Journal articles: 'Species divergence'

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Bond, Jason E., David A. Beamer, Marshal C. Hedin, and Petra Sierwald. "Gradual evolution of male genitalia in a sibling species complex of millipedes (Diplopoda : Spirobolida : Rhinocricidae : Anadenobolus)." Invertebrate Systematics 17, no. 6 (2003): 711. http://dx.doi.org/10.1071/is03026.

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Jamaican millipedes in the Anadenobolus species complex provide an unusual case study of arthropods having undergone speciation in the absence of conspicuous divergence of male genitalia. Using landmark-based morphometrics, we examined shape deformation of the male anterior copulatory device in three genetically divergent yet morphologically cryptic species. A multivariate analysis of variance and relative warp analysis of nonuniform components show that although male genitalic shape is statistically different among species, many specimens are 'misplaced' in morphological space, perhaps consistent with a condition analogous to incomplete lineage sorting. A simulation of neutral nuclear gene coalescence suggests that such incomplete sorting is expected, given the depth of mtDNA divergences observed across species. The pronounced contrast between deep molecular v. incomplete genitalic divergence is at odds with the paradigm of selection-driven rapid change in male copulatory structure during arthropod speciation. Alternatively, we suggest that male genitalic divergence is evolving neutrally or in concert with other components of the genome (pleiotropy). Although we recognise the empirical validity of rapid genitalic divergence via sexual selection or sexual conflict, such models must be empirically tested using multiple lines of evidence. Accepting the rapid and divergent hypothesis without such multiple evidence scrutiny may result in a gross underestimation of evolutionary diversity and, subsequently, the misinterpretation of processes shaping genitalic change.

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Sun, Xin, Anne Bedos, and Louis Deharveng. "Unusually low genetic divergence at COI barcode locus between two species of intertidalThalassaphorura(Collembola: Onychiuridae)." PeerJ 6 (June 18, 2018): e5021. http://dx.doi.org/10.7717/peerj.5021.

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Species classification is challenging when taxa display limited morphological differences. In this paper, we combined morphology and DNA barcode data to investigate the complicated taxonomy of two Onychiurid Collembolan species.Thalassaphorura thalassophilaandThalassaphorura debilisare among the most common arthropod species in intertidal ecosystems and are often considered to be synonymous. Based on morphological and barcode analyses of fresh material collected in their type localities, we redescribed and compared the two species. However, their morphological distinctiveness was supported by a molecular divergence much smaller than previously reported at the interspecific level among Collembola. This divergence was even smaller than inter-population divergences recognized in the related edaphic speciesT. zschokkei, as well as those known between MOTUs within many Collembolan species. Our results may indicate a link between low genetic interspecific divergence and intertidal habitat, as the only biological peculiarity of the two species of interest compared to other Collembolan species analyzed to date is their strict intertidal life.

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Chantangsi, Chitchai, Denis H. Lynn, Maria T. Brandl, Jeffrey C. Cole, Neil Hetrick, and Pranvera Ikonomi. "Barcoding ciliates: a comprehensive study of 75 isolates of the genus Tetrahymena." International Journal of Systematic and Evolutionary Microbiology 57, no. 10 (October 1, 2007): 2412–23. http://dx.doi.org/10.1099/ijs.0.64865-0.

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The mitochondrial cytochrome-c oxidase subunit 1 (cox1) gene has been proposed as a DNA barcode to identify animal species. To test the applicability of the cox1 gene in identifying ciliates, 75 isolates of the genus Tetrahymena and three non-Tetrahymena ciliates that are close relatives of Tetrahymena, Colpidium campylum, Colpidium colpoda and Glaucoma chattoni, were selected. All tetrahymenines of unproblematic species could be identified to the species level using 689 bp of the cox1 sequence, with about 11 % interspecific sequence divergence. Intraspecific isolates of Tetrahymena borealis, Tetrahymena lwoffi, Tetrahymena patula and Tetrahymena thermophila could be identified by their cox1 sequences, showing <0.65 % intraspecific sequence divergence. In addition, isolates of these species were clustered together on a cox1 neighbour-joining (NJ) tree. However, strains identified as Tetrahymena pyriformis and Tetrahymena tropicalis showed high intraspecific sequence divergence values of 5.01 and 9.07 %, respectively, and did not cluster together on a cox1 NJ tree. This may indicate the presence of cryptic species. The mean interspecific sequence divergence of Tetrahymena was about 11 times greater than the mean intraspecific sequence divergence, and this increased to 58 times when all isolates of species with high intraspecific sequence divergence were excluded. This result is similar to DNA barcoding studies on animals, indicating that congeneric sequence divergences are an order of magnitude greater than conspecific sequence divergences. Our analysis also demonstrated low sequence divergences of <1.0 % between some isolates of T. pyriformis and Tetrahymena setosa on the one hand and some isolates of Tetrahymena furgasoni and T. lwoffi on the other, suggesting that the latter species in each pair is a junior synonym of the former. Overall, our study demonstrates the feasibility of using the mitochondrial cox1 gene as a taxonomic marker for ‘barcoding’ and identifying Tetrahymena species and some other ciliated protists.

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Head, Megan L., Emily A. Price, and Janette W. Boughman. "Body size differences do not arise from divergent mate preferences in a species pair of threespine stickleback." Biology Letters 5, no. 4 (May 27, 2009): 517–20. http://dx.doi.org/10.1098/rsbl.2009.0216.

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Ecological speciation can be driven by divergent natural and/or sexual selection. The relative contribution of these processes to species divergence, however, is unknown. Here, we investigate how sexual selection in the form of male and female mate preferences contributes to divergence of body size. This trait is known be under divergent natural selection and also contributes to sexual isolation in species pairs of threespine sticklebacks ( Gasterosteus aculeatus ). We show that neither female nor male size preferences contribute to body size divergence in this species pair, suggesting that size-based sexual isolation arises primarily through natural selection.

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Oneal, Elen, and L. Lacey Knowles. "Ecological selection as the cause and sexual differentiation as the consequence of species divergence?" Proceedings of the Royal Society B: Biological Sciences 280, no. 1750 (January 7, 2013): 20122236. http://dx.doi.org/10.1098/rspb.2012.2236.

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Key conceptual issues about speciation go unanswered without consideration of non-mutually exclusive factors. With tests based on speciation theory, we exploit the island distribution and habitat differences exhibited by the Caribbean cricket Amphiacusta sanctaecrucis , and with an analysis of divergent ecological selection, sexually selected differentiation and geographical isolation, address how these different factors interact. After testing for divergent selection by comparing neutral genetic and morphological divergence in one ecological (mandible shape) and one sexual (male genitalia shape) trait, we examine whether ecological or sexual selection is the primary mechanism driving population divergence. We find that all three factors—isolation, ecological and sexual selection—contribute to divergence, and that their interaction determines the stage of completeness achieved during the speciation process, as measured by patterns of genetic differentiation. Moreover, despite the striking diversity in genitalic shapes across the genus Amphiacusta , which suggests that sexual selection drives speciation, the significant differences in genitalia shape between forest habitats revealed here implies that ecological divergence may be the primary axis of divergence. Our work highlights critical unstudied aspects in speciation—differentiating the cause from the consequence of divergence—and suggests avenues for further disentangling the roles of natural and sexual selection in driving divergence in Amphiacusta .

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Ma, Tao, Kun Wang, Quanjun Hu, Zhenxiang Xi, Dongshi Wan, Qian Wang, Jianju Feng, et al. "Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex." Proceedings of the National Academy of Sciences 115, no. 2 (December 26, 2017): E236—E243. http://dx.doi.org/10.1073/pnas.1713288114.

