving the diversification of Mexican highland taxa. Location Highlands of mainland Mexico and the south‐western United States (Texas, New Mexico, and Arizona). Methods A synthesis of inferences was used to address several associated questions about the biogeography of the Mexican highlands and the evolutionary drivers of phylogeographical diversity in co‐distributed taxa. We combined extensive range‐wide sampling (130 individuals representing five putative species) and mixed‐model phylogenetic analyses of 2408 base pairs of mitochondrial DNA to estimate genealogical relationships and divergence times within the C. triseriatus species group. We then assessed the tempo of diversification using a maximum likelihood framework based on the birth–death process. Estimated times of divergences provided a probabilistic temporal component and questioned whether diversification rates have remained constant or varied over time. Finally, we looked for phylogeographical patterns in other co‐distributed taxa. Results We identified eight major lineages within the C. triseriatus group, and inferred strong correspondence between maternal and geographic history within most lineages. At least one cryptic species was detected. Relationships among lineages were generally congruent with previous molecular studies, with differences largely attributable to our expanded taxonomic and geographic sampling. Estimated divergences between most major lineages occurred in the Late Miocene and Pliocene. Phylogeographical structure within each lineage appeared to have been generated primarily during the Pleistocene. Although the scale of genetic diversity recognized affected estimated rates of diversification, rates appeared to have been constant through time. Main conclusions The biogeographical history of the C. triseriatus group implies a dynamic history for the highlands of Mexico. The Neogene formation of the Transvolcanic Belt appears responsible for structuring geographic diversity among major lineages. Pleistocene glacial–interglacial climatic cycles and resultant expansions and contractions of the Mexican pine–oak forest appear to have driven widespread divergences within lineages. Climatic change, paired with the complex topography of Mexico, probably produced a myriad of species‐specific responses in co‐distributed Mexican highland taxa. The high degree of genetic differentiation recovered in our study and others suggests that the Mexican highlands may contain considerably more diversity than currently recognized.     

Evolution and biogeography of the endemic Roucela complex (Campanulaceae: Campanula) in the Eastern Mediterranean

At the intersection of geological activity, climatic fluctuations, and human pressure, the Mediterranean Basin – a hotspot of biodiversity – provides an ideal setting for studying endemism, evolution, and biogeography. Here, we focus on the Roucela complex (Campanula subgenus Roucela), a group of 13 bellflower species found primarily in the eastern Mediterranean Basin. Plastid and low‐copy nuclear markers were employed to reconstruct evolutionary relationships and estimate divergence times within the Roucela complex using both concatenation and species tree analyses. Niche modeling, ancestral range estimation, and diversification analyses were conducted to provide further insights into patterns of endemism and diversification through time. Diversification of the Roucela clade appears to have been primarily the result of vicariance driven by the breakup of an ancient landmass. We found geologic events such as the formation of the mid‐Aegean trench and the Messinian Salinity Crisis to be historically important in the evolutionary history of this group. Contrary to numerous past studies, the onset of the Mediterranean climate has not promoted diversification in the Roucela complex and, in fact, may be negatively affecting these species. This study highlights the diversity and complexity of historical processes driving plant evolution in the Mediterranean Basin.     

Evolutionary history inferred from the de novo assembly of a nonmodel organism,the blue‐eyed black lemur

Lemurs, the living primates most distantly related to humans, demonstrate incredible diversity in behaviour, life history patterns and adaptive traits. Although many lemur species are endangered within their native Madagascar, there is no high‐quality genome assembly from this taxon, limiting population and conservation genetic studies. One critically endangered lemur is the blue‐eyed black lemur Eulemur flavifrons. This species is fixed for blue irises, a convergent trait that evolved at least four times in primates and was subject to positive selection in humans, where 5′ regulatory variation of OCA2 explains most of the brown/blue eye colour differences. We built a de novo genome assembly for E. flavifrons, providing the most complete lemur genome to date, and a high confidence consensus sequence for close sister species E. macaco, the (brown‐eyed) black lemur. From diversity and divergence patterns across the genomes, we estimated a recent split time of the two species (160 Kya) and temporal fluctuations in effective population sizes that accord with known environmental changes. By looking for regions of unusually low diversity, we identified potential signals of directional selection in E. flavifrons at MITF, a melanocyte development gene that regulates OCA2 and has previously been associated with variation in human iris colour, as well as at several other genes involved in melanin biosynthesis in mammals. Our study thus illustrates how whole‐genome sequencing of a few individuals can illuminate the demographic and selection history of nonmodel species.     

