Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species

Genomic and ecological divergence support recognition of a new species of endangered Satyrium butterfly (Lepidoptera, Lycaenidae)

We describe a highly isolated population of hairstreak butterfly from Waterton Lakes National Park, Alberta, Canada, as a new species, Satyriumcuriosolus sp. nov., previously recognized as Satyriumsemiluna (Half-moon Hairstreak). We propose "Curiously Isolated Hairstreak" as the common name due to its disjunct and unusual distribution. Previous whole-genome analyses revealed S.curiosolus has extremely low genomic diversity and is highly divergent from the nearest S.semiluna populations in British Columbia and Montana, more than 400 km distant. Further analysis suggested prolonged inbreeding and isolation for up to ~40,000 years BP. Ecological niche modeling indicated that S.curiosolus occupies environmental conditions that are distinct from S.semiluna, suggesting niche divergence driven by long-term geographical and ecological separation. While host plant and ant associations have not been definitively resolved, they likely differ between S.curiosolus and S.semiluna. As part of this description, we provide whole-genome consensus sequences for each individual of the type series and identify 21,985 single nucleotide polymorphisms (SNPs) that are divergently fixed between S.curiosolus and S.semiluna, including 117 unlinked SNPs distributed across the genome as putative diagnostic markers. Previously listed as Endangered in Canada as the Waterton population of S.semiluna, S.curiosolus should retain this conservation status due to its extreme isolation, small population size, and flatlined genomic diversity. We propose species recognition as a testable hypothesis under the General Lineage Concept and recommend further research to explore the taxonomy, ecological relationships, and conservation of the greater species complex, including S.curiosolus, S.semiluna, and S.fuliginosa.

A New Look at an Old Face: The Hoà Binh Late Pleistocene Pongo Skull and Other Faciodental Fragments From Breccia Caves in Vietnam-A Morphometric Assessment With Taxonomic Implications

OBJECTIVES

The taxonomic status of the Middle and Late Pleistocene pongines from northern Vietnam remains obscure. Two current schemes dominate. The first has multiple species of Pongo and Langsonia occupying the region during the late Middle and Late Pleistocene. The second has just two species, with the large species P. weidenreichi from the Early to Late Pleistocene of China evolving into the smaller P. devosi from the Middle/Late Pleistocene transition. Here, we generate several multivariate analyses against the available faciodental specimens from present-day northern Vietnam to test these two schemes and assess the morphotypes of these specimens.

MATERIALS AND METHODS

Discriminant factor and principal components analyses were both used against 51 extant hominids (Pongo, Gorilla and the two species of Pan) with 105 faciodental variables to examine the near-complete subfossil Hoà Binh skull. Additional fossils from the Late Pleistocene of this region were also analyzed. All specimens used were original.

RESULTS

We conclude that there was a diverse range of Pongo species in the region of northern Vietnam. We recognize two large and two small species during the Late Pleistocene. One of the larger species occupied this region toward the end of the Late Pleistocene, thus refuting the chronospecies hypothesis.

DISCUSSION

This study suggests the extinction of mainland Pongo species is associated with the rapid decline in habitat during the Late Pleistocene. Orangutan populations further south in Sumatra and Borneo (still then part of Mainland Asia) survived in safe havens of relic rainforests.

Phylogenetic Signal in Primate Tooth Enamel Proteins and its Relevance for Paleoproteomics

Ancient tooth enamel, and to some extent dentin and bone, contain characteristic peptides that persist for long periods of time. In particular, peptides from the enamel proteome (enamelome) have been used to reconstruct the phylogenetic relationships of fossil taxa. However, the enamelome is based on only about 10 genes, whose protein products undergo fragmentation in vivo and post mortem. This raises the question as to whether the enamelome alone provides enough information for reliable phylogenetic inference. We address these considerations on a selection of enamel-associated proteins that has been computationally predicted from genomic data from 232 primate species. We created multiple sequence alignments for each protein and estimated the evolutionary rate for each site. We examined which sites overlap with the parts of the protein sequences that are typically isolated from fossils. Based on this, we simulated ancient data with different degrees of sequence fragmentation, followed by phylogenetic analysis. We compared these trees to a reference species tree. Up to a degree of fragmentation that is similar to that of fossil samples from 1 to 2 million years ago, the phylogenetic placements of most nodes at family level are consistent with the reference species tree. We tested phylogenetic analysis on combinations of different enamel proteins and found that the composition of the proteome can influence deep splits in the phylogeny. With our methods, we provide guidance for researchers on how to evaluate the potential of paleoproteomics for phylogenetic studies before sampling valuable ancient specimens.

A comprehensive framework for the delimitation of species within the Bemisia tabaci cryptic complex, a global pest-species group

Identifying cryptic species poses a substantial challenge to both biologists and naturalists due to morphological similarities. Bemisia tabaci is a cryptic species complex containing more than 44 putative species; several of which are currently among the world's most destructive crop pests. Interpreting and delimiting the evolution of this species complex has proved problematic. To develop a comprehensive framework for species delimitation and identification, we evaluated the performance of distinct data sources both individually and in combination among numerous samples of the B. tabaci species complex acquired worldwide. Distinct datasets include full mitogenomes, single-copy nuclear genes, restriction site-associated DNA sequencing, geographic range, host speciation, and reproductive compatibility datasets. Phylogenetically, our well-supported topologies generated from three dense molecular markers highlighted the evolutionary divergence of species of the B. tabaci complex and suggested that the nuclear markers serve as a more accurate representation of B. tabaci species diversity. Reproductive compatibility datasets facilitated the identification of at least 17 different cryptic species within our samples. Native geographic range information provides a complementary assessment of species recognition, while the host range datasets provide low rate of delimiting resolution. We further summarized different data performances in species classification when compared with reproductive compatibility, indicating that combination of mtCOI divergence, nuclear markers, geographic range provide a complementary assessment of species recognition. Finally, we represent a model for understanding and untangling the cryptic species complexes based on the evidence from this study and previously published articles.

