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1.  Growth in fossil and extant deer and implications for body size and life history evolution 
Background
Body size variation within clades of mammals is widespread, but the developmental and life-history mechanisms by which this variation is achieved are poorly understood, especially in extinct forms. An illustrative case study is that of the dwarfed morphotypes of Candiacervus from the Pleistocene of Crete versus the giant deer Megaloceros giganteus, both in a clade together with Dama dama among extant species. Histological analyses of long bones and teeth in a phylogenetic context have been shown to provide reliable estimates of growth and life history patterns in extant and extinct mammals.
Results
Similarity of bone tissue types across the eight species examined indicates a comparable mode of growth in deer, with long bones mainly possessing primary plexiform fibrolamellar bone. Low absolute growth rates characterize dwarf Candiacervus sp. II and C. ropalophorus compared to Megaloceros giganteus displaying high rates, whereas Dama dama is characterized by intermediate to low growth rates. The lowest recorded rates are those of the Miocene small stem cervid Procervulus praelucidus. Skeletal maturity estimates indicate late attainment in sampled Candiacervus and Procervulus praelucidus. Tooth cementum analysis of first molars of two senile Megaloceros giganteus specimens revealed ages of 16 and 19 years whereas two old dwarf Candiacervus specimens gave ages of 12 and 18 years.
Conclusions
There is a rich histological record of growth across deer species recorded in long bones and teeth, which can be used to understand ontogenetic patterns within species and phylogenetic ones across species. Growth rates sensu Sander & Tückmantel plotted against the anteroposterior bone diameter as a proxy for body mass indicate three groups: one with high growth rates including Megaloceros, Cervus, Alces, and Dama; an intermediate group with Capreolus and Muntiacus; and a group showing low growth rates, including dwarf Candiacervus and Procervulus. Dwarf Candiacervus, in an allometric context, show an extended lifespan compared to other deer of similar body size such as Mazama which has a maximum longevity of 12 years in the wild. Comparison with other clades of mammals reveals that changes in size and life history in evolution have occurred in parallel, with various modes of skeletal tissue modification.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-015-0295-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-015-0295-3
PMCID: PMC4332446
Island evolution; Pleistocene; Cervidae; Candiacervus; Megaloceros; Bone histology; Cementum analysis; Growth rates; Longevity; Skeletal maturity
2.  Nymphalid eyespots are co-opted to novel wing locations following a similar pattern in independent lineages 
Background
Variation in the number of repeated traits, or serial homologs, has contributed greatly to animal body plan diversity. Eyespot color patterns of nymphalid butterflies, like arthropod and vertebrate limbs, are an example of serial homologs. These eyespot color patterns originated in a small number of wing sectors on the ventral hindwing surface and later appeared in novel wing sectors, novel wings, and novel wing surfaces. However, the details of how eyespots were co-opted to these novel wing locations are currently unknown.
Results
We used a large data matrix of eyespot/presence absence data, previously assembled from photographs of contemporary species, to perform a phylogenetic investigation of eyespot origins in nine independent nymphalid lineages. To determine how the eyespot gene regulatory network acquired novel positional information, we used phylogenetic correlation analyses to test for non-independence in the origination of eyespots. We found consistent patterns of eyespot gene network redeployment in the nine lineages, where eyespots first redeployed from the ventral hindwing to the ventral forewing, then to new sectors within the ventral wing surface, and finally to the dorsal wing surface. Eyespots that appeared in novel wing sectors modified the positional information of their serial homolog ancestors in one of two ways: by changing the wing or surface identity while retaining sector identity, or by changing the sector identity while retaining wing and surface identity.
Conclusions
Eyespot redeployment to novel sectors, wings, and surfaces happened multiple times in different nymphalid subfamilies following a similar pattern. This indicates that parallel mutations altering expression of the eyespot gene regulatory network led to its co-option to novel wing locations over time.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-015-0300-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-015-0300-x
PMCID: PMC4335541
Serial homology; Correlation analysis; Ancestral states; Phylogeny; Wing patterns
3.  Female control of mate plugging in a female-cannibalistic spider (Micaria sociabilis) 
BMC Evolutionary Biology  2015;15(1):18.
Background
Sperm competition imposes a strong selective pressure on males, leading to the evolution of various physiological, morphological and behavioral traits. Sperm competition can be prevented by blocking or impeding the access to female genitalia by means of a mating plug. We investigated the factors responsible for plug production and function in the promiscuous female-cannibalistic spider Micaria sociabilis (Gnaphosidae).
Results
We performed mating trials using females with and without a plug that consists of an amorphous mass. The mating trials demonstrated that the probability of male plugging increased non-linearly with the duration of copulation. Copulation duration and plug production seem to be controlled by the female. We found that females terminated matings later if males were fast at genital coupling. Whereas incomplete plugs had disappeared on the day following copulation, complete plugs persisted (40%). In matings with females with complete plugs, only a small proportion of males (7%) were able to remove the plug, indicating the high effectiveness of plugging. Moreover, males ceased attempts to copulate with plugged females with higher probability. 3D X-ray microscopy of the female and male genitalia showed that the plug material can extend far into the female genital tract and that the plug material is produced by a massive gland inside the palpal organ of the modified male pedipalps.
Conclusions
Our study demonstrates that the mating plug in M. sociabilis constitutes an effective male strategy to avoid sperm competition that seems to be under female control.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-014-0278-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-014-0278-9
PMCID: PMC4327802
Secretory plugs; Sperm competition; Cryptic female choice; Multiple mating; X-ray microscopy
4.  Annual acknowledgement of reviewers 
BMC Evolutionary Biology  2015;15(1):17.
Contributing reviewers
The editors of BMC Evolutionary Biology would like to thank all our reviewers who have contributed to the journal in Volume 14 (2014).
doi:10.1186/s12862-015-0282-8
PMCID: PMC4322815
5.  Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates 
BMC Evolutionary Biology  2015;15(1):13.