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How genome divergence eventually leads to speciation is a topic of prime evolutionary interest. Genomic islands of elevated divergence are frequently reported between diverging lineages, and their size is expected to increase with time and gene flow under the speciation-with-gene-flow model. However, such islands can also result from divergent sorting of ancient polymorphisms, recent ecological selection regardless of gene flow, and/or recurrent background selection and selective sweeps in low-recombination regions. It is challenging to disentangle these nonexclusive alternatives, but here we attempt to do this in an analysis of what drove genomic divergence between four lineages comprising a species complex of desert poplar trees. Within this complex we found that two morphologically delimited species, Populus euphratica and Populus pruinosa, were paraphyletic while the four lineages exhibited contrasting levels of gene flow and divergence times, providing a good system for testing hypotheses on the origin of divergence islands. We show that the size and number of genomic islands that distinguish lineages are not associated with either rate of recent gene flow or time of divergence. Instead, they are most likely derived from divergent sorting of ancient polymorphisms and divergence hitchhiking. We found that highly diverged genes under lineage-specific selection and putatively involved in ecological and morphological divergence occur both within and outside these islands. Our results highlight the need to incorporate demography, absolute divergence measurement, and gene flow rate to explain the formation of genomic islands and to identify potential genomic regions involved in speciation.

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Hou, Zhong-e., Zhu Li, and Shu-qiang Li. "Identifying Chinese species of Gammarus (Crustacea: Amphipoda) using DNA barcoding." Current Zoology 55, no. 2 (April 1, 2009): 158–64. http://dx.doi.org/10.1093/czoolo/55.2.158.

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Abstract Using a standard cytochrome c oxidase I sequence, DNA barcoding has been shown to be effective to distinguish known species and to discover cryptic species. Here we assessed the efficiency of DNA barcoding for the amphipod genus Gammarus from China. The maximum intraspecific divergence for widespread species, Gammarus lacustris, was 3.5%, and mean interspecific divergence reached 21. 9%. We presented a conservative benchmark for determining provisional species using maximum intraspecific divergence of Gammarus lacustris. Thirty-one species possessed distinct barcode clusters. Two species were comprised of highly divergent clades with strong neighbor-joining bootstrap values, and likely indicated the presence of cryptic species. Although DNA barcoding is effective, future identification of species of Gammarus should incorporate DNA barcoding and morphological detection.

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Assis, G. M. L., R. F. Euclydes, C. D. Cruz, and C. B. Valle. "Genetic divergence in Brachiaria species." Cropp Breeding and Applied Biotechnology 2, no. 3 (September 30, 2002): 331–38. http://dx.doi.org/10.12702/1984-7033.v02n03a02.

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9

Fahrenkamp-Uppenbrink, J. "Ancient patterns reveal species divergence." Science 345, no. 6196 (July 31, 2014): 526–28. http://dx.doi.org/10.1126/science.345.6196.526-p.

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Livshits, M. A., and M. V. Volkenstein. "On the divergence of species." Biosystems 24, no. 4 (January 1991): 301–3. http://dx.doi.org/10.1016/0303-2647(91)90048-p.

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11

Rannala, Bruce. "Conceptual issues in Bayesian divergence time estimation." Philosophical Transactions of the Royal Society B: Biological Sciences 371, no. 1699 (July 19, 2016): 20150134. http://dx.doi.org/10.1098/rstb.2015.0134.

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Bayesian inference of species divergence times is an unusual statistical problem, because the divergence time parameters are not identifiable unless both fossil calibrations and sequence data are available. Commonly used marginal priors on divergence times derived from fossil calibrations may conflict with node order on the phylogenetic tree causing a change in the prior on divergence times for a particular topology. Care should be taken to avoid confusing this effect with changes due to informative sequence data. This effect is illustrated with examples. A topology-consistent prior that preserves the marginal priors is defined and examples are constructed. Conflicts between fossil calibrations and relative branch lengths (based on sequence data) can cause estimates of divergence times that are grossly incorrect, yet have a narrow posterior distribution. An example of this effect is given; it is recommended that overly narrow posterior distributions of divergence times should be carefully scrutinized. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

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CATALANO, SARAH R., IAN D. WHITTINGTON, STEPHEN C. DONNELLAN, TERRY BERTOZZI, and BRONWYN M. GILLANDERS. "First comparative insight into the architecture ofCOImitochondrial minicircle molecules of dicyemids reveals marked inter-species variation." Parasitology 142, no. 8 (April 16, 2015): 1066–79. http://dx.doi.org/10.1017/s0031182015000384.

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SUMMARYDicyemids, poorly known parasites of benthic cephalopods, are one of the few phyla in which mitochondrial (mt) genome architecture departs from the typical ~16 kb circular metazoan genome. In addition to a putative circular genome, a series of mt minicircles that each comprises the mt encoded units (I–III) of the cytochromecoxidase complex have been reported. Whether the structure of the mt minicircles is a consistent feature among dicyemid species is unknown. Here we analyse the complete cytochromecoxidase subunit I (COI) minicircle molecule, containing theCOIgene and an associated non-coding region (NCR), for ten dicyemid species, allowing for first time comparisons between species of minicircle architecture, NCR function and inferences of minicircle replication. Divergence inCOInucleotide sequences between dicyemid species was high (average net divergence = 31·6%) while within species diversity was lower (average net divergence = 0·2%). The NCR and putative 5′ section of theCOIgene were highly divergent between dicyemid species (average net nucleotide divergence of putative 5′COIsection = 61·1%). No tRNA genes were found in the NCR, although palindrome sequences with the potential to form stem-loop structures were identified in some species, which may play a role in transcription or other biological processes.

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Jančúchová-Lásková, Jitka, Eva Landová, and Daniel Frynta. "Are genetically distinct lizard species able to hybridize? A review." Current Zoology 61, no. 1 (February 1, 2015): 155–80. http://dx.doi.org/10.1093/czoolo/61.1.155.

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Abstract Animal species are delimited by reproductive isolation mechanisms (RIMs). Postzygotic RIMs are mainly products of genetic differences and thus their strength increases with elapsed divergence time. The relationship between postzygotic reproductive isolation and genetic divergence, however, differs considerably among major clades of vertebrates. We reviewed the available literature providing empirical evidence of natural and/or experimental hybridization between distinct species of lizards (squamates except snakes). We found that hybridization events are widely distributed among nearly all major lizard clades. The majority of research focuses on parthenogenetic species and/or polyploid hybrids in families Lacertidae, Teiidae and Gekkonidae. Homoploid bisexual hybrids are mainly reported within Lacertidae and Iguania groups. As a proxy of genetic divergence of the hybridizing taxa we adopted nucleotide sequence distance (HKY85) of mitochondrial cyt b gene. The upper limit of genetic divergence was similar with regard to both parthenogenetic and bisexual hybrids. Maximum values of these distances between hybridizing species of lizards approached 18%?21%, which is comparable to or even exceeds the corresponding values reported for other principal clades of vertebrates. In spite of this, F1 hybrids are typically at least partially fertile in lizards and thus genetic in-trogression between highly divergent species is possible. The relationship between the genetic distance and hybrid fertility was not found.

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Li, Kexin, Wei Hong, Hengwu Jiao, Guo-Dong Wang, Karl A. Rodriguez, Rochelle Buffenstein, Yang Zhao, Eviatar Nevo, and Huabin Zhao. "Sympatric speciation revealed by genome-wide divergence in the blind mole rat Spalax." Proceedings of the National Academy of Sciences 112, no. 38 (September 4, 2015): 11905–10. http://dx.doi.org/10.1073/pnas.1514896112.

