Global determinants and conservation of evolutionary and geographic rarity in land vertebrates

Deciphering global trends in phylogenetic endemism is crucial for understanding broad-scale evolutionary patterns and the conservation of key elements of biodiversity. However, knowledge to date on global phylogenetic endemism and its determinants has been lacking. Here, we conduct the first global analysis of phylogenetic endemism patterns of land vertebrates (>30,000 species), their environmental correlates, and threats. We found that low temperature seasonality and high topographic heterogeneity were the main global determinants of phylogenetic endemism. While phylogenetic endemism hotspots cover 22% of Earth, these regions currently have a high human footprint, low natural land cover, minimal protection, and will be greatly affected by climate change. Evolutionarily unique, narrow-range species are crucial for sustaining biodiversity in the face of environmental change. Our global study advances the current understanding of this imperilled yet previously overlooked facet of biodiversity.

Evolutionary dynamics of the elevational diversity gradient in passerine birds

Low-elevation regions harbour the majority of the world's species diversity compared to high-elevation areas. This global gradient suggests that lowland species have had more time to diversify, or that net diversification rates have been higher in the lowlands. However, highlands seem to be cradles of diversity as they contain many young endemics, suggesting that their rates of speciation are exceptionally fast. Here we use a phylogenetic diversification model that accounts for the dispersal of species between different elevations to examine the evolutionary dynamics of the elevational diversity gradient in passerine birds, a group that has radiated globally to occupy almost all elevations and latitudes. We find strong support for a model in which passerines diversify at the same rate in the highlands and the lowlands but in which the per-capita rate of dispersal from high to low elevations is more than twice as fast as that in the reverse direction. This suggests that while there is no consistent trend in diversification across elevations, part of the diversity generated by highland regions migrates into the lowlands, thus setting up the observed gradient in passerine diversity. We find that this process drives tropical regions but for temperate areas, the analysis could be hampered by their lower richness. Despite their lower diversity, highland regions are disproportionally important for maintaining diversity in the adjacent lowlands.

Cradles and museums of generic plant diversity across tropical Africa

Determining where species diversify (cradles) and persist (museums) over evolutionary time is fundamental to understanding the distribution of biodiversity and for conservation prioritization. Here, we identify cradles and museums of angiosperm generic diversity across tropical Africa, one of the most biodiverse regions on Earth. Regions containing nonrandom concentrations of young (neo-) and old (paleo-) endemic taxa were identified using distribution data of 1719 genera combined with a newly generated time-calibrated mega-phylogenetic tree. We then compared the identified regions with the current network of African protected areas (PAs). At the generic level, phylogenetic diversity and endemism are mainly concentrated in the biogeographically complex region of Eastern Africa. We show that mountainous areas are centres of both neo- and paleo-endemism. By contrast, the Guineo-Congolian lowland rain forest region is characterized by widespread and old lineages. We found that the overlap between centres of phylogenetic endemism and PAs is high (> 85%). We show the vital role played by mountains acting simultaneously as cradles and museums of tropical African plant biodiversity. By contrast, lowland rainforests act mainly as museums for generic diversity. Our study shows that incorporating large-scale taxonomically verified distribution datasets and mega-phylogenies lead to an improved understanding of tropical plant biodiversity evolution.

Geographic variation in the laryngeal morphology of a widely distributed South-American anuran: behavioural and evolutionary implications

Sound-producing organs generate acoustic signals that have a fundamental role in communication systems. In species exhibiting different biogeographic patterns, variations of these structures can explain a large part of interpopulation differences of their signals. Pleurodema thaul is an anuran with an extensive geographic distribution in Chile and presents an evident divergence in its acoustic signals among three genetic/bioacoustic groups (i.e. northern, central and southern). By means of classic histology and 3D-reconstructions, we study the geographic variation in the larynx of P. thaul males from these three groups. In addition, volumes of six laryngeal structures are used as predictors of acoustic characteristics of advertisement calls recorded in previous studies for the same subjects used in the current study. After removing the effect of body size, the arytenoid cartilage, dilator muscle and vocal cords show significant differences between the three bioacoustic groups. Furthermore, arytenoid cartilage and dilator muscle volumes predict some temporal parameters and also the dominant frequency of advertisement calls. Our results show important geographic variation in laryngeal morphology, which is in correspondence with acoustic, behavioural and genetic variation in this species.

