Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent

Exact calculation of the expected SFS in structured populations

The Site Frequency Spectrum (SFS), summary statistic of the distribution of derived allele frequencies in a sample of DNA sequences, provides information about genetic variation and can be used to make population inferences. The exact calculation of the expected SFS in a panmictic population under the infinite-site model of mutation has been known in the Markovian coalescent theory for decades, but its generalization to the structured coalescent is hampered by the almost exponential growth of the states space. We show here how to obtain this expected SFS as the solution of a linear system. More precisely, we propose a complete algorithmic procedure, from how to build a suitable state space and sort it, to how to take advantage of the sparsity of the rate matrix and to solve numerically the linear system using an iterative method. We then build a specialization for the simplest case of the symmetrical n-island model to arrive at a ready-to-use software called SISiFS from which a demographic parameters inference framework could easily be developed.

Low Genetic Diversity and Complex Population Structure in Black Piranha (Serrasalmus rhombeus), a Key Amazonian Predator

The black piranha (Serrasalmus rhombeus), a widely spread species in the rivers of the Amazon basin, plays a vital role as both key predator and important prey. Despite its essential contribution to ecosystem stability, there is a lack of information regarding its genetic diversity and population dynamics in the central Amazon region. As the Amazon continues to undergo environmental changes in the context of growing anthropogenic threats, such knowledge is fundamental for assist in the conservation of this species. This study is the first to analyze the genetic diversity and population structure of S. rhombeus in the central Amazon region using high-resolution genomic data. We employed a Genotyping-by-Sequencing approach with 248 samples across 14 study sites from various tributaries, encompassing diverse water types (black, white, and clear water) and characterized by 34 physiochemical parameters. The data reveals low diversity accompanied by pronounced signs of inbreeding in half of the sites and robust genetic differentiation and variation among sites and within-sites. Surprisingly, we also found evidence of higher dispersal capacity than previously recognized. Our analysis exposed a complex and high population structure with genetic groups exclusive to some sites. Gene flow was low and some groups presented ambiguous genealogical divergence index (gdi) signals, suggesting the occurrence of potential cryptic species. Moreover, our results suggest that the population structure of black piranha appears more influenced by historical events than contemporary factors. These results underscore the need to give greater attention to this keystone species, for which no regulatory framework or conservation strategies is presently in effect.

Integrative taxonomy clarifies the evolution of a cryptic primate clade

Global biodiversity is under accelerating threats, and species are succumbing to extinction before being described. Madagascar's biota represents an extreme example of this scenario, with the added complication that much of its endemic biodiversity is cryptic. Here we illustrate best practices for clarifying cryptic diversification processes by presenting an integrative framework that leverages multiple lines of evidence and taxon-informed cut-offs for species delimitation, while placing special emphasis on identifying patterns of isolation by distance. We systematically apply this framework to an entire taxonomically controversial primate clade, the mouse lemurs (genus Microcebus, family Cheirogaleidae). We demonstrate that species diversity has been overestimated primarily due to the interpretation of geographic variation as speciation, potentially biasing inference of the underlying processes of evolutionary diversification. Following a revised classification, we find that crypsis within the genus is best explained by a model of morphological stasis imposed by stabilizing selection and a neutral process of niche diversification. Finally, by clarifying species limits and defining evolutionarily significant units, we provide new conservation priorities, bridging fundamental and applied objectives in a generalizable framework.

Secondary contact erodes Pleistocene diversification in a wide-ranging freshwater mussel (Quadrula)

The isolated river drainages of eastern North America serve as a natural laboratory to investigate the roles of allopatry and secondary contact in the evolutionary trajectories of recently diverged lineages. Drainage divides facilitate allopatric speciation, but due to their sensitivity to climatic and geomorphological changes, neighboring rivers frequently coalesce, creating recurrent opportunities of isolation and contact throughout the history of aquatic lineages. The freshwater mussel Quadrula quadrula is widely distributed across isolated rivers of eastern North America and possesses high phenotypic and molecular variation across its range. We integrate sequence data from three genomes, including female- and male-inherited mitochondrial markers and thousands of nuclear encoded SNPs with morphology and geography to illuminate the group's divergence history. Across contemporary isolated rivers, we found continuums of molecular and morphological variation, following a pattern of isolation by distance. In contact zones, hybridization was frequent with no apparent fitness consequences, as advanced hybrids were common. Accordingly, we recognize Q. quadrula as a single cohesive species with subspecific variation (Q. quadrula rumphiana). Demographic modeling and divergence dating supported a divergence history characterized by allopatric vicariance followed by secondary contact, likely driven by river rearrangements and Pleistocene glacial cycles. Despite clinal range-wide variation and hybridization in contact zones, the process-based species delimitation tool delimitR, which considers demographic scenarios like secondary contact, supported the delimitation of the maximum number of species tested. As such, when interpreting species delimitation results, we suggest careful consideration of spatial sampling and subsequent geographic patterns of biological variation, particularly for wide-ranging taxa.

Cryptic divergence in and evolutionary dynamics of endangered hybrid Picea brachytyla sensu stricto in the Qinghai-Tibet Plateau

BACKGROUND

The visual similarities observed across various plant groups often conceal underlying genetic distinctions. This occurrence, known as cryptic diversity, underscores the key importance of identifying and understanding cryptic intraspecific evolutionary lineages in evolutionary ecology and conservation biology.

RESULTS

In this study, we conducted transcriptome analysis of 81 individuals from 18 natural populations of a northern lineage of Picea brachytyla sensu stricto that is endemic to the Qinghai-Tibet Plateau. Our analysis revealed the presence of two distinct local lineages, emerging approximately 444.8 thousand years ago (kya), within this endangered species. The divergence event aligns well with the geographic and climatic oscillations that occurred across the distributional range during the Mid-Pleistocene epoch. Additionally, we identified numerous environmentally correlated gene variants, as well as many other genes showing signals of positive selection across the genome. These factors likely contributed to the persistence and adaptation of the two distinct local lineages.

