29 results on '"Alter, S. Elizabeth"'
Search Results
2. Impacts of Quaternary Climatic Changes on the Diversification of Riverine Cichlids in the Lower Congo River.
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Kurata, Naoko P, Stiassny, Melanie L J, Hickerson, Michael J, and Alter, S Elizabeth
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QUATERNARY Period ,ENDEMIC species ,GENE flow ,CLIMATE change ,SPECIES diversity - Abstract
Climatic and geomorphological changes during the Quaternary period impacted global patterns of speciation and diversification across a wide range of taxa, but few studies have examined these effects on African riverine fish. The lower Congo River is an excellent natural laboratory for understanding complex speciation and population diversification processes, as it is hydrologically extremely dynamic and recognized as a continental hotspot of diversity harboring many narrowly endemic species. A previous study using genome-wide SNP data highlighted the importance of dynamic hydrological regimes to the diversification and speciation in lower Congo River cichlids. However, historical climate and hydrological changes (e.g. reduced river discharge during extended dry periods) have likely also influenced ichthyofaunal diversification processes in this system. The lower Congo River offers a unique opportunity to study climate-driven changes in river discharge, given the massive volume of water from the entire Congo basin flowing through this short stretch of the river. Here, we, for the first time, investigate the impacts of paleoclimatic factors on ichthyofaunal diversification in this system by inferring divergence times and modeling patterns of gene flow in four endemic lamprologine cichlids, including the blind cichlid, Lamprologus lethops. Our results suggest that Quaternary climate changes associated with river discharge fluctuations may have impacted the diversification of species along the system and the emergence of cryptophthalmic phenotype in some endemic species. Our study, using reduced representation sequencing (2RADseq), indicates that the lower Congo River lamprologines emerged during the Early-Middle Pleistocene transition, characterized as one of the earth's major climatic transformation periods. Modeling results suggest that gene flow across populations and between species was not constant but occurred in temporally constrained pulses. We show that these results correlate with glacial–interglacial fluctuations. The current hyper-diverse fish assemblages of the lower Congo River riverscape likely reflect the synergistic effects of multiple drivers fueling complex evolutionary processes through time. [ABSTRACT FROM AUTHOR]
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- 2024
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3. A Framework for Effective Dissemination of Innovative STEM Curricula
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Alter, S. Elizabeth and Gafney, Leo
- Abstract
The last decade has seen an explosion of new pedagogical programs, modules, and curricula in undergraduate STEM courses. Despite the importance of effective dissemination in spreading such programs to a broader community of users, relatively little attention is typically given to the needs of potential adopters. In this paper, we build on previous literature on dissemination and examine specific strategies implemented by programs that seek to develop new curricula across several STEM fields. We consider factors that affect likelihood of adoption from the perspectives of both potential disseminators and adopters, reviewing a set of case studies. Finally, we lay out a framework for effective dissemination of research-based STEM curricula, highlighting features that include demonstration of relative advantage over previous pedagogical methods, compatibility with departmental curricula, complexity, and trialability.
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- 2020
4. A Framework for Effective Dissemination of Innovative STEM Curricula
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Alter, S. Elizabeth and Gafney, Leo
