Phylogeographic structure, gene flow and species status in blue grouse (Dendragapus obscurus)

Abstract We examined phylogeographic structure in the direct-developing New Zealand endemic intertidal mud whelk, Cominella glandiformis. Two hundred and ninety-six whelks from 12 sites were collected from sheltered shores around New Zealand’s four largest islands (North Island, South Island, Stewart Island and Chatham Island), encompassing the geographical range of this species. Despite being direct developers, gene flow among C. glandiformis populations may occur over short distances by adult floating, and over larger distances by rafting of egg masses. Primers were developed to amplify variable microsatellite regions at six loci. All loci were variable, with 8–34 alleles/loci. Observed and expected heterozygosities were high across all alleles, with minimal evidence of null alleles. The average number of alleles varied from 3.5 (Chatham Island) to 7.5 (Waitemata Harbour). Strong genetic structure was evident, with distinct ‘eastern’ and ‘western’ groups. Each group extended over a large geographic area, including regions of unsuitable habitat, but were linked by oceanic currents. We suggest that the intraspecific geographic genetic structure in C. glandiformis has arisen due a combination of ocean currents (promoting gene flow between geographically distant regions) and upwelling areas (limiting gene flow between certain regions).

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Mitochondrial DNA Variation, Species Limits, and Rapid Evolution of Plumage Coloration and Size in the Savannah Sparrow

The Condor ◽

10.1093/condor/107.1.21 ◽

2005 ◽

Vol 107 (1) ◽

pp. 21-28 ◽

Cited By ~ 1

Author(s):

Robert M. Zink ◽

James D. Rising ◽

Steve Mockford ◽

Andrew G. Horn ◽

Jonathan M. Wright ◽

...

Keyword(s):

Mitochondrial Dna ◽

Nova Scotia ◽

San Diego ◽

Baja California ◽

Rapid Evolution ◽

Plumage Coloration ◽

Phylogeographic Structure ◽

Species Status ◽

Passerculus Sandwichensis ◽

Savannah Sparrows

Abstract We compared sequences from two mitochondrial DNA (mtDNA) genes (ND2, ND3) in Savannah Sparrows (Passerculus sandwichensis; n = 112) sampled from Baja California (five sites), coastal Sonora and the continental range (eight sites). Populations from Baja California, San Diego and Sonora formed a clade within which there was no phylogeographic structure; this clade merits species status (Passerculus rostratus). The other clade, consisting of phenotypically “typical” savannah sparrows, should be classified as P. sandwichensis. Among the typical sparrows, there was no phylogeographic structure, although two major clades were discovered. Representatives of each of the two main clades occurred at most sampling localities, excluding Suisan Bay, California and Sable Island, Nova Scotia, Canada. Haplotypes found on Sable Island, representing the “Ipswich Sparrow,” were not distinctive, thereby failing to support species status for this taxon. On Isla San Benito, a single haplotype was found, which also occurred in other Mexican localities. The results for Sable Island and Isla San Benito show that size and plumage coloration can evolve rapidly. Variación en ADN Mitocondrial, Límites entre Especies y Evolución Rápida de la Coloración del Plumaje y el Tamaño en Passerculus sandwichensis Resumen. En este estudio comparamos secuencias de dos genes mitocondriales (ND2 y ND3) entre individuos de la especie Passerculus sandwichensis (n = 112) muestreados en Baja California (5 sitios), la costa de Sonora y el rango de distribución continental (8 sitios). Las poblaciones de Baja California, San Diego y Sonora formaron un clado, al interior del cual no existió estructura filogeográfica; este clado merece estatus de especie (Passerculus rostratus). El otro clado, conformado por individuos fenotípicamente “típicos”, debe clasificarse como P. sandwichensis. Entre los individuos típicos no existió estructura filogeográfica, aunque se descubrieron dos clados principales. Individuos representativos de cada uno de estos dos clados se encontraron en la mayoría de las localidades, excepto Suisan Bay, California y Sable Island, Nova Scotia. Los haplotipos encontrados en Sable Island, correspondientes al “gorrión de Ipswich” no fueron distintivos, lo que no apoya el estatus de especie para este taxón. En Isla San Benito se encontró un solo halpotipo, el cual también se encontraba en otras localidades mexicanas. Los resultados de Sable Island e Isla San Benito muestran que el tamaño y la coloración del plumaje pueden evolucionar rápidamente.

