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Winding up the molecular clock in the genus Carabus (Coleoptera: Carabidae): assessment of methodological decisions on rate and node age estimation.

ABSTRACT: BACKGROUND: Rates of molecular evolution are known to vary across taxa and among genes, and this requires rate calibration for each specific dataset based on external information. Calibration is sensitive to evolutionary model parameters, partitioning schemes and clock model. However, the way in which these and other analytical aspects affect both the rates and the resulting clade ages from calibrated phylogenies are not yet well understood. To investigate these aspects we have conducted calibration analyses for the genus Carabus (Coleoptera, Carabidae) on five mitochondrial and four nuclear DNA fragments with 7888 nt total length, testing different clock models and partitioning schemes to select the most suitable using Bayes Factors comparisons. RESULTS: We used these data to investigate the effect of ambiguous character and outgroup inclusion on both the rates of molecular evolution and the TMRCA of Carabus. We found considerable variation in rates of molecular evolution depending on the fragment studied (ranging from 5.02% in cob to 0.26% divergence/My in LSU-A), but also on analytical conditions. Alternative choices of clock model, partitioning scheme, treatment of ambiguous characters, and outgroup inclusion resulted in rate increments ranging from 28% (HUWE1) to 1000% (LSU-B and ITS2) and increments in the TMRCA of Carabus ranging from 8.4% (cox1-A) to 540% (ITS2). Results support an origin of the genus Carabus during the Oligocene in the Eurasian continent followed by a Miocene differentiation that originated all main extant lineages. CONCLUSIONS: The combination of several genes is proposed as the best strategy to minimise both the idiosyncratic behaviors of individual markers and the effect of analytical aspects in rate and age estimations. Our results highlight the importance of estimating rates of molecular evolution for each specific dataset, selecting for optimal clock and partitioning models as well as other methodological issues potentially affecting rate estimation.

SUBMITTER: Andujar C

PROVIDER: S-EPMC3368785 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Winding up the molecular clock in the genus Carabus (Coleoptera: Carabidae): assessment of methodological decisions on rate and node age estimation.

Andújar Carmelo C Serrano José J Gómez-Zurita Jesús J

BMC evolutionary biology 20120328

<h4>Background</h4>Rates of molecular evolution are known to vary across taxa and among genes, and this requires rate calibration for each specific dataset based on external information. Calibration is sensitive to evolutionary model parameters, partitioning schemes and clock model. However, the way in which these and other analytical aspects affect both the rates and the resulting clade ages from calibrated phylogenies are not yet well understood. To investigate these aspects we have conducted ...[more]

PMID: 22455387

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Project description:Molecular clocks have become powerful tools given increasing sequencing and fossil resources. However, calibration analyses outcomes depend on the choice of priors. Here, we revisited the seminal dating study published by Andújar and coworkers of the genus Carabus proposing that prior choices need re-evaluation. We hypothesized that reflecting fossil evidence and the Gondwanan split properly significantly rewinds the molecular clock. We re-used the dataset including five mitochondrial and four nuclear DNA fragments with a total length of 7888 nt. Fossil evidence for Oligocene occurrence of Calosoma was considered. Root age was set based on the fossil evidence of Harpalinae ground beetles in the Upper Cretaceous. Paleogene divergence of the outgroup taxa Ceroglossini and Pamborini is introduced as a new prior based on current paleontological and geological literature. The ultrametric time-calibrated tree of the extended nd5 dataset resulted in a median TMRCA Carabus of 53.92 Ma (HPD 95% 45.01-63.18 Ma), roughly 30 Ma older than in the Andújar study. The splits among C. rugosus and C. morbillosus (A), C. riffensis from the European Mesocarabus (B), and Eurycarabus and Nesaeocarabus (C) were dated to 17.58 (12.87-22.85), 24.14 (18.02-30.58), and 21.6 (16.44-27.43) Ma. They were decidedly older than those previously reported (7.48, 10.93, and 9.51 Ma). These changes were driven almost entirely by constraining the Carabidae time-tree root with a Harpalinae amber fossil at ~99 Ma. Utilizing the nd5 dating results of three well-supported Carabus clades as secondary calibration points for the complete MIT-NUC dataset led to a TMRCA of Carabus of 44.72 (37.54-52.22) Ma, compared with 25.16 Ma (18.41-33.04 Ma) in the previous study. Considering fossil evidence for Oligocene Calosoma and Late Cretaceous Harpalini together with the Gondwanan split as a new prior, our new approach supports the origin of genus Carabus in the Eocene. Our results are preliminary because of the heavy reliance on the nd5 gene, and thus will have to be tested with a sufficient set of nuclear markers. Additionally, uncertainties due to dating root age of the tree based on a single fossil and outgroup taxon affect the results. Improvement of the fossil database, particularly in the supertribe Carabitae, is needed to reduce these uncertainties in dating Carabus phylogeny.

