Hebertetal Astraptes 2004
Hebertetal Astraptes 2004
Hebertetal Astraptes 2004
net/publication/8249566
Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W. Ten species in
one: DNA barcoding reveals cryptic species in the neotropical skipper
butterfly Astraptes fulgerator. Proc N...
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Astraptes fulgerator, first described in 1775, is a common and mitochondrial gene cytochrome c oxidase I (COI), whereas
widely distributed neotropical skipper butterfly (Lepidoptera: Hes- divergences among conspecific individuals average only 0.25%
periidae). We combine 25 years of natural history observations in (11). Similar values were obtained in birds, with intraspecific
northwestern Costa Rica with morphological study and DNA bar- divergences at COI averaging 0.27%, whereas congener diver-
coding of museum specimens to show that A. fulgerator is a gences averaged 7.93% (14).
complex of at least 10 species in this region. Largely sympatric, In this study, the addition of DNA barcodes to data on food
these taxa have mostly different caterpillar food plants, mostly plants, ecological distributions, caterpillar color patterns, and
distinctive caterpillars, and somewhat different ecosystem prefer- adult facies indicates that A. fulgerator consists of 10 largely
ences but only subtly differing adults with no genitalic divergence. sympatric species in the ACG. This result raises the prospect
Our results add to the evidence that cryptic species are prevalent that, over its huge neotropical range, A. fulgerator may comprise
in tropical regions, a critical issue in efforts to document global many more hidden species. Imagine the biodiversity implications
species richness. They also illustrate the value of DNA barcoding, of this result for other wide-ranging, common, and ‘‘somewhat
especially when coupled with traditional taxonomic tools, in dis- variable’’ species of neotropical animals and plants.
closing hidden diversity.
Materials and Methods
Field Biology. The ACG is a 110,000-hectare mosaic of many ages
W e are driven to find and describe our planet’s unrecog-
nized biodiversity because it is disappearing before our
eyes. Yet some of this uncharacterized biodiversity has been
of succession and old growth tropical dry forest, rain forest, and
cloud forest, as well as their various intergrades under conser-
staring us in the face, almost from the taxonomic start. Consider vation in northwestern Costa Rica (www.acguanacaste.ac.cr and
the neotropical skipper butterfly Astraptes fulgerator (Hesperi- http:兾兾janzen.sas.upenn.edu). Since 1978, tens of thousands of
idae) (Fig. 1) described in 1775 (1). This butterfly has long been caterpillars have been reared annually from thousands of species
regarded as a single species that is common, variable, and of plants (e.g., refs. 2–5 and 15). Through 2003, these rearings
wide-ranging: from the far southern United States to northern included 2,592 caterpillars of A. fulgerator. Each caterpillar was
Argentina, from the near desert to deep rain forest, from reared individually, and its rearing data were collated under a
lowlands to middle elevations, and from urban gardens to unique voucher code (e.g., 93-SRNP-3774), which is accessible
pristine habitats. However, this view blocks perception of its real on the project web site (http:兾兾janzen.sas.upenn.edu).
complexity. Approximately half of these A. fulgerator caterpillars produced
The rearing of ⬎2,500 wild-caught caterpillars of A. fulgerator adults; 968 were frozen on the day of eclosion, thawed within 2
during 25 years of biodiversity inventory in the dry forest, rain months, pinned, spread, oven-dried, and stored at ambient
forest, and cloud forest of the Area de Conservación Guanacaste temperatures. These specimens were collected under multiple
(ACG) in northwestern Costa Rica (http:兾兾janzen.sas. research and export permits issued to D.H.J. by the Ministerio
upenn.edu; refs. 2–5) revealed a range of dicotyledonous food del Ambiente y Energı́a of Costa Rica, and they have been
plants far too broad for one species of pyrgine hesperiid (as deposited in the National Museum of Natural History, where
demonstrated by some 31,000 other ACG pyrgine rearing they remain stored at ambient temperatures.
records (http:兾兾janzen.sas.upenn.edu). Moreover, divergent We attempted to assign DNA barcodes to 484 of these adults.
color patterns of the caterpillars (Fig. 2) segregated in accord Where possible, those chosen included at least 20 individuals
with food plants. Although dissections of 67 male and female reared from each species of food plant, extremes and interme-
genitalia disclosed none of the morphological differentiation diates of adult and caterpillar color variation, and representa-
that often distinguishes cryptic species of skippers (see, for tives from the three major ACG terrestrial ecosystems (dry
example, refs. 6–9), close study of adults, sorted by their forest, cloud forest, and rain forest) and their intergrades. All 30
caterpillar food plant, showed subtle differences in color, pat- available individuals from wild-caught pupae were barcoded
tern, size, and wing shape. Synthesis of information on food plant even though their food plants are unknown (caterpillars of A.