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Phylogeographic structure of a freshwater crayfish (Decapoda:Parastacidae:Cherax preissii) in south-western Australia

Marine and Freshwater Research ◽

10.1071/mf05248 ◽

2006 ◽

Vol 57 (8) ◽

pp. 837 ◽

Cited By ~ 20

Author(s):

Gavin Gouws ◽

Barbara A. Stewart ◽

Savel R. Daniels

Keyword(s):

Gene Flow ◽

Western Australia ◽

Molecular Dating ◽

Phylogeographic Structure ◽

Freshwater Crayfish ◽

The North ◽

South West ◽

Biogeographical Regions ◽

Freshwater Decapods ◽

North Western

Although phylogeographic patterns of freshwater decapods elsewhere in Australia are well documented, little is known of the phylogeography and biogeography of the endemic freshwater fauna of south-western Australia. Here, the phylogeographic structure of a freshwater crayfish, Cherax preissii Erichson, 1846, was investigated to determine contemporary and historical patterns of gene flow and to examined evolutionary and biogeographical scenarios. Allozyme and cytochrome c oxidase subunit I mitochondrial DNA data were collected from 15 populations, sampled across the known C. preissii distribution. Both markers revealed a clear distinction and separation among populations occurring in the north-western and southern portions of the distribution. Inferences of allopatric fragmentation and molecular dating attributed the divergence of the aquatic fauna of these regions to periods of Pliocene–Pleistocene aridity. Connectivity appeared to be greater within each of these regions. Evidence suggested contemporary, but not ongoing, gene flow, particularly within the southern region. This was possibly facilitated by dispersal during pluvial Pleistocene periods or drainage connectivity during episodic marine regressions. The divergence and distributions of these lineages parallels patterns seen in other freshwater crayfish of the region. More explicit investigation of these and further fine-scale phylogeographic studies may contribute to the understanding of biogeography and evolution in the south-west, and may further refine currently recognised biogeographical regions.

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Barriers to gene flow along the Brazilian coast: a synthesis and data analysis

10.22541/au.161358135.51187023/v1 ◽

2021 ◽

Author(s):

Nuno Martins ◽

Leonardo Macagnan ◽

Valéria Cassano ◽

CARLOS GURGEL

Keyword(s):

Gene Flow ◽

Strong Association ◽

Continuous Distribution ◽

Significant Negative Correlation ◽

Additive Models ◽

Phylogeographic Structure ◽

Brazilian Coast ◽

Published Data ◽

Brazil Current ◽

North Brazil

Barriers to gene flow (BGF) play a pivotal role in the dynamics of population genetics promoting genetic differentiation, thus, are inexorably associated with the development and maintenance of phylogeographic structure. Phylogeographic structure resulting from BGF represents data that help the management of natural genetic resources, aiding in the recognition of areas of conservation interest. Several geographic and oceanographic processes found along the Brazilian coast have been proposed as BGF. However, no consensus exist identifying which of them represents the most important in shaping biodiversity. Therefore, this study provides a synthesis of the scientific literature on Brazilian marine phylogeography and used published data to build datasets that allowed us apply linear (lm) and generalized additive models (gam) to identify spatially congruent phylogeographic breaks among marine species (as areas of high BGF frequency occurrence). Lm identified a significant negative correlation between the occurrence of BGF and latitude, suggesting that population in the tropics are genetically more structured than in higher latitudes. This result bears strong association with the latitude species diversity gradient observed worldwide. Gam identified Cape São Roque (05° 28’ S) as the main BGF for populations with continuous distribution along the Brazilian coast. Cape São Roque is located near the center point region where the South Equatorial Current splits into the northward North Brazil Current and the southward Brazil Current. This study represents the first literature synthesis of Brazil’s marine phylogeography and provides a novel explicit quantitative approach to comparative phylogeography.

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

The Auk ◽

10.1093/auk/122.4.1149 ◽

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?