CONCLUSIONS

Our findings shed light on the highly dynamic evolutionary processes underlying the remarkably similar phenotypes of the two lineages of this endangered species. Importantly, these results enhance our understanding of the evolutionary past for this and for other endangered species with similar histories, and also provide guidance for the development of conservation plans.

Morphological variability or inter-observer bias? A methodological toolkit to improve data quality of multi-researcher datasets for the analysis of morphological variation

OBJECTIVES

The investigation of morphological variation in animals is widely used in taxonomy, ecology, and evolution. Using large datasets for meta-analyses has dramatically increased, raising concerns about dataset compatibilities and biases introduced by contributions of multiple researchers.

MATERIALS AND METHODS

We compiled morphological data on 13 variables for 3073 individual mouse lemurs (Cheirogaleidae, Microcebus spp.) from 25 taxa and 153 different sampling locations, measured by 48 different researchers. We introduced and applied a filtering pipeline and quantified improvements in data quality (Shapiro-Francia statistic, skewness, and excess kurtosis). The filtered dataset was then used to test for genus-wide sexual size dimorphism and the applicability of Rensch's, Allen's, and Bergmann's rules.

RESULTS

Our pipeline reduced inter-observer bias (i.e., increased normality of data distributions). Inter-observer reliability of measurements was notably variable, highlighting the need to reduce data collection biases. Although subtle, we found a consistent pattern of sexual size dimorphism across Microcebus, with females being the larger (but not heavier) sex. Sexual size dimorphism was isometric, providing no support for Rensch's rule. Variations in tail length but not in ear size were consistent with the predictions of Allen's rule. Body mass and length followed a pattern contrary to predictions of Bergmann's rule.

DISCUSSION

We highlighted the usefulness of large multi-researcher datasets for testing ecological hypotheses after correcting for inter-observer biases. Using genus-wide tests, we outlined generalizable patterns of morphological variability across all mouse lemurs. This new methodological toolkit aims to facilitate future large-scale morphological comparisons for a wide range of taxa and applications.

Genomic divergence and introgression between cryptic species of a widespread North American songbird

Analysis of genomic variation among related populations can sometimes reveal distinct species that were previously undescribed due to similar morphological appearances, and close examination of such cases can provide much insight regarding speciation. Genomic data can also reveal the role of reticulate evolution in differentiation and speciation. White-breasted nuthatches (Sitta carolinensis) are widely distributed North American songbirds that are currently classified as a single species but have been suspected to represent a case of cryptic speciation. Previous genetic analyses suggested four divergent groups, but it was unclear whether these represented multiple reproductively isolated species. Using extensive genomic sampling of over 350 white-breasted nuthatches from across North America and a new chromosome-level reference genome, we asked if white-breasted nuthatches are comprised of multiple species and whether introgression has occurred between divergent populations. Genomic variation of over 300,000 loci revealed four highly differentiated populations (Pacific, n = 45; Eastern, n = 23; Rocky Mountains North, n = 138; and Rocky Mountains South, n = 150) with geographic ranges that are adjacent. We observed a moderate degree of admixture between Rocky Mountain populations but only a small number of hybrids between the Rockies and the Eastern population. The rarity of hybrids together with high levels of differentiation between populations is supportive of populations having some level of reproductive isolation. Between populations, we show evidence for introgression from a divergent ghost lineage of white-breasted nuthatches into the Rocky Mountains South population, which is otherwise closely related to Rocky Mountains North. We conclude that white-breasted nuthatches are best considered at least three species and that ghost lineage introgression has contributed to differentiation between the two Rocky Mountain populations. White-breasted nuthatches provide a dramatic case of morphological similarity despite high genomic differentiation, and the varying levels of reproductive isolation among the four groups provide an example of the speciation continuum.

Estimation of species divergence times in presence of cross-species gene flow

Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene flow is ignored in the analysis. Using advances in analytical methods under the multispecies coalescent (MSC) model, we demonstrate that by accounting for incomplete lineage sorting and introgression using large phylogenomic data sets this problem can be avoided. The multispecies-coalescent-with-introgression (MSci) model is capable of accurately estimating both divergence times and ancestral effective population sizes, even when only a single diploid individual per species is sampled. We characterize some general expectations for biases in divergence time estimation under three different scenarios: 1) introgression between sister species, 2) introgression between non-sister species, and 3) introgression from an unsampled (i.e., ghost) outgroup lineage. We also conducted simulations under the isolation-with-migration (IM) model and found that the MSci model assuming episodic gene flow was able to accurately estimate species divergence times despite high levels of continuous gene flow. We estimated divergence times under the MSC and MSci models from two published empirical datasets with previous evidence of introgression, one of 372 target-enrichment loci from baobabs (Adansonia), and another of 1000 transcriptome loci from 14 species of the tomato relative, Jaltomata. The empirical analyses not only confirm our findings from simulations, demonstrating that the MSci model can reliably estimate divergence times but also show that divergence time estimation under the MSC can be robust to the presence of small amounts of introgression in empirical datasets with extensive taxon sampling. [divergence time; gene flow; hybridization; introgression; MSci model; multispecies coalescent].

