Eight microsatellite loci in Phaedranassa schizantha Baker (Amaryllidaceae) and cross-amplification in other Phaedranassa species

Phaedranassa schizantha is a species endemic to Ecuador from which eight polymorphic microsatellite loci were isolated from an enriched genomic library. A total of 31 alleles with an average of four alleles per locus were detected across 29 individuals from a single natural population of P. schizantha. Observed heterozygosity ranged from 0.05 to 0.68. Most of the eight loci were successfully amplified in six Phaedranassa species. Five of those species are either “Vulnerable” or “Endangered” under IUCN criteria. These loci will be used to investigate patterns of inter- and intraspecific variation of Phaedranassa species, which will contribute data relevant to their conservation status.     

Comparative Phylogeography of Direct-Developing Frogs (Anura: Craugastoridae: Pristimantis) in the Southern Andes of Colombia

The Andes of South America hosts perhaps the highest amphibian species diversity in the world, and a sizable component of that diversity is comprised of direct-developing frogs of the genus Pristimantis (Anura: Craugastoridae). In order to better understand the initial stages of species formation in these frogs, this study quantified local-scale spatial genetic structuring in three species of Pristimantis. DNA sequences of two mitochondrial gene fragments (16S and COI) were obtained from P. brevifrons, P. palmeri and P. jubatus at different locations in the Cordillera Occidental. We found high levels of genetic diversity in the three species, with highly structured populations (as measured by F _ST) in P. brevifrons and P. palmeri while P. jubatus showed panmixia. Large effective population sizes, inferred from the high levels of genetic diversity, were found in the three species and two highly divergent lineages were detected within P. jubatus and P. palmeri. Estimated divergence times among populations within P. brevifrons and P. palmeri coincide with the Pleistocene, perhaps due to similar responses to climatic cycling or recent geological history. Such insights have important implications for linking alpha and beta diversity, suggesting regional scale patterns may be associated with local scale processes in promoting differentiation among populations in the Andes.     

Genetic structure of the threatened Phaedranassa schizantha (Amaryllidaceae)

Phaedranassa schizantha (Amaryllidaceae) is an endangered species endemic to Ecuador and two varieties have been described: P. schizantha var. schizantha and P. schizantha var. ignea. We assessed population genetic structure and demographic patterns in 11 populations across the range of the species using 13 microsatellite loci. Our data show that genetic diversity was generally lower in the southern part of the range and was especially low in populations closest to cities. We found significant population differentiation (F_ST = 0.14, D_EST = 0.34) and evidence of a genetic bottleneck. Genetic variation did not show isolation by distance. Instead, results suggest genetic barriers around two main cities. Bayesian analysis identified two genetic groups, neither of which represents either of the two varieties previously recognized. Coalescent analysis indicates a relatively recent colonization pattern between the two genetic groups (< 3000 generations). Conservation efforts need to be taken to facilitate genetic exchange between the groups, especially between locations that seem to be genetically isolated.     

Migration through a Major Andean Ecogeographic Disruption as a Driver of Genetic and Phenotypic Diversity in a Wild Tomato Species

Evolutionary dynamics at the population level play a central role in creating the diversity of life on our planet. In this study, we sought to understand the origins of such population-level variation in mating systems and defensive acylsugar chemistry in Solanum habrochaites—a wild tomato species found in diverse Andean habitats in Ecuador and Peru. Using Restriction-site-Associated-DNA-Sequencing (RAD-seq) of 50 S. habrochaites accessions, we identified eight population clusters generated via isolation and hybridization dynamics of 4–6 ancestral populations. Detailed characterization of mating systems of these clusters revealed emergence of multiple self-compatible (SC) groups from progenitor self-incompatible populations in the northern part of the species range. Emergence of these SC groups was also associated with fixation of deleterious alleles inactivating acylsugar acetylation. The Amotape-Huancabamba Zone—a geographical landmark in the Andes with high endemism and isolated microhabitats—was identified as a major driver of differentiation in the northern species range, whereas large geographical distances contributed to population structure and evolution of a novel SC group in the central and southern parts of the range, where the species was also inferred to have originated. Findings presented here highlight the role of the diverse ecogeography of Peru and Ecuador in generating population differentiation, and enhance our understanding of the microevolutionary processes that create biological diversity.     