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- 2020
5. Geography, Climate, and Habitat Shape the Microbiome of the Endangered Rock Gnome Lichen (Cetradonia linearis).
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Paulsen, Julianna, Allen, Jessica L., Morris, Nathan, Dorey, Jenna, Walke, Jenifer B., and Alter, S. Elizabeth
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LICHENS ,BIOLOGICAL systems ,BACTERIAL diversity ,ECOSYSTEM management ,ENDANGERED species ,ENDANGERED ecosystems ,HABITATS ,BACTERIAL communities - Abstract
Bacterial symbionts are essential components of healthy biological systems. They are increasingly recognized as important factors in the study and management of threatened species and ecosystems. Despite management shifts at the ecosystem level, microbial communities are often neglected in discussions of holobiont conservation in favor of the primary members of a symbiosis. In this study, we addressed the bacterial community knowledge gap for one of two federally endangered lichen species in the United States, Cetradonia linearis (Cladoniaceae). We collected 28 samples of the endangered rock gnome lichen (Cetradonia linearis) from 13 sites and characterized bacterial communities in thalli using 16S rRNA metabarcoding to investigate the factors influencing the microbiome composition and diversity within the thallus. We found that Proteobacteria (37.8% ± 10.3) and Acidobacteria (25.9% ± 6.0) were the most abundant phyla recovered. Cyanobacteria were a major component of the microbiome in some individuals, despite this species associating with a green algal symbiont. Habitat, climate, and geography were all found to have significant influences on bacterial community composition. An analysis of the core microbiome at a 90% threshold revealed shared amplicon sequence variants in the microbiomes of other lichens in the family Cladoniaceae. We concluded that the bacterial microbiome of Cetradonia linearis is influenced by environmental factors and that some bacterial taxa may be core to this group. Further exploration into the microbiomes of rare lichen species is needed to understand the importance of bacterial symbionts to lichen diversity and distributions. [ABSTRACT FROM AUTHOR]
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- 2024
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6. First genome-wide analysis of the endangered, endemic lichen Cetradonia linearis reveals isolation by distance and strong population structure
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Allen, Jessica L., McKenzie, Sean K., Sleith, Robin S., and Alter, S. Elizabeth
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- 2018
7. Contemporary and historical effective population sizes of Atlantic sturgeon Acipenser oxyrinchus oxyrinchus
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Waldman, John, Alter, S. Elizabeth, Peterson, Douglas, Maceda, Lorraine, Roy, Nirmal, and Wirgin, Isaac
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- 2019
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8. DNA Evidence for Historic Population Size and past Ecosystem Impacts of Gray Whales
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Alter, S. Elizabeth, Rynes, Eric, and Palumbi, Stephen R.
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- 2007
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9. Riverscape genomics of cichlid fishes in the lower Congo: Uncovering mechanisms of diversification in an extreme hydrological regime.
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Kurata, Naoko P., Hickerson, Michael J., Hoffberg, Sandra L., Gardiner, Ned, Stiassny, Melanie L. J., and Alter, S. Elizabeth
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CICHLIDS ,GENE flow ,AQUATIC biodiversity ,SURFACE of the earth ,GENOMICS ,FRESHWATER fishes ,FRESHWATER habitats - Abstract
Freshwater fishes are notably diverse, given that freshwater habitat represents a tiny fraction of the earth's surface, but the mechanisms generating this diversity remain poorly understood. Rivers provide excellent models to understand how freshwater diversity is generated and maintained across heterogeneous habitats. In particular, the lower Congo River (LCR) consists of a dynamic hydroscape exhibiting extraordinary aquatic biodiversity, endemicity, morphological and ecological specialization. Previous studies have suggested that the numerous high‐energy rapids throughout the LCR form physical barriers to gene flow, thus facilitating diversification and speciation, generating ichthyofaunal diversity. However, this hypothesis has not been fully explored using genome‐wide SNPs for fish species distributed across the LCR. Here, we examined four lamprologine cichlids endemic to the LCR that are distributed along the river without range overlap. Using genome‐wide SNP data, we tested the hypotheses that high‐energy rapids serve as physical barriers to gene flow that generate genetic divergence at interspecific and intraspecific levels, and that gene flow occurs primarily in a downstream direction. Our results are consistent with the prediction that powerful rapids sometimes act as a barrier to gene flow but also suggest that, at certain temporal and spatial scales, they may provide multidirectional dispersal opportunities for riverine rheophilic cichlid fishes. These results highlight the complexity of diversification processes in rivers and the importance of assessing such processes across different riverscapes. [ABSTRACT FROM AUTHOR]
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- 2022
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10. Comparing Evolutionary Patterns and Variability in the Mitochondrial Control Region and Cytochrome b in Three Species of Baleen Whales
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Alter, S. Elizabeth and Palumbi, Stephen R.
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- 2009
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11. Environmental DNA metabarcoding is a promising method for assaying fish diversity in cenotes of the Yucatán Peninsula, Mexico.
