Phylogeography and genetic characteristics of a putative secondary-contact zone of the loggerhead shrike in central and eastern North America

2001 ◽  
Vol 79 (12) ◽  
pp. 2221-2227 ◽  
Author(s):  
M Vallianatos ◽  
S C Lougheed ◽  
P T Boag
Keyword(s):  
North America ◽  
Contact Zone ◽  
Sequence Data ◽  
Phylogeographic Structure ◽  
Secondary Contact ◽  
Eastern North America ◽  
Management Units ◽  
Genetic Characteristics ◽  
Loggerhead Shrike ◽  
The Impact

The loggerhead shrike (Lanius ludovicianus) is found throughout North America in grassland and open scrub habitats. We previously described four loggerhead shrike management units found in central and eastern North America within the geographic ranges of three subspecies, L. l. migrans, L. l. ludovicianus, and L. l. excubitorides. A contact zone has been suggested to occur between L. l. migrans and L. l. excubitorides. The present study uses mitochondrial DNA sequence data to explore historical, ecological, and geographical factors that may have played a role in the genetic differentiation of these four management units, and examines the evidence for and characteristics of the migrans–excubitorides contact zone. Geographically discrete, monophyletic clades were not evident, but the distribution of haplotypes (especially those exceeding 10% overall frequency) indicated some phylogeographic structure that perhaps reflects an intermediate stage of differentiation between paraphyly and reciprocal monophyly. The contact zone between L. l. migrans and L. l. excubitorides is supported by the mixing of haplotypes unique to each of the hybridizing populations and intermediate frequencies of common haplotypes. We interpret these patterns as possibly reflecting the impact of both glacial refugial dynamics and anthropogenic changes to habitat in eastern North America.

scholarly journals Evolutionary lessons from California plant phylogeography

2016 ◽  
Vol 113 (29) ◽  
pp. 8064-8071 ◽  
Author(s):  
Victoria L. Sork ◽  
Paul F. Gugger ◽  
Jin-Ming Chen ◽  
Silke Werth
Keyword(s):  
Genetic Variation ◽  
Spatial Distribution ◽  
Plant Traits ◽  
Sequence Data ◽  
Population Expansion ◽  
Phylogeographic Structure ◽  
Adaptive Genetic Variation ◽  
Local Selection ◽  
Isolation By Environment ◽  
The Impact

Phylogeography documents the spatial distribution of genetic lineages that result from demographic processes, such as population expansion, population contraction, and gene movement, shaped by climate fluctuations and the physical landscape. Because most phylogeographic studies have used neutral markers, the role of selection may have been undervalued. In this paper, we contend that plants provide a useful evolutionary lesson about the impact of selection on spatial patterns of neutral genetic variation, when the environment affects which individuals can colonize new sites, and on adaptive genetic variation, when environmental heterogeneity creates divergence at specific loci underlying local adaptation. Specifically, we discuss five characteristics found in plants that intensify the impact of selection: sessile growth form, high reproductive output, leptokurtic dispersal, isolation by environment, and the potential to evolve longevity. Collectively, these traits exacerbate the impact of environment on movement between populations and local selection pressures—both of which influence phylogeographic structure. We illustrate how these unique traits shape these processes with case studies of the California endemic oak, Quercus lobata, and the western North American lichen, Ramalina menziesii. Obviously, the lessons we learn from plant traits are not unique to plants, but they highlight the need for future animal, plant, and microbe studies to incorporate its impact. Modern tools that generate genome-wide sequence data are now allowing us to decipher how evolutionary processes affect the spatial distribution of different kinds of genes and also to better model future spatial distribution of species in response to climate change.

scholarly journals Phylogeography of southern New Zealand: Implications of Pliocene and Pleistocene Processes and Evolutionary Concordance Across Independent  Loci

2021 ◽  
Author(s):  
◽  
Shay B. O'Neill
Keyword(s):  
New Zealand ◽  
Sequence Data ◽  
Genetic Data ◽  
Phylogeographic Structure ◽  
The South ◽  
The North ◽  
Genealogical Concordance ◽  
Cook Strait ◽  
The Impact ◽  
Genetic Break