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Sympatric speciation (SS), i.e., speciation within a freely breeding population or in contiguous populations, was first proposed by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection] and is still controversial despite theoretical support [Gavrilets S (2004) Fitness Landscapes and the Origin of Species (MPB-41)] and mounting empirical evidence. Speciation of subterranean mammals generally, including the genus Spalax, was considered hitherto allopatric, whereby new species arise primarily through geographic isolation. Here we show in Spalax a case of genome-wide divergence analysis in mammals, demonstrating that SS in continuous populations, with gene flow, encompasses multiple widespread genomic adaptive complexes, associated with the sharply divergent ecologies. The two abutting soil populations of S. galili in northern Israel habituate the ancestral Senonian chalk population and abutting derivative Plio-Pleistocene basalt population. Population divergence originated ∼0.2–0.4 Mya based on both nuclear and mitochondrial genome analyses. Population structure analysis displayed two distinctly divergent clusters of chalk and basalt populations. Natural selection has acted on 300+ genes across the genome, diverging Spalax chalk and basalt soil populations. Gene ontology enrichment analysis highlights strong but differential soil population adaptive complexes: in basalt, sensory perception, musculature, metabolism, and energetics, and in chalk, nutrition and neurogenetics are outstanding. Population differentiation of chemoreceptor genes suggests intersoil population's mate and habitat choice substantiating SS. Importantly, distinctions in protein degradation may also contribute to SS. Natural selection and natural genetic engineering [Shapiro JA (2011) Evolution: A View From the 21st Century] overrule gene flow, evolving divergent ecological adaptive complexes. Sharp ecological divergences abound in nature; therefore, SS appears to be an important mode of speciation as first envisaged by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection].

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Noguchi, Hideyuki, Akira Itoh, Takashi Mizuno, Kriangsak Sri-ngernyuang, Mamoru Kanzaki, Sakhan Teejuntuk, Witchaphart Sungpalee, et al. "Habitat divergence in sympatric Fagaceae tree species of a tropical montane forest in northern Thailand." Journal of Tropical Ecology 23, no. 5 (August 16, 2007): 549–58. http://dx.doi.org/10.1017/s0266467407004403.

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Spatial distributions of many tropical trees are skewed to specific habitats, i.e. habitat specialization. However, habitats of specialist species must be divergent, i.e. habitat divergence, to coexist in a local community. When a pair of species specialize in the same habitat, i.e. habitat convergence, they could not coexist by way of habitat specialization. Thus, analyses of habitat divergence, in addition to habitat specialization, are necessary to discuss coexistence mechanisms of sympatric species. In this study, the habitat specialization and habitat divergence along topographic gradients of eight sympatric tree species of the Fagaceae were studied in a 15-ha study plot in a tropical lower montane forest in northern Thailand. A statistical test with torus shift randomizations for 9673 trees of Fagaceae revealed significantly biased distributions for all of the species, for at least one of the four topographic variables used: elevation, slope inclination, aspect and convexity. Slope convexity was the most critical topographic variable, along which all but one species had significantly skewed distributions. Out of 112 possible combinations of species pairs and topographic variables, 18 (16%) and two pairs (1.8%) showed significant habitat divergence and habitat convergence, respectively. The observed habitat divergence alone could not completely explain the coexistence of the eight species. There was a gradation in the habitat position of each species, with relatively large overlaps between species distributed in similar habitats, and small overlaps between species associated with contrasting habitats, respectively. The gradual changes in the habitats of the species suggested that dividing the species into a small number of distinct habitat groups, such as ridge and valley specialists, would not be straightforward.

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Crawford, Daniel J., and Elias Landolt. "Allozyme divergence among species ofWolffia (Lemnaceae)." Plant Systematics and Evolution 197, no. 1-4 (1995): 59–69. http://dx.doi.org/10.1007/bf00984632.

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Pouwels, Peter H., and Jack A. M. Leunissen. "Divergence in codon usage ofLactobacillus species." Nucleic Acids Research 22, no. 6 (1994): 929–36. http://dx.doi.org/10.1093/nar/22.6.929.

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Whitaker, Rachel J. "Allopatric origins of microbial species." Philosophical Transactions of the Royal Society B: Biological Sciences 361, no. 1475 (October 11, 2006): 1975–84. http://dx.doi.org/10.1098/rstb.2006.1927.

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Although allopatric divergence is a well-accepted mechanism of speciation for eukaryotic macro-organisms, the importance of geographical barriers to divergence in microbial populations is a subject of great debate. Do geographically separated populations of micro-organisms diverge independently, or does their structure fit the often quoted Bass-Becking description ‘everything is everywhere; the environment selects’? Aided by high-resolution genetic and genomic tools, the search for ‘microbial marsupials’ has revealed that in fact both are true; some species of micro-organisms demonstrate allopatric divergence, while others do not. This discovery opens the door for comparative analyses, where questions about the differences in evolutionary and ecological mechanisms that drive divergence and speciation in different microbial species can begin to be explored. Investigating these differences in evolutionary mechanisms will greatly enhance interest in, and understanding of, the dynamic processes that create and maintain the vast diversity of the microbial world.

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Lobo, Jorge, Maria S. Ferreira, Ilisa C. Antunes, Marcos A. L. Teixeira, Luisa M. S. Borges, Ronaldo Sousa, Pedro A. Gomes, Maria Helena Costa, Marina R. Cunha, and Filipe O. Costa. "Contrasting morphological and DNA barcode-suggested species boundaries among shallow-water amphipod fauna from the southern European Atlantic coast." Genome 60, no. 2 (February 2017): 147–57. http://dx.doi.org/10.1139/gen-2016-0009.

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In this study we compared DNA barcode-suggested species boundaries with morphology-based species identifications in the amphipod fauna of the southern European Atlantic coast. DNA sequences of the cytochrome c oxidase subunit I barcode region (COI-5P) were generated for 43 morphospecies (178 specimens) collected along the Portuguese coast which, together with publicly available COI-5P sequences, produced a final dataset comprising 68 morphospecies and 295 sequences. Seventy-five BINs (Barcode Index Numbers) were assigned to these morphospecies, of which 48 were concordant (i.e., 1 BIN = 1 species), 8 were taxonomically discordant, and 19 were singletons. Twelve species had matching sequences (<2% distance) with conspecifics from distant locations (e.g., North Sea). Seven morphospecies were assigned to multiple, and highly divergent, BINs, including specimens of Corophium multisetosum (18% divergence) and Dexamine spiniventris (16% divergence), which originated from sampling locations on the west coast of Portugal (only about 36 and 250 km apart, respectively). We also found deep divergence (4%–22%) among specimens of seven species from Portugal compared to those from the North Sea and Italy. The detection of evolutionarily meaningful divergence among populations of several amphipod species from southern Europe reinforces the need for a comprehensive re-assessment of the diversity of this faunal group.

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Nadeau, Nicola J., Annabel Whibley, Robert T. Jones, John W. Davey, Kanchon K. Dasmahapatra, Simon W. Baxter, Michael A. Quail, et al. "Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1587 (February 5, 2012): 343–53. http://dx.doi.org/10.1098/rstb.2011.0198.

