Thomas J Near’s research while affiliated with Yale University and other places

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Publications (42)


Figure 1. Molecular dating (BEAST) analysis for the 'Big Africa' tree using both nuclear and mitochondrial markers. Scale bar is in millions of years. Node bars represent 95% confidence intervals around the node ages.
Figure 4. Disparity through time (DDT) plot using the rank envelope method for the LT claroteine radiation based on the MCC tree. Disparity profiles are indicated by solid lines (PC1-4), the dashed line is predicted disparity under Brownian motion, and 95% confidence intervals from 5000 simulations are given by the grey polygon. The relative time axis shows the proportion of time from the origin of the radiation (0) to the present.
Figure 5. Scatter plots of stable isotope values for (A) the claroteines and (B) Synodontis from the southern Lake Tanganyika basin. Ellipses show the standard ellipse area of each species.
Overlap of standard ellipse values (carbon and nitrogen data) for Claroteinae and Synodontis taxa from the Southern Lake Tanganyika Basin.
Do sympatric catfish radiations in Lake Tanganyika show eco-morphological diversification?
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August 2024

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81 Reads

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1 Citation

Evolutionary Journal of the Linnean Society

Claire R Peart

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Roger Bills

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[...]

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Adaptive radiation is characterised by eco-morphological differentiation, in which niche partitioning has been shown to be a central response to natural selection during the diversification of animal clades. This process is suggested to have generated the exceptional biodiversity in the East African rift lakes; however aside from the cichlid fishes, the nature of the divergence, over time, or among species is less clear in the other radiations. To address this, we focus on two distantly related sympatric Lake Tanganyika catfish clades, the genus Synodontis, considered to be Müllerian mimics, and the sub-family Claroteinae. We investigate to what extent, if any, these radiations have undergone eco-morphological diversification. We place these radiations in a common phylogenetic context, and test for morphological divergence and trophic niche partitioning using novel trait data and stable isotope signatures. Diversification of both catfish clades was recent, with the Synodontis radiation synchronised in time with individual genera within the claroteine radiation, suggesting initial diversification was facilitated by lake basin dynamics and/or lake level fluctuations. There is evidence for eco-morphological diversification within the claroteine radiation, as inferred from observed morphological disparity and divergence in diet both between and within genera; however, several species show significant overlap in dietary isotopic signatures. In contrast, the Synodontis radiation has greater overlap between taxa both in morphology and isotopic signatures potentially indicating niche conservatism, suggesting different selective forces maybe driving these radiations.

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Colonization of the ocean floor by jawless vertebrates across three mass extinctions

June 2024

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138 Reads

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2 Citations

BMC Ecology and Evolution

Background The deep (> 200 m) ocean floor is often considered to be a refugium of biodiversity; many benthic marine animals appear to share ancient common ancestry with nearshore and terrestrial relatives. Whether this pattern holds for vertebrates is obscured by a poor understanding of the evolutionary history of the oldest marine vertebrate clades. Hagfishes are jawless vertebrates that are either the living sister to all vertebrates or form a clade with lampreys, the only other surviving jawless fishes. Results We use the hagfish fossil record and molecular data for all recognized genera to construct a novel hypothesis for hagfish relationships and diversification. We find that crown hagfishes persisted through three mass extinctions after appearing in the Permian ~ 275 Ma, making them one of the oldest living vertebrate lineages. In contrast to most other deep marine vertebrates, we consistently infer a deep origin of continental slope occupation by hagfishes that dates to the Paleozoic. Yet, we show that hagfishes have experienced marked body size diversification over the last hundred million years, contrasting with a view of this clade as morphologically stagnant. Conclusion Our results establish hagfishes as ancient members of demersal continental slope faunas and suggest a prolonged accumulation of deep sea jawless vertebrate biodiversity.




