Browsing by Subject "SPECIATION"

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  • Byers, Kelsey J. R. P.; Darragh, Kathy; Musgrove, Jamie; Abondano Almeida, Diana; Fernanda Garza, Sylvia; Warren, Ian A.; Rastas, Pasi M.; Kucka, Marek; Chan, Yingguang Frank; Merrill, Richard M.; Schulz, Stefan; Owen McMillan, W.; Jiggins, Chris D. (2020)
    Understanding the production, response, and genetics of signals used in mate choice can inform our understanding of the evolution of both intraspecific mate choice and reproductive isolation. Sex pheromones are important for courtship and mate choice in many insects, but we know relatively little of their role in butterflies. The butterfly Heliconius melpomene uses a complex blend of wing androconial compounds during courtship. Electroantennography in H. melpomene and its close relative Heliconius cydno showed that responses to androconial extracts were not species specific. Females of both species responded equally strongly to extracts of both species, suggesting conservation of peripheral nervous system elements across the two species. Individual blend components provoked little to no response, with the exception of octadecanal, a major component of the H. melpomene blend. Supplementing octadecanal on the wings of octadecanal-rich H. melpomene males led to an increase in the time until mating, demonstrating the bioactivity of octadecanal in Heliconius. Using quantitative trait locus (QTL) mapping, we identified a single locus on chromosome 20 responsible for 41% of the parental species' difference in octadecanal production. This QTL does not overlap with any of the major wing color or mate choice loci, nor does it overlap with known regions of elevated or reduced F-ST. A set of 16 candidate fatty acid biosynthesis genes lies underneath the QTL. Pheromones in Heliconius carry information relevant for mate choice and are under simple genetic control, suggesting they could be important during speciation.
  • Li, Xiaodong; Meng, Shuo; Puhakka, Eini; Ikonen, Jussi; Liu, Longcheng; Siitari-Kauppi, Marja (2020)
    To determine the diffusion and sorption properties of radionuclides in intact crystalline rocks, a new electromigration device was built and tested by running with I- and Se(IV) ions. By introducing a potentiostat to impose a constant voltage over the studied rock sample, the electromigration device can give more stable and accurate experimental results than those from the traditional electromigration devices. In addition, the variation in the pH of the background electrolytes was minimised by adding a small amount of NaHCO3 as buffers. To interpret the experimental results with more confidence, an advection-dispersion model was also developed in this study, which accounts for the most important mechanisms governing ionic transport in the electromigration experiments. Data analysis of the breakthrough curves by the advection-dispersion model, instead of the traditional ideal plug-flow model, suggest that the effective diffusivities of I- and Se(IV) are (1.15 +/- 0.06) x 10(-13) m(2)/s and (3.50 +/- 0.86) x 10(-14) m(2)/s, respectively. The results also show that I- is more mobile than Se(IV) ions when migrating through the same intact rock sample and that their sorption properties are almost identical.
  • Zhang, Yanjun; Peräkylä, Otso; Yan, Chao; Heikkinen, Liine; Äijälä, Mikko; Dällenbach, Kaspar; Zha, Qiaozhi; Riva, Matthieu; Garmash, Olga; Junninen, Heikki; Paatero, Pentti; Worsnop, Douglas; Ehn, Mikael (2019)
    Recent advancements in atmospheric mass spectrometry provide huge amounts of new information but at the same time present considerable challenges for the data analysts. High-resolution (HR) peak identification and separation can be effort- and time-consuming yet still tricky and inaccurate due to the complexity of overlapping peaks, especially at larger mass-to-charge ratios. This study presents a simple and novel method, mass spectral binning combined with positive matrix factorization (binPMF), to address these problems. Different from unit mass resolution (UMR) analysis or HR peak fitting, which represent the routine data analysis approaches for mass spectrometry datasets, binPMF divides the mass spectra into small bins and takes advantage of the positive matrix factorization's (PMF) strength in separating different sources or processes based on different temporal patterns. In this study, we applied the novel approach to both ambient and synthetic datasets to evaluate its performance. It not only succeeded in separating overlapping ions but was found to be sensitive to subtle variations as well. Being fast and reliable, binPMF has no requirement for a priori peak information and can save much time and effort from conventional HR peak fitting, while still utilizing nearly the full potential of HR mass spectra. In addition, we identify several future improvements and applications for binPMF and believe it will become a powerful approach in the data analysis of mass spectra.
