Burton K. Lim

The role of DNA barcodes in understanding and conservation of mammal diversity in southeast Asia.

Background Southeast Asia is recognized as a region of very high biodiversity, much of which is currently at risk due to habitat loss and other threats. However, many aspects of this diversity, even for relatively well-known groups such as mammals, are poorly known, limiting ability to develop conservation plans. This study examines the value of DNA barcodes, sequences of the mitochondrial COI gene, to enhance understanding of mammalian diversity in the region and hence to aid conservation planning. Methodology and Principal Findings DNA barcodes were obtained from nearly 1900 specimens representing 165 recognized species of bats. All morphologically or acoustically distinct species, based on classical taxonomy, could be discriminated with DNA barcodes except four closely allied species pairs. Many currently recognized species contained multiple barcode lineages, often with deep divergence suggesting unrecognized species. In addition, most widespread species showed substantial genetic differentiation across their distributions. Our results suggest that mammal species richness within the region may be underestimated by at least 50%, and there are higher levels of endemism and greater intra-specific population structure than previously recognized. Conclusions DNA barcodes can aid conservation and research by assisting field workers in identifying species, by helping taxonomists determine species groups needing more detailed analysis, and by facilitating the recognition of the appropriate units and scales for conservation planning.

DNA barcoding in surveys of small mammal communities: a field study in Suriname.

The performance of DNA barcoding as a tool for fast taxonomic verification in ecological assessment projects of small mammals was evaluated during a collecting trip to a lowland tropical rainforest site in Suriname. We also compared the performance of tissue sampling onto FTA CloneSaver cards vs. liquid nitrogen preservation. DNA barcodes from CloneSaver cards were recovered from 85% of specimens, but DNA degradation was apparent, because only 36% of sequence reads were long (over 600 bp). In contrast, cryopreserved tissue delivered 99% barcode recovery (97% > 600 bp). High humidity, oversampling or tissue type may explain the poor performance of CloneSaver cards. Comparison of taxonomic assignments made in the field and from barcode results revealed inconsistencies in just 3.4% of cases and most of the discrepancies were due to field misidentifications (3%) rather than sampling/analytical error (0.5%). This result reinforces the utility of DNA barcoding as a tool for verification of taxonomic identifications in ecological surveys, which is especially important when the collection of voucher specimens is not possible.

Species diversity of bats (Mammalia: Chiroptera) in Iwokrama Forest, Guyana, and the Guianan subregion: implications for conservation

Fourteen species of bats are reported for the first time from Guyana (Saccopteryx gymnura, Micronycteris brachyotis, M. homezi, Lichonycteris obscura, Anoura latidens, Vampyressa pusilla, Vampyrodes caraccioli, Eptesicus chiriquinus, Cynomops paranus, Molossops neglectus, Molossus sp., Molossus coibensis, Molossus sinaloae, and Promops centralis) bringing the known bat diversity for the country to 121 species. Information including measurements, reproductive data, distribution, and taxonomy are provided for these species. Seven of these new records were collected in the Iwokrama International Rain Forest Programme site in central Guyana. Eighty-six bat species are now documented from Iwokrama Forest which is the highest species diversity for bats reported from any protected area in the world. There are, however, few tropical sites that have relatively complete inventories. A summary for bat species diversity in southern Venezuela, Guyana, Suriname, and French Guiana indicates that at least 146 species of bats are known from the Guianan subregion. Intense inventory surveys, especially in the often neglected subcanopy, suggest that species richness is probably underestimated in most Neotropical areas. Likewise, species-level diversity in the Guianan subregion is higher than previously suggested. Surveying and monitoring biodiversity are critical to developing a National Protected Areas System in Guyana.

