Ben Evans

• PhD
• Professor at McMaster University

Sex chromosomes of some closely related species are not homologous, and sex chromosome turnover is often attributed to mechanisms that involve linkage to or recombination arrest around sex-determining loci. We examined sex chromosome turnover and recombination landscapes in African clawed frogs (genus Xenopus) with reduced representation genome seq...

Genetic triggers for sex determination are frequently co-inherited with other linked genes that may also influence one or more sex-specific phenotypes. To better understand how sex-limited regions evolve and function, we studied a small W chromosome-specific region of the frog Xenopus laevis that contains only three genes (dm-w, scan-w, ccdc69-w) a...

The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of regional diversification, this has rarely been tested in the context of an explicit geological framework. Her...

In most eukaryotes, aerobic respiration requires interactions between autosomally-encoded genes (Ninteract genes) and mitochondrial DNA, RNA, and protein. In species where females are philopatric, contrasting distributions of genetic variation in mitochondrial and nuclear genomes creates variation in mitonuclear interactions that may be subject to...

Allotetraploid genomes have two distinct genomic components called subgenomes that are derived from separate diploid ancestral species. Many genomic characteristics such as gene function, expression, recombination and transposable element mobility may differ significantly between subgenomes. To explore the possibility that subgenome population stru...

Allopolyploid genomes are divided into compartments called subgenomes that are derived from lower ploidy ancestors. In African clawed frogs of the subgenus Xenopus (genus Xenopus), allotetraploid species have two subgenomes (L and S) with morphologically distinct homoeologous chromosomes. In allotetraploid species of the sister subgenus Silurana, i...

In many groups, sex chromosomes change frequently but the drivers of their rapid evolution are varied and often poorly characterized. With an aim of further understanding sex chromosome turnover, we investigated the polymorphic sex chromosomes of the Marsabit clawed frog, Xenopus borealis, using genomic data and a new chromosome-scale genome assemb...

Allotetraploid genomes have two distinct genomic compartments called subgenomes that are derived from separate diploid ancestral species. Many genomic characteristics such as gene function, expression, recombination, and transposable element mobility may differ significantly between subgenomes. To explore the possibility that subgenome population s...

Abstract Genital divergence is thought to contribute to reproductive barriers by establishing a “lock‐and‐key" mechanism for reproductive compatibility. One such example, Macaca arctoides, the bear macaque, has compensatory changes in both male and female genital morphology as compared to close relatives. M. arctoides also has a complex evolutionar...

Allopolyploid genomes are divided into compartments called subgenomes that are derived from lower ploidy ancestors. In African clawed frogs of the subgenus Xenopus (genus Xenopus), allotetraploid species have two subgenomes (L and S) with morphologically distinct homoeologous chromosomes. In allotetraploid species of the sister subgenus Silurana, i...

Allopolyploid genomes are divided into compartments called subgenomes that are derived from lower ploidy ancestors. In African clawed frogs of the subgenus Xenopus (genus Xenopus ), allotetraploid species have two subgenomes (L and S) with morphologically distinct homoeologous chromosomes. In allotetraploid species of the sister subgenus Silurana ,...

In most macaques, females are philopatric and males migrate from their natal ranges, which results in pronounced divergence of mitochondrial genomes within and among species. We therefore predicted that some nuclear genes would have to acquire compensatory mutations to preserve compatibility with diverged interaction partners from the mitochondria....

Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information...

The tempo of sex chromosome evolution—how quickly, in what order, why and how their particular characteristics emerge during evolution—remains poorly understood. To understand this further, we studied three closely related species of African clawed frog (genus Xenopus), that each has independently evolved sex chromosomes. We identified population p...

In many species, sexual differentiation is a vital prelude to reproduction, and disruption of this process can have severe fitness effects, including sterility. It is thus interesting that genetic systems governing sexual differentiation vary among—and even within—species. To understand these systems more, we investigated a rare example of a frog w...

Wallace's Line demarcates a biogeographical boundary between the Indomalaya and Australasian ecoregions. Most placental mammalian genera, for example, occur to the west of this line, whereas most marsupial genera occur to the east. However, macaque monkeys are unusual because they naturally occur on both western and eastern sides. To further explor...

This document includes supplementary methods and supplementary results.