The genomic signatures of evolutionary stasis

March 2024

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707 Reads

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3 Citations

Evolution

Evolutionary stasis characterizes lineages that seldom speciate and show little phenotypic change over long stretches of geological time. Although lineages that appear to exhibit evolutionary stasis are often called living fossils, no single mechanism is thought responsible for their slow rates of morphological evolution and low species diversity. Some analyses of molecular evolutionary rates in a handful of living fossil lineages have indicated they exhibit slow rates of genomic change. Here, we investigate mechanisms of evolutionary stasis using a dataset of 1,105 exons for 481 vertebrate species. We demonstrate that two ancient clades of ray-finned fishes classically called living fossils, gars and sturgeons, exhibit the lowest rates of molecular substitution in protein coding genes among all jawed vertebrates. Comparably low rates of evolution are observed at four-fold degenerate sites in gars and sturgeons, implying a mechanism of stasis decoupled from selection that we speculate is linked to a highly effective DNA repair apparatus. We show that two gar species last sharing common ancestry over 100 million years ago naturally produce morphologically intermediate and fertile hybrids. This makes gars the oldest naturally hybridizing divergence among eukaryotes and supports a theoretical prediction that slow rates of nucleotide substitution across the genome slows the accumulation of genetic incompatibilities, enabling hybridization across deeply divergent lineages and perhaps slowing the rate of speciation. Our results help establish molecular stasis as a barrier to speciation and phenotypic innovation and provide a mechanism to explain the low species diversity in living fossil lineages.


Figure 1. Phylogenetic relationships, geographic distribution, and morphological stasis of gars. (A) Tip-dated phylogenetic tree of gars based on three subsets of the 90 largest exons and with positions of fossils fixed based on morphological phylogenies. The circle marks the timing of divergence between Atractosteus and Lepisosteus at approximately 105 million years ago. MRCA = most recent common ancestor. The time-calibrated phylogeny is from Brownstein et al. (2023). (B) Morphological stasis in gars is exemplified by nearly identical species separated by over 50 million years in time. Photographs of Eocene Green River Formation gar fossils are by Lance Grande, and photographs of living gars are by Zachary Miller, both used with permission.
Figure 2. Genomic substitution rates across vertebrates reveal the slow tempo of gar molecular evolution. (A) Combined, annotated time-calibrated phylogeny of all 478 vertebrate species included in the exon rate estimation analysis. For the purposes of combining the subtrees used into a single figure, divergence dates between independently analyzed subclades are taken from Timetree.org. (B) Violin and box plot showing distributions of estimated exon log substitution rates in different vertebrate clades relative to the mean rate in gar (black line). (C) Estimated substitution rates at fourfold degenerate sites in different clades of vertebrates. Silhouettes are public domain from Phylopic.org.
Results of tests using reduced sampling
The genomic signatures of evolutionary stasis

March 2024

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208 Reads

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12 Citations

Evolution

Evolutionary stasis characterizes lineages that seldom speciate and show little phenotypic change over long stretches of geological time. Although lineages that appear to exhibit evolutionary stasis are often called living fossils, no single mechanism is thought to be responsible for their slow rates of morphological evolution and low species diversity. Some analyses of molecular evolutionary rates in a handful of living fossil lineages have indicated that they exhibit slow rates of genomic change. Here, we investigate mechanisms of evolutionary stasis using a dataset of 1,105 exons for 481 vertebrate species. We demonstrate that two ancient clades of ray-finned fishes classically called living fossils, gars and sturgeons, exhibit the lowest rates of molecular substitution in protein-coding genes among all jawed vertebrates. Comparably low rates of evolution are observed at fourfold degenerate sites in gars and sturgeons, implying a mechanism of stasis decoupled from selection that we speculate is linked to a highly effective DNA repair apparatus. We show that two gar species last sharing common ancestry over 100 million years ago produce morphologically intermediate and fertile hybrids in the wild. This makes gars the oldest naturally hybridizing divergence among eukaryotes and supports a theoretical prediction that slow rates of nucleotide substitution across the genome slow the accumulation of genetic incompatibilities, enabling hybridization across deeply divergent lineages and slowing the rate of speciation over geological timescales. Our results help establish molecular stasis as a barrier to speciation and phenotypic innovation and provide a mechanism to explain the low species diversity in living fossil lineages.


Evolutionary origins of the lampriform pelagic radiation

October 2023

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94 Reads

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2 Citations

Zoological Journal of the Linnean Society

Ray-finned fishes, which compose nearly half of living vertebrate diversity, provide an excellent system for studying the evolution of novel body forms. Lampriformes is a species-poor lineage of acanthomorph ray-finned fishes that has evolved two very different and highly specialized body plans suited to life in pelagic oceanic habitats: the deep, round-bodied bathysomes and the ribbon-like taeniosomes. Here, we present a new phylogenetic hypothesis and divergence time estimates for lampriform fishes based on an updated morphological dataset and DNA sequences from nuclear genes for all but one of the living lampriform families and 55% of recognized extant genera. Our analyses resolve two major clades in Lampriformes: the Bathysomi and the Taeniosomi. A time calibrated phylogeny shows that the origin of living lampriforms coincides with the aftermath of the Cretaceous–Palaeogene extinction and that anatomically modern pelagic morphotypes evolved 10 Myr after the start of the Palaeogene.