Ecuadorian novelties in Blakea and Topobea (Melastomataceae)

Three new species of Melastomataceae (Blakeeae) are described:Blakea subpanduriformis, Topobea adscendens, andT. bullata. All are climbers endemic to the montane forests of the eastern slopes of the Andes in southern Ecuador. In this region, 35% of the Ecuadorian species and 41% of the endemic Ecuadorian species of Melastomataceae occur. The discovery of these three new endemic species underlines the diversity of Melastomataceae occurring on the slopes of the Andes in southeastern Ecuador.     

Progenitor-derivative speciation in Pozoa (Apiaceae, Azorelloideae) of the southern Andes

Background and Aims

Studies examining patterns and processes of speciation in South America are fewer than in North America and Europe. One of the least well documented processes has been progenitor–derivative speciation. A particularly instructive example occurs in the southern Andes in the genus Pozoa (Apiaceae, Azorelloideae), which consists of only two diploid outcrossing species, the widespread P. coriacea and the geographically and ecologically restricted P. volcanica. This paper tests the hypothesis that the latter species originated from the former through local geographical and ecological isolation by progenitor–derivative speciation.

Methods

DNA sequences were analysed from Pozoa and the related South American genera Asteriscium, Eremocharis and Gymnophyton from non-coding regions of the plastid genome, ndhF-rpl32 and rpl32-trnL, plus incorporation of previously reported rpl16 intron and trnD-trnT intergenic spacer sequences. Amplified fragment length polymorphism (AFLP) data from 105 individuals in 21 populations throughout the entire range of distribution of the genus were used for estimation of genetic diversity, divergence and SplitsTree network analysis. Ecological factors, including habitat and associated species, were also examined.

Key Results

Pozoa coriacea is more similar genetically to the outgroup genera, Asteriscium and Eremocharis, than is P. volcanica. At the population level, only P. volcanica is monophyletic, whereas P. coriacea is paraphyletic. Analyses of genetic differentiation among populations and genetic divergence and diversity of the species show highest values in P. coriacea and clear reductions in P. volcanica. Pozoa coriacea occurs in several types of high elevation habitats, whereas P. volcanica is found only in newly formed open volcanic ash zones.

Conclusions

All facts support that Pozoa represents a good example of progenitor–derivative speciation in the Andes of southern South America.     

Population dynamics of the endangered plant, Phaedranassa tunguraguae, from the Tropical Andean hotspot

The Tropical Andes is a diversity hotspot for plants, but there is a scant knowledge about patterns of genetic variation within its constituent species. Phaedranassa tunguraguae is an IUCN endangered plant species endemic to a single valley in the Ecuadorian Andes. We estimate the levels of genetic differentiation across the geographic distribution of P. tunguraguae using 12 microsatellite loci. We discuss factors that might influence the genetic structure of this species. Genetic distance was used to evaluate relationship among populations and geographic patterns. Bayesian methods were used to investigate population structure, migration, evidence of recent bottlenecks, and time of divergence. The 7 populations form 2 genetic clusters. These clusters show highly significant differentiation between them, along with isolation by distance. Allele richness decreases from the most diverse westernmost population to the least diverse easternmost population. The species overall shows an excess of homozygotes, with highest levels of inbreeding in the easternmost population. We found evidence of recent bottleneck events. Migration rates were in general low but were higher between populations within each of the clusters. Time of divergence between populations was related to historical volcanic activity in the area. Based on our results, we propose 2 management units for P. tunguraguae.     

