mt DNA PHYLOGENY OF ANDEAN MICE: A TEST OF DIVERSIFICATION ACROSS ECOLOGICAL GRADIENTS

Unlocking Andean sigmodontine diversity: five new species of Chilomys (Rodentia: Cricetidae) from the montane forests of Ecuador

The Andean cloud forests of Ecuador are home to several endemic mammals. Members of the Thomasomyini rodents are well represented in the Andes, with Thomasomys being the largest genus (47 species) of the subfamily Sigmodontinae. Within this tribe, however, there are genera that have escaped a taxonomic revision, and Chilomys Thomas, 1897, constitutes a paradigmatic example of these "forgotten" Andean cricetids. Described more than a century ago, current knowledge of this externally unmistakable montane rodent is very limited, and doubts persist as to whether or not it is monotypic. After several years of field efforts in Ecuador, a considerable quantity of specimens of Chilomys were collected from various localities representing both Andean chains. Based on an extensive genetic survey of the obtained material, we can demonstrate that what is currently treated as C. instans in Ecuador is a complex comprising at least five new species which are described in this paper. In addition, based on these noteworthy new evidence, we amend the generic diagnosis in detail, adding several key craniodental traits such as incisor procumbency and microdonty. These results indicate that Chilomys probably has a hidden additional diversity in large parts of the Colombian and Peruvian territories, inviting a necessary revision of the entire genus.

The formation of avian montane diversity across barriers and along elevational gradients

Tropical mountains harbor exceptional concentrations of Earth's biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. We test how barrier strength and relative elevational distribution predict population differentiation, rates of historical gene flow, and changes in effective population sizes through time. We find population differentiation to be consistently and positively correlated with barrier strength and a species' altitudinal floor. Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area. Surprisingly, even the most divergent taxon pairs at the highest elevations experience gene flow across barriers, implying that dispersal between montane regions is important for the formation of montane assemblages.

The Evolution of Trait Disparity during the Radiation of the Plant Genus Macrocarpaea (Gentianaceae) in the Tropical Andes

The evolutionary processes responsible for the extraordinary diversity in the middle elevation montane forests of the Tropical Andes (MMF; 1000-3500 m) remain poorly understood. It is not clear whether adaptive divergence, niche conservatism or geographical processes were the main contributors to the radiation of the respective lineages occurring there. We investigated the evolutionary history of plant lineages in the MMF. We used the vascular plant genus Macrocarpaea (Gentianaceae) as a model, as it consists of 118 morphologically diverse species, a majority of which are endemic to the MMF. We used a time-calibrated molecular phylogeny and morphological and climatic data to compare a set of evolutionary scenarios of various levels of complexity in a phylogenetic comparative framework. In this paper, we show that the hypothesis of adaptive radiation for Macrocarpaea in the MMF is unlikely. The genus remained confined to the upper montane forests (UMF > 1800 m) during more than a half of its evolutionary history, possibly due to evolutionary constraints. Later, coinciding with the beginning of the Pleistocene (around 2.58 Ma), a phylogenetically derived (recently branching) clade, here referred to as the M. micrantha clade (25 species), successfully colonized and radiated in the lower montane forests (LMF < 1800 m). This colonization was accompanied by the evolution of a new leaf phenotype that is unique to the species of the M. micrantha clade that likely represents an adaptation to life in this new environment (adaptive zone). Therefore, our results suggest that niche conservatism and geographical processes have dominated most of the diversification history of Macrocarpaea, but that a rare adaptive divergence event allowed a transition into a new adaptive zone and enabled progressive radiation in this zone through geographical processes.