Figure 1. Evolutionary history of lake-river divergence. A) Map of sampling localities within the Waccamaw and Pee Dee River systems. Site 5 is located within Lake Waccamaw immediately above the outlet, site 6 is 0-350 meters downstream of the lake. Insert map shows range of Etheostoma maculaticeps in pink with sampling area highlighted in yellow. Gray areas indicate the Pee Dee River basin. B) Maximum likelihood ddRAD phylogeny of E. maculaticeps and E. perlongum. Outgroup taxa are not shown. Nodes with <50% bootstrap support are collapsed, nodes with >95% bootstrap support are unlabeled. Branches colored according to hybrid classification results. C), PCA of 10,628 SNPs with <10% missing data. D) Genetic clustering analyses. Each vertical bar represents a sample, bar colors represent admixture coefficients (SNMF) or assignment probabilities (SNAPCLUST). Sampling sites are delimited by vertical white bars. E) Parameter estimates from model with the best AIC score (Fig. S4, model 2, 11,000 generations of lake-river divergence). Non-parametric bootstrap 95% HDIs are indicated in parentheses.
Figure 2. Morphological and ecological divergence associated with genomic divergence. A) Position of 16 landmarks (red) and 24 sliding semilandmarks (black) and the linear measurements. B) Morphospace of first and second principal components of the geometric morphometric analysis. Filled regions are convex hulls with 95% credible interval ellipsoids around the mean for each group. Gray outlines represent body shapes in different regions of morphospace. C) Boxplots of PC2 scores plus linear regression residuals of caudal length and head length versus standard length. Boxplots center line shows the median; box limits show 25th and 75th quartiles; whiskers show 1.5x interquartile range; all data points shown. Compact letter displays of Tukey HSD tests indicated above each plot. D) Linear regressions of osteological traits versus genomic ancestry coefficients estimated by SNMF (Fig. 1D). Points are colored by sampling location (lake, outlet, or river). E) Results of non-metric multi-dimensional scaling (NMDS) with fish stomach contents. Circles indicate fish specimens (colored by sampling location) while triangles represent prey categories. Filled regions are convex hulls with 95% credible interval ellipsoids around the mean for each group.
Figure 3. Genomic outliers of lake-river divergence are concentrated on chromosome 9. A) Scatter plot of estimated cline centers vs cline widths for each ddRAD SNP. The outlet of Lake Waccamaw is located at 0 km on the x-axis. Black points represent SNPs within the inversion. B) Boxplots of cline center and cline width for SNPs within the chromosome 9 inversion versus the genomic background. C) SNP density along the 24 largest Etheostoma perlongum scaffolds, histograms bins in 1 Mbp windows. Gray bars show the distribution of all analyzed SNPs. Black bars show the distribution of SNPs with estimated cline centers within 1 km of the lake-river boundary and with estimated cline widths < 10 km. D) Genome-wide estimates of FST (relative divergence), Dxy (absolute divergence), and π (nucleotide diversity) between Lake Waccamaw (E. perlongum) and the Waccamaw River (E. maculaticeps). FST estimates for individual SNPs are indicated by dots or crosses, sliding window FST estimates are indicated by the black line. Point color indicates how many methods identified a particular SNP as an outlier. Dxy plot shows sliding window estimates, black points indicate outliers. π plot shows sliding window estimates for Lake Waccamaw (black) and the Waccamaw River (pink). All sliding window estimates used a 1 Mbp window size with a 100 Kbp step size.
Figure 4. Etheostoma perlongum chromosome 9 contains a likely inversion supergene. A) Chromosome 9 patterns of nucleotide diversity (π) and genomic differentiation (FST and Dxy). FST estimates for individual SNPs are indicated by dots or crosses, sliding window FST estimates are indicated by the black line. Point color indicates how many methods identified a particular SNP as an outlier. Dxy and π plots show sliding window estimates with a 1 Mbp window size with a 100 Kbp step size. The FST plateau (black bar) and Dxy peaks (grey bars) indicate outlier regions used for gene ontology enrichment analyses. B) Genotypes of SNPs in the chromosome 9 single outlier cluster of high LD (SOC-1). Individuals are ordered by increasing downstream distance from the north shore of Lake Waccamaw. C) Linkage disequilibrium (LD) heatmap for 1 Mbp windows along chromosome 9. Locations of SNPs in SOC-1 are noted. Bar plot on the top margin shows per-SNP linkage metric calculated as the sum of distances between SNPs in high LD (R2 > 0.8). Histogram on the right margin shows the distribution of ddRAD SNPs in 1 Mbp windows along chromosome 9. D) Nucmer alignment dot plot of E. perlongum chromosome 9 versus E. nigrum scaffold 6. Red indicates forward strand alignments, blue indicates reverse strand alignments. E) Alignment of E. nigrum contig 3336 spanning the E. perlongum inversion. F) Position of vision, olfaction, and circadian genes within the
Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes

