Download the Free Unbound MEDLINE PubMed App to your smartphone or tablet.
Available for iPhone, iPad, iPod touch, and Android.
Mol Phylogenet Evol [journal]
- Cryptic diversity within the Anatololacerta species complex (Squamata: Lacertidae) in the Anatolian Peninsula: evidence from a multi-locus approach. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Oct 11.
The rapid development of innovative molecular tools for characterizing biodiversity is leading to an extensive and sometimes unexpected renovation of taxonomic classifications. Particularly, for species having allopatric or parapatric distributions or resulting from recent speciation processes, the absence of clear phenotypic differentiation may hinder the recognition of closely related taxa, while intraspecific polymorphism may be confused with the presence of more than one single species. In the present work, we apply different phylogenetic methods in order to infer relationships within the genus Anatololacerta, and to assess the taxonomy of this morphologically diversified group of lizards endemic to western and southern Anatolia and some neighbouring Aegean islands. According to morphology, three species have been recognized (Anatolocerta anatolica, A. oertzeni and A. danfordi) as well as several subspecies, but small variation at immunological markers led some authors to join all the populations into one single taxon, A. danfordi. By selecting both mitochondrial and nuclear informative markers, we tested the effectiveness of classical "gene tree" (i.e. Bayesian Inference) vs. innovative (i.e. coalescent-based) "species tree" methods in resolving the Anatololacerta taxonomic enigma, as a case in point for similar studies on species complexes resulting from non-obvious and cryptic diversification patterns. According to our results, the "gene tree" method failed in resolving phylogenetic relationships among clades, whereas the multi-locus "species tree" approach, coupled with species delimitation methods, allowed the identification of four well distinct species. These species probably diversified in different allopatric refugia located in southern and western Anatolia, where isolated populations may have persisted during Pleistocene glacial cycles.
- When Do Species-Tree and Concatenated Estimates Disagree? An Empirical Analysis with Higher-Level Scincid Lizard Phylogeny. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Oct 11.
Simulation studies suggest that coalescent-based species-tree methods are generally more accurate than concatenated analyses. However, these species-tree methods remain impractical for many large datasets. Thus, a critical but unresolved issue is when and why concatenated and coalescent species-tree estimates will differ. We predict such differences for branches in concatenated trees that are short, weakly supported, and have conflicting gene trees. We test these predictions in Scincidae, the largest lizard family, with data from 10 nuclear genes for 17 ingroup taxa and 44 genes for 12 taxa. We support our initial predictions, andsuggest that simply considering uncertainty in concatenated trees may sometimes encompass the differences between these methods. We also found that relaxed-clock concatenated trees can be surprisingly similar to the species-tree estimate. Remarkably, the coalescent species-tree estimates had slightly lower support values when based on many more genes (44 vs. 10) and a small (∼30%) reduction in taxon sampling. Thus, taxon sampling may be more important than gene sampling when applying species-tree methods to deep phylogenetic questions. Finally, our coalescent species-tree estimates tentatively support division of Scincidae into three monophyletic subfamilies, a result otherwise found only in concatenated analyses with extensive species sampling.
- Phylogeny and biogeography of Ficedula flycatchers (Aves: Muscicapidae): novel results from fresh source material. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Oct 9.
The avian genus Ficedula has been a model system for studying speciation, genomics, biogeography, and the evolution of migratory behavior. However, no multi-locus molecular phylogenetic hypothesis exists for the genus. We expanded taxon and character sampling over previous studies and produced a robust hypothesis of relationships for the genus. Many previous findings, such as the inclusion of Muscicapella and exclusion of Ficedula monileger from the genus, were verified, but many relationships differed compared to previous work. Some of the differences were due to increased sampling, but others were due to problematic sequence data produced from DNA extracted from historical museum specimens. The new phylogenetic hypothesis resulted in a simpler biogeographic scenario with fewer transitions between regions and fewer transitions between seasonally migratory and resident character states. Notably, all species endemic to the Philippines and Wallacea formed a clade, which included Ficedula dumetoria of the Sunda Shelf and Lesser Sundas. In addition, Ficedula hyperythra was not monophyletic; samples from Philippine populations formed a clade distantly related to a clade that comprised all other sampled populations.