Heads up-Four Giraffa species have distinct cranial morphology

Giraffe (Giraffa spp.) are among the most unique extant mammals in terms of anatomy, phylogeny, and ecology. However, aspects of their evolution, ontogeny, and taxonomy are unresolved, retaining lingering questions that are pivotal for their conservation. We assembled the largest known dataset of Giraffa skulls (n = 515) to investigate patterns of cranial variability using 3D geometric morphometrics. The results show distinct sexual dimorphism and divergent ontogenetic trajectories of skull shape for the north clade (G. camelopardalis antiquorum, G. c. camelopardalis, G. c. peralta, and G. reticulata) and the south clade (G. giraffa angolensis, G. g. giraffa, G. tippelskirchi tippelskirchi, and G. t. thornicrofti) which was further supported statistically. Discriminant functions found statistically significant cranial shape differences between all four Giraffa species, and in some cases also between subspecies of the same species. Our 3D morphometric analysis shows that the four genetically distinct Giraffa spp. also have distinct cranial morphologies, largely addressable to features of display (ossicones). Our results highlight the importance of focusing future giraffe conservation efforts on each taxon to maintain their unique characteristics and biodiversity in the wild.

Delimitation of Endangered Telmatobius Species (Anura: Telmatobiidae) of the Chilean Salt Puna

Clarifying the taxonomic status and distribution of endangered species is crucial to their conservation. In this study, we contrasted different lines of evidence (morphology, mtDNA, and nucDNA: microsatellites and SNP) to clarify the taxonomic status of endangered Telmatobius water frog species and unidentified populations that inhabit the Salt Puna in Chile. We studied population differentiation and species divergence by performing morphometric, population genetic and species delimitation analyses. The results confirmed the species status of Telmatobius fronteriensis and T. philippii, as they exhibited morphometric, mitochondrial and genomic SNP divergence. Although Bayes factor delimitation analysis indicated that the Telmatobius populations of Ascotán and Carcote could represent a new species, their few mitochondrial differences and similar morphology with respect to T. philippii suggested otherwise. Instead, they can be considered an evolutionarily significant unit of T. philippii that has differentiated from the type locality. These results extend the geographic distribution of T. philippii, which is categorized as critically endangered by the IUCN.

Pongo's ecological diversity from dental macrowear analysis

OBJECTIVES

Orangutans are found in tropical rainforests of Borneo (Pongo pygmaeus) and Sumatra (Pongo abelii and Pongo tapanuliensis), and they are primarily considered frugivorous species. However, ecological studies reported differences in feeding behavior between these species. P. pygmaeus spend more time feeding on low-quality foods, such as bark and tough vegetation than do P. abelii. The aim of this study is to investigate if there is any geographic variation in molar macrowear pattern between the two species.

METHODS

We analyzed the macrowear pattern of second mandibular molars of 58 orangutan specimens combining dental topographic measurements (occlusal relief index, percentage of dentine exposure, and percentage of enamel wear) with the occlusal fingerprint analysis method.

RESULTS

The molar macrowear patterns of P. abelii and P. pygmaeus show no significant differences in most of the variables examined in this study. While P. pygmaeus molars are generally characterized by flatter occlusal morphology with slightly larger crushing and grinding areas than those of P. abelii, these differences are not statistically significant. However, we do observe a more variable wear in P. pygmaeus.

CONCLUSIONS

Similarities in molar macrowear patterns between the two species could be linked to overlapping long-term diets, primarily composed of ripe and pulpy fruits. Dental macrowear is a cumulative process that occurs during the individual's lifetime, and it may be difficult to detect seasonal changes through its examination. Future studies could integrate tooth micro- and macrowear data for a better understanding of primate dental ecology.

Deep genetic substructure within bonobos

Establishing the genetic and geographic structure of populations is fundamental, both to understand their evolutionary past and preserve their future. Nevertheless, the patterns of genetic population structure are unknown for most endangered species. This is the case for bonobos (Pan paniscus), which, together with chimpanzees (Pan troglodytes), are humans' closest living relatives. Chimpanzees live across equatorial Africa and are classified into four subspecies,1 with some genetic population substructure even within subspecies. Conversely, bonobos live exclusively in the Democratic Republic of Congo and are considered a homogeneous group with low genetic diversity,2 despite some population structure inferred from mtDNA. Nevertheless, mtDNA aside, their genetic structure remains unknown, hampering our understanding of the species and conservation efforts. Mapping bonobo genetic diversity in space is, however, challenging because, being endangered, only non-invasive sampling is possible for wild individuals. Here, we jointly analyze the exomes and mtDNA from 20 wild-born bonobos, the whole genomes of 10 captive bonobos, and the mtDNA of 136 wild individuals. We identify three genetically distinct bonobo groups of inferred Central, Western, and Far-Western geographic origin within the bonobo range. We estimate the split time between the central and western populations to be ∼145,000 years ago and genetic differentiation to be in the order of that of the closest chimpanzee subspecies. Furthermore, our estimated long-term Ne for Far-West (∼3,000) is among the lowest estimated for any great ape lineage. Our results highlight the need to attend to the bonobo substructure, both in terms of research and conservation.

Evidence for the smallest fossil Pongo in southern China

The rarity of Pongo fossils with precise absolute dating from the Middle Pleistocene hampers our understanding of the taxonomy and spatiotemporal distribution of Quaternary orangutans in southern China. Here, we report a newly discovered sample of 113 isolated teeth of fossil Pongo from Zhongshan Cave in the Bubing Basin, Guangxi, southern China. We describe the Pongo specimens from Zhongshan Cave and compare them metrically to other samples of fossil Pongo species (i.e., Pongo weidenreichi, Pongo devosi, Pongo duboisi, Pongo palaeosumatrensis, Pongo javensis, and Pongo sp.) and to extant orangutans (i.e., Pongo pygmaeus and Pongo abelii). The Zhongshan Pongo assemblage is dated using U-series and coupled electron spin resonance/U-series methods. Our results reasonably constrain the Zhongshan Pongo assemblage to 184 ± 16 ka, which is consistent with the biostratigraphic evidence. The Zhongshan Pongo teeth are only 6.5% larger on average than those of extant Pongo. The Zhongshan teeth are smaller overall than those of Pongo from all other cave sites in southern China, and they currently represent the smallest fossil orangutans in southern China. Based on their dental size, and the presence of a well-developed lingual pillar and lingual cingulum on the upper and lower incisors, an intermediate frequency of lingual cingulum remnants on the upper molars, and a higher frequency of moderate to heavy wrinkling on the upper and lower molars, we provisionally assign the Zhongshan fossils to P. devosi. Our results confirm earlier claims that P. weidenreichi is replaced by a smaller species in southern China, P. devosi, by the late Middle Pleistocene. The occurrence of P. devosi in Zhongshan Cave further extends its spatial and temporal distribution. The Pongo specimens from Zhongshan provide important new evidence to demonstrate that the dental morphological features of Pongo in southern China changed substantially during the late Middle Pleistocene.

