J. Andrés López

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Verified

J. verified their affiliation via an institutional email.

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• Ph.D.
• Professor (Associate) at University of Alaska Fairbanks

Despite numerous studies aimed at resolving relationships among basal euteleost lineages, many aspects of their phylogeny remain the subject of debate. The Esociformes have proven particularly difficult to place, and although a hypothesis of relationships within this group first proposed by Nelson has been generally accepted, a recent hypothesis ba...

We present a study of inter- and intra-familial relationships of the carcharhiniform shark family Triakidae aimed at testing existing hypotheses of relationships for this group and at improving understanding of the evolution of reproductive traits in elasmobranchs. Our analyses and conclusions are based on evidence from DNA sequences of four protei...

The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about t...

The family Colocongridae and the genus Thalassenchelys are two enigmatic anguilliform taxa whose phylogenetic affinities are poorly understood. Here we present results from parsimony and Bayesian phylogenetic analyses of mitochondrial ribosomal RNA sequences from a taxonomic sample designed to test alternative placements of colocongrids and Thalass...

The Upper Cretaceous Prince Creek Formation (PCF) of northern Alaska offers a unique glimpse into northern high-latitude, non-marine vertebrate assemblages, providing critical data on polar ecosystems during the late Campanian (c. 73 Ma). This study presents a comprehensive taxonomic assessment of fish fossils from the PCF, including macrofossils a...

Forage fishes are biological drivers throughout the Pacific Ocean, from the Arctic to nearly subtropical latitudes. As a critical trophic link, the health and stability of Pacific herring ( Clupea pallasii ) populations have implications for other marine species, including several targeted by large, productive fisheries. Previous research has indic...

We developed this protocol in 2021 to for standardized eDNA sample collection at salmon escapement assessment sites in non-glacial, boreal rivers in the Arctic-Yukon-Kuskokwim Region of Alaska. The protocol is designed to allow researchers without any prior training in molecular techniques to collect eDNA samples and store them for up to several mo...

The thermally dynamic nearshore Beaufort Sea, Alaska, is experiencing climate change-driven temperature increases. Measuring thermal tolerance of broad whitefish (Coregonus nasus) and saffron cod (Eleginus gracilis), both important species in the Arctic ecosystem, will enhance understanding of species-specific thermal tolerances. The objectives of...

The production of offspring of mixed ancestry from genetically distinct populations, hybridization, is a single word encompassing extremely varied circumstances. Why and how much the parental populations are genetically distinct on one side has diverse causes. The temporal and spatial distribution of hybridization, as well as its frequency may vary...

Significant progress in our knowledge of Beringian biodiversity and in the technologies available for biodiversity research has been made in the several decades since a comprehensive biogeographic synthesis of Beringian freshwater fishes was compiled and published in 1986. Further, the fish fauna of Beringia and, more broadly, of high latitude fres...

The development and application of approaches to detect and quantify environmental DNA (eDNA) have potential to improve our understanding of the distribution, abundance, and health of Atlantic Salmon Salmo salar and Pacific salmon Oncorhynchus spp. Here, we review 61 articles focusing on eDNA applications pertaining to salmon occupying natural habi...

Seascape genomics provides a powerful framework to evaluate the presence and strength of environmental pressures on marine organisms, as well as to forecast long term species stability under various perturbations. In the highly productive North Pacific, forage fishes, key trophic links across ecosystems, are also contending with a rapidly warming c...

Rapid and effective quantification of total mercury concentrations ([THg]) in fish muscle is an important part of ongoing monitoring to provide reliable and near real-time public health guidance. Methods for quantifying THg in fish muscle frequently require the use of large sample mass and numerous preparation steps. Wet (aka fresh weight) biopsy p...

Arctic lamprey (Lethenteron camtschaticum) is an important dietary resource for rural and indigenous communities in parts of Alaska, with some commercial use. As with many fish species harvested for human consumption, there are concerns regarding mercury concentrations ([Hg]) in Arctic lamprey that may impact human health. To date, information rega...

