Selected). Barrowclough, G.F., R.J. Gutiérrez, J.G. Groth, J.E. Lai, and D. Rock. 2011. The hybrid zone between Northern and California Spotted Owls in the Cascade-Sierran suture zone. Condor 113:581-589.. Barrowclough, G.F., J.G. Groth, K.J. Odom, and J.E. Lai. 2011. Phylogeography of the Barred Owl (Strix varia): species limits, multiple refugia, and range expansion. Auk 128:696-706.. Perktas, U., G.F. Barrowclough, and J.G. Groth. 2011. Phylogeography and species limits in the green woodpecker (Picus viridis) complex; Pleistocene refugia and range expansion across Europe and the Near East. Biological Journal of the Linnaean Society 104:710-723.. Zink, R.M., J.G. Groth, H. Vazquez-Miranda, and G.F. Barrowclough. 2013. Phylogeography of the California Gnatcatcher (Polioptila californica) using multi-locus DNA sequences and ecological niche modeling: implications for conservation. Auk 130:449-458.. Barrowclough, G.F., J.G. Groth, J.E. Lai, and S.M. Tsang. 2014. The phylogenetic relationships of ...
Human immunodeficiency virus type 2 (HIV-2) emerged in West Africa and has spread further to countries that share socio-historical ties with this region. However, viral origins and dispersal patterns at a global scale remain poorly understood. Here, we adopt a Bayesian phylogeographic approach to investigate the spatial dynamics of HIV-2 group A (HIV-2A) using a collection of 320 partial pol and 248 partial env sequences sampled throughout 19 countries worldwide ...
Background The marginal seas of northwestern Pacific are characterized by unique topography and intricate hydrology. Two hypotheses have been proposed to explain genetic patterns of marine species inhabiting the region: the historical glaciations hypothesis suggests population genetic divergence between sea basins, whereas the Changjiang River outflow hypothesis suggests genetic break in line with the Changjiang Estuary. Here the phylogeography of bivalve Cyclina sinensis was investigated to test the validity of these two hypotheses for intertidal species in three marginal seas-the East China Sea (ECS), the South China Sea (SCS), and the Japan Sea (JPS). Methodology/Principal Findings Fragments of two markers (mitochondrial COI and nuclear ITS-1) were sequenced for 335 individuals collected from 21 populations. Significant pairwise ΦST were observed between different marginal sea populations. Network analyses illustrated restricted distribution of haplogroups/sub-haplogroups to sea basins, with a
Liu, Y. P., Ren, Z. M., Harris, AJ, Peterson, Paul M., Wen, Jun, and Su, X. 2018. "Phylogeography of Orinus (Poaceae), a dominant grass genus on the Qinhai-Tibet Plateau." Botanical Journal of the Linnean Society. 186:202-223. https://doi.org/10.1093/botlinnean/box091 ...
Novel HIV-1 Recombinants Spreading across Multiple Risk Groups in the United Kingdom: The Identification and Phylogeography of Circulating Recombinant Form CRF 50 A1D. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Simulated mismatch distributions for each species and molecular marker.Observed mismatch distributions are represented by the bar graphs, while the curve repres
The application of phylogenetic and genomic analyses to the study of animal biodiversity and evolution, with a specific focus on mammals, is the main goal of the Phylogeny and Phylogeography of Mammals lab. Using next-generation sequencing techniques and advanced bioinformatics tools, the population divergence and speciation process in different species complexes are analysed in order to obtain a better description of our biological diversity. These modern methodologies are also used to study kinship relationships and connectivity between populations in some species of great conservation importance, such as the Pyrenean desman.. Lab website: Castresana Lab. ...
Outline Concept & Development The main scientific questions To infer the demographic history of important species To understand the mechanisms of speciation To identify the different species Perspectives
Having a phylogenetic hypothesis of a group of interest is fundamental for understanding the evolution of species traits, species relations in space and time, and factors promoting their diversification. I have investigated this in detail in a number of fish groups, such as Iberian nases and Iberian and Italian barbels. I have recently used phylogenomic…
Aim Analytical methods are commonly used to identify historical processes of vicariance and dispersal in the evolution of taxa. Currently, dispersal-vicariance analysis implemented in the software diva is the most widely used method. Despite some recognized shortcomings of the method, it has been treated as error-free in many cases and used extensively as the sole method to reconstruct histories of taxa. In light of this, an evaluation of the limitations of the method is needed, especially in relation to several newer alternatives.. Methods In an approach similar to simulation studies in phylogenetics, I use hypothetical taxa evolving in specific geological scenarios and test how well diva reconstructs their histories.. Results diva reconstructs histories accurately when evolution has been simple; that is, where speciation is driven mainly by vicariance. Ancestral areas are wrongly identified under several conditions, including complex patterns of dispersals and within-area speciation events. ...