Background
Model selection is a vital part of most phylogenetic analyses, and accounting for the heterogeneity in evolutionary patterns across sites is particularly important. Mixture models and partitioning are commonly used to account for this variation, and partitioning is the most popular approach. Most current partitioning methods require some a priori partitioning scheme to be defined, typically guided by known structural features of the sequences, such as gene boundaries or codon positions. Recent evidence suggests that these a priori boundaries often fail to adequately account for variation in rates and patterns of evolution among sites. Furthermore, new phylogenomic datasets such as those assembled from ultra-conserved elements lack obvious structural features on which to define a priori partitioning schemes. The upshot is that, for many phylogenetic datasets, partitioned models of molecular evolution may be inadequate, thus limiting the accuracy of downstream phylogenetic analyses.
Results
We present a new algorithm that automatically selects a partitioning scheme via the iterative division of the alignment into subsets of similar sites based on their rates of evolution. We compare this method to existing approaches using a wide range of empirical datasets, and show that it consistently leads to large increases in the fit of partitioned models of molecular evolution when measured using AICc and BIC scores. In doing so, we demonstrate that some related approaches to solving this problem may have been associated with a small but important bias.
Conclusions
Our method provides an alternative to traditional approaches to partitioning, such as dividing alignments by gene and codon position. Because our method is data-driven, it can be used to estimate partitioned models for all types of alignments, including those that are not amenable to traditional approaches to partitioning.
doi:10.1186/s12862-015-0283-7
PMCID: PMC4327964
Model selection; Partitioning; Partitionfinder; Phylogenetics; Phylogenomics; K-means; Clustering; Ultra-conserved elements; UCE’s
6.  The alveolate translation initiation factor 4E family reveals a custom toolkit for translational control in core dinoflagellates 
BMC Evolutionary Biology  2015;15(1):14.
Background
Dinoflagellates are eukaryotes with unusual cell biology and appear to rely on translational rather than transcriptional control of gene expression. The eukaryotic translation initiation factor 4E (eIF4E) plays an important role in regulating gene expression because eIF4E binding to the mRNA cap is a control point for translation. eIF4E is part of an extended, eukaryote-specific family with different members having specific functions, based on studies of model organisms. Dinoflagellate eIF4E diversity could provide a mechanism for dinoflagellates to regulate gene expression in a post-transcriptional manner. Accordingly, eIF4E family members from eleven core dinoflagellate transcriptomes were surveyed to determine the diversity and phylogeny of the eIF4E family in dinoflagellates and related lineages including apicomplexans, ciliates and heterokonts.
Results
The survey uncovered eight to fifteen (on average eleven) different eIF4E family members in each core dinoflagellate species. The eIF4E family members from heterokonts and dinoflagellates segregated into three clades, suggesting at least three eIF4E cognates were present in their common ancestor. However, these three clades are distinct from the three previously described eIF4E classes, reflecting diverse approaches to a central eukaryotic function. Heterokonts contain four clades, ciliates two and apicomplexans only a single recognizable eIF4E clade. In the core dinoflagellates, the three clades were further divided into nine sub-clades based on the phylogenetic analysis and species representation. Six of the sub-clades included at least one member from all eleven core dinoflagellate species, suggesting duplication in their shared ancestor. Conservation within sub-clades varied, suggesting different selection pressures.
Conclusions
Phylogenetic analysis of eIF4E in core dinoflagellates revealed complex layering of duplication and conservation when compared to other eukaryotes. Our results suggest that the diverse eIF4E family in core dinoflagellates may provide a toolkit to enable selective translation as a strategy for controlling gene expression in these enigmatic eukaryotes.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-015-0301-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-015-0301-9
PMCID: PMC4330643
Dinoflagellates; Translation initiation; eIF4E; Phylogeny; Alveolate; Heterokont
7.  Spatiotemporal abnormality dynamics of the pale grass blue butterfly: three years of monitoring (2011–2013) after the Fukushima nuclear accident 
Background
Long-term monitoring of the biological impacts of the radioactive pollution caused by the Fukushima nuclear accident in March 2011 is required to understand what has occurred in organisms living in the polluted areas. Here, we investigated spatial and temporal changes of the abnormality rate (AR) in both field-caught adult populations and laboratory-reared offspring populations of the pale grass blue butterfly, Zizeeria maha, which has generation time of approximately one month. We monitored 7 localities (Fukushima, Motomiya, Hirono, Iwaki, Takahagi, Mito, and Tsukuba) every spring and fall over 3 years (2011–2013).
Results
The adult ARs of these localities quickly increased and peaked in the fall of 2011, which was not observed in non-contaminated localities. In the offspring generation, the total ARs, which include deaths at the larval, prepupal, and pupal stages and morphological abnormalities at the adult stage, peaked either in the fall of 2011 or in the spring of 2012, with much higher levels than those of the parent field populations, suggesting that high incidence of deaths and abnormalities might have occurred in the field populations. Importantly, the elevated ARs of the field and offspring populations settled back to a normal level by the fall of 2012 and by the spring of 2013, respectively. Similar results were obtained not only in the spatiotemporal dynamics of the number of individuals caught per minute but also in the temporal dynamics of the correlation coefficient between the adult abnormality rate and the ground radiation dose or the distance from the Power Plant.
Conclusions
These results demonstrated an occurrence and an accumulation of adverse physiological and genetic effects in early generations, followed by their decrease and leveling off at a normal level, providing the most comprehensive record of biological dynamics after a nuclear accident available today. This study also indicates the importance of considering generation time and adaptive evolution in evaluating the biological impacts of artificial pollution in wild organisms.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-015-0297-1) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-015-0297-1
PMCID: PMC4335452
Adaptive evolution; Fukushima nuclear accident; Long-term monitoring; Pale grass blue butterfly; Radioactive contamination
8.  Parallel evolution in Ugandan crater lakes: repeated evolution of limnetic body shapes in haplochromine cichlid fish 
BMC Evolutionary Biology  2015;15(1):9.
