The importance of environmental heterogeneity and spatial distance in generating phylogeographic structure in edaphic specialist and generalist tree species of Protium (Burseraceae) across the Amazon Basin

Aim Edaphic heterogeneity may be an important driver of population differentiation in the Amazon but remains to be investigated in trees. We compared the phylogeographic structure across the geographic distribution of two Protium (Burseraceae) species with different degrees of edaphic specialization: Protium alvarezianum, an edaphic specialist of white‐sand habitat islands; and Protium subserratum, an edaphic generalist found in white sand as well as in more widespread soil types. We predicted that in the edaphic specialist, geographic distance would structure populations more strongly than in the edaphic generalist, and that soil type would not structure populations in the edaphic generalist unless habitat acts as a barrier promoting population differentiation. Location Tropical rain forests of the Peruvian and Brazilian Amazon, Guyana and French Guiana. Methods We sequenced 1209–1211 bp of non‐coding nuclear ribosomal DNA (internal transcribed spacer and external transcribed spacer) and a neutral low‐copy nuclear gene (phytochrome C) from P. subserratum (n = 65, 10 populations) and P. alvarezianum (n = 19, three populations). We conducted a Bayesian phylogenetic analysis, constructed maximum parsimony haplotype networks and assessed population differentiation among groups (soil type or geographic locality) using analysis of molecular variance and spatial analysis of molecular variance. Results The edaphic specialist exhibited considerable genetic differentiation among geographically distant populations. The edaphic generalist showed significant genetic differentiation between the Guianan and Amazon Basin populations. Within Peru, soil type and not geographic distance explained most of the variation among populations. Non‐white‐sand populations in Peru exhibited lower haplotype/nucleotide diversity than white‐sand populations, were each other’s close relatives, and formed an unresolved clade derived from within the white‐sand populations. Main conclusions Geographic distance is a stronger driver of population differentiation in the edaphic specialist than in the generalist. However, this difference did not appear to be related to edaphic generalism per se as adjacent populations from both soil types in the edaphic generalist did not share many haplotypes. Populations of the edaphic generalist in white‐sand habitats exhibited high haplotype diversity and shared haplotypes with distant white‐sand habitat islands, indicating that they have either efficient long‐distance dispersal and/or larger ancestral effective population sizes and thus retain ancestral polymorphisms. These results highlight the importance of edaphic heterogeneity in promoting population differentiation in tropical trees.     

THE CONTRIBUTION OF EDAPHIC HETEROGENEIYT TO THE EVOLUTION AND DIVERSITY OF BURSERACEAR TREES IN THE WESTERN AMAZON

Abstract —Environmental heterogeneity in the tropics is thought to lead to specialization in plants and thereby contribute to the diversity of the tropical flora. We examine this idea with data on the habitat specificity of 35 western Amazonian species from the genera Protium, Crepidospermum, and Tetragastris in the monophyletic tribe Protieae (Burseraceae) mapped on a molecular‐based phylogeny. We surveyed three edaphic habitats that occur throughout terra firme Amazonia: white‐sand, clay, and terrace soils in eight forests across more than 2000 km in the western Amazon. Twenty‐six of the 35 species were found to be associated with only one of three soil types, and no species was associated with all three habitats; this pattern of edaphic specialization was consistent across the entire region. Habitat association mapped onto the phylogenetic tree shows association with terrace soils to be the probable ancestral state in the group, with subsequent speciation events onto clay and white‐sand soils. The repeated gain of clay association within the clade likely coincides with the emergence of large areas of clay soils in the Miocene deposited during the Andean uplift. Character optimizations revealed that soil association was not phylogenetically clustered for white‐sand and clay specialists, suggesting repeated independent evolution of soil specificity is common within the Protieae. This phylogenetic analysis also showed that multiple cases of putative sister taxa with parapatric distributions differ in their edaphic associations, suggesting that edaphic heterogeneity was an important driver of speciation in the Protieae in the Amazon basin.     