<p>The endemic fauna of the South Island has proven to be an ideal taxonomic group to examine the impact of climatic and geological processes on the evolution of New Zealand's biota since the Pliocene. This thesis examines the phylogeography of McCann's skink (Oligosoma maccanni) in order to provide insight into the relative contribution of Pliocene and Pleistocene processes on patterns of genetic structure in South Island biota. This thesis also investigates the phylogeography of the brown skink (O. zelandicum) to examine whether Cook Strait landbridges facilitated gene flow between the North and South Island in the late-Pleistocene. This thesis also investigates the presence of genealogical concordance across independent loci for the endemic alpine stick insect, Niveaphasma. I obtained mitochondrial DNA (mtDNA) sequence data (ND2 and ND4; 1284 bp) from across the range of both skink species and mtDNA (COI; 762 bp) and nuclear sequence data (EF1 ; 590 bp) from across the range of Niveaphasma. I used DGGE in order to resolve nuclear EF1 alleles and examined phylogeographic patterns in each species using Neighbour-Joining, Maximum Likelihood and Bayesian methods. Substantial phylogeographic structure was found within O. maccanni, with divergences among clades estimated to have occurred during the Pliocene. Populations in the Otago/Southland region formed a well-supported lineage within O. maccanni. A genetic break was evident between populations in east and west Otago, while north-south genetic breaks were evident within the Canterbury region. There was relatively minor phylogeographic structure within O. zelandicum. Our genetic data supports a single colonization of the North Island by O. zelandicum from the South Island, with the estimated timing of this event (0.46 Mya) consistent with the initial formation of Cook Strait. There was substantial genetic structuring identified within Niveaphasma, with a well-supported lineage present in the Otago/Southland region. There was also a genetic break between populations in Canterbury and eastern Otago with those in central Otago and Southland. The genetic data provided strong genealogical concordance between mtDNA haplotypes and nuclear alleles suggesting an accurate depiction of the historical isolation identified between the major clades of Niveaphasma. This finding offers compelling evidence for the use of nuclear gene  phylogeography alongside mtDNA for future evolutionary studies within New Zealand.</p>

scholarly journals Phylogeography of the American Woodcock (Scolopax Minor): Are Management Units Based on Band Recovery Data Reflected in Genetically Based Management Units?

The Auk ◽  
2005 ◽  
Vol 122 (4) ◽  
pp. 1149-1160
Author(s):  
Judith M. Rhymer ◽  
Daniel G. McAuley ◽  
Heather L. Ziel
Keyword(s):  
Gene Flow ◽  
North America ◽  
Haplotype Diversity ◽  
Bird Species ◽  
Population Expansion ◽  
Phylogeographic Structure ◽  
Eastern Region ◽  
Management Units ◽  
American Woodcock ◽  
Scolopax Minor

Abstract Information on population connectivity throughout the annual cycle has become more crucial, because populations of many migratory birds are in decline. One such species is the American Woodcock (Scolopax minor), which inhabits early-successional forests in eastern North America. Although band recoveries have proved useful for dividing populations of this game bird species into an Eastern Region and Central Region for management purposes, these data do not provide enough detail to determine the breeding population of origin of birds recovered on stopover and wintering areas. To obtain more fine-scale data, we undertook a phylogeographic study of American Woodcock populations throughout their primary breeding range in the eastern United States and Canada using mitochondrial DNA (mtDNA) sequences from the hypervariable control region I (CRI) and ND6 gene. Despite high haplotype diversity, nucleotide diversity was low and there was no phylogeographic structure among American Woodcock populations across the species range, with birds from many states and provinces in both management regions sharing identical haplotypes. Results suggest recent or ongoing gene flow among populations, with asymmetric movement of birds between migration flyways. As has been demonstrated for several other avian species in North America, American Woodcock appear to have undergone a rapid population expansion following the late Pleistocene glacial retreat. Thus, a combination of historical demographic factors and recent or ongoing gene flow mask any population structure based on mtDNA that might accrue from philopatry to breeding areas observed in studies of marked birds. Phylogéographie de Scolopax minor: Est-ce que les Unités de Gestion Basées sur les Données de Retour de Bagues Reflètent les Unités de Gestion Basées sur la Génétique?

