ResearchPad - evolutionary-studies https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Performance in a novel environment subject to ghost competition]]> https://www.researchpad.co/article/elastic_article_12830 A central tenet of the evolutionary theory of communities is that competition impacts evolutionary processes such as local adaptation. Species in a community exert a selection pressure on other species and may drive them to extinction. We know, however, very little about the influence of unsuccessful or ghost species on the evolutionary dynamics within the community.MethodsHere we report the long-term influence of a ghost competitor on the performance of a more successful species using experimental evolution. We transferred the spider mite Tetranychus urticae onto a novel host plant under initial presence or absence of a competing species, the congeneric mite T. ludeni.ResultsThe competitor species, T. ludeni, unintentionally went extinct soon after the start of the experiment, but we nevertheless completed the experiment and found that the early competitive pressure of this ghost competitor positively affected the performance (i.e., fecundity) of the surviving species, T. urticae. This effect on T. urticae lasted for at least 25 generations.DiscussionOur study suggests that early experienced selection pressures can exert a persistent evolutionary signal on species’ performance in novel environments. ]]> <![CDATA[Phylogeography of the widespread Caribbean spiny orb weaver <i>Gasteracantha cancriformis</i>]]> https://www.researchpad.co/article/elastic_article_12766 Modern molecular analyses are often inconsistent with pre-cladistic taxonomic hypotheses, frequently indicating higher richness than morphological taxonomy estimates. Among Caribbean spiders, widespread species are relatively few compared to the prevalence of single island endemics. The taxonomic hypothesis Gasteracantha cancriformis circumscribes a species with profuse variation in size, color and body form. Distributed throughout the Neotropics, G. cancriformis is the only morphological species of Gasteracantha in the New World in this globally distributed genus.MethodsWe inferred phylogenetic relationships across Neotropical populations of Gasteracantha using three target genes. Within the Caribbean, we estimated genetic diversity, population structure, and gene flow among island populations.ResultsOur findings revealed a single widespread species of Gasteracantha throughout the Caribbean, G. cancriformis, while suggesting two recently divergent mainland populations that may represent separate species, diverging linages, or geographically isolated demes. The concatenated and COI (Cytochrome c oxidase subunit 1) phylogeny supported a Caribbean clade nested within the New World. Genetic variability was high between island populations for our COI dataset; however, gene flow was also high, especially between large, adjacent islands. We found structured genetic and morphological variation within G. cancriformis island populations; however, this variation does not reflect genealogical relationships. Rather, isolation by distance and local morphological adaptation may explain the observed variation. ]]> <![CDATA[Time matters: genetic composition and evaluation of effective population size in temperate coastal fish species]]> https://www.researchpad.co/article/N3c941b76-3ff8-49b6-a56c-740a41f92c9a Extensive knowledge on the genetic characterization of marine organisms has been assembled, mainly concerning the spatial distribution and structuring of populations. Temporal monitoring assesses not only the stability in genetic composition but also its trajectory over time, providing critical information for the accurate forecast of changes in genetic diversity of marine populations, particularly important for both fisheries and endangered species management. We assessed fluctuations in genetic composition among different sampling periods in the western Portuguese shore in three fish species.MethodsWhite seabream Diplodus sargus, sand smelt Atherina presbyter and shanny Lipophrys pholis were chosen, because of their genetic patterns in distinct ecological environments, insight into historical and contemporary factors influencing population effective size (Ne), and degree of commercial exploitation. Samples were obtained near Lisbon between 2003 and 2014 and screened for genetic variation with mitochondrial and nuclear markers. Analyses included genealogies, genetic diversities, temporal structures and contemporary Ne.ResultsFor mtDNA no temporal structure was detected, while for nDNA significant differences were recorded between some sampling periods for the shanny and the sand smelt. Haplotype networks revealed deep genealogies, with various levels of diversification. The shanny revealed a smaller Ne/generation when compared to the other species, which, in turn, revealed no evidence of genetic drift for most study periods. These results highlight the fact that temporal variations in genetic pool composition should be considered when evaluating the population structure of fish species with long distance dispersal, which are more vulnerable to recruitment fluctuations. ]]> <![CDATA[Dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence]]> https://www.researchpad.co/article/Nf925bd92-5f9c-4397-b631-1d827df41b5c

