Robert W Meredith

• PhD
• Professor (Associate) at Montclair State University

Objectives The new data provide an important genomic resource for the Critically Endangered Cuban crocodile ( Crocodylus rhombifer ). Cuban crocodiles are restricted to the Zapata Swamp in southern Matanzas Province, Cuba, and readily hybridize with the widespread American crocodile ( Crocodylus acutus ) in areas of sympatry. The reported de novo a...

An annual life cycle is characterized by short-lived adults that exploit seasonally productive but temporary habitats, paired with a hardy embryo stage that survives unfavourable environmental conditions, such as winter or the dry season. This life cycle is rare amongst vertebrates but has evolved independently several times in African and South Am...

All biological species undergo change over time due to the evolutionary process. These changes can occur rapidly and unpredictably. Due to their high potential to spread quickly, it is critical to be able to monitor changes and detect viral variants. Phylogenetic trees serve as good methods to study evolutionary relationships. Complex big data in b...

Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300–1400 year old specimens (n = 2) of th...

p>In live-bearing animal lineages, the evolution of the placenta is predicted to create an arena for genomic conflict during pregnancy, drive patterns of male sexual selection, and increase the rate of speciation. Here we test these predictions of the viviparity driven conflict hypothesis (VDCH) in live-bearing poecilid fishes, a group showing mult...

Climate change has increased hurricane activity and intensity, leading to greater destructive forces impacting coastal communities. Barnegat Bay, New Jersey, USA, is a shallow Mid-Atlantic estuary with considerable anthropogenic development which shows vulnerability to elevated storm surges and coastal flooding. Gelatinous zooplankton were sampled...

The fish subfamily Poeciliinae (sensu Parenti, 1981) is widely distributed across the Western Hemisphere and a dominant component of the fish communities of Central America. Poeciliids have figured prominently in previous studies on the roles of dispersal and vicariance in shaping current geographic distributions. Most recently, Hrbek et al. combin...

Complete time trees which served as the basis for Fig 1 and Fig 2. (DOCX)

Area assignments. (DOC)

Details of colonization events summarized in Table 4. (DOCX)

Next generation sequencing (NGS) methodologies have proven useful in deciphering the food items of generalist predators, but have yet to be applied to gelatinous animal gut and tentacle content. NGS can potentially supplement traditional methods of visual identification. Chrysaora quinquecirrha (Atlantic sea nettle) has progressively become more ab...

Recent phylogenetic analyses of a large dataset for mammalian families (169 taxa, 26 loci) portray contrasting results. Supermatrix (concatenation) methods support a generally robust tree with only a few inconsistently resolved polytomies, whereas MP-EST coalescence analysis of the same dataset yields a weakly supported tree that conflicts with man...

We reassessed the phylogenetic relationships of dasyuromorphians using a large molecular database comprising previously published and new sequences for both nuclear (nDNA) and mitochondrial (mtDNA) genes from the numbat (Myrmecobius fasciatus), most living species of Dasyuridae, and the recently extinct marsupial wolf, Thylacinus cynocephalus. Our...

Retinal opsin photopigments initiate mammalian vision when stimulated by light. Most mammals possess a short wavelength-sensitive opsin 1 (SWS1) pigment that is primarily sensitive to either ultraviolet or violet light, leading to variation in colour perception across species. Despite knowledge of both ultraviolet- and violet-sensitive SWS1 classes...

Annual killifish adapted to life in seasonally ephemeral water-bodies exhibit desiccation resistant eggs that can undergo diapause, a period of develop-mental arrest, enabling them to traverse the otherwise inhospitable dry season. Environmental cues that potentially indicate the season can govern whether eggs enter a stage of diapause mid-way thro...

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific...

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific...

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific...

Edentulism, the absence of teeth, has evolved convergently among vertebrates, including birds, turtles, and several lineages of mammals. Instead of teeth, modern birds (Neornithes) use a horny beak (rhamphotheca) and a muscular gizzard to acquire and process food. We performed comparative genomic analyses representing lineages of nearly all extant...

The evolution of the placenta from a non-placental ancestor causes a shift of maternal investment from pre- to post-fertilization, creating a venue for parent-offspring conflicts during pregnancy. Theory predicts that the rise of these conflicts should drive a shift from a reliance on pre-copulatory female mate choice to polyandry in conjunction wi...

