Restricted gene flow in the endangered Capricorn Yellow Chat Epthianura crocea macgregori: consequences for conservation management

2017 ◽  
Vol 28 (1) ◽  
pp. 116-125 ◽  
Author(s):  
WAYNE A. HOUSTON ◽  
WILLIAM J. ASPDEN ◽  
ROD ELDER ◽  
ROBERT L. BLACK ◽  
LINDA E. NEAVES ◽  
...  

SummaryThe Yellow Chat Epthianura crocea is comprised of three disjunct subspecies. Subspecies E. c. macgregori (Capricorn Yellow Chat) is listed as Critically Endangered under the EPBC Act and has a distribution that also appears to be disjunct, with a limited geographic area of less than 7,000 ha. Some populations are threatened by rapid industrial development, and it is important for conservation of the subspecies to determine the extent to which the putative populations are connected. We used 14 microsatellite markers to measure genetic diversity and to determine the extent of gene flow between two disjunct populations at the northern and southern extremes of the subspecies’ range. No significant differences in genetic diversity (number of alleles and heterozygosity) were observed, but clear population structuring was apparent, with obvious differentiation between the northern and southern populations. The most likely explanation for reduced gene flow between the two populations is either the development of a geographic barrier as a consequence of shrinkage of the marine plains associated with the rise in sea levels following the last glacial maxima, or reduced connectivity across the largely unsuitable pasture and forest habitat that now separates the two populations, exacerbated by declining population size and fewer potential emigrants. Regardless of the mechanism, restricted gene flow between these two populations has important consequences for their ongoing conservation. The relative isolation of the smaller southern groups (the Fitzroy River delta and Curtis Island) from the much larger northern group (both sides of the Broad Sound) makes the southern population more vulnerable to local extinction. Conservation efforts should focus on nature refuge agreements with land owners agreeing to maintain favourable grazing management practices in perpetuity, particularly in the northern area where most chats occur. Supplemental exchanges of individuals from northern and southern populations should be explored as a way of increasing genetic diversity and reducing inbreeding.

Genetics ◽  
2002 ◽  
Vol 161 (2) ◽  
pp. 873-888
Author(s):  
Jon F Wilkins ◽  
John Wakeley

Abstract In this article we present a model for analyzing patterns of genetic diversity in a continuous, finite, linear habitat with restricted gene flow. The distribution of coalescent times and locations is derived for a pair of sequences sampled from arbitrary locations along the habitat. The results for mean time to coalescence are compared to simulated data. As expected, mean time to common ancestry increases with the distance separating the two sequences. Additionally, this mean time is greater near the center of the habitat than near the ends. In the distant past, lineages that have not undergone coalescence are more likely to have been at opposite ends of the population range, whereas coalescent events in the distant past are biased toward the center. All of these effects are more pronounced when gene flow is more limited. The pattern of pairwise nucleotide differences predicted by the model is compared to data collected from sardine populations. The sardine data are used to illustrate how demographic parameters can be estimated using the model.


Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 97 ◽  
Author(s):  
Xiaofeng Chi ◽  
Faqi Zhang ◽  
Qingbo Gao ◽  
Rui Xing ◽  
Shilong Chen