Conservation genetics of an endangered orchid in eastern Canada

Platanthera leucophaea, the Eastern Prairie Fringed-orchid, is a globally imperilled species native to the USA and Canada, with its Canadian distribution limited to the Province of Ontario. In Canada, where P. leucophaea is listed as endangered, approximately 40 % of populations have been extirpated in recent years, and many remaining populations have experienced substantial declines. In this study, we investigated whether reduced population sizes have led to low genetic diversity and inbreeding. We also investigated the extent to which hybridization with Platanthera psycodes may be threatening the genetic integrity of P. leucophaea populations. We found that overall, genetic diversity is low, and inbreeding is high. This is despite evidence of regular gene flow between proximate populations, although more distant populations show high levels of genetic differentiation. At sites where P. leucophaea is sympatric with P. psycodes, interspecific hybridization occurs in a bidirectional manner, i.e. with both parental species acting as either pollen donor or pollen recipient. Inbreeding and low genetic diversity in all populations, and hybridization in some populations, may pose future threats to P. leucophaea, and should be considered in the future by biodiversity managers.     

Taxonomic revision of the olingos (Bassaricyon), with description of a new species,the Olinguito

We present the first comprehensive taxonomic revision and review the biology of the olingos, the endemic Neotropical procyonid genus Bassaricyon, based on most specimens available in museums, and with data derived from anatomy, morphometrics, mitochondrial and nuclear DNA, field observations, and geographic range modeling. Species of Bassaricyon are primarily forest-living, arboreal, nocturnal, frugivorous, and solitary, and have one young at a time. We demonstrate that four olingo species can be recognized, including a Central American species (Bassaricyon gabbii), lowland species with eastern, cis-Andean (Bassaricyon alleni) and western, trans-Andean (Bassaricyon medius) distributions, and a species endemic to cloud forests in the Andes. The oldest evolutionary divergence in the genus is between this last species, endemic to the Andes of Colombia and Ecuador, and all other species, which occur in lower elevation habitats. Surprisingly, this Andean endemic species, which we call the Olinguito, has never been previously described; it represents a new species in the order Carnivora and is the smallest living member of the family Procyonidae. We report on the biology of this new species based on information from museum specimens, niche modeling, and fieldwork in western Ecuador, and describe four Olinguito subspecies based on morphological distinctions across different regions of the Northern Andes.     

Axinaea fernando‐cabiesii and A. reginae spp. nov. (Melastomataceae) from upper Amazonia of Peru,with notes on the conservation status of A. flava

Two new Peruvian species of Axinaea (Melastomataceae) are described. Axinaea francisco‐cabiesii and Axinaea reginae are small trees, endemic to the cloud forest zone in the northern Andean region of Peru. The border region of Peru and Ecuador is one of the Earth's most biologically diverse areas. The Huancabamba depression of the central Andean Cordillera allows for dispersal of flora and fauna between the Amazon Basin and the Pacific lowlands. Additionally, the region is characterized by a fast transition between the humid mountain forests of the northern Andes and the dry, deciduous forests of the northern Peruvian lowlands, making it a hotspot for endemic species. Field observations indicate that both new Axinaea species have small population sizes, occurring in a very restricted habitat. Axinaea flava was described only a few years ago from the cloud forest – paramo transition zone in southernmost Ecuador between 3400 and 3800 m a.s.l. This small tree is the only yellow‐flowered species of the genus. The original assessment counted about 100 individuals. In the last decade, livestock grazing and widespread burning have intensified in the region, and a new assessment yielded only 10 individuals, four of which were damaged by fire. This puts the species in danger of extinction. We encourage search for other populations in southern Ecuador and northern Peru.     

Barcoding,population structure,and demographic history of Prodiplosis longifila associated with the Andes

Prodiplosis longifila Gagné (Diptera: Cecidomyiidae) is an insect pest that attacks various types of crops, including tomato, Solanum lycopersicum L. (Solanaceae), a vegetable with substantial economic significance worldwide. Prodiplosis longifila is a widely distributed pest in Colombia, Ecuador, and Peru, countries characterized by the presence of significant geographic barriers like the Andes Mountains. It has been reported that geographic barriers affect the dynamics and genetic differentiation of insect populations. Therefore, the aim of this study was to assess the diversity, genetic structure, and demographic history of P. longifila through the analysis of sequences within the mitochondrial region of cytochrome oxidase I (COI) and rDNA‐ITS2 in 27 populations located in Colombia and Ecuador. Analyses were performed on populations distributed in three geographic groups separated by the presence of the Andes Mountains. A total of 11 haplotypes were identified with the COI gene and only one haplotype in the rDNA‐ITS2 was found. Analyses of population structure and demographic history revealed that there is a structure associated with the Andes, which is reflected in an uneven distribution of the haplotype frequencies between regions, but even so, gene flow between populations was detected which produces low genetic differentiation. Because P. longifila has a short‐range dispersion that determines its territorial nature, it would be expected that other factors are producing the genetic exchange between populations. We suggest that the anthropogenic effect produced by farming practices, such as the use of seedlings as seed, which may carry P. longifila larvae, cause passive dispersal of pest throughout the Andes, particularly in Colombia.     

