scholarly journals Slender salamanders (genus Batrachoseps) reveal Southern California to be a center for the diversification, persistence, and introduction of salamander lineages

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9599
Author(s):  
Elizabeth L. Jockusch ◽  
Robert W. Hansen ◽  
Robert N. Fisher ◽  
David B. Wake
Keyword(s):  
Southern California ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
San Joaquin Valley ◽  
Phylogeographic Structure ◽  
Geological History ◽  
Sea Level Changes ◽  
Salamander Species

Background The southern California biodiversity hotspot has had a complex geological history, with both plate tectonic forces and sea level changes repeatedly reconfiguring the region, and likely driving both lineage splittings and extinctions. Here we investigate patterns of genetic divergence in two species of slender salamanders (Plethodontidae: Batrachoseps) in this region. The complex geological history in combination with several organismal traits led us to predict that these species harbor multiple ancient mitochondrial lineages endemic to southern California. These species belong to a clade characterized by fine-scale mitochondrial structure, which has been shown to track ancient splits. Both focal species, Batrachoseps major and B. nigriventris, are relatively widely distributed in southern California, and estimated to have persisted there across millions of years. Recently several extralimital populations of Batrachoseps were found in the San Joaquin Valley of California, a former desert area that has been extensively modified for agriculture. The origins of these populations are unknown, but based on morphology, they are hypothesized to result from human-mediated introductions of B. major. Methods We sequenced the mitochondrial gene cytochrome b from a geographically comprehensive sampling of the mitochondrial lineages of B. major and B. nigriventris that are endemic to southern California. We used phylogenetic analyses to characterize phylogeographic structure and identify mitochondrial contact zones. We also included the San Joaquin Valley samples to test whether they resulted from introductions. We used a bootstrap resampling approach to compare the strength of isolation-by-distance in both Batrachoseps species and four other salamander species with which they co-occur in southern California. Results The northern lineage of B. major harbors at least eight deeply differentiated, geographically cohesive mitochondrial subclades. We identify geographic contact between many of these mtDNA lineages and some biogeographic features that are concordant with lineage boundaries. Batrachoseps nigriventris also has multiple deeply differentiated clades within the region. Comparative analyses highlight the smaller spatial scales over which mitochondrial divergence accumulates in Batrachoseps relative to most other salamander species in southern California. The extralimital populations of Batrachoseps from the San Joaquin Valley are assigned to B. major and are shown to result from at least two independent introductions from different source populations. We also suggest that B. major on Catalina Island, where it is considered native, may be the result of an introduction. Some of the same traits that facilitate the build-up of deep phylogeographic structure in Batrachoseps likely also contribute to its propensity for introductions, and we anticipate that additional introduced populations will be discovered.

Species relationships in the dasyurid marsupial genus Pseudantechinus (Marsupialia : Dasyuridae): a re-examination of the taxonomic status of Pseudantechinus roryi

2017 ◽  
Vol 65 (4) ◽  
pp. 240 ◽  
Author(s):  
L. S. Umbrello ◽  
P. A. Woolley ◽  
M. Westerman
Keyword(s):  
Dna Sequences ◽  
Isolation By Distance ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Taxonomic Status ◽  
Museum Collections ◽  
Species Relationships ◽  
Type Specimens ◽  
Network Analyses ◽  
The Status

The status of Pseudantechinus roryi relative to its congeners has been determined from DNA sequences obtained from both nuclear and mitochondrial gene loci. Although all other recognised species of Pseudantechinus form reciprocally monophyletic lineages in phylogenetic analyses, individuals identified in museum collections as Ps. roryi (including type specimens) were indistinguishable from those identified as Ps. macdonnellensis. Ps. roryi is thus considered to be a synonym of Ps. macdonnellensis. Neighbour-joining network analyses failed to reveal any clear biogeographic differences between populations of Ps. macdonnellensis other than some evidence of isolation by distance.

scholarly journals Phylogeography of the New Zealand whelks Cominella maculosa and C. virgata

2021 ◽  
Author(s):  
◽  
Kerry Walton
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
High Frequency ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Nuclear Gene ◽  
Disjunct Distribution ◽  
Phylogeographic Structure ◽  
Interglacial Period ◽  
Cook Strait