- Molecular phylogeny of the Afroedura nivaria (Reptilia: Gekkonidae) species complex in South Africa provides insight on cryptic speciation. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Oct 9.
The Afroedura nivaria species complex (A. nivaria, A. karroica, A. amatolica, A. tembulica and A. halli) is a morphologically conservative group of medium-sized flat geckos endemic to South Africa and Lesotho. Species are allopatric, as are some populations within species that are separated by large expanses of unsuitable habitat. Because of this isolation of populations we hypothesised that several cryptic species may be present. To investigate this hypothesis we constructed a molecular phylogeny using multiple markers, and included representatives of other Afroedura species. Bayesian inference and maximum likelihood analyses (439 bp 16S, 593 bp ND4, 948 bp RAG1) strongly supported the genetic distinctiveness of the five described species. However, the A. nivaria species complex as currently described is not monophyletic, as A. karroica was positioned outside a clade containing all other Afroedura species, and A. pondolia (which was presumed to belong to a different species complex) was recovered within the A. nivaria complex. Several distinct clades within A. halli and A. nivaria were also recovered, and the narrowly-distributed A. amatolica consisted of two highly divergent clades. We also conducted a multivariate analysis using 19 morphological characters to investigate whether the clades recovered by the phylogeny were distinct in terms of head, body and limb shape. The analysis showed some variation between clades in terms of locomotor apparatus (forelimbs and feet), head and body dimensions, but overall the morphological differences were minor. This morphological conservatism in the A. nivaria complex may be a result of adaptation to similar microhabitats. Exclusive of A. karroica, the results suggest that there are at least nine species in this complex, of which four are cryptic and undescribed.
- Biogeography of squirrel monkeys (genus Saimiri): South-central Amazon origin and rapid pan-Amazonian diversification of a lowland primate. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Oct 8.
The squirrel monkey, Saimiri, is a pan-Amazonian Pleistocene radiation. We use statistical phylogeographic methods to create a mitochondrial DNA-based timetree for 118 squirrel monkey samples across 68 localities spanning all Amazonian centers of endemism, with the aim of better understanding (1) the effects of rivers as barriers to dispersal and distribution; (2) the area of origin for modern Saimiri; (3) whether ancestral Saimiri was a lowland lake-affiliated or an upland forest taxa; and (4) the effects of Pleistocene climate fluctuation on speciation. We also use our topology to help resolve current controversies in Saimiri taxonomy and species relationships. The Rondônia and Inambari centers in the southern Amazon were recovered as the most likely areas of origin for Saimiri. The Amazon River proved a strong barrier to dispersal, and squirrel monkey expansion and diversification was rapid, with all speciation events estimated to occur between 1.4 and 0.6Ma, predating the last three glacial maxima and eliminating climate extremes as the main driver of squirrel monkey speciation. Saimiri expansion was concentrated first in central and western Amazonia, which according to the "Young Amazon" hypothesis was just becoming available as floodplain habitat with the draining of the Amazon Lake. Squirrel monkeys also expanded and diversified east, both north and south of the Amazon, coincident with the formation of new rivers. This evolutionary history is most consistent with a Young Amazon Flooded Forest Taxa model, suggesting Saimiri has always maintained a lowland wetlands niche and was able to greatly expand its range with the transition from a lacustrine to a riverine system in Amazonia. Saimiri vanzolinii was recovered as the sister group to one clade of Saimiri ustus, discordant with the traditional Gothic vs. Roman morphological division of squirrel monkeys. We also found paraphyly within each of the currently recognized species: S. sciureus, S. ustus, and S. macrodon. We discuss evidence for taxonomic revision within the genus Saimiri, and the need for future work using nuclear markers.