Preliminary analysis of the genetic diversity and population structure of mortiño (Vaccinium floribundum Kunth)

Mortiño (Vaccinium floribundum Kunth) is a deciduous perennial shrub endemic to the high Andes of South America. Despite a rich ethnobotanic history among indigenous communities, mortiño remains a wild species vulnerable to extinction from the ongoing fragmentation of its natural habitat. This study assessed the degree of genetic diversity and population structure of Ecuadorian V. floribundum as a preliminary step towards the establishment of effective conservation and sustainable-agriculture strategies. Mortiño individuals (126 in total) sampled from 3 regions in the northern highlands of Ecuador were characterized using 11 heterologous SSR markers originally developed for Vaccinium corymbosum. Expected heterozygosity (He = 0.49) revealed a moderate degree of genetic diversity for Ecuadorian mortiño, and pairwise F statistics between sampling regions (0.019≤ Fst ≤0.041) demonstrated low-to-moderate population differentiation. Population structure analysis clustered mortiño germplasm into 3 groups, each representing the 3 distinct regions from where samples were collected. The geographic patterning of genetic diversity for V. floribundum could be explained by an isolation-by-distance model, where physical barriers along the Andean highlands reduce genetic exchange between distanced populations. To confirm the latter, this study should extend to a wider sampling range, covering other regions along the Andean alley where the species is found.     

Revision of the rhinoceros beetle genus Oryctophileurus Kolbe with description of a new species,the male of O. varicosus Prell,and notes on biogeography (Scarabaeoidea,Dynastinae, Phileurini)

The genus Oryctophileurus is reviewed and its validity is supported by a combination of the following apomorphic characters: a single cephalic horn with lateral carina, pronotal cavity with ocellate punctures and two teeth or tubercles close behind the anterior pronotal margin. The male of Oryctophileurus varicosus Prell, 1934, is described for the first time. A new species, Oryctophileurus guerrai Perger & Grossi sp. n., from subhumid Tucuman-Bolivian forest in the Southern Bolivian Andes is described. The new species is distinguished from its closest relative, O. armicollis Prell, 1911, by a narrower distance between the inner teeth of the dorsal pronotal protuberances and a reduced area of weakly developed ocellate punctures above the posterolateral pronotal margin. The occurrence of Oryctophileurus species in areas of endemism along the eastern slope of the tropical Andes suggests that these populations represent biogeographic “relicts”, and the discovery of Oryctophileurus guerrai sp. n. in the southern Bolivian Andes suggests that this area is underrated with respect to insect diversity and endemism.     

Conservation genetics of the central newt (Notophthalmus viridescens) in Iowa: the importance of a biogeographic framework

In light of global declines in amphibian populations, genetic data have become increasingly important for understanding population structure and for revealing hidden diversity. At the species level, Notophthalmus viridescens is an IUCN species of “least concern”, but the subspecies N. v. louisianensis (central newt) is listed as “threatened” in Iowa, a state on the western periphery of the species range. Genetic data were collected from 282 N. v. louisianensis from 14 sites in Iowa. Sequences from 1,054 nucleotides of mitochondrial DNA from Iowa newts revealed unexpected diversity in the form of two major haplotype groups that are not sister clades, with southern Iowa N. v. louisianensis being more closely related to N. v. piaropicola (peninsula newt) from Florida than to consubspecifics in Iowa. Sequence differentiation indicates that the two lineages of newts present in Iowa diverged near the beginning of the Pleistocene. Northern and southern Iowa haplotypes were found together at one site, indicating an opportunity for hybridization near Remington’s biogeographic suture zone 1, a hotspot for hybridization in other species. Three microsatellite loci provided additional evidence for distinctness of northern and southern Iowa newt populations. This study highlights the relevance of historical biogeography to conservation, as management strategies for N. v. louisianensis in Iowa must reflect previously unrecognized diversity in this species. Nuclear and mitochondrial data indicate genetic isolation of nearby populations on the same drainage, and field data suggest the decline of one study population, emphasizing the need for identification and protection of newt breeding sites in Iowa.     