<p>Cominella maculosa and C. virgata are common rocky shore whelk species from New Zealand. This study used DNA sequences from the mitochondrial gene cytochrome c oxidase subunit 1 (CO1) to expand an earlier unpublished dataset and examine the phylogeographic structure of both species in the Cook Strait region, of C. maculosa in the Chatham Islands, and of C. virgata in the northern North Island. Both species are found to have a considerable degree of phylogeographic structure, concordant with that reported by an earlier study and for other species with direct development.  South Island sites sampled for C. maculosa had several private haplotypes and a high frequency haplotype that is shared with populations from the southern North Island. Together, these formed a ‘southern haplogroup’. Low diversity in ‘southern’ populations may reflect founder effects that would have occurred as part of a southward range expansion during the onset of the present interglacial period. The Chatham Islands samples had two haplotypes that formed a separate sub-group to the ‘southern haplogroup’, suggesting Chatham Islands populations are moderately isolated from those on mainland New Zealand but may have been founded from ‘southern’ populations relatively recently.  The high frequency haplotype present in South Island samples of C. virgata is absent in Wellington samples but widespread in those from the north-eastern North Island. South Island populations may have been founded from the Hauraki Gulf through human-mediated translocation events. Phylogenetic analyses with a focus on C. virgata were conducted using the mitochondrial genes CO1 and 16SrRNA, and the nuclear gene 18S rRNA, to expand an earlier published dataset. The purported northern subspecies C. virgata brookesi does not form a monophyletic lineage and voucher specimens fluidly intergrade with the nominal subspecies, with which it is synonymised. A lectotype is designated for Buccinum lineolatum Quoy & Gaimard, 1833, for which Cominella virgata is a replacement name. Potential causes of the disjunct distribution patterns of C. virgata and other mollusc taxa are discussed with particular reference to the formation and timing of marine straits through the Auckland Isthmus and Cook Strait.</p>

scholarly journals Phylogeography of the New Zealand whelks Cominella maculosa and C. virgata

2021 ◽  
Author(s):  
◽  
Kerry Walton
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
High Frequency ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Nuclear Gene ◽  
Disjunct Distribution ◽  
Phylogeographic Structure ◽  
Interglacial Period ◽  
Cook Strait

<p>Cominella maculosa and C. virgata are common rocky shore whelk species from New Zealand. This study used DNA sequences from the mitochondrial gene cytochrome c oxidase subunit 1 (CO1) to expand an earlier unpublished dataset and examine the phylogeographic structure of both species in the Cook Strait region, of C. maculosa in the Chatham Islands, and of C. virgata in the northern North Island. Both species are found to have a considerable degree of phylogeographic structure, concordant with that reported by an earlier study and for other species with direct development.  South Island sites sampled for C. maculosa had several private haplotypes and a high frequency haplotype that is shared with populations from the southern North Island. Together, these formed a ‘southern haplogroup’. Low diversity in ‘southern’ populations may reflect founder effects that would have occurred as part of a southward range expansion during the onset of the present interglacial period. The Chatham Islands samples had two haplotypes that formed a separate sub-group to the ‘southern haplogroup’, suggesting Chatham Islands populations are moderately isolated from those on mainland New Zealand but may have been founded from ‘southern’ populations relatively recently.  The high frequency haplotype present in South Island samples of C. virgata is absent in Wellington samples but widespread in those from the north-eastern North Island. South Island populations may have been founded from the Hauraki Gulf through human-mediated translocation events. Phylogenetic analyses with a focus on C. virgata were conducted using the mitochondrial genes CO1 and 16SrRNA, and the nuclear gene 18S rRNA, to expand an earlier published dataset. The purported northern subspecies C. virgata brookesi does not form a monophyletic lineage and voucher specimens fluidly intergrade with the nominal subspecies, with which it is synonymised. A lectotype is designated for Buccinum lineolatum Quoy & Gaimard, 1833, for which Cominella virgata is a replacement name. Potential causes of the disjunct distribution patterns of C. virgata and other mollusc taxa are discussed with particular reference to the formation and timing of marine straits through the Auckland Isthmus and Cook Strait.</p>

scholarly journals A molecular and morphological investigation of species boundaries and phylogenetic relationships in Australian free-tailed bats Mormopterus (Chiroptera : Molossidae)

2014 ◽  
Vol 62 (2) ◽  
pp. 109 ◽  
Author(s):  
T. B. Reardon ◽  
N. L. McKenzie ◽  
S. J. B. Cooper ◽  
B. Appleton ◽  
S. Carthew ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Phylogeographic Structure ◽  
Species Boundaries ◽  
Base Pairs ◽  
Nadh Dehydrogenase Subunit 2 ◽  
The Family ◽  
Taxonomic Uncertainty ◽  
History Of ◽  
Phylogenetic Affinities

The taxonomic uncertainty surrounding several prominent genera of Australian microbat has been a long-standing impediment to research and conservation efforts on these groups. The free-tail bat genus Mormopterus is perhaps the most significant example, with a long history of acknowledged species-level confusion. This study uses a combined molecular and morphological approach to conduct a comprehensive assessment of species and subgeneric boundaries, between-species phylogenetic affinities and within-species phylogeographic structure in Australian members of Mormopterus. Phylogenetic analyses based on 759 base pairs of the NADH Dehydrogenase subunit 2 mitochondrial gene were concordant with species boundaries delineated using an expanded allozyme dataset and by phallic morphology, and also revealed strong phylogeographic structure within two species. The levels of divergence evident in the molecular and morphological analyses led us to recognise three subgenera within Australia: Micronomus, Setirostris subgen. nov. and Ozimops subgen. nov. Within Ozimops we recognise seven Australian species, three of which are new, and none are conspecific with Indo-Papuan species. The family Molossidae now comprises eleven species across three subgenera in Australia, making it the continent’s second most speciose family of bats.