Regional phylogeographical studies involving co-distributed animal and plant species have been conducted for several areas, most notably for Europe and the Pacific Northwest of North America. Until recently, phylogeographical studies in unglaciated eastern North America have been largely limited to animals. As more studies emerge for diverse lineages (including plants), it seems timely to assess the phylogeography across this region: (i) comparing and contrasting the patterns seen in plants and animals; (ii) assessing the extent of pseudocongruence; and (iii) discussing the potential applications of regional phylogeography to issues in ecology, such as response to climatic change. Unglaciated eastern North America is a large, geologically and topographically complex area with the species examined having diverse distributions. Nonetheless, some recurrent patterns emerge: (i) maritime - Atlantic vs. Gulf Coast; (ii) Apalachicola River discontinuity; (iii) Tombigbee River discontinuity; (iv) the ...
Aquatic vascular plants are a distinctive group, differing from terrestrial plants in their growth forms and habitats. Among the various aquatic plant life forms, the evolutionary processes of freshwater submerged species are most likely distinct due to their exclusive occurrence in the discrete and patchy aquatic habitats. Using the chloroplast trnL-F region sequence data, we investigated the phylogeographic structure of a submerged macrophyte, Hydrilla verticillata, the single species in the genus Hydrilla, throughout China, in addition to combined sample data from other countries to reveal the colonisation and diversification processes of this species throughout the world. We sequenced 681 individuals from 123 sampling locations throughout China and identified a significant phylogeographic structure (NST | GST, p | 0.01), in which four distinct lineages occurred in different areas. A high level of genetic differentiation among populations (global FST = 0.820) was detected. The divergence of Hydrilla
Read "Phylogeography of the Siberian newt Salamandrella keyserlingii by mitochondrial DNA sequence analysis, Russian Journal of Genetics" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Aim We carried out a phylogeographic study across the range of the herbaceous plant species Monotropa hypopitys L. in North America to determine whether its current disjunct distribution is due to ...
Since the beginning of the semester, we have been learned that the geographic distributions of organisms are determined by historical and ecological mechanisms. We also have learned some of the methodology that has been applied in historical biogeography studies. My last two posts were dedicated to historical biogeography, its pattern-based methodology, and assumptions. But I have not yet described an event-based methodology…. In event-based approaches, the processes responsible for taxa distribution are analyzed and the events are weight modeled. One example of event-based approach is the Dispersal-vicariance analysis -DIVA. It reconstructs the ancestral range distribution of a particular group of organisms, minimizing the dispersal events needed for explaining the distributions. In this approach, the vicariance events have no cost, while the dispersals and extinctions cost one per area unit added to the distribution (Gomez & Lobo, 2006). This method was first applied to the theory of ...
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If a pond is located within 500 m of your development site then the potential presence of great crested newts will have to be considered. This is usually incorporated into a Preliminary Ecological Appraisal (PEA) where local biological records and a habitat suitability assessment will determine whether further surveys are required. Following on from this eDNA can be used to determine presence/absence of great crested newts however more in depth surveying to determine the population size will be required if a pond to be impacted by works is found to have great crested newts.. Natterjack toad surveys will be required where historical records suggest they may be present and suitable habitat is located within or near to your development site. The distribution of natterjack toads is quite restricted in the UK, being almost exclusively confined to coastal sand dunes, grazing marshes and sandy heaths.. If you have any queries regarding the services your project may require, please contact our ...
Varieties distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political difficulties for data collection across such areas. genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may symbolize currently unrecognized unique varieties. One major clade, comprising 25 divergent lineages, includes samples from the type locality of complex. The remaining lineages together with the complex constitute the varieties group. Historic analyses support an Amazonian source for the varieties group having a subsequent dispersal to eastern Brazil where the complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km2. One of them occupies an certain part of nearly a single million kilometres2 encompassing multiple biomes. Our results, at a spatial quality ...
