Significant population genetic structuring but a lack of phylogeographic structuring in the endemic Tasmanian tree frog (Litoria burrowsae)

2014 ◽  
Vol 62 (3) ◽  
pp. 238 ◽  
Author(s):  
Z. Y. Zhang ◽  
S. Cashins ◽  
A. Philips ◽  
C. P. Burridge
Keyword(s):  
Population Genetic ◽  
Nuclear Dna ◽  
Isolation By Distance ◽  
Global Climate ◽  
Haplotype Diversity ◽  
Habitat Destruction ◽  
Phylogeographic Structure ◽  
Tree Frog ◽  
Genetic Structuring ◽  
Management Units

Conservation of frogs is of global concern, owing to declines resulting from habitat destruction, global climate change, and disease. Knowledge of genetic variation in frog species is therefore desirable for the identification of management units. Here we surveyed mitochondrial DNA sequence variation in the Tasmanian endemic hylid frog Litoria burrowsae, which is infected by chytrid fungus, Batrachochytrium dendrobatidis, and may be declining. Neither phylogeographic structure nor deep phylogenetic divergence was detected in the species, although its populations were highly differentiated with respect to haplotype frequencies. The low-haplotype diversity in L. burrowsae suggests a recent bottleneck in the species, and population genetic structuring may reflect isolation by distance as well as founder effects associated with range expansion. Three putative management units were identified that require verification based on nuclear DNA variation and adaptation to local environments.

scholarly journals Phylogeography of the oyster borer (Haustrum scobina)

2021 ◽  
Author(s):  
◽  
Sebastian Logan
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Haplotype Diversity ◽  
Genetic Connectivity ◽  
Long Distance Dispersal ◽  
Genetic Structuring ◽  
Long Distance ◽  
Ecological Processes

<p>An effective investigation of the underlying ecological processes that shape genetic diversity and connectivity typically requires comparisons among phylogeographic studies of multiple species. Phylogeographic studies of New Zealand’s coastal marine benthos have historically relied on post hoc speculation rather than directed research questions to investigate ecological processes. There has also been a lack of studies on direct developing marine molluscs. Direct developers are expected to have a low potential for dispersal and thus show a pattern of genetic isolation by distance across their distributions. Recent research indicates that this assumption may frequently be violated by instances of long distance dispersal/translocation. The oyster borer (Haustrum scobina) is an endemic direct-developing marine mollusc found in high abundances at rocky intertidal environments across the entirety of New Zealand. This distribution and life history makes H. scobina an ideal target to study genetic connectivity in a species expected to show low realised dispersal and high population genetic structuring. This thesis research used 379 new DNA sequences from the mitochondrial gene cytochrome c oxidase subunit 1 (COI) to investigate the phylogeography of H. scobina across the southern North Island. In addition 16 new COI sequences were inadvertently sequenced from the morphologically similar congener Haustrum albomarginatum. Results from both species support the recently proposed division of H. scobina and H. albomarginatum as separate species. H. scobina populations show significant geographic structure and a lack of haplotype diversity across the south-eastern North Island concordant with results of another previous study of a direct developer. This finding suggests that ecological processes may be producing similar population genetic structures for direct developers generally. Contrast between high and low haplotype diversities in northern and southern H. scobina populations respectively, indicates that southern H. scobina populations may have originated via recolonisation from northern populations following a range contraction during the Last Glacial Maximum. Evidence of multiple long distance dispersal/translocation events was found indicating that long distance dispersal via rafting and/or inadvertent human-mediated translocations may have occurred frequently. Results are then discussed with a view to inform further research in to New Zealand direct developers.</p>

scholarly journals Phylogeography of the oyster borer (Haustrum scobina)

2021 ◽  
Author(s):  
◽  
Sebastian Logan
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Haplotype Diversity ◽  
Genetic Connectivity ◽  
Long Distance Dispersal ◽  
Genetic Structuring ◽  
Long Distance ◽  
Ecological Processes