Relative leg-to-arm skeletal strength proportions in orangutans by species and sex

Among extant great apes, orangutans climb most frequently. However, Bornean orangutans (Pongo pygmaeus) exhibit higher frequencies of terrestrial locomotion than do Sumatran orangutans (Pongo abelii). Variation in long bone cross-sectional geometry is known to reflect differential loading of the limbs. Thus, Bornean orangutans should show greater relative leg-to-arm strength than their Sumatran counterparts. Using skeletal specimens from museum collections, we measured two cross-sectional geometric measures of bone strength: the polar section modulus (Zpol) and the ratio of maximum to minimum area moments of inertia (Imax/Imin), at the midshaft of long bones in Bornean (n = 19) and Sumatran adult orangutans (n = 12) using medical CT and peripheral quantitative CT scans, and compared results to published data of other great apes. Relative leg-to-arm strength was quantified using ratios of femur and tibia over humerus, radius, and ulna, respectively. Differences between orangutan species and between sexes in median ratios were assessed using Wilcoxon rank sum tests. The tibia of Bornean orangutans was stronger relative to the humerus and the ulna than in Sumatran orangutans (p = 0.008 and 0.025, respectively), consistent with behavioral studies that indicate higher frequencies of terrestrial locomotion in the former. In three Zpol ratios, adult female orangutans showed greater leg-to-arm bone strength compared to flanged males, which may relate to females using their legs more during arboreal locomotion than in adult flanged males. A greater amount of habitat discontinuity on Borneo compared to Sumatra has been posited as a possible explanation for observed interspecific differences in locomotor behaviors, but recent camera trap studies has called this into question. Alternatively, greater frequencies of terrestriality in Pongo pygmaeus may be due to the absence of tigers on Borneo. The results of this study are consistent with the latter explanation given that habitat continuity was greater a century ago when our study sample was collected.

Orangutan males make increased use of social learning opportunities, when resource availability is high

Humans' colonization of diverse habitats relied on our ancestors' abilities to innovate and share innovations with others. While ecological impacts on innovations are well studied, their effect on social learning remains poorly understood. We examined how food availability affects social learning in migrant orangutan unflanged males, who may learn from local orangutans through peering (i.e., observational social learning). We analyzed 1,384 dyadic associations, including 360 peering events, among 46 wild Sumatran orangutan and 25 Bornean orangutan males, collected over 18 years. Migrants' peering rates significantly increased with higher food availability and time spent in proximity to others. Furthermore, migrants in the more sociable Sumatran population exhibited significantly higher peering rates compared to the Borneans, suggesting intrinsic and/or developmental effects of food availability on social learning. These findings emphasize the importance of investigating ecological effects on social learning on the immediate, developmental, and intrinsic levels for our understanding of cultural evolution.

Specimens as individuals: Four interventions and recommendations for great ape skeletal collections research and curation

Extensive discourse surrounds the ethics of human skeletal research and curation, but there has yet to be a similar discussion of the treatment of great ape skeletal remains, despite the clear interest in their ethical treatment when alive. Here we trace the history of apes who were killed and collected for natural history museums during the early 20th century and showcase how the guiding research questions of the colonial era continue to influence scholarship. We discuss best practices for improving industry and academic standards of research on, and the curation of, ape remains. The suggested interventions involve restoring individual identity and narrative to great apes while engaging with contextual reflexivity and decolonial theory. The resulting recommendations include contextualizing the individual, piecing individuals back together, challenging/questioning the captive-wild dichotomy, and collaborative international conversations. Our objective is to encourage a conversation regarding ethical and theoretical considerations in great ape skeletal remains research.

Lithocarpustapanuliensis (Fagaceae), a new stone oak from northern Sumatra and its role as an important resource for critically endangered orangutans

A new species of stone oak, Lithocarpustapanuliensis Harapan, W.H.Tan, Nurainas & Strijk from South Tapanuli, North Sumatra, Indonesia is described. We provide colour photographs, a distribution map and a new IUCN conservation status assessment for inclusion on the global Red List. The unique cupule morphology, particularly the shape, placement and distinctness of the cupule protuberances, are distinctive from other Lithocarpus species in the region. Ecological interactions (e.g. consumption and nesting) with Tapanuli orangutans were recorded in the field.

Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution

Our ancestors acquired morphological, cognitive and metabolic modifications that enabled humans to colonize diverse habitats, develop extraordinary technologies and reshape the biosphere. Understanding the genetic, developmental and molecular bases for these changes will provide insights into how we became human. Connecting human-specific genetic changes to species differences has been challenging owing to an abundance of low-effect size genetic changes, limited descriptions of phenotypic differences across development at the level of cell types and lack of experimental models. Emerging approaches for single-cell sequencing, genetic manipulation and stem cell culture now support descriptive and functional studies in defined cell types with a human or ape genetic background. In this Review, we describe how the sequencing of genomes from modern and archaic hominins, great apes and other primates is revealing human-specific genetic changes and how new molecular and cellular approaches - including cell atlases and organoids - are enabling exploration of the candidate causal factors that underlie human-specific traits.

Phylogenomic analyses provide insights into primate evolution

Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.

Middle Pleistocene Pongo from Ganxian Cave in southern China with implications for understanding dental size evolution in orangutans

The Pongo fossil record of China extends from the Early Pleistocene to the Late Pleistocene, but to date, no late Middle Pleistocene samples of Pongo with precise absolute dating have been identified in southern China. Here, we report the recovery of 106 fossil teeth of Pongo from Ganxian Cave in the Bubing Basin, Guangxi, southern China. We dated the speleothems using Uranium-series and dated the two rhinoceros teeth using coupled electron spin resonance/Uranium-series dating methods to between 168.9 ± 2.4 ka and 362 ± 78 ka, respectively. These dates are consistent with the biostratigraphic and magnetostratigraphic age estimates. We further describe the fossil teeth from Ganxian Cave and compare them metrically to samples of fossil Pongo (i.e., Pongo weidenreichi, Pongo duboisi, Pongo palaeosumatrensis, Pongo javensis, and Pongo sp.) from the Early, Middle, and Late Pleistocene and to extant Pongo (i.e., Pongo pygmaeus and Pongo abelii) from Southeast Asia. Based on overall dental size, a high frequency of lingual cingulum remnants on the upper molars, and a low frequency of moderate to heavy wrinkling on the molars, we attribute the Ganxian fossils to P. weidenreichi. Compared with Pongo fossils from other mainland Southeast Asia sites, those from Ganxian confirm that dental size reduction of Pongo occurred principally during the Early and Middle Pleistocene. From the Middle to Late Pleistocene, all teeth except the P³ show little change in occlusal area, indicating that the size of these teeth remained relatively stable over time. The evolutionary trajectory of the Pongo dentition through time may be more complex than previously thought. More orangutan fossils with precise dating constraints are the keys to solving this issue.