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Heliconius butterflies represent a recent radiation of species, in which wing pattern divergence has been implicated in speciation. Several loci that control wing pattern phenotypes have been mapped and two were identified through sequencing. These same gene regions play a role in adaptation across the whole Heliconius radiation. Previous studies of population genetic patterns at these regions have sequenced small amplicons. Here, we use targeted next-generation sequence capture to survey patterns of divergence across these entire regions in divergent geographical races and species of Heliconius . This technique was successful both within and between species for obtaining high coverage of almost all coding regions and sufficient coverage of non-coding regions to perform population genetic analyses. We find major peaks of elevated population differentiation between races across hybrid zones, which indicate regions under strong divergent selection. These ‘islands’ of divergence appear to be more extensive between closely related species, but there is less clear evidence for such islands between more distantly related species at two further points along the ‘speciation continuum’. We also sequence fosmid clones across these regions in different Heliconius melpomene races. We find no major structural rearrangements but many relatively large (greater than 1 kb) insertion/deletion events (including gain/loss of transposable elements) that are variable between races.

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McIntyre, Sarah R. N., Charles H. Lineweaver, Colin P. Groves, and Aditya Chopra. "Global biogeography since Pangaea." Proceedings of the Royal Society B: Biological Sciences 284, no. 1856 (June 7, 2017): 20170716. http://dx.doi.org/10.1098/rspb.2017.0716.

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The break-up of the supercontinent Pangaea around 180 Ma has left its imprint on the global distribution of species and resulted in vicariance-driven speciation. Here, we test the idea that the molecular clock dates, for the divergences of species whose geographical ranges were divided, should agree with the palaeomagnetic dates for the continental separations. Our analysis of recently available phylogenetic divergence dates of 42 pairs of vertebrate taxa, selected for their reduced ability to disperse, demonstrates that the divergence dates in phylogenetic trees of continent-bound terrestrial and freshwater vertebrates are consistent with the palaeomagnetic dates of continental separation.

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Monjardim, Marina, Celso O. Azevedo, and Valeria Fagundes. "DNA barcoding and hypopygium shape support delimitation of sympatric Dissomphalus species (Hymenoptera, Bethylidae) from the Atlantic rainforest." ZooKeys 959 (August 14, 2020): 87–97. http://dx.doi.org/10.3897/zookeys.959.53737.

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Dissomphalus is a cosmopolitan genus of Bethylidae and has 269 Neotropical species divided into 32 species-groups, mostly defined by the genital and the tergal process structures. Dissomphalus rectilineus and D. concavatus are sympatric species in the ulceratus species-group. Members of the species-group share many similarities in the morphology of the head, hypopygium, tergal process and genitalia, but may be distinguished by the structure of the hypopygium. Previous studies have found intermediate structures of the hypopygium in the sympatric areas and raised questions about the distinctiveness of these two species. We sequenced 340 bp of the mitochondrial gene cytochrome oxidase I of 29 specimens from Brazil and Paraguay, calculated the genetic divergence among specimens, and recovered the phylogenetic relationships between taxa. In addition, we compared the morphology of the hypopygium to evaluate its use as a species-specific diagnostic character using the genetic divergence values. We recovered three well-supported monophyletic groups (intraclade divergence from 1.3 to 13.4%) and three hypopygium morphologies associated with each clade, two of them associated with D. rectilineus and D. concavatus (as described in the literature); the third one is new, not associated with any known species. The divergence between the D. rectilineus and D. concavatus clades was 19%, while the third clade is divergent from each species by 19–20%. If fully described, the hypopygium shape associated with the COI sequence will represent an extremely promising approach to the diagnosis of Dissomphalus species.

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Kamran, Muhammad, Atif Yaqub, Naila Malkani, Khalid Mahmood Anjum, Muhammad Nabeel Awan, and Hamid Paknejad. "Identification and Phylogenetic Analysis of Channa Species from Riverine System of Pakistan Using COI Gene as a DNA Barcoding Marker." Journal of Bioresource Management 7, no. 2 (July 18, 2020): 88–98. http://dx.doi.org/10.35691/jbm.0202.0135.

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Channa are the freshwater and important food fish species in Pakistan belonging to family Channidae. However, identification and phylogenetic analysis based on molecular tools of these species in Pakistan was not well known. Herein, the current investigation was conceptualized, which dealt with mitochondrial DNA sequences from three geographically distinct populations of this species from Pakistan’s water system. DNA from fin tissues was extracted. COI region of mtDNA was amplified using universal primers for fish. PCR products were sequenced. Phylogenetic analysis conducted in the present study, i.e. neighbor-joining (NJ) cladogram, maximum likelihood, K2P genetic divergence and histogram suggests that the studied species of family Channidae are genetically different. The K2P intraspecific divergences were lower than interspecific divergences. The clades in the evolutionary tree for three species were clearly separated.Channa are the freshwater and important food fish species in Pakistan belonging to family Channidae. However, identification and phylogenetic analysis based on molecular tools of these species in Pakistan was not well known. Herein, the current investigation was conceptualized, which dealt with mitochondrial DNA sequences from three geographically distinct populations of this species from Pakistan’s water system. DNA from fin tissues was extracted. COI region of mtDNA was amplified using universal primers for fish. PCR products were sequenced. Phylogenetic analysis conducted in the present study, i.e. neighbor-joining (NJ) cladogram, maximum likelihood, K2P genetic divergence and histogram suggests that the studied species of family Channidae are genetically different. The K2P intraspecific divergences were lower than interspecific divergences. The clades in the evolutionary tree for three species were clearly separated.

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Abdussamad, E. M., A. Gopalakrishnan, K. G. Mini, S. Sukumaran, P. R. Divya, T. B. Retheesh, A. A. Muhammed, et al. "Description of a new species of queenfish, Scomberoides pelagicus from Indian seas." Journal of Environmental Biology 43, no. 1 (January 7, 2022): 105–14. http://dx.doi.org/10.22438/jeb/43/1/mrn-1975.

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Aim: The study was carried out to ascertain whether morphotype of Scomberoides commersonnianus (Talang queenfish) existing along the Indian coast is a new species or not. Methodology: Talang queenfish and the morphotype were tested for their uniqueness using systematic and molecular tools. The morphometric and meristic details including otolith morphometry were analysed and compared for taxonomic divergence and Cytochrome Oxidase I and Cytochrome b gene sequences for quantifying genetic divergences. Results: The systematic analysis indicated significant morphometric differences between both. The otolith morphometry and phylogeny also confirmed the divergence between them, and qualified the morphotype as an independent species status and named Scomberoides pelagicus sp. nov. Interpretation: The new species is distinct by deep ovate body, concave dorsal head profile, anal fin origin anterior to second dorsal fin and pelvic to pectoral fin, helical arrangement of body scale and stout and less numerous gill rakers on the first gill arch. The phylogeny as on Cytochrome b and Cytochrome Oxidase 1 sequences are very distinct, with 11.2% and 2.0% divergence respectively. Their known distributional range are peninsular region of Indian coast, Malaysian region of the South China Sea and Manila Bay, Philippines.

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Li, Xueying C., and Justin C. Fay. "Cis-Regulatory Divergence in Gene Expression between Two Thermally Divergent Yeast Species." Genome Biology and Evolution 9, no. 5 (May 2017): 1120–29. http://dx.doi.org/10.1093/gbe/evx072.

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Cahill, James A., André E. R. Soares, Richard E. Green, and Beth Shapiro. "Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data." Philosophical Transactions of the Royal Society B: Biological Sciences 371, no. 1699 (July 19, 2016): 20150138. http://dx.doi.org/10.1098/rstb.2015.0138.