scholarly journals Introduced Prophysaon andersonii (J.G. Cooper, 1872) in Quebec, Canada: first record of Prophysaon (Gastropoda, Eupulmonata, Arionoidea) in eastern North America, confirmed by partial-COI gene sequence

Check List ◽  
2020 ◽  
Vol 16 (2) ◽  
pp. 307-316
Author(s):  
Annegret Nicolai ◽  
Robert G. Forsyth
Keyword(s):  
North America ◽  
New Record ◽  
Gene Sequence ◽  
Sequence Data ◽  
First Record ◽  
Coi Gene ◽  
Eastern North America ◽  
Western North America ◽  
Native Range ◽  
First Time

We report for the first time the terrestrial slug Prophysaon andersonii (J.G. Cooper, 1872) from Quebec, Canada. Two specimens were collected in Parc national du Bic. The identification was determined by the external morphology and partial-COI gene sequence data. The genus Prophysaon is endemic to western North America, and the new record indisputably represents an introduction. No species of Prophysaon has, until now, been noticed in North America from outside its native range.

An exotic insect and pathogen disease complex reduces aboveground tree biomass in temperate forests of eastern North America

2011 ◽  
Vol 41 (2) ◽  
pp. 401-411 ◽  
Author(s):  
Posy E. Busby ◽  
Charles D. Canham
Keyword(s):  
North America ◽  
Negative Relationship ◽  
Fagus Grandifolia ◽  
Carbon Accumulation ◽  
Host Tree ◽  
Eastern North America ◽  
Tree Biomass ◽  
Growth And Survival ◽  
The Impact ◽  
Aboveground Tree Biomass

Forests store a large portion of global carbon in tree and soil biomass. However, our understanding of the factors that may reduce rates of forest carbon accumulation is incomplete. This study examines the impact of an exotic insect and fungal pathogen disease on aboveground tree biomass in forests of eastern North America. We determine how beech bark disease (BBD) — a pervasive but nonextirpating disease — influences the growth and survival of its host tree, Fagus grandifolia Ehrh., and the effects of changes in the demography of this late-successional dominant tree species on total stand-level aboveground tree biomass. Our analyses use US Forest Service Forest Inventory and Analysis data from eastern states located along a gradient in the time since introduction of BBD. In Maine, where BBD has been present for >50 years, we observed reduced growth and survival of the host tree and reduced overall stand-level aboveground tree biomass compared with states where BBD arrived more recently. Additionally, there is a negative relationship between host tree abundance and overall stand-level aboveground tree biomass. Where beech is most abundant, BBD results in substantial declines in aboveground tree biomass (e.g., 11% in Maine); where beech is less abundant, we expect more modest declines (1%–4%).

scholarly journals Phylogeography of southern New Zealand: Implications of Pliocene and Pleistocene Processes and Evolutionary Concordance Across Independent  Loci

2021 ◽  
Author(s):  
◽  
Shay B. O'Neill
Keyword(s):  
New Zealand ◽  
Sequence Data ◽  
Genetic Data ◽  
Phylogeographic Structure ◽  
The South ◽  
The North ◽  
Genealogical Concordance ◽  
Cook Strait ◽  
The Impact ◽  
Genetic Break