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Alter, S. Elizabeth and Arroyave, Jairo
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FISH diversity ,SINKHOLES ,GROUNDWATER ,AQUIFERS ,BIODIVERSITY - Abstract
The karst aquifer of the Yucatán Peninsula (YP) in southeastern Mexico is a unique ecosystem in which water-filled sinkholes, locally known as cenotes, connect subterranean waters with the surface. This system is home to around 20 species of freshwater fishes, including several that are endemic and/or threatened. Studies on this unique ichthyofauna have been partially hampered by the technical difficulties associated with sampling these habitats, particularly submerged caves. In this proof-of-concept study, we use environmental DNA (eDNA) metabarcoding to survey the diversity of freshwater fishes associated with the YP karst aquifer by sampling six cenotes from across the Ring of Cenotes region in northwestern Yucatán, a 180-km-diameter semicircular band of abundant karst sinkholes. Through a combination of conventional sampling (direct observation, fishing) and eDNA metabarcoding, we detected eight species of freshwater fishes across the six sampled cenotes. Overall, our eDNA metabarcoding approach was effective at detecting the presence of fishes from cenote water samples, including one of the two endemic cave-dwelling fish species restricted to the subterranean section of the aquifer. Although our study was focused on detecting fishes via eDNA, we also recovered DNA from several other vertebrate groups, particularly bats. These results suggest that the eDNA metabarcoding approach represents a promising and largely noninvasive method to assay aquatic biodiversity in these vulnerable habitats, allowing more effective, frequent, and wide-ranging surveys. Our detection of DNA from aerial and terrestrial vertebrate fauna implies that eDNA from cenotes, besides being a means to survey aquatic fauna, may also offer an effective way to quickly survey non-aquatic biodiversity associated with these persistent water bodies. [ABSTRACT FROM AUTHOR]
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- 2022
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12. Mitochondrial and Nuclear Genetic Variation across Calving Lagoons in Eastern North Pacific Gray Whales (Eschrichtius robustus)
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Alter, S. Elizabeth, Ramirez, Sergio Flores, Nigenda, Sergio, Ramirez, Jorge Urbán, Bracho, Lorenzo Rojas, and Palumbi, Stephen R.
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- 2009
13. Two New Phenacogrammus (Characoidei; Alestidae) from the Ndzaa River (Mfimi-Lukenie Basin) of Central Africa, Democratic Republic of Congo.
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Stiassny, Melanie L.J., Alter, S. Elizabeth, Monsembula Iyaba, Raoul J.C., and Liyandja, Tobit L.D.
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CYPRINIFORMES , *MORPHOMETRICS , *DIAGNOSIS , *SPECIES , *PERSONAL property - Abstract
Two new Phenacogrammus are described from the Ndzaa River, a small left-bank tributary of the Mfimi-Lukenie River in the central Congo basin. They share with P. deheyni, a congener endemic to the Cuvette Centrale to the north, a prominent anterior expansion of the first pleural rib; a feature interpreted here as a synapomorphy diagnostic for this species assemblage. The two new species are readily differentiated from P. deheyni based on differences in pigmentation patterning, a lower number of scales in longitudinal series (26–28 vs. 29–33) and a longer head length (m. 24.9% SL vs. 21.7 and 23.2% SL). Phenacogrammus flexus, new species, is distinguished from all congeners in the possession of 6 (vs. 7) supraneural bones, and a characteristic zigzag pattern of black pigmentation along and below the midline extending from the posterior border of the opercle to the base of the caudal peduncle. While no unambiguous morphological autapomorphies have been located to diagnose P. concolor, new species, it is nonetheless readily distinguished from all congeners, except P. deheyni and P. flexus, in the possession of a prominent anterior expansion of the first pleural rib. It differs from both P. deheyni and P. flexus in the absence of a dominant pigmentation patterning over the flanks and caudal peduncle. Additionally, it differs from P. flexus in a shallower body depth (m. 24.9% vs. 27.0% SL) and in the possession of 7 (vs. 6) supraneurals. The three species exhibit extensive divergence in mt-COI sequence (P. flexus vs. P. concolor 10.2%–11%; P. flexus vs deheyni 12.9%–13.5%; P. concolor vs. deheyni 11.3%–12.9%). Furthermore, analysis of shape variation utilizing geometric morphometrics indicates that each species differs significantly in body shape. [ABSTRACT FROM AUTHOR]
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- 2021
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14. Trade‐offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on "Environmental DNA: What's behind the term?" by Pawlowski et al., (2020).
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Rodriguez‐Ezpeleta, Naiara, Morissette, Olivier, Bean, Colin W., Manu, Shivakumara, Banerjee, Pritam, Lacoursière‐Roussel, Anaïs, Beng, Kingsly C., Alter, S. Elizabeth, Roger, Fabian, Holman, Luke E., Stewart, Kathryn A., Monaghan, Michael T., Mauvisseau, Quentin, Mirimin, Luca, Wangensteen, Owen S., Antognazza, Caterina M., Helyar, Sarah J., de Boer, Hugo, Monchamp, Marie‐Eve, and Nijland, Reindert
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DNA ,TERMS & phrases ,ENVIRONMENTAL sampling - Abstract
In a recent paper, "Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring," Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra‐organismal DNA from macro‐organisms. We agree with this view. However, we are concerned that their proposed two‐level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. This terminology is based on categories that are often difficult to assign and uninformative, and it overlooks a fundamental distinction within eDNA: the type of DNA (organismal or extra‐organismal) from which ecological interpretations are derived. [ABSTRACT FROM AUTHOR]
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- 2021
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15. Regional‐scale aquifer hydrogeology as a driver of phylogeographic structure in the Neotropical catfish Rhamdia guatemalensis (Siluriformes: Heptapteridae) from cenotes of the Yucatán Peninsula, Mexico.