Diversification processes in Gerp's mouse lemur demonstrate the importance of rivers and altitude as biogeographic barriers in Madagascar's humid rainforests

Madagascar exhibits exceptionally high levels of biodiversity and endemism. Models to explain the diversification and distribution of species in Madagascar stress the importance of historical variability in climate conditions which may have led to the formation of geographic barriers by changing water and habitat availability. The relative importance of these models for the diversification of the various forest-adapted taxa of Madagascar has yet to be understood. Here, we reconstructed the phylogeographic history of Gerp's mouse lemur (Microcebus gerpi) to identify relevant mechanisms and drivers of diversification in Madagascar's humid rainforests. We used restriction site associated DNA (RAD) markers and applied population genomic and coalescent-based techniques to estimate genetic diversity, population structure, gene flow and divergence times among M. gerpi populations and its two sister species M. jollyae and M. marohita. Genomic results were complemented with ecological niche models to better understand the relative barrier function of rivers and altitude. We show that M. gerpi diversified during the late Pleistocene. The inferred ecological niche, patterns of gene flow and genetic differentiation in M. gerpi suggest that the potential for rivers to act as biogeographic barriers depended on both size and elevation of headwaters. Populations on opposite sides of the largest river in the area with headwaters that extend far into the highlands show particularly high genetic differentiation, whereas rivers with lower elevation headwaters have weaker barrier functions, indicated by higher migration rates and admixture. We conclude that M. gerpi likely diversified through repeated cycles of dispersal punctuated by isolation to refugia as a result of paleoclimatic fluctuations during the Pleistocene. We argue that this diversification scenario serves as a model of diversification for other rainforest taxa that are similarly limited by geographic factors. In addition, we highlight conservation implications for this critically endangered species, which faces extreme habitat loss and fragmentation.

Genome-wide data reveal cryptic diversity and hybridization in a group of tree ferns

Discovery of cryptic diversity is essential to understanding both the process of speciation and the conservation of species. Determining species boundaries in fern lineages represents a major challenge due to lack of morphologically diagnostic characters and frequent hybridization. Genomic data has substantially enhanced our understanding of the speciation process, increased the resolution of species delimitation studies, and led to the discovery of cryptic diversity. Here, we employed restriction-site-associated DNA sequencing (RAD-seq) and integrated phylogenomic and population genomic analyses to investigate phylogenetic relationships and evolutionary history of 16 tree ferns with marginate scales (Cyatheaceae) from China and Vietnam. We conducted multiple species delimitation analyses using the multispecies coalescent (MSC) model and novel approaches based on genealogical divergence index (gdi) and isolation by distance (IBD). In addition, we inferred species trees using concatenation and several coalescent-based methods, and assessed hybridization patterns and rate of gene flow across the phylogeny. We obtained highly supported and generally congruent phylogenies inferred from concatenated and summary-coalescent methods, and the monophyly of all currently recognized species were strongly supported. Our results revealed substantial evidence of cryptic diversity in three widely distributed Gymnosphaera species, each of which was composite of two highly structure lineages that may correspond to cryptic species. We found that hybridization was fairly common between not only closely related species, but also distantly related species. Collectively, it appears that scaly tree ferns may contain cryptic diversity and hybridization has played an important role throughout the evolutionary history of this group.

Repeated divergence of amphibians and reptiles across an elevational gradient in northern Madagascar

How environmental factors shape patterns of biotic diversity in tropical ecosystems is an active field of research, but studies examining the possibility of ecological speciation in terrestrial tropical ecosystems are scarce. We use the isolated rainforest herpetofauna on the Montagne d'Ambre (Amber Mountain) massif in northern Madagascar as a model to explore elevational divergence at the level of populations and communities. Based on intensive sampling and DNA barcoding of amphibians and reptiles along a transect ranging from ca. 470-1470 m above sea level (a.s.l.), we assessed a main peak in species richness at an elevation of ca. 1000 m a.s.l. with 41 species. The proportion of local endemics was highest (about 1/3) at elevations >1100 m a.s.l. Two species of chameleons (Brookesia tuberculata, Calumma linotum) and two species of frogs (Mantidactylus bellyi, M. ambony) studied in depth by newly developed microsatellite markers showed genetic divergence up the slope of the mountain, some quite strong, others very weak, but in each case with genetic breaks between 1100 and 1270 m a.s.l. Genetic clusters were found in transect sections significantly differing in bioclimate and herpetological community composition. A decrease in body size was detected in several species with increasing elevation. The studied rainforest amphibians and reptiles show concordant population genetic differentiation across elevation along with morphological and niche differentiation. Whether this parapatric or microallopatric differentiation will suffice for the completion of speciation is, however, unclear, and available phylogeographic evidence rather suggests that a complex interplay between ecological and allopatric divergence processes is involved in generating the extraordinary species diversity of Madagascar's biota. Our study reveals concordant patterns of diversification among main elevational bands, but suggests that these adaptational processes are only part of the complex of processes leading to species formation, among which geographical isolation is probably also important.

Molecular phylogenetics of the sucking louse genus Lemurpediculus (Insecta: Phthiraptera), ectoparasites of lemurs, with descriptions of three new species

Sucking lice live in intimate association with their hosts and often display a high degree of host specificity. The present study investigated sucking lice of the genus Lemurpediculus from six mouse lemur (Microcebus) and two dwarf lemur (Cheirogaleus) species endemic to the island of Madagascar, considered a biodiversity hotspot. Louse phylogenetic trees were created based on cytochrome C oxidase subunit I (COI), elongation factor 1α (EF1α) and internal transcribed spacer 1 (ITS1) sequences. While clustering according to host species was generally observed for COI and ITS1, suggesting high host specificity of the examined lice, EF1α sequences alone did not distinguish between lice of different Microcebus species, possibly due to rather recent divergence. As bootstrap support for basal tree structure was rather low, further data are necessary to resolve the evolutionary history of louse-mouse lemur associations. Three new species of sucking lice are described: Lemurpediculus zimmermanni sp. Nov. From Microcebus ravelobensis, Lemurpediculus gerpi sp.nov. from Microcebus gerpi, and Lemurpediculus tsimanampesotsae sp. nov. from Microcebus griseorufus. These new species are compared with all known congeneric species and identifying features are illustrated for all known species of Lemurpediculus.