The ecogeographical differentiation of Amazonian inundation forests

Due to the considerable annual fluctuations of water level of the Amazonian rivers, their river banks are fringed with periodically flooded forests of vast extension. The biota of these communities are adapted to annual inundations that can last for more than half a year. Water chemistry is most important for the floristic differentiation of these flooded forests. White water rivers, which carry a rich load of suspended material originating from the erosion of the Andes, have a floristic composition related to that of the noninundatable Amazonian forest. Clear water and black water rivers, which originate in the Amazon Basin or its adjacent crystalline shields, are nutrient-poor and more or less acidic; their flora is related to that of peculiar woodland and savannah vegetation on oligotrophic white sand. The distribution patterns of floodplain species of nutrient-poor waters point to a centre of diversity in the Upper Rio Negro region, and another one in the Guayana lowland. These coincide with diversity centres for species of non-flooded habitats. Hence it seems unlikely that species diversity is directly influenced by pluviosity. The flooded forests have developed biotic interactions with the fish fauna of the Amazon Basin, which are vital for their continued existence. It is assumed that the origin of these habitats, their biota and their interactions dates back long into the Tertiary.     

Marine species formation along the rise of Central America: The anomuran crab Megalobrachium

The evolution of marine neotropical shallow water species is expected to have been greatly affected by physical events related to the emergence of the Central American Isthmus. The anomuran crab Megalobrachium, a strictly neotropical porcellanid genus, consists of four species in the West Atlantic (WA) and nine in the East Pacific (EP). Dispersal is limited to a relatively short planktonic phase, which lasts approximately two weeks. We obtained DNA sequences of three mitochondrial and two nuclear genes of all but one species of Megalobrachium to construct a time‐calibrated phylogeny of the genus and its historical phylogeography, based on the reconstruction of ancestral areas. The topology of the phylogenetic trees of Megalobrachium produced by Bayesian Inference (BI) and Maximum Likelihood (ML) were virtually congruent. The genus is monophyletic with respect to other porcellanids. Ancestral area reconstruction indicates that it arose in the eastern Pacific 18 million years ago and diversified into at least 13 species that are currently formally recognized and three additional species indicated by our data. Most morphological variation appears to have followed phylogenetic differentiation, though some cryptic speciation has also occurred. Four geminate clades in this genus implicate the gradual emergence of the Central American Isthmus in this diversification, but events preceding the final separation of the oceans as well as within‐ocean events after the cessation of water connections were also important.     

Multigene phylogeny reveals convergent evolution in small interstitial catfishes from the Amazon and Atlantic forests (Siluriformes: Trichomycteridae)

Interstitial trichomycterid catfishes of the Glanapteryginae and Sarcoglanidinae with uncommon morphology have been known for long time from taxa endemic to the Amazon. In most recent decades, two genera, Listrura and Microcambeva, respectively, placed in Glanapteryginae and Sarcoglanidinae on the basis of morphological characters, have been described from the Atlantic Forest of eastern South America, about 1,500 km from the area inhabited by those Amazon taxa. Herein, we first test the phylogenetic positioning of Listrura and Microcambeva using a multigene data set, including two nuclear and three mitochondrial genes for nine species of Listrura and Microcambeva and 11 species representing all closely related subfamilies (TSVSG-clade), as well as five used as outgroups. The phylogenetic analyses generated a robust tree with high support values in all nodes, where monophyly of Glanapteryginae and Sarcoglanidinae is refuted. In contrast, Listrura and Microcambeva form a highly supported clade, herein formally described as a new subfamily, sister to a clade containing taxa representing the Glanapteryginae, Sarcoglanidinae, Stegophilinae, Tridentinae and Vandelliinae. This study also indicates that Microcambeva and Listrura exhibit divergent evolutionary trends in ecological and morphological attributes. Species of Microcambeva inhabit patches of loose sand and possess morphological traits that were convergently acquired by Amazon sand-dwelling sarcoglanidines, including loss of body pigmentation and long maxilla. Species of Listrura live burrowed inside small stretches of dense leaf litter and have morphological traits that were convergently acquired by Amazon glanapterygines inhabiting leaf litter bottom rivers, including elongate body, with numerous vertebrae and loss or reduction of all fins.     

