Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide

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.

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The Coalescent in a Continuous, Finite, Linear Population

Genetics ◽

10.1093/genetics/161.2.873 ◽

2002 ◽

Vol 161 (2) ◽

pp. 873-888

Author(s):

Jon F Wilkins ◽

John Wakeley

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Simulated Data ◽

Restricted Gene Flow ◽

Demographic Parameters ◽

Common Ancestry ◽

Linear Habitat ◽

Mean Time ◽

Finite Linear

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.

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Genetic Structure and Eco-Geographical Differentiation of Lancea tibetica in the Qinghai-Tibetan Plateau

Genes ◽

10.3390/genes10020097 ◽

2019 ◽

Vol 10 (2) ◽

pp. 97 ◽

Cited By ~ 2

Author(s):

Xiaofeng Chi ◽

Faqi Zhang ◽

Qingbo Gao ◽

Rui Xing ◽

Shilong Chen

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Gene Flow ◽

Tibetan Plateau ◽

Environmental Changes ◽

Restricted Gene Flow ◽

Principal Coordinates Analysis ◽

Principal Coordinates ◽

Genetic Diversity And Structure ◽

Tanggula Mountains

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.

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Genetic diversity and extent of gene flow in the endangered Japanese population of Hodgson's hawk-eagle, Spizaetus nipalensis

Bird Conservation International ◽

10.1017/s0959270906000050 ◽

2006 ◽

Vol 16 (2) ◽

pp. 113-129 ◽

Cited By ~ 18

Author(s):

SHIGEKI ASAI ◽

YOSHIHIRO YAMAMOTO ◽

SATOSHI YAMAGISHI

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Japanese Population ◽

Isolation By Distance ◽

Cladistic Analysis ◽

Variable Region ◽

Complete Sequence ◽

Restricted Gene Flow ◽

Critical Situation ◽

Mtdna Sequence

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.

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Location and Species Matters: Variable Influence of the Environment on the Gene Flow of Imperiled, Native and Invasive Cottontails

Frontiers in Genetics ◽

10.3389/fgene.2021.708871 ◽

2021 ◽

Vol 12 ◽

Author(s):

Thomas J. McGreevy ◽

Sozos Michaelides ◽

Mihajla Djan ◽

Mary Sullivan ◽

Diana M. Beltrán ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

New England ◽

Environmental Variables ◽

Negative Impact ◽

Genomic Variation ◽

Restricted Gene Flow ◽

New England Cottontail ◽

Eastern Cottontail ◽

Northeast Us

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.

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Population connectivity and larval dispersal of the exploited mangrove crab Ucides cordatus along the Brazilian coast

PeerJ ◽

10.7717/peerj.4702 ◽

2018 ◽

Vol 6 ◽

pp. e4702 ◽

Cited By ~ 4

Author(s):

Fábio B. Britto ◽

Anders J. Schmidt ◽

Adriana M.F. Carvalho ◽

Carolina C.M.P. Vasconcelos ◽

Antonia M. Farias ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Flow ◽

Population Connectivity ◽

Brazilian Coast ◽

Fishery Resource ◽

Ucides Cordatus ◽

Migration Rates ◽

Mangrove Crab ◽

Key Species

Background The mangrove crab Ucides cordatus is considered a key species for the ecological balance of mangrove forests and a major source of employment and income for traditional crab collectors in Brazil. Several studies evidenced weak genetic variation among populations due to an efficient larval transport. However, gene flow patterns of the species is poorly understood, with no information about migration rates. The influence of the two main Brazilian currents in larval dispersion is also not clear. In order to provide baseline information for conservation, planning and management of this important fishery resource, the present study aimed to estimate and evaluate spatial distribution of genetic diversity, migration rates and gene flow directivity among populations of U. cordatus in Brazil. Methods Nine microsatellites were used to resolve population structure of 319 crabs collected from six sites located along the Brazilian coast. The degree of geographical differentiation included estimates of genetic diversity, population structure and gene flow models, with spatial analysis of shared alleles (SAShA), isolation by distance tests, AMOVA, discriminant analysis of principal components (DAPC) and Bayesian clustering. We estimated the amount of ongoing gene flow between clusters using the coalescent-based method implemented in Migrate-N. Results Loci were highly polymorphic (average of 12.4 alleles per locus) evidencing high genetic variability. There was significant differentiation among localities, despite of the low value of FST (= 0.019; P < 0.001). FST and Jost’s D indexes were also estimated in pairwise comparisons and showed significant differences between most of the surveyed site pairs (P < 0.05). Structure evidenced a single genetic group among samples, however SAShA pointed to a non-panmictic condition (P = 0.011). AMOVA detected four statistical significant clusters with low level of differentiation (FCT = 0.037; P = 0.023). The gene flow model that best described the population connectivity was the island model, with ∼24 crabs being exchanged among localities per generation. Discussion The high migration rates found among localities seem to be the main force acting to sustain the distribution of the genetic diversity of U. cordatus. Despite the high gene flow and the weak population structure among samples, the significant genetic differences found suggest that gene flow alone does not bypass the effects of genetic drift, natural selection and/or human exploitation. These findings are vital for the establishment of a database to be used in the development of conservation programs.

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

Bird Conservation International ◽

10.1017/s0959270917000284 ◽

2017 ◽

Vol 28 (1) ◽

pp. 116-125 ◽

Cited By ~ 1

Author(s):

WAYNE A. HOUSTON ◽

WILLIAM J. ASPDEN ◽

ROD ELDER ◽

ROBERT L. BLACK ◽

LINDA E. NEAVES ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Industrial Development ◽

Management Practices ◽

Geographic Area ◽

Restricted Gene Flow ◽

Sea Levels ◽

Population Structuring ◽

Epbc Act ◽

Two Populations

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.