Long-term host-pathogen evolution of endogenous beta- and gammaretroviruses in mouse lemurs with little evidence of recent retroviral introgression

Madagascar's flora and fauna have evolved in relative isolation since the island split from the African and Indian continents. When the last common ancestors of lemurs left Africa between 40 and 70 million years ago, they carried a subset of the viral diversity of the mainland population within them, which continued to evolve throughout the lemur radiation. Relative to other primate radiations, we know very little about the past or present viral diversity of lemurs, particularly mouse lemurs. Using high-throughput sequencing, we identified two gammaretroviruses and three betaretroviruses in the genomes of four species of wild mouse lemurs. The two gammaretroviruses and two betaretroviruses have not previously been described. One betaretrovirus was previously identified. All identified viruses are present in both Lorisiformes and Lemuriformes but absent from haplorrhine primates. The estimated ages of these viruses are consistent with the estimated divergence dates of the host lineages, suggesting they colonized the lemur genome after the Haplorrhine-Strepsirrhine split, but before the Lorisiformes-Lemuriformes split and before the colonization of Madagascar. The viral phylogenies connect multiple lineages of retroviruses from non-lemur and non-Madagascar-native species, suggesting substantial cross-species transmission occurred deep in the primate clade prior to its geographic dispersal. These phylogenies provide novel insights into known retroviral clades. They suggest that the origin of gammaretroviruses in rodents or bats may be premature and that the Jaagsiekte sheep virus clade may be older and more broadly distributed among mammals than previously thought.

Genome-wide species delimitation analyses of a silverside fish species complex in central Mexico indicate taxonomic over-splitting

BACKGROUND

Delimiting species across a speciation continuum is a complex task, as the process of species origin is not generally instantaneous. The use of genome-wide data provides unprecedented resolution to address convoluted species delimitation cases, often unraveling cryptic diversity. However, because genome-wide approaches based on the multispecies coalescent model are known to confound population structure with species boundaries, often resulting in taxonomic over-splitting, it has become increasingly evident that species delimitation research must consider multiple lines of evidence. In this study, we used phylogenomic, population genomic, and coalescent-based species delimitation approaches, and examined those in light of morphological and ecological information, to investigate species numbers and boundaries comprising the Chirostoma "humboltianum group" (family Atherinidae). The humboltianum group is a taxonomically controversial species complex where previous morphological and mitochondrial studies produced conflicting species delimitation outcomes. We generated ddRADseq data for 77 individuals representing the nine nominal species in the group, spanning their distribution range in the central Mexican plateau.

RESULTS

Our results conflict with the morphospecies and ecological delimitation hypotheses, identifying four independently evolving lineages organized in three geographically cohesive clades: (i) chapalae and sphyraena groups in Lake Chapala, (ii) estor group in Lakes Pátzcuaro and Zirahuén, and (iii) humboltianum sensu stricto group in Lake Zacapu and Lerma river system.

CONCLUSIONS

Overall, our study provides an atypical example where genome-wide analyses delineate fewer species than previously recognized on the basis of morphology. It also highlights the influence of the geological history of the Chapala-Lerma hydrological system in driving allopatric speciation in the humboltianum group.

RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results

Microsatellites have been a workhorse of evolutionary genetic studies for decades and are still commonly in use for estimating signatures of genetic diversity at the population and species level across a multitude of taxa. Yet, the very high mutation rate of these loci is a double-edged sword, conferring great sensitivity at shallow levels of analysis (e.g. paternity analysis) but yielding considerable uncertainty for deeper evolutionary comparisons. For the present study, we used reduced representation genome-wide data (restriction site-associated DNA sequencing (RADseq)) to test for patterns of interspecific hybridization previously characterized using microsatellite data in a contact zone between two closely related mouse lemur species in Madagascar (Microcebus murinus and Microcebus griseorufus). We revisit this system by examining populations in, near, and far from the contact zone, including many of the same individuals that had previously been identified as hybrids with microsatellite data. Surprisingly, we find no evidence for admixed nuclear ancestry. Instead, re-analyses of microsatellite data and simulations suggest that previously inferred hybrids were false positives and that the program NewHybrids can be particularly sensitive to erroneously inferring hybrid ancestry. Combined with results from coalescent-based analyses and evidence for local syntopic co-occurrence, we conclude that the two mouse lemur species are in fact completely reproductively isolated, thus providing a new understanding of the evolutionary rate whereby reproductive isolation can be achieved in a primate.

Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests

Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The historical perspective was that Madagascar's grasslands had anthropogenic origins, but emerging evidence suggests that grasslands were a component of the pre-human Central Highlands vegetation. Consequently, there is now vigorous debate regarding the extent to which these grasslands have expanded due to anthropogenic pressures. Here, we shed light on the temporal dynamics of Madagascar's vegetative composition by conducting a population genomic investigation of Goodman's mouse lemur (Microcebus lehilahytsara; Cheirogaleidae). These small-bodied primates occur both in Madagascar's eastern rainforests and in the Central Highlands, making them a valuable indicator species. Population divergences among forest-dwelling mammals will reflect changes to their habitat, including fragmentation, whereas patterns of post-divergence gene flow can reveal formerly wooded migration corridors. To explore these patterns, we used RADseq data to infer population genetic structure, demographic models of post-divergence gene flow, and population size change through time. The results offer evidence that open habitats are an ancient component of the Central Highlands, and that wide-spread forest fragmentation occurred naturally during a period of decreased precipitation near the Last Glacial Maximum. Models of gene flow suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene via riparian corridors. Though our findings support the hypothesis that Central Highland grasslands predate human arrival, we also find evidence for human-mediated population declines. This highlights the extent to which species imminently threatened by human-mediated deforestation may already be vulnerable from paleoclimatic conditions.