Background
The enormous diversity found in East African cichlid fishes in terms of morphology, coloration, and behavior have made them a model for the study of speciation and adaptive evolution. In particular, haplochromine cichlids, by far the most species-rich lineage of cichlids, are a well-known textbook example for parallel evolution. Southwestern Uganda is an area of high tectonic activity, and is home to numerous crater lakes. Many Ugandan crater lakes were colonized, apparently independently, by a single lineage of haplochromine cichlids. Thereby, this system could be considered a natural experiment in which one can study the interaction between geographical isolation and natural selection promoting phenotypic diversification.
Results
We sampled 13 crater lakes and six potentially-ancestral older lakes and, using both mitochondrial and microsatellite markers, discovered strong genetic and morphological differentiation whereby (a) geographically close lakes tend to be genetically more similar and (b) three different geographic areas seem to have been colonized by three independent waves of colonization from the same source population. Using a geometric morphometric approach, we found that body shape elongation (i.e. a limnetic morphology) evolved repeatedly from the ancestral deeper-bodied benthic morphology in the clear and deep crater lake habitats.
Conclusions
A pattern of strong genetic and morphological differentiation was observed in the Ugandan crater lakes. Our data suggest that body shape changes have repeatedly evolved into a more limnetic-like form in several Ugandan crater lakes after independent waves of colonization from the same source population. The observed morphological changes in crater lake cichlids are likely to result from a common selective regime.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-015-0287-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-015-0287-3
PMCID: PMC4322459  PMID: 25648727
Parallel evolution; Benthic-limnetic; Speciation
9.  Lack of evolutionary adjustment to ambient temperature in highly specialized cave beetles 
BMC Evolutionary Biology  2015;15(1):10.
Background
A key question in evolutionary biology is the relationship between species traits and their habitats. Caves offer an ideal model to test the adjustment of species to their surrounding temperature, as they provide homogeneous and simple environments. We compared two species living under different thermal conditions within a lineage of Pyrenean beetles highly modified for the subterranean life since the Miocene. One, Troglocharinus fonti, is found in caves at 4-11°C in the ancestral Pyrenean range. The second, T. ferreri, inhabits the coastal area of Catalonia since the early Pliocene, and lives at 14-16°C.
Results
We found no differences in their short term upper thermal limit (ca. 50°C), similar to that of most organisms, or their lower thermal limit (ca. -2.5°C), higher than for most temperate insects and suggesting the absence of cryoprotectants. In longer term tests (7 days) survival between 6-20°C was almost 100% for both species plus two outgroups of the same lineage, but all four died between 23-25°C, without significant differences between them.
Conclusions
Our results suggest that species in this lineage have lost some of the thermoregulatory mechanisms common in temperate insects, as their inferred default tolerance range is larger than the thermal variation experienced through their whole evolutionary history.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-015-0288-2) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-015-0288-2
PMCID: PMC4324670  PMID: 25648857
Acclimation; Adaptation; Pyrenees; Thermal tolerance; Subterranean environment
10.  The fossil record and taphonomy of butterflies and moths (Insecta, Lepidoptera): implications for evolutionary diversity and divergence-time estimates 
BMC Evolutionary Biology  2015;15(1):12.
Background
It is conventionally accepted that the lepidopteran fossil record is significantly incomplete when compared to the fossil records of other, very diverse, extant insect orders. Such an assumption, however, has been based on cumulative diversity data rather than using alternative statistical approaches from actual specimen counts.
Results
We reviewed documented specimens of the lepidopteran fossil record, currently consisting of 4,593 known specimens that are comprised of 4,262 body fossils and 331 trace fossils. The temporal distribution of the lepidopteran fossil record shows significant bias towards the late Paleocene to middle Eocene time interval. Lepidopteran fossils also record major shifts in preservational style and number of represented localities at the Mesozoic stage and Cenozoic epoch level of temporal resolution. Only 985 of the total known fossil specimens (21.4%) were assigned to 23 of the 40 extant lepidopteran superfamilies. Absolute numbers and proportions of preservation types for identified fossils varied significantly across superfamilies. The secular increase of lepidopteran family-level diversity through geologic time significantly deviates from the general pattern of other hyperdiverse, ordinal-level lineages.
Conclusion
Our statistical analyses of the lepidopteran fossil record show extreme biases in preservation type, age, and taxonomic composition. We highlight the scarcity of identified lepidopteran fossils and provide a correspondence between the latest lepidopteran divergence-time estimates and relevant fossil occurrences at the superfamily level. These findings provide caution in interpreting the lepidopteran fossil record through the modeling of evolutionary diversification and in determination of divergence time estimates.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-015-0290-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-015-0290-8
PMCID: PMC4326409  PMID: 25649001
Lepidoptera; Fossil record; Taphonomy; Diversity; Divergence-time estimation
11.  Phenotype and animal domestication: A study of dental variation between domestic, wild, captive, hybrid and insular Sus scrofa 
BMC Evolutionary Biology  2015;15(1):6.
Background
Identifying the phenotypic responses to domestication remains a long-standing and important question for researchers studying its early history. The great diversity in domestic animals and plants that exists today bears testament to the profound changes that domestication has induced in their ancestral wild forms over the last millennia. Domestication is a complex evolutionary process in which wild organisms are moved to new anthropogenic environments. Although modern genetics are significantly improving our understanding of domestication and breed formation, little is still known about the associated morphological changes linked to the process itself. In order to explore phenotypic variation induced by different levels of human control, we analysed the diversity of dental size, shape and allometry in modern free-living and captive wild, wild x domestic hybrid, domestic and insular Sus scrofa populations.