Rugged relief and climate promote isolation and divergence between two neotropical cold-associated birds

The role of historical factors in establishing patterns of diversity in tropical mountains is of interest to understand the buildup of megadiverse biotas. In these regions, the historical processes of range fragmentation and contraction followed by dispersal are thought to be mediated by the interplay between rugged relief (complex topography) and climate fluctuations and likely explain most of the dynamics of diversification in plants and animals. Although empirical studies addressing the interaction between climate and topography have provided invaluable insights into population divergence and speciation patterns in tropical montane organisms, a more detailed and robust test of such processes in an explicit spatio-temporal framework is still lacking. Consequently, our ability to gain insights into historical range shifts over time and the genomic footprint left by them is limited. Here, we used niche modeling and subgenomic population-level datasets to explore the evolution of two species of warbling finches (genus Microspingus) disjunctly distributed across the Montane Atlantic Forest, a Neotropical region with complex geological and environmental histories. Population structure inferences suggest a scenario of three genetically differentiated populations, which are congruent with both geography and phenotypic variation. Demographic simulations support asynchronous isolation of these populations as recently as ∼40,000 years ago, relatively stable population sizes over recent time, and past gene flow subsequent to divergence. Throughout the last 800,000 years, niche models predicted extensive expansion into lowland areas with increasing overlap of species distributions during glacial periods, with prominent retractions and isolation into higher altitudes during interglacials, which are in line with signs of introgression of currently isolated populations. These results support a dual role of cyclical climatic changes: population divergence and persistence in mountain tops during warm periods followed by periods of expansion and admixture in lower elevations during cold periods. Our results underscore the role of the interplay between landscape and climate as an important mechanism in the evolution of the Neotropical montane biota.

Speciation and gene flow across an elevational gradient in New Guinea kingfishers

Closely related species with parapatric elevational ranges are ubiquitous in tropical mountains worldwide. The gradient speciation hypothesis proposes that these series are the result of in situ ecological speciation driven by divergent selection across elevation. Direct tests of this scenario have been hampered by the difficulty inferring the geographic arrangement of populations at the time of divergence. In cichlids, sticklebacks and Timema stick insects, support for ecological speciation driven by other selective pressures has come from demonstrating parallel speciation, where divergence proceeds independently across replicated environmental gradients. Here, we take advantage of the unique geography of the island of New Guinea to test for parallel gradient speciation in replicated populations of Syma kingfishers that show extremely subtle differentiation across elevation and between historically isolated mountain ranges. We find that currently described high-elevation and low-elevation species have reciprocally monophyletic gene trees and form nuclear DNA clusters, rejecting this hypothesis. However, demographic modelling suggests selection has likely maintained species boundaries in the face of gene flow following secondary contact. We compile evidence from the published literature to show that although in situ gradient speciation in labile organisms such as birds appears rare, divergent selection and post-speciation gene flow may be an underappreciated force in the origin of elevational series and tropical beta diversity along mountain slopes.

Mountaintops phylogeography: A case study using small mammals from the Andes and the coast of central Chile

We evaluated if two sigmodontine rodent taxa (Abrothrix olivacea and Phyllotis darwini) from the Andes and Coastal mountaintops of central Chile, experienced distributional shifts due to altitudinal movements of habitat and climate change during and after the Last Glacial Maximum (LGM). We tested the hypothesis that during LGM populations of both species experienced altitudinal shifts from the Andes to the lowlands and the coastal Cordillera, and then range retractions during interglacial towards higher elevations in the Andes. These distributional shifts may have left remnants populations on the mountaintops. We evaluated the occurrence of intraspecific lineages for each species, to construct distribution models at LGM and at present, as extreme climatic conditions for each lineage. Differences in distribution between extreme climatic conditions were interpreted as post-glacial distributional shifts. Abrothrix olivacea displayed a lineage with shared sequences between both mountain systems, whereas a second lineage was restricted to the Andes. A similar scenario of panmictic unit in the past was recovered for A. olivacea in the Andes, along with an additional unit that included localities from the rest of its distribution. For P. darwini, both lineages recovered were distributed in coastal and Andean mountain ranges at present as well, and structuring analyses for this species recovered coastal and Andean localities as panmictic units in the past. Niche modeling depicted differential postglacial expansions in the recovered lineages. Results suggest that historical events such as LGM triggered the descending of populations to Andean refuge areas (one of the A. olivacea's lineages), to the lowlands, and to the coastal Cordillera. Backward movements of populations after glacial retreats may have left isolates on mountaintops of the coastal Cordillera, suggesting that current species distribution would be the outcome of climate change and habitat reconfiguration after LGM.