Genomics reveals broad hybridization in deeply divergent Palearctic grass and water snakes (Natrix spp.)

Understanding speciation is one of the cornerstones of biological diversity research. Currently, speciation is often understood as a continuous process of divergence that continues until genetic or other incompatibilities minimize or prevent interbreeding. The Palearctic snake genus Natrix is an ideal group to study speciation, as it comprises taxa representing distinct stages of the speciation process, ranging from widely interbreeding parapatric taxa through parapatric species with very limited gene flow in narrow hybrid zones to widely sympatric species. To understand the evolution of reproductive isolation through time, we have sequenced the genomes of all five species within this genus and two additional subspecies. We used both long-read and short-read methods to sequence and de-novo-assemble two high-quality genomes (Natrix h. helvetica, Natrix n. natrix) to their 1.7 Gb length with a contig N50 of 4.6 Mbp and 1.5 Mbp, respectively, and used these as references to assemble the remaining short-read-based genomes. Our phylogenomic analyses yielded a well-supported dated phylogeny and evidence for a surprisingly complex history of interspecific gene flow, including between widely sympatric species. Furthermore, evidence for gene flow was also found for currently allopatric species pairs. Genetic exchange among these well-defined, distinct, and several million-year-old reptile species emphasizes that speciation and maintenance of species distinctness can occur despite continued genetic exchange.

Single-inlet univentricular heart with persistent truncus arteriosus in a Sumatran orangutan (Pongo abelii)

Univentricular heart malformations are rarely described in the veterinary literature. This case report describes a single-inlet univentricular heart with persistent truncus arteriosus as a cause of death of a captive-bred, 2-day-old, female Sumatran orangutan (Pongo abelii), a critically endangered species.

DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs

DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.

Molecular phylogeny reveals distinct evolutionary lineages of the banded krait, Bungarus fasciatus (Squamata, Elapidae) in Asia

The banded krait, Bungarus fasciatus is a widespread elapid snake, likely to comprise several distinct species in different geographic regions of Asia. Therefore, based on molecular phylogenetics and comparative morphology data, we present an overview of the systematic composition of the species to delimit potential biogeographic boundaries. Our phylogenetic analyses, based on four mitochondrial genes, reveal the existence of at least three evolutionary lineages within B. fasciatus, corresponding to Indo-Myanmar, Sundaic and eastern Asian lineages. We are convinced that there are at least three taxonomic entities within the nomen B. fasciatus and restrict the distribution of B. fasciatus sensu stricto to the Indo-Myanmar region. We also provide additional natural history data of the taxon from eastern India. Finally, we advocate further studies to establish the degree of reproductive isolation among these diverging evolutionary lineages and to reassess the systematic status of this species complex especially the Sundaic and eastern Asian lineages.

Taxonomic review of Saguinus mystax (Spix, 1823) (Primates, Callitrichidae), and description of a new species

Although the Amazon has the greatest diversity of primates, there are still taxonomic uncertainties for many taxa, such as the species of the Saguinus mystax group. The most geographically broadly distributed and phenotypically diverse species in this group is S. mystax, and its phenotypic diversity has been recognized as three subspecies-S. mystax mystax, S. mystax pileatus and S. mystax pluto-with non-overlapping geographic distributions. In this sense, we carried out an extensive field survey in their distribution areas and used a framework of taxonomic hypothesis testing of genomic data combined with an integrative taxonomic decision-making framework to carry out a taxonomic revision of S. mystax. Our tests supported the existence of three lineages/species. The first species corresponds to Saguinus mystax mystax from the left bank of the Juruá River, which was raised to the species level, and we also discovered and described animals from the Juruá-Tefé interfluve previously attributed to S. mystax mystax as a new species. The subspecies S. m. pileatus and S. m. pluto are recognized as a single species, under a new nomenclatural combination. However, given their phenotypic distinction and allopatric distribution, they potentially are a manifestation of an early stage of speciation, and therefore we maintain their subspecific designations.

Current advances in primate genomics: novel approaches for understanding evolution and disease

Primate genomics holds the key to understanding fundamental aspects of human evolution and disease. However, genetic diversity and functional genomics data sets are currently available for only a few of the more than 500 extant primate species. Concerted efforts are under way to characterize primate genomes, genetic polymorphism and divergence, and functional landscapes across the primate phylogeny. The resulting data sets will enable the connection of genotypes to phenotypes and provide new insight into aspects of the genetics of primate traits, including human diseases. In this Review, we describe the existing genome assemblies as well as genetic variation and functional genomic data sets. We highlight some of the challenges with sample acquisition. Finally, we explore how technological advances in single-cell functional genomics and induced pluripotent stem cell-derived organoids will facilitate our understanding of the molecular foundations of primate biology.

Mitogenomic analysis of Rüppell's fox (Vulpes rueppellii) confirms phylogenetic placement within the Palaearctic clade shared with its sister species, the red fox (Vulpes vulpes)

The Rüppell's fox (Vulpes rueppellii) inhabits desert regions across North Africa, the Arabian Peninsula and southwestern Asia. Its phylogenetic relationship with other fox species, especially within the phylogeographic context of its sister species, V. vulpes, remain unclear. We here report the sequencing and de-novo assembly of the first annotated mitogenome of V. rueppellii, analysed with data from other foxes (tribe Vulpini, subfamily Caninae). We used four bioinformatic approaches to reconstruct the V. rueppellii mitogenome, obtaining identical sequences except for the incompletely assembled tandem-repeat region within the D-loop. The mitogenome displayed an identical organization, number and length of genes as V. vulpes. We found high support for clustering of both known subclades of V. rueppellii within the Palearctic clade of V. vulpes, rendering the latter species paraphyletic, consistent with previous analyses of shorter mtDNA fragments. More work is needed for a full understanding of the evolutionary drivers and consequences of hybridization in foxes.

