scholarly journals Molecular Systematics and Biogeography of Antillean Thrashers, Tremblers, and Mockingbirds (Aves: Mimidae)

The Auk ◽  
2001 ◽  
Vol 118 (1) ◽  
pp. 35-55 ◽  
Author(s):  
Jeffrey S. Hunt ◽  
Eldredge Bermingham ◽  
Robert E. Ricklefs
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Sequence Divergence ◽  
The West ◽  
Island Populations ◽  
Mimus Polyglottos ◽  
History Of ◽  
Dumetella Carolinensis ◽  
Phylogenetic Hypotheses

Abstract We constructed phylogenetic hypotheses for Greater and Lesser Antillean Mimidae, including five endemic species of tremblers and thrashers that represent the best plausible example of an avian radiation within the Lesser Antilles. Phylogenetic relationships were inferred from analysis of 3,491 base pairs (bp) of mitochondrial DNA (mtDNA) and roughly 780 bp of the nuclear-encoded myoglobin gene. We used a subset of mtDNA gene sequences and pcrRFLP analysis to evaluate the phylogeographic relationships among individuals representing island populations of the Brown and Gray tremblers (Cinclocerthia ruficauda and C. gutturalis), Pearly-eyed Thrasher (Margarops fuscatus), Scaly-breasted Thrasher (Margarops fuscus), and Antillean and continental populations of the Tropical (Mimus gilvus) and Northern mockingbirds (Mimus polyglottos). Phylogeographic analysis distinguished three strongly differentiated mtDNA clades among tremblers, as well as distinct southern (St. Lucia and Martinique) and northern (Dominica to Montserrat) mtDNA lineages of the Scaly-breasted Thrasher. Minor geographic subdivision was also observed between continental and Antillean populations of the Tropical Mockingbird. Phylogenetic analyses of species-level Mimidae relationships that are based on mtDNA and nuclear sequences provide strong support for the monophyly and Antillean origin of a clade that consists of the tremblers, Pearly-eyed Thrasher, and Scaly-breasted Thrasher, but reject the monophyly of the genus Margarops. Phylogenetic analysis cannot confirm the monophyly of all endemic Antillean mimids because of the apparently contemporaneous diversification of the Antillean White-breasted Thrasher (Ramphocinclus brachyurus) with the continental Gray Catbird (Dumetella carolinensis) and Black Catbird (Melanoptila glabrirostris). However, an insertion and a deletion in the myoglobin intron 2 sequence support grouping the West Indian thrashers and tremblers, from which we infer that the endemic Lesser Antillean mimids are an indigenous radiation. Assuming a constant mtDNA clock for the Mimidae, the splitting of the Northern and Tropical mockingbird lineages is roughly contemporaneous with the separation of the three trembler clades, as well as the two Scaly-breasted Thrasher clades. Application of a mitochondrial DNA clock ticking at 2% sequence divergence per million years (Ma), suggests that the history of the endemic thrasher and trembler lineage in the West Indies extends back about 4 Ma, and the three distinct clades of tremblers split about 2 Ma ago.

Evidence of cryptic speciation in mesostigmatid mites from South Africa

Parasitology ◽  
2014 ◽  
Vol 141 (10) ◽  
pp. 1322-1332 ◽  
Author(s):  
ADRIAAN ENGELBRECHT ◽  
CONRAD A. MATTHEE ◽  
EDWARD A. UECKERMANN ◽  
SONJA MATTHEE
Keyword(s):  
South Africa ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Sequence Divergence ◽  
Morphological Diversity ◽  
Morphometric Analyses ◽  
Mtdna Sequence ◽  
History Of ◽  
Complex Life History

SUMMARYLaelaps giganteus and Laelaps muricola (Mesostigmata; Laelapidae) are widespread and locally abundant host generalists on small mammals in southern Africa. The large host range and complex life history of these ectoparasites may allude to possible intraspecific cryptic diversity in these taxa. To assess genetic and morphological diversity in L. giganteus and L. muricola, we sampled 228 rodents at eight localities in South Africa. This sample included nine previously recorded host species and on these, L. muricola was only recorded from Mastomys natalensis and Micaelamys namaquensis while L. giganteus was found on Rhabdomys dilectus and Lemniscomys rosalia. Phylogenetic analyses of partial mtDNA cytochrome oxidase subunit I (COI) and nuclear ITS1 data strongly supported the recognition of L. giganteus and L. muricola, a scenario partly supported by the Tropomyosin intron. Strong support for evolutionary distinct lineages within L. giganteus is found: L. giganteus lineage 1 is confined to R. dilectus and L. giganteus lineage 2 is confined to L. rosalia. These host specific monophyletic lineages were also separated by 9·84% mtDNA sequence divergence and 3·44% nuclear DNA sequence divergence. Since quantitative morphometric analyses were not congruent with these findings, these two lineages more than likely represent cryptic species.