The uplift of the Qinghai-Tibetan Plateau (QTP) had a profound impact on the plant speciation rate and genetic diversity. High genetic diversity ensures that species can survive and adapt in the face of geographical and environmental changes. The Tanggula Mountains, located in the central of the QTP, have unique geographical significance. The aim of this study was to investigate the effect of the Tanggula Mountains as a geographical barrier on plant genetic diversity and structure by using Lancea tibetica. A total of 456 individuals from 31 populations were analyzed using eight pairs of microsatellite makers. The total number of alleles was 55 and the number per locus ranged from 3 to 11 with an average of 6.875. The polymorphism information content (PIC) values ranged from 0.2693 to 0.7761 with an average of 0.4378 indicating that the eight microsatellite makers were efficient for distinguishing genotypes. Furthermore, the observed heterozygosity (Ho), the expected heterozygosity (He), and the Shannon information index (I) were 0.5277, 0.4949, and 0.9394, respectively, which indicated a high level of genetic diversity. We detected high genetic differentiation among all sampling sites and restricted gene flow among populations. Bayesian-based cluster analysis (STRUCTURE), principal coordinates analysis (PCoA), and Neighbor-Joining (NJ) cluster analysis based on microsatellite markers grouped the populations into two clusters: the southern branch and the northern branch. The analysis also detected genetic barriers and restricted gene flow between the two groups separated by the Tanggula Mountains. This study indicates that the geographical isolation of the Tanggula Mountains restricted the genetic connection and the distinct niches on the two sides of the mountains increased the intraspecific divergence of the plants.


2006 ◽  
Vol 16 (2) ◽  
pp. 113-129 ◽  
Author(s):  
SHIGEKI ASAI ◽  
YOSHIHIRO YAMAMOTO ◽  
SATOSHI YAMAGISHI

The Japanese subspecies of Hodgson's Hawk-eagle, Spizaetus nipalensis orientalis, is considered threatened and has been designated as Endangered by the Japanese government. We determined the complete mitochondrial DNA (mtDNA) sequence of this species and designed a primer set to amplify a highly variable region of mtDNA, part of the control region (CR), based on this complete sequence. Using the primers, we amplified the CR and then determined the haplotypes of 178 samples collected at different sites in Japan. A nested cladistic analysis indicated that gene flow within some clades was restricted. The inference key implied that isolation by distance had caused the restriction of gene flow. Moreover, the ranges of the clades in which restricted gene flow was detected overlapped with the ranges of other clades. These results suggest that there is no fragmental population of Hodgson's Hawk-eagle in Japan and that this species has dispersed within short distances, at least in some lineages. Genetic diversity was high in comparison with other species. Therefore, at least in terms of genetic diversity, the Japanese population of Hodgson's Hawk-eagle is probably not in a critical situation.


2021 ◽  
Vol 12 ◽  
Author(s):  
Thomas J. McGreevy ◽  
Sozos Michaelides ◽  
Mihajla Djan ◽  
Mary Sullivan ◽  
Diana M. Beltrán ◽  
...  

The environment plays an important role in the movement of individuals and their associated genes among populations, which facilitates gene flow. Gene flow can help maintain the genetic diversity both within and between populations and counter the negative impact of genetic drift, which can decrease the fitness of individuals. Sympatric species can have different habitat preferences, and thus can exhibit different patterns of genetic variability and population structure. The specialist-generalist variation hypothesis (SGVH) predicts that specialists will have lower genetic diversity, lower effective population sizes (Ne), and less gene flow among populations. In this study, we used spatially explicit, individual-based comparative approaches to test SGVH predictions in two sympatric cottontail species and identify environmental variables that influence their gene flow. New England cottontail (Sylvilagus transitionalis) is the only native cottontail in the Northeast US, an early successional habitat specialist, and a species of conservation concern. Eastern cottontail (S. floridanus) is an invasive species in the Northeast US and a habitat generalist. We characterized each species’ genomic variation by developing double-digest Restriction-site Associated DNA sequence single nucleotide polymorphism markers, quantified their habitat with Geographic Information System environmental variables, and conducted our analyses at multiple scales. Surprisingly, both species had similar levels of genetic diversity and eastern cottontail’s Ne was only higher than New England cottontail in one of three subregions. At a regional level, the population clusters of New England cottontail were more distinct than eastern cottontail, but the subregional levels showed more geographic areas of restricted gene flow for eastern cottontail than New England cottontail. In general, the environmental variables had the predicted effect on each species’ gene flow. However, the most important environmental variable varied by subregion and species, which shows that location and species matter. Our results provide partial support for the SGVH and the identification of environmental variables that facilitate or impede gene flow can be used to help inform management decisions to conserve New England cottontail.