Accurate reconstructions of phylogeny are essential for studying the evolution of a clade, and morphological characters are necessarily used for the reconstruction of the relationships of fossil organisms. However, variation in their evolutionary modes (for example rate variation and character non-independence) not accounted for in analyses may be leading to unreliable phylogenies. A recent study suggested that phylogenetic analyses of mammals may be suffering from a dominance of dental characters, which were shown to have lower phylogenetic signal than osteological characters and produced phylogenies less congruent with molecularly-derived benchmarks. Here we build on this previous work by testing five additional morphological partitions for phylogenetic signal and examining what aspects of dental and other character evolution may be affecting this, by fitting models of discrete character evolution to phylogenies inferred and time calibrated using molecular data. Results indicate that the phylogenetic signal of discrete characters correlate most strongly with rates of evolution, with increased rates driving increased homoplasy. In a dataset covering all Mammalia, dental characters have higher rates of evolution than other partitions. They do not, however, fit a model of independent character evolution any worse than other regions. Primates and marsupials show different patterns to other mammal clades, with dental characters evolving at slower rates and being more heavily integrated (less independent). While the dominance of dental characters in analyses of mammals could be leading to inaccurate phylogenies, the issue is not unique to dental characters and the results are not consistent across datasets. Molecular benchmarks (being entirely independent of the character data) provide a framework for examining each dataset individually to assess the evolution of the characters used.

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<![CDATA[Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice]]> https://www.researchpad.co/article/N1859479f-adf6-472d-b1b5-f88f77b9db88

Most animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes (“minicircles”) are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between nine and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation. Nevertheless, other work indicates a lesser degree of fragmentation (2–3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genus Columbicola (Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling the Columbicola mitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome of Pediculus humanus from shotgun sequencing reads, a species known to have minicircles. Columbicola spp. genomes are highly fragmented into 15–17 minicircles between ∼1,100 and ∼3,100 bp in length, with 1–4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species of Columbicola represent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice.

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<![CDATA[Plastomes of the green algae Hydrodictyon reticulatum and Pediastrum duplex (Sphaeropleales, Chlorophyceae)]]> https://www.researchpad.co/article/5989db5dab0ee8fa60be050c

Background

Comparative studies of chloroplast genomes (plastomes) across the Chlorophyceae are revealing dynamic patterns of size variation, gene content, and genome rearrangements. Phylogenomic analyses are improving resolution of relationships, and uncovering novel lineages as new plastomes continue to be characterized. To gain further insight into the evolution of the chlorophyte plastome and increase the number of representative plastomes for the Sphaeropleales, this study presents two fully sequenced plastomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae), one from Hydrodictyon reticulatum and the other from Pediastrum duplex.

Methods

Genomic DNA from Hydrodictyon reticulatum and Pediastrum duplex was subjected to Illumina paired-end sequencing and the complete plastomes were assembled for each. Plastome size and gene content were characterized and compared with other plastomes from the Sphaeropleales. Homology searches using BLASTX were used to characterize introns and open reading frames (orfs) ≥ 300 bp. A phylogenetic analysis of gene order across the Sphaeropleales was performed.

Results

The plastome of Hydrodictyon reticulatum is 225,641 bp and Pediastrum duplex is 232,554 bp. The plastome structure and gene order of H. reticulatum and P. duplex are more similar to each other than to other members of the Sphaeropleales. Numerous unique open reading frames are found in both plastomes and the plastome of P. duplex contains putative viral protein genes, not found in other Sphaeropleales plastomes. Gene order analyses support the monophyly of the Hydrodictyaceae and their sister relationship to the Neochloridaceae.