Glaciations, gradients, and geography: multiple drivers of diversification of bush frogs in the Western Ghats Escarpment

The historical processes underlying high diversity in tropical biodiversity hotspots like the Western Ghats of Peninsular India remain poorly understood. We sampled bush frogs on 13 massifs across the Western Ghats Escarpment and examined the relative influence of Quaternary glaciations, ecological gradients and geological processes on the spatial patterns of lineage and clade diversification. The results reveal a large in situ radiation (more than 60 lineages), exhibiting geographical structure and clade-level endemism, with two deeply divergent sister clades, North and South, highlighting the biogeographic significance of an ancient valley, the Palghat Gap. A majority of the bush frog sister lineages were isolated on adjacent massifs, and signatures of range stasis provide support for the dominance of geological processes in allopatric speciation. In situ diversification events within the montane zones (more than 1800 m) of the two highest massifs suggest a role for climate-mediated forest-grassland persistence. Independent transitions along elevational gradients among sub-clades during the Miocene point to diversification along the elevational gradient. The study highlights the evolutionary significance of massifs in the Western Ghats with the high elevations acting as centres of lineage diversification and the low- and mid-elevations of the southern regions, with deeply divergent lineages, serving as museums.

Molecular systematics and biogeography of lowland antpittas (Aves, Grallariidae): The role of vicariance and dispersal in the diversification of a widespread Neotropical lineage

We infer phylogenetic relationships, divergence times, and the diversification history of the avian Neotropical antpitta genera Hylopezus and Myrmothera (Grallariidae), based on sequence data (3,139 base pairs) from two mitochondrial (ND2 and ND3) and three nuclear nuclear introns (TGFB2, MUSK and FGB-I5) from 142 individuals of the 12 currently recognized species in Hylopezus and Myrmothera and 5 outgroup species. Phylogenetic analyses recovered 19 lineages clustered into two major clades, both distributed in Central and South America. Hylopezus nattereri, previously considered a subspecies of H. ochroleucus, was consistently recovered as the most divergent lineage within the Grallaricula/Hylopezus/Myrmothera clade. Ancestral range estimation suggested that modern lowland antpittas probably originated in the Amazonian Sedimentary basin during the middle Miocene, and that most lineages within the Hylopezus/Myrmothera clade appeared in the Plio-Pleistocene. However, the rate of diversification in the Hylopezus/Myrmothera clade appeared to have remained constant through time, with no major shifts over the 20 million years. Although the timing when most modern lineages of the Hylopezus/Myrmothera clade coincides with a period of intense landscape changes in the Neotropics (Plio-Pleistocene), the absence of any significant shifts in diversification rates over the last 20 million years challenges the view that there is a strict causal relationship between intensification of landscape changes and cladogenesis. The relative old age of the Hylopezus/Myrmothera clade coupled with an important role ascribed to dispersal for its diversification, favor an alternative scenario whereby long-term persistence and dispersal across an ever-changing landscape might explain constant rates of cladogenesis through time.

Gene flow during glacial habitat shifts facilitates character displacement in a Neotropical flycatcher radiation

BACKGROUND

Pleistocene climatic fluctuations are known to be an engine of biotic diversification at higher latitudes, but their impact on highly diverse tropical areas such as the Andes remains less well-documented. Specifically, while periods of global cooling may have led to fragmentation and differentiation at colder latitudes, they may - at the same time - have led to connectivity among insular patches of montane tropical habitat with unknown consequences on diversification. In the present study we utilized ~5.5 kb of DNA sequence data from eight nuclear loci and one mitochondrial gene alongside diagnostic morphological and bioacoustic markers to test the effects of Pleistocene climatic fluctuations on diversification in a complex of Andean tyrant-flycatchers of the genus Elaenia.

RESULTS

Population genetic and phylogenetic approaches coupled with coalescent simulations demonstrated disparate levels of gene flow between the taxon chilensis and two parapatric Elaenia taxa predominantly during the last glacial period but not thereafter, possibly on account of downward shifts of montane forest habitat linking the populations of adjacent ridges. Additionally, morphological and bioacoustic analyses revealed a distinct pattern of character displacement in coloration and vocal traits between the two sympatric taxa albiceps and pallatangae, which were characterized by a lack of gene flow.