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Understanding when species diverged aids in identifying the drivers of speciation, but the end of gene flow between populations can be difficult to ascertain from genetic data. We explore the use of pairwise sequential Markovian coalescent (PSMC) modelling to infer the timing of divergence between species and populations. PSMC plots generated using artificial hybrid genomes show rapid increases in effective population size at the time when the two parent lineages diverge, and this approach has been used previously to infer divergence between human lineages. We show that, even without high coverage or phased input data, PSMC can detect the end of significant gene flow between populations by comparing the PSMC output from artificial hybrids to the output of simulations with known demographic histories. We then apply PSMC to detect divergence times among lineages within two real datasets: great apes and bears within the genus Ursus . Our results confirm most previously proposed divergence times for these lineages, and suggest that gene flow between recently diverged lineages may have been common among bears and great apes, including up to one million years of continued gene flow between chimpanzees and bonobos after the formation of the Congo River. This article is part of the themed issue ‘Dating species divergences using rocks and clocks'.

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Genty, Gabrielle, Carlos E. Guarnizo, Juan P. Ramírez, Lucas S. Barrientos, and Andrew J. Crawford. "Landscape Genetics and Species Delimitation in the Andean Palm Rocket Frog (Aromobatidae, Rheobates)." Journal of Zoological Systematics and Evolutionary Research 2022 (February 9, 2022): 1–12. http://dx.doi.org/10.1155/2022/6774225.

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The complex topography of the species-rich northern Andes creates heterogeneous environmental landscapes that are hypothesized to have promoted population fragmentation and diversification by processes such as vicariance or local adaptation. Previous phylogenetic work on the palm rocket frog (Anura: Aromobatidae: Rheobates spp.), endemic to midelevation forests of Colombia, suggested that valleys were important in promoting divergence between lineages. In this study, we first evaluated previous hypotheses of species-level diversity, then fitted an isolation-with-migration (IM) historical demographic model, and tested two landscape genetic models to explain genetic divergence within Rheobates: isolation by distance and isolation by environment. The data consisted of two mitochondrial and four nuclear genes from 24 samples covering most of the geographic range of the genus. Species delimitation by Bayesian Phylogenetics and Phylogeography recovered five highly divergent genetic lineages within Rheobates, among which few to no migrants are exchanged according to IM. We found that isolation by environment provided the only variable significantly correlated with genetic distances for both mitochondrial and nuclear genes, suggesting that local adaptation may have a role in driving the genetic divergence within this frog genus. Thus, genetic divergence in Rheobates may be driven more by variation among the local environments where these frogs live rather than by geographic distance.

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Oliver, Paul M., Mozes P. K. Blom, Harold G. Cogger, Robert N. Fisher, Jonathan Q. Richmond, and John C. Z. Woinarski. "Insular biogeographic origins and high phylogenetic distinctiveness for a recently depleted lizard fauna from Christmas Island, Australia." Biology Letters 14, no. 6 (June 2018): 20170696. http://dx.doi.org/10.1098/rsbl.2017.0696.

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Striking faunal turnover across Asia and Australasia, most famously along the eastern edge of the Sunda Shelf or ‘Wallace's Line’, has been a focus of biogeographic research for over 150 years. Here, we investigate the origins of a highly threatened endemic lizard fauna (four species) on Christmas Island. Despite occurring less 350 km south of the Sunda Shelf, this fauna mostly comprises species from clades centred on the more distant regions of Wallacea, the Pacific and Australia (more than 1000 km east). The three most divergent lineages show Miocene (approx. 23–5 Ma) divergences from sampled relatives; and have recently become extinct or extinct in the wild, likely owing to the recent introduction of a southeast Asian snake ( Lycodon capucinus ). Insular distributions, deep phylogenetic divergence and recent decline suggest that rather than dispersal ability or recent origins, environmental and biotic barriers have impeded these lineages from diversifying on the continental Sunda Shelf, and thereby, reinforced faunal differentiation across Wallace's Line. Our new phylogenetically informed perspective further highlights the rapid loss of ancient lineages that has occurred on Christmas Island, and underlines how the evolutionary divergence and vulnerability of many island-associated lineages may continue to be underestimated.

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Matsuo, Y., and T. Yamazaki. "Nucleotide variation and divergence in the histone multigene family in Drosophila melanogaster." Genetics 122, no. 1 (May 1, 1989): 87–97. http://dx.doi.org/10.1093/genetics/122.1.87.

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Abstract Nucleotide differences in the histone H3 gene family in Drosophila melanogaster were studied on three levels: (1) within a chromosome, (2) within a population and (3) between species (D. melanogaster and Drosophila simulans). The average difference within the H3 gene within a chromosome was 0.0040 per nucleotide site, about 52% of that within a population (0.0077). The proportion of divergent sites between the two species was 0.0575, which is about 8.5 times the difference within a species. The distribution of divergence between species was similar to that of variation within a species. Divergence and variation were noted to be greatest in the 3' noncoding region and least in the coding region. Values intermediate between these were found for the 5' noncoding region. Divergence and variation in silent sites exceeded those in the total coding region, thus indicating possible purifying selection for amino-acid-altering change. Phylogenetic relations among H3 genes and genetic differences on these three levels are evidence for the concerted evolution of the histone gene family. The molecular mechanism by which variation is produced and maintained is discussed.

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Isabel, Sandra, Éric Leblanc, Maurice Boissinot, Dominique K. Boudreau, Myrian Grondin, François J. Picard, Eric A. Martel, et al. "Divergence among Genes Encoding the Elongation Factor Tu of Yersinia Species." Journal of Bacteriology 190, no. 22 (September 12, 2008): 7548–58. http://dx.doi.org/10.1128/jb.01067-08.

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ABSTRACT Elongation factor Tu (EF-Tu), encoded by tuf genes, carries aminoacyl-tRNA to the ribosome during protein synthesis. Duplicated tuf genes (tufA and tufB), which are commonly found in enterobacterial species, usually coevolve via gene conversion and are very similar to one another. However, sequence analysis of tuf genes in our laboratory has revealed highly divergent copies in 72 strains spanning the genus Yersinia (representing 12 Yersinia species). The levels of intragenomic divergence between tufA and tufB sequences ranged from 8.3 to 16.2% for the genus Yersinia, which is significantly greater than the 0.0 to 3.6% divergence observed for other enterobacterial genera. We further explored tuf gene evolution in Yersinia and other Enterobacteriaceae by performing directed sequencing and phylogenetic analyses. Phylogenetic trees constructed using concatenated tufA and tufB sequences revealed a monophyletic genus Yersinia in the family Enterobacteriaceae. Moreover, Yersinia strains form clades within the genus that mostly correlate with their phenotypic and genetic classifications. These genetic analyses revealed an unusual divergence between Yersinia tufA and tufB sequences, a feature unique among sequenced Enterobacteriaceae and indicative of a genus-wide loss of gene conversion. Furthermore, they provided valuable phylogenetic information for possible reclassification and identification of Yersinia species.

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Wang, Guo-Hong, He Li, Hai-Wei Zhao, and Wei-Kang Zhang. "Detecting climatically driven phylogenetic and morphological divergence among spruce (<i>Picea</i>) species worldwide." Biogeosciences 14, no. 9 (May 5, 2017): 2307–19. http://dx.doi.org/10.5194/bg-14-2307-2017.

