Genetic Diversity of Neotropical Myotis (Chiroptera: Vespertilionidae) with an Emphasis on South American Species

Background

Cryptic morphological variation in the Chiropteran genus Myotis limits the understanding of species boundaries and species richness within the genus. Several authors have suggested that it is likely there are unrecognized species-level lineages of Myotis in the Neotropics. This study provides an assessment of the diversity in New World Myotis by analyzing cytochrome-b gene variation from an expansive sample ranging throughout North, Central, and South America. We provide baseline genetic data for researchers investigating phylogeographic and phylogenetic patterns of Myotis in these regions, with an emphasis on South America.

Methodology and Principal Findings

Cytochrome-b sequences were generated and phylogenetically analyzed from 215 specimens, providing DNA sequence data for the most species of New World Myotis to date. Based on genetic data in our sample, and on comparisons with available DNA sequence data from GenBank, we estimate the number of species-level genetic lineages in South America alone to be at least 18, rather than the 15 species currently recognized.

Conclusions

Our findings provide evidence that the perception of lower species richness in South American Myotis is largely due to a combination of cryptic morphological variation and insufficient sampling coverage in genetic-based systematic studies. A more accurate assessment of the level of diversity and species richness in New World Myotis is not only helpful for delimiting species boundaries, but also for understanding evolutionary processes within this globally distributed bat genus.     

2C DNA variation and relationships among New World species of the genus Lupinus (Fabaceae)

The 2C DNA values in 38 species and accessions of the genus Lupinus (Fabaceae) from the New World have been analysed using flow cytometry. They are representatives of North and South American species (the Atlantic and the Andean regions). Estimated 2C DNA values ranged from 1.08 pg in L. pusillus to 2.68 pg in L. albicaulis (both from North America), that is a variation of more than 2.5-fold. The variation for North American lupins was much higher than that for South American ones. Statistical analysis of the data resulted in a grouping that showed for North American lupins some correlation with the length of life cycle. Discussion concerns some aspects of the evolution of the genus.     

Ecogeographical Variation in Skull Shape of South-American Canids: Abiotic or Biotic Processes?

Species morphological changes can be mutually influenced by environmental or biotic factors, such as competition. South American canids represent a quite recent radiation of taxa that evolved forms very disparate in phenotype, ecology and behaviour. Today, in the central part of South America there is one dominant large species (the maned wolf, Chrysocyon brachyurus) that directly influence sympatric smaller taxa via interspecific killing. Further south, three species of similar sized foxes (Lycalopex spp.) share the same habitats. Such unique combination of taxa and geographic distribution makes South American dogs an ideal group to test for the simultaneous impact of climate and competition on phenotypic variation. Using geometric morphometrics, we quantified skull size and shape of 431 specimens belonging to the eight extant South American canid species: Atelocynus microtis, Cerdocyon thous, Ch. brachyurus, Lycalopex culpaeus, L. griseus, L. gymnocercus, L. vetulus and Speothos venaticus. South American canids are significantly different in both skull size and shape. The hypercarnivorous bush dog is mostly distinct in shape from all the other taxa while a degree of overlap in shape—but not size—occurs between species of the genus Lycalopex. Both climate and competition impacts interspecific morphological variation. We identified climatic adaptations as the main driving force of diversification for the South American canids. Competition has a lower degree of impact on their skull morphology although it might have played a role in the past, when canid community was richer in morphotypes.     

Moisture variables, and not temperature, are responsible for climate filtering and genetic bottlenecks in the South African endemic terrestrial mollusc Prestonella (Orthalicoidea)

Non-vagile taxa such as terrestrial molluscs are susceptible to stochastic environmental events that can cause local extinctions or population declines, and extinctions of terrestrial mollusc species are among the highest documented. Many terrestrial snails are habitat specialists, and genetic studies using both allozyme and DNA sequence data have indicated that many species contain substantial and geographically structured genetic variation. In this study, we assess the genetic variation within two species of the rare terrestrial snail genus Prestonella, an inhabitant of rocky areas along water courses in the southern Great Escarpment of South Africa, and correlate genetic diversity to climatic variables. DNA sequence data from mitochondrial 16S rDNA and partial cytochrome oxidase I genes indicate that neither species is monophyletic, and that populations are deeply divergent, even over distances of a few hundred metres. Principal components anaylsis of climatic variables derived from two databases indicates that genetic diversity of the populations is correlated to moisture-related climatic variables. Populations with little or no diversity occur in more arid regions, and are thus most at risk from any future climatic changes that would increase aridification. These moisture variables are thus potent drivers of genetic bottlenecks and may have resulted in historical climate filtering or limitation of the distribution of these species. Temperature appears to be a less important variable, a finding supported by physiological data based on heart rates that show that death occurs only at temperatures far higher than found in their environment.     