Project description:Carabus (Cathoplius) aliai was described as a separate species by Escalera in 1944 but since the 1950-60s it has been considered as a subspecies of Carabus (Cathoplius) stenocephalus Lucas, 1866. This downgrading was adopted after examining only a few specimens, due to their rarity in collections. In recent years, an important population of this taxon was rediscovered in the Tan-Tan area in southern Morocco. By combining field observations with laboratory breeding experiments including hybridization trials, and through the morphological examination of a representative number of individuals, it is confirmed that Carabusaliai is indeed a valid species. Despite close geographic distribution, the morphological and biological characteristics of Carabusaliai and Carabusstenocephalusifniensis Zarco, 1941, its northern substitutive taxon, are very different. Carabusaliai adults are characterized by a smaller size, a slender silhouette, a more brilliant aspect, a narrower pronotum, a coarser elytral sculpture, longer legs, and a wider and a little more curved apex of the median lobe of the aedeagus. Carabusaliai larvae are also characterized by a much smaller size and the Carabusaliai pupa has a narrower thoracic area and a different chaetotaxy compared to that of Carabusstenocephalusifniensis. Contrary to this, Carabusaliai has a life cycle belonging to the annual univoltine winter semelparous type. Moreover, the duration of its development cycle is shorter. Carabusaliai is a sabulicolous steppe-wandering species with an intensive running activity, while Carabusstenocephalusifniensis is a more sedentary taxon. Crossbreeding experiments showed a marked reproductive isolation between Carabusaliai and Carabusstenocephalusifniensis. When F1 hybrids were crossed with one another, a very high mortality rate during embryonic, larval and pupal development was evident and no vital F2 neo-adults were obtained. Morphological and biological differences, together with the reproductive failure in Carabusaliai × Carabusstenocephalusifniensis hybrids, clearly indicate that Carabusaliai is a separate Cathoplius species that is distributed in an area south of the Anti-Atlas chain, from Plage Blanche (Guelmim) to Lemsid and Bou Kra (south of Laâyoune). Carabusaliai is therefore both a Saharan desert endemic and an Atlantic resident. Moreover, it is the southernmost Carabus species of the western Palaearctic region.

Project description:The Brasiella tiger beetle fauna on Hispaniola, the second largest island of the Greater Antilles, has more species diversity than currently recognized as all populations previously have been assigned to the insular endemic Brasiella dominicana (Mandl). A comparative study of adult morphology, particularly male genitalic and female abdominal characters, for available Brasiella specimens from populations on Hispaniola, proposes eight additional new species also endemic to this island. Except for three sympatric species in the Sierra de Baoruco in southern Dominican Republic occurring in different habitats, all the Brasiella on Hispaniola appear to be allopatric. Most species occur in the major mountainous regions of Hispaniola. Two species, however, are known only from river floodplains in the southern coastal plain of the Dominican Republic. Brasiella dominicana (Mandl) and Brasiella ocoa, new species, occur along river floodplains emanating from the eastern end of the Cordillera Central in the Dominican Republic. Two new Brasiella species, Brasiella bellorum, and Brasiella philipi, occur in the Cordillera Central, Dominican Republic, the former species from central portions, and the latter species from north slopes of this mountain range, respectively. Three new Brasiella species, Brasiella rawlinsi, Brasiella iviei, and Brasiella youngi, are isolated in the Sierra de Baoruco, Dominican Republic, where each occupies a different habitat along an altitudinal gradient. The two new Brasiella species in Haiti are Brasiella darlingtoniana, in the Massif de la Selle, and Brasiella davidsoni, in the Massif de la Hotte. All nine Brasiella species on Hispaniola, along with Brasiella viridicollis (Dejean) and its two subspecies on Cuba, belong to the viridicollis species group of the genus Brasiella based on criteria presented in earlier published phylogenetic studies of Brazilian and West Indian tiger beetles. The subspecies Brasiella viridicollis fernandozayasi (Kippenhan, Ivie and Hopp) may represent a distinct species within this species group, whereas removal of Brasiella wickhami (W. Horn) from this species group seems warranted based on evidence presented. A general overview of species relationships for the Brasiella on Hispaniola are discussed, along with the current and ancestral geographic distributions of the Brasiella viridicollis species group in the West Indies.

Dataset Information

Winding up the molecular clock in the genus Carabus (Coleoptera: Carabidae): assessment of methodological decisions on rate and node age estimation.

Publications

Winding up the molecular clock in the genus Carabus (Coleoptera: Carabidae): assessment of methodological decisions on rate and node age estimation.

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