Results
We show that domestication has created completely new dental phenotypes not found in wild boar (although the amount of variation amongst domestic pigs does not exceed that found in the wild). Wild boar tooth shape also appears to be biogeographically structured, likely the result of post-glacial recolonisation history. Furthermore, distinct dental phenotypes were also observed among domestic breeds, probably the result of differing types and intensity of past and present husbandry practices. Captivity also appears to impact tooth shape. Wild x domestic hybrids possess second molars that are strictly intermediate in shape between wild boar and domestic pigs (third molars, however, showing greater shape similarity with wild boar) while their size is more similar to domestic pigs. The dental phenotypes of insular Sus scrofa populations found on Corsica and Sardinia today (originally introduced by Neolithic settlers to the islands) can be explained either by feralization of the original introduced domestic swine or that the founding population maintained a wild boar phenotype through time.
Conclusions
Domestication has driven significant phenotypic diversification in Sus scrofa. Captivity (environmental control), hybridization (genome admixture), and introduction to islands all correspond to differing levels of human control and may be considered different stages of the domestication process. The relatively well-known genetic evolutionary history of pigs shows a similar complexity at the phenotypic level.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-014-0269-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-014-0269-x
PMCID: PMC4328033  PMID: 25648385
Teeth; Molars; Geometric morphometrics; Biogeography; Artificial selection; Natural selection
12.  Impact of the terrestrial-aquatic transition on disparity and rates of evolution in the carnivoran skull 
BMC Evolutionary Biology  2015;15(1):8.
Background
Which factors influence the distribution patterns of morphological diversity among clades? The adaptive radiation model predicts that a clade entering new ecological niche will experience high rates of evolution early in its history, followed by a gradual slowing. Here we measure disparity and rates of evolution in Carnivora, specifically focusing on the terrestrial-aquatic transition in Pinnipedia. We analyze fissiped (mostly terrestrial, arboreal, and semi-arboreal, but also including the semi-aquatic otter) and pinniped (secondarily aquatic) carnivorans as a case study of an extreme ecological transition. We used 3D geometric morphometrics to quantify cranial shape in 151 carnivoran specimens (64 fissiped, 87 pinniped) and five exceptionally-preserved fossil pinnipeds, including the stem-pinniped Enaliarctos emlongi. Range-based and variance-based disparity measures were compared between pinnipeds and fissipeds. To distinguish between evolutionary modes, a Brownian motion model was compared to selective regime shifts associated with the terrestrial-aquatic transition and at the base of Pinnipedia. Further, evolutionary patterns were estimated on individual branches using both Ornstein-Uhlenbeck and Independent Evolution models, to examine the origin of pinniped diversity.
Results
Pinnipeds exhibit greater cranial disparity than fissipeds, even though they are less taxonomically diverse and, as a clade nested within fissipeds, phylogenetically younger. Despite this, there is no increase in the rate of morphological evolution at the base of Pinnipedia, as would be predicted by an adaptive radiation model, and a Brownian motion model of evolution is supported. Instead basal pinnipeds populated new areas of morphospace via low to moderate rates of evolution in new directions, followed by later bursts within the crown-group, potentially associated with ecological diversification within the marine realm.
Conclusion
The transition to an aquatic habitat in carnivorans resulted in a shift in cranial morphology without an increase in rate in the stem lineage, contra to the adaptive radiation model. Instead these data suggest a release from evolutionary constraint model, followed by aquatic diversifications within crown families.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-015-0285-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-015-0285-5
PMCID: PMC4328284  PMID: 25648618
Disparity; Carnivora; Fissiped; Pinniped; Cranial morphology; Radiation; Ecological transition; Aquatic mammal
13.  Genetic and morphological variation in sexual and asexual parasitoids of the genus Lysiphlebus – an apparent link between wing shape and reproductive mode 
Background
Morphological divergence often increases with phylogenetic distance, thus making morphology taxonomically informative. However, transitions to asexual reproduction may complicate this relationship because asexual lineages capture and freeze parts of the phenotypic variation of the sexual populations from which they derive. Parasitoid wasps belonging to the genus Lysiphlebus Foerster (Hymenoptera: Braconidae: Aphidiinae) are composed of over 20 species that exploit over a hundred species of aphid hosts, including many important agricultural pests. Within Lysiphlebus, two genetically and morphologically well-defined species groups are recognised: the “fabarum” and the “testaceipes” groups. Yet within each group, sexual as well as asexual lineages occur, and in L. fabarum different morphs of unknown origin and status have been recognised. In this study, we selected a broad sample of specimens from the genus Lysiphlebus to explore the relationship between genetic divergence, reproductive mode and morphological variation in wing size and shape (quantified by geometric morphometrics).
Results
The analyses of mitochondrial and nuclear gene sequences revealed a clear separation between the “testaceipes” and “fabarum” groups of Lysiphlebus, as well as three well-defined phylogenetic lineages within the “fabarum” species group and two lineages within the “testaceipes” group. Divergence in wing shape was concordant with the deep split between the “testaceipes” and “fabarum” species groups, but within groups no clear association between genetic divergence and wing shape variation was observed. On the other hand, we found significant and consistent differences in the shape of the wing between sexual and asexual lineages, even when they were closely related.
Conclusions
Mapping wing shape data onto an independently derived molecular phylogeny of Lysiphlebus revealed an association between genetic and morphological divergence only for the deepest phylogenetic split. In more recently diverged taxa, much of the variation in wing shape was explained by differences between sexual and asexual lineages, suggesting a mechanistic link between wing shape and reproductive mode in these parasitoid wasps.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-015-0293-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-015-0293-5
PMCID: PMC4332431
Parasitoid wasps; Wing shape; Reproductive mode; COI
14.  Higher speciation and lower extinction rates influence mammal diversity gradients in Asia 
Background
Little is known about the patterns and correlates of mammal diversity gradients in Asia. In this study, we examine patterns of species distributions and phylogenetic diversity in Asia and investigate if the observed diversity patterns are associated with differences in diversification rates between the tropical and non-tropical regions. We used species distribution maps and phylogenetic trees to generate species and phylogenetic diversity measures for 1° × 1° cells across mainland Asia. We constructed lineage-through-time plots and estimated diversification shift-times to examine the temporal patterns of diversifications across orders. Finally, we tested if the observed gradients in Asia could be associated with geographical differences in diversification rates across the tropical and non-tropical biomes. We estimated speciation, extinction and dispersal rates across these two regions for mammals, both globally and for Asian mammals.