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Abstract. This study aimed to elucidate the relationship between climate and the phylogenetic and morphological divergence of spruces (Picea) worldwide. Climatic and georeferenced data were collected from a total of 3388 sites distributed within the global domain of spruce species. A phylogenetic tree and a morphological tree for the global spruces were reconstructed based on DNA sequences and morphological characteristics. Spatial evolutionary and ecological vicariance analysis (SEEVA) was used to detect the ecological divergence among spruces. A divergence index (D) with (0, 1) scaling was calculated for each climatic factor at each node for both trees. The annual mean values, extreme values and annual range of the climatic variables were among the major determinants for spruce divergence. The ecological divergence was significant (P < 0. 001) for 185 of the 279 comparisons at 31 nodes in the phylogenetic tree, as well as for 196 of the 288 comparisons at 32 nodes in the morphological tree. Temperature parameters and precipitation parameters tended to be the main driving factors for the primary divergences of spruce phylogeny and morphology, respectively. Generally, the maximum D of the climatic variables was smaller in the basal nodes than in the remaining nodes. Notably, the primary divergence of morphology and phylogeny among the investigated spruces tended to be driven by different selective pressures. Given the climate scenario of severe and widespread drought over land areas in the next 30–90 years, our findings shed light on the prediction of spruce distribution under future climate change.

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Mavengere, Heidi, Kathleen Mattox, Marcus M. Teixeira, Victoria E. Sepúlveda, Oscar M. Gomez, Orville Hernandez, Juan McEwen, and Daniel R. Matute. "Paracoccidioides Genomes Reflect High Levels of Species Divergence and Little Interspecific Gene Flow." mBio 11, no. 6 (December 22, 2020): e01999-20. http://dx.doi.org/10.1128/mbio.01999-20.

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ABSTRACTThe fungus Paracoccidioides is a prevalent human pathogen endemic to South America. The genus is composed of five species. In this report, we use 37 whole-genome sequences to study the allocation of genetic variation in Paracoccidioides. We tested three genome-wide predictions of advanced speciation, namely, that all species should be reciprocally monophyletic, that species pairs should be highly differentiated along the whole genome, and that there should be low rates of interspecific gene exchange. We find support for these three hypotheses. Species pairs with older divergences show no evidence of gene exchange, while more recently diverged species pairs show evidence of modest rates of introgression. Our results indicate that as divergence progresses, species boundaries become less porous among Paracoccidioides species. Our results suggest that species in Paracoccidioides are at different stages along the divergence continuum.IMPORTANCEParacoccidioides is the causal agent of a systemic mycosis in Latin America. Most of the inference of the evolutionary history of Paracoccidioides has used only a few molecular markers. In this report, we evaluate the extent of genome divergence among Paracoccidioides species and study the possibility of interspecific gene exchange. We find that all species are highly differentiated. We also find that the amount of gene flow between species is low and in some cases is even completely absent in spite of geographic overlap. Our study constitutes a systematic effort to identify species boundaries in fungal pathogens and to determine the extent of gene exchange among fungal species.

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de Moya, Robert S., Judith K. Brown, Andrew D. Sweet, Kimberly K. O. Walden, Jorge R. Paredes-Montero, Robert M. Waterhouse, and Kevin P. Johnson. "Nuclear Orthologs Derived from Whole Genome Sequencing Indicate Cryptic Diversity in the Bemisia tabaci (Insecta: Aleyrodidae) Complex of Whiteflies." Diversity 11, no. 9 (August 29, 2019): 151. http://dx.doi.org/10.3390/d11090151.

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The Bemisia tabaci complex of whiteflies contains globally important pests thought to contain cryptic species corresponding to geographically structured phylogenetic clades. Although mostly morphologically indistinguishable, differences have been shown to exist among populations in behavior, plant virus vector capacity, ability to hybridize, and DNA sequence divergence. These differences allow for certain populations to become invasive and cause great economic damage in a monoculture setting. Although high mitochondrial DNA divergences have been reported between putative conspecifics of the B. tabaci species complex, there is limited data that exists across the whole genome for this group. Using data from 2184 orthologs obtained from whole genome sequencing (Illumina), a phylogenetic analysis using maximum likelihood and coalescent methodologies was completed on ten individuals of the B. tabaci complex. In addition, automatic barcode gap discovery methods were employed, and results suggest the existence of five species. Although the divergences of the mitochondrial cytochrome oxidase I gene are high among members of this complex, nuclear divergences are much lower in comparison. Single-copy orthologs from whole genome sequencing demonstrate divergent population structures among members of the B. tabaci complex and the sequences provide an important resource to aid in future genomic studies of the group.

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Simpson, Richard K., David R. Wilson, Allison F. Mistakidis, Daniel J. Mennill, and Stéphanie M. Doucet. "Sympatry drives colour and song evolution in wood-warblers (Parulidae)." Proceedings of the Royal Society B: Biological Sciences 288, no. 1942 (January 13, 2021): 20202804. http://dx.doi.org/10.1098/rspb.2020.2804.

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Closely related species often exhibit similarities in appearance and behaviour, yet when related species exist in sympatry, signals may diverge to enhance species recognition. Prior comparative studies provided mixed support for this hypothesis, but the relationship between sympatry and signal divergence is likely nonlinear. Constraints on signal diversity may limit signal divergence, especially when large numbers of species are sympatric. We tested the effect of sympatric overlap on plumage colour and song divergence in wood-warblers (Parulidae), a speciose group with diverse visual and vocal signals. We also tested how number of sympatric species influences signal divergence. Allopatric species pairs had overall greater plumage and song divergence compared to sympatric species pairs. However, among sympatric species pairs, plumage divergence positively related to the degree of sympatric overlap in males and females, while male song bandwidth and syllable rate divergence negatively related to sympatric overlap. In addition, as the number of species in sympatry increased, average signal divergence among sympatric species decreased, which is likely due to constraints on warbler perceptual space and signal diversity. Our findings reveal that sympatry influences signal evolution in warblers, though not always as predicted, and that number of sympatric species can limit sympatry's influence on signal evolution.

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Ladner, Jason T., Nazir Savji, Loreen Lofts, Amelia Travassos da Rosa, Michael R. Wiley, Marie C. Gestole, Gail E. Rosen, et al. "Genomic and phylogenetic characterization of viruses included in the Manzanilla and Oropouche species complexes of the genus Orthobunyavirus, family Bunyaviridae." Journal of General Virology 95, no. 5 (May 1, 2014): 1055–66. http://dx.doi.org/10.1099/vir.0.061309-0.

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A thorough characterization of the genetic diversity of viruses present in vector and vertebrate host populations is essential for the early detection of and response to emerging pathogenic viruses, yet genetic characterization of many important viral groups remains incomplete. The Simbu serogroup of the genus Orthobunyavirus, family Bunyaviridae, is an example. The Simbu serogroup currently consists of a highly diverse group of related arboviruses that infect both humans and economically important livestock species. Here, we report complete genome sequences for 11 viruses within this group, with a focus on the large and poorly characterized Manzanilla and Oropouche species complexes. Phylogenetic and pairwise divergence analyses indicated the presence of high levels of genetic diversity within these two species complexes, on a par with that seen among the five other species complexes in the Simbu serogroup. Based on previously reported divergence thresholds between species, the data suggested that these two complexes should actually be divided into at least five species. Together these five species formed a distinct phylogenetic clade apart from the rest of the Simbu serogroup. Pairwise sequence divergences among viruses of this clade and viruses in other Simbu serogroup species complexes were similar to levels of divergence among the other orthobunyavirus serogroups. The genetic data also suggested relatively high levels of natural reassortment, with three potential reassortment events present, including two well-supported events involving viruses known to infect humans.