April 2023

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267 Reads

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2 Citations

Evolution

Geographic isolation is the primary driver of speciation in many vertebrate lineages. This trend is exemplified by North American darters, a clade of freshwater fishes where nearly all sister species pairs are allopatric and separated by millions of years of divergence. One of the only exceptions is the Lake Waccamaw endemic Etheostoma perlongum and its riverine sister species E. maculaticeps, which have no physical barriers to gene flow. Here we show that lacustrine speciation of E. perlongum is characterized by morphological and ecological divergence likely facilitated by a large chromosomal inversion. While Etheostoma perlongum is phylogenetically nested within the geographically widespread E. maculaticeps, there is a sharp genetic and morphological break coinciding with the lake-river boundary in the Waccamaw River system. Despite recent divergence, an active hybrid zone, and ongoing gene flow, analyses using a de novo reference genome reveal a 9 Mb chromosomal inversion with elevated divergence between E. perlongum and E. maculaticeps. This region exhibits striking synteny with known inversion supergenes in two distantly related fish lineages, suggesting deep evolutionary convergence of genomic architecture. Our results illustrate that rapid, ecological speciation with gene flow is possible even in lineages where geographic isolation is the dominant mechanism of speciation.


The biogeography of extant lungfishes traces the breakup of Gondwana

April 2023

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85 Reads

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5 Citations

Journal of Biogeography

Aim Lungfishes are one of the two surviving clades from the once diverse grade of lobe‐finned fishes leading to tetrapods. This classic living fossil lineage, which is the living sister to four‐limbed terrestrial vertebrates, appeared approximately 425 million years ago and rapidly diversified. However, the evolution of lungfishes after their initial radiation is poorly understood, and whether their present distribution tracks ancient geographical change is a classic problem in biogeography. Location Global. Taxon Lungfishes (Dipnoi). Methods Here, we combine mitogenomic, nuclear gene and fossil data to reconstruct the timing of lungfish diversification a Bayesian tip‐dating approach to quantitatively test hypotheses of lungfish historical biogeography and divergence times. We sample all major living and extinct lungfish lineages, including three of the four species of African lungfishes ( Protopterus spp.), the Australian lungfish Neoceratodus forsteri , the South American lungfish Lepidosiren paradoxa and 13 fossils representing extinct lineages from across the globe. Results Our results demonstrate that the divergences of the three major living lungfish clades closely recapitulate the stepwise fragmentation of the Gondwana during the Mesozoic. All of our model‐based biogeographical reconstructions support a Gondwanan vicariance model for the origins of the present distribution of lungfish lineages. Conclusions In turn, lungfishes provide an excellent example of how the integration of fossil data may drastically change support for historical biogeographical hypotheses previously discounted by molecular data and are one of the few living animal lineages that record incredibly ancient geographical changes in their phylogeny.


Citations (21)


... This species was described based on museum specimens collected from Lake Tanganyika [28]. Since its description, it has been reported only once in the literature, quite recently [49]. The holotype and paratypes of the species originate from the same locality, Kajaga in Burundi; a locality not far from the region studied here (Figure 1). ...

Reference:

Catfishes from the North-Western Part of Lake Tanganyika: Contribution to a Reference Library of DNA Barcodes
Do sympatric catfish radiations in Lake Tanganyika show eco-morphological diversification?

Evolutionary Journal of the Linnean Society

... Given their ancient common ancestry with other vertebrates, deep water chimaeras and ghost sharks lend credence to the hypothesis that mesopelagic and bathypelagic environments have served as a refuge for ancient biodiversity that has become rare or extinct in other ecosystems [22,23]. Evidence from the fossil record [24] and phylogenomic analyses of diverse living deep-sea vertebrate clades [25][26][27][28][29][30][31][32][33] suggest younger origins for these deep water radiations. Thus, chimaeras and ghost sharks stand as one of the remaining potential relict vertebrate lineages that have survived in the mesopelagic and bathypelagic zones. ...