<p>An effective investigation of the underlying ecological processes that shape genetic diversity and connectivity typically requires comparisons among phylogeographic studies of multiple species. Phylogeographic studies of New Zealand’s coastal marine benthos have historically relied on post hoc speculation rather than directed research questions to investigate ecological processes. There has also been a lack of studies on direct developing marine molluscs. Direct developers are expected to have a low potential for dispersal and thus show a pattern of genetic isolation by distance across their distributions. Recent research indicates that this assumption may frequently be violated by instances of long distance dispersal/translocation. The oyster borer (Haustrum scobina) is an endemic direct-developing marine mollusc found in high abundances at rocky intertidal environments across the entirety of New Zealand. This distribution and life history makes H. scobina an ideal target to study genetic connectivity in a species expected to show low realised dispersal and high population genetic structuring. This thesis research used 379 new DNA sequences from the mitochondrial gene cytochrome c oxidase subunit 1 (COI) to investigate the phylogeography of H. scobina across the southern North Island. In addition 16 new COI sequences were inadvertently sequenced from the morphologically similar congener Haustrum albomarginatum. Results from both species support the recently proposed division of H. scobina and H. albomarginatum as separate species. H. scobina populations show significant geographic structure and a lack of haplotype diversity across the south-eastern North Island concordant with results of another previous study of a direct developer. This finding suggests that ecological processes may be producing similar population genetic structures for direct developers generally. Contrast between high and low haplotype diversities in northern and southern H. scobina populations respectively, indicates that southern H. scobina populations may have originated via recolonisation from northern populations following a range contraction during the Last Glacial Maximum. Evidence of multiple long distance dispersal/translocation events was found indicating that long distance dispersal via rafting and/or inadvertent human-mediated translocations may have occurred frequently. Results are then discussed with a view to inform further research in to New Zealand direct developers.</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 Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters

ZooKeys ◽  
2020 ◽  
Vol 911 ◽  
pp. 139-160 ◽  
Author(s):  
Shyama Sundari Devi Chanthran ◽  
Phaik-Eem Lim ◽  
Yuan Li ◽  
Te-Yu Liao ◽  
Sze-Wan Poong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Genetic ◽  
Haplotype Diversity ◽  
Dispersal Ability ◽  
Human Consumption ◽  
Stock Management ◽  
Genetic Structuring ◽  
Migration Ability ◽  
Mtdna Coi

A background study is important for the conservation and stock management of a species. Terapon jarbua is a coastal Indo-Pacific species, sourced for human consumption. This study examined 134 samples from the central west and east coasts of Peninsular (West) Malaysia and East Malaysia. A 1446-bp concatenated dataset of mtDNA COI and Cyt b sequences was used in this study and 83 haplotypes were identified, of which 79 are unique haplotypes and four are shared haplotypes. Populations of T. jarbua in Malaysia are genetically heterogenous as shown by the high level of haplotype diversity ranging from 0.9167–0.9952, low nucleotide diversity ranging from 0.0288–0.3434, and high FST values (within population genetic variation). Population genetic structuring is not distinct as shown by the shared haplotypes between geographic populations and mixtures of haplotypes from different populations within the same genetic cluster. The gene flow patterns and population structuring observed among these regions are likely attributed to geographical distance, past historical events, allopatric speciation, dispersal ability and water currents. For instance, the mixture of haplotypes revealed an extraordinary migration ability of T. jarbua (&gt;1200 km) via ancient river connectivity. The negative overall value of the neutrality test and a non-significant mismatch distribution are consistent with demographic expansion(s) in the past. The median-joining network concurred with the maximum likelihood haplotype tree with three major clades resolved. The scarcity of information on this species is an obstacle for future management and conservation purposes. Hence, this study aims to contribute information on the population structure, genetic diversity, and historical demography of T. jarbua in Malaysia.