Results
Our results demonstrate strong latitudinal and longitudinal gradients of species and phylogenetic diversity with Southeast Asia and the Himalayas showing highest diversity. Importantly, our results demonstrate that differences in diversification (speciation, extinction and dispersal) rates between the tropical and the non-tropical biomes influence the observed diversity gradients globally and in Asia. For the first time, we demonstrate that Asian tropics act as both cradles and museums of mammalian diversity.
Conclusions
Temporal and spatial variation in diversification rates across different lineages of mammals is an important correlate of species diversity gradients observed in Asia.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-015-0289-1) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-015-0289-1
PMCID: PMC4333168  PMID: 25648944
Biomes; Biogeography; Tropical diversity; Diversification rates; Latitudinal gradients; Phylogenetic diversity
15.  The origin of the ADAR gene family and animal RNA editing 
BMC Evolutionary Biology  2015;15(1):4.
Background
ADAR (adenosine deaminase acting on RNA) proteins convert adenosine into inosine in double-stranded RNAs and have been shown to increase gene product diversity in a number of bilaterians, particularly mammals and flies. This enzyme family appears to have evolved from an ADAT (adenosine deaminase acting on tRNA) ancestor, via the addition of a double-stranded RNA binding domain. The modern vertebrate ADAR family is comprised of ADAD, ADAR2 and ADAR1, each of which has a conserved domain architecture. To reconstruct the origin of this protein family, we identified and categorised ADAR family members encoded in the genomes and/or transcriptomes of early-branching metazoan and closely related non-metazoan taxa, including thirteen sponge and ten ctenophore species.
Results
We demonstrate that the ADAR protein family is a metazoan innovation, with the three ADAR subtypes being present in representatives of the earliest phyletic lineages of animals – sponges and ctenophores – but not in other closely related choanoflagellate and filasterean holozoans. ADAR1 is missing from all ctenophore genomes and transcriptomes surveyed. Depending on the relationship of sponges and ctenophores to the rest of the Metazoa, this is consistent with either ADAR1 being lost in ctenophores, as it has been in multiple metazoan lineages, or being an innovation that evolved after ctenophores diverged from the rest of the animal kingdom. The presence of Z-DNA binding domains in some sponge ADARs indicates an ancestral ADAR included this domain and it has been lost in multiple animal lineages.
Conclusions
The ADAR family appears to be a metazoan innovation, with all family members in place in the earliest phyletic branches of the crown Metazoa. The presence of ADARs in sponges and ctenophores is consistent with A-to-I editing being a post-transcriptional regulatory mechanism that was used by the last common ancestor to all living animals and subsequently has been preserved in most modern lineages.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-015-0279-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-015-0279-3
PMCID: PMC4323055  PMID: 25630791
A-to-I editing; Adenosine deaminase acting on RNA (ADAR); Evolution; RNA editing; Domain evolution; Sponge; Ctenophore; Metazoa; Domain architecture
16.  Chimpanzee population structure in Cameroon and Nigeria is associated with habitat variation that may be lost under climate change 
BMC Evolutionary Biology  2015;15(1):2.
Background
The Nigeria-Cameroon chimpanzee (Pan troglodytes ellioti) is found in the Gulf of Guinea biodiversity hotspot located in western equatorial Africa. This subspecies is threatened by habitat fragmentation due to logging and agricultural development, hunting for the bushmeat trade, and possibly climate change. Although P. t. ellioti appears to be geographically separated from the neighboring central chimpanzee (P. t. troglodytes) by the Sanaga River, recent population genetics studies of chimpanzees from across this region suggest that additional factors may also be important in their separation. The main aims of this study were: 1) to model the distribution of suitable habitat for P. t. ellioti across Cameroon and Nigeria, and P. t. troglodytes in southern Cameroon, 2) to determine which environmental factors best predict their optimal habitats, and 3) to compare modeled niches and test for their levels of divergence from one another. A final aim of this study was to examine the ways that climate change might impact suitable chimpanzee habitat across the region under various scenarios.
Results
Ecological niche models (ENMs) were created using the software package Maxent for the three populations of chimpanzees that have been inferred to exist in Cameroon and eastern Nigeria: (i) P. t. troglodytes in southern Cameroon, (ii) P. t. ellioti in northwestern Cameroon, and (iii) P. t. ellioti in central Cameroon. ENMs for each population were compared using the niche comparison test in ENMtools, which revealed complete niche divergence with very little geographic overlap of suitable habitat between populations.
Conclusions
These findings suggest that a positive relationship may exist between environmental variation and the partitioning of genetic variation found in chimpanzees across this region. ENMs for each population were also projected under three different climate change scenarios for years 2020, 2050, and 2080. Suitable habitat of P. t. ellioti in northwest Cameroon / eastern Nigeria is expected to remain largely unchanged through 2080 in all considered scenarios. In contrast, P. t. ellioti in central Cameroon, which represents half of the population of this subspecies, is expected to experience drastic reductions in its ecotone habitat over the coming century.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-014-0275-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-014-0275-z
PMCID: PMC4314735  PMID: 25608567
17.  The population genetics of wild chimpanzees in Cameroon and Nigeria suggests a positive role for selection in the evolution of chimpanzee subspecies 
BMC Evolutionary Biology  2015;15(1):3.