use, caterpillar color pattern, and adult external phenotypes fulgerator often pupate off their food plant). One leg was plucked
indicated that A. fulgerator from the ACG was a complex of at from each individual, placed in a dry Eppendorf tube, and sent
least six or seven species. However, it seemed that several more to the University of Guelph for DNA analysis. Sampled adults
years of linking caterpillar and adult characteristics with food
plants would be needed to fully delimit species.
While this query was proceeding, it became apparent that Freely available online through the PNAS open access option.
DNA sequencing of a standard gene region or ‘‘DNA barcoding’’ Abbreviations: ACG, Area de Conservación Guanacaste; COI, cytochrome c oxidase I; NJ,
(10) might speed a solution. DNA barcoding can be helpful in neighbor-joining.
species diagnosis because sequence divergences are ordinarily Data deposition: The sequences reported in this paper have been deposited in the GenBank
much lower among individuals of a species than between closely database (accession nos. AY666597–AY667060, AY7224411, and AY7224412).
related species (11–13). For example, congeneric species of †To whom correspondence should be addressed. E-mail: phebert@uoguelph.ca.
moths show an average sequence divergence of 6.5% in the © 2004 by The National Academy of Sciences of the USA
Results
COI Divergences. A full-length PCR product was recovered from
465 of the 484 individuals (96%), and a 350-bp product was
recovered from 14 of the 19 remaining specimens. The COI
sequences were easily aligned, as no insertions or deletions were
detected. However, 13 sequences showed heterozygosity (as
evidenced by dual peaks of similar height in the electrophero-
grams) at 16–28 nucleotide sites, suggesting either heteroplasmy
or coamplification of a nuclear pseudogene with its mitochon-
drial counterpart. A second DNA extraction from these 13
individuals, followed by sequence analysis, confirmed their
heterozygosity. We discuss these individuals below, but we
Fig. 1. Newly eclosed female A. fulgerator (species LOHAMP, voucher code excluded them from our initial analyses. The 137 different COI
02-SRNP-9770) from the ACG. sequences among the remaining individuals displayed consider-
able divergence (Appendix 1, which is published as supporting
information on the PNAS web site), with Kimura-2-Parameter
received yellow labels stating ‘‘Legs away兾for DNA.’’ Digital distances among individuals averaging 2.76% (range, 0.0 –
photographs of the upper and lower side of each adult, together 7.95%).
ECOLOGY
with its collection details, are available on the Barcodes of Life
(BoLD) web site (www.barcodinglife.com) and on the inventory The 10 Taxa. Mapping caterpillar兾adult morphology and food
web site, which also has images of hundreds of the adults and plants onto the NJ tree of COI divergences reveals 10 haplotype
their caterpillars. clusters that covary with morphological and ecological traits
(Fig. 3), suggesting the presence of 10 species. Sequence diver-
Genetic Analysis. Total DNA was extracted from each of the 484 gences for the 45 pairwise NJ comparisons among these 10 taxa
dry legs by using the GenElute Mammalian Genomic DNA average 2.97% and range from 0.32% to 6.58% (Appendix 2,
Miniprep kit (Sigma Genosys) according to the manufacturer’s which is published as supporting information on the PNAS web
specifications, and the resultant DNA was eluted in 30 l of site). To aid discussion, we code each species by key biological
double-distilled H20. Analysis ordinarily examined sequence attributes: 7 of the 10 taxa are coded according to their primary
diversity in a specific 648-bp fragment of the mitochondrial COI food plants (TRIGO, CELT, LONCHO, LOHAMP, HIHAMP,
gene (the COI 5⬘ region). This sequence was amplified by using BYTTNER, and INGCUP), and the other three taxa are coded
the following primer pair designed for Lepidoptera: LEP-F1, by their main food plants plus a color character of the adult
5⬘-ATTCAACCAATCATAAAGATAT-3⬘; and LEP-R1, 5⬘- (SENNOV, YESENN, and FABOV). Two small COI groups of
TAAACTTCTGGATGTCCAAAAA-3⬘. When PCR amplifi- three (MYST) and four (NUMT) individuals are treated sepa-
cation with these primers failed to generate a product, the rately for reasons that are justified later. In the remainder of this
LEP-F1 primer was combined with another reverse primer section, we briefly describe key features (ecological, ethological,
(5⬘-CTTATATTATTTATTCGTGGGAAAGC-3⬘) to generate and morphological) for each of the 10 presumptive taxa.