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Arroyave, Jairo, Martinez, Christopher M., Martínez‐Oriol, Fausto H., Sosa, Erick, and Alter, S. Elizabeth
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HYDROGEOLOGY ,AQUIFERS ,SINKHOLES ,CATFISHES ,FISH populations ,GROUNDWATER flow - Abstract
The Yucatán Peninsula (YP) contains one of the most spectacular and developed karstic aquifers in the world, which connects to the surface through water‐filled sinkholes locally known as cenotes. Cenotes and their associated submerged caves are home to a remarkable diversity of aquatic fauna, yet very little is known about spatial patterns of intraspecific genetic and morphological variation across the aquifer. The strong affinity to cenotes (vs. submerged caves) exhibited by most fishes inhabiting the YP aquifer raises a fundamental question about the ecology and evolutionary history of its ichthyofauna: how genetically structured and morphologically divergent are fish populations from different cenotes across the YP? To shed light on this question, we investigated phylogeographic structure in the Neotropical catfish Rhamdia guatemalensis, arguably the most ubiquitous representative of the YP aquifer ichthyofauna.Geographic patterns of genetic variation were determined through phylogeographic and population genetics analyses of mitochondrial (mt)DNA sequence data. Body shape variation was investigated using both traditional and geometric morphometrics. Dense sampling across the previously overlooked YP region, coupled with the inclusion of samples from basins unrepresented in past studies, allowed for revision of previous estimates of phylogeographic structuring across the species' range.Our results reveal a striking spatial correspondence between major mtDNA lineages and physiographic regions defined on the basis of broad‐scale patterns of groundwater flow. Morphological variation in populations from the YP, although considerable, neither reflects the observed spatial signal of genetic differentiation nor displays any other discernible geographic pattern. The resulting range‐wide phylogeographic pattern is largely consistent with a latitudinal, isolation‐by‐distance gradient, and the expectations from catchment hydrology, while revealing an unexpectedly close relationship between YP aquifer and epigean populations (both inside and outside the YP).Although the inferred range‐wide phylogeographic history is consistent with a single aquifer colonisation event followed by multiple instances of dispersal out of the aquifer and into neighbouring epigean basins, hypotheses regarding the colonisation and exodus of the YP by R. guatemalensis require further investigation. Within the YP aquifer, regional‐scale hydrogeological differences might impose limits to underground dispersal, potentially driving genetic divergence in populations of R. guatemalensis, and possibly in other cenote‐dwelling fishes as well. Future research focused on other YP aquifer species, however, is needed to test the generality of our findings.Phylogeographic research on the stygofauna of the YP aquifer is a relatively nascent field of inquiry. Besides shedding novel light into the patterns and drivers of genetic differentiation in fish populations from across the aquifer, this study sets the stage for future research aimed at unravelling the evolutionary history of the stygofauna that inhabits the cenotes and submerged caves of the YP. The remarkable and hitherto undocumented phylogeographic pattern revealed herein (i.e. correspondence of major mtDNA lineages with physiographic regions defined by regional‐scale fracture zones) adds to a growing body of evidence in support of the notion that the architecture of freshwater aquifers may include physical barriers that can act as regional‐scale drivers of groundwater faunal distributions and genetic structuring. [ABSTRACT FROM AUTHOR]
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- 2021
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16. Genomic Analysis of the Only Blind Cichlid Reveals Extensive Inactivation in Eye and Pigment Formation Genes.