  • Kilpi-Koski, Johanna; Penttinen, Olli-Pekka; Väisänen, Ari O.; van Gestel, Cornelis A. M. (2019)
    The aim of this study was to determine the bioavailability of metals in field soils contaminated with chromated copper arsenate (CCA) mixtures. The uptake and elimination kinetics of chromium, copper, and arsenic were assessed in the earthworm Eisenia andrei exposed to soils from a gradient of CCA wood preservative contamination near Hartola, Finland. In soils contaminated with 1480–1590 mg Cr/kg dry soil, 642–791 mg Cu/kg dry soil, and 850–2810 mg Ag/kg dry soil, uptake and elimination kinetics patterns were similar for Cr and Cu. Both metals were rapidly taken up and rapidly excreted by Eisenia andrei with equilibrium reached within 1 day. The metalloid As, however, showed very slow uptake and elimination in the earthworms and body concentrations did not reach equilibrium within 21 days. Bioaccumulation factors (BAF) were low for Cu and Cr (
  • Sampaio, Larissa; Ferraz, Dnilson Oliveira; Moreira da Costa, Ana Carolina; Aleixo, Alexandre; Cerqueira, Pablo Vieira; Araripe, Juliana; do Rego, Pericles Sena (2020)
    The present study aimed to confirm the occurrence of a hybridization event between the band-tailed manakin (Pipra fasciicauda) and the crimson-hooded manakin (Pipra aureola), based on the existence of a specimen that presents morphological traits of both taxa. We analyzed 297 taxidermized skins of adult males of the two species, including the potential hybrid. We also analyzed the mitochondrial (ND2, ND3 e COI) and nuclear (FGB-I5, MB-I2 e GAPDH-I3) genes of 12 adult specimens of the two taxa, diagnosed phenotypically, in addition to the potential hybrid. The analyses of the plumage indicated that the potential hybrid has an intermediate pattern of white banding on the tail that is less extensive than that found in Pipra fasciicauda, but that its other phenotypic traits are characteristic of Pipra aureola. The molecular topologies revealed two clades, one that groups P. aureola together with the potential hybrid, and the other that corresponds to P. fasciicauda. These findings allowed us to confirm the occurrence of a process of hybridization and potential introgression through secondary events in the P. aureola lineage.
  • Ribas, Talita Fernanda Augusto; Pieczarka, Julio Cesar; Griffin, Darren K.; Kiazim, Lucas G.; Nagamachi, Cleusa Yoshiko; O' Brien, Patricia Caroline Mary; Ferguson-Smith, Malcolm Andrew; Yang, Fengtang; Aleixo, Alexandre; O'Connor, Rebecca E. (2021)
    Background Thamnophilidae birds are the result of a monophyletic radiation of insectivorous Passeriformes. They are a diverse group of 225 species and 45 genera and occur in lowlands and lower montane forests of Neotropics. Despite the large degree of diversity seen in this family, just four species of Thamnophilidae have been karyotyped with a diploid number ranging from 76 to 82 chromosomes. The karyotypic relationships within and between Thamnophilidae and another Passeriformes therefore remain poorly understood. Recent studies have identified the occurrence of intrachromosomal rearrangements in Passeriformes using in silico data and molecular cytogenetic tools. These results demonstrate that intrachromosomal rearrangements are more common in birds than previously thought and are likely to contribute to speciation events. With this in mind, we investigate the apparently conserved karyotype of Willisornis vidua, the Xingu Scale-backed Antbird, using a combination of molecular cytogenetic techniques including chromosome painting with probes derived from Gallus gallus (chicken) and Burhinus oedicnemus (stone curlew), combined with Bacterial Artificial Chromosome (BAC) probes derived from the same species. The goal was to investigate the occurrence of rearrangements in an apparently conserved karyotype in order to understand the evolutionary history and taxonomy of this species. In total, 78 BAC probes from the Gallus gallus and Taeniopygia guttata (the Zebra Finch) BAC libraries were tested, of which 40 were derived from Gallus gallus macrochromosomes 1-8, and 38 from microchromosomes 9-28. Results The karyotype is similar to typical Passeriformes karyotypes, with a diploid number of 2n = 80. Our chromosome painting results show that most of the Gallus gallus chromosomes are conserved, except GGA-1, 2 and 4, with some rearrangements identified among macro- and microchromosomes. BAC mapping revealed many intrachromosomal rearrangements, mainly inversions, when comparing Willisornis vidua karyotype with Gallus gallus, and corroborates the fissions revealed by chromosome painting. Conclusions Willisornis vidua presents multiple chromosomal rearrangements despite having a supposed conservative karyotype, demonstrating that our approach using a combination of FISH tools provides a higher resolution than previously obtained by chromosome painting alone. We also show that populations of Willisornis vidua appear conserved from a cytogenetic perspective, despite significant phylogeographic structure.
