Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation

Abstract

High-throughput DNA sequencing has the potential to accelerate species discovery if it is able to recognize evolutionary entities from sequence data that are comparable to species. The general mixed Yule-coalescent (GMYC) model estimates the species boundary from DNA surveys by identifying independently evolving lineages as a transition from coalescent to speciation branching patterns on a phylogenetic tree. Applied here to 12 families from 4 orders of insects in Madagascar, we used the model to delineate 370 putative species from mitochondrial DNA sequence variation among 1614 individuals. These were compared with data from the nuclear genome and morphological identification and found to be highly congruent (98% and 94%). We developed a modified GMYC that allows for a variable transition from coalescent to speciation among lineages. This revised model increased the congruence with morphology (97%), suggesting that a variable threshold better reflects the clustering of sequence data into biological species. Local endemism was pronounced in all 5 insect groups. Most species (60-91%) and haplotypes (88-99%) were found at only 1 of the 5 study sites (40-1000 km apart). This pronounced endemism resulted in a 37% increase in species numbers using diagnostic nucleotides in a population aggregation analysis. Sample sizes between 7 and 10 individuals represented a threshold above which there was minimal increase in genetic diversity, broadly agreeing with coalescent theory and other empirical studies. Our results from > 1.4 Mb of empirical data suggest that the GMYC model captures species boundaries comparable to those from traditional methods without the need for prior hypotheses of population coherence. This provides a method of species discovery and biodiversity assessment using single-locus data from mixed or environmental samples while building a globally available taxonomic database for future identifications.

Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama

“…The K2P model was chosen to facilitate comparison of our genetic distance data with previously published reports. We also estimated the number of lineages or evolutionary "entities" using a likelihoodbased analysis of a GMYC model that assumes an ultrametric gene genealogy and identifies the points of transition between within-population rates of coalescence versus interspecific rates of lineage coalescence (47,48). Using the code gmyc (47), written for R (69), a likelihood ratio test of a single-threshold model versus a multiple-threshold model rejected the former (χ 2 9 = 1956.236, P < 10 −10 ), inferring four transition points and 112 entities including 60 clusters of more than one sample.…”

“…1). Application of a general mixed Yule coalescent (GMYC) model-based approach to identifying discrete evolutionary clusters (47,48) yielded an additional 40 "entities" beyond the 74 identified by the bivariate barcode gap analysis. The restricted geographic sampling in our study, however, could be hampering the GMYC analysis (49,50), and we therefore prefer the more conservative estimate of 74 total species named and candidate.…”

Whole-community DNA barcoding reveals a spatio-temporal continuum of biodiversity at species and genetic levels

“…Field identifications were used to maximize the diversity and to obtain a good representation of the total variation, but these identifications were not further utilized. Hence the data reflect the evolutionary history of the target taxa as inferred from a single locus, but any inconsistencies that may result from gene tree-species tree incongruence presumably are avoided due to the very large number of lineages sampled and the relatively rare occurrence of incongruence 25 . Note that with only the mtDNA sequenced, gene tree incongruence could only be assessed indirectly against the morphological species limits; where such incongruence with the mtDNA groups was evident, this usually affected only some portions of the species ranges 26 , that is, any resulting error would affect the details of geographic turnover but not the discovery of species-level groups per se.…”

A phylogeographic evaluation of the Amolops mantzorum species group: Cryptic species and plateau uplift

“…Our GMYC analyses were performed with the consensus tree under the single-threshold model, using the R package SPLITS (Monaghan et al, 2009). The genealogical sorting index (gsi) statistic quantifies the degree of exclusive ancestry of pre-defined groups on a phylogenetic tree (Cummings et al, 2008).…”