a 350-bp product. This combination was necessary in ⬇5% of the The yellow-ringed caterpillars of TRIGO eat the two species
extractions; it was necessary more frequently with specimens of Trigonia (Trigoniaceae) in the ACG, whereas those of CELT
10–20 years old than with newer material. eat only Celtis iguanaea (Celtidaceae兾Ulmaceae). These food
All PCR mixes had a total volume of 50 l and contained 2.5 plants are ignored by the remainder of the A. fulgerator complex
mM MgCl2, 5 pmol of each primer, 20 M dNTPs, 10 mM (and by other ACG hesperiids, as well). Conversely, TRIGO and
Tris䡠HCl (pH 8.3), 50 mM KCl, 10–50 ng (1–5 l) of genomic CELT do not use the food plants of the other eight members of
DNA, and 1 unit of TaqDNA polymerase. The thermocycling the complex. The lone record of TRIGO eating Licania arborea
profile consisted of one cycle of 1 min at 94°C, six cycles of 1 min (Chrysobalanaceae) is real but exceptional (the other ⱖ750
at 94°C, 1 min and 30 sec at 45°C, and 1 min and 15 sec at 72°C, caterpillar records from this species of plant are of other species
followed by 36 cycles of 1 min at 94°C, 1 min and 30 sec at of Lepidoptera). CELT and TRIGO are sympatric in the ACG
51°C, and 1 min and 15 sec at 72°C, with a final step of 5 min at lowland rain forest (up to ⬇400 m), but only TRIGO extends
72°C. PCR products were electrophoresed in 1.0% TBE agarose into the dry forest.
gels, stained with ethidium bromide, and visualized under UV LOHAMP and LONCHO, which have similar yellow-disk-
light. Two microliters (20–50 ng) of the PCR products from these marked caterpillars, are likewise faithful to their food plants,
reactions were cycle sequenced without further cleanup by using although with some instructional exceptions. LOHAMP normally
the LEP-F1 primer, the ABI Prism TaqFS dye terminator kit eats Hampea appendiculata (Malvaceae), but 1 of 47 barcoded
(Applied Biosystems), and BIG DYE (version 3.1). Sequencing individuals ate Lonchocarpus oliganthus (Fabaceae), and 2 individ-
reactions had a total volume of 10 l and included 10 pmol of ual ate Styrax argenteus (Styracaceae), a plant that was not other-
each primer. The sequencing amplification protocol consisted of wise fed on by any member of the A. fulgerator complex. LONCHO
one cycle of 1 min at 96°C, followed by 30 cycles of 10 sec at 96°C, regularly eats L. oliganthus or L. costaricensis, but 9 of 41 barcoded
5 sec at 55°C, and 4 min at 60°C. Sequences were analyzed on an individuals used Senna (Fabaceae), and 2 used H. appendiculata.
ABI 377 sequencer (Applied Biosystems) and were aligned Hence, LOHAMP and LONCHO can survive on each other’s
subsequently by eye in BIOEDIT (16). Sequence divergences principal food plant, whereas LONCHO also rarely eats the pri-
among individuals were quantified by using the Kimura-2- mary food plants (Senna) of three other A. fulgerator species.
Parameter distance model (17) and graphically displayed in a LONCHO is sympatric with five species in the complex at the lower
Hebert et al. PNAS 兩 October 12, 2004 兩 vol. 101 兩 no. 41 兩 14813
Fig. 2. Last-instar caterpillars of 10 species in the A. fulgerator complex from the ACG. Interim names reflect the primary larval food plant and, in some cases,
a color character of the adult.