CONCLUSION

Our study demonstrates that global periods of cooling are likely to have facilitated gene flow among Andean montane Elaenia flycatchers that are more isolated from one another during warm interglacial periods such as the present era. We also identify a hitherto overlooked case of plumage and vocal character displacement, underpinning the complexities of gene flow patterns caused by Pleistocene climate change across the Andes.

Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens)

The little greenbul, a common rainforest passerine from sub-Saharan Africa, has been the subject of long-term evolutionary studies to understand the mechanisms leading to rainforest speciation. Previous research found morphological and behavioural divergence across rainforest-savannah transition zones (ecotones), and a pattern of divergence with gene flow suggesting divergent natural selection has contributed to adaptive divergence and ecotones could be important areas for rainforests speciation. Recent advances in genomics and environmental modelling make it possible to examine patterns of genetic divergence in a more comprehensive fashion. To assess the extent to which natural selection may drive patterns of differentiation, here we investigate patterns of genomic differentiation among populations across environmental gradients and regions. We find compelling evidence that individuals form discrete genetic clusters corresponding to distinctive environmental characteristics and habitat types. Pairwise F_ST between populations in different habitats is significantly higher than within habitats, and this differentiation is greater than what is expected from geographic distance alone. Moreover, we identified 140 SNPs that showed extreme differentiation among populations through a genomewide selection scan. These outliers were significantly enriched in exonic and coding regions, suggesting their functional importance. Environmental association analysis of SNP variation indicates that several environmental variables, including temperature and elevation, play important roles in driving the pattern of genomic diversification. Results lend important new genomic evidence for environmental gradients being important in population differentiation.

DISPERSAL, VICARIANCE, AND CLOCKS: HISTORICAL BIOGEOGRAPHY AND SPECIATION IN A COSMOPOLITAN PASSERINE GENUS (ANTHUS: MOTACILLIDAE)

Dispersal and vicariant hypotheses have for decades been at odds with each other, notwithstanding the fact that both are well-established natural processes with important histories in biogeographic analyses. Despite their importance, neither dispersal nor vicariant methodologies are problem-free. The now widely used molecular techniques for generating phylogenies have provided a mechanism by which both dispersal- and vicariance-driven speciation can be better tested via the application of molecular clocks; unfortunately, substantial problems can also exist in the employment of those clocks. To begin to assess the relative roles of dispersal and vicariance in the establishment of avifaunas, especially intercontinental avifaunas, I applied a test for clocklike behavior in molecular data, as well as a program that infers ancestral areas and dispersal events, to a phylogeny of a speciose, cosmopolitan avian genus (Anthus; Motacillidae). Daughter-lineages above just 25 of 40 nodes in the Anthus phylogeny are evolving in a clocklike manner and are thus dateable by a molecular clock. Dating the applicable nodes suggests that Anthus arose nearly 7 million yr ago, probably in eastern Asia, and that between 6 and 5 million yr ago, Anthus species were present in Africa, the Palearctic, and North and South America. Speciation rates have been high throughout the Pliocene and quite low during the Pleistocene; further evidence that the Pleistocene may have had little effect in generating modern species. Intercontinental movements since 5 million yr ago have been few and largely restricted to interchange between Eurasia and Africa. Species swarms on North America, Africa, and Eurasia (but not South America or Australia) are the product of multiple invasions, rather than being solely the result of within-continent speciation. Dispersal has clearly played an important role in the distribution of this group.

Divergence at the edges: peripatric isolation in the montane spiny throated reed frog complex

Background

Peripatric speciation and peripheral isolation have uncertain importance in species accumulation, and are largely overshadowed by assumed dominance of allopatric modes of speciation. Understanding the role of different speciation mechanisms within biodiversity hotspots is central to understanding the generation of biological diversity. Here, we use a phylogeographic analysis of the spiny-throated reed frogs and examine sister pairings with unbalanced current distributional ranges for characteristics of peripatric speciation. We further investigate whether forest/grassland mosaic adapted species are more likely created through peripatric speciation due to instability of this habitat type.