Sexual selection can increase morphological diversity within and among species. Little is known regarding how interspecific variation produced through sexual selection affects other functional systems. Here we examine how morphological diversity resulting from sexual selection impacts aerobic locomotor performance. Using Xiphophorus (swordtail fish...

We assessed the relationships of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) with high throughput genomic sequencing data with an average coverage of 25× for each species. A total of 1.4 billion 100-bp paired-end reads were assembled using the polar bear and annotated giant panda (Ailuropoda melanoleuca)...

O'Leary et al. (Research Article, 8 February 2013, p. 662) examined mammalian relationships and divergence times and concluded that a single placental ancestor crossed the Cretaceous-Paleogene (K-Pg) boundary. This conclusion relies on phylogenetic analyses that fail to discriminate between homology and homoplasy and further implies virus-like rate...

Parsimony reconstruction of the 4-bp frameshift deletion in SWS1. Branch colors are as follows: gray, odontocetes; black, mysticetes, blue, stem Cetacea; green, non-cetacean. Plio = Pliocene; P = Pleistocene. Paintings are by Carl Buell. Also see Text S1. (PDF)

Maximum likelihood phylogram based on SWS1 exons and introns. (PDF)

Additional Materials and Methods. (PDF)

Maximum likelihood phylogram based on RH1 exons. (PDF)

Chromatograms that illustrate inactivating mutations found in cetacean LWS sequences. Taxa exhibiting the deleterious mutations for the indicated exon are in red font. Deletions are highlighted in red and insertions are highlighted in green. (PDF)

Primers used in this study (all 5′ to 3′). SWS1 primer pairs were designed to amplify four complete exons (1–4), four complete introns (1–4), and part of exon 5 in five overlapping segments. RHI and LWS primers were designed to amplify each exon and part of the flanking 5′ and 3′ introns. Ex = exon. (PDF)

Fourteen alignments in nexus format. Alignment 1 = SWS1 Introns + Exons (RAxML); Alignment 2 = SWS1 Exons (PAML, RAxML); Alignment 3 = LWS Exons (PAML, RAxML); Alignment 4 = LWS Exon 1 amplicon; Alignment 5 = LWS Exon 2 amplicon; Alignment 6 = LWS Exon 3 amplicon; Alignment 7 = LWS Exon 4 amplicon; Alignment 8 = LWS Exon 5 amplicon; Alignment 9 = L...

Cetaceans have a long history of commitment to a fully aquatic lifestyle that extends back to the Eocene. Extant species have evolved a spectacular array of adaptations in conjunction with their deployment into a diverse array of aquatic habitats. Sensory systems are among those that have experienced radical transformations in the evolutionary hist...

Background Secondary edentulism (toothlessness) has evolved on multiple occasions in amniotes including several mammalian lineages (pangolins, anteaters, baleen whales), birds, and turtles. All edentulous amniote clades have evolved from ancestors with enamel-capped teeth. Previous studies have documented the molecular decay of tooth-specific genes...

Nexus alignment of ENAM exon 9 sequences for two crocodylians, one testudine, and five birds. The stop codon in crocodylians and Chrysemys picta occurs at positions 3788–3790. A 406 bp deletion that is shared by all five birds occurs near the 3’ end of the coding region at positions 3353–3758. Additional frameshift mutations are shared by four of f...

Nexus alignment of AMBN exon sequences for two crocodylians, one testudine, and one bird. The start and stop codons in crocodylians occur at positions 127–129 (exon 2) and 1374–1376 (exon 11), respectively.

Nexus alignment of AMBN exon sequences forHomo sapiens, Orycteropus aferand six other afrotherians, Dasypus novemcinctus, and Choloepus hoffmanni. The start and stop codons in Homo occur at positions 121–123 (exon 1) and 1468–1470 (exon 13), respectively. The presumed start codon in Dasypus occurs at positions 151–153. Dasypus shares the same stop...

Nexus alignment of AMEL exon sequences in nexus format for two crocodylians, two testudines, and five birds. The start and stop codons in crocodylians occur at positions 69–71 (exon 1) and 731–733 (exon 5), respectively. A putative one-bp frameshift deletion that is shared by all five birds species occurs at position 242 in exon 4.