- Diversification of the silverspot butterflies (Nymphalidae) in the Neotropics inferred from multi-locus DNA sequences. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Oct 6.
The tribe Heliconiini (Lepidoptera: Nymphalidae) is a diverse group of butterflies distributed throughout the Neotropics, which has been studied extensively, in particular the genus Heliconius. However, most of the other lineages, such as Dione, which are less diverse and considered basal within the group, have received little attention. Basic information, such as species limits and geographical distributions remain uncertain for this genus. Here we used multilocus DNA sequence data and the geographical distribution analysis across the entire range of Dione in the Neotropical region in order to make inferences on the evolutionary history of this poorly explored lineage. Bayesian time-tree reconstruction allows inferring two major diversification events in this tribe around 25mya. Lineages thought to be ancient, such as Dione and Agraulis, are as recent as Heliconius. Dione formed a monophyletic clade, sister to the genus Agraulis. Dione juno, D. glycera and D. moneta were reciprocally monophyletic and formed genetic clusters, with the first two more close related than each other in relation to the third. Divergence time estimates support the hypothesis that speciation in Dione coincided with both the rise of Passifloraceae (the host plants) and the uplift of the Andes. Since the sister species D. glycera and D. moneta are specialized feeders on passion-vine lineages that are endemic to areas located either within or adjacent to the Andes, we inferred that they co-speciated with their host plants during this vicariant event.
- Through thick and thin: cryptic sympatric speciation in the submersed genus Najas (Hydrocharitaceae). [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Oct 6.
Cryptic sympatric species arise when reproductive isolation is established in sympatry, leading to genetically divergent lineages that are highly similar morphologically or virtually indistinguishable. Although cryptic sympatric species have been reported in various animals, fungi, and protists, there are few compelling examples for plants. This investigation presents a case for cryptic sympatric speciation in Najas flexilis, a widespread aquatic plant, which extends throughout northern North America and Eurasia. The taxon is noted for its variable seed morphology, which earlier research associated with cytotypes; i.e., diploids were characterized by thicker seeds and tetraploids by thinner seeds. However, cytotypes are not patterned geographically with diploid and tetraploid plants often found in close proximity within the same lake. Using digital image and DNA sequence analyses, we found that diploids and tetraploids are well-isolated and remain genetically distinct throughout their sympatric range, where sterile hybrids occur frequently. Incorporation of sequence data from the single-copy nuclear phytoene desaturase locus revealed further that the tetraploids are allopolyploid derivatives of N. flexilis and N. guadalupensis, the latter a closely related species with an overlapping distribution. We conclude that the taxon widely known as N. flexilis actually comprises two cryptic, sibling species, which diverged in sympatry by interspecific hybridization and subsequent chromosomal isolation. By comparing seed morphology of type specimens, we associated the names N. flexilis and N. canadensis to the diploids and tetraploids respectively. Additionally, the narrowly restricted taxon known formerly as N. muenscheri is shown via morphological and genetic evidence to be synonymous with N. canadensis.
- The origins and radiation of Australian Coptotermes termites: From rainforest to desert dwellers. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Oct 6.
