Cryptic diversity in museum collections

1. Cryptic diversity in museum collections May 7, 2013 Sang Il Kim

2. Key Concepts • Cryptic species • Comparative morphology • Morphological species concept • Principal components analysis (PCA) • Phylogenetic reconstruction • Sequenced-based species delimitation • Phylogenetic species concept • Generalized mixed Yule-coalescent (GMYC) model

3. Cryptic Species • Cryptic species are defined as one or more species that are morphologically similar, but genetically different. • The advent of inexpensive DNA sequencing has facilitated the discovery of cryptic species in recent years. • Unveiling cryptic diversity has importance in evolutionary biology and conservation effort. • Integrative taxonomy as a means of discovering undetected diversity. Bickford et al. 2006

4. Cryptic Species: Examples

5. Cryptic Species: Examples

6. Cryptic Species • Cryptic species are defined as one or more species that are morphologically similar, but genetically different. • The advent of inexpensive DNA sequencing has facilitated the discovery of cryptic species in recent years. • Unveiling cryptic diversity is importance for evolutionary biology and conservation effort. • Integrative taxonomy as a means of discovering undetected diversity.

7. Museum Collections • A traditional entomological collection includes: ①Collection data (locality, date, collector’s name) e.g., Locality: Padong, BrithshBootan Date: 1913 Collector’s name: L. Durel ②Determination label e.g., Species name: Dorcusursulus Determined by: M. E. Bacchus Determination year: 1975 ③Voucher information e.g., Holotype ④Unique identifier e.g., Brit. Mus. 1938-113

8. Comparative Morphology • Morphological species conceptstipulates that species are delimited by gaps in morphology (Darwin 1859). • Dorcusvelutinus species group is a group of stag beetles (Lucanidae: Coleoptera) showing subtle morphological disparity, despite the large interspecific genetic distances.

9. Comparative Morphology Internal tooth sharply angulated Internal tooth sharply angulated Internal tooth roundly broadened Thailand, Burma, Vietnam, China Cambodia India Paramere sharp at apex Paramereangulated at apex Lateral margins of basal piece diverging toward base Lateral margins of basal piece almost parallel Thailand, Burma, Vietnam, China Cambodia India

10. Quantitative Morphological Characters ①BL – body length ② BW – body width ③ EL – elytron length ④ AWP – anterior width of pronotum ⑤ PWP – posterior width of pronotum ⑥ MLP – median length of pronotum ⑦ MLM – median length of mentum ⑧ PWM – posterior width of mentum ⑨ PSML – median length of prosternum ⑩ PPW – prosternal process width ** The images were produced with the Auto-Montage system to obtain a full depth of field.

11. Quantitative Morphological Characters • Use ImageJv1.46r to collect quantitative morphological data. • Perform a principal components analysis (PCA) using SPSSv21 to assess morphological heterogeneity among geographically diverse populations. • PCAis a mathematical procedure to convert a set of observations of possibly correlated variables into a set of linearly uncorrelated variables called principal components (i.e., dimension reduction of the observed variables).

12. Quantitative Morphological Characters • Result of the principal component analysis based on eight quantitative characters. • By examining the clustering patterns of these data points, we may be able to discriminate species boundaries amongst geographically diverse populations. • However, no apparent grouping observed in this result. • The two step cluster analysis produced the following two clusters: • 1, 2, 3, 6, 10, 11, 12, 14 • 4, 5, 7, 8, 9, 13 ** Our data of quantitative characters failed to discriminate cryptic species among the D. velutinus populations.

13. Phylogenetic Reconstruction • Sequence one or more phylogenetically informative markers (e.g., 16S, COI of the mtDNA, and wingless, EF1a, 28S of nuclear DNA). • The provided alignment includes the 16S rRNA sequences of 47 individuals. • Use BEAST v1.7.5 to reconstruct an ultrametricBayesian tree.

14. Sequence-Based Species Delimitation • Phylogenetic species concept: The smallest set of organisms that share an ancestor (monophyletic group). • Exclusivity criteria: Monophyletic grouping and large genetic distances. • A problem with the phylogenetic species concept: Where to draw the species boundary? • Species boundary can be estimated using the Generalized Mixed Yule-coalescent (GMYC) model (Pons et al. 2006).

15. Species Delimitation Using GMYC Model • The GMYC model estimates the species boundary from DNA sequence data by identifying independently evolving lineages as a transition from coalescent to speciation branching patterns on a phylogenetic tree. • Using the Splits package in R to optimize the GMYC model onto our tree (vignette provided). • Lineage-through-time plot shows the sharp increase in branching rate which corresponds to the transition from inter-species (speciation and extinction) to intra-species (coalescence) branching events.

16. Results and Conclusions Cambodia population Dorcus sp. nov. 2 Thailand-Burma-Vietnam-China population Dorcus sp. nov. 1 FROM COMPARATIVE MORPHOLOGY: India population True Dorcusvelutinus

17. Acknowledgement I would like to thank Prof. Scott Edwards and Dr. Mark Liu for their support throughout the semester. Thank you!