skip to main content


Title: Genetic differentiation among populations of the blackfin goodea Goodea atripinnis (Cyprinodontiformes: Goodeidae): implications for its evolutionary history
Abstract

Central Mexico is characterized by a complex topography that is the result of historic and contemporary tectonic and climatic factors. These events have influenced the evolutionary history of numerous freshwater fishes in the region. Nonetheless, recent studies have shown that life‐history traits and ecological characteristics of species may influence dispersal capabilities and the degree of genetic connectivity.Goodea(Cyprinodontiformes: Goodeidae) is one of the most widely distributed and environmentally tolerant genera of goodeids. In this study, the authors analysed variation in the mitochondrial cytochrome b gene to evaluate the phylogeographic relationships, genetic structure, genetic diversity and demographic history ofGoodeafrom across its distribution range. They found low genetic differentiation and identified shared haplotypes among several regions. Geographic segregation was found in samples southwest and northeast of the Lower Lerma region, with some internal isolated groups showing phylogeographic differentiation and unique haplotypes. The AMOVA best explained genetic structure when grouped by haplogroups rather than when grouped by recognized biogeographic regions. Several regions showed null genetic diversity, raising the possibility of dispersal mediated by humans. Finally, Bayesian Skyline Plot analysis showed a population expansion for the Southwest haplogroup, except for the Armería population and sub‐group II of the Northeast haplogroup. All this suggests a recent colonization ofGoodea atripinnisthroughout some of the biogeographic regions currently inhabited by this species.

 
more » « less
NSF-PAR ID:
10452472
Author(s) / Creator(s):
 ;  ;  ;  ;  ;  
Publisher / Repository:
Wiley-Blackwell
Date Published:
Journal Name:
Journal of Fish Biology
Volume:
98
Issue:
5
ISSN:
0022-1112
Page Range / eLocation ID:
p. 1253-1266
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract Aim

    Present Amazonian diversity patterns can result from many different mechanisms and, consequently, the factors contributing to divergence across regions and/or taxa may differ. Nevertheless, the river‐barrier hypothesis is still widely invoked as a causal process in divergence of Amazonian species. Here we use model‐based phylogeographic analyses to test the extent to which major Amazonian rivers act similarly as barriers across time and space in two broadly distributed Amazonian taxa.

    Local

    Amazon rain forest.

    Taxon

    The lizardGonatodes humeralis(Sphaerodactylidae) and the tree frogDendropsophus leucophyllatus(Hylidae).

    Methods

    We obtained RADseq data for samples distributed across main river barriers, representing main Areas of Endemism previously proposed for the region. We conduct model‐based phylogeographic and genetic differentiation analyses across each population pair.

    Results

    Measures of genetic differentiation (based onFSTcalculated from genomic data) show that all rivers are associated with significant genetic differentiation. Parameters estimated under investigated divergence models showed that divergence times for populations separated by each of the 11 bordering rivers were all fairly recent. The degree of differentiation consistently varied between taxa and among rivers, which is not an artifact of any corresponding difference in the genetic diversities of the respective taxa, or to amounts of migration based on analyses of the site‐frequency spectrum.

    Main conclusions

    Taken together, our results support a dispersal (rather than vicariance) history, without strong evidence of congruence between these species and rivers. However, once a species crossed a river, populations separated by each and every river have remained isolated—in this sense, rivers act similarly as barriers to any further gene flow. This result suggests differing degrees of persistence and gives rise to the seeming contradiction that the divergence process indeed varies across time, space and species, even though major Amazonian rivers have acted as secondary barriers to gene flow in the focal taxa.

     
    more » « less
  2. The Indo-Malay Archipelago is regarded as a barrier that separates organisms of the Indian and Pacific Oceans. Previous studies of marine biota from this region have found a variety of biogeographic barriers, seemingly dependent on taxon and methodology. Several hypotheses, such as emergence of the Sunda Shelf and recent physical oceanography, have been proposed to account for the genetic structuring of marine organisms in this region. Here, we used six microsatellite loci to infer genetic diversity, population differentiation and phylogeographic patterns ofEnhalus acoroidesacross the Indo-Malay Archipelago. Heterozygosities were consistently high, and significant isolation-by-distance, consistent with restricted gene flow, was observed. Both a neighbour joining tree based onDAdistance and Bayesian clustering revealed three major clusters ofE. acoroides. Our results indicate that phylogeographic patterns ofE. acoroideshave possibly been influenced by glaciation and deglaciation during the Pleistocene. Recent physical oceanography such as the South Java Current and the Seasonally Reversing Current may also play a role in shaping the genetic patterns ofE. acoroides.