Three evolutionarily significant units for conservation in the iguanid genus Brachylophus

2006 ◽  
Vol 12 (1) ◽  
pp. 64
Author(s):  
Emma L. Burns ◽  
Brian H. Costello ◽  
Bronwyn A. Houlden
Keyword(s):  
Pacific Islands ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Conservation Priorities ◽  
Separate Species ◽  
Island Populations ◽  
Evolutionarily Significant Units ◽  
Average Sequence Divergence ◽  
History Of ◽  
South Pacific Islands

We examined phylogenetic relationships within the genus Brachylophus, which comprises two endangered iguana species endemic to the South Pacific islands of Fiji and Tonga. Genetic variation among Fijian Crested Iguanas B. vitiensis and Fijian and Tongan Banded Iguanas B. fasciatus was analysed using mitochondrial DNA (mtDNA) cytochrome b (cyt b) characterized from 35 individuals from island populations. Three distinct clades of Brachylophus were identified. The most divergent clade comprised B. fasciatus from Tonga, which supports the recognition of Tongan iguanas as a separate species. Molecular clock estimates suggested that the average sequence divergence (6.4%) between Tongan and Fijian B. fasciatus clades equated to 7 - 15.8 MY of separation, confirming that extant Brachylophus species have a long history of evolution in situ in the Fijian and Tongan archipelago. Phylogenetic analyses also revealed that Fijian B. fasciatus and B. vitiensis iguana populations were not reciprocally monophyletic. One clade comprised two mtDNA haplotypes from the Fijian islands of Monu, Monuriki, Devuilau, Waya and Yadua Taba. The other clade comprised B. fasciatus haplotypes from Kadavu and Gau, which was divergent from both the aforementioned Fijian clade (dA = 3.5%), and the Tongan clade (dA = 6.4%). In addition to mtDNA data, variation was assessed at microsatellite loci, and significant differentiation between iguana populations was detected. Based on both mtDNA and microsatellite analysis, the conservation priorities for these endangered lizards must be reassessed to protect iguanas as three distinct evolutionarily significant units.

scholarly journals Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia

2016 ◽  
Author(s):  
Patricia Marrero ◽  
Khaled K. Abu-Amero ◽  
Jose M Larruga ◽  
Vicente M Cabrera
Keyword(s):  
Mitochondrial Dna ◽  
Arabian Peninsula ◽  
Indian Subcontinent ◽  
Modern Humans ◽  
The West ◽  
West Side ◽  
Human Mitochondrial Dna ◽  
Phylogeographic Analysis ◽  
History Of ◽  
Out Of Africa

ABSTRACTObjetivesWe suggest that the phylogeny and phylogeography of mtDNA macrohaplogroup M in Eurasia and Australasia is better explained supposing an out of Africa of modern humans following a northern route across the Levant than the most prevalent southern coastal route across Arabia and India proposed by others.MethodsA total 206 Saudi samples belonging to macrohaplogroup M have been analyzed. In addition, 4107 published complete or nearly complete Eurasian and Australasian mtDNA genomes ascribed to the same macrohaplogroup have been included in a global phylogeographic analysis.ResultsMacrohaplogroup M has only historical implantation in West Eurasia including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side.ConclusionsThe existence of a northern route previously advanced by the phylogeography of mtDNA macrohaplogroup N is confirmed here by that of macrohaplogroup M. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa.

scholarly journals A revised global biogeography of turtles

2015 ◽  
Author(s):  
Walter G. Joyce ◽  
Márton Rabi
Keyword(s):  
Middle Jurassic ◽  
Fossil Record ◽  
Phylogenetic Analyses ◽  
Sensu Stricto ◽  
Early History ◽  
Marine Turtles ◽  
Biogeographic History ◽  
Global Presence ◽  
History Of ◽  
Phylogenetic Hypotheses