Phylogenetic relationships among populations of the Nacobbus aberrans (Nematoda,Pratylenchidae) complex reveal the existence of cryptic species

The plant‐parasitic nematode Nacobbus aberrans sensu lato is an agricultural pest of quarantine importance. Due to the morphometric, physiological and genetic variability observed within the species, there is no agreement on the taxonomy of this nematode. The objective of this study was to analyse the ITS rDNA region and the D2–D3 expansion segments of 28S rDNA in 10 Argentine populations and one from Ecuador and to establish their phylogenetic relationship with other known sequences from South and North America. Phylogenetic trees of the ITS gene showed seven statistically well‐supported clades; the high and significant F_st values obtained among these groups confirmed this partitioning. The Argentine populations here considered were separated into three clades: one comprising a population from the Andean region and two grouping nematodes from lower altitudes. Three other clades were distinguished for South American populations, which included known sequences of individuals from Peru, Bolivia and north of Argentina. The other clade included sequences from Mexico, Ecuador and two Argentine populations of unknown origin. The important degree of genetic divergence observed among Andean populations suggests that the Andes may have played a crucial role in speciation of Nacobbus, which would have originated in this region. Although D2–D3 segments exhibited lower variation, they were useful for establishing phylogenetic relationships among the Argentine populations considered in this work. As there are no other GenBank sequences available for these segments, it was not possible to make comparisons with other populations from South and North America. The considerable genetic differentiation observed in ITS rDNA region among Nacobbus populations showed evidence of cryptic species within the N. aberrans s.l. complex. Integration of morphological and morphometric studies and molecular analyses considering other genes may aid in the identification of species and their phylogenetic relationships within this genus.     

A new revision of Joosia (Rubiaceae-Cinchoneae)

Joosia comprises 11 species, three of which are here described as new: J. longisepala, J. multiflora, and J. obtusa. Joosia pulcherrima Steere is resurrected from synonymy. Joosia is a close relative of Cinchona, Ladenbergia, and Remijia, from all of which it differs in having wilting rather than caducous stipules, an inflorescence of predominantly monochasial cymes, and corolla lobes with marginal showy appendages. It occurs from western Panama along the Andes south to northern Bolivia, with a pronounced center of diversity in Ecuador. On the basis of a cladistic and biogeographical analysis, it is hypothesized that the genus originated in the lowland forest of the westernmost Amazon Basin.     

Bats,Trypanosomes, and Triatomines in Ecuador: New Insights into the Diversity,Transmission, and Origins of Trypanosoma cruzi and Chagas Disease

The generalist parasite Trypanosoma cruzi has two phylogenetic lineages associated almost exclusively with bats—Trypanosoma cruzi Tcbat and the subspecies T. c. marinkellei. We present new information on the genetic variation, geographic distribution, host associations, and potential vectors of these lineages. We conducted field surveys of bats and triatomines in southern Ecuador, a country endemic for Chagas disease, and screened for trypanosomes by microscopy and PCR. We identified parasites at species and genotype levels through phylogenetic approaches based on 18S ribosomal RNA (18S rRNA) and cytochrome b (cytb) genes and conducted a comparison of nucleotide diversity of the cytb gene. We document for the first time T. cruzi Tcbat and T. c. marinkellei in Ecuador, expanding their distribution in South America to the western side of the Andes. In addition, we found the triatomines Cavernicola pilosa and Triatoma dispar sharing shelters with bats. The comparisons of nucleotide diversity revealed a higher diversity for T. c. marinkellei than any of the T. c. cruzi genotypes associated with Chagas disease. Findings from this study increased both the number of host species and known geographical ranges of both parasites and suggest potential vectors for these two trypanosomes associated with bats in rural areas of southern Ecuador. The higher nucleotide diversity of T. c. marinkellei supports a long evolutionary relationship between T. cruzi and bats, implying that bats are the original hosts of this important parasite.     