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Aardema, Matthew L, Stiassny, Melanie L J, and Alter, S Elizabeth
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GENETIC mutation ,GENETIC drift ,GENES ,HETEROZYGOSITY ,EYE color ,STATISTICAL power analysis ,NUCLEOTIDE sequencing - Abstract
Trait loss represents an intriguing evolutionary problem, particularly when it occurs across independent lineages. Fishes in light-poor environments often evolve "troglomorphic" traits, including reduction or loss of both pigment and eyes. Here, we investigate the genomic basis of trait loss in a blind and depigmented African cichlid, Lamprologus lethops , and explore evolutionary forces (selection and drift) that may have contributed to these losses. This species, the only known blind cichlid, is endemic to the lower Congo River. Available evidence suggests that it inhabits deep, low-light habitats. Using genome sequencing, we show that genes related to eye formation and pigmentation, as well as other traits associated with troglomorphism, accumulated inactivating mutations rapidly after speciation. A number of the genes affected in L. lethops are also implicated in troglomorphic phenotypes in Mexican cavefish (Astyanax mexicanus) and other species. Analysis of heterozygosity patterns across the genome indicates that L. lethops underwent a significant population bottleneck roughly 1 Ma, after which effective population sizes remained low. Branch-length tests on a subset of genes with inactivating mutations show little evidence of directional selection; however, low overall heterozygosity may reduce statistical power to detect such signals. Overall, genome-wide patterns suggest that accelerated genetic drift from a severe bottleneck, perhaps aided by directional selection for the loss of physiologically expensive traits, caused inactivating mutations to fix rapidly in this species. [ABSTRACT FROM AUTHOR]
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- 2020
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17. Mitochondrial and nuclear genetic variation across calving lagoons in Eastern North Pacific gray wheels(Eschrichtius robustus)
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Alter, S. Elizabeth, Ramirez, Sergio Flores, Nigenda, Sergio, Ramirez, Jorge Urban, Bracho, Lorenzo Rojas, and Palumbi, Stephen R.
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Gray whale -- Genetic aspects ,Gray whale -- Demographic aspects ,Lagoons -- Environmental aspects ,Population ecology -- Research ,Biological sciences - Published
- 2009
18. Fishes in the desert: mitochondrial variation and phylogeography of Danakilia (Actinopterygii: Cichlidae) and Aphanius (Actinopterygii: Cyprinodontidae) in the Danakil Depression of northeastern Africa.
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Chiozzi, Giorgio, Stiassny, Melanie L. J., Alter, S. Elizabeth, De Marchi, Giuseppe, Mebrahtu, Yohannes, Tessema, Misikire, Asmamaw, Berhan, Fasola, Mauro, and Bellati, Adriana
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PHYLOGEOGRAPHY ,MITOCHONDRIAL DNA ,CICHLIDS ,ACTINOPTERYGII ,GENETICS - Abstract
The Danakil Depression in northeastern Africa represents one of the harshest arid environments on Earth, yet two genera of fishes, Danakilia (Cichlidae) and Aphanius (Cyprinodontidae), share its sparse aquatic habitats. The evolutionary history of these fishes is investigated here in the context of genetic, geological and paleoenvironmental information. We collected samples from seven sites and assessed phylogeographic relationships using concatenated COI and cytb mtDNA genes. Danakilia morphospecies show low differentiation at mitochondrial markers, but variation is partitioned between a northern cluster containing D. dinicolai plus three undescribed riverine populations, and a southern cluster including two creek populations of D. franchettii separated by the hypersaline waters of Lake Afrera. Aphanius displayed four genetically distinct clades (A. stiassnyae in Lake Afrera; one distributed across the entire area; one in Lake Abaeded; and one in the Shukoray River), but without clear large-scale geographic structure. However, Danakil Aphanius are clearly differentiated from A. dispar sensu stricto from the Sinai Peninsula. Geological evidence suggests that after the Late Pleistocene closure of the Danakil-Red Sea connection, increased post-glacial groundwater availability caused the formation of a brackish paleo-lake flooding the entire region below the -50 m contour. Fish populations previously isolated in coastal oases during glaciation were able to mix in the paleo-lake. Subsequently, in a more arid phase starting ∼7300 BP, paleo-lake regression isolated fishes in separate drainages, triggering their still ongoing diversification. [ABSTRACT FROM AUTHOR]
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- 2018
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19. Genomewide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids-adapted clade of cichlids from the Congo River.
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Alter, S. Elizabeth, Munshi‐South, Jason, and Stiassny, Melanie L. J.