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.

Limited Dispersal and Significant Fine - Scale Genetic Structure in a Tropical Montane Parrot Species

Tropical montane ecosystems are biodiversity hotspots harbouring many endemics that are confined to specific habitat types within narrow altitudinal ranges. While deforestation put these ecosystems under threat, we still lack knowledge about how heterogeneous environments like the montane tropics promote population connectivity and persistence. We investigated the fine-scale genetic structure of the two largest subpopulations of the endangered El Oro parakeet (Pyrrhura orcesi) endemic to the Ecuadorian Andes. Specifically, we assessed the genetic divergence between three sites separated by small geographic distances but characterized by a heterogeneous habitat structure. Although geographical distances between sites are small (3-17 km), we found genetic differentiation between all sites. Even though dispersal capacity is generally high in parrots, our findings indicate that dispersal is limited even on this small geographic scale. Individual genotype assignment revealed similar genetic divergence across a valley (~ 3 km distance) compared to a continuous mountain range (~ 13 km distance). Our findings suggest that geographic barriers promote genetic divergence even on small spatial scales in this endangered endemic species. These results may have important implications for many other threatened and endemic species, particularly given the upslope shift of species predicted from climate change.

Patterns of Species Richness and Turnover for the South American Rodent Fauna

Understanding the spatial distribution of species sheds light on the group’s biogeographical history, offers clues to the drivers of diversity, and helps to guide conservation strategies. Here, we compile geographic range information for South America’s diverse rodents, whose 14 families comprise ~50% of the continent’s mammalian species. The South American rodent fauna is dominated by independent and temporally staggered radiations of caviomorph and sigmodontine groups. We mapped species richness and turnover of all rodents and the principal clades to identify the main predictors of diversity patterns. Species richness was highest in the Andes, with a secondary hotspot in Atlantic Forest and some regions of considerable richness in Amazonia. Differences in richness were evident between the caviomorphs and sigmodontines, the former showing the greatest richness in tropical forests whereas the latter show—and largely determine—the all-rodent pattern. Elevation was the main predictor of sigmodontine richness, whereas temperature was the principal variable correlated with richness of caviomorphs. Across clades, species turnover was highest along the Andes and was best explained by elevational relief. In South America, the effects of the familiar latitudinal gradient in species richness are mixed with a strong longitudinal effect, triggered by the importance of elevation and the position of the Andes. Both latitudinal and elevational effects help explain the complicated distribution of rodent diversity across the continent. The continent’s restricted-range species—those seemingly most vulnerable to localized disturbance—are mostly distributed along the Andes and in Atlantic Forest, with the greatest concentration in Ecuador. Both the Andes and Atlantic Forest are known hotspots for other faunal and floral components. Contrasting patterns of the older caviomorph and younger sigmodontine radiations underscore the interplay of both historical and ecological factors in determining present-day diversity patterns.

The dual role of Andean topography in primary divergence: functional and neutral variation among populations of the hummingbird, Metallura tyrianthina

Background

The ridges and valleys of the Andes create physical barriers that limit animal dispersal and cause deterministic local variation in rainfall. This has resulted in physical isolation of animal populations and variation in habitats, each of which has likely contributed to the evolution of high species diversity in the region. However, the relative influences of geographic isolation, ecoclimatic conditions, and their potential interactions remain poorly understood. To address this, we compared patterns of genetic and morphological diversity in Peruvian populations of the hummingbird Metallura tyrianthina.