Phenotypic invariance - the outcome of purifying selection - is a hallmark of biological importance. Alternatively, invariant phenotypes might be controlled by diverged genetic systems in different species. Here we explore how an important and invariant phenotype - the development of sexually differentiated individuals - is controlled in over two d...

In many species, vocal communication is essential for coordinating social behaviors including courtship, mating, parenting, rivalry, and alarm signaling. Effective communication requires accurate production, detection, and classification of signals, as well as selection of socially appropriate responses. Understanding how signals are generated and...

A comprehensive, accurate, and revisable alpha taxonomy is crucial for biodiversity studies, but is challenging when data from reference specimens are difficult to collect or observe. However, recent technological advances can overcome some of these challenges. To illustrate this, we used modern approaches to tackle a centuries-old taxonomic enigma...

During the late Pleistocene, isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myriad outcomes arisi...

Whole genome duplication (WGD), the doubling of the nuclear DNA of a species, contributes to biological innovation by creating ge‐netic redundancy. One mode of WGD is allopolyploidization, wherein each genome from two ancestral species becomes a ‘subgenome’ of a polyploid descendant species. The evolutionary trajectory of a dupli‐cated gene that ar...

During the late Pleistocene, genetically isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and the associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myria...

[This corrects the article DOI: 10.1098/rsos.170351.].

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and t...

There exists extraordinary variation among species in the degree and nature of sex chromosome divergence. However, much of our knowledge about sex chromosomes is based on comparisons between deeply diverged species with different ancestral sex chromosomes, making it difficult to establish how fast and why sex chromosomes acquire variable levels of...

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and tha...

Many genera of terrestrial vertebrates diversified exclusively on one or the other side of Wallace’s Line, which lies between Borneo and Sulawesi islands in Southeast Asia, and demarcates one of the sharpest biogeographic transition zones in the world. Macaque monkeys are unusual among vertebrate genera in that they are distributed on both sides of...

The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about 5 Ma. The mechanism for this rapid genome expansio...

Whole genome duplication (WGD) generates new species and genomic redundancy. In African clawed frogs of the genus Xenopus, this phenomenon has been especially important in that (i) all but one extant species are polyploid and (ii) whole genome sequences of some species provide an evidence for genomic rearrangements prior to or after WGD. Within Xen...

The Cape platanna, Xenopus gilli, an endangered frog, hybridizes with the African clawed frog, X. laevis, in South Africa. Estimates of the extent of gene flow between these species range from pervasive to rare. Efforts have been made in the last 30 years to minimize hybridization between these two species in the west population of X. gilli, but no...

The vertebrate hindbrain includes neural circuits that govern essential functions including breathing, blood pressure and heart rate. Hindbrain circuits also participate in generating rhythmic motor patterns for vocalization. In most tetrapods, sound production is powered by expiration and the circuitry underlying vocalization and respiration must...

Sexual differentiation is fundamentally important for reproduction, yet the genetic triggers of this developmental process can vary, even between closely related species. Recent studies have uncovered, for example, variation in the genetic triggers for sexual differentiation within and between species of African clawed frogs (genus Xenopus). Here,...

Background Cytomegaloviruses belong to a large, ancient, genus of DNA viruses comprised of a wide array of species-specific strains that occur in diverse array of hosts. Methods In this study we sequenced the ~217 Kb genome of a cytomegalovirus isolated from a Mauritius cynomolgus macaque, CyCMV Mauritius, and compared it to previously sequenced cy...

Background: The primate Y chromosome is distinguished by a lack of inter-chromosomal recombination along most of its length, extensive gene loss, and a prevalence of repetitive elements. A group of genes on the male-specific portion of the Y chromosome known as the "ampliconic genes" are present in multiple copies that are sometimes part of palind...

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...

Full size version of Fig 6, part two of three. (TIF)

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Photographs of type material from several previously described Xenopus taxa part two of six. (TIF)

Photographs of type material from several previously described Xenopus taxa part three of six. (TIF)

Photographs of type material from several previously described Xenopus taxa part four of six. (TIF)

X-ray of X. eysoole holotype (MCZ A-138016). (TIF)

Analysis of mitochondrial DNA data using the calibration from [9]. Labeling follows Fig 2. (TIF)

Photographs of type material from several previously described Xenopus taxa part six of six. (TIF)

Specimens for which sequence data were obtained. (XLSX)

Full size version of Fig 6, part one of three. (TIF)

Full size version of Fig 7, part one of three. (TIF)

Full size version of Fig 7, part three of three. (TIF)

Photographs of type material from several previously described Xenopus taxa part one of six. Images include, from subgenus Silurana: X. tropicalis (BMNH 1947.2.24.83) and X. epitropicalis (BMNH 1982.462), from amieti species group: X. amieti (MHNG 2030.80), X. andrei (MHNG 2088.32), X. boumbaensis (MHNG 2080.31), X. itombwensis (MCZ A-138192), X. l...