margin of the ACG cloud forest but does not follow the many pillars of HIHAMP are ringed (whereas those of LOHAMP bear
species of Lonchocarpus into the rain forest or dry forest lowlands. yellow discs), and they feed on mature foliage in the Hampea crown,
By contrast, LOHAMP follows H. appendiculata throughout its whereas those of LOHAMP feed on low, young foliage (usually on
highland to lowland range and so coexists with eight other members saplings). HIHAMP appears to be a middle-elevation cloud-forest
of the A. fulgerator complex. The blue on the upperside of the wings species that coexists with five other members of the A. fulgerator
of fresh reared adults is perceptibly deeper and darker in LONCHO complex, whereas the partly sympatric LOHAMP ranges down into
than it is in LOHAMP. the rain forest lowlands. However, HIHAMP is ecologically and
DNA barcoding revealed HIHAMP in an unexpected manner. microgeographically parapatric with FABOV, which is closest to it
The original HIHAMP group included just three adults reared in the NJ tree, and feeds on a very different plant family than
from caterpillars but 11 adults from wild-caught pupae. Each of FABOV.
these pupae was found 1–2 m above the ground, under a different The ringed caterpillars of BYTTNER resemble those of
tall adult H. appendiculata. One caterpillar was in mature foliage of several other A. fulgerator species. Their apparent monophagy on
an adult Hampea crown, whereas both records ‘‘from’’ Capparis Byttneria catalpaefolia (Sterculiaceae) is still tentative because
frondosa (Capparidaceae) were likely prepupal caterpillars de- just four adults of this dry forest species were available for
scended from the Hampea overhead. A directed search in 2004 analysis. Despite their rarity, these specimens were obtained
located three more HIHAMP caterpillars in the crowns of adult over a 15-year period, providing evidence for a persistent linkage
Hampea, two of which survived to produce adults. Both had between this food plant and a particular COI lineage.
sequences identical with those of the other HIHAMP. The cater- INGCUP is striking because it eats multiple species in two
ECOLOGY
(FABOV), whose adults were initially grouped by J.M.B. with
SENNOV because of their orange venters and their caterpillar
food plants. However, when FABOV was revealed, it was seen
that, on average, its ventral orange is slightly paler than that of
SENNOV. Although predominantly Senna eaters (21 of 33
cases), the ringed caterpillars of FABOV feed on at least seven
species in six other genera of Fabaceae. This taxon occurs in the
lowland ACG, mostly in dry forest and in the intergrade between
dry forest and rain forest (once recorded in deep rain forest), but
it is not common anywhere.
Hebert et al. PNAS 兩 October 12, 2004 兩 vol. 101 兩 no. 41 兩 14815
Discussion pattern of mitochondrial divergence as it includes one individual
Despite the infancy of DNA barcoding protocols, our study from Inga and two from Senna, suggesting that it is shared by
demonstrates that dry museum specimens up to 23 years old can INGCUP and FABOV. As such, this likely represents a case in
be sequenced with considerable success (⬇98%; but often only which lineage sorting is incomplete, a result that might have been
350-bp sequences were obtained from older specimens). Al- expected given the low genetic divergence (and presumed recent
though preservation methods can damage DNA (21, 22), earlier origin) of these groups.
studies have recovered PCR products from insect specimens Past work has provided conflicting perspectives on the likely
over 1 century old (23, 24). Moreover, augmented PCR protocols efficacy of mtDNA markers in delineating species boundaries.
with an initial DNA repair step promise advances in DNA Some studies, including extensive analyses of GenBank data,
recovery, suggesting that a comprehensive barcode library could have indicated that even closely related species ordinarily show
be assembled through the sequencing of museum specimens. marked mitochondrial divergence (10, 12). However, others
Numts pose a potential interpretational hazard for any PCR- suggest that mtDNA markers will often encounter problems in
based survey of mitochondrial DNA diversity (25), and 2.8% of species resolution (28–30). For example, a review of case studies
our COI sequences showed probable coamplification of a Numt (31) concluded that nearly one-fourth of all animal species fail
with its mitochondrial counterpart. However, the taxonomic the test of mitochondrial monophyly. The A. fulgerator complex
impact of these coamplifications was small; all such individuals represents a case in which mitochondrial markers might have
were identified as belonging to the A. fulgerator complex, and been expected to fail because its component species are both
most individuals could be assigned to one of its 10-component extremely similar and sympatric, providing opportunities for
taxa when the pseudogene sequence was determined. We em- hybridization. However, our detection of reciprocal monophyly
phasize, as well, that when sequencing is done with fresh for COI variants among its members means that shared ancestral
specimens, the use of RT-PCR provides strong protection polymorphisms have been lost, either as a consequence of
against Numt amplification (26), suggesting the use of this stochastic lineage pruning or selective sweeps. Moreover, the
approach in taxa with COI pseudogenes. lack of shared haplotypes indicates either strict reproductive
Our sequencing results support the prior conclusion that A. isolation or ongoing selection against mitochondrial exchange
fulgerator is a species complex. Its levels of COI diversity are between members of the complex. Female Lepidoptera are both
much higher than those typical of single-species populations. the heterogametic sex and the primary agents of food plant
More importantly, there is clear covariation of the COI se- selection, which are factors that can also act to ensure rapid
quences with morphological, ethological, and ecological traits. divergence in mitochondrial markers (32, 33).
