Paleoclimatic modeling and phylogeography of least killifish, Heterandria formosa: insights into Pleistocene expansion-contraction dynamics and evolutionary history of North American Coastal Plain freshwater biota

Biogeography and the evolution of acoustic communication in the polyploid North American grey treefrog complex

After polyploid species are formed, interactions between diploid and polyploid lineages may generate additional diversity in novel cytotypes and phenotypes. In anurans, mate choice by acoustic communication is the primary method by which individuals identify their own species and assess suitable mates. As such, the evolution of acoustic signals is an important mechanism for contributing to reproductive isolation and diversification in this group. Here, we estimate the biogeographical history of the North American grey treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid Hyla versicolor, focusing specifically on the geographical origin of whole genome duplication and the expansion of lineages out of glacial refugia. We then test for lineage-specific differences in mating signals by applying comparative methods to a large acoustic data set collected over 52 years that includes >1500 individual frogs. Along with describing the overall biogeographical history and call diversity, we found evidence that the geographical origin of H. versicolor and the formation of the midwestern polyploid lineage are both associated with glacial limits, and that the southwestern polyploid lineage is associated with a shift in acoustic phenotype relative to the diploid lineage with which they share a mitochondrial lineage. In H. chrysoscelis, we see that acoustic signals are largely split by Eastern and Western lineages, but that northward expansion along either side of the Appalachian Mountains is associated with further acoustic diversification. Overall, results of this study provide substantial clarity on the evolution of grey treefrogs as it relates to their biogeography and acoustic communication.

Insight into the evolutionary history of Indoplanorbis exustus (Bulinidae: Gastropoda) at the scale of population and species

The history of a lineage is intertwined with the history of the landscape it inhabits. Here we showcase how the geo-tectonic and climatic evolution of South Asia and surrounding landmasses have shaped the biogeographical history of Indoplanorbis exustus, a tropical Asian, freshwater snail. We amplified partial COI gene fragments from all over India and combined this with a larger dataset from South and Southeast Asia to carry out phylogenetic reconstruction, species delimitation analysis and population genetic analyses. Two nuclear genes were also amplified from a few individuals per putative species to carry out divergence dating and ancestral area reconstruction analyses. The results suggest that I. exustus dispersed out of Africa into India during the Eocene. Furthermore, molecular data suggest I. exustus is a species complex consisting of multiple putative species. Primary diversification took place in the Northern Indian plains or in Northeast India. The speciation events appear to be primarily allopatric caused by a series of aridification events starting from the late Miocene to early Pleistocene. None of the species appears to have any underlying genetic structure suggestive of high vagility. All the species underwent population fluctuations during the Pleistocene, probably driven by the Quaternary climatic fluctuations.

Influence of climate change on the predicted distributions of the genus Tympanoctomys (Rodentia, Hystricomorpha, Octodontidae), and their conservation implications

Viscacha rats (genus Tympanoctomys Yepes, 1942) are ecologically, physiologically, and behaviorally unusual octodontid rodents endemic to the Monte and Patagonian desert biomes of Argentina. The geographic ranges of the different species of Tympanoctomys have been described in general terms but have not been associated with spatial and climate data. Within species, populations are patchily distributed and genetically distinct. We investigated the predicted distribution of Tympanoctomys and the influence of climate fluctuations on their geographic range in historical, current, and future, scenarios. Our objectives were to characterize the environmental niche of the genus, propose a paleoclimatic context for the oldest fossils, characterize the environmental niches for T. barrerae and T. kirchnerorum, and forecast potential future distributions for these taxa. Ecological niche models were constructed using occurrence records from 1941 to the present wherein we identified several precipitation and temperature variables as important predictors of the geographic distributions of the genus, and the species T. barrerae and T. kirchnerorum. Based on our models’ results, we hypothesize that the distribution of Tympanoctomys has contracted from historical to modern times. At the species level, T. kirchnerorum likely experienced the most dramatic change, suffering a large contraction of its historical distribution resulting in its limited present distribution. Given these findings, projected future climate fluctuations and global warming are expected to affect the distributions and persistence of these species.

Climate change models predict decreases in the range of a microendemic freshwater fish in Honduras

Despite their incredible diversity, relatively little work has been done to assess impacts of climate change on tropical freshwater organisms. Chortiheros wesseli is a species of Neotropical cichlid (Cichlidae: Cichlinae) restricted to only a few river drainages in the Caribbean-slope of Honduras. Little is known about this species and few specimens had been collected until recently; however, our work with this species in the wild has led to a better understanding of its ecology and habitat preferences making it an excellent model for how freshwater fishes can be affected by climate change. This study assesses the distribution and habitats of Chortiheros wesseli using a combination of field data and species distribution modeling. Results indicate this species is largely limited to its current range, with no realistic suitable habitat nearby. Empirical habitat data show that this species is limited to narrow and shallow flowing waters with rapids and boulders. This habitat type is highly influenced by precipitation, which contributed the greatest influence on the models of present and future habitat suitability. Although several localities are within boundaries of national protected areas, species distribution models all predict a reduction in the range of this freshwater fish based on climate change scenarios. The likelihood of a reduced range for this species will be intensified by adverse changes to its preferred habitats.