Photographs of type material from several previously described Xenopus taxa part five of six. (TIF)

Analysis of mitochondrial DNA data using the calibration from [9]. Labeling follows Fig 1. (TIF)

Full size version of Fig 6, part three of three. (TIF)

Specimens examined and morphological data. (XLSX)

Information on CT scan settings (excluding X. calcaratus type). (XLSX)

This review summarizes the current status of the known extant genuine polyploid anuran and urodelan species, as well as spontaneously originated and/or experimentally produced amphibian polyploids. The mechanisms by which polyploids can originate, the meiotic pairing configurations, the diploidization processes operating in polyploid genomes, the p...

Genome duplication creates redundancy in proteins and their interaction networks, and subsequent smaller-scale gene duplication can further amplify genetic redundancy. Mutations then lead to the loss, maintenance or functional divergence of duplicated genes. Genome duplication occurred many times in African clawed frogs (genus Xenopus), and almost...

The African clawed frog Xenopus laevis has a large native distribution over much of sub-Saharan Africa and is a model organism for research, a proposed disease vector, and an invasive species. Despite its prominent role in research and abundance in nature, surprisingly little is known about the phylogeography and evolutionary history of this group....

We describe a new species of fanged frog (Limnonectes larvaepartus) that is unique among anurans in having both internal fertilization and birth of tadpoles. The new species is endemic to Sulawesi Island, Indonesia. This is the fourth valid species of Limnonectes described from Sulawesi despite that the radiation includes at least 15 species and po...

In species with separate sexes, social systems can differ in the relative variances of male versus female reproductive success. Papion monkeys (macaques, mangabeys, mandrills, drills, baboons, geladas) exhibit hallmarks of a high variance in male reproductive success, including a female-biased adult sex ratio and prominent sexual dimorphism. To exp...

In theory, competition among species in a shared habitat results in niche separation. In the case of small recondite mammals such as shrews, little is known about their autecologies, leaving open questions regarding the degree to which closely related species co-occur and how or whether ecological niches are partitioned. The extent to which species...

Sex chromosome divergence has been documented across phylogenetically diverse species, with amphibians typically having cytologically nondiverged (“homomorphic”) sex chromosomes. With an aim of further characterizing sex chromosome divergence of an amphibian, we used “RAD-tags” and Sanger sequencing to examine sex specificity and heterozygosity in...

Transposable elements (TEs) are repetitive DNA sequences that can make new copies of themselves that are inserted elsewhere in a host genome. The abundance and distributions of TEs vary considerably among phylogenetically diverse hosts. With the aim of exploring the basis of this variation, we evaluated correlations between several genomic variable...

Aim Widespread species found in disturbed habitats are often expected to be human commensals. In island systems, this association predicts that dispersal will be mediated by humans. We investigated the biogeographical relationships among populations of a widespread tree skink that inhabits coastal forest and human‐cultivated plantations in Southeas...

The effective population size (N(e)) quantifies the effectiveness of genetic drift in finite populations. When generations overlap, theoretical expectations for N(e) typically assume that the sampling of offspring genotypes from a given individual is independent among successive breeding events, even though this is not true in many species, includi...

Genome duplication, including polyploid speciation and spontaneous polyploidy in diploid species, occurs more frequently in amphibians than mammals. One possible explanation is that some amphibians, unlike almost all mammals, have young sex chromosomes that carry a similar suite of genes (apart from the genetic trigger for sex determination). These...

Prospects for a comprehensive inventory of global biodiversity would be greatly improved by automating methods of species delimitation. The general mixed Yule-coalescent (GMYC) was recently proposed as a potential means of increasing the rate of biodiversity exploration. We tested this method with simulated data and applied it to a group of poorly...

The estimation of phylogenetic relationships is an essential component of understanding evolution. Accurate phylogenetic estimation is difficult, however, when internodes are short and old, when genealogical discordance is common due to large ancestral effective population sizes or ancestral population structure, and when homoplasy is prevalent. In...