Nuclear and Mitochondrial Phylogenomics of the Sifakas Reveal Cryptic Variation in the Diademed Sifaka

The most comprehensive phylogenomic reconstruction to date was generated on all nominal taxa within the lemur genus Propithecus. Over 200 wild-caught individuals were included in this study to evaluate the intra and interspecific relationships across this genus. Ultraconserved Elements (UCEs) resulted in well-supported phylogenomic trees. Complete mitochondrial genomes (CMGs) largely agreed with the UCEs, except where a mitochondrial introgression was detected between one clade of the diademed sifaka (Propithecus diadema) and the Milne-Edwards sifaka (P. edwardsi). Additionally, the crowned (P. coronatus) and Von der Decken’s (P. deckeni) sifakas belonged to a single admixed lineage from UCEs. Further sampling across these two species is warranted to determine if our sampling represents a hybrid zone. P. diadema recovered two well-supported clades, which were dated and estimated as being ancient as the split between the Perrier’s (P. perrierii) and silky (P. candidus) sifakas. The reconstructed demographic history of the two clades also varied over time. We then modeled the modern ecological niches of the two cryptic P. diadema clades and found that they were significantly diverged (p < 0.01). These ecological differences result in a very limited zone of geographic overlap for the P. diadema clades (<60 km2). Niche models also revealed that the Onive River acts as a potential barrier to dispersal between P. diadema and P. edwardsi. Further taxonomic work is required on P. diadema to determine if its taxonomic status should be revised. This first genomic evaluation of the genus resolved the relationships between the taxa and the recovered cryptic diversity within one species.

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.

RADseq Data Suggest Occasional Hybridization between Microcebus murinus and M. ravelobensis in Northwestern Madagascar

The occurrence of natural hybridization has been reported in a wide range of organisms, including primates. The present study focuses on the endemic lemurs of Madagascar, primates for which only a few species occur in sympatry or parapatry with congeners, thereby creating limited opportunity for natural hybridization. This study examines RADseq data from 480 individuals to investigate whether the recent expansion of Microcebus murinus towards the northwest and subsequent secondary contact with Microcebus ravelobensis has resulted in the occurrence of hybridization between the two species. Admixture analysis identified one individual with 26% of nuclear admixture, which may correspond to an F2- or F3-hybrid. A composite-likelihood approach was subsequently used to test the fit of alternative phylogeographic scenarios to the genomic data and to date introgression. The simulations yielded support for low levels of gene flow (2Nm0 = 0.063) between the two species starting before the Last Glacial Maximum (between 54 and 142 kyr). Since M. murinus most likely colonized northwestern Madagascar during the Late Pleistocene, the rather recent secondary contact with M. ravelobensis has likely created the opportunity for occasional hybridization. Although reproductive isolation between these distantly related congeners is not complete, it is effective in maintaining species boundaries.

Molecular phylogeny and systematics of bald uakaris, genus Cacajao Lesson, 1840 (Primates: Pitheciidae), with the description of a new species

Bald uakaris, genus Cacajao, are Amazonian primates currently classified as one species and four subspecies based on the patterns of pelage coloration. In this study, we test if their current taxonomy is represented by the phylogenetic relationship of the main lineages retrieved from molecular data. We included, for the first time, all bald uakari taxa in a mitochondrial (cytochrome b) and genome-wide (ddRAD) phylogenetic analyses. We also examined the pattern of pelage colouration in specimens from zoological collections. Having determined the number of lineages using Maximum Likelihood and the species tree using coalescent analyses, we test their divergence time using a Bayesian approach. While the cytochrome b analysis only recovered two clades, the ddRAD analysis supported the reciprocal monophyly of five lineages of bald uakaris, with all clades including only individuals with distinct and exclusive diagnostic phenotypic characters. We found that species diversification in Cacajao occurred during the last 300 Kya and may have been influenced by the formation of rivers and flooded forests in western Amazonia. We propose that the four bald uakari subspecies currently recognised can be upgraded to species level and we describe the white uakaris from the basin of the Rio Tarauacá as a new species.

Rocks and clocks revised: New promises and challenges in dating the primate tree of life

In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.

Species boundaries in the messy middle-A genome-scale validation of species delimitation in a recently diverged lineage of coastal fog desert lichen fungi

Species delimitation among closely related species is challenging because traditional phenotype-based approaches, for example, using morphology, ecological, or chemical characteristics, may not coincide with natural groupings. With the advent of high-throughput sequencing, it has become increasingly cost-effective to acquire genome-scale data which can resolve previously ambiguous species boundaries. As the availability of genome-scale data has increased, numerous species delimitation analyses, such as BPP and SNAPP+Bayes factor delimitation (BFD*), have been developed to delimit species boundaries. However, even empirical molecular species delimitation approaches can be biased by confounding evolutionary factors, for example, hybridization/introgression and incomplete lineage sorting, and computational limitations. Here, we investigate species boundaries and the potential for micro-endemism in a lineage of lichen-forming fungi, Niebla Rundel & Bowler, in the family Ramalinaceae by analyzing single-locus and genome-scale data consisting of (a) single-locus species delimitation analysis using ASAP, (b) maximum likelihood-based phylogenetic tree inference, (c) genome-scale species delimitation models, e.g., BPP and SNAPP+BFD, and (d) species validation using the genealogical divergence index (gdi). We specifically use these methods to cross-validate results between genome-scale and single-locus datasets, differently sampled subsets of genomic data and to control for population-level genetic divergence. Our species delimitation models tend to support more speciose groupings that were inconsistent with traditional taxonomy, supporting a hypothesis of micro-endemism, which may include morphologically cryptic species. However, the models did not converge on robust, consistent species delimitations. While the results of our analysis are somewhat ambiguous in terms of species boundaries, they provide a valuable perspective on how to use these empirical species delimitation methods in a nonmodel system. This study thus highlights the challenges inherent in delimiting species, particularly in groups such as Niebla, with complex, relatively recent phylogeographic histories.