While freshwater and anadromous fish have been critical economic resources for late prehistoric and modern Native Americans, the origin and development of fishing is not well understood. We document the earliest known human use of freshwater and anadromous fish in North America by 13,000 and 11,800 years ago, respectively, from primary anthropogeni...

Invasive species are a major threat to global biodiversity, yet also represent large‐scale unplanned ecological and evolutionary experiments to address fundamental questions in nature. Here we analyzed both native and invasive populations of predatory northern pike (Esox lucius) to characterize landscape genetic variation, determine the most likely...

Piscivorous ducks such as the common merganser (Mergus merganser) can be important predators of juvenile salmonids. Mergansers are regularly observed feeding near known Chinook salmon (Oncorhynchus tshawytscha) rearing areas in the Yukon River Basin. However, it is unclear whether merganser predation in these areas is inhibiting recovery of depress...

Predation on anadromous salmon can have important consequences for both predators and prey. Salmon provide large seasonal pulses of energy and nutrients via carcasses, eggs and juveniles to many freshwater consumers, and conversely, predation can represent a significant source of mortality for juvenile salmon. Recent declines of Chinook salmon (Onc...

The relentless role of invasive species in the extinction of native biota requires predictions of ecosystem vulnerability to inform proactive management strategies. The worldwide invasion and range expansion of predatory northern pike (Esox lucius) has been linked to the decline of native fishes and tools are needed to predict the vulnerability of...

The understanding of the evolution of variable sex determination mechanisms across taxa requires comparative studies among closely related species. Following the fate of a known master sex-determining gene, we traced the evolution of sex determination in an entire teleost order (Esociformes). We discovered that the northern pike (Esox lucius) maste...

Recent and continued progress in the scale and sophistication of phylogenetic research has yielded substantial advances in knowledge of the tree of life; however, segments of that tree remain unresolved and continue to produce contradicting or unstable results. These poorly resolved relationships may be the product of methodological shortcomings or...

Sexual reproduction is a ubiquitous basic feature of life and genetic sex determination is thus widespread, at least among eukaryotes. Understanding the remarkable diversity of sex determination mechanisms, however, is limited by the paucity of empirical studies. Here, we traced back the evolution of sex determination in an entire clade of vertebra...

The chapter describes the describes the ecology, morphology, reproduction, distribution, behavior, taxonomy, conservation, and the fossil record of the esociform fishes. Although the number of living species of Esociformes is relatively small, they are remarkable for their diverse adaptations, habits and habitats.

The detection of fish by using environmental DNA (eDNA) analysis has been shown to be more cost‐effective than traditional sampling methods are in certain situations, but this method has not been assessed under extreme winter conditions. We conducted a multiyear pilot study to test the effectiveness of eDNA for detecting fish under ice. In the spri...

Yukon Chinook salmon (Oncorhynchus tshawytscha) returns since 2014 have been declining, which has led to strong regulations on both commercial and subsistence harvests. There is a large information gap on the overwintering habitat and behavior of Chinook salmon. Assessing overwintering habitat of juveniles is important in helping to manage potentia...

The State of Alaska assesses human exposure to mercury (Hg) via fish consumption producing consumption guidelines for fish tailored for children and women of childbearing age. Under these guidelines, unrestricted consumption is suggested for many fish species, while limited consumption is recommended for others. Subsequent questions have arisen reg...

Several species found in the Bering Sea show significant spatial variation in total mercury concentrations ([THg]) longitudinally along the Aleutian Island chain. We assessed [THg] in other members of the Bering Sea food web to better understand the factors shaping regional differences. [THg] and stable carbon and nitrogen isotope ratios (δ ¹⁵ N an...

To understand the marine feeding ecology of Arctic lamprey (Lethenteron camtschaticum) in the eastern Bering Sea, visual observations and DNA metabarcoding of gut contents (N = 250) were used to characterize Arctic lamprey diet composition in 2014 and 2015. Differences among individual diets were evaluated by collection year, capture site, and fish...