Results

Phylogenetic and variation partitioning analyses showed that geographic isolation rather than climatic dissimilarity explained the greatest proportion of genetic variance. In contrast, bill length variation was explained by climatic seasonality, but not by genetic divergence. We found that mutation-scaled migration rate (m) between persistently humid and semi-humid environments was nearly 20 times higher when the habitats were contiguous (m = 39.9) than when separated by a barrier, the Cordillera de Vilcanota (m = 2.1). Moreover, the population experiencing more gene flow exhibited a lesser degree of bill length divergence despite similar differences in climate.

Conclusions

Geographic isolation is necessary for genetic divergence. Ecological differences, represented here by climate characteristics, are necessary for functional divergence. Gene flow appears to hinder the evolution of functional traits toward local adaptive optima. This suggests that functional diversification requires geographic isolation followed or accompanied by a shift in ecological conditions. Andean topography causes both isolation and climatic variation, underscoring its dual role in biotic diversification.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0595-2) contains supplementary material, which is available to authorized users.

Glaciation effects on the phylogeographic structure of Oligoryzomys longicaudatus (Rodentia: Sigmodontinae) in the southern Andes

The long-tailed pygmy rice rat Oligoryzomys longicaudatus (Sigmodontinae), the major reservoir of Hantavirus in Chile and Patagonian Argentina, is widely distributed in the Mediterranean, Temperate and Patagonian Forests of Chile, as well as in adjacent areas in southern Argentina. We used molecular data to evaluate the effects of the last glacial event on the phylogeographic structure of this species. We examined if historical Pleistocene events had affected genetic variation and spatial distribution of this species along its distributional range. We sampled 223 individuals representing 47 localities along the species range, and sequenced the hypervariable domain I of the mtDNA control region. Aligned sequences were analyzed using haplotype network, bayesian population structure and demographic analyses. Analysis of population structure and the haplotype network inferred three genetic clusters along the distribution of O. longicaudatus that mostly agreed with the three major ecogeographic regions in Chile: Mediterranean, Temperate Forests and Patagonian Forests. Bayesian Skyline Plots showed constant population sizes through time in all three clusters followed by an increase after and during the Last Glacial Maximum (LGM; between 26,000-13,000 years ago). Neutrality tests and the "g" parameter also suggest that populations of O. longicaudatus experienced demographic expansion across the species entire range. Past climate shifts have influenced population structure and lineage variation of O. longicaudatus. This species remained in refugia areas during Pleistocene times in southern Temperate Forests (and adjacent areas in Patagonia). From these refugia, O. longicaudatus experienced demographic expansions into Patagonian Forests and central Mediterranean Chile using glacial retreats.

Plant and animal endemism in the eastern Andean slope: challenges to conservation

BACKGROUND

The Andes-Amazon basin of Peru and Bolivia is one of the most data-poor, biologically rich, and rapidly changing areas of the world. Conservation scientists agree that this area hosts extremely high endemism, perhaps the highest in the world, yet we know little about the geographic distributions of these species and ecosystems within country boundaries. To address this need, we have developed conservation data on endemic biodiversity (~800 species of birds, mammals, amphibians, and plants) and terrestrial ecological systems (~90; groups of vegetation communities resulting from the action of ecological processes, substrates, and/or environmental gradients) with which we conduct a fine scale conservation prioritization across the Amazon watershed of Peru and Bolivia. We modelled the geographic distributions of 435 endemic plants and all 347 endemic vertebrate species, from existing museum and herbaria specimens at a regional conservation practitioner's scale (1:250,000-1:1,000,000), based on the best available tools and geographic data. We mapped ecological systems, endemic species concentrations, and irreplaceable areas with respect to national level protected areas.

RESULTS

We found that sizes of endemic species distributions ranged widely (< 20 km2 to > 200,000 km2) across the study area. Bird and mammal endemic species richness was greatest within a narrow 2500-3000 m elevation band along the length of the Andes Mountains. Endemic amphibian richness was highest at 1000-1500 m elevation and concentrated in the southern half of the study area. Geographical distribution of plant endemism was highly taxon-dependent. Irreplaceable areas, defined as locations with the highest number of species with narrow ranges, overlapped slightly with areas of high endemism, yet generally exhibited unique patterns across the study area by species group. We found that many endemic species and ecological systems are lacking national-level protection; a third of endemic species have distributions completely outside of national protected areas. Protected areas cover only 20% of areas of high endemism and 20% of irreplaceable areas. Almost 40% of the 91 ecological systems are in serious need of protection (= < 2% of their ranges protected).