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FRESHWATER biodiversity , *ENDEMIC fishes , *PHYLOGEOGRAPHY , *CICHLIDS , *FISH phylogeny - Abstract
The lower Congo River is a freshwater biodiversity hot spot in Africa characterized by some of the world's largest rapids. However, little is known about the evolutionary forces shaping this diversity, which include numerous endemic fishes. We investigated phylogeographic relationships in Teleogramma, a small clade of rheophilic cichlids, in the context of regional geography and hydrology. Previous studies have been unable to resolve phylogenetic relationships within Teleogramma due to lack of variation in nuclear genes and discrete morphological characters among putative species. To sample more broadly across the genome, we analysed double-digest restriction-associated sequencing (dd RAD) data from 53 individuals across all described species in the genus. We also assessed body shape and mitochondrial variation within and between taxa. Phylogenetic analyses reveal previously unrecognized lineages and instances of microallopatric divergence across as little as ~1.5 km. Species ranges appear to correspond to geographic regions broadly separated by major hydrological and topographic barriers, indicating these features are likely important drivers of diversification. Mitonuclear discordance indicates one or more introgressive hybridization events, but no clear evidence of admixture is present in nuclear genomes, suggesting these events were likely ancient. A survey of female fin patterns hints that previously undetected lineage-specific patterning may be acting to reinforce species cohesion. These analyses highlight the importance of hydrological complexity in generating diversity in certain freshwater systems, as well as the utility of dd RAD-Seq data in understanding diversification processes operating both below and above the species level. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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20. Melting barriers to faunal exchange across ocean basins.
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McKeon, C. Seabird, Weber, Michele X., Alter, S. Elizabeth, Seavy, Nathaniel E., Crandall, Eric D., Barshis, Daniel J., Fechter‐Leggett, Ethan D., and Oleson, Kirsten L. L.
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BIODIVERSITY research ,MARINE mammals ,MARINE ecosystem management ,MARINE ecology ,GEOLOGICAL basins - Abstract
Accelerated loss of sea ice in the Arctic is opening routes connecting the Atlantic and Pacific Oceans for longer periods each year. These changes may increase the ease and frequency with which marine birds and mammals move between the Pacific and Atlantic Ocean basins. Indeed, recent observations of birds and mammals suggest these movements have intensified in recent decades. Reconnection of the Pacific and Atlantic Ocean basins will present both challenges to marine ecosystem conservation and an unprecedented opportunity to examine the ecological and evolutionary consequences of interoceanic faunal exchange in real time. To understand these changes and implement effective conservation of marine ecosystems, we need to further develop modeling efforts to predict the rate of dispersal and consequences of faunal exchange. These predictions can be tested by closely monitoring wildlife dispersal through the Arctic Ocean and using modern methods to explore the ecological and evolutionary consequences of these movements. [ABSTRACT FROM AUTHOR]
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- 2016
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21. Molecular phylogenetics reveals convergent evolution in lower Congo River spiny eels.
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Alter, S. Elizabeth, Brown, Bianca, and Stiassny, Melanie L. J.
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SPECIES diversity , *MASTACEMBELIDAE , *PHENOTYPES , *BIODIVERSITY , *MITOCHONDRIAL proteins ,ENVIRONMENTAL aspects - Abstract
Background: The lower Congo River (LCR) is a region of exceptional species diversity and endemism in the Congo basin, including numerous species of spiny eels (genus Mastacembelus). Four of these exhibit distinctive phenotypes characterized by greatly reduced optic globes deeply embedded into the head (cryptophthalmia) and reduced (or absent) melanin pigmentation, among other characteristics. A strikingly similar cryptophthalmic phenotype is also found in members of a number of unrelated fish families, strongly suggesting the possibility of convergent evolution. However, little is known about the evolutionary processes that shaped diversification in LCR Mastacembelus, their biogeographic origins, or when colonization of the LCR occurred. Methods: We sequenced mitochondrial and nuclear genes from Mastacembelus species collected in the lower Congo River, and compared them with other African species and Asian representatives as outgroups. We analyzed the sequence data using Maximum Likelihood and Bayesian phylogenetic inference. Results: Bayesian and Maximum Likelihood phylogenetic analyses, and Bayesian coalescent methods for species tree reconstruction, reveal that endemic LCR spiny eels derive from two independent origins, clearly demonstrating convergent evolution of the cryptophthalmic phenotype. Mastacembelus crassus, M. aviceps, and M. simbi form a clade, allied to species found in southern, eastern and central Africa. Unexpectedly, M. brichardi and brachyrhinus fall within a clade otherwise endemic to Lake Tanganikya (LT) ca. 1500 km east of the LCR. Divergence dating suggests the ages of these two clades of LCR endemics differ markedly. The age of the crassus group is estimated at ~4 Myr while colonization of the LCR by the brichardi-brachyrhinus progenitor was considerably more recent, dated at ~0.5 Myr. Conclusions: The phylogenetic framework of spiny eels presented here, the first to include LCR species, demonstrates that cryptophthalmia and associated traits evolved at least twice in Mastacembelus: once in M. brichardi and at least once in the M. crassus clade. Timing of diversification is broadly consistent with the onset of modern high-energy flow conditions in the LCR and with previous studies of endemic cichlids. The close genetic relationship between M. brichardi and M. brachyrhinus is particularly notable given the extreme difference in phenotype between these species, and additional work is needed to better understand the evolutionary history of diversification in this clade. The findings presented here demonstrate strong, multi-trait convergence in LCR spiny eels, suggesting that extreme selective pressures have shaped numerous phenotypic attributes of the endemic species of this region. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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22. Phylogenetics of Teleogramma, a Riverine Clade of African Cichlid Fishes, with a Description of the Deepwater Molluskivore- Teleogramma obamaorum- from the Lower Reaches of the Middle Congo River.