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Genetic structure and diversity in Juniperus communis populations in Saxony, Germany

Biodiversity Research and Conservation ◽

10.1515/biorc-2016-0008 ◽

2016 ◽

Vol 42 (1) ◽

pp. 9-18 ◽

Cited By ~ 1

Author(s):

Stefanie Reim ◽

Frank Lochschmidt ◽

Anke Proft ◽

Ute Tröber ◽

Heino Wolf

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Differentiation ◽

Land Use Changes ◽

Rapid Decline ◽

Restricted Gene Flow ◽

Negative Effects ◽

Population Isolation ◽

High Genetic Diversity ◽

Chloroplast Markers

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.

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Everything you always wanted to know about gene flow in tropical landscapes (but were afraid to ask)

PeerJ ◽

10.7717/peerj.6446 ◽

2019 ◽

Vol 7 ◽

pp. e6446 ◽

Cited By ~ 6

Author(s):

Waléria Pereira Monteiro ◽

Jamille Costa Veiga ◽

Amanda Reis Silva ◽

Carolina da Silva Carvalho ◽

Éder Cristian Malta Lanes ◽

...

Keyword(s):

Gene Flow ◽

Habitat Loss ◽

Forest Cover ◽

Habitat Degradation ◽

Population Level ◽

Tropical Species ◽

Natural Habitats ◽

Tropical Regions ◽

Landscape Effects ◽

Statistical Approaches

The bulk of the world’s biodiversity is found in tropical regions, which are increasingly threatened by the human-led degradation of natural habitats. Yet, little is known about tropical biodiversity responses to habitat loss and fragmentation. Here we review all available literature assessing landscape effects on gene flow in tropical species, aiming to help unravel the factors underpinning functional connectivity in the tropics. We map and classify studies by focus species, the molecular markers employed, statistical approaches to assess landscape effects on gene flow, and the evaluated landscape and environmental variables. We then compare qualitatively and quantitatively landscape effects on gene flow across species and units of analysis. We found 69 articles assessing landscape effects on gene flow in tropical organisms, most of which were published in the last five years, were concentrated in the Americas, and focused on amphibians or mammals. Most studies employed population-level approaches, microsatellites were the preferred type of markers, and Mantel and partial Mantel tests the most common statistical approaches used. While elevation, land cover and forest cover were the most common gene flow predictors assessed, habitat suitability was found to be a common predictor of gene flow. A third of all surveyed studies explicitly assessed the effect of habitat degradation, but only 14 of these detected a reduced gene flow with increasing habitat loss. Elevation was responsible for most significant microsatellite-based isolation by resistance effects and a single study reported significant isolation by non-forested areas in an ant. Our study reveals important knowledge gaps on the study of landscape effects on gene flow in tropical organisms, and provides useful guidelines on how to fill them.

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Conservation implications of distinct genetic structuring in the endangered freshwater fish Nannoperca oxleyana (Percichthyidae)

Marine and Freshwater Research ◽

10.1071/mf08022 ◽

2009 ◽

Vol 60 (1) ◽

pp. 34 ◽

Cited By ~ 14

Author(s):

James T. Knight ◽

Catherine J. Nock ◽

Martin S. Elphinstone ◽

Peter R. Baverstock

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Sand Dunes ◽

Restricted Gene Flow ◽

Genetic Structuring ◽

Conservation Implications ◽

South Wales ◽

Haplotypic Diversity ◽

Genetic Diversity And Structure ◽

Fragmented Distribution

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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Population and landscape genetic analysis of the Malayan sun bear Helarctos malayanus

Conservation Genetics ◽

10.1007/s10592-019-01233-w ◽

2019 ◽

Vol 21 (1) ◽

pp. 123-135

Author(s):

Miriam N. Kunde ◽

Renata F. Martins ◽

Joe Premier ◽

Joerns Fickel ◽

Daniel W. Förster

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Unknown Origin ◽

Population Connectivity ◽

The Sun ◽

Conservation Action ◽

Helarctos Malayanus ◽

Assignment Probability ◽

Sun Bear ◽

Landscape Genetic

AbstractConservation genetics can provide data needed by conservation practitioners for their decisions regarding the management of vulnerable or endangered species, such as the sun bear Helarctos malayanus. Throughout its range, the sun bear is threatened by loss and fragmentation of its habitat and the illegal trade of both live bears and bear parts. Sharply declining population numbers and population sizes, and a lack of natural dispersal between populations all threaten the genetic diversity of the remaining populations of this species. In this first population genetics study of sun bears using microsatellite markers, we analyzed 68 sun bear samples from Cambodia to investigate population structure and genetic diversity. We found evidence for two genetically distinct populations in the West and East of Cambodia. Ongoing or recent gene flow between these populations does not appear sufficient to alleviate loss of diversity in these populations, one of which (West Cambodia) is characterized by significant inbreeding. We were able to assign 85% of sun bears of unknown origin to one of the two populations with high confidence (assignment probability ≥ 85%), providing valuable information for future bear reintroduction programs. Further, our results suggest that developed land (mostly agricultural mosaics) acts as a barrier to gene flow for sun bears in Cambodia. We highlight that regional sun bear conservation action plans should consider promoting population connectivity and enforcing wildlife protection of this threatened species.

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