Discussion

The complete plastomes of Hydrodictyon reticulatum and Pediastrum duplex, representing the largest of the Sphaeropleales sequenced thus far, once again highlight the variability in size, architecture, gene order and content across the Chlorophyceae. Novel intron insertion sites and unique orfs indicate recent, independent invasions into each plastome, a hypothesis testable with an expanded plastome investigation within the Hydrodictyaceae.

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<![CDATA[The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models]]> https://www.researchpad.co/article/N8f14fcc2-0524-4065-b708-e2a60b264d8d

Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics. Recent analyses of both nuclear and chloroplast genome data of land plants (embryophytes) have, controversially, been shown to support monophyly of both bryophytes (mosses, liverworts, and hornworts) and tracheophytes (lycopods, ferns, and seed plants), with mosses and liverworts forming the clade Setaphyta. However, relationships inferred from mitochondria are incongruent with these results, and typically indicate paraphyly of bryophytes with liverworts alone resolved as the earliest-branching land plant group. Here, we reconstruct the mitochondrial land plant phylogeny from a newly compiled data set. When among-lineage composition heterogeneity is accounted for in analyses of codon-degenerate nucleotide and amino acid data, the clade Setaphyta is recovered with high support, and hornworts are supported as the earliest-branching lineage of land plants. These new mitochondrial analyses demonstrate partial congruence with current hypotheses based on nuclear and chloroplast genome data, and provide further incentive for revision of how plants arose on land.

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<![CDATA[Size matters: micro-evolution in Polynesian rats highlights body size changes as initial stage in evolution]]> https://www.researchpad.co/article/N2dd55868-5849-4fff-8cf7-11bb065f2041

Microevolutionary patterns in populations of introduced rodent species have often been the focus of analytic studies for their potential relevance to understanding vertebrate evolution. The Polynesian rat (Rattus exulans) is an excellent proxy species because of its wide geographic and temporal distribution: its native and introduced combined range spans half the globe and it has been living for at least seven centuries wherever it was introduced. The objective of this study was to assess the effects of long-term isolation (insularity; up to 4,000 years) and geographic variables on skull shape variation using geometric morphometrics. A sample of 513 specimens from 103 islands and four mainland areas was analysed. This study, to my knowledge the first to extensively sample introduced rats, analysed 59 two-dimensional landmarks on the skull. Landmarks were obtained in three separate aspects (dorsal, lateral, ventral skull view). The coordinate data were then subjected to a multivariate ordination analysis (principal components analysis, or PCA), multivariate regressions, and a canonical variates analysis (CVA). Three measures of disparity were evaluated for each view. The results show that introduced Polynesian rats evolve skull shapes that conform to the general mammalian interspecific pattern of cranial evolutionary allometry (CREA), with proportionally longer snouts in larger specimens. In addition, larger skulls are more tubular in shape than the smaller skulls, which are more balloon-shaped with a rounder and wider braincase relative to those of large skulls. This difference is also observed between the sexes (sexual dimorphism), due to the slightly larger average male size. Large, tubular skulls with long snouts are typical for Polynesia and Remote Oceania, where no native mammals occur. The greater disparity of Polynesian rats on mammal species-poor islands (’exulans-only’ region) provides further insight into how diversity may affect diversification through ecological release from predators and competitors.

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<![CDATA[The GAR domain integrates functions that are necessary for the proper localization of fibrillarin (FBL) inside eukaryotic cells]]> https://www.researchpad.co/article/N7b58627b-d58f-4103-8a4f-5386839b85f8

Fibrillarin (FBL) is an essential nucleolar protein that participates in pre-rRNA methylation and processing. The methyltransferase domain of FBL is an example of an extremely well-conserved protein domain in which the amino acid sequence was not substantially modified during the evolution from Archaea to Eukaryota. An additional N-terminal glycine–arginine-rich (GAR) domain is present in the FBL of eukaryotes. Here, we demonstrate that the GAR domain is involved in FBL functioning and integrates the functions of the nuclear localization signal and the nucleolar localization signal (NoLS). The methylation of the arginine residues in the GAR domain is necessary for nuclear import but decreases the efficiency of nucleolar retention via the NoLS. The presented data indicate that the GAR domain can be considered an evolutionary innovation that integrates several functional activities and thereby adapts FBL to the highly compartmentalized content of the eukaryotic cell.