Monograph of the neotropical species of Callipteris with anastomosing veins (Woodsiaceae)

Callipteris is a pantropical fern genus defined by two synapomorphies of its rhizome scales: 1) dark-castaneous to black borders, and 2) bifid marginal teeth. This monograph treats 15 neotropical species ofCallipteris that are further defined by the synapomorphy of anastomosing veins (free-veined species of the genus occur in the Neotropics and elsewhere). Three species are newly described here; the remaining 12 were previously classified inDiplazium. All the species ofCallipteris grow on wet forest floors at 100–2300 m. In the Neotropics the genus occurs from Guatemala to Bolivia, northern Brazil, and the Lesser Antilles. It has two centers of species richness. The first is the Chocó region on the western side of the Andes in Colombia and northwestern Ecuador. This region contains eight species, five of which are endemic. The second center is the mountains of Costa Rica and Panama, where six species occur, three of which are endemic. Only one species, an endemic, occurs in the Lesser Antilles in Martinique, St. Vincent, and Grenada. Four species occur only on the eastern side of the Andes, and these apparently represent at least two separate dispersal events from the western side of the Andes.     

Paraphyly of Cinclodes fuscus (Aves: Passeriformes: Furnariidae): Implications for taxonomy and biogeography

The Andes are a hotspot of global avian diversity, but studies on the historical diversification of Andean birds remain relatively scarce. Evolutionary studies on avian lineages with Andean–Patagonian distributions have focused on reconstructing species-level phylogenies, whereas no detailed phylogeographic studies on widespread species have been conducted. Here, we describe phylogeographic patterns in the Bar-winged Cinclodes (Cinclodes fuscus), a widespread and common species of ovenbird (Furnariidae) that breeds from Tierra del Fuego to the northern Andes. Traditionally, C. fuscus has been considered a single species composed of nine subspecies, but its long and narrow range suggests the possibility of considerable genetic variation among populations. Sequences of two mitochondrial genes revealed three discrete and geographically coherent groups of C. fuscus, occupying the southern, central, and northern Andes. Surprisingly, phylogenetic analyses indicated that these groups were more closely related to other species of Cinclodes than to each other. Relationships of the southern and northern C. fuscus clades to other species of Cinclodes were straightforward; in combination with available information on plumage, behavioral, and vocal variation, this suggests that each should be recognized as a distinct biological species. The central Andean group was paraphyletic with respect to C. oustaleti, and relationships among these taxa and C. olrogi were poorly resolved. We suggest that the central Andean C. fuscus should also be considered a different species, pending new information to clarify species limits in this group. These new phylogenetic data, along with recently developed methods, allowed us to review the biogeography of the genus, confirming southern South America and the central Andes as important areas for the diversification of these birds.     

Lack of genetic structure in endangered large yellow croaker Larimichthys crocea from China inferred from mitochondrial control region sequence data

The large yellow croaker Larimichthys crocea is an important commercial marine fish species in China. However, information about the population structure of this species is limited. In the present study, mitochondrial DNA (mtDNA) control region was sequenced from four populations of the yellow croaker in the southern Yellow Sea, East China Sea and South China Sea to investigate the genetic structure of this species. A total of 54 haplotypes were detected among 62 individuals of large yellow croaker. High levels of population genetic diversity were observed. Among the four populations, the haplotype diversity was between 0.9895 ± 0.0193 (Xiamen) and 1.0000 ± 0.0524 (Lvsi, Zhoushan). The nucleotide diversity ranged from 0.0208 ± 0.0108 (Xuwen) to 0.0246 ± 0.0138 (Lvsi). The results of AMOVA detected no significant differences among populations. The conventional F_ST statistics were negative and insignificant values. These indicated lack of population genetic structure throughout the Yellow Sea, East China Sea and South China Sea, and random mixing of individuals among the samples. Biological characters of large yellow croaker and lack of physical barrier in the studied area could be the reasons for lack of genetic structure in this species.