<p>The endemic fauna of the South Island has proven to be an ideal taxonomic group to examine the impact of climatic and geological processes on the evolution of New Zealand's biota since the Pliocene. This thesis examines the phylogeography of McCann's skink (Oligosoma maccanni) in order to provide insight into the relative contribution of Pliocene and Pleistocene processes on patterns of genetic structure in South Island biota. This thesis also investigates the phylogeography of the brown skink (O. zelandicum) to examine whether Cook Strait landbridges facilitated gene flow between the North and South Island in the late-Pleistocene. This thesis also investigates the presence of genealogical concordance across independent loci for the endemic alpine stick insect, Niveaphasma. I obtained mitochondrial DNA (mtDNA) sequence data (ND2 and ND4; 1284 bp) from across the range of both skink species and mtDNA (COI; 762 bp) and nuclear sequence data (EF1 ; 590 bp) from across the range of Niveaphasma. I used DGGE in order to resolve nuclear EF1 alleles and examined phylogeographic patterns in each species using Neighbour-Joining, Maximum Likelihood and Bayesian methods. Substantial phylogeographic structure was found within O. maccanni, with divergences among clades estimated to have occurred during the Pliocene. Populations in the Otago/Southland region formed a well-supported lineage within O. maccanni. A genetic break was evident between populations in east and west Otago, while north-south genetic breaks were evident within the Canterbury region. There was relatively minor phylogeographic structure within O. zelandicum. Our genetic data supports a single colonization of the North Island by O. zelandicum from the South Island, with the estimated timing of this event (0.46 Mya) consistent with the initial formation of Cook Strait. There was substantial genetic structuring identified within Niveaphasma, with a well-supported lineage present in the Otago/Southland region. There was also a genetic break between populations in Canterbury and eastern Otago with those in central Otago and Southland. The genetic data provided strong genealogical concordance between mtDNA haplotypes and nuclear alleles suggesting an accurate depiction of the historical isolation identified between the major clades of Niveaphasma. This finding offers compelling evidence for the use of nuclear gene  phylogeography alongside mtDNA for future evolutionary studies within New Zealand.</p>

scholarly journals Genomewide evidence of environmentally mediated secondary contact of European green crab (Carcinus maenas) lineages in eastern North America

2018 ◽  
Vol 11 (6) ◽  
pp. 869-882 ◽  
Author(s):  
Nicholas W. Jeffery ◽  
Ian R. Bradbury ◽  
Ryan R. E. Stanley ◽  
Brendan F. Wringe ◽  
Mallory Van Wyngaarden ◽  
...  
Keyword(s):  
North America ◽  
Carcinus Maenas ◽  
Green Crab ◽  
Secondary Contact ◽  
Eastern North America ◽  
European Green Crab

Characterization of a secondary contact zone of the Great Tit Parus major and the Japanese Tit P. minor (Aves: Passeriformes) in Far Eastern Siberia with DNA markers

Zootaxa ◽  
2006 ◽  
Vol 1325 (1) ◽  
pp. 55 ◽  
Author(s):  
LAURA KVIST ◽  
SEPPO RYTKÖNEN
Keyword(s):  
Contact Zone ◽  
Dna Sequences ◽  
Parus Major ◽  
Great Tit ◽  
Secondary Contact ◽  
Hybrid Fitness ◽  
Genetic Characteristics ◽  
Phenotypic Characters ◽  
Secondary Contact Zone ◽  
Far Eastern

The Great Tit Parus major and the Japanese Tit P. minor meet and hybridize in a secondary contact zone in Far Eastern Amur River Valley. The genetic characteristics of this hybrid zone were studied by nuclear microsatellites and mitochondrial DNA sequences. Patterns of introgression of nuclear markers, mitochondrial markers and phenotypic characters were found to be different. The possible reasons, such as stronger selection against heterogametic females according to Haldane’s rule, lowered hybrid fitness, assortative mating and factors enforcing introgression, like density-dependent pair-formation, are discussed.

scholarly journals The Influence of Chronic Ozone Exposure on Global Carbon and Water Cycles

2014 ◽  
Vol 28 (1) ◽  
pp. 292-305 ◽  
Author(s):  
D. Lombardozzi ◽  
Samuel Levis ◽  
G. Bonan ◽  
P. G. Hess ◽  
J. P. Sparks
Keyword(s):  
United States ◽  
Stomatal Conductance ◽  
North America ◽  
Southeast Asia ◽  
Greenhouse Gas ◽  
Eastern North America ◽  
Plant Responses ◽  
Eastern United States ◽  
Community Land Model ◽  
The Impact