Background. Over the course of the last decades, much effort has gone into unraveling the biogeographic history of turtles, but while much progress has been achieved in resolving post- Jurassic dispersal events, traditional phylogenetic hypotheses have yielded incongruous results in regards to the early history of the group. Methods. We re-evaluate the fossil record of turtles in context of recent phylogenetic analyses and fossil finds, including the extensive record of fragmentary but diagnostic remains. Given that near-coastal and marine turtles readily disperse across aquatic barriers, a broad set of neritic to pelagic groups were disregarded from consideration. Significant disagreement still exists among current phylogenetic hypotheses and we therefore place much effort into tracing the fossil record of unambiguously monophyletic groups. We finally employed molecular backbone constraints, given that the molecular phylogenies are more consistent with the fossil record than current, morphological phylogenies. Results. Among derived, aquatic turtles, we recognize four clades that can be traced back to discrete biogeographic centers: Paracryptodira in North America and Europe, Pan- Cryptodira in Asia, Pan-Pelomedusoides in northern Gondwanan landmasses and Pan- Chelidae in southern Gondwanan landmasses. This pattern is partially mirrored by three clades of primarily terrestrial, basal turtles: Solemydidae in North American and Europe, Sichuanchelyidae in Asia, and Meiolaniformes sensu stricto in southern Gondwanan landmasses. Although the exact interrelationships of these clades remain unclear, most can be traced back to the Middle Jurassic. Discussion. The conclusion that the two primary lineages of pleurodires and paracryptodires can be traced back to mutually exclusive land masses is not novel, but the realization that the early history of pan-cryptodires is restricted to Asia has not been realized previously, because traditional phylogenies implied an early, global presence of pan-cryptodires. The timing of the origin of the three primary clades of derived turtles (i.e., Pan-Pleurodira, Pan-Cryptodira, and Paracryptodira) correlates with the opening of the central Atlantic and the formation of the Turgai Strait in the Middle Jurassic, somewhat later than predicted by molecular calibration studies. The primary diversity of extant turtles therefore appears to have been driven by vicariance. A similar hypothesis could also be formulated for the three clades of basal turtles that survive at least into the Late Cretaceous, but given that their combined monophyly remains uncertain, it is unclear if their diversity was also driven by vicariance, or if they emulate a vicariance-like pattern. Although most groups remained within their primary geographic range throughout their evolutionary history, the dominant vicariance signal was thoroughly obfuscated by rich dispersal from littoral to marine turtles and crown cryptodires.

scholarly journals Mitochondrial DNA suggests recent origins in two coastal avian subspecies in northwestern North America

2016 ◽  
Author(s):  
Rebecca Cheek ◽  
Kyle K Campbell ◽  
Robert Dickerman ◽  
Berry Wijdeven ◽  
Kevin Winker
Keyword(s):  
Mitochondrial Dna ◽  
Population Divergence ◽  
Phenotypic Data ◽  
Southeast Alaska ◽  
Island Populations ◽  
Queen Charlotte Islands ◽  
Great Blue Heron ◽  
Accipiter Striatus ◽  
History Of ◽  
Northwestern North America

Genetic studies of subspecies endemic to Haida Gwaii (Queen Charlotte Islands), British Columbia and the Alexander Archipelago of southeast Alaska have frequently found genetic corroboration for these phenotypically based taxa. Divergence and speciation are common among island populations of birds, and evidence suggests this region has fostered such divergence during previous glacial maxima. We examined genetic divergence in mitochondrial DNA (mtDNA) of two coastal subspecies endemic to this region: sharp-shinned hawk (Accipiter striatus perobscurus) and great blue heron (Ardea herodias fannini). Genetic diversity in both species was remarkably low, with both coastal subspecies possessing only the most common haplotype found in continental populations. We found low but significant population divergence between A. s. perobscurus and continental populations of sharp-shinned hawks and no significant population divergence in the herons. The refugial history of the region suggests that these subspecies may have arisen relatively recently compared with other regional endemics for which genetic and phenotypic data both show divergence. Alternatively, species-wide selective sweeps of mtDNA prior to divergence may have rendered this genetic marker less useful for tracking that divergence.

scholarly journals Molecular Systematics and the Role of The “Várzea”–“Terra-Firme” Ecotone in the Diversification of Xiphorhynchus Woodcreepers (Aves: Dendrocolaptidae)

The Auk ◽  
2002 ◽  
Vol 119 (3) ◽  
pp. 621-640 ◽  
Author(s):  
Alexandre Aleixo
Keyword(s):  
Strong Support ◽  
Sequence Divergence ◽  
Decisive Role ◽  
Biological Species ◽  
Habitat Specialization ◽  
Terra Firme ◽  
Sister Relationship ◽  
As Species ◽  
History Of ◽  
Distinct Lineage