In the original publication, a part of funding information was missed out in the acknowledgement section. The corrected acknowledgement is given below: Acknowledgements: Partial funding was kindly provided by the Alaska Herpetological Society, the University of Alaska Fairbanks Department of Biology and Wildlife (Calvin J. Lensink Graduate Fellowsh...

The absence of information on genetic variation and population structure of brook lampreys Lethenteron spp. in the eastern part of their distribution limits our understanding of the migration ecology and spatial population genetic structure of the species. We examined genetic variation within and among three aggregations of Lethenteron spp. larvae...

Bering Cisco Coregonus laurettae is an anadromous coregonine species known almost exclusively from northwestern North America and with only three documented spawning populations, all in Alaska. Previous studies of Bering Cisco phenotypic variation examined individuals collected primarily in coastal rearing habitats where population affiliation was...

Alaska Blackfish Dallia pectoralis are an understudied but ecologically important mudminnow occurring in lentic ecosystems of subarctic and Arctic Alaska. We sampled a population of Alaska Blackfish during the winter months in an upland pond near Fairbanks, Alaska, and used a simple mark-recapture estimator to provide the first population estimate...

Identification and protection of water bodies used by anadromous species are critical in light of increasing threats to fish populations, yet often challenging given budgetary and logistical limitations. Noninvasive, rapid‐assessment, sampling techniques may reduce costs and effort while increasing species detection efficiencies. We used an intrins...

We developed and describe a qPCR assay for the detection of wood frogs (Rana sylvatica) using environmental DNA (eDNA) sampling. A single primer set was designed to amplify a 115-bp region of the wood frog cytochrome B gene and assessed for target specificity. There was no evidence of amplification in 11 non-target species. We evaluated the utility...

Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to...

Assemblies of sequence data generated for this study, the alignment examined for this study, and PartitionFinder configuration and partition files

Sampling scheme with classification of taxa included in this study following Betancur-R et al. (2013)

Methods and results of additional phylogenetic analyses

While intertidal habitats are often productive, species-rich environments, they are also harsh and highly dynamic. Organisms that live in these habitats must possess morphological and physiological adaptations that enable them to do so. Intertidal fishes are generally small, often lack scales, and the diverse families represented in intertidal habi...

Ancestral state reconstruction of tide pool occupancy for the sculpin subfamily Oligocottinae and the outgroup taxon Chitonotus pugetensis The most recent common ancestor (MRCA) of Oligocottinae and the MRCA of the Leiocottus lineage are each indicated with an arrow. See text for details.

Ancestral state reconstruction of the presence of copulation for the sculpin subfamily Oligocottinae and the outgroup taxon Chitonotus pugetensis The most recent common ancestor (MRCA) of Oligocottinae is indicated with an arrow. Tips and nodes without a pie symbol are taxa for which no data are available or the state is not reconstructable due to...

Phenogram showing the inferred evolutionary history of maximum length of extant oligocottine species and the outgroup taxon Chitonotus pugetensis The most recent common ancestor (MRCA) of Oligocottinae is indicated with an arrow. Phylogenetic relationships are represented by white edges and bifurcation points represent inferred speciation events. P...

Morphological variation in enlarged male genital papillae Species and museum lot numbers are as follows, (A) Artedius harringtoni, OSIC 04533, 91 mm SL; (B) Clinocottus acuticeps, UAM 47713, 30 mm SL; (C) Oligocottus maculosus, OSU 07467, 73 mm SL; (D) Chitonotus pugetensis, OSU 14872, 76 mm SL; (E) Clinocottus analis, OSU 3241, 72 mm SL; (F) Clino...

Museum collection data for all 16 species of the subfamily Oligocottinae and the outgroup taxon Chitonotus pugetensis Comma separated values (csv) format.

Summary of collection depth data for museum records of oligocottine sculpins and the outgroup taxon Chitonotus pugetensis Comma separated values (csv) format. Catalog numbers, depth, and locality data are provided in Table S2.

Folder containing R script, data matrix, shape data, and phylogenetic tree The R script is titled ”LitorallyAdaptiveScript.R” and contains a heavily annotated list of commands for importing the data matrix (”LitorallyAdaptive.datamatrix.csv”), shape data (”MorphoJcoords.csv”), and phylogenetic tree (”sculpin˙birthdeath˙mcc˙starbeast.tree”), and per...