Interspecific Genetic Differences and Historical Demography in South American Arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum)

The South American arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum) are emblematic species widely distributed in the Amazon and surrounding basins. Arowana species are under strong anthropogenic pressure as they are extensively exploited for ornamental and food purposes. Until now, limited genetic and cytogenetic information has been available, with only a few studies reporting to their genetic diversity and population structure. In the present study, cytogenetic and DArTseq-derived single nucleotide polymorphism (SNP) data were used to investigate the genetic diversity of the two Osteoglossum species, the silver arowana O. bicirrhosum, and the black arowana O. ferreirai. Both species differ in their 2n (with 2n = 54 and 56 for O. ferreirai and O. bicirrhosum, respectively) and in the composition and distribution of their repetitive DNA content, consistent with their taxonomic status as different species. Our genetic dataset was coupled with contemporary and paleogeographic niche modeling, to develop concurrent demographic models that were tested against each other with a deep learning approach in O. bicirrhosum. Our genetic results reveal that O. bicirrhosum colonized the Tocantins-Araguaia basin from the Amazon basin about one million years ago. In addition, we highlighted a higher genetic diversity of O. bicirrhosum in the Amazon populations in comparison to those from the Tocantins-Araguaia basin.

Unique maternal and environmental effects on the body morphology of the Least Killifish, Heterandria formosa

An important step in diagnosing local adaptation is the demonstration that phenotypic variation among populations is at least in part genetically based. To do this, many methods experimentally minimize the environmental effect on the phenotype to elucidate the genetic effect. Minimizing the environmental effect often includes reducing possible environmental maternal effects. However, maternal effects can be an important factor in patterns of local adaptation as well as adaptive plasticity. Here, we report the results of an experiment with males from two populations of the poeciliid fish, Heterandria formosa, designed to examine the relative influence of environmental maternal effects and environmental effects experienced during growth and development on body morphology, and, in addition, whether the balance among those effects is unique to each population. We used a factorial design that varied thermal environment and water chemistry experienced by mothers and thermal environment and water chemistry experienced by offspring. We found substantial differences between the two populations in their maternal and offspring norms of reaction of male body morphology to differences in thermal environment and water chemistry. We also found that the balance between maternal effects and postparturition environmental effects differed from one thermal regime to another and among traits. These results indicate that environmental maternal effects can be decidedly population-specific and, as a result, might either contribute to the appearance of or blur evidence for local adaptation. These results also suggest that local adaptation might also occur through the evolution of maternal norms of reaction to important, and varying, environmental factors.

Cryptic lineage divergence in marine environments: genetic differentiation at multiple spatial and temporal scales in the widespread intertidal goby Gobiosoma bosc

The adaptive radiation of the seven-spined gobies (Gobiidae: Gobiosomatini) represents a classic example of how ecological specialization and larval retention can drive speciation through local adaptation. However, geographically widespread and phenotypically uniform species also do occur within Gobiosomatini. This lack of phenotypic variation across large geographic areas could be due to recent colonization, widespread gene flow, or stabilizing selection acting across environmental gradients. We use a phylogeographic approach to test these alternative hypotheses in the naked goby Gobiosoma bosc, a widespread and phenotypically invariable intertidal fish found along the Atlantic Coast of North America. Using DNA sequence from 218 individuals sampled at 15 localities, we document marked intraspecific genetic structure in mitochondrial and nuclear genes at three main geographic scales: (i) between Gulf of Mexico and Atlantic Coast, (ii) between the west coast of the Florida peninsula and adjacent Gulf of Mexico across the Apalachicola Bay, and (iii) at local scales of a few hundred kilometers. Clades on either side of Florida diverged about 8 million years ago, whereas some populations along the East Cost show divergent phylogroups that have differentiated within the last 200,000 years. The absence of noticeable phenotypic or ecological differentiation among lineages suggests the role of stabilizing selection on ancestral phenotypes, together with isolation in allopatry due to reduced dispersal and restricted gene flow, as the most likely explanation for their divergence. Haplotype phylogenies and spatial patterns of genetic diversity reveal frequent population bottlenecks followed by rapid population growth, particularly along the Gulf of Mexico. The magnitude of the genetic divergence among intraspecific lineages suggests the existence of cryptic species within Gobiosoma and indicates that modes of speciation can vary among lineages within Gobiidae.