Results

We reconstructed a multi-locus molecular phylogeny of spiny-throated reed frogs which we then combined with comparative morphologic data to delimit species and analyze historical demographic change; identifying three new species. Three potential peripatric speciation events were identified along with one case of allopatric speciation. Peripatric speciation is supported through uneven potential and realized distributions and uneven population size estimates based on field collections. An associated climate shift was observed in most potentially peripatric splits. Morphological variation was highest in sexually dimorphic traits such as body size and gular shape, but this variation was not limited to peripatric species pairs as hypothesized. The potentially allopatric species pair showed no niche shifts and equivalent effective population sizes, ruling out peripatry in that speciation event. Two major ecological niche shifts were recovered within this radiation, possibly as adaptations to occupy areas of grassland that became more prevalent in the last 5 million years. Restricted and fluctuating grassland mosaics within forests might promote peripatric speciation in the Eastern Arc Biodiversity Hotspot (EABH).

Conclusions

In our case study, peripatric speciation appears to be an important driver of diversity within the EABH biodiversity hotspot, implying it could be a significant speciation mechanism in highly fragmented ecosystems. Extensive peripatric speciation in this montane archipelago may explain the abundance of discrete lineages within the limited area of the EABH, as inferred in remote island archipelagos. Future phylogenetic studies incorporating demographic and spatial analyses will clarify the role of peripatric speciation in creating biodiversity hotspots.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0384-3) contains supplementary material, which is available to authorized users.

Niche divergence promotes rapid diversification of East African sky island white-eyes (Aves: Zosteropidae)

The Eastern Afromontane biodiversity hotspot composed of highly fragmented forested highlands (sky islands) harbours exceptional diversity and endemicity, particularly within birds. To explain their elevated diversity within this region, models founded on niche conservatism have been offered, although detailed phylogeographic studies are limited to a few avian lineages. Here, we focus on the recent songbird genus Zosterops, represented by montane and lowland members, to test the roles of niche conservatism versus niche divergence in the diversification and colonization of East Africa's sky islands. The species-rich white-eyes are a typically homogeneous family with an exceptional colonizing ability, but in contrast to their diversity on oceanic islands, continental diversity is considered depauperate and has been largely neglected. Molecular phylogenetic analysis of ~140 taxa reveals extensive polyphyly among different montane populations of Z. poliogastrus. These larger endemic birds are shown to be more closely related to taxa with divergent habitat types, altitudinal distributions and dispersal abilities than they are to populations of restricted endemics that occur in neighbouring montane forest fragments. This repeated transition between lowland and highland habitats over time demonstrate that diversification of the focal group is explained by niche divergence. Our results also highlight an underestimation of diversity compared to morphological studies that has implications for their taxonomy and conservation. Molecular dating suggests that the spatially extensive African radiation arose exceptionally rapidly (1-2.5 Ma) during the fluctuating Plio-Pleistocene climate, which may have provided the primary driver for lineage diversification.

Little ecological divergence associated with speciation in two African rain forest tree genera

BACKGROUND

The tropical rain forests (TRF) of Africa are the second largest block of this biome after the Amazon and exhibit high levels of plant endemism and diversity. Two main hypotheses have been advanced to explain speciation processes that have led to this high level of biodiversity: allopatric speciation linked to geographic isolation and ecological speciation linked to ecological gradients. Both these hypotheses rely on ecology: in the former conservation of ecological niches through time is implied, while in the latter adaptation via selection to alternative ecological niches would be a prerequisite. Here, we investigate the role of ecology in explaining present day species diversity in African TRF using a species level phylogeny and ecological niche modeling of two predominantly restricted TRF tree genera, Isolona and Monodora (Annonaceae). Both these genera, with 20 and 14 species, respectively, are widely distributed in African TRFs, with a few species occurring in slightly less humid regions such as in East Africa.

RESULTS

A total of 11 sister species pairs were identified most of them occurring in allopatry or with little geographical overlap. Our results provide a mixed answer on the role of ecology in speciation. Although no sister species have identical niches, just under half of the tests suggest that sister species do have more similar niches than expected by chance. PCA analyses also support little ecological differences between sister species. Most speciation events within both genera predate the Pleistocene, occurring during the Late Miocene and Pliocene periods.

CONCLUSIONS

Ecology is almost always involved in speciation, however, it would seem to have had a little role in species generation within Isolona and Monodora at the scale analyzed here. This is consistent with the geographical speciation model for TRF diversification. These results contrast to other studies for non-TRF plant species where ecological speciation was found to be an important factor of diversification. The Pliocene period appears to be a vital time in the generation of African TRF diversity, whereas Pleistocene climatic fluctuations have had a smaller role on speciation than previously thought.Ecological niche modeling, species level phylogeny, ecological speciation, African tropics, Isolona, Monodora, Annonaceae.