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Stiassny, Melanie L.J. and Alter, S. Elizabeth
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PHYLOGENY , *CICHLIDS , *ANIMAL morphology , *SEXUAL dichromatism (Animals) , *RIVER ecology , *ECOSYSTEM health - Abstract
The lower Congo River and nearby habitats harbor numerous endemic lineages of cichlid fishes, including some with highly specialized morphologies. Based on morphological and molecular data, we herein describe a new species of Teleogramma, a member of the chromidotilapiine clade found on rocky outcrops in the lower reaches of the middle Congo River. The new species, T. obamaorum, is distinguished from congeners by numerous morphological and ecological attributes, including the lack of dorsoventral head and body depression, absence of sexual dichromatism, and features of laterosensory anatomy, pharyngeal and gut morphology, and dietary preference. Phylogenetic analyses of two nuclear and two mitochondrial loci using Bayesian and maximum-likelihood inference lend strong support for the taxonomic validity of T. obamaorum and provide preliminary estimates of species relationships within the genus. The discovery of a new, ecomorphologically distinctive cichlid species in the Congo River suggests that additional research focus on riverine clades has the potential to greatly contribute to our understanding of evolutionary dynamics in this hyperdiverse group of teleost fishes. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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23. Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100.
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Alter, S. Elizabeth, Meyer, Matthias, Post, Klaas, Czechowski, Paul, Gravlund, Peter, Gaines, Cork, Rosenbaum, Howard C., Kaschner, Kristin, Turvey, Samuel T., Plicht, Johannes, Shapiro, Beth, and Hofreiter, Michael
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GRAY whale , *HABITAT modification , *CLIMATE change , *PLEISTOCENE Epoch , *WHALING , *MARINE species diversity - Abstract
Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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24. Pre-Whaling Genetic Diversity and Population Ecology in Eastern Pacific Gray Whales: Insights from Ancient DNA and Stable Isotopes.
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Alter, S. Elizabeth, Newsome, Seth D., and Palumbi, Stephen R.
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WHALING , *POPULATION genetics , *POPULATION ecology , *WHALE populations , *FOSSIL DNA , *STABLE isotopes - Abstract
Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ∼5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region) and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
25. An impediment to consumer choice: Overfished species are sold as Pacific red snapper
- Author
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Logan, Cheryl A., Alter, S. Elizabeth, Haupt, Alison J., Tomalty, Katharine, and Palumbi, Stephen R.
- Subjects
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SEAFOOD , *LUTJANUS campechanus , *BIOPHYSICAL labeling , *MITOCHONDRIAL DNA , *DNA fingerprinting , *SEBASTES , *CONSUMER goods , *FISHERIES - Abstract
Concern over the collapse of many wild-caught fisheries has led to a recent focus on seafood-certification and consumer-driven support of sustainable seafood. However, such conservation strategies depend critically on the accurate labeling of seafood species in marketplaces. Pacific rockfish, a group of >60 species in the genus Sebastes, are often marketed as Pacific red snapper, but little is known about the number and identity of rockfish species sold under this name. We used a molecular approach to identify species sold as Pacific red snapper by grocery chains, local fish markets, and sushi restaurants in California and Washington. Using genetic data from two mitochondrial markers (cytochrome-b and control region), we identified seven species of rockfish (Sebastes spp.), tilapia (Oreochromis spp.), and one true red snapper (Lutjanus campechanus) in our samples. Among samples identified as rockfish, 56% were identified as species listed as overfished by the National Marine Fisheries Service within the past three years. By effectively permitting all species of rockfish to be sold under a common vernacular name, state and federal agencies compromise the ability of consumers to make informed choices when buying seafood. [Copyright &y& Elsevier]