Greater variation in boreal plant community composition and community-level traits at local- than regional-scale

Questions

Rapid climate change in northern latitudes is expected to influence plant functional traits of the whole community (community-level traits) through species compositional changes and/or trait plasticity, limiting our ability to anticipate climate warming impacts on northern plant communities. We explored differences in plant community composition and community-level traits within and among four boreal peatland sites and determined whether intra- or interspecific variation drives community-level traits.

Location

Boreal biome of western North America.

Methods

We collected plant community composition and functional trait data along dominant topoedaphic and/or hydrologic gradients at four peatland sites spanning the latitudinal extent of the boreal biome of western North America. We characterized variability in community composition and community-level traits of understorey vascular and moss species both within (local-scale) and among sites (regional-scale).

Results

Against expectations, community-level traits of vascular plant and moss species were generally consistent among sites. Furthermore, interspecific variation was more important in explaining community-level trait variation than intraspecific variation. Within-site variation in both community-level traits and community composition was greater than among-site variation, suggesting that local environmental gradients (canopy density, organic layer thickness, etc.) may be more influential in determining plant community processes than regional-scale gradients.

Conclusions

Given the importance of interspecific variation to within-site shifts in community-level traits and greater variation of community composition within than among sites, we conclude that climate-induced shifts in understorey community composition may not have a strong influence on community-level traits in boreal peatlands unless local-scale environmental gradients are substantially altered.     

Mitochondrial DNA based phylogeny of the woodpecker genera Colaptes and Piculus,and implications for the history of woodpecker diversification in South America

The woodpecker genus Colaptes (flickers) has its highest diversity in South America and the closely related genus Piculus is restricted to South and Central America. Two species of flickers occur in North America, and one species is endemic to Cuba. We conducted a Bayesian phylogenetic analysis of three mitochondrial encoded genes (cyt b, COI, 12S rRNA) and confirmed that the two genera are paraphyletic. Three species historically classified as Piculus are actually flickers. We found that the Cuban endemic C. fernandinae is the most basal species within the flickers and that the Northern Flicker is the next most basal species within the Colaptes lineage. The South American clade is most derived. The age of the South American diversification is estimated to be 3.6 MY, which is synchronous with the emergence of the Isthmus of Panama. The pattern of diversification of South American flickers is common among South American woodpeckers. Although woodpeckers have their greatest diversity in South America, we hypothesize that woodpeckers (Family Picidae) originated in Eurasia, dispersed to North America via the Bering land bridge, and multiple lineages entered South America as the Isthmus approached its final closing.     

Comparative Mitochondrial Genomics within and among Yeast Species of the Lachancea Genus

Yeasts are leading model organisms for mitochondrial genome studies. The explosion of complete sequence of yeast mitochondrial (mt) genomes revealed a wide diversity of organization and structure between species. Recently, genome-wide polymorphism survey on the mt genome of isolates of a single species, Lachancea kluyveri, was also performed. To compare the mitochondrial genome evolution at two hierarchical levels: within and among closely related species, we focused on five species of the Lachancea genus, which are close relatives of L. kluyveri. Hence, we sequenced the complete mt genome of L. dasiensis, L. nothofagi, L. mirantina, L. fantastica and L. meyersii. The phylogeny of the Lachancea genus was explored using these data. Analysis of intra- and interspecific variability across the whole Lachancea genus led to the same conclusions regarding the mitochondrial genome evolution. These genomes exhibit a similar architecture and are completely syntenic. Nevertheless, genome sizes vary considerably because of the variations of the intergenic regions and the intron content, contributing to mitochondrial genome plasticity. The high variability of the intergenic regions stands in contrast to the high level of similarity of protein sequences. Quantification of the selective constraints clearly revealed that most of the mitochondrial genes are under purifying selection in the whole genus.     