GADMA2: more efficient and flexible demographic inference from genetic data

BACKGROUND

Inference of complex demographic histories is a source of information about events that happened in the past of studied populations. Existing methods for demographic inference typically require input from the researcher in the form of a parameterized model. With an increased variety of methods and tools, each with its own interface, the model specification becomes tedious and error-prone. Moreover, optimization algorithms used to find model parameters sometimes turn out to be inefficient, for instance, by being not properly tuned or highly dependent on a user-provided initialization. The open-source software GADMA addresses these problems, providing automatic demographic inference. It proposes a common interface for several likelihood engines and provides global parameters optimization based on a genetic algorithm.

RESULTS

Here, we introduce the new GADMA2 software and provide a detailed description of the added and expanded features. It has a renovated core code base, new likelihood engines, an updated optimization algorithm, and a flexible setup for automatic model construction. We provide a full overview of GADMA2 enhancements, compare the performance of supported likelihood engines on simulated data, and demonstrate an example of GADMA2 usage on 2 empirical datasets.

CONCLUSIONS

We demonstrate the better performance of a genetic algorithm in GADMA2 by comparing it to the initial version and other existing optimization approaches. Our experiments on simulated data indicate that GADMA2's likelihood engines are able to provide accurate estimations of demographic parameters even for misspecified models. We improve model parameters for 2 empirical datasets of inbred species.

Ape femoral-humeral rigidities and arboreal locomotion

OBJECTIVES

This study investigates patterns of bone functional adaptations in extant apes through comparing hindlimb to forelimb bone rigidity ratios in groups with varying levels of arboreality.

MATERIALS AND METHODS

Using CT scans, bone rigidity (J) was calculated at three regions of interest (ROI) along femoral and humeral diaphyses in Homo, Pongo, Pan, and Gorilla with further comparisons made between species and subspecies divisions within Pan and Gorilla.

RESULTS

Consistent with previous work on extant hominoids, species exhibited differences in midshaft femoral to humeral (F/H) rigidity ratios. Results of the present study confirm that these midshaft differences extend to 35% and 65% diaphyseal ROIs. Modern humans, exhibiting larger ratios, and orangutans, exhibiting smaller ratios, bracketed the intermediate African apes in comparisons. Within some African apes, limb rigidity ratios varied significantly between taxonomic groups. Eastern gorillas exhibited the highest mean ratios and chimpanzees the lowest at all three ROIs. In posthoc comparisons, chimpanzees and bonobos did not differ in relative limb rigidity ratios at any of the three ROIs. However, western gorillas were more similar to bonobos than eastern gorillas at 50% and 35% ROIs, but not at the 65% ROI.

CONCLUSION

Species, and to a lesser extent subspecies, can be distinguished by F/H limb rigidity ratios according to broad positional behavior patterns at multiple regions of interest along the diaphyses. Similarity of bonobos and western gorillas is in line with behavioral data of bonobos being the most terrestrial of Pan species, and western gorillas the most arboreal of the Gorilla groups.

Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes

BACKGROUND

The pseudoautosomal region 1 (PAR1) is a 2.7 Mb telomeric region of human sex chromosomes. PAR1 has a crucial role in ensuring proper segregation of sex chromosomes during male meiosis, exposing it to extreme recombination and mutation processes. We investigate PAR1 evolution using population genomic datasets of extant humans, eight populations of great apes, and two archaic human genome sequences.

RESULTS

We find that PAR1 is fast evolving and closer to evolutionary nucleotide equilibrium than autosomal telomeres. We detect a difference between substitution patterns and extant diversity in PAR1, mainly driven by the conflict between strong mutation and recombination-associated fixation bias at CpG sites. We detect excess C-to-G mutations in PAR1 of all great apes, specific to the mutagenic effect of male recombination. Despite recent evidence for Y chromosome introgression from humans into Neanderthals, we find that the Neanderthal PAR1 retained similarity to the Denisovan sequence. We find differences between substitution spectra of these archaics suggesting rapid evolution of PAR1 in recent hominin history. Frequency analysis of alleles segregating in females and males provided no evidence for recent sexual antagonism in this region. We study repeat content and double-strand break hotspot regions in PAR1 and find that they may play roles in ensuring the obligate X-Y recombination event during male meiosis.

CONCLUSIONS

Our study provides an unprecedented quantification of population genetic forces governing PAR1 biology across extant and extinct hominids. PAR1 evolutionary dynamics are predominantly governed by recombination processes with a strong impact on mutation patterns across all species.

Evidence for the latest fossil Pongo in southern China

Pongo fossils with precise absolute age brackets are rare, limiting our understanding of their taxonomy and spatiotemporal distribution in southern China during the Late Pleistocene. Twenty-four isolated teeth of fossil orangutans were recently discovered during excavations at Yicun Cave in Guangxi Zhuang Autonomous Region, southern China. Here, we dated the fossil-bearing layer using Uranium-series dating of the associated flowstone and soda straw stalactites. Our results date the Yicun orangutan fossils to between 66 ± 0.32 ka and 57 ± 0.26 ka; thus, these fossils currently represent the last appearance datum of Pongo in southern China. We further conducted a detailed morphological comparison of the Yicun fossil teeth with large samples of fossil (n = 2454) and extant (n = 441) orangutans from mainland and island Southeast Asia to determine their taxonomic position. Compared to other fossil and extant orangutan samples, the Yicun Pongo assemblage has larger teeth and displays greater variation in occlusal structure. Based on the high frequency of cingular remnants and light to moderate enamel wrinkling of the molars, we assigned the Yicun fossils to Pongo weidenreichi, a species that was widespread in southern China throughout the Pleistocene. Lastly, we used published stable carbon isotope data of Early to Late Pleistocene mammalian fossil teeth from mainland Southeast Asia to reconstruct changes in the paleoenvironment and to interpret dental size variation of Pongo assemblages in a broader temporal and environmental context. The carbon isotope data show that dental size reduction in Pongo is associated with environmental changes. These morphological changes in Pongo appear to coincide with the expansion of savannah biomes and the contraction of forest habitats from the Middle Pleistocene onward. The variation in dental size of forest-dwelling Pongo in mainland Southeast Asia may have resulted from habitat differentiation during the Pleistocene.