  • Momigliano, Paolo; Florin, Ann-Britt; Merilä, Juha (2021)
    Testing among competing demographic models of divergence has become an important component of evolutionary research in model and non-model organisms. However, the effect of unaccounted demographic events on model choice and parameter estimation remains largely unexplored. Using extensive simulations, we demonstrate that under realistic divergence scenarios, failure to account for population size (N-e) changes in daughter and ancestral populations leads to strong biases in divergence time estimates as well as model choice. We illustrate these issues reconstructing the recent demographic history of North Sea and Baltic Sea turbots (Scophthalmus maximus) by testing 16 isolation with migration (IM) and 16 secondary contact (SC) scenarios, modeling changes in N-e as well as the effects of linked selection and barrier loci. Failure to account for changes in N-e resulted in selecting SC models with long periods of strict isolation and divergence times preceding the formation of the Baltic Sea. In contrast, models accounting for N-e changes suggest recent (
  • Savriama, Yoland; Valtonen, Mia; Kammonen, Juhana I.; Rastas, Pasi; Smolander, Olli-Pekka; Lyyski, Annina; Häkkinen, Teemu J.; Corfe, Ian J.; Gerber, Sylvain; Salazar-Ciudad, Isaac; Paulin, Lars; Holm, Liisa; Löytynoja, Ari; Auvinen, Petri; Jernvall, Jukka (2018)
    An increasing number of mammalian species have been shown to have a history of hybridization and introgression based on genetic analyses. Only relatively few fossils, however, preserve genetic material, and morphology must be used to identify the species and determine whether morphologically intermediate fossils could represent hybrids. Because dental and cranial fossils are typically the key body parts studied in mammalian palaeontology, here we bracket the potential for phenotypically extreme hybridizations by examining uniquely preserved cranio-dental material of a captive hybrid between grey and ringed seals. We analysed how distinct these species are genetically and morphologically, how easy it is to identify the hybrids using morphology and whether comparable hybridizations happen in the wild. We show that the genetic distance between these species is more than twice the modern human–Neanderthal distance, but still within that of morphologically similar species pairs known to hybridize. By contrast, morphological and developmental analyses show grey and ringed seals to be highly disparate, and that the hybrid is a predictable intermediate. Genetic analyses of the parent populations reveal introgression in the wild, suggesting that grey–ringed seal hybridization is not limited to captivity. Taken together, we postulate that there is considerable potential for mammalian hybridization between phenotypically disparate taxa.