Niche conservatism drives elevational diversity patterns in Appalachian salamanders

Many biodiversity hotspots are in montane regions, and many plant and animal groups have their highest species richness at intermediate elevations. Yet, the explanation for this hump-shaped diversity pattern has remained unclear because no studies have addressed both the ecological and evolutionary causes. Here, we address these causes in North American plethodontid salamanders, using a near-comprehensive phylogeny and environmental data. We develop a null model for assessing the relationship between the time that an area has been occupied and its species richness, and we apply a new approach that tests whether clades exhibit long-term stasis in their climatic niches (niche conservatism). Evolutionarily, the midelevation peak in species richness is explained by the time-for-speciation effect, with intermediate-elevation habitats seemingly being inhabited longest and accumulating more species. We find that this pattern is associated with evolutionary stasis in species' climatic niches, driving the midelevation peak by constraining the dispersal of lineages to environments at lower and higher elevations. These processes may help explain elevational diversity patterns in many montane regions around the world. The results also suggest that montane biotas may harbor high levels of both species diversity and phylogenetic diversity but may be particularly susceptible to rapid climate change.

The scramble for Africa: pan-temperate elements on the African high mountains

The composition of isolated floras has long been thought to be the result of relatively rare long-distance dispersal events. However, it has recently become apparent that the recruitment of lineages may be relatively easy and that many dispersal events from distant but suitable habitats have occurred, even at an infraspecific level. The evolution of the flora on the high mountains of Africa has been attributed to the recruitment of taxa not only from the African lowland flora or the Cape Floristic Region, but also to a large extent from other areas with temperate climates. We used the species rich, pan-temperate genera Carex, Ranunculus and Alchemilla to explore patterns in the number of recruitment events and region of origin. Molecular phylogenetic analyses, parametric bootstrapping and ancestral area optimizations under parsimony indicate that there has been a high number of colonization events of Carex and Ranunculus into Africa, but only two introductions of Alchemilla. Most of the colonization events have been derived from Holarctic ancestors. Backward dispersal out of Africa seems to be extremely rare. Thus, repeated colonization from the Northern Hemisphere in combination with in situ radiation has played an important role in the composition of the flora of African high mountains.

Climatic change as an engine for speciation in flightless Orthoptera species inhabiting African mountains

Many East African mountains are characterized by an exceptionally high biodiversity. Here we assess the hypothesis that climatic fluctuations during the Plio-Pleistocene led to ecological fragmentation with subsequent genetic isolation and speciation in forest habitats in East Africa. Hypotheses on speciation in savannah lineages are also investigated. To do this, mitochondrial DNA sequences from a group of bush crickets consisting of both forest and savannah inhabiting taxa were analysed in relation to Plio-Pleistocene range fragmentations indicated by palaeoclimatic studies. Coalescent modelling and mismatch distributions were used to distinguish between alternative biogeographical scenarios. The results indicate two radiations: the earliest one overlaps in time with the global spread of C4 grasslands and only grassland inhabiting lineages originated in this radiation. Climatically induced retraction of forest to higher altitudes about 0.8 million years ago, promoting vicariant speciation in species inhabiting the montane zone, can explain the second radiation. Although much of the biodiversity in East Africa is presently threatened by climate change, past climatic fluctuations appear to have contributed to the species richness observed in the East African hot spots. Perceiving forests as centres of speciation reinforces the importance of conserving the remaining forest patches in the region.

Complex population history of two Anopheles dirus mosquito species in Southeast Asia suggests the influence of Pleistocene climate change rather than human-mediated effects

Anopheles dirus and Anopheles baimaii are closely related species which feed on primates, particularly humans, and transmit malaria in the tropical forests of mainland Southeast Asia. Here, we report an in-depth phylogeographic picture based on 269 individuals from 21 populations from mainland Southeast Asia. Analysis of 1537 bp of mtDNA sequence revealed that the population history of A. baimaii is far more complex than previously thought. An old expansion (pre-300 kyr BP) was inferred in northern India/Bangladesh with a wave of south-eastwards expansion arriving at the Thai border (ca 135-173 kyr BP) followed by leptokurtic dispersal very recently (ca 16 kyr BP) into peninsular Thailand. The long and complex population history of these anthropophilic species suggests their expansions are not in response to the relatively recent (ca 40 kyr BP) human expansions in mainland Southeast Asia but, rather, fit well with our understanding of Pleistocene climatic change there.