Ecological niche modeling and geographical distribution of pollinator and plants: A case study of Peponapis fervens (Smith, 1879) (Eucerini: Apidae) and Cucurbita species (Cucurbitaceae)

The bees of the Peponapis genus (Eucerini, Apidae) have a Neotropical distribution with the center of species diversity located in Mexico and are specialized in Cucurbita plants, which have many species of economic importance, such as squashes and pumpkins. Peponapis fervens is the only species of the genus known from southern South America. The Cucurbita species occurring in the same area as P. fervens include four domesticated species (C. ficifolia, C. maxima maxima, C. moschata and C. pepo) and one non-domesticated species (Cucurbita maxima andreana). It was suggested that C. m. andreana was the original pollen source to P. fervens, and this bee expanded its geographical range due to the domestication of Cucurbita. The potential geographical areas of these species were determined and compared using ecological niche modeling that was performed with the computational system openModeller and GARP with best subsets algorithm. The climatic variables obtained through modeling were compared using Cluster Analysis. Results show that the potential areas of domesticated species practically spread all over South America. The potential area of P. fervens includes the areas of C. m. andreana but reaches a larger area, where the domesticated species of Cucurbita also occur. The Cluster Analysis shows a high climatic similarity between P. fervens and C. m. andreana. Nevertheless, P. fervens presents the ability to occupy areas with wider ranges of climatic variables and to exploit resources provided by domesticated species.     

Spatial predictability and resource specialization of bees (Hymenoptera: Apoidea) at a superabundant, widespread resource

For reciprocal specialization (coevolution) to occur among floral visitors and their host plants the interactions must be temporally and spatially persistent. However, studies repeatedly have shown that species composition and relative abundance of floral visitors vary dramatically at all spatial and temporal scales. We test the hypothesis that, on average, pollen specialist bee species occur more predictably at their floral hosts than pollen generalist bee species. Taxonomic floral specialization reaches its extreme among species of solitary, pollen-collecting bees, yet few studies have considered how pollen specialization by floral visitors influences their spatial constancy. We test this hypothesis using an unusually diverse bee guild that visits creosote bush (Larrea tridentatd), the most widespread, dominant plant of the warm deserts of North America. Twenty-two strict pollen specialist and 80 + generalist bee species visit Larrea for its floral resources. The sites we sampled were separated by 0.5 to > 1450 km, and spanned three distinct deserts and four vegetation zones. We found that species of Larrea pollen specialist bees occurred at more sites and tended to be more abundant than generalists. Surprisingly, spatial turnover was high for both pollen specialist and generalist bee species at all distances, and species composition of samples from sites 1–5 km apart varied as much as repeat samples made at single sites. Nevertheless, the pattern of bee species turnover was not haphazard. As distance among sites increased faunal similarity of sites decreased. Faunal similarities among sites within 250 km of each other were generally greater than if randomly distributed over all sites (the null model). No single ecological category of species (widespread, localized, Larrea pollen specialist, floral generalist) accounted for this spatial predictability. Evidently, concordant local distribution patterns of many ecologically diverse species contribute to the non-random spatial pattern. The ecological dominance of creosote bush does not confer obvious ecological advantages to its specialist floral visitors. Spatial turnover is comparable to that found for bee guilds from other biogeographic regions of the world and is not therefore limited to those bee species that inhabit highly seasonal climates, such as deserts. Philopatry and differences in bloom predictability among sites are probably more important causes for spatial turnover of bee species than are interspecific competition for nest sites or floral resources.     