  • Rasmussen, Christian M. Ø.; Kröger, Björn; Nielsen, Morten L.; Colmenar, Jorge (2019)
    The greatest relative changes in marine biodiversity accumulation occurred during the Early Paleozoic. The precision of temporal constraints on these changes is crude, hampering our understanding of their timing, duration, and links to causal mechanisms. We match fossil occurrence data to their lithostratigraphical ranges in the Paleobiology Database and correlate this inferred taxon range to a constructed set of biostratigraphically defined high-resolution time slices. In addition, we apply capture-recapture modeling approaches to calculate a biodiversity curve that also considers taphonomy and sampling biases with four times better resolution of previous estimates. Our method reveals a stepwise biodiversity increase with distinct Cambrian and Ordovician radiation events that are clearly separated by a 50-million-year-long period of slow biodiversity accumulation. The Ordovician Radiation is confined to a 15-million-year phase after which the Late Ordovician extinctions lowered generic richness and further delayed a biodiversity rebound by at least 35 million years. Based on a first-differences approach on potential abiotic drivers controlling richness, we find an overall correlation with oxygen levels, with temperature also exhibiting a coordinated trend once equatorial sea surface temperatures fell to present-day levels during the Middle Ordovician Darriwilian Age. Contrary to the traditional view of the Late Ordovician extinctions, our study suggests a protracted crisis interval linked to intense volcanism during the middle Late Ordovician Katian Age. As richness levels did not return to prior levels during the Silurian-a time of continental amalgamation-we further argue that plate tectonics exerted an overarching control on biodiversity accumulation.
  • Sirkiä, Päivi M.; McFarlane, S. Eryn; Jones, William; Wheatcroft, David; Ålund, Murielle; Rybinski, Jakub; Qvarnstrom, Anna (2018)
    Divergence in the onset of reproduction can act as an important source of reproductive isolation (i.e., allochronic isolation) between co-occurring young species, but evidence for the evolutionary processes leading to such divergence is often indirect. While advancing spring seasons strongly affect the onset of reproduction in many taxa, it remains largely unexplored whether contemporary spring advancement directly affects allochronic isolation between young species. We examined how increasing spring temperatures affected onset of reproduction and thereby hybridization between pied and collared flycatchers (Ficedula spp.) across habitat types in a young secondary contact zone. We found that both species have advanced their timing of breeding in 14 years. However, selection on pied flycatchers to breed earlier was weaker, resulting in a slower response to advancing springs compared to collared flycatchers and thereby build-up of allochronic isolation between the species. We argue that a preadaptation to a broader niche use (diet) of pied flycatchers explains the slower response to raising spring temperature, but that reduced risk to hybridize may contribute to further divergence in the onset of breeding in the future. Our results show that minor differences in the response to environmental change of co-occurring closely related species can quickly cause allochronic isolation.
  • Sheppard, Samuel K.; Cheng, Lu; Meric, Guillaume; De Haan, Caroline P. A.; Llarena, Ann-Katrin; Marttinen, Pekka; Vidal, Ana; Ridley, Anne; Clifton-Hadley, Felicity; Connor, Thomas R.; Strachan, Norval J. C.; Forbes, Ken; Colles, Frances M.; Jolley, Keith A.; Bentley, Stephen D.; Maiden, Martin C. J.; Hänninen, Marja-Liisa; Parkhill, Julian; Hanage, William P.; Corander, Jukka (2014)
  • Berner, Daniel; Roesti, Marius; Bilobram, Steven; Chan, Simon K.; Kirk, Heather; Pandoh, Pawan; Taylor, Gregory A.; Zhao, Yongjun; Jones, Steven J. M.; DeFaveri, Jacquelin (2019)
    The threespine stickleback is a geographically widespread and ecologically highly diverse fish that has emerged as a powerful model system for evolutionary genomics and developmental biology. Investigations in this species currently rely on a single high-quality reference genome, but would benefit from the availability of additional, independently sequenced and assembled genomes. We present here the assembly of four new stickleback genomes, based on the sequencing of microfluidic partitioned DNA libraries. The base pair lengths of the four genomes reach 92-101% of the standard reference genome length. Together with their de novo gene annotation, these assemblies offer a resource enhancing genomic investigations in stickleback. The genomes and their annotations are available from the Dryad Digital Repository (
  • Acanski, Jelena; Vujic, Ante; Djan, Mihajla; Obreht Vidakovic, Dragana; Ståhls, Gunilla; Radenkovic, Snezana (2016)
    Several recent studies have detected and described complexes of cryptic and sibling species in the genus Merodon (Diptera, Syrphidae). One representative of these complexes is the Merodon avidus complex that contains four sibling species, which have proven difficult to distinguish using traditional morphological characters. In the present study, we use two geometric morphometric approaches, as well as molecular characters of the 5' -end of the mtDNA COI gene, to delimit sibling taxa. Analyses based on these data were used to strengthen species boundaries within the complex, and to validate the status of a previously-recognized cryptic taxon from Lesvos Island (Greece), here described as Merodon megavidus Vujic & Radenkovic sp. nov. Geometric morphometric results of both wing and surstylus shape confirm the present classification for three sibling species-M. avidus (Rossi, 1790), M. moenium Wiedemann in Meigen, 1822 and M. ibericus Vujic, 2015-and, importantly, clearly discriminate the newly-described taxon Merodon megavidus sp. nov. In addition to our geometric morphometric results, supporting characters were obtained from molecular analyses of mtDNA COI sequences, which clearly differentiated M. megavidus sp. nov. from the other members of the M. avidus complex. Molecular analyses revealed that the earliest divergence of M. ibericus occurred around 800 ky BP, while the most recent separation happened between M. avidus and M. moenium around 87 ky BP.