Climatic zonation drives latitudinal variation in speciation mechanisms

Many groups of organisms show greater species richness in the tropics than in the temperate zone, particularly in tropical montane regions. Forty years ago, Janzen suggested that more limited temperature seasonality in the tropics leads to greater climatic zonation and more climatic barriers to organismal dispersal along elevational gradients in the tropics relative to temperate regions. These factors could lead to differences in how species arise in tropical versus temperate regions and possibly contribute to greater tropical diversity. However, no studies have compared the relationships among climate, elevational distribution and speciation in a group inhabiting both tropical and temperate regions. Here, we compare elevational and climatic divergence among 30 sister-species pairs (14 tropical, 16 temperate) within a single family of salamanders (Plethodontidae) that reaches its greatest species richness in montane Mesoamerica. In support of Janzen's hypothesis, we find that sister species are more elevationally and climatically divergent in the tropics than in the temperate zone. This pattern seemingly reflects regional variation in the role of climate in speciation, with niche conservatism predominating in the temperate zone and niche divergence in the tropics. Our study demonstrates how latitudinal differences in elevational climatic zonation may increase opportunities for geographical isolation, speciation and the associated build-up of species diversity in the tropics relative to the temperate zone.

The role of Pleistocene refugia and rivers in shaping gorilla genetic diversity in central Africa

The role of Pleistocene forest refugia and rivers in the evolutionary diversification of tropical biota has been the subject of considerable debate. A range-wide analysis of gorilla mitochondrial and nuclear variation was used to test the potential role of both refugia and rivers in shaping genetic diversity in current populations. Results reveal strong patterns of regional differentiation that are consistent with refugial hypotheses for central Africa. Four major mitochondrial haplogroups are evident with the greatest divergence between eastern (A, B) and western (C, D) gorillas. Coalescent simulations reject a model of recent east-west separation during the last glacial maximum but are consistent with a divergence time within the Pleistocene. Microsatellite data also support a similar regional pattern of population genetic structure. Signatures of demographic expansion were detected in eastern lowland (B) and Gabon/Congo (D3) mitochondrial haplogroups and are consistent with a history of postglacial expansion from formerly isolated refugia. Although most mitochondrial haplogroups are regionally defined, limited admixture is evident between neighboring haplogroups. Mantel tests reveal a significant isolation-by-distance effect among western lowland gorilla populations. However, mitochondrial genetic distances also correlate with the distance required to circumnavigate intervening rivers, indicating a possible role for rivers in partitioning gorilla genetic diversity. Comparative data are needed to evaluate the importance of both mechanisms of vicariance in other African rainforest taxa.

Molecular phylogenetics of the bee-eaters (Aves: Meropidae) based on nuclear and mitochondrial DNA sequence data

The bee-eaters (family Meropidae) comprise a group of brightly colored, but morphologically homogeneous, birds with a wide variety of life history characteristics. A phylogeny of bee-eaters was reconstructed using nuclear and mitochondrial DNA sequence data from 23 of the 25 named bee-eater species. Analysis of the combined data set provided a well-supported phylogenetic hypothesis for the family. Nyctiornis is the sister taxon to all other bee-eaters. Within the genus Merops, we recovered two well-supported clades that can be broadly separated into two groups along geographic and ecological lines, one clade with mostly African resident species and the other clade containing a mixture of African and Asian taxa that are mostly migratory species. The clade containing resident African species can be further split into two groups along ecological lines by habitat preference into lowland forest specialists and montane forest and forest edge species. Intraspecific sampling in several of the taxa revealed moderate to high (3.7-6.5%, ND2) levels of divergence in the resident taxa, whereas the lone migratory taxon showed negligible levels of intraspecific divergence. This robust molecular phylogeny provides the phylogenetic framework for future comparative tests of hypotheses about the evolution of plumage patterns, sociality, migration, and delayed breeding strategies.