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Vendrami, David L. J., Joseph I. Hoffman, and Craig S. Wilding. "Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species." Genes 14, no. 1 (December 21, 2022): 14. http://dx.doi.org/10.3390/genes14010014.

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Two commercially important scallop species of the genus Pecten are found in Europe: the north Atlantic Pecten maximus and the Mediterranean Pecten jacobaeus whose distributions abut at the Almeria–Orán front. Whilst previous studies have quantified genetic divergence between these species, the pattern of differentiation along the Pecten genome is unknown. Here, we mapped RADseq data from 235 P. maximus and 27 P. jacobaeus to a chromosome-level reference genome, finding a heterogeneous landscape of genomic differentiation. Highly divergent genomic regions were identified across 14 chromosomes, while the remaining five showed little differentiation. Demographic and comparative genomics analyses suggest that this pattern resulted from an initial extended period of isolation, which promoted divergence, followed by differential gene flow across the genome during secondary contact. Single nucleotide polymorphisms present within highly divergent genomic regions were located in areas of low recombination and contrasting patterns of LD decay were found between the two species, hinting at the presence of chromosomal inversions in P. jacobaeus. Functional annotations revealed that highly differentiated regions were enriched for immune-related processes and mRNA modification. While future work is necessary to characterize structural differences, this study provides new insights into the speciation genomics of P. maximus and P. jacobaeus.

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CIANFERONI, FRANCO, ROMINA P. YÁÑEZ, R. EDUARDO PALMA, CARLOS F. GARIN, and FERNANDO TORRES-PÉREZ. "Deep Divergences within Liolaemus nigroviridis (Squamata, Liolaemidae) Lineages Associated with Sky Islands in Central Chile." Zootaxa 3619, no. 1 (February 26, 2013): 59–69. http://dx.doi.org/10.11646/zootaxa.3619.1.3.

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Evolution of montane species may be strongly influenced by climate oscillations, particularly species distributed in isolated high-elevation areas (sky islands). Chilean topography is exemplified by montane environments including the Andesand CoastalMountains. To test hypotheses related to genetic divergence associated with sky islands, we explored population genetics and phylogenetic signatures in the montane lizard Liolaemus nigroviridis Müller and Hellmich 1932. We sequenced the mitochondrial cytochrome b for samples collected from six montane areas in central Chile. We found high genetic divergence among populations, congruent with well-supported clades from phylogeny reconstructions. The most recent common ancestor of all samples of L. nigroviridis was dated around the limit of Pliocene-Pleistocene (2.7 Mya), congruent with early vicariance of Andean and coastal populations. Deep lineage divergences suggest that allopatric populations accumulated high nucleotide differences and maintained long periods without gene exchange. We discuss potential taxonomic revisions considering relative genetic divergence.

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Renaut, S., N. Maillet, E. Normandeau, C. Sauvage, N. Derome, S. M. Rogers, and L. Bernatchez. "Genome-wide patterns of divergence during speciation: the lake whitefish case study." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1587 (February 5, 2012): 354–63. http://dx.doi.org/10.1098/rstb.2011.0197.

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The nature, size and distribution of the genomic regions underlying divergence and promoting reproductive isolation remain largely unknown. Here, we summarize ongoing efforts using young (12 000 yr BP) species pairs of lake whitefish ( Coregonus clupeaformis ) to expand our understanding of the initial genomic patterns of divergence observed during speciation. Our results confirmed the predictions that: (i) on average, phenotypic quantitative trait loci (pQTL) show higher F ST values and are more likely to be outliers (and therefore candidates for being targets of divergent selection) than non-pQTL markers; (ii) large islands of divergence rather than small independent regions under selection characterize the early stages of adaptive divergence of lake whitefish; and (iii) there is a general trend towards an increase in terms of numbers and size of genomic regions of divergence from the least (East L.) to the most differentiated species pair (Cliff L.). This is consistent with previous estimates of reproductive isolation between these species pairs being driven by the same selective forces responsible for environment specialization. Altogether, dwarf and normal whitefish species pairs represent a continuum of both morphological and genomic differentiation contributing to ecological speciation. Admittedly, much progress is still required to more finely map and circumscribe genomic islands of speciation. This will be achieved through the use of next generation sequencing data but also through a better quantification of phenotypic traits moulded by selection as organisms adapt to new environmental conditions.

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Hsieh, Wen-Ping, Tzu-Ming Chu, Russell D. Wolfinger, and Greg Gibson. "Mixed-Model Reanalysis of Primate Data Suggests Tissue and Species Biases in Oligonucleotide-Based Gene Expression Profiles." Genetics 165, no. 2 (October 1, 2003): 747–57. http://dx.doi.org/10.1093/genetics/165.2.747.

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Abstract An emerging issue in evolutionary genetics is whether it is possible to use gene expression profiling to identify genes that are associated with morphological, physiological, or behavioral divergence between species and whether these genes have undergone positive selection. Some of these questions were addressed in a recent study (Enard et al. 2002) of the difference in gene expression among human, chimp, and orangutan, which suggested an accelerated rate of divergence in gene expression in the human brain relative to liver. Reanalysis of the Affymetrix data set using analysis of variance methods to quantify the contributions of individuals and species to variation in expression of 12,600 genes indicates that as much as one-quarter of the genome shows divergent expression between primate species at the 5% level. The magnitude of fold change ranges from 1.2-fold up to 8-fold. Similar conclusions apply to reanalysis of Enard et al.'s (2002) parallel murine data set. However, biases inherent to short oligonucleotide microarray technology may account for some of the tissue and species effects. At high significance levels, more differences were observed in the liver than in the brain in each of the pairwise species comparisons, so it is not clear that expression divergence is accelerated in the human brain. Further, there is an apparent bias toward upregulation of gene expression in the brain in both primates and mice, whereas genes are equally likely to be up- or downregulated in the liver when these species diverge. A small subset of genes that are candidates for adaptive divergence may be identified on the basis of a high ratio of interspecific to intraspecific divergence.

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Hui, Feng-Li, Qiu-Hong Niu, Tao Ke, and Zheng Liu. "Candida ficus sp. nov., a novel yeast species from the gut of Apriona germari larvae." International Journal of Systematic and Evolutionary Microbiology 62, Pt_11 (November 1, 2012): 2805–9. http://dx.doi.org/10.1099/ijs.0.044214-0.

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A novel yeast species is described based on three strains from the gut of wood-boring larvae collected in a tree trunk of Ficus carica cultivated in parks near Nanyang, central China. Phylogenetic analysis based on sequences of the D1/D2 domains of the large subunit rRNA gene showed that these strains occurred in a separate clade that was genetically distinct from all known ascomycetous yeasts. In terms of pairwise sequence divergence, the novel strains differed by 15.3 % divergence from the type strain of Pichia terricola, and by 15.8 % divergence from the type strains of Pichia exigua and Candida rugopelliculosa in the D1/D2 domains. All three are ascomycetous yeasts in the Pichia clade. Unlike P. terricola, P. exigua and C. rugopelliculosa, the novel isolates did not ferment glucose. The name Candida ficus sp. nov. is proposed to accommodate these highly divergent organisms, with STN-8T ( = CICC 1980T = CBS 12638T) as the type strain.

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Giraud, Tatiana, Lorys M. M. A. Villaréal, Frédéric Austerlitz, Mickaël Le Gac, and Claire Lavigne. "Importance of the Life Cycle in Sympatric Host Race Formation and Speciation of Pathogens." Phytopathology® 96, no. 3 (March 2006): 280–87. http://dx.doi.org/10.1094/phyto-96-0280.