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<![CDATA[Estimating the evolutionary rates in mosasauroids and plesiosaurs: discussion of niche occupation in Late Cretaceous seas]]> https://www.researchpad.co/article/Nb43041e3-0d7b-4b14-b137-bc2977fa6cd1

Observations of temporal overlap of niche occupation among Late Cretaceous marine amniotes suggest that the rise and diversification of mosasauroid squamates might have been influenced by competition with or disappearance of some plesiosaur taxa. We discuss that hypothesis through comparisons of the rates of morphological evolution of mosasauroids throughout their evolutionary history with those inferred for contemporary plesiosaur clades. We used expanded versions of two species-level phylogenetic datasets of both these groups, updated them with stratigraphic information, and analyzed using the Bayesian inference to estimate the rates of divergence for each clade. The oscillations in evolutionary rates of the mosasauroid and plesiosaur lineages that overlapped in time and space were then used as a baseline for discussion and comparisons of traits that can affect the shape of the niche structures of aquatic amniotes, such as tooth morphologies, body size, swimming abilities, metabolism, and reproduction. Only two groups of plesiosaurs are considered to be possible niche competitors of mosasauroids: the brachauchenine pliosaurids and the polycotylid leptocleidians. However, direct evidence for interactions between mosasauroids and plesiosaurs is scarce and limited only to large mosasauroids as the predators/scavengers and polycotylids as their prey. The first mosasauroids differed from contemporary plesiosaurs in certain aspects of all discussed traits and no evidence suggests that early representatives of Mosasauroidea diversified after competitions with plesiosaurs. Nevertheless, some mosasauroids, such as tylosaurines, might have seized the opportunity and occupied the niche previously inhabited by brachauchenines, around or immediately after they became extinct, and by polycotylids that decreased their phylogenetic diversity and disparity around the time the large-sized tylosaurines started to flourish.

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<![CDATA[Intraspecific variation in the cochleae of harbour porpoises (Phocoena phocoena) and its implications for comparative studies across odontocetes]]> https://www.researchpad.co/article/Nc373f22c-a1da-404f-a8f7-c6cf6a14d889

In morphological traits, variation within species is generally considered to be lower than variation among species, although this assumption is rarely tested. This is particularly important in fields like palaeontology, where it is common to use a single individual as representative of a species due to the rarity of fossils. Here, we investigated intraspecific variation in the cochleae of harbour porpoises (Phocoena phocoena). Interspecific variation of cochlear morphology is well characterised among odontocetes (toothed whales) because of the importance of the structure in echolocation, but generally these studies use only a single cochlea to represent each species. In this study we compare variation within the cochleae of 18 specimens of P. phocoena with variations in cochlear morphology across 51 other odontocete species. Using both 3D landmark and linear measurement data, we performed Generalised Procrustes and principal component analyses to quantify shape variation. We then quantified intraspecific variation in our sample of P. phocoena by estimating disparity and the coefficient of variation for our 3D and linear data respectively. Finally, to determine whether intraspecific variation may confound the results of studies of interspecific variation, we used multivariate and univariate analyses of variance to test whether variation within the specimens of P. phocoena was significantly lower than that across odontocetes. We found low levels of intraspecific variation in the cochleae of P. phocoena, and that cochlear shape within P. phocoena was significantly less variable than across odontocetes. Although future studies should attempt to use multiple cochleae for every species, our results suggest that using just one cochlea for each species should not strongly influence the conclusions of comparative studies if our results are consistent across Cetacea.