- Published
- 2008
- Full Text
- View/download PDF
26. Enhanced growth of sagebrush (Artemisia tridentata ) in response to manipulated ecosystem warming.
- Author
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PERFORS, TRACY, HARTE, JOHN, and ALTER, S. ELIZABETH
- Subjects
CLIMATE change ,BIOTIC communities ,ACCLIMATIZATION ,ECOLOGY - Abstract
Abstract Global models project impending climate changes that could significantly alter plant species composition in ecosystems. Climate manipulation experiments provide an opportunity to investigate such effects. Here we describe and apply a method for extracting the age-detrended growth rate of sagebrush (Artemisia tridentata Nutt.) and show that experimental ecosystem warming enhances the growth rate of this shrub. Snowmelt date, not soil temperature or moisture, is demonstrated to be the dominant climate variable controlling the observed effect. Our findings suggest that global climate change will result in increased growth and range expansion of sagebrush near northern or high-elevation range boundaries in the Western United States. [ABSTRACT FROM AUTHOR]
- Published
- 2003
- Full Text
- View/download PDF
27. The virus evolves: four public health priorities for reducing the evolutionary potential of SARS-CoV-2.
- Author
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Fitzpatrick, Courtney L, Alter, S Elizabeth, Boughman, Janette W, Débarre, Florence, Edmands, Suzanne, Moehring, Amanda, Moyle, Leonie, Otto, Sarah P, Ronce, Ophélie, Rubin, Matthew J, and Sweigart, Andrea L
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- *
SARS-CoV-2 , *PUBLIC health - Published
- 2021
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28. Cover Image.
- Author
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Arroyave, Jairo, Martinez, Christopher M., Martínez‐Oriol, Fausto H., Sosa, Erick, and Alter, S. Elizabeth
- Subjects
IMAGE ,SINKHOLES ,CATFISHES ,AQUIFERS - Published
- 2021
- Full Text
- View/download PDF
29. From refugia to rookeries: Phylogeography of Atlantic green turtles.
- Author
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Naro-Maciel, Eugenia, Reid, Brendan N., Alter, S. Elizabeth, Amato, George, Bjorndal, Karen A., Bolten, Alan B., Martin, Meredith, Nairn, Campbell J., Shamblin, Brian, and Pineda-Catalan, Oscar
- Subjects
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GREEN turtle , *ANIMAL migration , *MITOCHONDRIAL DNA , *MITOCHONDRIA , *PHILOPATRY - Abstract
Investigating species' distribution and abundance over time is central to evolutionary biology, and provides important context for conservation and management. With respect to population genetic structure in green sea turtles ( Chelonia mydas ), certain processes such as female philopatry to natal rookeries are well understood, while others, such as male philopatry and historical changes in distribution and abundance, remain relatively understudied. Further, although inferences from mitochondrial DNA and nuclear microsatellites have both been critical in identifying management units, comparisons of these units based on both markers are still rare. Here we analyzed novel data from fifteen microsatellite markers gathered at six green turtle rookeries in the western Atlantic as well as previously published mitochondrial sequences from 13 regional rookeries. We detected low, but significant, population structure at microsatellite loci, which coincides with previous delineations of local and regional management units as well as reports of male philopatry. However, we also detected a discord between nuclear and mitochondrial data, in which two tropical rookeries (Aves Island, Venezuela; and Matapica, Surinam) clustered with the Caribbean and Mediterranean based on microsatellite data, but displayed a mitochondrial lineage characteristic of the southern Atlantic and Africa. To investigate the possible causes of this discord, we used both classical and Bayesian methods to estimate historical migration rates and the timing and magnitude of changes in population size. We detected a strong barrier to dispersal between the northern and southern Atlantic, as well as an expansion in the southern mitochondrial lineage during the Wisconsin glacial period and a later expansion in the northern lineage following the Last Glacial Maximum. We propose that the Aves and Surinam rookeries were colonized by females from a southern glacial refugium, after which they experienced male-biased gene flow from the Caribbean. This study highlights the utility of incorporating data from multiple types of molecular markers in accurately identifying conservation units and in elucidating the complex historical and contemporary processes underlying population genetic structure in marine species. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
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