Nine out of ten samples were mistakenly switched by The Orang-utan Genome Consortium

The Sumatran orang-utan (Pongo abelii) reference genome was first published in 2011, in conjunction with ten re-sequenced genomes from unrelated wild-caught individuals. Together, these published data have been utilized in almost all great ape genomic studies, plus in much broader comparative genomic research. Here, we report that the original sequencing Consortium inadvertently switched nine of the ten samples and/or resulting re-sequenced genomes, erroneously attributing eight of these to the wrong source individuals. Among them is a genome from the recently identified Tapanuli (P. tapanuliensis) species: thus, this genome was sequenced and published a full six years prior to the species’ description. Sex was wrongly assigned to five known individuals; the numbers in one sample identifier were swapped; and the identifier for another sample most closely resembles that of a sample from another individual entirely. These errors have been reproduced in countless subsequent manuscripts, with noted implications for studies reliant on data from known individuals.

Human-Borne Pathogens: Are They Threatening Wild Great Ape Populations?

Climate change and anthropic activities are the two main factors explaining wild great ape habitat reduction and population decline. The extent to which human-borne infectious diseases are contributing to this trend is still poorly understood. This is due to insufficient or fragmented knowledge on the abundance and distribution of current wild great ape populations, the difficulty obtaining optimal biological samples for diagnostic testing, and the scarcity of pathogen typing data of sufficient quality. This review summarises current information on the most clinically relevant pathogens of viral, bacterial, parasitic, and fungal nature for which transmission from humans to wild great apes is suspected. After appraising the robustness of available epidemiological and/or molecular typing evidence, we attempt to categorise each pathogen according to its likelihood of truly being of human origin. We further discuss those agents for which anthroponotic transmission is more likely. These include two viral (Human Metapneumovirus and Respiratory Syncytial Virus), one bacterial (diarrhoeagenic Escherichia coli), and two parasitic (Cryptosporidium spp. and Giardia duodenalis) pathogens. Finally, we identify the main drawbacks impairing research on anthroponotic pathogen transmission in wild great apes and propose research lines that may contribute to bridging current knowledge gaps.

Genomics of Serrasalmidae teleosts through the lens of microbiome fingerprinting

Associations between host genotype and host-associated microbiomes have been shown in a variety of animal clades, but studies on teleosts mostly show weak associations. Our study aimed to explore these relationships in four sympatric Serrasalmidae (i.e. piranha) teleosts from an Amazonian lake, using datasets from the hosts genomes (SNPs from GBS), skin and gut microbiomes (16S rRNA gene metataxonomics), and diets (COI metabarcoding) from the same fish individuals. Firstly, we investigated whether there were significant covariations of microbiome and fish genotypes at the inter and intraspecific levels. We also assessed the extent of co-variation between Serrasalmidae diet and microbiome, to isolate genotypic from dietary effects on community structure. We observed a significant covariation of skin microbiomes and host genotypes at interspecific (R² =24.4%) and intraspecific (R² =6.2%) levels, whereas gut microbiomes correlated poorly with host genotypes. Serrasalmidae diet composition was significantly correlated to fish genotype only at the interspecific level (R² =5.4%), but did not covary with gut microbiome composition (mantel R=-0.04). Secondly, we investigated whether the study of interspecific differentiation could benefit from considering host associated microbial communities in addition to host genotypes. By using a NMDS ordination-based approach, we observed that ordinations from skin and gut species-specific bacterial biomarkers identified through a random forest algorithm, could significantly increase the average interspecific differentiation detected through host genotype data alone. Although future studies encompassing additional species and environments are needed, our results suggest Serrasalmidae microbiomes could constitute an insightful trait to be considered when studying the interspecific differences between members of this clade.

Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)

Informed management and conservation efforts are vital to sustainable recreational fishing and biodiversity conservation. Because the taxonomic rank of species is important in conservation and management strategies, success of these efforts depends on accurate species delimitation. The Black Basses (Micropterus) are an iconic lineage of freshwater fishes that include some of the world’s most popular species for recreational fishing and world's most invasive species. Despite their popularity, previous studies to delimit species and lineages in Micropterus suffer from insufficient geographic coverage and uninformative molecular markers. Our phylogenomic analyses of ddRAD data result in the delimitation of 19 species of Micropterus, which includes 14 described species, the undescribed but well-known Altamaha, Bartram’s, and Choctaw basses, and two additional undescribed species currently classified as Smallmouth Bass (M. dolomieu). We provide a revised delimitation of species in the Largemouth Bass complex that necessitates a change in scientific nomenclature: Micropterus salmoides is retained for the Florida Bass and Micropterus nigricans is elevated from synonymy for the Largemouth Bass. The new understanding of diversity, distribution, and systematics of Black Basses will serve as important basis for the management and conservation of this charismatic and economically important clade of fishes.

Population dynamics and genetic connectivity in recent chimpanzee history

Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees.

Morphological variation of the maxilla in modern humans and African apes

Differences in morphology among modern humans and African apes are frequently used when assessing whether hominin fossils should be attributed to a single species or represent evidence for taxic diversity. A good understanding of the degree and structure of the intergeneric, interspecific, and intraspecific variation, including aspects such as sexual dimorphism and age, are key in this context. Here we explore the variation and differences shown by the maxilla of extant hominines, as maxillary morphology is central in the diagnosis of several hominin taxa. Our sample includes adults of all currently recognized hominine species and subspecies, with a balanced species sex ratio. In addition, we compared the adults with a small sample of late juveniles. The morphology of the maxillae was captured using three-dimensional landmarks, and the size and shape were analyzed using geometric morphometric methods. Key observations are that 1) the maxillae of all extant hominine species and subspecies show statistically significant differences, but complete separation in shape is only seen at the genus level; 2) the degree of variation is not consistent between genera, with subspecies of Gorilla being more different from each other than are species of Pan; 3) the pattern of sexual shape dimorphism is different in Pan, Gorilla, and Homo, often showing opposite trends; and 4) differentiation between maxillary shapes is increased after adjustment for static intraspecific allometry. These results provide a taxonomically up-to-date comparative morphological framework to help interpret the hominin fossil record, and we discuss the practical implications in that context.