Background
Chimpanzees (Pan troglodytes) can be divided into four subspecies. Substantial phylogenetic evidence suggests that these subspecies can be grouped into two distinct lineages: a western African group that includes P. t. verus and P. t. ellioti and a central/eastern African group that includes P. t. troglodytes and P. t. schweinfurthii. The geographic division of these two lineages occurs in Cameroon, where the rages of P. t. ellioti and P. t. troglodytes appear to converge at the Sanaga River. Remarkably, few population genetic studies have included wild chimpanzees from this region.
Results
We analyzed microsatellite genotypes of 187 wild, unrelated chimpanzees, and mitochondrial control region sequencing data from 604 chimpanzees. We found that chimpanzees in Cameroon and eastern Nigeria comprise at least two, and likely three populations. Both the mtDNA and microsatellite data suggest that there is a primary separation of P. t. troglodytes in southern Cameroon from P. t. ellioti north and west of the Sanaga River. These two populations split ~200-250 thousand years ago (kya), but have exchanged one migrant per generation since separating. In addition, P. t. ellioti consists of two populations that split from one another ~4 kya. One population is located in the rainforests of western Cameroon and eastern Nigeria, whereas the second population appears to be confined to a savannah-woodland mosaic in central Cameroon.
Conclusions
Our findings suggest that there are as many as three genetically distinct populations of chimpanzees in Cameroon and eastern Nigeria. P. t. troglodytes in southern Cameroon comprises one population that is separated from two populations of P. t. ellioti in western and central Cameroon, respectively. P. t. ellioti and P. t. troglodytes appear to be characterized by a pattern of isolation-with-migration, and thus, we propose that neutral processes alone can not explain the differentiation of P. t. ellioti and P. t. troglodytes.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-014-0276-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-014-0276-y
PMCID: PMC4314757  PMID: 25608610
18.  Environmental variation and rivers govern the structure of chimpanzee genetic diversity in a biodiversity hotspot 
BMC Evolutionary Biology  2015;15(1):1.
Background
The mechanisms that underlie the diversification of tropical animals remain poorly understood, but new approaches that combine geo-spatial modeling with spatially explicit genetic data are providing fresh insights on this topic. Data about the diversification of tropical mammals remain particularly sparse, and vanishingly few opportunities exist to study endangered large mammals that increasingly exist only in isolated pockets. The chimpanzees of Cameroon represent a unique opportunity to examine the mechanisms that promote genetic differentiation in tropical mammals because the region is home to two chimpanzee subspecies: Pan troglodytes ellioti and P. t. trogolodytes. Their ranges converge in central Cameroon, which is a geographically, climatically and environmentally complex region that presents an unparalleled opportunity to examine the roles of rivers and/or environmental variation in influencing the evolution of chimpanzee populations.
Results
We analyzed microsatellite genotypes and mtDNA HVRI sequencing data from wild chimpanzees sampled at a fine geographic scale across Cameroon and eastern Nigeria using a spatially explicit approach based upon Generalized Dissimilarity Modeling. Both the Sanaga River and environmental variation were found to contribute to driving separation of the subspecies. The importance of environmental variation differed among subspecies. Gene-environment associations were weak in P. t. troglodytes, whereas environmental variation was found to play a much larger role in shaping patterns of genetic differentiation in P. t. ellioti.
Conclusions
We found that both the Sanaga River and environmental variation likely play a role in shaping patterns of chimpanzee genetic diversity. Future studies using single nucleotide polymorphism (SNP) data are necessary to further understand how rivers and environmental variation contribute to shaping patterns of genetic variation in chimpanzees.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-014-0274-0) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-014-0274-0
PMCID: PMC4314796  PMID: 25608511
19.  Colony size is linked to paternity frequency and paternity skew in yellowjacket wasps and hornets 
BMC Evolutionary Biology  2014;14(1):2625.
Background
The puzzle of the selective benefits of multiple mating and multiple paternity in social insects has been a major focus of research in evolutionary biology. We examine paternity in a clade of social insects, the vespine wasps (the yellowjackets and hornets), which contains species with high multiple paternity as well as species with single paternity. This group is particularly useful for comparative analyses given the wide interspecific variation in paternity traits despite similar sociobiology and ecology of the species in the genera Vespula, Dolichovespula and Vespa. We describe the paternity of 5 species of yellowjackets (Vespula spp.) and we perform a phylogenetically controlled comparative analysis of relatedness, paternity frequency, paternity skew, colony size, and nest site across 22 vespine taxa.
Results
We found moderate multiple paternity in four small-colony Vespula rufa-group species (effective paternity 1.5 – 2.1), and higher multiple paternity in the large-colony Vespula flavopilosa (effective paternity ~3.1). Our comparative analysis shows that colony size, but not nest site, predicts average intracolony relatedness. Underlying this pattern, we found that greater colony size is associated with both higher paternity frequency and reduced paternity skew.
Conclusions
Our results support hypotheses focusing on the enhancement of genetic diversity in species with large colonies, and run counter to the hypothesis that multiple paternity is adaptively maintained due to sperm limitation associated with large colonies. We confirm the patterns observed in taxonomically widespread analyses by comparing closely related species of wasps with similar ecology, behavior and social organization. The vespine wasps may be a useful group for experimental investigation of the benefits of multiple paternity in the future.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-014-0277-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-014-0277-x
PMCID: PMC4298054  PMID: 25547876
Social insects; Polyandry; Multiple paternity; Paternity skew; Vespula; Dolichovespula; Vespa; Social evolution
20.  Concatenated alignments and the case of the disappearing tree 
BMC Evolutionary Biology  2014;14(1):266.
Background
Analyzed individually, gene trees for a given taxon set tend to harbour incongruent or conflicting signals. One popular approach to deal with this circumstance is to use concatenated data. But especially in prokaryotes, where lateral gene transfer (LGT) is a natural mechanism of generating genetic diversity, there are open questions as to whether concatenation amplifies or averages phylogenetic signals residing in individual genes. Here we investigate concatenations of prokaryotic and eukaryotic datasets to investigate possible sources of incongruence in phylogenetic trees and to examine the level of overlap between individual and concatenated alignments.