scholarly journals Genealogy and phylogeography of Cyprinid fish Labeo rohita (Hamilton, 1822) inferred from ATPase 6 and 8 mitochondrial DNA gene analysis

2014 ◽  
Vol 60 (4) ◽  
pp. 460-471 ◽  
Author(s):  
Rupesh K. Luhariya ◽  
Kuldeep K. Lal ◽  
Rajeev K. Singh ◽  
Vindhya Mohindra ◽  
Arti Gupta ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Labeo Rohita ◽  
Isolation By Distance ◽  
Haplotype Diversity ◽  
Population Variation ◽  
Population Substructure ◽  
Distribution Analysis ◽  
Genetic Structuring ◽  
Potential Marker ◽  
Atpase 6

Abstract ATPase 6/8 gene (842 bp) of mitochondrial DNA was sequenced in Labeo rohita samples (n = 253) collected from nine rivers belonging to four river basins; Indus, Ganges, Brahmaputra and Mahanadi. Analysis revealed 44 haplotypes with high haplotype diversity (Hd) 0.694 and low nucleotide diversity (π) 0.001. The within population variation was larger (83.44%) than among population differences (16.56%). The mean FST value (0.166; P &lt; 0.05) for overall populations revealed moderate level of genetic structuring in the wild L. rohita populations. The haplotype network presented a single clade for wild L. rohita population, from different rivers. Negative values for Fu’s index (FS), mismatch distribution analysis indicated period of expansion in L. rohita population. The time after recent expansion was estimated for each population, between 0.042 to 0.167 mya. The pattern of Isolation by Distance (IBD) was not significant (r = -0.113, P &lt; 0.287), when all the sampling locations were compared (Mantel test), however, when an outlier (Indus, Brahmaputra and Mahanadi) was removed from the whole population set, a clear positive correlation between pairwise FST and geographic distance (Km) was seen. The analysis of data demonstrated that ATPase6/8 gene polymorphism is a potential marker to understand genetic population structure of wild L. rohita existing in different rivers. The study identified population substructure in wild L. rohita with common ancestral origin [Current Zoology 60 (4): 460–471, 2014].

Genetic variation and phylogeography of Psammosilene tunicoides (Caryophyllaceae), a narrowly distributed and endemic species in south-western China

2011 ◽  
Vol 59 (5) ◽  
pp. 450 ◽  
Author(s):  
Qing-Ying Zhang ◽  
Yu-Juan Zhao ◽  
Xun Gong
Keyword(s):  
Genetic Differentiation ◽  
Endemic Species ◽  
Nuclear Dna ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Population History ◽  
Western China ◽  
Phylogeographic Structure ◽  
Population Subdivision ◽  
Chloroplast Haplotypes

Psammosilene tunicoides is a narrowly distributed and endemic species in south-western China. An investigation of sequence variation at two chloroplast DNA (cpDNA) regions (rpL16, trnQ-5′rps16) and one nuclear DNA (nDNA) locus (GPA1) were carried out to survey the population structure and population history of the species. Among the 22 populations across its geographical range, nine chloroplast haplotypes and 17 nuclear alleles were identified. Both cpDNA and nDNA consistently revealed high levels of population differentiation (GST = 0.604 and 0.540, respectively), suggesting a distinct phylogeographic structure (NST > GST, P < 0.01). This high genetic differentiation might be a combined effect of breeding system, limited pollen and seed dispersal and geographic isolation of populations. The level of haplotype diversities (cpDNA, hT = 0.575; nDNA, hT = 0.724) were high, but the nucleotide diversities (cpDNA, π = 0.00099; nDNA, π = 0.00105) were low. These results together with the star-like phylogenetic pattern and neutrality tests indicate that P. tunicoides has experienced a population expansion event in its evolution. Limited genetic exchange after population expansion was supported by the pronounced genetic differentiation among populations as well as evidence for ‘isolation-by-distance’ revealed by cpDNA. Due to high population subdivision and complex landscape, as many populations as possible should be considered for genetic conservation.