The gray mouse lemur (Microcebus murinus) as a model for early primate brain evolution

The gray mouse lemur (Microcebus murinus), one of the world's smallest primates, is thought to share a similar ecological niche and many anatomical traits with early euprimates. As a result, it has been considered a suitable model system for early primate physiology and behavior. Moreover, recent studies have demonstrated that mouse lemurs have comparable cognitive abilities and cortical functional organization as haplorhines. Finally, the small brain size of mouse lemurs provides us with actual lower limits for miniaturization of functional brain circuits within the primate clade. Considering its phylogenetic position and early primate-like traits, the mouse lemurs are a perfect model species to study the early evolution of primate brains.

Impact of model assumptions on demographic inferences: the case study of two sympatric mouse lemurs in northwestern Madagascar

BACKGROUND

Quaternary climate fluctuations have been acknowledged as major drivers of the geographical distribution of the extraordinary biodiversity observed in tropical biomes, including Madagascar. The main existing framework for Pleistocene Malagasy diversification assumes that forest cover was strongly shaped by warmer Interglacials (leading to forest expansion) and by cooler and arid glacials (leading to forest contraction), but predictions derived from this scenario for forest-dwelling animals have rarely been tested with genomic datasets.

RESULTS

We generated genomic data and applied three complementary demographic approaches (Stairway Plot, PSMC and IICR-simulations) to infer population size and connectivity changes for two forest-dependent primate species (Microcebus murinus and M. ravelobensis) in northwestern Madagascar. The analyses suggested major demographic changes in both species that could be interpreted in two ways, depending on underlying model assumptions (i.e., panmixia or population structure). Under panmixia, the two species exhibited larger population sizes across the Last Glacial Maximum (LGM) and towards the African Humid Period (AHP). This peak was followed by a population decline in M. ravelobensis until the present, while M. murinus may have experienced a second population expansion that was followed by a sharp decline starting 3000 years ago. In contrast, simulations under population structure suggested decreasing population connectivity between the Last Interglacial and the LGM for both species, but increased connectivity during the AHP exclusively for M. murinus.

CONCLUSION

Our study shows that closely related species may differ in their responses to climatic events. Assuming that Pleistocene climatic conditions in the lowlands were similar to those in the Malagasy highlands, some demographic dynamics would be better explained by changes in population connectivity than in population size. However, changes in connectivity alone cannot be easily reconciled with a founder effect that was shown for M. murinus during its colonization of the northwestern Madagascar in the late Pleistocene. To decide between the two alternative models, more knowledge about historic forest dynamics in lowland habitats is necessary. Altogether, our study stresses that demographic inferences strongly depend on the underlying model assumptions. Final conclusions should therefore be based on a comparative evaluation of multiple approaches.

Living in tiny fragments: a glimpse at the ecology of Goodman's mouse lemurs (Microcebus lehilahytsara) in the relic forest of Ankafobe, Central Highlands, Madagascar

Habitat fragmentation is one of the major types of anthropogenic change, though fragmented landscapes predate human intervention. At present, the Central Highlands of Madagascar are covered by extensive grasslands interspersed with small discrete forest patches of unknown antiquity. Ankafobe, an actively protected site, comprises two such fragments of 12 and 30 ha, respectively, known to harbor three lemur species and other endemic wildlife. At this location, we conducted a survey of resident Goodman's mouse lemurs, Microcebus lehilahytsara, to determine baseline behavioral and ecological conditions for this isolated population. By studying primates in forest fragments, investigators can characterize the effects of shrinking habitats and decreasing connectivity on species diversity and survival, thus providing a glimpse into the potential resilience of species in the face of anthropogenic disturbance. Investigating the behavioral ecology of Goodman's mouse lemurs across their geographic range could help us understand their metabolic and ecological flexibility and predict species long-term survival prospects. We conducted night transect walks, using capture techniques and telemetry, to track eight radio-collared individuals. Preliminary density estimates based on a limited number of sightings (n = 18) were 2.19 ind/ha, and home range assessments ranged between 0.22 and 3.67 ha. Mouse lemurs traveled an average of 425 m nightly during the 5-h tracking periods and primarily fed on fruits of the mistletoe Bakerella clavata. The finding that Goodman's mouse lemurs apparently thrive in the seasonally cold and arid forest fragments in the Central Highlands indicates that they may be among the most tolerant and adaptable lemur species in Madagascar. These results point towards an exciting research program that focuses on ecological tolerance as a mechanism for long-term species survival.

Past environmental changes affected lemur population dynamics prior to human impact in Madagascar

Quaternary climatic changes have been invoked as important drivers of species diversification worldwide. However, the impact of such changes on vegetation and animal population dynamics in tropical regions remains debated. To overcome this uncertainty, we integrated high-resolution paleoenvironmental reconstructions from a sedimentary record covering the past 25,000 years with demographic inferences of a forest-dwelling primate species (Microcebus arnholdi), in northern Madagascar. Result comparisons suggest that climate changes through the African Humid Period (15.2 - 5.5 kyr) strongly affected the demographic dynamics of M. arnholdi. We further inferred a population decline in the last millennium which was likely shaped by the combination of climatic and anthropogenic impacts. Our findings demonstrate that population fluctuations in Malagasy wildlife were substantial prior to a significant human impact. This provides a critical knowledge of climatically driven, environmental and ecological changes in the past, which is essential to better understand the dynamics and resilience of current biodiversity.

Measuring Phylogenetic Information of Incomplete Sequence Data

Widely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon probabilistic models of nucleotide substitution or amino-acid replacement. The phylogenetic information that can be extracted depends on the number of columns in the sequence alignment and will be decreased when the alignment contains gaps due to insertion or deletion events. Motivated by the measurement of information loss, we suggest assessment of the Effective Sequence Length (ESL) of an aligned data set. The ESL can differ from the actual number of columns in a sequence alignment because of the presence of alignment gaps. Furthermore, the estimation of phylogenetic information is affected by model misspecification. Inevitably, the actual process of molecular evolution differs from the probabilistic models employed to describe this process. This disparity means the amount of phylogenetic information in an actual sequence alignment will differ from the amount in a simulated data set of equal size, which motivated us to develop a new test for model adequacy. Via theory and empirical data analysis, we show how to disentangle the effects of gaps and model misspecification. By comparing the Fisher information of actual and simulated sequences, we identify which alignment sites and tree branches are most affected by gaps and model misspecification.

Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur

Mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of de novo mutations have been directly characterized in relatively few lineages. Our study provides the first direct mutation-rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprises nearly half of the primate clade. Using high-coverage linked-read sequencing for a focal quartet of gray mouse lemurs (Microcebus murinus), we estimated the mutation rate to be among the highest calculated for a mammal at 1.52 × 10-8 (95% credible interval: 1.28 × 10-8-1.78 × 10-8) mutations/site/generation. Further, we found an unexpectedly low count of paternal mutations, and only a modest overrepresentation of mutations at CpG sites. Despite the surprising nature of these results, we found both the rate and spectrum to be robust to the manipulation of a wide range of computational filtering criteria. We also sequenced a technical replicate to estimate a false-negative and false-positive rate for our data and show that any point estimate of a de novo mutation rate should be considered with a large degree of uncertainty. For validation, we conducted an independent analysis of context-dependent substitution types for gray mouse lemur and five additional primate species for which de novo mutation rates have also been estimated. These comparisons revealed general consistency of the mutation spectrum between the pedigree-based and the substitution-rate analyses for all species compared.

Phylogenomic Assessment of Biodiversity Using a Reference-Based Taxonomy: An Example With Horned Lizards (Phrynosoma)

Phylogenomic investigations of biodiversity facilitate the detection of fine-scale population genetic structure and the demographic histories of species and populations. However, determining whether or not the genetic divergence measured among populations reflects species-level differentiation remains a central challenge in species delimitation. One potential solution is to compare genetic divergence between putative new species with other closely related species, sometimes referred to as a reference-based taxonomy. To be described as a new species, a population should be at least as divergent as other species. Here, we develop a reference-based taxonomy for Horned Lizards (Phrynosoma; 17 species) using phylogenomic data (ddRADseq data) to provide a framework for delimiting species in the Greater Short-horned Lizard species complex (P. hernandesi). Previous species delimitation studies of this species complex have produced conflicting results, with morphological data suggesting that P. hernandesi consists of five species, whereas mitochondrial DNA support anywhere from 1 to 10 + species. To help address this conflict, we first estimated a time-calibrated species tree for P. hernandesi and close relatives using SNP data. These results support the paraphyly of P. hernandesi; we recommend the recognition of two species to promote a taxonomy that is consistent with species monophyly. There is strong evidence for three populations within P. hernandesi, and demographic modeling and admixture analyses suggest that these populations are not reproductively isolated, which is consistent with previous morphological analyses that suggest hybridization could be common. Finally, we characterize the population-species boundary by quantifying levels of genetic divergence for all 18 Phrynosoma species. Genetic divergence measures for western and southern populations of P. hernandesi failed to exceed those of other Phrynosoma species, but the relatively small population size estimated for the northern population causes it to appear as a relatively divergent species. These comparisons underscore the difficulties associated with putting a reference-based approach to species delimitation into practice. Nevertheless, the reference-based approach offers a promising framework for the consistent assessment of biodiversity within clades of organisms with similar life histories and ecological traits.

The challenge and promise of estimating the de novo mutation rate from whole-genome comparisons among closely related individuals

Germline mutations are the raw material for natural selection, driving species evolution and the generation of earth's biodiversity. Without this driver of genetic diversity, life on earth would stagnate. Yet, it is a double-edged sword. An excess of mutations can have devastating effects on fitness and population viability. It is therefore one of the great challenges of molecular ecology to determine the rate and mechanisms by which these mutations accrue across the tree of life. Advances in high-throughput sequencing technologies are providing new opportunities for characterizing the rates and mutational spectra within species and populations thus informing essential evolutionary parameters such as the timing of speciation events, the intricacies of historical demography, and the degree to which lineages are subject to the burdens of mutational load. Here, we will focus on both the challenge and promise of whole-genome comparisons among parents and their offspring from known pedigrees for the detection of germline mutations as they arise in a single generation. The potential of these studies is high, but the field is still in its infancy and much uncertainty remains. Namely, the technical challenges are daunting given that pedigree-based genome comparisons are essentially searching for needles in a haystack given the very low signal to noise ratio. Despite the challenges, we predict that rapidly developing methods for whole-genome comparisons hold great promise for integrating empirically derived estimates of de novo mutation rates and mutation spectra across many molecular ecological applications.

The latitudinal taxonomy gradient

Emerging large-scale datasets coupled with statistical advances have provided new insights into the processes that generate the latitudinal diversity gradient (LDG). But many of these studies run into an old, if often underappreciated, problem: The interpretation of the data critically depends on the consistent application of criteria to define what constitutes a species. This is particularly pernicious for the LDG because good species have been easier to recognize in temperate than in tropical regions. We provide evidence that this latitudinal taxonomy gradient exists, discuss how this potentially impacts inferences about latitudinal variation in ecoevolutionary processes such as population differentiation and speciation, and provide a roadmap for how to mitigate taxonomic biases in the study of biodiversity patterns.