Results
We analyzed prokaryotic datasets comprising 248 invidual gene trees from 315 genomes at three taxonomic depths spanning gammaproteobacteria, proteobacteria, and prokaryotes (bacteria plus archaea), and eukaryotic datasets comprising 279 invidual gene trees from 85 genomes at two taxonomic depths: across plants-animals-fungi and within fungi. Consistent with previous findings, the branches in trees made from concatenated alignments are, in general, not supported by any of their underlying individual gene trees, even though the concatenation trees tend to possess high bootstrap proportions values. For the prokaryote data, this observation is independent of phylogenetic depth and sequence conservation. The eukaryotic data show much better agreement between concatenation and single gene trees. LGT frequencies in trees were estimated using established methods. Sequence length in individual alignments, but not sequence divergence, was found to correlate with the generation of branches that correspond to the concatenated tree.
Conclusions
The weak correspondence of concatenation trees with single gene trees gives rise to the question where the phylogenetic signal in concatenated trees is coming from. The eukaryote data reveals a better correspondence between individual and concatenation trees than the prokaryote data. The question of whether the lack of correspondence between individual genes and the concatenation tree in the prokaryotic data is due to LGT or phylogenetic artefacts remains unanswered. If LGT is the cause of incongruence between concatenation and individual trees, we would have expected to see greater degrees of incongruence for more divergent prokaryotic data sets, which was not observed, although estimated rates of LGT suggest that LGT is responsible for at least some of the observed incongruence.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-014-0266-0) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-014-0266-0
PMCID: PMC4302582  PMID: 25547755
Phylogeny; Concatenation; Conflicting signals; Bootstrapping
21.  Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome 
BMC Evolutionary Biology  2014;14(1):1.
Background
Although the plastid genome is highly conserved across most angiosperms, multiple lineages have increased rates of structural rearrangement and nucleotide substitution. These lineages exhibit an excess of nonsynonymous substitutions (i.e., elevated dN/dS ratios) in similar subsets of plastid genes, suggesting that similar mechanisms may be leading to relaxed and/or positive selection on these genes. However, little is known regarding whether these mechanisms continue to shape sequence diversity at the intraspecific level.
Results
We examined patterns of interspecific divergence and intraspecific polymorphism in the plastid genome of Campanulastrum americanum, and across plastid genes found a significant correlation between dN/dS and pN/pS (i.e., the within-species equivalent of dN/dS). A number of genes including ycf1, ycf2, clpP, and ribosomal protein genes exhibited high dN/dS ratios. McDonald-Kreitman tests detected little evidence for positive selection acting on these genes, likely due to the presence of substantial intraspecific divergence.
Conclusions
These results suggest that mechanisms leading to increased nucleotide substitution rates in the plastid genome are continuing to act at the intraspecific level. Accelerated plastid genome evolution may increase the likelihood of intraspecific cytonuclear genetic incompatibilities, and thereby contribute to the early stages of the speciation process.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-014-0268-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-014-0268-y
PMCID: PMC4300152  PMID: 25539645
Plastid; Selection; dN/dS; pN/pS; Reproductive isolation; Intraspecific; Chloroplast; Sequence evolution
22.  Paternal X inactivation does not correlate with X chromosome evolutionary strata in marsupials 
BMC Evolutionary Biology  2014;14(1):267.
Background
X chromosome inactivation is the transcriptional silencing of one X chromosome in the somatic cells of female mammals. In eutherian mammals (e.g. humans) one of the two X chromosomes is randomly chosen for silencing, with about 15% (usually in younger evolutionary strata of the X chromosome) of genes escaping this silencing. In contrast, in the distantly related marsupial mammals the paternally derived X is silenced, although not as completely as the eutherian X. A chromosome wide examination of X inactivation, using RNA-seq, was recently undertaken in grey short-tailed opossum (Monodelphis domestica) brain and extraembryonic tissues. However, no such study has been conduced in Australian marsupials, which diverged from their American cousins ~80 million years ago, leaving a large gap in our understanding of marsupial X inactivation.
Results
We used RNA-seq data from blood or liver of a family (mother, father and daughter) of tammar wallabies (Macropus eugenii), which in conjunction with available genome sequence from the mother and father, permitted genotyping of 42 expressed heterozygous SNPs on the daughter’s X. These 42 SNPs represented 34 X loci, of which 68% (23 of the 34) were confirmed as inactivated on the paternally derived X in the daughter’s liver; the remaining 11 X loci escaped inactivation. Seven of the wallaby loci sampled were part of the old X evolutionary stratum, of which three escaped inactivation. Three loci were classified as part of the newer X stratum, of which two escaped inactivation. A meta-analysis of previously published opossum X inactivation data revealed that 5 of 52 genes in the old X stratum escaped inactivation.
Conclusions
We demonstrate that chromosome wide inactivation of the paternal X is common to an Australian marsupial representative, but that there is more escape from inactivation than reported for opossum (32% v 14%). We also provide evidence that, unlike the human X chromosome, the location of loci within the oldest evolutionary stratum on the marsupial X does not correlate with their probability of escape from inactivation.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-014-0267-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-014-0267-z
PMCID: PMC4302592  PMID: 25539578
X inactivation; Marsupial; Imprinting; X chromosome; Escape; RNA-seq; SNP; Evolution; Strata
23.  Seasonality in the migration and establishment of H3N2 Influenza lineages with epidemic growth and decline 
BMC Evolutionary Biology  2014;14(1):3.
Background
Influenza A/H3N2 has been circulating in humans since 1968, causing considerable morbidity and mortality. Although H3N2 incidence is highly seasonal, how such seasonality contributes to global phylogeographic migration dynamics has not yet been established. In this study, we incorporate time-varying migration rates in a Bayesian MCMC framework. We focus on migration within China, and to and from North-America as case studies, then expand the analysis to global communities.
