Daniel M Portik

Pacific Biosciences

The reproductive modes of anurans (frogs and toads) are the most diverse of terrestrial vertebrates, and a major challenge is identifying selective factors that promote the evolution or retention of reproductive modes across clades. Terrestrialized anuran breeding strategies have evolved repeatedly from the plesiomorphic fully aquatic reproductive...

The accumulation of biodiversity in tropical forests can occur through multiple allopatric and parapatric models of diversification, including forest refugia, riverine barriers, and ecological gradients. Considerable debate surrounds the major diversification process, particularly in the West African Lower Guinea forests, which contain a complex ge...

1. Phylogenies with extensive taxon sampling have become indispensable for many types of ecological and evolutionary studies. Many large‐scale trees are based on a “supermatrix” approach, which involves amalgamating thousands of published sequences for a group. Constructing up‐to‐date supermatrices can be challenging, especially as new sequences ma...

Detailed natural history information is lacking for a large number of African amphibians, including many species of the diverse family Hyperoliidae. A total of 18 hyperoliid species are known from Mt. Kupe, making it one of the most species-rich locationsfor hyperoliid frogs. The presence of seven species of Hyperolius and three species of Afrixalu...

The geographically widespread species Afrixalus laevis (Anura: Hyperoliidae) currently has a disjunct distribution in western Central Africa (Cameroon, Equatorial Guinea, Gabon, and possibly adjacent countries) and the area in and near the Albertine Rift in eastern Democratic Republic of the Congo and neighboring countries. At least two herpetologi...

De novo assembly of metagenome samples is a common approach to the study of microbial communities. Current metagenome assemblers developed for short sequence reads or noisy long reads were not optimized for accurate long reads. We thus developed hifiasm-meta, a metagenome assembler that exploits the high accuracy of recent data. Evaluated on seven...

Microbial communities might include distinct lineages of closely related organisms that complicate metagenomic assembly and prevent the generation of complete metagenome-assembled genomes (MAGs). Here we show that deep sequencing using long (HiFi) reads combined with Hi-C binning can address this challenge even for complex microbial communities. Us...

A long-standing challenge in human microbiome research is achieving the taxonomic and functional resolution needed to generate testable hypotheses about the gut microbiota’s impact on health and disease. With a growing number of live microbial interventions in clinical development, this challenge is renewed by a need to understand the pharmacokinet...

A bstract Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics analyses, including taxonomic profiling. The development of long-read specific tools for taxonomic profiling is accelerating, yet ther...

Current metagenome assemblers developed for short sequence reads or noisy long readswere not optimized for accurate long reads. Here we describe hifiasm-meta, a new metagenome assembler that exploits the high accuracy of recent data. Evaluated on seven empirical datasets, hifiasm-meta reconstructed tens to hundreds of complete circular bacterial ge...

A longstanding challenge in human microbiome research is achieving the taxonomic and functional resolution needed to generate testable hypotheses about the gut microbiome’s impact on health and disease. More recently, this challenge has extended to a need for in-depth understanding of the pharmacokinetics and pharmacodynamics of clinical microbiome...

Secondary sympatry among sister lineages is strongly associated with genetic and ecological divergence. This pattern suggests that for closely related species to coexist in secondary sympatry, they must accumulate differences in traits that mediate ecological and/or reproductive isolation. Here, we characterized inter‐ and intra‐specific divergence...

Despite the prevalence of high‐throughput sequencing in phylogenetics, many relationships remain difficult to resolve because of conflicting signal among genomic regions. Selection of different types of molecular markers from different genomic regions is required to overcome these challenges. For evolutionary studies in frogs, we introduce the publ...

Microbial communities in many environments include distinct lineages of closely related organisms which have proved challenging to separate in metagenomic assembly, preventing generation of complete metagenome-assembled genomes (MAGs). The advent of long and accurate HiFi reads presents a possible means to address this challenge by generating compl...

Alignment is a crucial issue in molecular phylogenetics because different alignment methods can potentially yield very different topologies for individual genes. But it is unclear if the choice of alignment methods remains important in phylogenomic analyses, which incorporate data from dozens, hundreds, or thousands of genes. For example, problemat...

Sexual size dimorphism (SSD) is shaped by multiple selective forces that drive the evolution of sex-specific body size, resulting in male or female-biased SSD. Stronger selection on one sex can result in an allometric body-size scaling relationship consistent with Rensch's rule or its converse. Anurans (frogs and toads) generally display female-bia...

Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly o...

Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly o...

Despite the increasing use of high-throughput sequencing in phylogenetics, many phylogenetic relationships remain difficult to resolve because of conflict between gene trees and species trees. Selection of different types of markers (i.e. protein-coding exons, non-coding introns, ultra-conserved elements) is becoming important to alleviate these ph...

Species with wide distributions spanning the African Guinean and Congolian rain forests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models...

Biodiversity loss is one major outcome of human-mediated ecosystem disturbance. One way that humans have triggered wildlife declines is by transporting disease-causing agents to remote areas of the world. Amphibians have been hit particularly hard by disease due in part to a globally distributed pathogenic chytrid fungus (Batrachochytrium dendrobat...

Biodiversity loss is one major outcome of human-mediated ecosys- tem disturbance. One way that humans have triggered wildlife declines is by transporting disease-causing agents to remote areas of the world. Amphibians have been hit particularly hard by disease due in part to a globally distributed pathogenic chytrid fungus (Batrachochytrium dendrob...

Theory predicts that sexually dimorphic traits under strong sexual selection, particularly those involved with intersexual signaling, can accelerate speciation and produce bursts of diversification. Sexual dichromatism (sexual dimorphism in color) is widely used as a proxy for sexual selection and is associated with rapid diversification in several...