Phylogenetic perspectives on diversification and character evolution in the species‐rich genus Erysimum (Erysimeae; Brassicaceae) based on a densely sampled ITS approach

Erysimum includes 150–350 species distributed in the Northern Hemisphere, with Eurasia being the centre of greatest diversity. It is well known for its taxonomic complexity as a result of overlapping morphological characters. We present the first densely sampled phylogenetic analysis of Erysimum using internal transcribed spacer (ITS) DNA sequences from c. 85% of the species (117 for the first time), representing the full range of morphological variation and geographical distribution. We used several approaches to reconstruct phylogenetic relationships, dating of diversification and patterns of evolution of morphological characters in the genus. Ancestral‐state reconstructions of four morphological diagnostic characters were performed using maximum parsimony, maximum likelihood and Bayesian methods. Our phylogenetic framework strongly supports the monophyly of Erysimum and recovers some well‐supported clades that are geographically, rather than morphologically, correlated. Our study confirms the placement of Erysimum in lineage I and reveals two Malcolmia spp. (M. maritima and M. orsiniana) as its sister taxa. The results suggest that the biennial duration and caespitose habit (vs. annual or perennial duration and herbaceous or woody habit) and large, yellow, glabrous (vs. small, non‐yellow, pubescent) petals are ancestral in Erysimum. The ancestral‐state reconstruction results show that annual vs. perennial and woody vs. herbaceous features have been independently derived several times. The dating analyses suggest an early radiation of Erysimum during the late Pliocene or early Pleistocene. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175 , 497–522.     

Historical biogeography and diversification within the Neotropical parrot genus Pionopsitta (Aves: Psittacidae)

Aim We investigate spatial and temporal patterns of diversification within the Neotropical avifauna using the phylogenetic history of parrots traditionally belonging to the genus Pionopsitta Bonaparte 1854. This genus has long been of interest for those studying Neotropical biogeography and diversity, as it encompasses species that occur in most Neotropical forest areas of endemism. Location The Neotropical lowland forests in South and Central America. Methods Phylogenetic relationships were investigated for all species of the genus Pionopsitta and five other short‐tailed parrot genera using complete sequences of the mitochondrial genes cyt b and ND2 as well as 26 plumage characters. The resulting phylogeny was used to test the monophyly of the genus, investigate species limits, and as a framework for reconstructing their historical biogeography and patterns of diversification. Results We found that the genus Pionopsitta, as previously defined, is not monophyletic and thus the Chocó, Central American and Amazonian species will now have to be placed in the genus Gypopsitta. The molecular and morphological phylogenies are largely congruent, but disagree on the position of one of the Amazon basin taxa. Using molecular sequence data, we estimate that species within Gypopsitta diversified between 8.7 and 0.6 Ma, with the main divergences occurring between 3.3 and 6.4 Ma. These temporal results are compared to other taxa showing similar vicariance patterns. Main conclusions The results suggest that diversification in Gypopsitta was influenced mainly by geotectonic events, marine transgressions and river dynamics, whereas Quaternary glacial cycles of forest change seem to have played a minor role in the origination of the currently recognized species.     

Revision and phylogeny of the bee genus Paratetrapedia Moure,with description of a new genus from the Andean Cordillera (Hymenoptera,Apidae, Tapinotaspidini)

The bee genus Paratetrapedia represents a commonly collected group of bees and is especially diverse in forested areas of the Neotropics. Its taxonomy has remained poorly understood because of a lack of modern revisionary work and numerous species described as Tetrapedia whose type specimens have not been re‐examined in recent times. Here, a comprehensive study was carried out to review the taxonomy of the genus Paratetrapedia and to investigate cladistically the relationships amongst its species. Eighteen new species of Paratetrapedia are described, giving a total of 32 species in the genus. A phylogenetic analysis of the species of Paratetrapedia was carried out using 61 morphological characters for 41 terminal taxa. The phylogenetic results confirmed the monophyly of Paratetrapedia and allowed the recognition of five species groups: the lugubris, moesta, bicolor, lineata, and flavipennis groups. Nasutopedia gen. nov. , recognized as the sister group of Paratetrapedia and with its distribution restricted to the western forested portions of the Andean highlands, is proposed based on distinct morphology, its placement in the phylogenetic tree, and biogeographical patterns. Species of Paratetrapedia are especially diverse in the Amazon Forest; the eastern Brazilian Atlantic Forest contains four endemic species, and one species is endemic to the Cerrado of central Brazil. Paratetrapedia shows a biogeographical pattern similar to other Neotropical groups of bees and birds, with wide distribution and high diversity in lowland forests and whose sister taxon occurs on highlands of north‐western portions of the Andean cordillera. Identification keys for males and females of all species are provided, as well as distribution maps and illustrations of general external morphology and genitalia. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 351–442.     