Phylogenetic Relationships and Species Delimitation in Pinus Section Trifoliae Inferrred from Plastid DNA

Recent diversification followed by secondary contact and hybridization may explain complex patterns of intra- and interspecific morphological and genetic variation in the North American hard pines (Pinus section Trifoliae), a group of approximately 49 tree species distributed in North and Central America and the Caribbean islands. We concatenated five plastid DNA markers for an average of 3.9 individuals per putative species and assessed the suitability of the five regions as DNA bar codes for species identification, species delimitation, and phylogenetic reconstruction. The ycf1 gene accounted for the greatest proportion of the alignment (46.9%), the greatest proportion of variable sites (74.9%), and the most unique sequences (75 haplotypes). Phylogenetic analysis recovered clades corresponding to subsections Australes, Contortae, and Ponderosae. Sequences for 23 of the 49 species were monophyletic and sequences for another 9 species were paraphyletic. Morphologically similar species within subsections usually grouped together, but there were exceptions consistent with incomplete lineage sorting or introgression. Bayesian relaxed molecular clock analyses indicated that all three subsections diversified relatively recently during the Miocene. The general mixed Yule-coalescent method gave a mixed model estimate of only 22 or 23 evolutionary entities for the plastid sequences, which corresponds to less than half the 49 species recognized based on morphological species assignments. Including more unique haplotypes per species may result in higher estimates, but low mutation rates, recent diversification, and large effective population sizes may limit the effectiveness of this method to detect evolutionary entities.     

Genetic architecture and genomic patterns of gene flow between hybridizing species of Picea

Hybrid zones provide an opportunity to study the effects of selection and gene flow in natural settings. We employed nuclear microsatellites (single sequence repeat (SSR)) and candidate gene single-nucleotide polymorphism markers (SNPs) to characterize the genetic architecture and patterns of interspecific gene flow in the Picea glauca × P. engelmannii hybrid zone across a broad latitudinal (40–60 degrees) and elevational (350–3500 m) range in western North America. Our results revealed a wide and complex hybrid zone with broad ancestry levels and low interspecific heterozygosity, shaped by asymmetric advanced-generation introgression, and low reproductive barriers between parental species. The clinal variation based on geographic variables, lack of concordance in clines among loci and the width of the hybrid zone points towards the maintenance of species integrity through environmental selection. Congruency between geographic and genomic clines suggests that loci with narrow clines are under strong selection, favoring either one parental species (directional selection) or their hybrids (overdominance) as a result of strong associations with climatic variables such as precipitation as snow and mean annual temperature. Cline movement due to past demographic events (evidenced by allelic richness and heterozygosity shifts from the average cline center) may explain the asymmetry in introgression and predominance of P. engelmannii found in this study. These results provide insights into the genetic architecture and fine-scale patterns of admixture, and identify loci that may be involved in reproductive barriers between the species.     

DNA barcoding identification and genetic diversity of bamboo shoot wireworms (Coleoptera: Elateridae) in South China

Wireworms are recognized as economically important oligophagous pests of Phyllostachys bamboo shoot, which have caused a huge economic loss in South China. Studies of bamboo shoot wireworm control and management were seriously hampered by the lack of reliable identification of larvae. DNA barcoding has been proved to be an important and useful tool in species identification of morphologically cryptic insects. Accurate knowledge of damage-causing species and the phylogenic structure of elaterids will provide insight into their sustainable and effective management. Here, we use interspecific variation in COI and EF1-a as a robust method of identification and consider the intra- and interspecific genetic variation of bamboo wireworms. This approach has revealed that three Melanotus larvae occurred in Phyllostachys forest. The dominance of one species in different sampling location suggests there maybe underlying difference in habit and host plant preference. These data provide a starting point for determining the distribution of wireworm species feeding on bamboo shoots in South China. The inclusions would further aid identification of wireworm species and relationships between certain wireworm species with specific environments.     

A tale of North and South America: time and mode of dispersal of the amphitropical genus Munroa (Poaceae,Chloridoideae)