Biogeographic region: Biogeographic region, area of animal and plant distribution having similar or shared characteristics throughout. It is a matter of general experience that the plants and
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In statistics, coherent measures of fit of nested and overlapping composite hypotheses are technically those measures that are consistent with the constraints of formal logic. For example, the probability of the nested special case must be less than or equal to the probability of the general model within which the special case is nested. Any…
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Phylogeographical analyses on Squalidus argentatus samples from thirteen localities within mainland China and Taiwan were conducted for biogeographic studies, as their dispersal strictly depends on geological evolution of the landmasses. A total of 95 haplotypes were genotyped for mtDNA cyt b gene in 160 specimens from nine river systems. Relatively high levels of haplotype diversity (h = 0.984) and low levels of nucleotide diversity (π = 0.020) were detected in S. argentatus. Two major phylogenetic haplotype groups, A and B, were revealed via phylogenetic analysis. The degree of intergroup divergence (3.96%) indicates that these groups diverged about 4.55 myr (million years) ago. Haplotype network and population analyses indicated significant genetic structure (FST = 0.775), largely concordant with the geographical location of the populations. According to SAMOVA analysis, we divided these populations into four units: Yangtze-Pearl, Qiantang-Minjiang, Jiulong-Beijiang and Taiwan groups. Mismatch
Since Darwins time, waterbirds have been considered an important vector for the dispersal of continental aquatic invertebrates. Bird movements have facilitated the worldwide invasion of the American brine shrimp Artemia franciscana, transporting cysts (diapausing eggs), and favouring rapid range expansions from introduction sites. Here we address the impact of bird migratory flyways on the population genetic structure and phylogeography of A. franciscana in its native range in the Americas. We examined the sequence variation for two mitochondrial gene fragments (COI and 16S for a subset of the data) in a large set of population samples representing the entire native range of A. franciscana. Furthermore, we performed Mantel tests and redundancy analyses (RDA) to test the role of flyways, geography and human introductions on the phylogeography and population genetic structure at a continental scale. A. franciscanamitochondrial DNA was very diverse, with two main clades, largely corresponding to Pacific
Investigating variation in complete mitochondrial genomes across the red muntjac distribution range enabled us to examine the evolutionary history of these populations, including phylogeographic structure and historical demography. The high genetic diversity within, and large divergence among the main clades indicate a long-term separation of these clades, which in turn implies that red muntjacs had spread across South and Southeast Asia shortly after their split from other muntjac species. We found, however, evidence for two geographic barriers that (i) separated populations from northern India and Sri Lanka + Western Ghats and (ii) separated Sundaic and Mainland populations.. The Sri Lanka clade split first from the other two populations around 1.5 Mya and our data provides the first molecular evidence for its distinction. Due to the low number of samples obtained from this region we were unable to further assess their evolutionary history and genetic diversity. Other authors, who regarded the ...
The Biomeme Great Crested Newt (Triturus cristatus) M1 Go-Kit for eDNA is an end-to-end mobile solution for the detection of Great Crested Newt, also known as Northern Crested Newt or Warty Newt, environmental DNA from filtered water samples.
The Biomeme Great Crested Newt (Triturus cristatus) M1 Go-Kit for eDNA is an end-to-end mobile solution for the detection of Great Crested Newt, also known as Northern Crested Newt or Warty Newt, environmental DNA from filtered water samples.
The historical demography of the populations of domestic pigs in Europe and China was examined using mismatch distributions, which represent the frequency distribution of pairwise differences among all sampled haplotypes. Theoretical studies have shown that population bottlenecks and population expansions have a strong effect on the pattern of genetic polymorphism among haplotypes in the population (Rogers & Harpending 1992). For instance, populations in long and stable demographic equilibrium have multimodal mismatch distribution (ragged and chaotic) whereas the distribution appears unimodal after recent demographic expansions (Rogers & Harpending 1992; Harpending 1994). The mismatch distributions as well as the network analysis were consistent with population expansions in the ancestors for both contemporary Chinese and European domestic pigs (figures 3 and 4). The crucial question is whether the population expansion occurred before or after domestication. Similar signatures of population ...
The phylogeographic structure of Lampides boeticus was remarkable in two respects. While most sampled populations had little or no genetic variation across half the planet, a small number of specimens from widely spaced locales were highly divergent from the most common haplotypes, yet relatively similar to each other.. As currently circumscribed, L. boeticus appears to be monophyletic with respect to the outgroups included in this analyses, and is nested within a wholly African clade. While we acknowledge the possibility that some extant species may have relictual distributions, it seems plausible - given the number of exclusively African close relatives - that the most recent common ancestor from which Lampides and its sister taxon evolved originated in Africa and spread eastward across the Old World. Descendants from early expansion events (clades C and D) appear to have been largely replaced throughout much of the range by descendants from expansion events after one or more recent ...