Evolution of Annual Species of the GenusMedicago: A Molecular Phylogenetic Approach

We performed a molecular phylogenetic study based on the nuclear ribosomal internal and external transcribed spacer (ITS and ETS). Thirty-one annualMedicagospecies were included in the study, representing more than half of the genus and 85% of the annuals of the genus. Major incongruences were found between phylogenetic relationships and morphological classification of the genus. Morphological and cytological traits were mapped onto the phylogeny. The most parsimonious reconstruction suggested an ancestral spiny state and a recurrent transition from spiny to spineless state. From the ancestral state of 2n=16, three loss events of chromosomes must have occurred leading to the same specific number of 14 chromosomes whereas species having 30 chromosomes form a monophyletic clade.     

Phylogenetics and seed morphology of African Nymphoides (Menyanthaceae)

We evaluated the boundaries among Nymphoides (Menyanthaceae) species in Africa, a region where the genus has received relatively little attention. We gathered morphological data from seeds using light and scanning electron microscopy, and we conducted molecular phylogenetic analyses using nuclear sequence data from the internal transcribed spacer (ITS) region. Morphological and molecular features distinguished six species and affirmed their respective geographic ranges. No African specimens were attributable to Nymphoides indica, even though this paleotropical species previously had been understood to grow in Africa. We establish the new combination Nymphoides senegalensis (G. Don) Tippery, based on an established African basionym, to accommodate the specimens formerly identified as N. indica. Phylogenetic analyses resolved two distinct clades containing African species. The majority of African species are closely related to neotropical species, with which they share similar petal ornamentation. The morphologically distinct N. ezannoi shares floral and phylogenetic similarity with species from North America and Asia. Results presented here support prior hypotheses that allopolyploid species in the Americas may have originated from one or more parental lineages in Africa. Seed morphological characters remain some of the most reliable features for identifying species, particularly for herbarium specimens lacking observable floral characters.     

Molecular phylogeny of the entomopathogenic fungi of the genus Cordyceps (Ascomycota: Clavicipitaceae) and its evolutionary implications

Abstract Cordyceps is an endoparasite ascomycetous genus containing approximately 450 species with a diversity of insect hosts, traditionally included in the family Clavicipitaceae of Ascomycota. Establishing the relationships among species with a varied range of morphologies and hosts is of importance to our understanding of the phylogeny and co‐evolution of parasites and hosts in entomopathogenic ascomycetes. To this end, we used a combination of molecular index and morphological characters from 40 representative species to carry out comprehensive molecular phylogenetic analyses. Based on the phylogenetic tree, we used the program DISCRETE for inferring the rates of evolution and finding ancestral states of morphological character. The phylogenetic analyses revealed two important points. (i) Types of perithecia attached to stroma reflected an evolutionary trend in Cordyceps. The vertically immersed perithecia form was the ancestral state, superficial and obliquely immersed perithecia were derived characters, obliquely immersed was irreversible. Species with obliquely immersed perithecia were in a closely related group and were the derived group. (ii) A strong correlation between fungal relatedness and the microhabitat supported the hypothesis that the host jumps through commingling in soil microhabitats. Based on the results of these analyses, host switching explains the diversity of entomopathogenic fungi of the genus Cordyceps.     

Ectomycorrhizal fungi diversity in a white sand forest in western Amazonia

The genera Dicymbe and Aldina (Fabaceae) host ectomycorrhizal fungi (EcM) and are common in white sand forests (WSFs), a highly specialized habitat with a high level of plant endemism compared with terra-firme forests. In this study, we visited four times a 1-ha permanent plot established in a small patch of a WSF in the south of Colombia Amazonia. Forty-eight species of EcM fungi were recovered from sporocarps and 15 ITS species-level were detected from root tips. Seventeen species were new reports to Colombia and seven corresponded to undescribed species. These results confirm that this WSF supports a significant EcM fungal diversity. Most of the species found in this study have been previously reported to be associated with other legume and/or dipterocarp species from geographically distant forests. The long-distance occurrence combined with low host specificity, suggest the possibility of gene flow between geographically distant populations of EcM fungi in neotropical lowland rainforests.     