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Exploring the Microdiversity Within Marine Bacterial Taxa: Toward an Integrated Biogeography in the Southern Ocean

Frontiers in Microbiology ◽

10.3389/fmicb.2021.703792 ◽

2021 ◽

Vol 12 ◽

Author(s):

Guillaume Schwob ◽

Nicolás I. Segovia ◽

Claudio González-Wevar ◽

Léa Cabrol ◽

Julieta Orlando ◽

...

Keyword(s):

Gene Flow ◽

Southern Ocean ◽

Taxonomic Resolution ◽

Phylogeographic Structure ◽

Rrna Gene ◽

Antarctic Polar Front ◽

Maritime Antarctica ◽

Biogeographic Patterns ◽

Biogeographic Provinces ◽

The Antarctic

Most of the microbial biogeographic patterns in the oceans have been depicted at the whole community level, leaving out finer taxonomic resolution (i.e., microdiversity) that is crucial to conduct intra-population phylogeographic study, as commonly done for macroorganisms. Here, we present a new approach to unravel the bacterial phylogeographic patterns combining community-wide survey by 16S rRNA gene metabarcoding and intra-species resolution through the oligotyping method, allowing robust estimations of genetic and phylogeographic indices, and migration parameters. As a proof-of-concept, we focused on the bacterial genus Spirochaeta across three distant biogeographic provinces of the Southern Ocean; maritime Antarctica, sub-Antarctic Islands, and Patagonia. Each targeted Spirochaeta operational taxonomic units were characterized by a substantial intrapopulation microdiversity, and significant genetic differentiation and phylogeographic structure among the three provinces. Gene flow estimations among Spirochaeta populations support the role of the Antarctic Polar Front as a biogeographic barrier to bacterial dispersal between Antarctic and sub-Antarctic provinces. Conversely, the Antarctic Circumpolar Current appears as the main driver of gene flow, connecting sub-Antarctic Islands with Patagonia and maritime Antarctica. Additionally, historical processes (drift and dispersal limitation) govern up to 86% of the spatial turnover among Spirochaeta populations. Overall, our approach bridges the gap between microbial and macrobial ecology by revealing strong congruency with macroorganisms distribution patterns at the populational level, shaped by the same oceanographic structures and ecological processes.

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Evaluating the taxonomic status of the Great White Heron (Ardea herodias occidentalis) using morphological, behavioral and genetic evidence

The Auk ◽

10.1093/auk/uky010 ◽

2019 ◽

Vol 136 (1) ◽

Author(s):

Heather L McGuire ◽

Sabrina S Taylor ◽

Frederick H Sheldon

Keyword(s):

Gene Flow ◽

Dna Analysis ◽

Incomplete Lineage Sorting ◽

Size Variation ◽

Florida Bay ◽

Taxonomic Status ◽

Morphological Characters ◽

Lineage Sorting ◽

Species Status ◽

Significant Difference

Abstract The Great White Heron (GWH) has an all-white plumage and occurs in the Gulf of Mexico and Caribbean. Described originally as Ardea occidentalis, it is now considered a subspecies of Great Blue Heron (GBH; A. herodias). GWH and GBH meet in Florida Bay at the southern tip of Florida, providing the opportunity to evaluate their interaction and species status. To this end, we examined size variation and mate choice across their contact zone and genetic variation range-wide. Measurements of 7 morphological characters indicate trends, but not a significant difference, in size between GBH and GWH in southern Florida. GBH and GWH nest mainly in different places (mainland vs. islands) and at different peak times. In Florida Bay, mixed pairs occur, but white-white and blue-blue pairs are more common than in a randomly mating population. Assessing mating, however, is complicated because most, if not all, nesting blue birds are of mixed parentage. Microsatellite DNA analysis indicates that white and blue herons in Florida Bay and the outer Keys (outside Florida Bay) form a group distinct from blue forms on Florida Peninsula and elsewhere in North America. However, some gene flow occurs from white herons on the outer Keys to white and blue herons in Florida Bay, and from blue herons in Florida Bay to GBH on the Florida Peninsula. GWH alleles occur in all North American populations, but whether this is from gene flow or incomplete lineage sorting is unknown. Deciding GWH's species status is difficult. GWH and GBH meet in an ecotone where some gene flow occurs, but behavior and habitat largely isolate them. We argue in favor of splitting GWH from GBH. Regardless of how it is ultimately classified, the GWH's small population needs to be actively managed as an isolate in an extremely vulnerable environment.