Sociality predicts orangutan vocal phenotype

In humans, individuals' social setting determines which and how language is acquired. Social seclusion experiments show that sociality also guides vocal development in songbirds and marmoset monkeys, but absence of similar great ape data has been interpreted as support to saltational notions for language origin, even if such laboratorial protocols are unethical with great apes. Here we characterize the repertoire entropy of orangutan individuals and show that in the wild, different degrees of sociality across populations are associated with different 'vocal personalities' in the form of distinct regimes of alarm call variants. In high-density populations, individuals are vocally more original and acoustically unpredictable but new call variants are short lived, whereas individuals in low-density populations are more conformative and acoustically consistent but also exhibit more complex call repertoires. Findings provide non-invasive evidence that sociality predicts vocal phenotype in a wild great ape. They prove false hypotheses that discredit great apes as having hardwired vocal development programmes and non-plastic vocal behaviour. Social settings mould vocal output in hominids besides humans.

Introgression and mating patterns between white-handed gibbons (Hylobates lar) and pileated gibbons (Hylobates pileatus) in a natural hybrid zone

Gibbons (Family Hylobatidae) are a suitable model for exploring hybridization in pair-living primates as several species form hybrid zones. In Khao Yai National Park, Thailand, white-handed gibbons (Hylobates lar) and pileated gibbons (Hylobates pileatus) are distributed parapatrically and hybridize in a narrow zone. Their phenotypic characteristics suggest limited inter-species gene flow, although this has never been assessed. To uncover the history and degree of gene flow between the two species, we studied the genetic structure of gibbons in the hybrid zone by analyzing fecal DNA samples, phenotypic characteristics, vocalizations and individuals’ social status. We determined eight autosomal single nucleotide variant (SNV) loci, and mitochondrial DNA (mtDNA) and Y-chromosomal haplotypes of 72 gibbons. We compared these markers with reference types of wild pureblood white-handed gibbons (n = 12) in Kaeng Krachan National Park and pureblood pileated gibbons (n = 4) in Khao Soi Dao Wildlife Sanctuary. Autosomal genotypic analyses confirmed the various levels of mixed ancestry for several adult gibbons with or without atypical phenotypic traits in Khao Yai National Park. In some other adult gibbons, the mixed ancestry was not detected in either autosomal SNVs or their phenotypic traits but the mtDNA. Both male and female adult hybrids formed reproductive units mainly with a phenotypic pureblood partner and many of them produced offspring. Taken together, our results suggest that once hybridization occurs, white-handed-pileated-gibbon hybrids can reproduce with either parental species and that the backcrossing and thus introgression may occur in successive generations, with no drastic changes in phenotypic appearance.

First fossil-leaf floras from Brunei Darussalam show dipterocarp dominance in Borneo by the Pliocene

The Malay Archipelago is one of the most biodiverse regions on Earth, but it suffers high extinction risks due to severe anthropogenic pressures. Paleobotanical knowledge provides baselines for the conservation of living analogs and improved understanding of vegetation, biogeography, and paleoenvironments through time. The Malesian bioregion is well studied palynologically, but there have been very few investigations of Cenozoic paleobotany (plant macrofossils) in a century or more. We report the first paleobotanical survey of Brunei Darussalam, a sultanate on the north coast of Borneo that still preserves the majority of its extraordinarily diverse, old-growth tropical rainforests. We discovered abundant compression floras dominated by angiosperm leaves at two sites of probable Pliocene age: Berakas Beach, in the Liang Formation, and Kampong Lugu, in an undescribed stratigraphic unit. Both sites also yielded rich palynofloral assemblages from the macrofossil-bearing beds, indicating lowland fern-dominated swamp (Berakas Beach) and mangrove swamp (Kampong Lugu) depositional environments. Fern spores from at least nine families dominate both palynological assemblages, along with abundant fungal and freshwater algal remains, rare marine microplankton, at least four mangrove genera, and a diverse rainforest tree and liana contribution (at least 19 families) with scarce pollen of Dipterocarpaceae, today's dominant regional life form. Compressed leaves and rare reproductive material represent influx to the depocenters from the adjacent coastal rainforests. Although only about 40% of specimens preserve informative details, we can distinguish 23 leaf and two reproductive morphotypes among the two sites. Dipterocarps are by far the most abundant group in both compression assemblages, providing rare, localized evidence for dipterocarp-dominated lowland rainforests in the Malay Archipelago before the Pleistocene. The dipterocarp fossils include winged Shorea fruits, at least two species of plicate Dipterocarpus leaves, and very common Dryobalanops leaves. We attribute additional leaf taxa to Rhamnaceae (Ziziphus), Melastomataceae, and Araceae (Rhaphidophora), all rare or new fossil records for the region. The dipterocarp leaf dominance contrasts sharply with the family's <1% representation in the palynofloras from the same strata. This result directly demonstrates that dipterocarp pollen is prone to strong taphonomic filtering and underscores the importance of macrofossils for quantifying the timing of the dipterocarps' rise to dominance in the region. Our work shows that complex coastal rainforests dominated by dipterocarps, adjacent to swamps and mangroves and otherwise similar to modern ecosystems, have existed in Borneo for at least 4-5 million years. Our findings add historical impetus for the conservation of these gravely imperiled and extremely biodiverse ecosystems.

Benefits and limitations of a new genome-based PCR-RFLP genotyping assay (GB-RFLP): A SNP-based detection method for identification of species in extremely young adaptive radiations

High-throughput DNA sequencing technologies make it possible now to sequence entire genomes relatively easily. Complete genomic information obtained by whole-genome resequencing (WGS) can aid in identifying and delineating species even if they are extremely young, cryptic, or morphologically difficult to discern and closely related. Yet, for taxonomic or conservation biology purposes, WGS can remain cost-prohibitive, too time-consuming, and often constitute a "data overkill." Rapid and reliable identification of species (and populations) that is also cost-effective is made possible by species-specific markers that can be discovered by WGS. Based on WGS data, we designed a PCR restriction fragment length polymorphism (PCR-RFLP) assay for 19 Neotropical Midas cichlid populations (Amphilophus cf. citrinellus), that includes all 13 described species of this species complex. Our work illustrates that identification of species and populations (i.e., fish from different lakes) can be greatly improved by designing genetic markers using available "high resolution" genomic information. Yet, our work also shows that even in the best-case scenario, when whole-genome resequencing information is available, unequivocal assignments remain challenging when species or populations diverged very recently, or gene flow persists. In summary, we provide a comprehensive workflow on how to design RFPL markers based on genome resequencing data, how to test and evaluate their reliability, and discuss the benefits and pitfalls of our approach.