Genetic and phenotypic variation in a colourful treefrog across five geographic barriers

Aim Understanding the patterns and processes underlying phenotype in a polytypic species provides key insights into microevolutionary mechanisms of diversification. The red‐eyed treefrog, Agalychnis callidryas, exhibits strong regional differentiation in colour pattern, corresponding to five admixed mitochondrial DNA clades. We evaluated spatial diversity patterns across multiple, putative barriers to examine the fine‐scale processes that mediate phenotypic divergence between some regions while maintaining homogeneity between others. Location We examined patterns of phenotypic diversification among 17 sites that span five putative biogeographic barriers in lower Central America (Costa Rica and Panama). Methods We tested the extent to which genetic distance (F_ST) derived from six multilocus nuclear genotypes covaried with measures of phenotypic distance (leg coloration) within and between biogeographic regions. We used linear regression analyses to determine the role of geographic and genetic factors in structuring spatial patterns of phenotypic diversity. Results The factors that best explained patterns of phenotypic diversity varied among biogeographic regions. We identified one geographic barrier that impeded gene exchange and resulted in concordant phenotypic divergence across the Continental Divide, isolating Caribbean and Pacific populations. Across Caribbean Costa Rican populations, one barrier structured phenotypic but not genetic diversity patterns, indicating a role for selection. In other regions, the putative barriers had no determining effect on either genetic or leg colour structure. Main conclusions The processes mediating the distribution and diversification of colour pattern in this polytypic, wide‐ranging treefrog varied among biogeographic regions. Spatially varying selection combined with the isolating effects of geographic factors probably resulted in the patchy distribution of colour diversity across Costa Rican and Panamanian populations.     

Explaining disparities in species richness between Mediterranean floristic regions: a case study in Gladiolus (Iridaceae)

Aim The causes of geographical variation in species richness in clades that do not follow the latitudinal diversity gradient have rarely been investigated. Here, we examine spatial asymmetries of diversity in Gladiolus (Iridaceae), a large genus (> 260 species) that is present in two mediterranean climate biomes: the Cape of southern Africa (106 species) and the Mediterranean Basin (7 species). Despite convergence of climatic conditions between the two regions, the species density of Gladiolus is over one order of magnitude higher in the Cape than in the Mediterranean Basin. We investigate whether the diversity disparities observed in the genus are better explained by recent colonization of species‐poor areas (temporal hypothesis) or by differential rates of diversification (evolutionary hypothesis). Location Africa, Madagascar and Eurasia Methods We employ a recently developed Bayesian method for the estimation of diversification rates and a biogeographical optimization approach within a phylogenetic framework. Results In Gladiolus, the ‘diversity anomaly’ between the two Mediterranean climate regions cannot be explained solely by the time available for speciation in the Cape, but is also due to locally reduced rates of diversification in the Mediterranean Basin. Furthermore, high overall diversity in southern Africa stems from an ancient origin in the Cape allied with high rates of diversification in the summer‐rainfall region of the subcontinent. Main conclusions Both evolutionary and temporal hypotheses must be taken into account in order to explain the diversity anomaly between the Mediterranean Basin and the Cape. Our results suggest that regions at comparable latitudes and/or with similar climate may not converge in diversity levels due to heterogeneity of diversification rates and contrasting biogeographical histories.     

Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genus Forpus

The temporal origins of the extraordinary biodiversity of the Neotropical region are highly debated. Recent empirical work has found support for alternative models on the tempo of speciation in Neotropical species further fuelling the debate. However, relationships within many Neotropical lineages are poorly understood, and it is unclear how this uncertainty impacts inferences on the evolution of taxa in the region. We examined the robustness of diversification patterns in the avian genus Forpus by testing whether the use of different units of biodiversity (i.e. biological species and statistically inferred species) impacted diversification rates and inferences regarding important biogeographic breaks in the genus. We found that the best‐fit model of diversification for the biological species data set was a declining rate of diversification; whereas a model of constant diversification was the best‐fit model for statistically inferred species or subspecies. Moreover, the relative importance of different landscape features in delimiting genetic structure across the landscape varied across data sets with differing units of biodiversity. Patterns based on divergence times among biological species indicated old speciation events across major geographic and river barriers. In contrast, data sets more inclusive of the diversity in Forpus illustrate the role of both old divergence across major landscape features and more recent divergences that are possibly attributed to Pleistocene climatic changes. Overall, these results indicate that conflicting models on the temporal origins of Neotropical birds may be attributable to sampling biases.     