CONCLUSIONS

We identify for the first time, areas of high endemic species concentrations and high irreplaceability that have only been roughly indicated in the past at the continental scale. We conclude that new complementary protected areas are needed to safeguard these endemics and ecosystems. An expansion in protected areas will be challenged by geographically isolated micro-endemics, varied endemic patterns among taxa, increasing deforestation, resource extraction, and changes in climate. Relying on pre-existing collections, publically accessible datasets and tools, this working framework is exportable to other regions plagued by incomplete conservation data.

Diversification across an altitudinal gradient in the Tiny Greenbul (Phyllastrephus debilis) from the Eastern Arc Mountains of Africa

BACKGROUND

The Eastern Arc Mountains of Africa have become one of the focal systems with which to explore the patterns and mechanisms of diversification among montane species and populations. One unresolved question is the extent to which populations inhabiting montane forest interact with those of adjacent lowland forest abutting the coast of eastern Africa. The Tiny Greenbul (Phyllastephus debilis) represents the only described bird species within the Eastern Arc/coastal forest mosaic, which is polytypic across an altitudinal gradient: the subspecies albigula (green head) is distributed in the montane Usambara and Nguru Mountains whereas the subspecies rabai (grey head) is found in Tanzanian lowland and foothill forest. Using a combination of morphological and genetic data, we aim to establish if the pattern of morphological differentiation in the Tiny Greenbul (Phyllastrephus debilis) is the result of disruptive selection along an altitudinal gradient or a consequence of secondary contact following population expansion of two differentiated lineages.

RESULTS

We found significant biometric differences between the lowland (rabai) and montane (albigula) populations in Tanzania. The differences in shape are coupled with discrete differences in the coloration of the underparts. Using multi-locus data gathered from 124 individuals, we show that lowland and montane birds form two distinct genetic lineages. The divergence between the two forms occurred between 2.4 and 3.1 Myrs ago.Our coalescent analyses suggest that limited gene flow, mostly from the subspecies rabai to albigula, is taking place at three mid-altitude localities, where lowland and montane rainforest directly abut. The extent of this introgression appears to be limited and is likely a consequence of the recent expansion of rabai further inland.

CONCLUSION

The clear altitudinal segregation in morphology found within the Tiny Greenbul is the result of secondary contact of two highly differentiated lineages rather than disruptive selection in plumage pattern across an altitudinal gradient. Based on our results, we recommend albigula be elevated to species rank.

Correlates of species richness in the largest Neotropical amphibian radiation

Although tropical environments are often considered biodiversity hotspots, it is precisely in such environments where least is known about the factors that drive species richness. Here, we use phylogenetic comparative analyses to study correlates of species richness for the largest Neotropical amphibian radiation: New World direct-developing frogs. Clade-age and species richness were nonsignificantly, negatively correlated, suggesting that clade age alone does not explain among-clade variation in species richness. A combination of ecological and morphological traits explained 65% of the variance in species richness. A more vascularized ventral skin, the ability to colonize high-altitude ranges, encompassing a large variety of vegetation types, correlated significantly with species richness, whereas larger body size was marginally correlated with species richness. Hence, whereas high-altitude ranges play a role in shaping clade diversity in the Neotropics, intrinsic factors, such as skin structures and possibly body size, might ultimately determine which clades are more speciose than others.