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Numerous morphological species of pathogenic fungi have been shown to actually encompass several genetically isolated lineages, often specialized on different hosts and, thus, constituting host races or sibling species. In this article, we explore theoretically the importance of some aspects of the life cycle on the conditions of sympatric divergence of host races, particularly in fungal plant pathogens. Because the life cycles classically modeled by theoreticians of sympatric speciation correspond to those of free-living animals, sympatric divergence of host races requires the evolution of active assortative mating or of active host preference if mating takes place on the hosts. With some particular life cycles with restricted dispersal between selection on the host and mating, we show that divergence can occur in sympatry and lead to host race formation, or even speciation, by a mere process of specialization, with strong divergent adaptive selection. Neither active assortative mating nor active habitat choice is required in these cases, and this may explain why the phylo-genetic species concept seems more appropriate than the biological species concept in these organisms.

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Costa e Silva, João, Brad M. Potts, and Peter A. Harrison. "Population Divergence along a Genetic Line of Least Resistance in the Tree Species Eucalyptus globulus." Genes 11, no. 9 (September 18, 2020): 1095. http://dx.doi.org/10.3390/genes11091095.

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The evolutionary response to selection depends on the distribution of genetic variation in traits under selection within populations, as defined by the additive genetic variance-covariance matrix (G). The structure and evolutionary stability of G will thus influence the course of phenotypic evolution. However, there are few studies assessing the stability of G and its relationship with population divergence within foundation tree species. We compared the G-matrices of Mainland and Island population groups of the forest tree Eucalyptus globulus, and determined the extent to which population divergence aligned with within-population genetic (co)variation. Four key wood property traits exhibiting signals of divergent selection were studied—wood density, extractive content, and lignin content and composition. The comparison of G-matrices of the mainland and island populations indicated that the G-eigenstructure was relatively well preserved at an intra-specific level. Population divergence tended to occur along a major direction of genetic variation in G. The observed conservatism of G, the moderate evolutionary timescale, and close relationship between genetic architecture and population trajectories suggest that genetic constraints may have influenced the evolution and diversification of the E. globulus populations for the traits studied. However, alternative scenarios, including selection aligning genetic architecture and population divergence, are discussed.

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Emelianova, Katie, and Catherine Kidner. "COMPARATIVE TRANSCRIPTOME ANALYSIS OF TWO CLOSELY RELATED BEGONIA SPECIES REVEALS DIVERGENT PATTERNS IN KEY LIGHT-REGULATED PATHWAYS." Edinburgh Journal of Botany 79 (August 18, 2022): 1–18. http://dx.doi.org/10.24823/ejb.2022.398.

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Begonia is one of the most diverse angiosperm genera, comprising more than 2000 described species. The wide morphological and ecological range represented in the genus makes it a good model for studying the generation and maintenance of diversity. Previous research has shown that strong population structure, poor seed dispersal, and high levels of drift contribute to high rates of speciation and morphological variation. In the present study, we used transcriptomics to compare two closely related but morphologically and ecologically divergent species, Begonia conchifolia A.Dietr. and B. plebeja Liebm., to identify genes putatively involved in ecological divergence. Using publicly available multitissue RNA-seq data, we asked what genetic pathways show species-specific patterns of divergence between our two study species. The results of differential expression and gene ontology enrichment analyses showed species-specific enrichment of light-regulated functions in Begonia plebeja. Concomitant enrichment of ethylene and jasmonate pathways in Begonia plebeja indicate an increased shade avoidance response, suggesting that light availability may be a key factor in the divergent adaptation of B. conchifolia and B. plebeja.

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Neupane, Swatantra, and Sen Xu. "Adaptive Divergence of Meiotic Recombination Rate in Ecological Speciation." Genome Biology and Evolution 12, no. 10 (August 28, 2020): 1869–81. http://dx.doi.org/10.1093/gbe/evaa182.

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Abstract Theories predict that directional selection during adaptation to a novel habitat results in elevated meiotic recombination rate. Yet the lack of population-level recombination rate data leaves this hypothesis untested in natural populations. Here, we examine the population-level recombination rate variation in two incipient ecological species, the microcrustacean Daphnia pulex (an ephemeral-pond species) and Daphnia pulicaria (a permanent-lake species). The divergence of D. pulicaria from D. pulex involved habitat shifts from pond to lake habitats as well as strong local adaptation due to directional selection. Using a novel single-sperm genotyping approach, we estimated the male-specific recombination rate of two linkage groups in multiple populations of each species in common garden experiments and identified a significantly elevated recombination rate in D. pulicaria. Most importantly, population genetic analyses show that the divergence in recombination rate between these two species is most likely due to divergent selection in distinct ecological habitats rather than neutral evolution.

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Wakeley, John. "Polymorphism and Divergence for Island-Model Species." Genetics 163, no. 1 (January 1, 2003): 411–20. http://dx.doi.org/10.1093/genetics/163.1.411.

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Abstract Estimates of the scaled selection coefficient, γ of Sawyer and Hartl, are shown to be remarkably robust to population subdivision. Estimates of mutation parameters and divergence times, in contrast, are very sensitive to subdivision. These results follow from an analysis of natural selection and genetic drift in the island model of subdivision in the limit of a very large number of subpopulations, or demes. In particular, a diffusion process is shown to hold for the average allele frequency among demes in which the level of subdivision sets the timescale of drift and selection and determines the dynamic equilibrium of allele frequencies among demes. This provides a framework for inference about mutation, selection, divergence, and migration when data are available from a number of unlinked nucleotide sites. The effects of subdivision on parameter estimates depend on the distribution of samples among demes. If samples are taken singly from different demes, the only effect of subdivision is in the rescaling of mutation and divergence-time parameters. If multiple samples are taken from one or more demes, high levels of within-deme relatedness lead to low levels of intraspecies polymorphism and increase the number of fixed differences between samples from two species. If subdivision is ignored, mutation parameters are underestimated and the species divergence time is overestimated, sometimes quite drastically. Estimates of the strength of selection are much less strongly affected and always in a conservative direction.

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Yatskievych, George, and Robbin C. Moran. "Primary Divergence and Species Concepts in Ferns." American Fern Journal 79, no. 2 (April 1989): 36. http://dx.doi.org/10.2307/1547158.

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Hosken, David J., C. Ruth Archer, Clarissa M. House, and Nina Wedell. "Penis evolution across species: divergence and diversity." Nature Reviews Urology 16, no. 2 (November 5, 2018): 98–106. http://dx.doi.org/10.1038/s41585-018-0112-z.

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Alcaide, Miguel, Elizabeth S. C. Scordato, Trevor D. Price, and Darren E. Irwin. "Genomic divergence in a ring species complex." Nature 511, no. 7507 (May 25, 2014): 83–85. http://dx.doi.org/10.1038/nature13285.

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Kawabe, Akira, Hazuka Y. Furihata, Yudai Tsujino, Takahiro Kawanabe, Sota Fujii, and Takanori Yoshida. "Divergence of RNA editing among Arabidopsis species." Plant Science 280 (March 2019): 241–47. http://dx.doi.org/10.1016/j.plantsci.2018.12.009.

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Chen, Yi, Qian-Qian Su, Jiao Qin, and Quan-Sheng Liu. "Call divergence in three sympatric Rattus species." Journal of the Acoustical Society of America 142, no. 1 (July 2017): 29–34. http://dx.doi.org/10.1121/1.4990022.

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Journal articles on the topic 'Species divergence'

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