2016 ◽  
Vol 42 (1) ◽  
pp. 9-18 ◽  
Author(s):  
Stefanie Reim ◽  
Frank Lochschmidt ◽  
Anke Proft ◽  
Ute Tröber ◽  
Heino Wolf

Abstract In recent years, land use changes led to a rapid decline and fragmentation of J. communis populations in Germany. Population isolation may lead to a restricted gene flow and, further, to negative effects on genetic variation. In this study, genetic diversity and population structure in seven fragmented J. communis populations in Saxony, Germany, were investigated using nuclear microsatellites (nSSR) and chloroplast single nucleotide polymorphism (cpSNP). In all Saxony J. communis populations, a high genetic diversity was determined but no population differentiation could be detected whatever method was applied (Bayesian cluster analysis, F-statistics, AMOVA). The same was true for three J. communis out-group samples originating from Italy, Slovakia and Norway, which also showed high genetic diversity and low genetic differences regarding other J. communis populations. Low genetic differentiation among the J. communis populations ascertained with nuclear and chloroplast markers indicated high levels of gene flow by pollen and also by seeds between the sampled locations. Low genetic differentiation may also provide an indicator of Juniper survival during the last glacial maximum (LGM) in Europe. The results of this study serve as a basis for the implementation of appropriate conservation measures in Saxony.


Author(s):  
Anayansi Valderrama Cumbrera ◽  
Mileyka Santos ◽  
Angélica Castro ◽  
José Dilermando Andrade Filho

<p><em>[Cryptic Species Lutzomyia longipalpis (Diptera: Phlebotominae) and its Implications in the Transmission of Leishmaniasis in Panama]</em></p><p><em>RESUMEN</em></p><p><em>Lutzomyia</em><em>longipalpis</em>es el principal vector de una importante enfermedad desatendida en América. La diversidad genética de este vector se estimó en la población colectada en dos áreas geográficas separadas por hasta 37 km. Analizamos la secuencia CB3-PDR / N1N-PDR de 22 individuos obteniendo un parámetro de: h = 0.43 y π = 0.0017 (Bo-na), h = 0.89, π = 0.004 (El Limón) con una diferenciación genética de kst = 0.03; p&gt; 0.05 entre ellos. Ocho haplotipos fueron detectados, de los cuales fue compartido. Se detectó una diferenciación significativa entre las poblaciones Panamá-Colombia (kst = 0.98), Panamá-Costa Rica (kst = 0.98) y Panamá-Brasil (kst = 0.72) bajo el modelo de aislamiento. Las inferencias genéticas de esta población pueden complementar la información de la capacidad de dispersión y brindar pistas importantes para comprender la ecología de <em>Lu</em>. <em>longiplapis</em>en Panamá.</p><p>ABSTRACT</p><p class="CuerpoA"><span class="Ninguno"><em><span lang="EN-US">Lutzomyia longipalpis</span></em></span><span class="Ninguno"><span lang="EN-US">is the main vector-borne of important neglected disease in America. The genetic diversity of this vector was estimated in population collected from two geographic area separated by up to </span></span><span class="Ninguno"><span lang="ES-TRAD">37</span></span><span class="Ninguno"><span lang="EN-US">km. We analyzed the sequence CB3-PDR/N1N-PDR of 22 individuals and the resulted of parameter was: h = 0.43 and π = 0.0017 (Bona), h = 0.89, π = 0.004 (El Limón) and genetic differentiation was kst = 0.03; p &gt; 0.05 among them. Eight haplotypes were detected, and one was shared. Significant differentiation was detected among populations Panama-Colombia (kst = 0.98), Panama-Costa Rica (kst = 0.98) and Panama-Brazil (kst = 0.72) and these were genetically isolated by distance. The existence of shared haplotypes among the populations suggests a gene flow despite the distance and geographic separation. Nevertheless, showed isolation it contrasted with individuals very distant.</span></span><span class="Ninguno"><span lang="EN-US">The genetic inferences of this population can supplement the information of dispersal capacity and provided important clues to understand the ecology of sandflies.</span></span></p>


2019 ◽  
Author(s):  
DR Trumbo ◽  
PE Salerno ◽  
KA Logan ◽  
M Alldredge ◽  
RB Gagne ◽  
...  