Plant disjunctions have provided some of the most intriguing distribution patterns historically addressed by biogeographers. We evaluated the three hypotheses that have been postulated to explain these patterns [vicariance, stepping‐stone dispersal and long‐distance dispersal (LDD)] using Munroa, an American genus of grasses with six species and a disjunct distribution between the desert regions of North and South America. The ages of clades, cytology, ancestral characters and areas of distribution were investigated in order to establish relationships among species, to determine the time of divergence of the genus and its main lineages, and to understand further the biogeographical and evolutionary history of this genus. Bayesian inference recovered the North American M. pulchella as sister species to the rest. Molecular dating and ancestral area analyses suggest that Munroa originated in North America in the late Miocene–Pliocene (7.2 Mya; 8.2–6.5 Mya). Based on these results, we postulate that two dispersal events modelled the current distribution patterns of Munroa: the first from North to South America (7.2 Mya; 8.2–6.5 Mya) and the second (1.8 Mya; 2–0.8 Mya) from South to North America. Arid conditions of the late Miocene–Pliocene in the Neogene and Quaternary climatic oscillations in North America and South America were probably advantageous for the establishment of populations of Munroa. We did not find any relationship between ploidy and dispersal events, and our ancestral character analyses suggest that shifts associated with dispersal and seedling establishment, such as habit, reproductive system, disarticulation of rachilla, and shape and texture of the glume, have been important in these species reaching new areas. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 110–125.     

Does the DNA barcoding gap exist? – a case study in blue butterflies (Lepidoptera: Lycaenidae)

Background

DNA barcoding, i.e. the use of a 648 bp section of the mitochondrial gene cytochrome c oxidase I, has recently been promoted as useful for the rapid identification and discovery of species. Its success is dependent either on the strength of the claim that interspecific variation exceeds intraspecific variation by one order of magnitude, thus establishing a "barcoding gap", or on the reciprocal monophyly of species.

Results

We present an analysis of intra- and interspecific variation in the butterfly family Lycaenidae which includes a well-sampled clade (genus Agrodiaetus) with a peculiar characteristic: most of its members are karyologically differentiated from each other which facilitates the recognition of species as reproductively isolated units even in allopatric populations. The analysis shows that there is an 18% overlap in the range of intra- and interspecific COI sequence divergence due to low interspecific divergence between many closely related species. In a Neighbour-Joining tree profile approach which does not depend on a barcoding gap, but on comprehensive sampling of taxa and the reciprocal monophyly of species, at least 16% of specimens with conspecific sequences in the profile were misidentified. This is due to paraphyly or polyphyly of conspecific DNA sequences probably caused by incomplete lineage sorting.

Conclusion

Our results indicate that the "barcoding gap" is an artifact of insufficient sampling across taxa. Although DNA barcodes can help to identify and distinguish species, we advocate using them in combination with other data, since otherwise there would be a high probability that sequences are misidentified. Although high differences in DNA sequences can help to identify cryptic species, a high percentage of well-differentiated species has similar or even identical COI sequences and would be overlooked in an isolated DNA barcoding approach.     

A New Fishfly Species (Megaloptera: Corydalidae: Neohermes Banks) Discovered from North America by a Systematic Revision,with Phylogenetic and Biogeographic Implications

The taxonomy of Megaloptera from the Nearctic region is fairly well known and their faunal diversity has been largely surveyed, even in relatively remote regions. However, the evolutionary history of Nearctic Megaloptera is still poorly known with phylogenetic and biogeographic studies lacking. In this paper, we report a new fishfly species of the endemic North American genus Neohermes Banks, 1908, increasing the total number known of species to six. This new species (Neohermes inexpectatus sp. nov.) is currently known to occur only in California (USA) and is apparently confined to the Northern Coastal Range. The new species resembles the three Neohermes species from eastern North America based on the relatively small body size and the presence of female gonostyli 9. However, our phylogenetic analysis using adult morphological data recovered the new species as the sister species to the remaining Neohermes, which includes two species from western North America and three from eastern North America. According to the present interspecific phylogeny of Neohermes, with reconstructed ancestral areas, the initial divergence within the genus was found to take place in western North America, with a subsequent eastward dispersal. This likely lead to the modern distribution of Neohermes in eastern North America with the closure of the Mid-Continental Seaway, which separated western and eastern North America in the Mid-Late Cretaceous (100–80 MYA) and finally disappeared at the end of the Cretaceous (70 MYA). The uplift of the Cordilleran System probably accounted for the divergence between the eastern and two western Neohermes species.     

Intra- and interspecific genome-size variation in the Salmonidae.