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<![CDATA[Temporal changes in the most effective pollinator of a bromeliad pollinated by bees and hummingbirds]]> https://www.researchpad.co/article/N12b518a3-59ac-4f63-b5f2-4beafdf115e9

A generalist pollination system may be characterized through the interaction of a plant species with two or more functional groups of pollinators. The spatiotemporal variation of the most effective pollinator is the factor most frequently advocated to explain the emergence and maintenance of generalist pollination systems. There are few studies merging variation in floral visitor assemblages and the efficacy of pollination by different functional groups. Thus, there are gaps in our knowledge about the variation in time of pollinator efficacy and frequency of generalist species. In this study, we evaluated the pollination efficacy of the floral visitors of Edmundoa lindenii (Bromeliaceae) and their frequency of visits across four reproductive events. We analyzed the frequency of the three groups of floral visitors (large bees, small bees, and hummingbirds) through focal observations in the reproductive events of 2015, 2016, 2017, and 2018. We evaluated the pollination efficacy (fecundity after one visit) through selective exposure treatments and the breeding system by manual pollinations. We tested if the reproductive success after natural pollination varied between the reproductive events and also calculated the pollen limitation index. E. lindenii is a self-incompatible and parthenocarpic species, requiring the action of pollinators for sexual reproduction. Hummingbirds had higher efficacy than large bees and small bees acted only as pollen larcenists. The relative frequency of the groups of floral visitors varied between the reproductive events. Pollen limitation has occurred only in the reproductive event of 2017, when visits by hummingbirds were scarce and reproductive success after natural pollination was the lowest. We conclude that hummingbirds and large bees were the main and the secondary pollinators of E. lindenii, respectively, and that temporal variations in the pollinator assemblages had effects on its reproductive success. Despite their lower pollination efficacy, large bees ensured seed set when hummingbirds failed. Thus, we provide evidence that variable pollination environments may favor generalization, even under differential effectiveness of pollinator groups if secondary pollinators provide reproductive assurance.

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<![CDATA[Masticatory musculature of the African mole-rats (Rodentia: Bathyergidae)]]> https://www.researchpad.co/article/N373b2037-1497-437f-abb5-970b008345b0

The Bathyergidae, commonly known as blesmols or African mole-rats, is a family of rodents well-known for their subterranean lifestyle and tunnelling behaviour. Four of the five extant bathyergid genera (Cryptomys, Fukomys, Georychus and Heliophobius) are chisel-tooth diggers, that is they dig through soil with their enlarged incisors, whereas the remaining genus (Bathyergus) is a scratch-digger, only using its forelimbs for burrowing. Heterocephalus glaber, the naked mole-rat, is also a chisel-tooth digger and was until recently included within the Bathyergidae (as the most basally branching genus), but has now been placed by some researchers into its own family, the Heterocephalidae. Given the importance of the masticatory apparatus in habitat construction in this group, knowledge and understanding of the morphology and arrangement of the jaw-closing muscles in Bathyergidae is vital for future functional analyses. Here, we use diffusible iodine-based contrast-enhanced microCT to reveal and describe the muscles of mastication in representative specimens of each genus of bathyergid mole-rat and to compare them to the previously described musculature of the naked mole-rat. In all bathyergids, as in all rodents, the masseter muscle is the most dominant component of the masticatory musculature. However, the temporalis is also a relatively large muscle, a condition normally associated with sciuromorphous rodents. Unlike their hystricomorphous relatives, the bathyergids do not show an extension of the masseter through the infraorbital foramen on to the rostrum (other than a very slight protrusion in Cryptomys and Fukomys). Thus, morphologically, bathyergids are protrogomorphous, although this is thought to be secondarily derived rather than retained from ancestral rodents. Overall, the relative proportions of the jaw-closing muscles were found to be fairly consistent between genera except in Bathyergus, which was found to have an enlarged superficial masseter and relatively smaller pterygoid muscles. It is concluded that these differences may be a reflection of the behaviour of Bathyergus which, uniquely in the family, does not use its incisors for digging.