Colonization of the ocean floor by jawless vertebrates across three mass extinctions

BMC Ecology and Evolution

... Speciation in many taxa occurs prior to the complete cessation of gene flow (Wu 2001;Nosil 2012;Caro et al. 2013;Wang et al. 2019). In fact gene flow in many species continues well over millions of generations past initial species divergence (Price and Bouvier 2002;Hewitt 2011;Barth et al. 2020;Brownstein et al. 2024). Therefore incomplete reproductive isolation may be a stable evolutionary endpoint, especially where hybrids zones serve to filter adaptive alleles from maladaptive alleles (Martinsen et al. 2001;Servedio and Hermisson 2020). ...

The genomic signatures of evolutionary stasis

Evolution

... The species in the linkage map collection belong to the main extant fish lineage, teleosts [20,31], except the outgroup species, spotted gar, that has been termed a living fossil [11] (Figure 1). Teleost fishes have two small and two large subdivisions Euteleostei and Otocephala. ...

The genomic signatures of evolutionary stasis

Evolution

... Evidence from the fossil record (Friedman, 2010;Friedman et al., 2023;Guinot & Cavin, 2016) and node-dated molecular studies (Alfaro et al., 2009(Alfaro et al., , 2018Brownstein & Near, 2023;Collar et al., 2022;Friedman et al., 2019;Ghezelayagh et al., 2022;Harrington et al., 2016;Miya et al., 2013) suggest that acanthomorph lineage diversity and body shape disparity exploded in the early Paleogene. Pelagic taxa in particular have been proposed to represent a case of parallel adaptive radiations, triggered by the conquest of ecological niches left vacant by the Cretaceous-Paleogene extinction event (Brownstein & Near, 2023;Friedman, 2010;Miya et al., 2013). ...

Evolutionary origins of the lampriform pelagic radiation
  • Citing Article
  • October 2023

Zoological Journal of the Linnean Society

... Previous time estimates for characiforms indicate a Campanian (82 and 76 Mya) cladogenesis of Alestidae and Hepsetus but with phylogenies lacking inclusion of Arnoldichthys and Lepidarchus (Melo et al. 2022a, b). In addition, time estimates using phylogenies and biogeographical reconstructions of other freshwater fish lineages have also shown Late Cretaceous to Early Cenozoic reconstructions for the origins of numerous other African clades such as Denticeps, Heterotis, kneriids, mormyrids, notopterids, Pantodon, various siluroids, and the sarcopterygian Protopterus (Lavoué et al. 2013, Lavoué 2016Near et al. 2013;Brownstein et al. 2023;Brito et al. 2024;Capobianco & Friedman, 2024). Yet despite temporal concordance none of these studies has considered, or even mentioned, the potential impact of the Trans-Saharan Seaway as a major hydrological barrier and therefore a potential driver of east-west allopatric divergence of freshwater fish lineages on the continent. ...

The biogeography of extant lungfishes traces the breakup of Gondwana
  • Citing Article
  • April 2023

Journal of Biogeography

... A member of the primitive Agnathans, the holarctic lamprey genera evolved over 450 million years ago, with much of the modern lamprey diversity appearing in the past 20 million years [14]. Lampreys are obligate ectotherms and are directly influenced by ambient water temperature. ...

Phylogenetics and the Cenozoic radiation of lampreys
  • Citing Article
  • December 2022

Current Biology

... Further complications emerge when considering the fossil record, as extinct species can often be found in geographical areas outside the distribution of their living relatives. Some notable cases include marsupials [10], lungfishes [11] and gars [12], all of which show more complex past geographical distributions. Because of such patterns, the importance of fossils for biogeographical studies has been appreciated for more than a century [2]. ...

Phylogenomics of the Ancient and Species-Depauperate Gars Tracks 150 Million Years of Continental Fragmentation in the Northern Hemisphere
  • Citing Article
  • December 2022

Systematic Biology

... Recent research on artedidraconids has focused on their evolutionary history and phylogenetic relationships, which can drive species trait patterns and thermal tolerance (Felsenstein 1985;Todgham and Mandic 2020). In their phylogenetic analysis, Parker and Near (2022) recovered artedidraconids as a group within Harpagiferidae as the subfamily Artedidraconinae (Andriashev 1965). One harpagiferid species, Harpagifer bispinis (Forster in Bloch and Schneider 1801), is found in the Magellan region of South America (Duhamel et al. 2014), where summer ocean temperatures can exceed 11 °C. ...

Phylogeny Reconciles Classification in Antarctic Plunderfishes
  • Citing Article
  • November 2022

Ichthyology & Herpetology