Schematic alignment showing regions of AMEL exons 1–5 that were identified in Chrysemys picta and Pelodiscus sinensis . Bars below sequence numbers show regions of sequence similarity between Alligator mississippiensis and both testudines (green) or A. mississippiensis and one testudine (chartreuse). Dark blue rectangles = numbered exons in A. miss...

Nexus alignment of Alligator mississippiensis AMEL exon 1 (positions 1–114), intron 1 (positions 115–813), and exon 2 (838–894) with exon 1 and flanking sequences from Chrysemys picta and Pelodiscus sinensis .

Schematic alignment showing regions of ENAM exon 9 that were identified in Chrysemys picta. Green bars below sequence numbers show regions of sequence similarity between C. picta and Alligator mississippiensis. Red rectangles = frameshift mutations in C. picta; light blue rectangles = indels within the coding sequence that are in multiples of three...

Nexus alignment of AMEL sequences (exons 2–7) for Homo sapiens, Orycteropus afer and six other afrotherians (Echinops telfairi, Chrysochloris asiatica, Elephantulus edwardii, Trichechus manatus, Loxodonta africana, Procavia capensis), Dasypus novemcinctus, and Choloepus hoffmanni. The start and stop codons in Homo occur at positions 13–15 (exon 2)...

Schematic alignment showing regions of AMBN exons 1–11 that were identified in Chrysemys picta. Green bars below sequence numbers show regions of sequence similarity between C. picta and Alligator mississippiensis. Dark blue rectangles = numbered exons in A. mississippiensis; red rectangles = frameshift mutations in C. picta; light blue rectangles...

Nexus alignment of protein-coding AMBN sequences for 20 mammals that was used in selection analyses with PAML 4.5 [36].

Nexus alignment of AMEL intron 4 (positions 1–662) and exon 5 (positions 663–844) sequences for Chrysemys picta and Pelodiscus sinensis .

Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extract...

Node labels for Table S1. (PDF)

Compendium of primate species that have been recognized subsequent to Groves [6]. (DOCX)

Timetrees and RAxML phylograms in Newick format. 1. Newick timetree with autocorrelated rates and hard-bounded constraints. 2. Newick timetree with autocorrelated rates and soft-bounded constraints. 3. Newick timetree with independent rates and hard-bounded constraints. 4. Newick timetree with independent rates and soft-bounded constraints. 5. RAxM...

Graphical representation of gene and taxon completeness. Black × = gene present in data set; red × = gene present in data set, but sequence length<50% of the length of the longest sequence. (PDF)

Mean, median, and 95% credibility intervals for four different methods. Node numbers are given in Figure S1. (XLS)

Fourteen minimum and 14 maximum calibrations that were employed in primate timetree analyses with mcmctree [140], [141]. Minimum calibrations were based on the oldest crown fossil belong to each clade. Maximum calibrations were based on stratigraphic bounding (two chronologic units), phylogenetic bracketing (two outgroups), and phylogenetic uncerta...

Compendium of modifications to Perelman et al.’s [12] data set. (DOCX)

List of GenBank accession numbers. (DOC)

List of genes that were included in eight different mcmctree partitions. (DOCX)

Bandicoots (Peramelemorphia) are a major order of australidelphian marsupials, which despite a fossil record spanning at least the past 25 million years and a pandemic Australasian range, remain poorly understood in terms of their evolutionary relationships. Many living peramelemorphians are critically endangered, making this group an important foc...

Bininda-Emonds and Purvis reanalyzed our mammalian phylogenetic supermatrix and claim that our results are not significantly different from their delayed-rise hypothesis. We show that our divergence times are ~11 million years later for placental inter- and intraordinal divergences—consistent with a post–Cretaceous-Paleogene (KPg) radiation of most...

Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted i...

Palaeobiogeographic reconstructions are underpinned by phylogenies, divergence times and ancestral area reconstructions, which together yield ancestral area chronograms that provide a basis for proposing and testing hypotheses of dispersal and vicariance. Methods for area coding include multi-state coding with a single character, binary coding with...