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<![CDATA[Miconia lucenae (Melastomataceae), a new species from montane Atlantic Forest in Espírito Santo, Brazil]]> https://www.researchpad.co/article/N7d672d70-165f-4fea-a22b-86d1d005f675

We describe Miconia lucenae R.Goldenb. & Michelang., a new species from the montane Atlantic Forest in Santa Teresa in the state of Espírito Santo. Our analysis, based on three plastid spacers (atpF-atpH, psbK-psbl and trnS-trnG), one plastid gene (ndhF, not available for M. lucenae), and two nuclear ribosomal loci (nrITS and nrETS), showed that it belongs to a small clade with Miconia paradoxa (Mart. ex DC.) Triana (Minas Gerais) and M. michelangeliana R.Goldenb. & L.Kollmann (Espírito Santo). The three species in the “Paradoxa clade” can be recognized by the plants with glabrous or glabrescent branches and leaves, white petals and yellow stamens, these with the connectives not prolonged below the thecae, ventrally unappendaged, dorsally unappendaged or with a minute tooth, the latter bilobed or not, glabrous ovary, and the fruits with a persistent calyx. Miconia lucenae can be recognized, among the species in this clade, by the shrubby plants with terete young branches, short inflorescences, usually with red axes, and the 2-bracteolate, sessile, 4-merous flowers, with a ciliolate inner portion of the sepals, lanceolate petals, and 4-celled ovaries. This species can be considered as endangered according to IUCN criteria.

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<![CDATA[Alternative splicing and thermosensitive expression of Dmrt1 during urogenital development in the painted turtle, Chrysemys picta]]> https://www.researchpad.co/article/Ne4a490eb-6b94-4eef-b56e-0ca83edfa95f

Background

The doublesex and mab-3 related transcription factor 1 (Dmrt1) is a highly conserved gene across numerous vertebrates and invertebrates in sequence and function. Small aminoacid changes in Dmrt1 are associated with turnovers in sex determination in reptiles. Dmrt1 is upregulated in males during gonadal development in many species, including the painted turtle, Chrysemys picta, a reptile with temperature-dependent sex determination (TSD). Dmrt1 is reported to play different roles during sex determination and differentiation, yet whether these functions are controlled by distinct Dmrt1 spliceoforms remains unclear. While Dmrt1 isoforms have been characterized in various vertebrates, no study has investigated their existence in any turtle.

Methods

We examine the painted turtle to identify novel Dmrt1 isoforms that may be present during urogenital development using PCR, profile their expression by RNA-seq across five embryonic stages at male- and female-producing temperatures, and validate their expression pattern via qPCR with transcript-specific fluorescent probes.

Results

A novel Dmrt1 spliceoform was discovered for the first time in chelonians, lacking exons 2 and 3 (Dmrt1 ΔEx2Ex3). Dmrt1 canonical and ΔEx2Ex3 transcripts were differentialy expressed by temperature at stages 19 and 22 in developing gonads of painted turtles, after the onset of sex determination, and displayed a significant male-biased expression pattern. This transcriptional pattern differs from studies in other turtles and vertebrates that reported Dmrt1 differential expression before or at the onset of sex determination. This study provides the first insight into Dmrt1 transcriptional diversity in turtles and opens the door for future functional studies of the alternative Dmrt1 transcript uncovered here.

Conclusions

The discovery of an isoform in turtles indicate that alternative splicing may be a common feature of Dmrt1 across vertebrates, as isoforms are also found in crocodilians, birds, mammals and fish, and this variation remains unexplained. The relatively late-onset of Dmrt1 expression observed here contrasts with other turtles, indicating that Dmrt1 is not the topmost male sex -determining factor in C. picta. When placed in a phylogenetic context, this discrepancy underscores the divergent regulation of Dmrt1, and of sexual development more generally, across vertebrates.