Although studies of classical characters indicated six or seven Should the 10 species of A. fulgerator identified in this study be
species, the addition of COI data raised the count to 10. This formally described despite their morphological similarity? Yes.
increase reflects the way in which the COI data added meaning Although their recognition was facilitated by DNA barcoding,
to isolated records on unusual food plants (e.g., Byttneria), to the combination of their genetic distinctiveness and their cova-
lineages with behavioral and caterpillar color pattern divergence rying caterpillar color patterns, food plant usage, and adult
(e.g., LOHAMP vs. HIHAMP), and to taxa with nearly indis- morphology demonstrates that they are reproductively isolated
tinguishable adult facies (e.g., SENNOV vs. FABOV). Whereas populations. The fact that these populations are largely sympa-
our study reveals the power of DNA barcoding in helping to tric argues even more strongly for traditional binomials.
resolve complex taxonomic situations, it also indicates the im- Diversification in the A. fulgerator complex is clearly linked to
perative of large sample sizes and supplemental morphology and food plants, suggesting the importance of a detailed analysis of
natural history. We emphasize that barcodes differ from the shifting food plant use. The complex likely derives from a species
standard traits used for species discrimination in the following that fed on Fabaceae because most other species of Astraptes and
important way: they can be obtained in a mechanized manner. many of those in 19 allied genera (34) feed largely on plants in
Hence, they can be used without much background knowledge, this family (2). Based on standard calibrations for rates of
both for routine identifications and for the detection of hidden mitochondrial evolution (e.g., refs. 35 and 36), TRIGO sepa-
species (13, 27). rated from the basal fulgerator clade ⬇4 million years ago,
Despite the variation in caterpillar color pattern and food probably onto Trigonia, whereas CELT separated ⬇2 million
plants, adults in the A. fulgerator complex show little phenotypic years ago, likely onto Celtis. Subsequent speciation has involved
diversity. Their similarity probably reflects not only recent less radical food plant shifts, but some of these events probably
common ancestry but also stabilizing selection arising from occurred within the last half-million years (e.g., FABOV, HI-
membership in a massive mimicry ring. At least 35 species in HAMP, and INGCUP). This diversification may be linked to
three subfamilies of hesperiids from the ACG range from regional variation in the species composition of plant commu-
general to exact mimics of A. fulgerator (see images of adults at nities and to the inclusion of novel species in the food plant
http:兾兾janzen.sas.upenn.edu). In the neotropics as a whole, repertoire of some taxa. For example, only SENNOV eats K.
many more skipper species swell this mimetic assemblage. As calderoni, a species that is chemically and morphologically
expected from their morphological similarity, members of the A. divergent from its standard food plants. If isolated in a setting
fulgerator complex show less sequence divergence than most lacking its usual food plants, SENNOV might rapidly evolve into
other congeneric species pairs (10, 13). Only two taxa (CELT a Karwinskia specialist.
and TRIGO) have minimum COI divergences (3.4% and 5.4%) Although members of the A. fulgerator complex are young in
from all other members of the complex that exceed the sequence evolutionary terms, their ranges have surely expanded well
threshold (3%) typically encountered between congeneric spe- beyond their areas of origin. As a result, we doubt that any of the
cies pairs recognized by morphological approaches (14). Diver- lineages revealed in this study are endemic to the ACG or to
gences among the remaining taxa are lower, but all exceed 1.1%, Costa Rica. Rather, we expect that most of their distributions
which is well above usual intraspecific values, except among span many degrees of latitude, extending wherever food plants
members of the triad FABOV, HIHAMP, and INGCUP, which and ecological conditions permit (37). Given the high diversity
show ⬍0.5% divergence. These three species possess distinct of the South American hesperiid fauna, and the fact that A.
COI sequence arrays (Fig. 3), feed on very different food plants, fulgerator ranges from the southern United States to northern
and show subtle differences in both caterpillar and adult facies. Argentina, a comprehensive survey might uncover many more
The MYST lineage apparently represents an exception to this species.
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