Modification of the anteriormost rays of the anal in males of the genus Oligocottus Illustration of anal fin is shown for all species: (A) O. rimensis, SIO 67-151; (B) O. maculosus, OS 287; (C) O. rubellio, OS 8133; (D) O. snyderi, OS 4366. Cladogram indicating phylogenetic relationship of species is indicated below anal fin illustrations, adapted...

GenBank accession numbers for all sequences used in this study from the dataset assembled in Buser & López (2015) Microsoft Excel (xlsx) format. See Buser & López (2015) for collection locality data and DNA isolation and amplification methodology.

Verbatim descriptions of depth ranges for members of the sculpin subfamily Oligocottinae (ingroup) and the outgroup taxon Chitonotus pugetensis Comma separated values (csv) format. Verbatim descriptions of depth ranges, primary literature references for tidepool occurrance, and museum lots where “tide pool” or the like is listed as the collection l...

Summary of collection depth data for museum records of oligocottine sculpins and the outgroup taxon Chitonotus pugetensis Microsoft Excel (xlsx) format. Catalog numbers, depth, and locality data are provided in Table S2.

Ancestral state reconstruction of the presence of squamation for the sculpin subfamily Oligocottinae and the outgroup taxon Chitonotus pugetensis The most recent common ancestor (MRCA) of Oligocottinae, the MRCA of the subgenus Clinocottus (Blennicottus), and the MRCA of the clade composed of Oligocottus snyderi, O. rubellio, and O. maculosus are e...

Morphospace of significant principal component axes showing inferred phenotypic optima for the sculpin subfamily Oligocottinae and the outgroup taxon Chitonotus pugetensis Taxa (small circles, labeled by species name) are color-coded to match their inferred phenotypic optimum (large circles). Optima inferred using “surface” (Ingram & Mahler, 2013)....

GenBank accession numbers for all sequences used in this study from the dataset assembled in Buser & López (2015) See Buser & López (2015) for collection locality data and DNA isolation and amplification methodology.

Museum collection data for all 16 species of the subfamily Oligocottinae and the outgroup taxon Chitonotus pugetensis Microsoft Excel (xlsx) format. Museum records where “tide pool” or the like is explicitly stated as the collection locality are highlighted in light green.

Verbatim descriptions of depth ranges for members of the sculpin subfamily Oligocottinae (ingroup) and the outgroup taxon Chitonotus pugetensis Microsoft Excel (xlsx) format. Verbatim descriptions of depth ranges, primary literature references for tide pool occurrence, and museum lots where “tide pool” or the like is listed as the collection locali...

While intertidal habitats are often productive, species-rich environments, they are also harsh and highly dynamic. Organisms that live in these habitats must possess morphological and physiological adaptations that enable them to do so. Intertidal fishes are generally small, often lack scales, and the diverse families represented in intertidal habi...

While intertidal habitats are often productive, species-rich environments, they are also harsh and highly dynamic. Organisms that live in these habitats must possess morphological and physiological adaptations that enable them to do so. Intertidal fishes are generally small, often lack scales, and the diverse families represented in intertidal habi...

Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to...

Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to...

This study presents the first detailed analysis of the mitochondrial DNA diversity of least cisco Coregonus sardinella in Alaska using a 678 bp segment of the control region (D-loop) of the mitochondrial genome. Findings suggest that the history of C. sardinella in Alaska differs from that of other species of Coregonus present in the state and surr...

Assimilation of mercury (Hg) into food webs is directly influenced by ecological factors such as local habitat characteristics, species feeding behavior, and movement patterns. Total Hg concentrations ([THg]) in biota from Subarctic latitudes are driven both by broad spatial processes such as long-range atmospheric transport and more local influenc...

Introduced non-native fishes have the potential to substantially alter aquatic ecology in the introduced range through competition and predation. The Alaska blackfish (Dallia pectoralis) is a freshwater fish endemic to Chukotka and Alaska north of the Alaska Range (Beringia); the species was introduced outside of its native range to the Cook Inlet...