Limits and convergence properties of the sequentially Markovian coalescent

Several methods based on the sequentially Markovian coalescent (SMC) make use of full genome sequence data from samples to infer population demographic history including past changes in population size, admixture, migration events and population structure. More recently, the original theoretical framework has been extended to allow the simultaneous estimation of population size changes along with other life history traits such as selfing or seed banking. The latter developments enhance the applicability of SMC methods to nonmodel species. Although convergence proofs have been given using simulated data in a few specific cases, an in-depth investigation of the limitations of SMC methods is lacking. In order to explore such limits, we first develop a tool inferring the best case convergence of SMC methods assuming the true underlying coalescent genealogies are known. This tool can be used to quantify the amount and type of information that can be confidently retrieved from given data sets prior to the analysis of the real data. Second, we assess the inference accuracy when the assumptions of SMC approaches are violated due to departures from the model, namely the presence of transposable elements, variable recombination and mutation rates along the sequence, and SNP calling errors. Third, we deliver a new interpretation of SMC methods by highlighting the importance of the transition matrix, which we argue can be used as a set of summary statistics in other statistical inference methods, uncoupling the SMC from hidden Markov models (HMMs). We finally offer recommendations to better apply SMC methods and build adequate data sets under budget constraints.

Inferring number of populations and changes in connectivity under the n-island model

Inferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes, ignoring population structure. Alternatively, when structure is assumed, it is defined a priori as a population tree and not inferred. Here we propose a framework based on the IICR (Inverse Instantaneous Coalescence Rate). The IICR can be estimated for a single diploid individual using the PSMC method of Li and Durbin (2011). For an isolated panmictic population, the IICR matches the population size history, and this is how the PSMC outputs are generally interpreted. However, it is increasingly acknowledged that the IICR is a function of the demographic model and sampling scheme with limited connection to population size changes. Our method fits observed IICR curves of diploid individuals with IICR curves obtained under piecewise stationary symmetrical island models. In our models we assume a fixed number of time periods during which gene flow is constant, but gene flow is allowed to change between time periods. We infer the number of islands, their sizes, the periods at which connectivity changes and the corresponding rates of connectivity. Validation with simulated data showed that the method can accurately recover most of the scenario parameters. Our application to a set of five human PSMCs yielded demographic histories that are in agreement with previous studies using similar methods and with recent research suggesting ancient human structure. They are in contrast with the view of human evolution consisting of one ancestral population branching into three large continental and panmictic populations with varying degrees of connectivity and no population structure within each continent.

Next-generation technologies applied to age-old challenges in Madagascar

Madagascar is a biodiversity hotspot that is facing rapid rates of deforestation, habitat destruction, and poverty. Urgent action is required to document the status of biodiversity to facilitate efficacious conservation plans. With the recent advent of portable and affordable genetic technologies, it is now possible to take genomic approaches out of the lab and into the field. Mobile genetics labs can produce scientifically reproducible data under field conditions, dramatically minimizing the time between sample collection and data analysis. Here, we show “proof of concept” by deploying miniPCR bio’s miniaturized thermal cycler alongside Oxford Nanopore’s MinION DNA sequencer in Madagascar. Specifically, we deployed this technology at Anjajavy, northwestern Madagascar for rapid biodiversity assessment. We successfully extracted mouse lemur DNA, amplified and sequenced a phylogenetically informative mitochondrial gene (cytochrome-b; cytb), and thereby confirmed the presence of Danfoss’ mouse lemur (M. danfossi) within the Anjajavy Reserve. We show that a mobile genetics lab can provide expeditious results, and allow scientists to conduct genetic analyses, potentially allowing for rapid interventions under emergency conditions in situ. Additionally, mobile labs offer powerful training opportunities for in-country scientists for whom training opportunities were previously confined to ex-situ locations. By bringing genomic technologies to Madagascar and other economically challenged and biodiverse regions of the world, the next generation of scientists and conservationists can more fully implement their leadership roles. Local laboratory and training facilities are changing the polarity of research programs in Madagascar and empowering national researchers to take charge of environmental stewardship.

Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species

Delimitation of cryptic species is increasingly based on genetic analyses but the integration of distributional, morphological, behavioral, and ecological data offers unique complementary insights into species diversification. We surveyed communities of nocturnal mouse lemurs (Microcebus spp.) in five different sites of northeastern Madagascar, measuring a variety of morphological parameters and assessing reproductive states for 123 individuals belonging to five different lineages. We documented two different non-sister lineages occurring in sympatry in two areas. In both cases, sympatric species pairs consisted of a locally restricted (M. macarthurii or M. sp. #3) and a more widespread lineage (M. mittermeieri or M. lehilahytsara). Estimated Extents of Occurrence (EOO) of these lineages differed remarkably with 560 and 1,500 km² versus 9,250 and 50,700 km² , respectively. Morphometric analyses distinguished unambiguously between sympatric species and detected more subtle but significant differences among sister lineages. Tail length and body size were most informative in this regard. Reproductive schedules were highly variable among lineages, most likely impacted by phylogenetic relatedness and environmental variables. While sympatric species pairs differed in their reproductive timing (M. sp. #3/M. lehilahytsara and M. macarthurii/M. mittermeieri), warmer lowland rainforests were associated with a less seasonal reproductive schedule for M. mittermeieri and M. lehilahytsara compared with populations occurring in montane forests. Distributional, morphological, and ecological data gathered in this study support the results of genomic species delimitation analyses conducted in a companion study, which identified one lineage, M. sp. #3, as meriting formal description as a new species. Consequently, a formal species description is included. Worryingly, our data also show that geographically restricted populations of M. sp. #3 and its sister species (M. macarthurii) are at high risk of local and perhaps permanent extinction from both deforestation and habitat fragmentation.

Molecular Clocks without Rocks: New Solutions for Old Problems

Molecular data have been used to date species divergences ever since they were described as documents of evolutionary history in the 1960s. Yet, an inadequate fossil record and discordance between gene trees and species trees are persistently problematic. We examine how, by accommodating gene tree discordance and by scaling branch lengths to absolute time using mutation rate and generation time, multispecies coalescent (MSC) methods can potentially overcome these challenges. We find that time estimates can differ - in some cases, substantially - depending on whether MSC methods or traditional phylogenetic methods that apply concatenation are used, and whether the tree is calibrated with pedigree-based mutation rates or with fossils. We discuss the advantages and shortcomings of both approaches and provide practical guidance for data analysis when using these methods.