Neotropical Bats: Estimating Species Diversity with DNA Barcodes

DNA barcoding using the cytochrome c oxidase subunit 1 gene (COI) is frequently employed as an efficient method of species identification in animal life and may also be used to estimate species richness, particularly in understudied faunas. Despite numerous past demonstrations of the efficiency of this technique, few studies have attempted to employ DNA barcoding methodologies on a large geographic scale, particularly within tropical regions. In this study we survey current and potential species diversity using DNA barcodes with a collection of more than 9000 individuals from 163 species of Neotropical bats (order Chiroptera). This represents one of the largest surveys to employ this strategy on any animal group and is certainly the largest to date for land vertebrates. Our analysis documents the utility of this tool over great geographic distances and across extraordinarily diverse habitats. Among the 163 included species 98.8% possessed distinct sets of COI haplotypes making them easily recognizable at this locus. We detected only a single case of shared haplotypes. Intraspecific diversity in the region was high among currently recognized species (mean of 1.38%, range 0–11.79%) with respect to birds, though comparable to other bat assemblages. In 44 of 163 cases, well-supported, distinct intraspecific lineages were identified which may suggest the presence of cryptic species though mean and maximum intraspecific divergence were not good predictors of their presence. In all cases, intraspecific lineages require additional investigation using complementary molecular techniques and additional characters such as morphology and acoustic data. Our analysis provides strong support for the continued assembly of DNA barcoding libraries and ongoing taxonomic investigation of bats.

Molecular Differentiation of Large Species of Fruit-Eating Bats (Artibeus) and Phylogenetic Relationships Based on the Cytochrome b Gene

We analyzed the phylogenetic relationships of all eleven currently recognized species of large Artibeus using the cytochrome b mitochondrial gene. The topology from a maximum parsimony analysis included: (1) A. obscurus and A. planirostris as sister species with successively basal lineages of (2) A. amplus, (3) a clade with A. lituratus and A. intermedius, (4) A. jamaicensis, (5) a clade of A. inopinatus sister to A. hirsutus and A. fraterculus, (6) A. fimbriatus, and (7) the most basal lineage of A. concolor. The individual species were monophyletic and well supported by bootstrap and decay values. The monophyletic clade of ((((obscurus + planirostris) + amplus) + (lituratus + intermedius)) + jamaicensis) was also highly supported, although some of the interspecific relationships were less so. Contrary to previous hypotheses of species limits based on a presumed intergradation in body size, A. jamaicensis and A. planirostris do not form a monophyletic group, refuting their conspecificity and supporting an earlier study concluding that these two taxa represent separate morphological populations. An analysis with A. jamaicensis and A. planirostris constrained as sister-taxa resulted in a tree 8 steps longer. In addition, the low genetic pair-wise difference between A. lituratus and A. intermedius (2.8% with Kimura-2 parameters) warrants closer examination of their species limits.

Bat community structure at Iwokrama Forest, Guyana

With 86 species, Iwokrama Forest in central Guyana has the highest reported bat biodiversity for a protected area in the world. Using standardized capture data for 73 of these 86 species, we document community structure of bats in terms of species diversity, relative abundance, gross biomass, feeding guilds, vertical stratification and a trophic-size niche matrix. Based on faunal surveys in 1997, with similar amounts of effort in the forest canopy and at ground level, the greater fruit-eating bat (Artibeus lituratus) was by far the most ecologically dominant species in terms of frequency of capture and biomass. In total, frugivores comprised 70% of the species diversity and 78% of the biomass. The most common species of bat were fully partitioned in a resource niche matrix of size and trophic guild when vertical stratification was included as a variable. We conclude that resource partitioning and species packing differentially affect relative size in tropical bats, and are better summarized and analysed in three dimensions.