Gene duplication is an important biological phenomenon associated with genomic redundancy, degeneration, specialization, innovation, and speciation. After duplication, both copies continue functioning when natural selection favors duplicated protein function or expression, or when mutations make them functionally distinct before one copy is silence...

The Ethiopian highlands - home to striking species diversity and endemism - are bisected by the Rift Valley, a zone of tectonic divergence. Using molecular data we examined the evolutionary history of two co-distributed species of African clawed frog (Xenopus clivii and X. largeni) that are endemic to this region. Our field collections substantiall...

Because island communities are derived from mainland communities, they are often less diverse by comparison. However, reduced complexity of island communities can also present ecological opportunities. For example, amphibian diversity on Sulawesi Island is lower than it is in the Philippines, but Sulawesi supports a surprising diversity of Sulawesi...

Indirect tests have detected recombination in mitochondrial DNA (mtDNA) from many animal lineages, including mammals. However, it is possible that features of the molecular evolutionary process without recombination could be incorrectly inferred by indirect tests as being due to recombination. We have identified one such example, which we call "pat...

We describe a new octoploid species of African clawed frog (Xenopus) from the Lendu Plateau in the northern Albertine Rift of eastern Democratic Republic of the Congo. This species is the sister taxon of Xenopus vestitus (another octoploid), but is distinguished by a unique morphology, vocalization and molecular divergence in mitochondrial and auto...

For most frogs, advertisement calls are essential for reproductive success, conveying information on species identity, male quality, sexual state and location. While the evolutionary divergence of call characters has been examined in a number of species, the relative impacts of genetic drift or natural and sexual selection remain unclear. Insights...

Southeast Asia’s widespread species offer unique opportunities to explore the effects of geographical barriers to dispersal on patterns of vertebrate lineage diversification. We analyzed mitochondrial gene sequences (16S rDNA) from a geographically widespread sample of 266 Southeast Asian tree frogs, including 244 individuals of Polypedates leucomy...

Contemporary global declines and mortality events in amphibian populations have been often attributed to infectious disease and climate change, separately and in combination. We report on an enigmatic mortality event in the only known population of the Critically Endangered frog species Xenopus longipes. This aquatic and biologically distinctive sp...

DM-W is a dominant, female-specific, regulator of sex determination in the African clawed frog Xenopus laevis. This gene is derived from partial duplication of DMRT1, a male-related autosomal gene. We set out to better understand sex determination in Xenopus by studying this pair of genes. We found that DM-W evolved in Xenopus after divergence from...

Sex-specific differences in dispersal, survival, reproductive success, and natural selection differentially affect the effective population size (N(e)) of genomic regions with different modes of inheritance such as sex chromosomes and mitochondrial DNA. In papionin monkeys (macaques, baboons, geladas, mandrills, drills, and mangabeys), for example,...

Genetic variation within species--a priority for biodiversity conservation--is influenced by natural selection, demography, and stochastic events such as genetic drift. We evaluated the role of these factors in 14 codistributed species of reptiles and amphibians on the Indonesian island of Halmahera by testing whether their molecular variation was...

Changes in gene expression contribute to reproductive isolation of species, adaptation, and development and may impact the genetic fate of duplicated genes. African clawed frogs (genus Xenopus) offer a useful model for examining regulatory evolution, particularly after gene duplication, because species in this genus are polyploid. Additionally, the...

Here we describe a new octoploid species of clawed frog from the Itombwe Massif of South Kivu Province, Democratic Republic of the Congo. This new species is the sister taxon of Xenopus wittei, but is substantially diverged in morphol-ogy, male vocalization, and mitochondrial and autosomal DNA. Analysis of mitochondrial "DNA barcodes" in polyploid...

Here we describe a new octoploid species of clawed frog from the Itombwe Massif of South Kivu Province, Democratic Republic of the Congo. This new species is the sister taxon of Xenopus wittei, but is substantially diverged in morphology, male vocalization, and mitochondrial and autosomal DNA. Analysis of mitochondrial “DNA barcodes” in polyploid c...

Isolation of populations eventually leads to divergence by genetic drift, but if connectivity varies over time, its impact on diversification may be difficult to discern. Even when the habitat patches of multiple species overlap, differences in their demographic parameters, molecular evolution and stochastic events contribute to differences in the...