Abstract Ozone (O3) is a phytotoxic greenhouse gas that has increased more than threefold at Earth’s surface from preindustrial values. In addition to directly increasing radiative forcing as a greenhouse gas, O3 indirectly impacts climate through altering the plant processes of photosynthesis and transpiration. While global estimates of gross primary productivity (GPP) have incorporated the effects of O3, few studies have explicitly determined the independent effects of O3 on transpiration. In this study, the authors include effects of O3 on photosynthesis and stomatal conductance from a recent literature review to determine the impact on GPP and transpiration and highlight uncertainty in modeling plant responses to O3. Using the Community Land Model, the authors estimate that present-day O3 exposure reduces GPP and transpiration globally by 8%–12% and 2%–2.4%, respectively. The largest reductions were in midlatitudes, with GPP decreasing up to 20% in the eastern United States, Europe, and Southeast Asia and transpiration reductions of up to 15% in the same regions. Larger reductions in GPP compared to transpiration decreased water-use efficiency 5%–10% in the eastern United States, Southeast Asia, Europe, and central Africa; increased surface runoff more than 15% in eastern North America; and altered patterns of energy fluxes in the tropics, high latitudes, and eastern North America. Future climate predictions will be improved if plant responses to O3 are incorporated into models such that stomatal conductance is modified independently of photosynthesis and the effects on transpiration are explicitly considered in surface energy budgets. Improvements will help inform regional decisions for managing changes in hydrology and surface temperatures in response to O3 pollution.

scholarly journals Phylogenomics and biogeography of Wisteria (Fabaceae), with implication on plastome evolution of inverted repeat-lacking clade

2019 ◽  
Author(s):  
Mao-Qin Xia ◽  
Ren-Yu Liao ◽  
Jin-Ting Zhou ◽  
Han-Yang Lin ◽  
Jian-Hua Li ◽  
...  
Keyword(s):  
North America ◽  
Late Miocene ◽  
North American ◽  
Inverted Repeat ◽  
Disjunct Distribution ◽  
Eastern North America ◽  
Eastern Asia ◽  
Asian Continent ◽  
The Impact ◽  
Japanese Islands

Abstract Background: The inverted repeat-lacking clade (IRLC) of Fabaceae is characterized by loss of an IR region in plastomes. Both the loss of an IR region and the life history may have affected the evolution of the plastomes in the clade. Nevertheless, few studies have been done to test the impact explicitly. Wisteria , an important member of IRLC and has a disjunct distribution between eastern Asia and eastern North America, has confused interspecific relationships and biogeography, which need to elucidate in depth. Results: The plastome of six newly sequenced Wisteria species and a Millettia japonica ranged from 130,116 to 132,547 bp. Phylogenetic analyses recognized two major clades in IRLC: Glycyrrhiza - Millettia - Wisteria clade and a clade containing the remaining genera. North American Wisteria species and Asian species formed reciprocal clades. Within Asian clade, each of the two Japanese species was sister to a species in the Asian continent. A ~16kb inversion from ndh F to ycf 1 in all IRLC species. Wisteria and Millettia japonica have two intron of rps 12 gene but all other IRLC species just have one. Synonymous substitution rates ( d S ) of protein coding genes were higher in the IRLC species than non-IRLC species. Woody species have lower substitutions rates than herbs. Wisteria may have originated in East Asia by the boundary of Oligocene and Miocene and the eastern Asian-eastern North American disjunction formed in the Late Miocene, while two vicariance events formed the disjunct distributions between the Asian continent and the Japanese islands in the Quaternary. Conclusions: In the IRLC clade, Wisteria , Milletia japonica and Glycyrrhiza form a clade to the remaining genera, most of which are herbaceous. Both the loss of one IR region and the herbaceous habit elevated mutation rates of the plastomes. Multiple vicariance events between eastern Asia and eastern North America, and between the Asian continent and the Japanese Islands may have promoted speciation of Wisteria since the Late Miocene. Plastomes contain rich genetic diversity for studying genetic structure and migration of populations in response to climatic changes, which benefits conservation of rare and endangered species.

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