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Annual aboveground carbon uptake enhancements from assisted gene flow in boreal black spruce forests are not long-lasting

Nature Communications ◽

10.1038/s41467-021-21222-3 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Martin P. Girardin ◽

Nathalie Isabel ◽

Xiao Jing Guo ◽

Manuel Lamothe ◽

Isabelle Duchesne ◽

...

Keyword(s):

Gene Flow ◽

Net Primary Productivity ◽

Black Spruce ◽

Carbon Sink ◽

Phenotypic Variability ◽

Common Garden ◽

Phylogeographic Structure ◽

Aboveground Net Primary Productivity ◽

Common Garden Experiments ◽

Positive Effect

AbstractAssisted gene flow between populations has been proposed as an adaptive forest management strategy that could contribute to the sequestration of carbon. Here we provide an assessment of the mitigation potential of assisted gene flow in 46 populations of the widespread boreal conifer Picea mariana, grown in two 42-year-old common garden experiments and established in contrasting Canadian boreal regions. We use a dendroecological approach taking into account phylogeographic structure to retrospectively analyse population phenotypic variability in annual aboveground net primary productivity (NPP). We compare population NPP phenotypes to detect signals of adaptive variation and/or the presence of phenotypic clines across tree lifespans, and assess genotype‐by‐environment interactions by evaluating climate and NPP relationships. Our results show a positive effect of assisted gene flow for a period of approximately 15 years following planting, after which there was little to no effect. Although not long lasting, well-informed assisted gene flow could accelerate the transition from carbon source to carbon sink after disturbance.

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Comparative phylogeography reveals how a barrier filters and structures taxa in North American warm deserts

10.1101/2020.06.17.157842 ◽

2020 ◽

Author(s):

Kaiya L. Provost ◽

Edward A. Myers ◽

Brian Tilston Smith

Keyword(s):

Gene Flow ◽

Model Selection ◽

Statistical Power ◽

Isolation By Distance ◽

Species Traits ◽

Phylogeographic Structure ◽

Spatially Explicit ◽

Isolation With Migration ◽

Demographic Models ◽

Isolation By Environment

AbstractThe study of biogeographic barriers have been instrumental in understanding the evolution and distribution of taxa. Now with the increased availability of empirical datasets, it is possible to infer emergent patterns from communities by synthesizing how barriers filter and structure populations across species. We assemble phylogeographic data for a barrier and perform spatially-explicit simulations to quantify temporal and spatial patterns of divergence, the influence of species traits on these patterns, and understand the statistical power of differentiating alternative diversification modes. We incorporate published datasets to examine taxa around the Cochise Filter Barrier, separating the Sonoran and Chihuahuan deserts of North America, to synthesize phylogeographic structuring across the community with respect to organismal functional traits. We then use a simulation and machine learning pipeline to assess the power of phylogeographic model selection. Taxa distributed across the Cochise Filter Barrier show heterogeneous responses to the barrier in levels of gene flow, phylogeographic structure, divergence timing, barrier width, and divergence mechanism. These responses vary concordantly with locomotor and thermoregulatory traits. Many taxa show a Pleistocene population genetic break, often with introgression after divergence. Allopatric isolation and isolation-by-environment are the primary mechanisms purported to structure taxa. Simulations reveal that in spatially-explicit isolation-with-migration models across the barrier, age of divergence, presence of gene flow, and presence of isolation-by-distance can confound the interpretation of evolutionary history and model selection by producing easily-confusable results. By synthesizing phylogeographic data for the Cochise Filter Barrier we show a pattern where barriers interact with species traits to differentiate taxa in communities over millions of years. Identifying the modes of differentiation across the barriers for these taxa remains challenging because commonly invoked demographic models may not be identifiable across a range of likely parameter space.

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