Phylogeography of the Northern Alligator Lizard (Squamata,Anguidae): Hidden diversity in a western endemic

Western North America includes the California Floristic Province and the Pacific Northwest, biologically diverse regions highlighted by a complex topography, geology, climate and history. A number of animals span these regions and show distinctive patterns of dispersal, vicariance and lineage diversification. Examining phylogeographic patterns in the fauna of this area aids in our understanding of the forces that have contributed to the generation and maintenance of regional biodiversity. Here, we investigate the biogeography and population structure of the Northern Alligator Lizard (Elgaria coerulea), a wide‐ranging anguid endemic to western North America. We sequenced two mtDNA fragments (ND2 and ND4) for 181 individuals across the range of the species and analysed these data with phylogenetic approaches to infer population and biogeographic history, and date major divergences within the taxon. We further used Bayesian clustering methods to assess major patterns of population structure and performed ecological niche modelling (ENM) to aid in our interpretation of geographic structure and diversification of E. coerulea lineages. Our phylogeographic examination of E. coerulea uncovered surprising diversity and structure, recovering 10 major lineages, each with substantial geographic substructure. While some divergences within the species are relatively old (Pliocene, 5.3–2.6 mya), most intraspecific variation appears to be of more recent origin (Pleistocene, 2.6 mya‐11,700 ya). Current diversity appears to have arisen in the Sierra Nevada Mountains and spread west and north since the Pliocene. Finally, our ENMs suggest that much of the Coast Ranges in California provided ideal habitat during the Last Glacial Maxima (LGM) that has since contracted dramatically and shifted northwards, whereas significant portions of the Sierra Nevada were unsuitable during the LGM and have since become more suitable. Interestingly, E. coerulea shares a number of genetic boundaries with other sympatric taxa, suggesting common historical events and geomorphological features have shaped the biota of this region.     

Phylogeography,historical demography and habitat suitability modelling of freshwater fishes inhabiting seasonally fluctuating Mediterranean river systems: a case study using the Iberian cyprinid Squalius valentinus

The Mediterranean freshwater fish fauna has evolved under constraints imposed by the seasonal weather/hydrological patterns that define the Mediterranean climate. These conditions have influenced the genetic and demographic structure of aquatic communities since their origins in the Mid‐Pliocene. Freshwater species in Mediterranean‐type climates will likely constitute genetically well‐differentiated populations, to varying extents depending on basin size, as a consequence of fragmentation resulting from drought/flood cycles. We developed an integrative framework to study the spatial patterns in genetic diversity, demographic trends, habitat suitability modelling and landscape genetics, to evaluate the evolutionary response of Mediterranean‐type freshwater fish to seasonal fluctuations in weather. To test this evolutionary response, the model species used was Squalius valentinus, an endemic cyprinid of the Spanish Levantine area, where seasonal weather fluctuations are extreme, although our findings may be extrapolated to other Mediterranean‐type species. Our results underscore the significant role of the Mediterranean climate, along with Pleistocene glaciations, in diversification of S. valentinus. We found higher nuclear diversity in larger drainage basins, but higher mitochondrial diversity correlated to habitat suitability rather than basin size. We also found strong correlation between genetic structure and climatic factors associated with Mediterranean seasonality. Demographic and migration analyses suggested population expansion during glacial periods that also contributed to the current genetic structure of S. valentinus populations. The inferred models support the significant contribution of precipitation and temperature to S. valentinus habitat suitability and allow recognizing areas of habitat stability. We highlight the importance of stable habitat conditions, fostered by typical karstic springs found on the Mediterranean littoral coasts, for the preservation of freshwater species inhabiting seasonally fluctuating river systems.     