The termite genus Coptotermes (Rhinotermitidae) is found in Asia, Africa, Central/South America and Australia, with greatest diversity in Asia. Some Coptotermes species are amongst the world's most damaging invasive termites, but the genus is also significant for containing the most sophisticated mound-building termites outside the family Termitidae. These mound-building Coptotermes occur only in Australia. Despite its economic and evolutionary significance, the biogeographic history of the genus has not been well investigated, nor has the evolution of the Australian mound-building species. We present here first phylogeny of the Australian Coptotermes to include representatives from all described species. We combined our new data with previously generated data to estimate the first phylogeny to include representatives from all continents where the genus is found. We also present the first estimation of divergence dates during the evolution of genus. We found the Australian Coptotermes to be monophyletic and most closely related to the Asian Coptotermes, with considerable genetic diversity in some Australian taxa possibly representing undescribed species. The Australian mound-building species did not form a monophyletic clade. Our ancestral state reconstruction analysis indicated that ancestral Australian Coptotermes was likely to have been a tree nester, and that mound-building behaviour has arisen multiple times. The Australian Coptotermes were found to have diversified ∼13million years ago, which plausibly matches with the narrowing of the Arafura Sea allowing Asian taxa to cross into Australia. The first diverging Coptotermes group was found to be African, casting doubt on the previously raised hypothesis that the genus has an Asian origin.
- Support for a 'Center of Origin' in the Coral Triangle: cryptic diversity, recent speciation, and local endemism in a diverse lineage of reef fishes (Gobiidae: Eviota). [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Oct 6.
The Coral Triangle is widely regarded as the richest marine biodiversity hot-spot in the world. One factor that has been proposed to explain elevated species-richness within the Coral Triangle is a high rate of in situ speciation within the region itself. Dwarfgobies (Gobiidae: Eviota) are a diverse genus of diminutive cryptobenthic reef fishes with limited dispersal ability, and life histories and ecologies that increase potential for speciation. We use molecular phylogenetic and biogeographic data from two clades of Eviota species to examine patterns, processes and timing associated with species origination within the Coral Triangle. Sequence data from mitochondrial and nuclear DNA were used to generate molecular phylogenies and median-joining haplotype networks for the genus Eviota, with emphasis on the E. nigriventris and E. bifasciata complexes - two species groups with distributions centered in the Coral Triangle. The E. nigriventris and E. bifasciata complexes both contain multiple genetically distinct, geographically restricted color morphs indicative of recently-diverged species originating within the Coral Triangle. Relaxed molecular-clock dating estimates indicate that most speciation events occurred within the Pleistocene, and the geographic pattern of genetic breaks between species corresponds well with similar breaks in other marine fishes and sessile invertebrates. Regional isolation due to sea-level fluctuations may explain some speciation events in these species groups, yet other species formed with no evidence of physical isolation. The timing of diversification events and present day distributions of Eviota species within the Coral Triangle suggest that both allopatric speciation (driven by ephemeral and/or 'soft' physical barriers to gene flow) and sympatric speciation (driven by niche partitioning and assortative mating) may be driving diversification at local scales within the Coral Triangle. The presence of multiple young, highly-endemic cryptic species of Eviota within the Coral Triangle suggests that (i) the Coral Triangle is indeed a "cradle" of reef fish biodiversity and that (ii) our current approximations of reef fish diversity in the region may be significantly underestimated.
- Phylogeography and species boundaries of Leptopelis (Anura: Arthroleptidae) from the Albertine Rift. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Oct 5.
The genus Leptopelis occurs in multiple habitats throughout sub-Saharan Africa, and it includes several species that have highly variable color patterns, which makes taxonomic studies challenging. In this study, we examined multiple populations of Leptopelis from the Albertine Rift (AR), a region known for its high levels of endemism and biodiversity. Currently, five species are recognized from the AR: L. anebos, L. fiziensis, L. karissimbensis, L. kivuensis, and L. mtoewaate, most of which are found in and around the Itombwe Plateau in Democratic Republic of the Congo (DRC). We sampled 90 individuals of Leptopelis from multiple localities in DRC, Uganda, Rwanda and Burundi. We employed concatenated gene-tree analyses, coalescent species-tree analyses, and divergence dating approaches to infer phylogenies and biogeographic patterns with a multi-locus data set consisting of two mitochondrial (16S and cyt b) and one nuclear gene (RAG1). All analyses revealed several cryptic lineages within the genus, suggesting that a revision of AR Leptopelis taxonomy is needed.