Abstract The phylogeny of all known Xiphorhynchus (Dendrocolaptidae) species and many of its subspecies was reconstructed to evaluate species limits in this taxonomically challenging genus and investigate the possible role played by the Amazonian “várzea” (floodplain forest)–“terra-firme” (upland forest) ecotone in its diversification. Phylogenies were inferred based on 2,430 bp of the mitochondrial DNA genes ND2, ND3, and cytochrome b. All phylogeny estimates supported the monophyly of all extant Xiphorhynchus species to the exclusion of the sibling species pair Straight-billed (X. picus) and Zimmer's (X. kienerii) woodcreeper. Confirming findings of previous molecular and anatomical studies, strong support was found to include the Lesser Woodcreeper (Lepidocolaptes fuscus) in Xiphorhynchus. Levels of sequence divergence among some subspecies of Buff-throated (X. guttatus), Ocellated (X. ocellatus), and Spix's (X. spixii) woodcreepers reached or exceeded those found between closely related, undisputed biological species of Xiphorhynchus. High levels of sequence differentiation and the paraphyly of some Xiphorhynchus species indicated that the following taxa should be recognized as species: Lafresnaye's (X. guttatoides), Tschudi's (X. chunchotambo), and Elegant (X. elegans) woodcreepers. All Xiphorhynchus species restricted to terra-firme forest in lowland Amazonia formed a well supported monophyletic group, whereas species restricted to várzea forest were either basal to a clade containing species found in a wide variety of habitats (Striped Woodcreeper [X. obsoletus]) or belonged to a distinct lineage likely to be regarded as a separate genus (X. kienerii). These findings falsified an anticipated sister relationship between várzea and terra-firme species, as expected if the várzea–terra-firme ecotone had played a decisive role in population differentiation and speciation within Xiphorhynchus. Instead, phylogeny estimates suggested that the várzea–terra-firme habitat specialization evolved early on in the evolutionary history of Xiphorhynchus and that subsequent differentiation occurred mostly within the terra-firme habitat.

Interspecific and intraspecific mitochondrial DNA variation in North American bears (Ursus)

1991 ◽  
Vol 69 (12) ◽  
pp. 2985-2992 ◽  
Author(s):  
Matthew A. Cronin ◽  
Steven C. Amstrup ◽  
Gerald W. Garner ◽  
Ernest R. Vyse
Keyword(s):  
Mitochondrial Dna ◽  
North American ◽  
Ursus Arctos ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Black Bears ◽  
Polar Bears ◽  
Brown Bears ◽  
Dna Variation ◽  
Base Substitutions

We assessed mitochondrial DNA variation in North American black bears (Ursus americanus), brown bears (Ursus arctos), and polar bears (Ursus maritimus). Divergent mitochondrial DNA haplotypes (0.05 base substitutions per nucleotide) were identified in populations of black bears from Montana and Oregon. In contrast, very similar haplotypes occur in black bears across North America. This discordance of haplotype phylogeny and geographic distribution indicates that there has been maintenance of polymorphism and considerable gene flow throughout the history of the species. Intraspecific mitochondrial DNA sequence divergence in brown bears and polar bears is lower than in black bears. The two morphological forms of U. arctos, grizzly and coastal brown bears, are not in distinct mtDNA lineages. Interspecific comparisons indicate that brown bears and polar bears share similar mitochondrial DNA (0.023 base substitutions per nucleotide) which is quite divergent (0.078 base substitutions per nucleotide) from that of black bears. High mitochondrial DNA divergence within black bears and paraphyletic relationships of brown and polar bear mitochondrial DNA indicate that intraspecific variation across species' ranges should be considered in phylogenetic analyses of mitochondrial DNA.

Mitochondrial DNA variation in water shrews (Sorex palustris, Sorex bendirii) from western North America: implications for taxonomy and phylogeography

2005 ◽  
Vol 83 (11) ◽  
pp. 1469-1475 ◽  
Author(s):  
M B O'Neill ◽  
D W Nagorsen ◽  
R J Baker
Keyword(s):  
Mitochondrial Dna ◽  
North America ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Vancouver Island ◽  
Western North America ◽  
Cytb Sequence ◽  
Dna Variation ◽  
Late Pliocene ◽  
Postglacial Colonization