Differing contributions of density dependence and climate to the population dynamics of three eruptive herbivores

1. Although both endogenous and exogenous processes regulate populations, the current understanding of the contributions from density dependence and climate to the population dynamics of eruptive herbivores remains limited. 2. Using a 17‐year time series of three cereal aphid species [Rhopalosiphum padi L., Metopolophium dirhodum (Walker), and Diuraphis noxia (Kurdumov)] compiled from a trapping network spanning the northwestern U.S.A., temporal and spatial patterns associated with population fluctuations, and modelled density dependence in aphid abundances were tested. These models were used to analyse correlations between climate and aphid abundances in the presence and absence of residual variance as a result of density‐dependent effects. 3. The temporal dynamics of aphid population fluctuations indicated periodicity, with no clear evidence for a spatial pattern underlying population fluctuations. 4. Aphid abundances oscillated in a manner consistent with delayed density dependence for all three aphid species, although the strength of these feedbacks differed among species. 5. Diuraphis noxia abundances were negatively correlated with increasing temperatures in the absence of density‐dependent effects, whereas M. dirhodum abundances were positively correlated with increasing cumulative precipitation in the presence of density‐dependent effects; yet, R. padi abundances were unrelated to climate variables irrespective of population feedbacks. 6. Our analysis suggests that endogenous feedbacks differentially regulate aphid populations in the northwestern U.S.A., and these feedbacks may operate at an expansive spatial scale. It is concluded that the contributions of density dependence and climate to aphid population dynamics are species‐specific in spite of similar ecological niches, with implications for assessing species responses to climate variability.     

A tale of the nearly tail‐less: the effects of Plio‐Pleistocene climate change on the diversification of the African avian genus Sylvietta

Sylvietta is a broadly distributed group of African species inhabiting a wide range of habitats and presents an interesting opportunity to investigate the historic mechanisms that have impacted the biogeography of African avian species. We collected sequence data from 50 individuals and used model‐based phylogenetic methods, molecular divergence estimates and ancestral area estimates to construct a time‐calibrated phylogeny and estimation of biogeographic history. We estimate a southern African origin for Sylvietta, with an initial divergence splitting the genus into two clades. The first consists of arid‐adapted species, with a southern African origin and subsequent diversification north into Ethiopia–Somalia. The second clade is estimated as having a Congolian forest origin with an eastward pattern of colonization and diversification as a result of Plio‐Pleistocene forest dynamics. Additionally, two members of the genus Sylvietta display interesting patterns of intraspecific diversification. Sylvietta rufescens is an arid‐adapted species inhabiting southern Africa, and we recover two subclades with a divergence dating to the Pleistocene, a unique pattern for avian species which may be explained via isolation in arid habitat fragments in the early Pleistocene. Second, Sylvietta virens, a species endemic to Afro‐tropical forests, is recovered with geographically structured genetic diversification across its broad range, an interesting result given that recent investigations of several avian forest species have found similar and substantial geographically structured genetic diversity relating to Plio‐Pleistocene forest fragmentation. Overall, Plio‐Pleistocene habitat cycling played a significant role in driving diversification in Sylvietta, and this investigation highlights the substantial impact of climate‐driven habitat dynamics on the history of sub‐Saharan species.     

Contrasting demographic history and gene flow patterns of two mangrove species on either side of the Central American Isthmus

Comparative phylogeography offers a unique opportunity to understand the interplay between past environmental events and life‐history traits on diversification of unrelated but co‐distributed species. Here, we examined the effects of the quaternary climate fluctuations and palaeomarine currents and present‐day marine currents on the extant patterns of genetic diversity in the two most conspicuous mangrove species of the Neotropics. The black (Avicennia germinans, Avicenniaceae) and the red (Rhizophora mangle, Rhizophoraceae) mangroves have similar geographic ranges but are very distantly related and show striking differences on their life‐history traits. We sampled 18 Atlantic and 26 Pacific locations for A. germinans (N = 292) and R. mangle (N = 422). We performed coalescence simulations using microsatellite diversity to test for evidence of population change associated with quaternary climate fluctuations. In addition, we examined whether patterns of genetic variation were consistent with the directions of major marine (historical and present day) currents in the region. Our demographic analysis was grounded within a phylogeographic framework provided by the sequence analysis of two chloroplasts and one flanking microsatellite region in a subsample of individuals. The two mangrove species shared similar biogeographic histories including: (1) strong genetic breaks between Atlantic and Pacific ocean basins associated with the final closure of the Central American Isthmus (CAI), (2) evidence for simultaneous population declines between the mid‐Pleistocene and early Holocene, (3) asymmetric historical migration with higher gene flow from the Atlantic to the Pacific oceans following the direction of the palaeomarine current, and (4) contemporary gene flow between West Africa and South America following the major Atlantic Ocean currents. Despite the remarkable differences in life‐history traits of mangrove species, which should have had a strong influence on seed dispersal capability and, thus, population connectivity, we found that vicariant events, climate fluctuations and marine currents have shaped the distribution of genetic diversity in strikingly similar ways.     

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.