The nuclear DNA contents of 22 salmonid taxa, estimated primarily by flow-cytometric analysis relative to a chicken internal standard, were evaluated to compare intra- and interspecific variation in DNA content within this fish family. The average variability within taxa exceeded that among taxa. Intraspecific genome-size variation was substantial and, in some cases, exceeded the mean genome size for the species. The flow-cytometric method used here allows for rapid and reliable comparison of nuclear DNA contents within and among individuals from natural animal populations.     

Phylogenetic relationships of Ochoterenatrema Caballero, 1943 (Digenea: Lecithodendriidae) with descriptions of two new species

Ochoterenatrema is a small genus of lecithodendriid digeneans that includes six species parasitic in Neotropical bats in North and South America. Members of this genus are characterized by the presence of a pseudogonotyl formed by thickened tegument on the left side of the ventral sucker. We examined morphology of specimens belonging to five species of Ochoterenatrema from Brazil, Ecuador and the USA and describe two new Ochoterenatrema spp. (Ochoterenatrema sphaerula n. sp. and Ochoterenatrema gracilis n. sp.). These new species are readily differentiated from their congeners by a combination of morphological characters, including the distribution of vitelline follicles and the body shape. We have provided the first DNA sequences for Ochoterenatrema. Newly generated partial nuclear 28S rDNA and mitochondrial cox1 gene sequences were used to differentiate among species and study the phylogenetic affinities of Ochoterenatrema spp., including one of the new species, O. gracilis n. sp., as well as Ochoterenatrema diminutum, Ochoterenatrema fraternum and Ochoterenatrema cf. labda. The phylogeny of the Microphalloidea based on 28S had well-supported topology, particularly at the family level. The Ochoterenatrema clade was strongly supported; however, the internal topology of the clade was weakly supported. Comparison of sequences revealed 0.4–1.3% interspecific divergence in 28S and 9.1–19.7% interspecific divergence in cox1 among Ochoterenatrema spp. We hypothesize that extremely diverse fauna of bats in South and Central America harbors multiple undescribed species of Ochoterenatrema. Several lecithodendriid genera from bats and other hosts are yet to be included in future molecular phylogenetic analyses to test the monophyly of this extremely diverse digenean family and analyze evolutionary affinities of its constituent taxa.     

Forager abundance and its relationship with colony activity level in three species of South American Pogonomyrmex harvester ants

The proportion of foragers in ant colonies is a fairly constant species-specific characteristic that could be determined by intrinsic or extrinsic factors. If intrinsic factors are relevant, species with similar life history characteristics (e.g., colony size and foraging strategies) would be expected to have a similar proportion of foragers in their colonies. Within the genus Pogonomyrmex, North American species can vary largely in their colony size, whereas only species with small colonies are known in South America. We studied the characteristics of the foraging subcaste in three sympatric South American species of Pogonomyrmex harvester ants, and compared it with the available information on other species of the same genus. We used two mark-recapture methods and colony excavations to estimate the number and proportion of foragers in the colonies of P. mendozanus, P. inermis, and P. rastratus, and to test the relationship between forager external activity levels and abundance per colony. Forager abundance in the three studied species was lower than in most North American species. The percentage of foragers in their colonies ranged 7–15 %, more similar to North American species with large colonies than to those with small colony size. Foraging activity was positively correlated with forager abundance in all three species, implying that colony allocation to number of foragers allows for higher food acquisition. Further comparative studies involving a wider range of traits in South and North American species would allow to unveil the role of environmental factors in shaping each species’ particular traits.     

Reappraisal of the Genus Tapirus (Perissodactyla, Tapiridae): Systematics and Phylogenetic Affinities of the South American Tapirs

The record of the genus Tapirus in South America is associated with the faunistic events of the Great American Biotic Interchange (GABI). The taxon is considered an immigrant of Holarctic origin. Although remains are scarce and incomplete during the Pleistocene, an analysis of these materials allowed us to consider valid seven fossil species : Tapirus tarijensis, T. cristatellus, T. greslebini, T. rioplatensis, T. oliverasi, T. mesopotamicus, and T. rondoniensis. A phylogenetic analysis was carried out in order to elucidate the relationships of the American fossil and extant species. Our result is consistent with a paraphyletic hypothesis for South American tapirs and suggests that a second dispersal event would have occurred from South America to North America, of a form closely related to T. cristatellus, resulting in the derived forms of North America.