An abundant and globally occurring marine picocyanobacterium, the genus Synechococcus is an important player in oceanic primary production and global carbon cycling. In the complex marine environment, this widespread organism has evolved to successfully colonize and inhabit different environmental niches. Their biogeographic distribution suggests that Synechococcus ecotypes exhibit thermal niche preferences. Temperature is a key environmental variable and the elucidation of the temperature stress acclimation in members of this genus can shed light on the molecular mechanisms involved in their adaptive capability. The growth of four representative Synechococcus isolates of various ecotypes from tropical and temperate regions were monitored under various temperature conditions. This revealed drastic differences in growth rates in correlation with their thermal niche preferences. The temperate strains CC9311 and BL107 displayed higher growth rates at lower temperatures while tropical strains WH8102 ...
We are interested in the mechanisms behind the proximal processes of evolution - those that lead to population differentiation, divergence and ultimately speciation. Our group specialises in terrestrial invertebrates because their abundance and low dispersal rates make them excellent models for addressing basic evolutionary principles. Currently we are studying huntsman and
inbreeding, if not totally selfing, and thus does not ex- perience sexual recombination. The equivalence of the number of genotypes with the number of hybrid origins, therefore, appears to be a valid assumption in this species.) Alternatively, the existing populations could be remnants of a once more continuous, southern Rocky Mountain metapopulation, most of which has gone extinct. Even under the latter scenario, however, one must invoke dis- persal from a single original point of hybridization with subsequent reduction in population size.. The genetic identities among the continental U.S. pop- ulations may be particularly significant in unraveling the biogeographic history of this species in light of its tetra- ploid nature. Werth and Windham (1991) proposed a model of speciation of allopatric populations of polyploid pteridophytes involving reciprocal silencing of alternate alleles at homoeologous loci, and several empirical studies have documented such reciprocal silencing in disjunct, ...
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The slender salamanders genus, Batrachoseps (Plethodontidae), is the most speciose groupof caudate amphibians in the western nearctic zone. All clades and even species within these groupsshow a marked phylogeographic structure, although there is often a discrepancy between mtDNAand nDNA (allozymes) datasets. Batrachoseps species are morphologically cryptic and ecologicallyvery similar. Slender salamander species do not merge when a parapatry occurs and sympatry islimited especially within clade ...
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Amorim, D. de S. and S. H. S. Tozzoni. 1994. Phylogenetic and biogeographic analysis of the Anisopodoidea (Diptera, Bibionomorpha), with an area cladogram for intercontinental relationships. Rev. Bras. Entomol. 38:517-543.. Amorim, D. de S. and E. Rindal. 2007. Phylogeny of the Mycetophiliformia, with proposal of subfamilies Heterotrichinae, Ohakuneinae, and Chiletrichinae for the Rangomaramidae (Dipter, Bibionomorpha. Zootaxa 1535:1-92.. Jaschhof, M. and R. K. Didham. 2002. Rangomaramidae fam. nov. from New Zealand and implications for the phylogeny of the Sciaroidea (Diptera: Bibionomorpha). Studia Dipt. Suppl. 11.. Oosterbroek, P. and G. Courtney. 1995. Phylogeny of the nematocerous families of Diptera (Insecta). Zool. J. Linn. Soc. 115:267-311.. Sinclair, B. J. 1992. A phylogenetic interpretation of the Brachycera (Diptera) based on the larval mandible and associated mouthpart structures. Syst. Entomol. 17:233-252.. Wood, D. M. and A. Borkent 1989. Phylogeny and classification of the ...
We sequenced 20 new, field-collected individuals for up to seven genes to explore the phylogeography and conservation genetics of the threatened Nile softshell turtle Trionyx triunguis, including the...
The importance of islands in revealing evolutionary processes has been recognized since Darwins work on the Galapagos (Darwin, 1909) and Wallaces work in the Malay Archipelago (Wallace, 1876). Since, island biogeography has provided many elegant...
Ive developed a mild interest in East-West phylogeography in Europe in regards to human populations. In the process I stumbled onto this paper, Geographical heterogeneity of Y-chromosomal lineages in Norway. Ive put the full PDF in the forum, here. Standard caveat, take this with a grain of salt!!! But, Ive put some maps below that readers might find of interest ...
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