Pleistocene to holocene expansion of the black-belt cichlid in Central America, Vieja maculicauda (Teleostei: Cichlidae)

The distributions of many Northern Hemisphere organisms have been influenced by fluctuations in sea level and climatic conditions during Pleistocene interglacial periods. These cycles are associated with range contraction and refugia for northern-distributed organisms as a response to glaciers. However, lower sea levels in the tropics and sub-tropics created available habitat for expansion of the ranges of freshwater organisms. The goal of this study was to use ecological niche modeling to test the hypothesis of north to south range expansion of Vieja maculicauda associated with Pleistocene glacial cycles. Understanding the biogeography of this widespread species may help us better understand the geology and interconnectivity of Central American freshwaters. Occurrence data for V. maculicauda was based on georeferencing of all museum records of specimens recovered from FishNet2. General patterns of phylogeographic structure were assessed with mtDNA. Present day niche models were generated and subsequently projected onto paleoclimatic maps of the region during the Last Interglacial, Last Glacial Maximum, and mid-Holocene. Phylogenetic analysis of mtDNA sequence data showed no phylogeographic structure throughout the range of this widespread species. Present day niche models were congruent with the observed distribution of V. maculicauda in Central America. Results showed a lack of suitable freshwater habitat in northern Central America and Mexico during the Last Interglacial, with greatest range expansion during the Last Glacial Maximum and mid-Holocene. Results support the hypothesis of a north to south range expansion of V. maculicauda associated with glacial cycles. The wide distribution of this species compared to other closely related cichlids indicates the latter did not respond to the degree of V. maculicauda in expansion of their distributions. Future work aimed at comparisons with other species and modeling of future climatic scenarios will be a fruitful area of investigation.

Genomic survey provides insights into the evolutionary changes that occurred during European expansion of the invasive mosquitofish (Gambusia holbrooki)

Biological invasions rank among the main global threats for biodiversity. The Eastern mosquitofish (Gambusia holbrooki) is considered one of the 100 world worst invasive species due to its high adaptation capability to new environments. Using the restriction-site-associated DNA tags (RADtags), introduced European locations were compared against native US mosquitofish populations to analyse genomic changes that occurred during invasive process of European locations. After filtering, 7724 RADtags containing only one SNP were retained for population studies. Comparative genomics indicated that 186 of these RADtags matched sequences in the transcriptome of Xyphophorus maculatus, the most closely related genome available. Genomic analyses showed that invasive populations show high reductions in diversity. Further, analyses of population structuring based on these data are concordant with previous analyses based on microsatellites. It is concluded that during the invasion process genetic drift was the main evolutionary force affecting patterns of diversity and population structure. While recognizing that positive selection could be masked by the strong drift during founder events, adaptive processes were evidenced in a reduced number of RADtags (<2%), with only one of these in a putative coding region. Surprisingly, balancing selection was detected in several coding RADtags, suggesting that the preservation of polymorphism in specific genes could be more important than the average population diversity for the population maintenance at any location, particularly for the survival of introduced populations.

Late Glacial Demographic Expansion Motivates a Clock Overhaul for Population Genetics

The molecular clock hypothesis is fundamental in evolutionary biology as by assuming constancy of the molecular rate it provides a timeframe for evolution. However, increasing evidence shows time dependence of inferred molecular rates with inflated values obtained using recent calibrations. As recent demographic calibrations are virtually non-existent in most species, older phylogenetic calibration points (>1 Ma) are commonly used, which overestimate demographic parameters. To obtain more reliable rates of molecular evolution for population studies, I propose the calibration of demographic transition (CDT) method, which uses the timing of climatic changes over the late glacial warming period to calibrate expansions in various species. Simulation approaches and empirical data sets from a diversity of species (from mollusk to humans) confirm that, when compared with other genealogy-based calibration methods, the CDT provides a robust and broadly applicable clock for population genetics. The resulting CDT rates of molecular evolution also confirm rate heterogeneity over time and among taxa. Comparisons of expansion dates with ecological evidence confirm the inaccuracy of phylogenetically derived divergence rates when dating population-level events. The CDT method opens opportunities for addressing issues such as demographic responses to past climate change and the origin of rate heterogeneity related to taxa, genes, time, and genetic information content.

Population genetic structure of Bellamya aeruginosa (Mollusca: Gastropoda: Viviparidae) in China: weak divergence across large geographic distances

Bellamya aeruginosa is a widely distributed Chinese freshwater snail that is heavily harvested, and its natural habitats are under severe threat due to fragmentation and loss. We were interested whether the large geographic distances between populations and habitat fragmentation have led to population differentiation and reduced genetic diversity in the species. To estimate the genetic diversity and population structure of B. aeruginosa, 277 individuals from 12 populations throughout its distribution range across China were sampled: two populations were sampled from the Yellow River system, eight populations from the Yangtze River system, and two populations from isolated plateau lakes. We used seven microsatellite loci and mitochondrial cytochrome oxidase I sequences to estimate population genetic parameters and test for demographic fluctuations. Our results showed that (1) the genetic diversity of B. aeruginosa was high for both markers in most of the studied populations and effective population sizes appear to be large, (2) only very low and mostly nonsignificant levels of genetic differentiation existed among the 12 populations, gene flow was generally high, and (3) relatively weak geographic structure was detected despite large geographic distances between populations. Further, no isolation by linear or stream distance was found among populations within the Yangtze River system and no signs of population bottlenecks were detected. Gene flow occurred even between far distant populations, possibly as a result of passive dispersal during flooding events, zoochoric dispersal, and/or anthropogenic translocations explaining the lack of stronger differentiation across large geographic distances. The high genetic diversity of B. aeruginosa and the weak population differentiation are likely the results of strong gene flow facilitated by passive dispersal and large population sizes suggesting that the species currently is not of conservation concern.