Bioregion heterogeneity correlates with extensive mitochondrial DNA diversity in the Namaqua rock mouse, Micaelamys namaquensis (Rodentia: Muridae) from southern Africa--evidence for a species complex

BACKGROUND

Intraspecific variation within the diverse southern African murine rodents has not been extensively investigated, yet cryptic diversity is evident in several taxa studied to date. The Namaqua rock mouse, Micaelamys namaquensis Smith, 1834 is a widespread endemic murine rodent from the subregion. Currently, a single species with four subspecies is recognised, but in the past up to 16 subspecies were described. Thus, this species is a good candidate for the investigation of patterns and processes of diversification in a diverse but under-studied mammalian subfamily and geographic region. Here, we report genetic differentiation based on mitochondrial DNA (mtDNA) cytochrome b (cyt b) sequences among samples collected over an extensive coverage of the species' range.

RESULTS

Cytochrome b sequences of 360 widely sampled individuals identified 137 unique maternal alleles. Gene tree and phylogeographic analyses of these alleles suggest the presence of at least eight lineages or haplogroups (A-H), with varying degrees of intra-lineage diversity. This differentiation is in contrast with the most recent taxonomic treatment based on cranial morphometrics which only recognised four subspecies. The mtDNA diversity strongly supports earlier views that this taxon may represent a species complex. We further show statistical support for the association of several of these lineages with particular vegetation biomes of southern Africa. The time to the most recent common ancestor (TMRCA) dates to the Pliocene (~5 Mya) whereas coalescent-based divergence time estimates between lineages vary between 813 Kya [0.22-1.36] and 4.06 Mya [1.21-4.47]. The major diversification within lineages occurred during the Pleistocene. The identification of several regions of sympatry of distinct lineages offers future opportunities for the elucidation of the underlying speciation processes in the suggested species complex.

CONCLUSIONS

Similar to other African murine rodents, M. namaquensis radiated during the Pliocene and Pleistocene coinciding with major periods of aridification and the expansion of savanna habitats. The suggested species complex is represented by at least eight lineages of which the majority are confined to only one or a few neighbouring biomes/bioregions. Contrasting intra-lineage phylogeographic patterns suggest differences in adaptation and responses to Plio-Pleistocene climatic and vegetation changes. The role of ecological factors in driving speciation in the group needs further investigation.

Population history, phylogeography, and conservation genetics of the last Neotropical mega-herbivore, the lowland tapir (Tapirus terrestris)

BACKGROUND

Understanding the forces that shaped Neotropical diversity is central issue to explain tropical biodiversity and inform conservation action; yet few studies have examined large, widespread species. Lowland tapir (Tapirus terrrestris, Perissodactyla, Tapiridae) is the largest Neotropical herbivore whose ancestors arrived in South America during the Great American Biotic Interchange. A Pleistocene diversification is inferred for the genus Tapirus from the fossil record, but only two species survived the Pleistocene megafauna extinction. Here, we investigate the history of lowland tapir as revealed by variation at the mitochondrial gene Cytochrome b, compare it to the fossil data, and explore mechanisms that could have shaped the observed structure of current populations.

RESULTS

Separate methodological approaches found mutually exclusive divergence times for lowland tapir, either in the late or in the early Pleistocene, although a late Pleistocene divergence is more in tune with the fossil record. Bayesian analysis favored mountain tapir (T. pinchaque) paraphyly in relation to lowland tapir over reciprocal monophyly, corroborating the inferences from the fossil data these species are sister taxa. A coalescent-based analysis rejected a null hypothesis of allopatric divergence, suggesting a complex history. Based on the geographic distribution of haplotypes we propose (i) a central role for western Amazonia in tapir diversification, with a key role of the ecological gradient along the transition between Andean subcloud forests and Amazon lowland forest, and (ii) that the Amazon river acted as an barrier to gene flow. Finally, the branching patterns and estimates based on nucleotide diversity indicate a population expansion after the Last Glacial Maximum.

CONCLUSIONS

This study is the first examining lowland tapir phylogeography. Climatic events at the end of the Pleistocene, parapatric speciation, divergence along the Andean foothill, and role of the Amazon river, have similarly shaped the history of other taxa. Nevertheless further work with additional samples and loci is needed to improve our initial assessment. From a conservation perspective, we did not find a correspondence between genetic structure in lowland tapir and ecogeographic regions proposed to define conservation priorities in the Neotropics. This discrepancy sheds doubt into this scheme's ability to generate effective conservation planning for vagile species.

