skip to main content

Attention:

The NSF Public Access Repository (NSF-PAR) system and access will be unavailable from 11:00 PM ET on Thursday, May 23 until 2:00 AM ET on Friday, May 24 due to maintenance. We apologize for the inconvenience.


Title: Species‐level view of population structure and gene flow for a critically endangered primate ( Varecia variegata )
Abstract

Lemurs are among the world's most threatened mammals. The critically endangered black‐and‐white ruffed lemur (Varecia variegata), in particular, has recently experienced rapid population declines due to habitat loss, ecological sensitivities to habitat degradation, and extensive human hunting pressure. Despite this, a recent study indicates that ruffed lemurs retain among the highest levels of genetic diversity for primates. Identifying how this diversity is apportioned and whether gene flow is maintained among remnant populations will help to diagnose and target conservation priorities. We sampled 209 individuals from 19 sites throughout the remainingV. variegatarange. We used 10 polymorphic microsatellite loci and ~550 bp of mtDNAsequence data to evaluate genetic structure and population dynamics, including dispersal patterns and recent population declines. Bayesian cluster analyses identified two distinct genetic clusters, which optimally partitioned data into populations occurring on either side of theMangoro River. Localities north of the Mangoro were characterized by greater genetic diversity, greater gene flow (lower genetic differentiation) and higher mtDNAhaplotype and nucleotide diversity than those in the south. Despite this, genetic differentiation across all sites was high, as indicated by high averageFST(0.247) and ΦST(0.544), and followed a pattern of isolation‐by‐distance. We use these results to suggest future conservation strategies that include an effort to maintain genetic diversity in the north and restore connectivity in the south. We also note the discordance between patterns of genetic differentiation and current subspecies taxonomy, and encourage a re‐evaluation of conservation management units moving forward.

 
more » « less
NSF-PAR ID:
10196882
Author(s) / Creator(s):
 ;  ;  ;  ;  ;  
Publisher / Repository:
Wiley Blackwell (John Wiley & Sons)
Date Published:
Journal Name:
Ecology and Evolution
Volume:
4
Issue:
13
ISSN:
2045-7758
Format(s):
Medium: X Size: p. 2675-2692
Size(s):
["p. 2675-2692"]
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    The paleback darter,Etheostoma pallididorsum, is considered imperilled and has recently been petitioned for listing under the Endangered Species Act. Previous allozyme‐based studies found evidence of a small effective population size, warranting conservation concern. The objective of this study was to assess the population dynamics and the phylogeographical history of the paleback darter, using a multilocus microsatellite approach and mitochondrial DNA.

    The predictions of this study were that: paleback darter populations will exhibit low genetic diversity and minimal gene flow; population structure will correspond to the river systems from which the samples are derived; reservoir dams impounding the reaches between the Caddo and Ouachita rivers would serve as effective barriers to gene flow; and the Caddo and Ouachita rivers are reciprocally monophyletic.

    Microsatellite DNA loci revealed significant structure among sampled localities (globalFst= 0.17,P< 0.001), with evidence of two distinct populations representing the Caddo and Ouachita rivers. However, Bayesian phylogeographical analyses resulted in three distinct clades: Caddo River, Ouachita River, and Mazarn Creek. Divergence from the most recent ancestor shared among the river drainages was estimated at 60 Kya. Population genetic diversity was relatively low (He= 0.65; mean alleles per locus,A= 6.26), but was comparable with the population genetic diversity found in the close relatives slackwater darter,Etheostoma boschungi(He= 0.65;A= 6.74), and Tuscumbia darter,Etheostoma tuscumbia(He= 0.57;A= 5.53).

    These results have conservation implications for paleback darter populations and can be informative for other headwater specialist species. Like other headwater species with population structuring and relatively low genetic diversity, the persistence of paleback darter populations is likely to be tied to the persistence and connectivity of local breeding and non‐breeding habitat. These results do not raise conservation concern for a population decline; however, the restricted distribution and endemic status of the species still renders paleback darter populations vulnerable to extirpation or extinction.

