Presentation on theme: "Cryptic diversity in museum collections"— Presentation transcript:
1 Cryptic diversity in museum collections May 7, 2013Sang Il Kim
2 Key Concepts Cryptic species Comparative morphology Morphological species conceptPrincipal components analysis (PCA)Phylogenetic reconstructionSequenced-based species delimitationPhylogenetic species conceptGeneralized mixed Yule-coalescent (GMYC) model
3 Cryptic SpeciesBickford et al. 2006Cryptic 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.
6 Cryptic SpeciesCryptic 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: ① Collection data (locality, date, collector’s name)e.g., Locality: Padong, Brithsh BootanDate: 1913Collector’s name: L. Durel② Determination labele.g., Species name: Dorcus ursulusDetermined by: M. E. BacchusDetermination year: 1975③ Voucher informatione.g., Holotype④ Unique identifiere.g., Brit. Mus
8 Comparative Morphology Defining species taxa within the Lucanidae requires the use of robust characters (e.g., genital structure) that have demonstrated importance in species-level recognition, rather than relying on small differences in few characters (such as the form of the male mandibles) that may result from geographic variation or allometry.Morphological species concept stipulates that species are delimited by gaps in morphology (Darwin 1859).Dorcus velutinus 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 angulatedInternal tooth sharply angulatedInternal tooth roundly broadenedThailand, Burma,Vietnam, ChinaCambodiaIndiaParamere angulated at apexParamere sharp at apexLateral margins of basal piece diverging toward baseLateral margins of basal piece almost parallelThailand, Burma,Vietnam, ChinaCambodiaIndia
10 Quantitative Morphological Characters ① BL – body length② BW – body width③ EL – elytron length④ AWP – anterior width ofpronotum⑤ PWP – posterior width of⑥ MLP – median length of⑦ MLM – median length ofmentum⑧ PWM – posterior width of⑨ PSML – median length ofprosternum⑩ PPW – prosternalprocess width** The images were produced with the Auto-Montage system to obtain a full depth of field.
11 Quantitative Morphological Characters Use ImageJ v1.46r to collect quantitative morphological data.Perform a principal components analysis (PCA) using SPSS v21 to assess morphological heterogeneity among geographically diverse populations.PCA is 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, 144, 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 ultrametric Bayesian 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.