AbstractApex predators are important indicators of intact natural ecosystems. They are also sensitive to urbanization because they require broad home ranges and extensive contiguous habitat to support their prey base. Pumas (Puma concolor) can persist near human developed areas, but urbanization may be detrimental to their movement ecology, population structure, and genetic diversity. To investigate potential effects of urbanization in population connectivity of pumas, we performed a landscape genomics study of 134 pumas on the rural Western Slope and more urbanized Front Range of Colorado, USA. Over 12,000 single nucleotide polymorphisms were genotyped using double-digest, restriction site-associated DNA sequencing (ddRADseq). We investigated patterns of gene flow and genetic diversity, and tested for correlations between key landscape variables and genetic distance to assess the effects of urbanization and other landscape factors on gene flow. Levels of genetic diversity were similar for the Western Slope and Front Range, but effective population sizes were smaller, genetic distances were higher, and there was more overall population substructure in the more urbanized Front Range. Forest cover was strongly positively associated with puma gene flow on the Western Slope, while impervious surfaces restricted gene flow and more open, natural habitats enhanced gene flow on the Front Range. Landscape genomic analyses revealed differences in puma movement and gene flow patterns in rural versus urban settings. Our results highlight the utility of dense, genome-scale markers to document subtle impacts of urbanization on a wide-ranging carnivore living near a large urban center.


2020 ◽  
Author(s):  
Cheng Jin ◽  
Huixia Kao ◽  
Shubin Dong

Abstract BackgroundStudying population genetic structure and gene flow of plant populations and their influence factors is crucial in field of conservation biology, especially rare and endangered plants. Tetraena mongolica Maxim (TM), belong to Zygophyllaceae family, a rare and endangered plant with narrow distribution. Due to excessive logging, urban expansion, industrial development and development of the scenic spot in the last decades, has caused habitat fragments and decline.ResultsIn this study, the genetic diversity, the population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found existing TM populations have moderate levels of genetic diversity, very low genetic differentiation and high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups, Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. The migration model indicated that the gene flow is more of an north to south migration pattern in history.ConclusionsOur study demonstrate that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. For recommendations of conservation management, all 8 populations should be protected as a whole population, rather than just those in the core area of TM nature reserve, especially the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.


2009 ◽  
Vol 60 (1) ◽  
pp. 34 ◽  
Author(s):  
James T. Knight ◽  
Catherine J. Nock ◽  
Martin S. Elphinstone ◽  
Peter R. Baverstock

The maintenance of genetic diversity and gene flow in threatened species is a vital consideration for recovery programs. The endangered Oxleyan pygmy perch Nannoperca oxleyana has a fragmented distribution within coastal freshwater drainages of southern Queensland and northern New South Wales, Australia. In the present study, mitochondrial DNA control region variation was used to assess genetic diversity and structure across the geographical range of this species. Haplotypic diversity was highest in a small NSW subcatchment south of Evans Head (h = 0.594) followed by Marcus Creek in Queensland (h = 0.475). Distinct genetic differentiation was evident among the Queensland localities and the NSW subcatchments, implying restricted gene flow between coastal river systems. One of the nine haplotypes detected was distributed over 83.4% of the species’ range, suggesting historical connectivity among the now fragmented populations. These patterns were concordant with eustatic changes associated with the last glacial maximum. High barrier sand dunes may also act as barriers to gene flow and dispersal between adjacent NSW subcatchments. Conservation efforts should focus on the preservation of genetic diversity by maintaining as many genetically differentiated populations as possible. The relatively diverse populations inhabiting the South Evans Head subcatchment and Marcus Creek require special management consideration.


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