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<![CDATA[Acoustic divergence in advertisement calls among three sympatric Microhyla species from East China]]> https://www.researchpad.co/article/Na4947a90-ee42-4dde-bbbf-c3a0e5e8d10b

Background

Species-specific advertisement calls are the main mechanism of transmitting information between individuals in anuran amphibians and are therefore indispensable for anuran survival and reproduction. Survey methods that monitor these calls can be used for rapid species recognition, behavioral experiments, and conservation monitoring. In this study, we described in detail 10 call parameters from three sympatric species in the genus Microhyla and analyzed the differences in call parameter among these species to provide a basis for systematic monitoring, acoustic analysis and taxonomic study of this genus.

Methods

The quantitative analyses of temporal and spectral call parameters were used in our study for the advertisement calls of three sympatric Microhyla species (M. beilunensis, M. fissipes and M. heymonsi) in Zhejiang Province, East China.

Results

Our results showed the following: (1) Significant differences existed among the three sympatric Microhyla species in call duration (CD), call interval (CI), number of pulses (NP), pulse rate, call intensity (CIT), dominant frequency (DF) and frequency of the first to fourth formants (F1, F2, F3 and F4). (2) Some spectral parameters (DF, F1 and F3) were negatively correlated with the body size of the vocalizing individuals in each species. (3) The coefficients of variation within individuals (CVw) for CIT, DF and F1–F4 were smaller than 5%, whereas the CVW for CI was larger than 10% in each species. (4) The principal component analysis and discriminant function analysis showed that call parameters could distinguish the three Microhyla species. (5) The phylogenetic generalized least squares analysis showed that phylogenetic relationships affected CD and NP against snout-vent length (SVL), DF and NP against CD, and NP against DF, but not of DF against SVL; based on the phylogenetic analysis, CD and NP were not related to SVL, but DF was negatively related to SVL.

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<![CDATA[Co-expression clustering across flower development identifies modules for diverse floral forms in Achimenes (Gesneriaceae)]]> https://www.researchpad.co/article/Nd3c840b0-b57b-490a-865f-a1cd159f3a43

Background

Genetic pathways involved with flower color and shape are thought to play an important role in the development of flowers associated with different pollination syndromes, such as those associated with bee, butterfly, or hummingbird pollination. Because pollination syndromes are complex traits that are orchestrated by multiple genes and pathways, the gene regulatory networks have not been explored. Gene co-expression networks provide a systems level approach to identify important contributors to floral diversification.

Methods

RNA-sequencing was used to assay gene expression across two stages of flower development (an early bud and an intermediate stage) in 10 species of Achimenes (Gesneriaceae). Two stage-specific co-expression networks were created from 9,503 orthologs and analyzed to identify module hubs and the network periphery. Module association with bee, butterfly, and hummingbird pollination syndromes was tested using phylogenetic mixed models. The relationship between network connectivity and evolutionary rates (dN/dS) was tested using linear models.

Results

Networks contained 65 and 62 modules that were largely preserved between developmental stages and contained few stage-specific modules. Over a third of the modules in both networks were associated with flower color, shape, and pollination syndrome. Within these modules, several hub nodes were identified that related to the production of anthocyanin and carotenoid pigments and the development of flower shape. Evolutionary rates were decreased in highly connected genes and elevated in peripheral genes.

Discussion

This study aids in the understanding of the genetic architecture and network properties underlying the development of floral form and provides valuable candidate modules and genes for future studies.