  • Marttinen, Pekka; Hanage, William P.; Croucher, Nicholas J.; Connor, Thomas R.; Harris, Simon R.; Bentley, Stephen D.; Corander, Jukka (2012)
  • Schultz, Eduardo D.; Pérez-Emán, Jorge; Aleixo, Alexandre; Miyaki, Cristina Y.; Brumfield, Robb T.; Cracraft, Joel; Ribas, Camila C. (2019)
    Dendrocincla woodcreepers are ant-following birds widespread throughout tropical America. Species in the genus are widely distributed and show little phenotypic variation. Notwithstanding, several subspecies have been described, but the validity of some of these taxa and the boundaries among them have been discussed for decades. Recent genetic evidence based on limited sampling has pointed to the paraphyly of D. fuliginosa, showing that its subspecies constitute a complex that also includes D. anabatina and D. turdina. In this study we sequenced nuclear and mitochondrial markers for over two hundred individuals belonging to the D. fuliginosa complex to recover phylogenetic relationships, describe intraspecific genetic diversity and provide historical biogeographic scenarios of diversification. Our results corroborate the paraphyly of D. fuliginosa, with D. turdina and D. anabatina nested within its recognized subspecies. Recovered genetic lineages roughly match the distributions of described subspecies and congruence among phylogenetic structure, phenotypic diagnosis and distribution limits were used to discuss current systematics and taxonomy within the complex, with special attention to Northern South America. Our data suggest the origin of the complex in western Amazonia, associated with the establishment of upland forests in the area during the early Pliocene. Paleoclimatic cycles and river rearrangements during the Pleistocene could have, at different times, both facilitated dispersal across large Amazonian rivers and the Andes and isolated populations, likely playing an important role in differentiation of extant species. Previously described hybridization in the headwaters of the Tapajós river represents a secondary contact of non-sister lineages that cannot be used to test the role of the river as primary source of diversification. Based on comparisons of D. fuliginosa with closely related understory upland forest taxa, we suggest that differential habitat use could influence diversification processes in a historically changing landscape, and should be considered for proposing general mechanisms of diversification.
  • Ribas, Camila C.; Aleixo, Alexandre (2019)
    Amazonia has been a focus of interest since the early days of biogeography as an intrinsically complex and extremely diverse region. This region comprises an intricate mosaic that includes diverse types of forest formations, flooded environments and open vegetation. Increased knowledge about the distribution of species in Amazonia has led to the recognition of complex biogeographic patterns. The confrontation of these biogeographic patterns with information on the geological and climatic history of the region has generated several hypotheses dedicated to explain the origin of the biological diversity. Genomic information, coupled with knowledge of Earth's history, especially the evolution of the Amazonian landscape. presents fascinating possibilities for understanding the mechanisms that govern the origin and maintenance of diversity patterns in one of the most diverse regions of the world. For this we will increasingly need more intense and coordinated interactions between researchers studying biotic diversification and the evolution of landscapes. From the interaction between these two fields of knowledge that are in full development, an increasingly detailed understanding of the historical mechanisms related to the origin of the species will surely arise.