Systematics of the genera Carollia and Rhinophylla based on the cytochrome-B gene

Intrageneric relationships within Carollia and Rhinophylla (Phyllostomidae) are examined using the 1,140 base pairs of the mitochondrial cytochrome-b gene. We also examined the proposed sister relationship of Carollia and Rhinophylla by comparing the cytochrome-b gene from those two taxa to that of representatives of Phyllonycteris, Lonchophylla, Uroderma, Artibeus, Dermanura, Enchisthenes, and Chiroderma. Within Carollia, representatives of C. brevicauda and C. perspicillata are most closely related, whereas C. subrufa is more closely related to these two species than is C. castanea, which forms the basal divergence for the genus. Within Rhinophylla, data for relationships of species are equivocal and suggest a concomitant divergence for all three species. If the rate of evolution is the same for the cytochrome-b gene in the two genera, then species within Rhinophylla diverged earlier than did any of the species of Carollia. If those two genera shared a common ancestor to the exclusion of the remainder of the Phyllostomidae, common ancestry was of short duration. The alternative hypothesis, that Carollia and Rhinophylla are not sister taxa and shared morphological characteristics are convergent, remains viable based on our data.

The Phylogenetic Position of the Rodent Genus Typhlomys and the Geographic Origin of Muroidea

Abstract In this report, we provide the 1st phylogenetic assessment of the evolutionary relationships of Platacanthomyidae. This enigmatic family of rodents comprises 2 genera, Platacanthomys and Typhlomys, that are distributed disjunctly in western India and southern Asia, respectively. We analyze sequence data from the nuclear genes encoding the interphotoreceptor retinoid-binding protein (IRBP) and the growth-hormone receptor (GHR) to address the relationships of Typhlomys cinereus to other rodents, with a particular focus on testing whether its evolutionary affinities lie with glirids or muroids. Our results provide compelling evidence that Typhlomys is a muroid and that it represents the earliest split within this clade. We use the resulting phylogeny to explore the origin and evolutionary history of muroid rodents. We conclude that both Myodonta and Muroidea originated in Eurasia and that the 3 earliest divergences within Muroidea were restricted to the Eurasian supercontinent. Moreover, our analyses support the view that global muroid diversity resulted from independent radiations in separate continental regions.

Differentiation and Species Status of the Neotropical Yellow-Eared Bats Vampyressa pusilla and V. thyone (Phyllostomidae) with a Molecular Phylogeny and Review of the Genus

A systematic re-evaluation of Vampyressa pusilla warrants the elevation of V. p. thyone from subspecies to species rank based on its distinction from the allopatric V. p. pusilla. Morphological, mensural, chromosomal, and mitochondrial differences define each of these two taxa as divergent lineages. Vampyressa pusilla is endemic to the Atlantic Forest of southeastern South America and V. thyone is found allopatrically in northwestern South America, Central America, and southern Mexico. A molecular phylogenetic analysis of the mtDNA ND3–4 gene region using restriction endonuclease cut sites resulted in a monophyletic, although weakly supported Vampyressa ingroup with Chiroderma, and a clade of Mesophylla and Ectophylla as successive basal outgroup lineages. The phylogeny within Vampyressa, with the exception of V. melissa which is most similar to V. thyone based on karyotypes and morphology, had a topology of ((pusilla + thyone) + ((brocki + nymphaea) + bidens))).

Mammals of Iwokrama Forest

Abstract As part of a larger project on biodiversity and conservation in Guyana, we documented 130 species of mammals from Iwokrama Forest. This included 7 marsupials, 4 xenarthrans, 86 bats, 5 primates, 8 carnivores, 1 perissodactyl, 4 artiodactyls, and 15 rodents. As is typical for most Neotropical sites, the 86 species of bats represent over half of the mammal diversity. Standardized collecting methods implemented in the 1997 faunal survey of Iwokrama Forest in central Guyana enabled us also to investigate species diversity and abundance resulting from the inventory of mammals. Four species of fruit-eating bats (Artibeus lituratus, A. obscurus, A. planirostris, and Carollia perspicillata) were the most abundant and accounted for 43% of the 2,097 total captures in mist nets and harp traps during 79 nights of sampling. For nonvolant mammals, terrestrial spiny rats (Proechimys spp.) represented over half (55%) of the 65 captures in primarily live box-style traps. We estimate that our inventory is approximately 70% complete with an additional 57 species of mammals expected to occur in Iwokrama Forest. More specialized field techniques are required to attain a complete inventory of mammals, and long-term monitoring should be established at several sites to study spatial and temporal variation.