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<![CDATA[Congenital feeding response to a novel prey in a Mexican gartersnake]]> https://www.researchpad.co/article/N44631003-18fb-419d-a8f5-3be852c12ef8

In this study, we explored chemosensory, ingestive and prey-catching responses of neonate Mexican Black-bellied Gartersnakes (Thamnophis melanogaster) to crayfish (Cambarellus montezumae). By comparing snakes from a recently discovered crayfish-eating population and a typical non-crayfish-eating population, we asked which behavioral components change as a species enlarges its feeding niche. In the crayfish-eating population chemosensory responsiveness to crayfish was not enhanced but its heritability was higher. Neonates of both populations showed similar preference for freshly-molted versus unmolted crayfish, and whereas the tendency to ingest both crayfish stages remained stable between ages 15 and 90 days in the non-crayfish-eating population, in the crayfish-eating population it actually decreased. Techniques to catch and manipulate molted crayfish were similar in the two populations. We discuss the possibility that there is no increase in the behavioral response to eat crayfish by the neonates of the crayfish-eating populations, possibly due to the absence of ecological and spatial isolation between the two T. melanogaster populations. The crayfish ingestion in some population of T. melanogaster can be explained by environmental differences between populations, or by recent origin of crayfish ingestion in T. melanogaster.

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<![CDATA[Recent advances on the estimation of the thermal reaction norm for sex ratios]]> https://www.researchpad.co/article/N8b02a14e-f059-4239-8077-c15cfe738bca

Temperature-dependent sex determination, or TSD, is a widespread phenomenon in reptiles. The shape of the relationship between constant incubation temperature and sex ratio defines the TSD pattern. The TSD pattern is considered a life-history parameter important for conservation because the wider the range of temperatures producing both sexes, the more resilient the species is to climate change impacts. We review the different published equations and methodologies that have been used to model TSD patterns. We describe a new flexible model that allows for an asymmetrical pattern around the pivotal temperature, which is the constant temperature producing both sexes in equal proportions. We show that Metropolis-Hastings with Markov chain produced by a Monte Carlo process has many advantages compared to maximum likelihood and is preferred. Finally, we apply the models to results from incubation experiments using eggs from the marine turtle Lepidochelys olivacea originating in Northeast Indian, East Pacific, and West Atlantic Regional Management Units (RMUs) and find large differences in pivotal temperatures but not in transitional ranges of temperatures.

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<![CDATA[The body plan of Halszkaraptor escuilliei (Dinosauria, Theropoda) is not a transitional form along the evolution of dromaeosaurid hypercarnivory]]> https://www.researchpad.co/article/N432dbd97-a628-42db-9154-776e4dbadb83

The dromaeosaurid theropod Halszkaraptor escuilliei is characterized by several unusual features absent in other paravians, part of which has been interpreted as diagnostic of a novel lineage adapted to a semiaquatic ecology. Recently, these evolutionary and ecological interpretations have been challenged, and Halszkaraptor has been claimed to be a transitional form between non-dromaeosaurid maniraptoriforms and other dromaeosaurids: following that reevaluation, its peculiar body plan would represent the retention of several maniraptoran plesiomorphies, lost among other dromaeosaurids, and not an adaptation to a novel ecology. This alternative scenario is here carefully investigated and tested. It is shown that most statements supporting this scenario are based on misinterpretation of anatomical traits and bibliography. Once these statements have been corrected, character state transition optimization over a well-supported phylogenetic framework indicates that the large majority of the peculiar features of the Halszkaraptor lineage are derived novelties acquired by the latter after its divergence from the last ancestor shared with eudromaeosaurs, and thus are not maniraptoriform plesiomorphies. At least seven novelties of the Halszkaraptor lineage are convergently acquired with spinosaurids, and are integrated in semiaquatic adaptations: one of these is reported here for the first time. The amount of morphological divergence of Halszkaraptorinae from the ancestral dromaeosaurid condition is comparable to those of Microraptorinae and Velociraptorinae. Among extant taxa, the sawbills (Mergini, Anseriformes) show the closest ecomorphological similarity with the peculiar body plan inferred for Halszkaraptor. The halszkaraptorine bauplan is thus confirmed as a derived amphibious specialization, and does not represent a “transitional” stage along the evolution of dromaeosaurids.

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