Build-up of the Himalayan avifauna through immigration: a biogeographical analysis of the Phylloscopus and Seicercus warblers

The Himalayan mountain range is one of the most species-rich areas in the world, harboring about 8% of the world's bird species. In this study, we compare the relative importance of immigration versus in situ speciation to the build-up of the Himalayan avifauna, by evaluating the biogeographic history of the Phylloscopus/Seicercus warblers, a speciose clade that is well represented in Himalayan forests. We use a comprehensive, multigene phylogeny in conjunction with dispersal-vicariance analysis to discern patterns of speciation and dispersal within this clade. The results indicate that virtually no speciation has occurred within the Himalayas. Instead, several speciation events are attributed to dispersal into the Himalayas followed by vicariance between the Himalayas and China/Southeast Asia. Most, perhaps all, of these events appear to be pre-Pleistocene. The apparent lack of speciation within the Himalayas stands in contrast to the mountain-driven Pleistocene speciation suggested for the Andes and the East African mountains.

A PHYLOGENETIC PERSPECTIVE ON ELEVATIONAL SPECIES RICHNESS PATTERNS IN MIDDLE AMERICAN TREEFROGS: WHY SO FEW SPECIES IN LOWLAND TROPICAL RAINFORESTS?

Differences in species richness at different elevations are widespread and important for conservation, but the causes of these patterns remain poorly understood. Here, we use a phylogenetic perspective to address the evolutionary and biogeographic processes that underlie elevational diversity patterns within a region. We focus on a diverse but well-studied fauna of tropical amphibians, the hylid frogs of Middle America. Middle American treefrogs show a "hump-shaped" pattern of species richness (common in many organisms and regions), with the highest regional diversity at intermediate elevations. We reconstructed phylogenetic relationships among 138 species by combining new and published sequence data from 10 genes and then used this phylogeny to infer evolutionary rates and patterns. The high species richness of intermediate elevations seems to result from two factors. First, a tendency for montane clades to have higher rates of diversification. Second, the early colonization of montane regions, leaving less time for speciation to build up species richness in lowland regions (including tropical rainforests) that have been colonized more recently. This "time-for-speciation" effect may explain many diversity patterns and has important implications for conservation. The results also imply that local-scale environmental factors alone may be insufficient to explain the high species richness of lowland tropical rainforests, and that diversification rates are lower in earth's most species-rich biome.

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.

Montane speciation patterns in Ithomiola butterflies (Lepidoptera: Riodinidae): are they consistently moving up in the world?

Tropical lowland areas have often been seen as the centres of terrestrial species proliferation, but recent evidence suggests that young species may be more frequent in montane areas. Several montane speciation modes have been proposed, but their relative frequencies and predominant evolutionary sequence remain unclear because so few biogeographic and phylogenetic studies have tested such questions. I use morphological data to generate a phylogenetic hypothesis for all 11 species of the riodinid butterfly genus Ithomiola (Riodininae: Mesosemiini: Napaeina). These species are shown here to be all strictly geographically and elevationally allo- or parapatrically distributed with respect to their closest relatives in lowland and montane regions throughout the Neotropics. The overwhelming pattern in Ithomiola is of repeated upward parapatric speciation across an elevational gradient, and the genus appears to provide the clearest example to date of vertical montane speciation. All of the young derived species are montane and all of the old basal species are confined to the lowlands, supporting the hypothesis of montane regions largely as 'species pumps' and lowland regions as 'museums'. Possible reasons for the post-speciation maintenance of parapatric ranges in Ithomiola are discussed.

Phylogenetic relationships of the bulbuls (Aves: Pycnonotidae) based on mitochondrial and nuclear DNA sequence data

Bulbuls (Aves: Pycnonotidae) are a fairly speciose (ca. 130 sp.) bird family restricted to the Old World. Family limits and taxonomy have been revised substantially over the past decade, but a comprehensive molecular phylogeny for the family has not been undertaken. Using nuclear and mitochondrial DNA sequences, we reconstructed a well-supported phylogenetic hypothesis for the bulbuls. Three basal lineages were identified: a large African clade, a large Asian clade that also included African Pycnonotus species, and the monotypic African genus Calyptocichla. The African clade was sister to the other two lineages, but this placement did not have high branch support. The genus Pycnonotus was not monophyletic because three species (eutilotus, melanoleucos, and atriceps) were highly diverged from the other species and sister to all other Asian taxa. Additional taxon sampling is needed to further resolve relationships and taxonomy within the large and variable Hypsipetes complex.