     
    more » « less
  3. Abstract

    A growing body of knowledge on the diversity and evolution of intertidal isopods across different regions worldwide has enhanced our understanding on biological diversification at the poorly studied, yet vast, sea–land interface. High genetic divergences among numerous allopatric lineages have been identified within presumed single broadly distributed species.Excirolana mayanais an intertidal isopod that is commonly found in sandy beaches throughout the Gulf of California. Its distribution in the Pacific extends from this basin to Colombia and in the Atlantic from Florida to Venezuela. Despite its broad distribution and ecological importance, its evolutionary history has been largely neglected. Herein, we examined phylogeographic patterns ofE. mayanain the Gulf of California and the Caribbean, based on maximum‐likelihood and Bayesian phylogenetic analyses ofDNAsequences from four mitochondrial genes (16SrDNA, 12SrDNA, cytochrome oxidase I gene, and cytochrome b gene). We compared the phylogeographic patterns ofE. mayanawith those of the coastal isopodsLigiaandExcirolana braziliensis(Gulf of California and Caribbean) andTylos(Gulf of California). We found highly divergent lineages in both, the Gulf of California and Caribbean, suggesting the presence of multiple species. We identified two instances of Atlantic–Pacific divergences. Some geographical structuring among the major clades found in the Caribbean is observed. Haplotypes from the Gulf of California form a monophyletic group sister to a lineage found in Venezuela. Phylogeographic patterns ofE. mayanain the Gulf of California differ from those observed inLigiaandTylosin this region. Nonetheless, several clades ofE. mayanahave similar distributions to clades of these two other isopod taxa. The high levels of cryptic diversity detected inE. mayanaalso pose challenges for the conservation of this isopod and its fragile environment, the sandy shores.

     
    more » « less
  4. Abstract

    Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB,Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here, we usedRADsequencing across the entireMPBrange in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X‐linked loci. Clustering and geneflow analyses revealed three distinct Y haplogroups geographically positioned within and on either side of the Great Basin Desert. Despite close geographic proximity between populations on the boundaries of each Y haplogroup, there was extremely low Y haplogroup mixing among populations, and gene flow on the autosomes was reduced across Y haplogroup boundaries. These results are consistent with a previous study suggesting that independent degradation of a recently evolved neo‐Y chromosome in previously isolated populations causes male sterility or inviability among Y haplotype lineages. Phylogeographic results supported historic contraction ofMPBinto three separate Pleistocene glacial refugia followed by postglacial range expansion and secondary contact. Distinct sets ofSNPs were statistically associated with environmental data among the most genetically distinct sets of geographic populations. This finding suggests that the process of adaptation to local climatic conditions is influenced by population genetic structure, with evidence for largely independent evolution in the most genetically isolated Y haplogroup.

     
    more » « less
  5. Abstract Aim

    The drivers of genetic diversity in Amazonia, the most species‐rich set of ecosystems on Earth, are still incompletely understood. Species from distinct Amazonian ecosystems have unique biogeographic histories that will reflect regional landscape and climatic drivers of genetic diversity. We studied bird species from patchy Amazonian white‐sand ecosystems (WSE) to evaluate the occurrence of shared biogeographic patterns to better understand the complex environmental and landscape history of Amazonia and its biodiversity.

    Location

    Northern South America; Amazonia.

    Taxon

    Passeriformes.

    Methods

    We sequenced Ultra‐conserved Elements (UCEs) from 177 samples of seven bird species associated with WSE that have overlapping ranges. We used the SNP matrices and sequence data to estimate genetic structure and migration surfaces using ‘conStruct’ andeems, performed model‐selection to obtain the most probable demographic histories on ‘PipeMasterand implemented analyses of shared demography withecoevolity.

    Results

    Shallow genetic structure patterns varied among species. The Amazon river was the only barrier shared among them. Population structure dates to no more than 450,000 years ago. Nine geographically structured populations showed signals of population size changes and eight of these occur in Northern Amazonia. Population expansion was inferred at two distinct times: ~100,000 and ~ 50,000 years ago. The timing of co‐expanding populations is consistent with differences in habitat preference, as species that prefer dense scrubby to forested vegetation expanded more recently compared to species that prefer open vegetation.

    Main conclusions

    WSE species responded in concert to environmental and landscape changes that occurred in the relatively recent past. Population expansions were likely driven by the genesis of new WSE patches and a return to wetter conditions after glacial periods. Pleistocene climatic cycles affected the distribution and dynamics of open vegetation habitats in Amazonia, especially in the Northern region, driving genetic diversity and demographic patterns of its associated biota.

     
    more » « less