High‐throughput sequencing data have greatly improved our ability to understand the processes that contribute to current biodiversity patterns. The “vanishing refuge” diversification model is speculated for the coastal forests of eastern Africa, whereby some taxa have persisted and diversified between forest refugia, while others have switched to b...

Theory predicts that sexually dimorphic traits under strong sexual selection, particularly those involved with intersexual signaling, can accelerate speciation and produce bursts of diversification. Sexual dichromatism (sexual dimorphism in color) is widely used as a proxy for sexual selection and is associated with rapid diversification in several...

Aim To investigate how putative barriers, forest refugia, and ecological gradients across the lower Guineo‐Congolian rain forest shape genetic and phenotypic divergence in the leaf‐folding frog Afrixalus paradorsalis, and examine the role of adjacent land bridge and sky‐islands in diversification. Location The Lower Guineo‐Congolian Forest, the Ca...

Frogs in the genus Amnirana (family Ranidae) are widely distributed across sub-Saharan Africa and present a model system for exploring the relationship between diversification and geography across the continent. Using multiple loci from the mitochondrial (16S) and nuclear genomes (DISP2, FICD, KIAA2013, REV3L), we generated a strongly supported spe...

A new species of African reed frog (genus Hyperolius Rapp, 1842) is described from the Coastal Forests of the Eastern Africa Biodiversity Hotspot in northeastern Mozambique. It is currently only known from less than ten localities associated with the Mozambican coastal pans system, but may also occur in the southeastern corner of Tanzania. Phylogen...

Ecological niche models (ENMs) have been used in a wide range of ecological and evolutionary studies. In biogeographic studies these models have, among other things, helped in the discovery of new allopatric populations, and even new species. However, small sample sizes and questionable taxonomic delimitation can challenge models, often decreasing...

Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and...

Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake (Crotalus atrox) to determine whethe...

We performed surveys at several lower elevation sites surrounding Mt. Kupe, a mountain at the southern edge of the Cameroonian Highlands. This work resulted in the sampling of 48 species, including 38 amphibian and 10 reptile species. By combining our data with prior survey results from higher elevation zones, we produce a checklist of 108 species...

Custom sequence capture experiments are becoming an efficient approach for gathering large sets of orthologous markers in non-model organisms. Transcriptome-based exon capture utilizes transcript sequences to design capture probes, typically using a reference genome to identify intron-exon boundaries to exclude shorter exons (< 200 bp). Here, we te...

African clawed frogs, genus Xenopus, are extraordinary among vertebrates in the diversity of their polyploid species and the high number of independent polyploidization events that occurred during their diversification. Here we update current understanding of the evolutionary history of this group and describe six new species from west and central...

The sequestration of alkaloids from prey items for the purpose of chemical defense has evolved independently in five frog families, and is documented for approximately 150 taxa. The number of currently recognized cases of defensive toxic sequestration is a conservative estimate, and there is a need for continued exploration of the occurrence of thi...

The Arabian Peninsula is home to a unique fauna that has assembled and evolved throughout the course of major geophysical events, including the separation of the Arabian Plate from Africa and subsequent collision with Eurasia. Opportunities for faunal exchanges with particular continents occurred in temporally distinct periods, and the presence of...

Custom sequence capture experiments are becoming an efficient approach for gathering large sets of orthologous markers with targeted levels of informativeness in non-model organisms. Transcriptome-based exon capture utilizes transcript sequences to design capture probes, often with the aid of a reference genome to identify intron-exon boundaries an...

Background The East African spiny-throated reed frog complex (Hyperolius spinigularis, H. tanneri, and H. minutissimus) is comprised of morphologically similar species with highly fragmented populations across the Eastern Afromontane Region. Recent genetic evidence has supported the distinctiveness of populations suggesting a number of cryptic spec...

A newly discovered population of Red-bellied Newts (Taricha rivularis) in the Stevens Creek watershed in Santa Clara County, California, represents a significant southerly range extension of this species, by approximately 130 km from the nearest records in Sonoma County, California. To investigate the origin of this population we sequenced two mito...

A new species of high elevation dwarf gecko (Gekkonidae: Lygodactylus) is described from Mount Namuli, northern Mozambique. This new species is distinguished from other closely related species in the genus Lygodactylus by body size, scalation, and color, and is genetically divergent from congeners. The species is most similar genetically and morpho...

A putative driver of global amphibian decline is the panzootic chytrid fungus Batrachochytrium dendrobatidis (Bd). While Bd has been documented across continental Africa, its distribution in West Africa remains ambiguous. We tested 793 West African amphibians (one caecilian and 61 anuran species) for the presence of Bd. The samples originated from...

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As the fields of molecular systematics and phylogeography are advancing, it is necessary to incorporate multiple loci in both population and species-level inference. Here, we present primer sets for 104 intronless orthologus exons designed for amplification in all squamates. When comparing the Anolis genome to the Gallus genome, all the markers hav...

Phylogeographic patterns in wide-ranging species in southern Africa remain largely unexplored, especially in areas north of South Africa. Here, we investigate population structuring, demographic history, and the colonization pattern of the western rock skink (Trachylepis sulcata), a rock-dwelling species with a range extending from southwestern Sou...

The phylogenetic affinities of the melanistic subspecies Trachylepis sulcata nigra have never been investigated, and it was unclear if this subspecies represented a locally adapted population or a distinct species. Sequences from the nuclear marker RAG-1 (1149 bp), two novel rapidly-evolving nuclear markers KIF24 and EXPH5 (554 bp and 941 bp respec...

Though sequences of formation and ossification of bony elements have been described for many taxa, controversy surrounds the formation of limb elements in turtles. Three hypotheses for patterns of formation of autopodial elements have been proposed, differing primarily in the origin of Distal Carpal/Tarsal 3, the digital arch, and Centrale 4. Patte...