     
    more » « less
  2. Abstract

    Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population‐specific and pairwiseFST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin,USA. Using 151 putatively neutral and 29 candidate adaptiveSNPloci, we found that climate‐related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables andFSTacross all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin‐wide to the metapopulation scale). Sensitivity analysis (leave‐one‐population‐out) revealed consistent relationships between climate variables andFSTwithinthree metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (= 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

     
    more » « less
  3. The extent and nature of genetic differentiation inSemotilus atromaculatus, one of the most abundant and widespread leuciscids in North America, were evaluated based on mitochondrial (mt) and nuclear DNA sequence variation. Phylogenetic relationships were first inferred based on a fragment of the cytochrome b (cytb) region and the nuclear introns7gene forS. atromaculatusand all other congeners as well as representative species from all other genera in the creek chub–plagopterin clade. The phylogeography of major haplogroups ofS. atromaculatuswas also assessed according to variation in a fragment of the mitochondrialcytbregion from 567 individuals across its range. All analyses identifiedS. thoreauianus,S. lumbeeandS. corporalisas reciprocally monophyletic groups. Analyses of nuclear sequence variation resolvedS. atromaculatusas a single clade, whereS. thoreauianusandS. lumbeewere recovered as the sister group toS. atromaculatus, andS. corporaliswas resolved as sister to all other species in the genus. Analyses of mtDNA sequence variation recoveredS. atromaculatusas three well supported and differentiated monophyletic groups, with a widespread genetically homogeneous lineage extending across most of the current range of the species; a more geographically restricted and geographically structured lineage in the southern Appalachians, sister group toS. lumbee; and a geographically restricted lineage was identified from two Gulf Slope basins. Evidence of complex mito‐nuclear discordance and phylogeographic differentiation withinS. atromaculatusillustrates that further analysis of widespread species is warranted to understand North American freshwater fish diversity and distributions.

     
    more » « less
  4. Abstract

    Despite substantial interest in coevolution's role in diversification, examples of coevolution contributing to speciation have been elusive. Here, we build upon past studies that have shown both coevolution between South Hills crossbills and lodgepole pine (Pinus contorta), and high levels of reproductive isolation between South Hills crossbills and other ecotypes in the North American red crossbill (Loxia curvirostra) complex. We used genotyping by sequencing to generate population genomic data and applied phylogenetic and population genetic analyses to characterize the genetic structure within and among nine of the ecotypes. Although genome‐wide divergence was slight between ecotypes (FST = 0.011–0.035), we found evidence of relative genetic differentiation (as measured byFST) between and genetic cohesiveness within many of them. As expected for nomadic and opportunistic breeders, we detected no evidence of isolation by distance. The one sedentary ecotype, the South Hills crossbill, was genetically most distinct because of elevated divergence at a small number of loci rather than pronounced overall genome‐wide divergence. These findings suggest that mechanisms related to recent local coevolution between South Hills crossbills and lodgepole pine (e.g. strong resource‐based density dependence limiting gene flow) have been associated with genome divergence in the face of gene flow. Our results further characterize a striking example of coevolution driving speciation within perhaps as little as 6000 years.

     
    more » « less
  5. Abstract

    The diversity and distribution of marine species in eastern Australia is influenced by one of the world's strongest western boundary currents, the East Australia Current, which propels water and propagules poleward, a flow intensifying due to climate change.

    Population genetic structure of the asterinid sea starMeridiastra calcarwas investigated across its range in eastern Australia (12° of latitude, 2,500 km) from northern New South Wales to its poleward‐extending range in Tasmania at the southern edge influence of the East Australia Current.

    Population structure and connectivity ofM. calcarwere examined across six bioregions using six microsatellite loci (nuclear DNA) and the control region (mitochondrial DNA). The potential influence of the extent ofM. calcar's intertidal rock platform habitat was also assessed.

    Genetic structure analysis indicated that the Hawkesbury Shelf contained distinct genetic clusters, whereas the two sites in the Batemans Shelf differed from each other, with Jervis Bay Marine Park having just one genetic cluster. The Manning Shelf, Twofold Shelf, and Bruny bioregions all had similar genetic composition.

    Strong self‐seeding (68–98%) was indicated by microsatellite loci for all bioregions, with lower (0.3–6.5%) migration between bioregions. Poleward (New South Wales to Tasmania) migration was low except from the Manning Shelf (30%).

    Contemporary population connectivity and genetic structure ofM. calcarappear to be influenced by ocean currents, habitat distribution, and its short planktonic larval duration, which was a minimum of 12–14 days, depending on availability of a settlement cue.

    The dominance of unique genetic groups in the Hawkesbury bioregion shows the importance of this region forM. calcarand possibly a diversity of co‐distributed rock platform species. This highlights how important it is to have a large marine park in the Hawkesbury bioregion, which is presently lacking.

     
    more » « less