Testing alternative mechanisms of evolutionary divergence in an African rain forest passerine bird

Abstract Models of speciation in African rain forests have stressed either the role of isolation or ecological gradients. Here we contrast patterns of morphological and genetic divergence in parapatric and allopatric populations of the Little Greenbul, Andropadus virens, within different and similar habitats. We sampled 263 individuals from 18 sites and four different habitat types in Upper and Lower Guinea. We show that despite relatively high rates of gene flow among populations, A. virens has undergone significant morphological divergence across the savanna-forest ecotone and mountain-forest boundaries. These data support a central component of the divergence-with-gene-flow model of speciation by suggesting that despite large amounts of gene flow, selection is sufficiently intense to cause morphological divergence. Despite evidence of isolation based on neutral genetic markers, we find little evidence of morphological divergence in fitness-related traits between hypothesized refugial areas. Although genetic evidence suggests populations in Upper and Lower Guinea have been isolated for over 2 million years, morphological divergence appears to be driven more by habitat differences than geographic isolation and suggests that selection in parapatry may be more important than geographic isolation in causing adaptive divergence in morphology.

African endemics span the tree of songbirds (Passeri): molecular systematics of several evolutionary 'enigmas'

The deep divergence between the African endemic passerines Picathartidae (rockfowl Picathartes and rockjumpers Chaetops, four species) and the Passerida (ca. 3500 species) suggests an older history of oscines on the African continent than has previously been assumed. In order to determine whether any additional, unexpectedly deep lineages occur in African endemic songbirds, 29 species--including 10 enigmatic focal taxa endemic to southern Africa--were added to a large nuclear sequence dataset gathered from oscine songbirds (Passeri). Phylogenetic analyses of these data resolve many long-standing questions about the affinities of these birds, not all of which were predicted by traditional approaches. The application of a molecular clock indicates that most basal divergences in Passerida occurred in the middle to late Eocene, with divergences between African and Australasian core corvoids occurring somewhat later in the early Miocene. Consistent with inferences for mammals, divergences between Malagasy endemic passerines and their mainland relatives suggests an asynchronous colonization history. This emerging phylogenetic picture reveals that relationships within Old World families are highly informative regarding the early dispersal and radiation of songbirds out of Gondwana. Future analyses will depend on improving resolution of higher-level phylogenetic relationships among these groups, and increasing the density of taxon sampling within them.

Phylogeography of an east Australian wet-forest bird, the satin bowerbird (Ptilonorhynchus violaceus), derived from mtDNA, and its relationship to morphology

Australian wet forests have undergone a contraction in range since the mid-Tertiary, resulting in a fragmented distribution along the east Australian coast incorporating several biogeographical barriers. Variation in mitochondrial DNA and morphology within the satin bowerbird was used to examine biogeographical structure throughout almost the entire geographical extent of these wet forest fragments. We used several genetic analysis techniques, nested clade and barrier analyses, that use patterns inherent in the data to describe the spatial structuring. We also examined the validity of the two previously described satin bowerbird subspecies that are separated by well-defined biogeographical barriers and tested existing hypotheses that propose divergence occurs within each subspecies across two other barriers, the Black Mountain corridor and the Hunter Valley. Our data showed that the two subspecies were genetically and morphologically divergent. The northern subspecies, found in the Wet Tropics region of Queensland, showed little divergence across the Black Mountain corridor, a barrier found to be significant in other Wet Tropics species. Biogeographical structure was found through southeastern Australia; three geographically isolated populations showed genetic differentiation, although minimal divergence was found across the proposed Hunter Valley barrier. A novel barrier was found separating inland and coastal populations in southern New South Wales. Little morphological divergence was observed within subspecies, bar a trend for birds to be larger in the more southerly parts of the species' range. The results from both novel and well-established genetic analyses were similar, providing greater confidence in the conclusions about spatial divergence and supporting the validity of these new techniques.

Mechanisms and tempo of evolution in the African Guineo-Congolian rainforest

This paper reviews how and when African rainforest diversity arose, presenting evidence from both plant and animal studies. Preliminary investigations show that these African forests are an assemblage of species of varying age. Phylogenetic evidence, from both African rainforest angiosperms and vertebrates, suggest a Tertiary origin for the major lineages in some of these groups. In groups where savannah species are well represented and rainforest species are a minority, the latter appear to be relics of a Mid-Tertiary rainforest. By contrast, species that are primarily adapted to rainforest have arisen in the past 10 Myr with the main morphological innovations dating from the Late Miocene, and Quaternary speciation dominating in large, morphologically homogeneous groups. The small number of species-level phylogenies for African rainforest plants hinders a more incisive and detailed study into the historical assembly of these continental forests.