Fish skeletal muscle is often used to monitor mercury concentrations and is used by regulatory agencies to develop fish consumption advisories. However, the distribution of mercury species (MeHg+ and THg) in muscle tissue and other organs is not well understood in a number of fish species. Here we evaluate the spatial distribution of THg and MeHg+...

Pleistocene climatic instability had profound and diverse effects on the distribution and abundance of Arctic organisms revealed by variation in phylogeographic patterns documented in extant Arctic populations. To better understand the effects of geography and paleoclimate on Beringian freshwater fishes, we examined genetic variability in the genus...

The genus Sphaeroforma previously encompassed organisms isolated exclusively from animal symbionts in marine systems. The first saprotrophic sphaeroformids (Mesomycetozoea) isolated from non-animal hosts are described here. Sphaeroforma sirkka and S. napiecek are also the first species in the genus possessing endogenous DNA-containing motile propag...

Given current and projected warming trends in the Arctic and the important role played by subsistence hunting and fishing in the life of northern rural communities, it is increasingly important to document local observations of climate change and its impacts on livelihood practices. We describe ethnographic research exploring local observations of...

Aim We test the hypothesis that the North Pacific coastline from British Columbia to the Kuril Islands forms a broad region of admixture between two divergent mitochondrial‐genome (mt DNA ) lineages in three‐spined stickleback ( Gasterosteus aculeatus ): the Euro‐North American ( ENA ) and Trans‐North‐Pacific ( TNP or Japanese) clades. We test whet...

Lampreys share many of the same habitats as salmonids in freshwater ecosystems, yet receive comparatively little management or research attention. The current belief is that two lamprey species reside in interior Alaska: anadromous Arctic lamprey Lethenteron camtschaticum and freshwater-resident Alaskan brook lamprey L. alaskense. We examined the l...

Betancur-R and Ortí (in press, in this issue) offer a criticism of our recent examination of the monophyly of extant flatfishes (Pleuronectiformes; Campbell et al., 2013). We welcome this opportunity to examine and respond to the main issues presented in Betancur-R and Ortí (in press). Briefly, this debate centers on the question of whether or not...

Mitochondrial genetic variability among populations of the blackfish genus Dallia (Esociformes) across Beringia was examined. Levels of divergence and patterns of geographic distribution of mitochondrial DNA lineages were characterized using phylogenetic inference, median-joining haplotype networks, Bayesian skyline plots, mismatch analysis and spa...

Cetaceans and seabirds frequently come into close contact when they target the same prey. Seabirds are generally thought to benefit from these associations; however, here we report a negative consequence for seabirds from associating with Humpback Whales Megaptera novaeangliae. We examined the remains of three seabirds found in a Humpback Whale fec...

The Elopomorpha (eels and relatives) is a morphologically diverse group of predominantly marine teleost fishes comprising about 1,000 species placed in 25 families and 157 genera. It is one of the three major living teleost lineages along with the Osteoglossomorpha and Clupeocephala. Among a few morphological synapomorphies that have been offered a...

All extant species of flatfish (order Pleuronectiformes) are thought to descend from a common ancestor, and therefore to represent a monophyletic group. This hypothesis is based largely on the dramatic bilateral asymmetry and associated ocular migration characteristics of all flatfish. Yet, molecular-based phylogenetic studies have been inconclusiv...

Blackfishes (Esociformes: Esocidae: Dallia), small fishes with relictual distributions, are unique in being the only primary freshwater fish genus endemic to Beringia. Although the number of species of Dallia is debated, disjunct populations and distinct mitochondrial divisions that predate the end of the last glacial maximum are apparent. We devel...

The zoonotic parasite Trichinella is the causative agent of trichinellosis outbreaks in the circumpolar Arctic. Subsistence communities are particularly prone to trichinellosis due to traditional meat preparation methods and regional presence of a freeze-tolerant Trichinella species (Trichinella nativa). This study is the first application of a val...