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.

Phylogenetics of the florally diverse Andean clade Iochrominae (Solanaceae)

Recent molecular phylogenetic studies of Solanaceae have identified many well-supported clades within the family and have permitted the creation of a phylogenetic system of classification. Here we estimate the phylogeny for Iochrominae, a clade of Physaleae sensu Olmstead et al. (1999), which contains 34 Andean species encompassing an immense diversity of floral forms and colors. Using three nuclear regions, ITS, the second intron of LEAFY, and exons 2 to 9 of the granule-bound starch synthase gene (waxy), we evaluated the monophyly of the traditional genera comprising Iochrominae and assessed the extent of interspecific hybridization within the clade. Only one of the six traditionally recognized genera of Iochrominae was supported as monophyletic. Further, comparison of the individual nuclear data sets revealed two interspecific hybrid taxa and a third possible case. These hybrid taxa occur in the Amotape-Huancabamba zone, a region between the northern and central Andes that has the greatest diversity of Iochroma species and offers frequent opportunities for hybridization in areas of sympatry. We postulate that periodic hybridization events in this area coupled with pollinator-mediated selection and the potential for microallopatry may have acted together to promote diversification in montane Andean taxa, such as Iochrominae.

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.

Comparative phylogeography of short-tailed bats (Carollia: Phyllostomidae)

This is the first study of comparative phylogeography involving closely related species of Neotropical bats of the family Phyllostomidae. We compared patterns of geographical variation within the five species of fruit-eating bats currently recognized in the genus Carollia using the complete mitochondrial cytochrome-b gene. Our results suggest that the combined effect of the uplift of the Andes and the Panamanian land bridge has been as important for bats as for terrestrial mammals in shaping present-day biodiversity in the New World tropics. Species in this genus can be arranged in two highly supported clades, with a deep subdivision within each that corresponds well to differences across the Andes. We found three congruent phylogeographical patterns across species in this genus. First, the closer relationship between samples from western Ecuador and those from Central America, compared with populations east of the Andes in C. brevicauda, C. castanea and C. perspicillata. Second, the likelihood of a similar timing in South America for the arrival and diversification of C. brevicauda and C. perspicillata from their Central America ancestors. Third, the expansion of C. perspicillata and C. sowelli into northwestern Central America in the relatively recent past. Using a molecular clock, with rates ranging from 2.3 to 5% per 10(6) years, diversification within Carollia would have occurred over the last 1-4.5 Myr. These estimates agree well with the last rise of the Northern Andes and the Panama isthmus.

Acoustic divergence in two cryptic Hipposideros species: a role for social selection?

We present evidence that a relatively widespread and common bat from South East Asia comprises two morphologically cryptic but acoustically divergent species. A population of the bicoloured leaf-nosed bat (Hipposideros bicolor) from Peninsular Malaysia exhibits a bimodal distribution of echolocation call frequencies, with peaks in the frequency of maximum energy at ca. 131 and 142 kHz. The two phonic types are genetically distinct, with a cytochrome b sequence divergence of just under 7%. We consider the mechanisms by which acoustic divergence in these species might arise. Differences in call frequency are not likely to effect resource partitioning by detectable prey size or functional range. However, ecological segregation may be achieved by differences in microhabitat use; the 131kHz H. bicolor is characterized by significantly longer forearms, lower wing loading, a lower aspect ratio and a more rounded wingtip, features that are associated with greater manoeuvrability in flight that may enable it to forage in more cluttered environments relative to the 142 kHz phonic type. We suggest that acoustic divergence in these species is a consequence of social selection for a clear communication channel, which is mediated by the close link between the acoustic signal and receptor systems imposed by the highly specialized nature of the hipposiderid and rhinolophid echolocation system.