scholarly journals Molecular evidence that the Channel Islands populations of the orange-crowned warbler (Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7388 ◽  
Author(s):  
Zachary R. Hanna ◽  
Carla Cicero ◽  
Rauri C.K. Bowie
Keyword(s):  
Southern California ◽  
Isolation By Distance ◽  
Mitochondrial Gene ◽  
Molecular Data ◽  
Channel Islands ◽  
Molecular Evidence ◽  
Western North America ◽  
Microsatellite Data ◽  
Distinct Evolutionary Lineage ◽  
Geographic Structure

We used molecular data to assess the degree of genetic divergence across the breeding range of the orange-crowned warbler (Oreothlypis celata) in western North America with particular focus on characterizing the divergence between O. celata populations on the mainland of southern California and on the Channel Islands. We obtained sequences of the mitochondrial gene ND2 and genotypes at ten microsatellite data for 192 O. celata from populations spanning all four recognized subspecies. We recovered shallow, but significant, levels of divergence among O. celata populations across the species range. Our results suggest that island isolation, subspecies (delineation by morphology, ecological, and life-history characteristics), and isolation-by-distance, in that order, are the variables that best explain the geographic structure detected across the range of O. celata. Populations on the Channel Islands were genetically divergent from those on the mainland. We found evidence for greater gene flow from the Channel Islands population to mainland southern California than from the mainland to the islands. We discuss these data in the context of differentiation in phenotypic and ecological characters.

scholarly journals Molecular evidence that the Channel Islands populations of the orange-crowned warbler (Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage

2018 ◽  
Author(s):  
Zachary R Hanna ◽  
Carla Cicero ◽  
Rauri CK Bowie
Keyword(s):  
Southern California ◽  
Isolation By Distance ◽  
Mitochondrial Gene ◽  
Molecular Data ◽  
Channel Islands ◽  
Molecular Evidence ◽  
Microsatellite Data ◽  
Distinct Evolutionary Lineage ◽  
Genetic Patterns ◽  
Low Levels

We used molecular data to assess the degree of genetic divergence across the breeding range of the orange-crowned warbler (Oreothlypis celata) in western North America with particular focus on characterizing the divergence between O. celata populations on the mainland of southern California and on the Channel Islands. We obtained sequences of the mitochondrial gene ND2 and genotypes at ten microsatellite data for 192 O. celata from populations spanning all four recognized subspecies. We recovered low levels of divergence between O. celata populations and genetic patterns were consistent with isolation by distance. However, populations on the Channel Islands were genetically divergent from those on the mainland. We found evidence for greater gene flow from the Channel Islands population to mainland southern California than from the mainland to the islands. We discuss these data in the context of differentiation in phenotypic and ecological characters.

scholarly journals Molecular evidence that the Channel Islands populations of the orange-crowned warbler (Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage

2018 ◽  
Author(s):  
Zachary R Hanna ◽  
Carla Cicero ◽  
Rauri CK Bowie
Keyword(s):  
Southern California ◽  
Isolation By Distance ◽  
Mitochondrial Gene ◽  
Molecular Data ◽  
Channel Islands ◽  
Molecular Evidence ◽  
Microsatellite Data ◽  
Distinct Evolutionary Lineage ◽  
Genetic Patterns ◽  
Low Levels

We used molecular data to assess the degree of genetic divergence across the breeding range of the orange-crowned warbler (Oreothlypis celata) in western North America with particular focus on characterizing the divergence between O. celata populations on the mainland of southern California and on the Channel Islands. We obtained sequences of the mitochondrial gene ND2 and genotypes at ten microsatellite data for 192 O. celata from populations spanning all four recognized subspecies. We recovered low levels of divergence between O. celata populations and genetic patterns were consistent with isolation by distance. However, populations on the Channel Islands were genetically divergent from those on the mainland. We found evidence for greater gene flow from the Channel Islands population to mainland southern California than from the mainland to the islands. We discuss these data in the context of differentiation in phenotypic and ecological characters.

scholarly journals Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1134
Author(s):  
Fei Ye ◽  
Hu Li ◽  
Qiang Xie
Keyword(s):  
Gene Rearrangement ◽  
Hot Spot ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Deep Understanding ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Current View ◽  
Novel Gene ◽  
Spot Group

Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran lineages confirm Reduviidae as a ‘hot-spot group’ of gene rearrangement in Heteroptera. The phylogenetic analyses corroborate the current view of phylogenetic relationships between basal groups of Reduviidae with high support values. Our study provides deeper insights into the evolution of mitochondrial gene arrangement in Heteroptera and the early divergence of reduviids.

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

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