  • Kekkonen, Mari; Hebert, Paul D. N. (2014)
    The analysis of DNA barcode sequences with varying techniques for cluster recognition provides an efficient approach for recognizing putative species (operational taxonomic units, OTUs). This approach accelerates and improves taxonomic workflows by exposing cryptic species and decreasing the risk of synonymy. This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths. OTUs supported by all three approaches were viewed as robust, but 20% of the OTUs were only recognized by one or two of the methods. These OTUs were examined for three criteria to clarify their status. Monophyly and diagnostic nucleotides were both uninformative, but information on ranges was useful as sympatric sister OTUs were viewed as distinct, while allopatric OTUs were merged. This approach revealed 124 OTUs of Hypertrophinae, a more than twofold increase from the currently recognized 51 species. Because this analytical protocol is both fast and repeatable, it provides a valuable tool for establishing a basic understanding of species boundaries that can be validated with subsequent studies.
  • Pulido-Santacruz, Paola; Aleixo, Alexandre; Weir, Jason T. (2020)
    The incidence of introgression during the diversification process and the timespan following divergence when introgression is possible are poorly understood in the neotropics where high species richness could provide extensive opportunities for genetic exchange. We used thousands of genome-wide SNPs to infer phylogenetic relationships, calculate ages of splitting, and to estimate the timing of introgression in a widespread avian neotropical genus of woodcreepers. Five distinct introgression events were reconstructed involving taxa classified both as subspecies and species including lineages descending from the basal-most split, dated to 7.3 million years ago. Introgression occurred between just a few hundred thousand to about 2.5 million years following divergence, suggesting substantial portions of the genome are capable of introgressing across taxa boundaries during a protracted time window of a few million years following divergence. Despite this protracted time window, we found that the proportion of the genome introgressing (6-11%) declines with the time of introgression following divergence, suggesting that the genome becomes progressively more immune to introgression as reproductive isolation increases.
  • Miraldo, Andreia; Duplouy, Anne (2019)
    Determining the drivers of diversity is a major topic in biology. Due to its high level of micro-endemism in many taxa, Madagascar has been described as one of Earth's biodiversity hotspot. The exceptional Malagasy biodiversity has been shown to be the result of various eco-evolutionary mechanisms that have taken place on this large island since its isolation from other landmasses. Extensive phylogenetic analyses have, for example, revealed that most of the dung beetle radiation events have arisen due to allopatric speciation, and adaptation to altitudinal and/or longitudinal gradients. But other biotic factors, that have yet to be identified, might also be at play. Wolbachia is a maternally transmitted endosymbiotic bacterium widespread in insects. The bacterium is well-known for its ability to modify its host reproductive system in ways that may lead to either discordance patterns between the host mitochondrial and nuclear phylogenies, and in some cases to speciation. Here, we used theMultiLocus Sequence Typing system, to identify and characterize five Wolbachia strains infecting several species within the Nanos clypeatus dung beetle clade. We discuss the implications of these Wolbachia strains for the evolution and diversification of their dung beetle hosts in Madagascar.
  • Penny, Amelia; Kroger, Bjorn (2019)
    The unprecedented diversifications in the fossil record of the early Palaeozoic (541-419 million years ago) increased both within-sample (alpha) and global (gamma) diversity, generating considerable ecological complexity. Faunal difference (beta diversity), including spatial heterogeneity, is thought to have played a major role in early Palaeozoic marine diversification, although alpha diversity is the major determinant of gamma diversity through the Phanerozoic. Drivers for this Phanerozoic shift from beta to alpha diversity are not yet resolved. Here, we evaluate the impacts of environmental and faunal heterogeneity on diversity patterns using a global spatial grid. We present early Palaeozoic genus-level alpha, beta and gamma diversity curves for molluscs, brachiopods, trilobites and echinoderms and compare them with measures of spatial lithological heterogeneity, which is our proxy for environmental heterogeneity. We find that alpha and beta diversity are associated with increased lithological heterogeneity, and that beta diversity declines over time while alpha increases. We suggest that the enhanced dispersal of marine taxa from the Middle Ordovician onwards facilitated increases in alpha diversity by encouraging the occupation of narrow niches and increasing the prevalence of transient species, simultaneously reducing spatial beta diversity. This may have contributed to a shift from beta to alpha diversity as the major determinant of gamma diversity increase over this critical evolutionary interval.