Comparative morphology and physiology of the vocal production apparatus and the brain in the extant primates

Objective data mainly from the comparative anatomy of various organs related to human speech and language is considered to unearth clues about the mechanisms behind language development. The two organs of the larynx and hyoid bone are considered to have evolved towards suitable positions and forms in preparation for the occurrence of the large repertoire of vocalization necessary for human speech. However, some researchers have asserted that there is no significant difference of these organs between humans and non-human primates. Speech production is dependent on the voluntary control of the respiratory, laryngeal, and vocal tract musculature. Such control is fully present in humans but only partially so in non-human primates, which appear to be able to voluntarily control only supralaryngeal articulators. Both humans and non-human primates have direct cortical innervation of motor neurons controlling the supralaryngeal vocal tract but only human appear to have direct cortical innervation of motor neurons controlling the larynx. In this review, we investigate the comparative morphology and function of the wide range of components involved in vocal production, including the larynx, the hyoid bone, the tongue, and the vocal brain. We would like to emphasize the importance of the tongue in the primary development of human speech and language. It is now time to reconsider the possibility of the tongue playing a definitive role in the emergence of human speech.

Island Biogeography Revisited: Museomics Reveals Affinities of Shelf Island Birds Determined by Bathymetry and Paleo-Rivers, Not by Distance to Mainland

Island biogeography is one of the most powerful subdisciplines of ecology: its mathematical predictions that island size and distance to mainland determine diversity have withstood the test of time. A key question is whether these predictions follow at a population-genomic level. Using rigorous ancient-DNA protocols, we retrieved approximately 1,000 genomic markers from approximately 100 historic specimens of two Southeast Asian songbird complexes from across the Sunda Shelf archipelago collected 1893-1957. We show that the genetic affinities of populations on small shelf islands defy the predictions of geographic distance and appear governed by Earth-historic factors including the position of terrestrial barriers (paleo-rivers) and persistence of corridors (Quaternary land bridges). Our analyses suggest that classic island-biogeographic predictors may not hold well for population-genomic dynamics on the thousands of shelf islands across the globe, which are exposed to dynamic changes in land distribution during Quaternary climate change.

King or royal family? Testing for species boundaries in the King Cobra, Ophiophagus hannah (Cantor, 1836), using morphology and multilocus DNA analyses

In widespread species, the diverse ecological conditions in which the populations occur, and the presence of many potential geographical barriers through their range are expected to have created ample opportunities for the evolution of distinct, often cryptic lineages. In this work, we tested for species boundaries in one such widespread species, the king cobra, Ophiophagus hannah (Cantor, 1836), a largely tropical elapid snake distributed across the Oriental realm. Based on extensive geographical sampling across most of the range of the species, we initially tested for candidate species (CS) using Maximum-Likelihood analysis of mitochondrial genes. We then tested the resulting CS using both morphological data and sequences of three single-copy nuclear genes. We used snapclust to determine the optimal number of clusters in the nuclear dataset, and Bayesian Phylogenetics and Phylogeography (BPP) to test for likely species status. We used non-metric multidimensional scaling (nMDS) analysis for discerning morphological separation. We recovered four independently evolving, geographically separated lineages that we consider Confirmed Candidate Species: (1) Western Ghats lineage; (2) Indo-Chinese lineage (3) Indo-Malayan lineage; (4) Luzon Island lineage, in the Philippine Archipelago. We discuss patterns of lineage divergence, particularly in the context of low morphological divergence, and the conservation implications of recognizing several endemic king cobra lineages.

Current Progress in Evolutionary Comparative Genomics of Great Apes

The availability of high-quality genome sequences of great ape species provides unprecedented opportunities for genomic analyses. Herein, we reviewed the recent progress in evolutionary comparative genomic studies of the existing great ape species, including human, chimpanzee, bonobo, gorilla, and orangutan. We elaborate discovery on evolutionary history, natural selection, structural variations, and new genes of these species, which is informative for understanding the origin of human-specific phenotypes.

Gene Flow in Volant Vertebrates: Species Biology, Ecology and Climate Change

Gene flow, the exchange of genetic material between populations is an important biological process, which shapes and maintains biodiversity. The successful movement of individuals between populations depends on multiple factors determined by species biology and the environment. One of the most important factors regulating gene flow is the ability to move, and flight allows individuals to easily move across geographical barriers. Volant vertebrates are found on some of the remotest islands and contribute significantly to the biodiversity and ecosystem. The availability of next-generation sequencing data for non-model animals has substantially improved our understanding of gene flow and its consequences, allowing us to look at fine-scale patterns. However, most of our understanding regarding gene flow comes from the temperate regions and the Neotropics. The lack of studies from species-rich Asia is striking. In this review, we outline the importance of gene flow and the factors affecting gene flow, especially for volant vertebrates. We especially discuss research studies from tropical biomes of South and Southeast Asia, highlight the lacuna in literature and provide an outline for future studies in this species-rich region.

Population dynamics of GC-changing mutations in humans and great apes

The nucleotide composition of the genome is a balance between origin and fixation rates of different mutations. For example, it is well-known that transitions occur more frequently than transversions, particularly at CpG sites. Differences in fixation rates of mutation types are less explored. Specifically, recombination-associated GC-biased gene conversion (gBGC) may differentially impact GC-changing mutations, due to differences in their genomic distributions and efficiency of mismatch repair mechanisms. Given that recombination evolves rapidly across species, we explore gBGC of different mutation types across human populations and great ape species. We report a stronger correlation between segregating GC frequency and recombination for transitions than for transversions. Notably, CpG transitions are most strongly affected by gBGC in humans and chimpanzees. We show that the overall strength of gBGC is generally correlated with effective population sizes in humans, with some notable exceptions, such as a stronger effect of gBGC on non-CpG transitions in populations of European descent. Furthermore, species of the Gorilla and Pongo genus have a greatly reduced gBGC effect on CpG sites. We also study the dependence of gBGC dynamics on flanking nucleotides and show that some mutation types evolve in opposition to the gBGC expectation, likely due to hypermutability of specific nucleotide contexts. Our results highlight the importance of different gBGC dynamics experienced by GC-changing mutations and their impact on nucleotide composition evolution.