Inter- and intra-specific variations in cytochrome b (Cytb) sequence were assessed in 22 specimens of Sorex palustris Richardson, 1828 and 6 specimens of Sorex bendirii (Merriam, 1884) from 20 locations in western North America. Phylogenetic analyses revealed three distinct clades: Boreal (S. p. palustris), Cordilleran (S. p. brooksi, S. p. navigator), and Coastal (S. b. palmeri, S. b. bendirii). Sequence divergence between the Boreal and the Coastal–Cordilleran lineages was 6.9%, while the divergence between the Coastal and the Cordilleran clades was 3.1%. Sorex palustris brooksi, a subspecies endemic to Vancouver Island, showed minor divergence from mainland samples of S. p. navigator. The results suggest that S. palustris may consist of two species: a boreal eastern form (S. palustris) and a Cordilleran form (S. navigator). The taxonomic validity of S. p. brooksi is unresolved. Distribution of the three clades are consistent with vicariance and isolation in coastal, Cordilleran, and eastern refugia in the Late Pliocene or Pleistocene. The Vancouver Island subspecies S. p. brooksi is probably derived from postglacial colonization in the Late Pleistocene.

scholarly journals Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequencing data

2020 ◽  
Author(s):  
Rafael G Albaladejo ◽  
Sara Martín-Hernanz ◽  
J Alfredo Reyes-Betancort ◽  
Arnoldo Santos-Guerra ◽  
María Olangua-Corral ◽  
...  
Keyword(s):  
Canary Islands ◽  
Ecological Niche ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Genotyping By Sequencing ◽  
Niche Conservatism ◽  
Sequencing Data ◽  
History Of ◽  
Spatio Temporal ◽  
Dispersal Events

Abstract Background and Aims Several biogeographical models have been proposed to explain the colonization and diversification patterns of Macaronesian lineages. In this study, we calculated the diversification rates and explored what model best explains the current distribution of the 15 species endemic to the Canary Islands belonging to Helianthemum sect. Helianthemum (Cistaceae). Methods We performed robust phylogenetic reconstructions based on genotyping-by-sequencing data and analysed the timing, biogeographical history and ecological niche conservatism of this endemic Canarian clade. Key Results Our phylogenetic analyses provided strong support for the monophyly of this clade, and retrieved five lineages not currently restricted to a single island. The pristine colonization event took place in the Pleistocene (~1.82 Ma) via dispersal to Tenerife by a Mediterranean ancestor. Conclusions The rapid and abundant diversification (0.75–1.85 species per million years) undergone by this Canarian clade seems the result of complex inter-island dispersal events followed by allopatric speciation driven mostly by niche conservatism, i.e. inter-island dispersal towards niches featuring similar environmental conditions. Nevertheless, significant instances of ecological niche shifts have also been observed in some lineages, making an important contribution to the overall diversification history of this clade.

Systematic affinities of island and mainland populations of the Dunnart Sminthopsis griseoventer in Western Australia: data from allozymes and mitochondrial DNA

1998 ◽  
Vol 4 (4) ◽  
pp. 289 ◽  
Author(s):  
A. Labrinidis ◽  
S. J. B. Cooper ◽  
M. Adams ◽  
N. Baczocha
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
Control Region Sequence ◽  
Island Population ◽  
Complex Species ◽  
Island Populations ◽  
Region Sequence ◽  
Allozyme Loci

The systematic affinities of Boullanger Island and Western Australian mainland populations of the Grey-bellied Dunnart Sminthopsis griseoventer were investigated using allozyme electrophoresis and phylogenetic analysis of a 404 bp region of the mitochondrial DNA (mtDNA) control region. Forty-six allozyme loci were screened for variation and found to be monomorphic in S. griseoventer from both Boullanger Island and one mainland population. Low levels of variation were also detected in the control region sequence, with just one haplotype observed among eight island individuals and three haplotypes among 10 mainland individuals, each differing at between two and four nucleotide sites (0.5?1.0% divergence). Phylogenetic analyses using maximum parsimony of control region sequence from mainland and island taxa, and four species of the "murina complex", S. aitkeni, S. murina, S. gilberti and S. dolichura, indicated that the island and mainland taxa formed a monophyletic group to the exclusion of the other "murina complex" species, but were paraphyletic at the level of the individual haplotypes. These results are consistent with the hypothesis that mainland and island populations of S. griseoventer comprise a single species, and suggest that there has been no long-term barrier to gene flow between these populations. Analyses of molecular variation provided evidence the island population represents a separate management unit for conservation, but are insufficient to determine whether there has been inbreeding or a recent bottleneck in the island population.

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