Close relatedness between mitochondrial DNA from seven Anser goose species

The phylogenetic relationships of seven goose species and two of the subspecies representing the genus Anser were studied by approximately 1180 bp of mitochondrial DNA tRNAglu, control region and tRNAphe sequences. Despite obvious morphological and behavioural affinities among the species, their evolutionary relationships have not been studied previously. The small amount of genetic differentiation observed in the mitochondrial DNA indicates an extremely close evolutionary relationship between the Anser species. The sequence divergences between the species (0.9–5.5%) are among the lowest reported for avian species with speciation events of Anser geese dating to late Pliocene and Pleistocene. The species grouped into four mtDNA lineages: (1) snow and Ross’ goose, (2) greylag goose, (3) white‐fronted goose, and (4) bean, pink‐footed and lesser white‐fronted goose. The phylogenetic relationships of the most closely related species, bean, pink‐footed and lesser white‐fronted goose, indicate a period of rapid cladogenesis. The poor agreement between morphological relationships and the phylogenetic relationships indicated by mtDNA sequences implies that either ancestral polymorphism and lineage sorting, hybridization and introgression or convergent evolution has been involved.     

Repeated evolution of dioecy from monoecy in Siparunaceae (Laurales)

Siparunaceae comprise Glossocalyx with one species in West Africa and Siparuna with 65 species in the neotropics; all have unisexual flowers, and 15 species are monoecious, 50 dioecious. Parsimony and maximum likelihood analyses of combined nuclear ribosomal ITS and chloroplast trnL-trnF intergenic spacer sequences yielded almost identical topologies, which were used to trace the evolution of the two sexual systems. The African species, which is dioecious, was sister to all neotropical species, and the monoecious species formed a grade basal to a large dioecious Andean clade. Dioecy evolved a second time within the monoecious grade. Geographical mapping of 6,496 herbarium collections from all species sorted by sexual system showed that monoecy is confined to low-lying areas (altitude < 700 m) in the Amazon basin and southern Central America. The only morphological trait with a strong phylogenetic signal is leaf margin shape (entire or toothed), although this character also correlates with altitude, probably reflecting selection on leaf shapes by temperature and rainfall regimes. The data do not reject the molecular clock, and branch lengths suggest that the shift to dioecy in the lowlands occurred many million years after the shift to dioecy in the ancestor of the Andean clade.     

Species poor but distinct: bird assemblages in white sand vegetation in Jaú National Park, Brazilian Amazon

There have been few studies of the fauna of the distinctive vegetation that grows on sandy soil in Amazonia. Leached and nutrient-poor sandy soil is associated with a vegetation type that varies in structure from open fields (campinas) to low canopy forests (campinaranas). During a bird inventory in sandy soil vegetation at Jaú National Park (JNP), I recorded 128 bird species, with 55 in campina and 94 in campinarana. Estimates suggested only 150 bird species should be expected to occur in these habitats, a reduced species diversity compared with other vegetation types in the Amazon region. This low species diversity is probably linked to the low productivity of this habitat and its relatively simple vegetation structure. Despite the relatively low diversity, at least 14 bird species (3% of the entire avifauna) appear to be restricted to white sand vegetation in JNP. In Amazonia as a whole, some 37 bird species are associated with vegetation in sandy soils. Biological inventories of other taxa are needed to understand the contribution of white sandy vegetation to the faunal distribution in Amazonia.     