Results
Incorporating seasonally varying migration rates improves the modeling of migration in our regional case studies, and also in a global context. In our global model, windows of increased immigration map to the seasonal timing of epidemic spread, while windows of increased emigration map to epidemic decline. Seasonal patterns also correlate with the probability that local lineages go extinct and fail to contribute to long term viral evolution, as measured through the trunk of the phylogeny. However, the fraction of the trunk in each community was found to be better determined by its overall human population size.
Conclusions
Seasonal migration and rapid turnover within regions is sustained by the invasion of 'fertile epidemic grounds' at the end of older epidemics. Thus, the current emphasis on connectivity, including air-travel, should be complemented with a better understanding of the conditions and timing required for successful establishment. Models which account for migration seasonality will improve our understanding of the seasonal drivers of influenza, enhance epidemiological predictions, and ameliorate vaccine updating by identifying strains that not only escape immunity but also have the seasonal opportunity to establish and spread. Further work is also needed on additional conditions that contribute to the persistence and long term evolution of influenza within the human population, such as spatial heterogeneity with respect to climate and seasonality.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-014-0272-2) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-014-0272-2
PMCID: PMC4316805  PMID: 25539729
Influenza; Migration; Phylogeography; Persistence; Seasonality; Evolution
24.  Towards a comprehensive characterization of durum wheat landraces in Moroccan traditional agrosystems: analysing genetic diversity in the light of geography, farmers’ taxonomy and tetraploid wheat domestication history 
BMC Evolutionary Biology  2014;14(1):264.
Background
Crop diversity managed by smallholder farmers in traditional agrosystems is the outcome of historical and current processes interacting at various spatial scales, and influenced by factors such as farming practices and environmental pressures. Only recently have studies started to consider the complexity of these processes instead of simply describing diversity for breeding purposes. A first step in that aim is to add multiple references to the collection of genetic data, including the farmers’ varietal taxonomy and practices and the historical background of the crop.
Results
On the basis of interview data collected in a previous study, we sampled 166 populations of durum wheat varieties in two traditional Moroccan agrosystems, in the Pre-Rif and Atlas Mountains regions. Using a common garden experiment, we detected a high phenotypic variability on traits indicative of taxonomical position and breeding status, namely spike shape and plant height. Populations often combined modern (short) with traditional-like (tall) statures, and classical durum squared spike shape (5 flowers/spikelet) with flat spike shape (3 flowers/ spikelet) representative of primitive domesticated tetraploid wheat (ssp. dicoccum). By contrast, the genetic diversity assessed using 14 microsatellite markers was relatively limited. When compared to the genetic diversity found in a large collection of tetraploid wheat, it corresponded to free-threshing tetraploid wheat. Within Morocco, the two studied regions differed for both genetic diversity and variety names. Within regions, neither geography nor variety names nor even breeding status constituted strong barriers to gene exchange despite a few significant patterns.
Conclusions
This first assessment of morphological and genetic diversity allowed pointing out some important factors that may have influenced the structure and evolutionary dynamics of durum wheat in Morocco: the significance of variety names, the occurrence of mixtures within populations, the relative strength of seed exchange between farmers and local adaptation, as well as the fate of modern varieties once they have been introduced. Further, multidisciplinary studies at different spatial scales are needed to better understand these complex agrosystems of invaluable importance for food security.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-014-0264-2) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-014-0264-2
PMCID: PMC4300848  PMID: 25528060
Genetic diversity; Traditional agrosystems; Variety names; Landraces; Durum wheat
25.  Mitochondrial genomes of the Baltic clam Macoma balthica (Bivalvia: Tellinidae): setting the stage for studying mito-nuclear incompatibilities 
BMC Evolutionary Biology  2014;14(1):259.
Background
Allopatric divergence across lineages can lead to post-zygotic reproductive isolation upon secondary contact and disrupt coevolution between mitochondrial and nuclear genomes, promoting emergence of genetic incompatibilities. A previous FST scan on the transcriptome of the Baltic clam Macoma balthica highlighted several genes potentially involved in mito-nuclear incompatibilities (MNIs). As proteins involved in the mitochondrial oxidative phosphorylation (OXPHO) chain are prone to MNIs and can contribute to the maintenance of genetic barriers, the mitochondrial genomes of six Ma. balthica individuals spanning two secondary contact zones were sequenced using the Illumina MiSeq plateform.
Results
The mitogenome has an approximate length of 16,806 bp and encodes 13 protein-coding genes, 2 rRNAs and 22 tRNAs, all located on the same strand. atp8, a gene long reported as rare in bivalves, was detected. It encodes 42 amino acids and is putatively expressed and functional. A large unassigned region was identified between rrnS and tRNAMet and could likely correspond to the Control Region. Replacement and synonymous mutations were mapped on the inferred secondary structure of all protein-coding genes of the OXPHO chain. The atp6 and atp8 genes were characterized by background levels of replacement mutations, relative to synonymous mutations. However, most nad genes (notably nad2 and nad5) were characterized by an elevated proportion of replacement mutations.
Conclusions
Six nearly complete mitochondrial genomes were successfully assembled and annotated, providing the necessary roadmap to study MNIs at OXPHO loci. Few replacement mutations were mapped on mitochondrial-encoded ATP synthase subunits, which is in contrast with previous data on nuclear-encoded subunits. Conversely, the high population divergence and the prevalence of non-synonymous mutations at nad genes are congruent with previous observations from the nuclear transcriptome. This further suggest that MNIs between subunits of Complex I of the OXPHO chain, coding for NADH dehydrogenase, may play a role in maintaining barriers to gene flow in Ma. balthica.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-014-0259-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-014-0259-z
PMCID: PMC4302422  PMID: 25527898
NADH dehydrogenase; ATP synthase; Next-generation sequencing; OXPHO chain; Positive selection; Inter-specific hybridization; Hybrid zone

Results 1-25 (2803)