scholarly journals Patterns of genetic divergence among populations of Aedes aegypti L. (Diptera: Culicidae) in the southeastern USA

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Kristen A. Hopperstad ◽  
Michael H. Reiskind ◽  
Paul E. Labadie ◽  
Martha O. Burford Reiskind
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Aedes Aegypti ◽  
Microsatellite Markers ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Health Concern ◽  
Genetic Structuring ◽  
Genetic Characteristics ◽  
Southeastern Usa

Abstract Background The yellow fever mosquito, Aedes aegypti is a public health concern in the USA, especially in the wake of emergent diseases such as Zika and chikungunya. Aedes aegypti populations dwindled after the invasion of Aedes albopictus in the 1980s and many populations were extirpated. However, in some areas Ae. aegypti persisted in small populations and there are reports of recent resurgences of Ae. aegypti in Florida, Louisiana, Nevada and California. We assessed the population genetic structure of Ae. aegypti in Florida and Georgia, which has concomitant consequences related to mosquito dispersal, pesticide resistance and vectorial capacity. Methods We collected Ae. aegypti across Florida and in Georgia using ovitraps. We hatched the eggs and reared them to adults, and after sacrifice we extracted their DNA. We then probed each individual for variation in 6 microsatellite markers, which we used to address population genetic characteristics. Results We collected Ae. aegypti and genotyped seven Florida populations and one Georgia population using microsatellite markers. We found evidence of isolation by distance model of gene flow supported by driving distance among cities within Florida and two theoretic genetic clusters. Conclusions Significant genetic structure between some populations with substantial gene flow between geographically distant cities suggests regional genetic structuring of Ae. aegypti in Florida. This study provides information on the genetic exchange between populations of Ae. aegypti in the southeastern USA and suggests potential routes of spread of this species.

scholarly journals Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex

2017 ◽  
Author(s):  
Md Rakeb-Ul Islam ◽  
Daniel J Schmidt ◽  
David A Crook ◽  
Jane M Hughes
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Cryptic Species ◽  
Isolation By Distance ◽  
Gene Tree ◽  
Phylogeographic Structure ◽  
Genetic Structuring ◽  
River Population ◽  
Genetic Population ◽  
Eastern Australia

Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinninae: Retropinna semoni) is a facultatively diadromous fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations at the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to potamodromous behaviour. We investigated populations corresponding with two putative cryptic species, the South East Queensland (SEQ), and Central East Queensland (CEQ) lineages. In agreement with our hypothesis, highly significant overall FST values suggested that both groups exhibit very low dispersal among rivers (SEQ FST = 0.13; CEQ FST = 0.30). The two putative cryptic species, formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within clades. Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting potamodromous behaviour does not homogenise populations at the within-river scale. Overall, northern groups in the smelt cryptic species exhibit higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units to guide future conservation management.

scholarly journals Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex

2017 ◽  
Author(s):  
Md Rakeb-Ul Islam ◽  
Daniel J Schmidt ◽  
David A Crook ◽  
Jane M Hughes
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Cryptic Species ◽  
Isolation By Distance ◽  
Gene Tree ◽  
Phylogeographic Structure ◽  
Genetic Structuring ◽  
River Population ◽  
Genetic Population ◽  
Eastern Australia

Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinninae: Retropinna semoni) is a facultatively diadromous fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations at the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to potamodromous behaviour. We investigated populations corresponding with two putative cryptic species, the South East Queensland (SEQ), and Central East Queensland (CEQ) lineages. In agreement with our hypothesis, highly significant overall FST values suggested that both groups exhibit very low dispersal among rivers (SEQ FST = 0.13; CEQ FST = 0.30). The two putative cryptic species, formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within clades. Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting potamodromous behaviour does not homogenise populations at the within-river scale. Overall, northern groups in the smelt cryptic species exhibit higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units to guide future conservation management.

Sign in / Sign up

Export Citation Format

Share Document