Cryptic diversity in the lizard genus Plica (Squamata): phylogenetic diversity and Amazonian biogeography

Intra‐ and interspecific genetic diversity of the lizard species Plica plica (9 localities) and Plica umbra (19 localities) from the Brazilian Amazon was analysed using two mitochondrial (16S rDNA and CO1) and one nuclear (prolactin receptor – PRLR) genes. We generated a maximum‐likelihood and Bayesian hypotheses of phylogenetic relationships, and using the bPTP and ABGD lineage delimiting methods inferred the most likely number of lineages within each species. Both methods delimited five distinct lineages in Plica plica and six lineages within Plica umbra. The nominal subspecies of Plica umbra was comprised of one lineage, while Plica umbra ochrocollaris was comprised of five lineages. In majority of the cases, lineages were restricted to the interfluves of major Amazonian rivers, and different lineages occupied distinct areas of endemism. Phylogenetic relationships of the lineages are largely concordant with the hypothesized formation of the areas of endemism. The geographic structuring of the clades and the delimitation of these clades as distinct lineages suggest the possibility that these lineages represent species. If the observed diversity of lineages within the genus Plica is characteristic of squamate reptiles of the Amazon region, the diversity of squamates is grossly underestimated.     

Biogeography and evolution of Dolichandra (Bignonieae,Bignoniaceae)

Little information on evolutionary relationships of Neotropical organisms or on the factors that have shaped the diversity currently encountered in this region is available. However, it is clear that biotic interactions and abiotic aspects have played important roles for species diversification in the region. This study focuses on Dolichandra (Bignonieae, Bignoniaceae), a clade of Neotropical lianas that is distributed broadly across different habitats and with diverse pollination and dispersal systems. We used sequences from two plastid DNA markers (ndhF and rpl32‐trnL) and one nuclear gene (PepC) to infer phylogenetic relationships in Dolichandra using parsimony and Bayesian approaches. We then used this phylogenetic framework as basis to study the biogeographic history, reconstruct the evolution of morphological characters and test the impact of morphology and environment on the diversification of the genus. More specifically, we: (1) time‐calibrate the phylogenetic tree of Dolichandra; (2) estimate the ancestral areas of the various lineages; (3) estimate the ancestral states of discrete and continuous morphological traits; (4) test for phylogenetic signal in environmental and phenotypic data; and (5) test whether morphological characters and/or niche evolution are correlated with cladogenesis. All Dolichandra spp. are monophyletic in the combined molecular phylogeny; relationships among species are generally well resolved, although poorly supported in some instances. The genus is inferred to have originated 36.43–26.23 Mya, possibly in eastern South America. Ancestral state reconstructions of continuous and discrete floral characters inferred a mixed morphology as the ancestral condition for the group. Phylogenetic signal differed between perianth and sexual whorls and gradual evolution was recovered for all traits except style length and anther length. Environmental variables showed no phylogenetic signal and a pattern of variation that was not correlated with branch length, suggesting that environmental transitions were concomitant with speciation. Dispersal is inferred to be the main driver of the differential distribution observed among species. In addition, climatic preferences and floral characters seem to have been important reproductive barriers in Dolichandra. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 403–420.     

Neue Arten der neotropischen Gattung Neolindus Scheerpeltz (Coleoptera,Staphylinidae)

New species of the neotropical genus Neolindus Scheerpeltz (Coleoptera, Staphylinidae). Five new species of the neotropical genus Neolindus from the Peruvian Amazon region and from Brazil (Rio de Janeiro) are described.     

Molecular phylogenetics of Atlantic Shield Platynectes diving beetles (Coleoptera: Dytiscidae): a first glance at the evolution of the genus in the Amazon Basin

Neotropical diving beetles of the genus Platynectes are distributed across Central America, the Andes and different Precambrian shields in the Amazon Basin. Species from the northern Guiana Shield form a monophyletic clade, yet the phylogenetic relationships of the eastern Atlantic Shield species remain unknown. Here, we augmented an existing molecular dataset with a species from the Atlantic Shield that was not previously sampled. We reconstructed the phylogenetic relationships and estimated divergence times to understand the evolution of lineages dwelling in this region. The newly sampled specimens from the Atlantic Shield are recovered as sister taxa to Guiana Shield species. The dating analyses suggest a split between these two lineages in the late Oligocene to mid-Miocene, contemporary with the Miocenic geological remodeling of the Amazon Basin. Additional sampling in the Atlantic and Central Brazilian Shields will be determinant to test the monophyly of Platynectes species distributed in these ancient shields, and to fully understand the biogeographical history of diving beetles in the Amazon Basin.