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Molecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate the extent to which the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices and phylogenetic inference method. We demonstrate that more stringent minor allele filters bias inferred trees away from the true species tree topology, and that these biased trees tend to be more imbalanced and have a higher center of gravity than the true trees. We find the greatest topological accuracy when filtering sites for minor allele count (MAC) >3–4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with MAC >1–2. In contrast, filtering for missing data increased accuracy in the inferred topologies; however, this effect was small in comparison to the effect of minor allele filters and may be undesirable due to a subsequent mutation spectrum distortion. The bias introduced by these filters differs based on the reference genome used in short read alignment, providing further support that choosing a reference genome for alignment is an important bioinformatic decision with implications for downstream analyses. These results demonstrate that attributes of the study system and dataset (and their interaction) add important nuance for how best to assemble and filter short-read genomic data for phylogenetic inference. [ABSTRACT FROM AUTHOR]

Species delineation has a long and contentious history, yet most agree that sympatric populations exhibiting high levels of reproductive isolation and evolving independently are species. In an opinion piece, Hill and Powers (2021; hereafter H&P) claim that several recognized species of crossbills (Loxia spp.) do not represent species because by no measure are they discrete, the vocalizations used to categorize crossbills are learned, modified and can switch to that of a different species, and reproductive isolation is incomplete and weak. We argue that the behavioral and genetic evidence indicate that Cassia crossbills L. sinesciuris, which we focus on because the data relevant to species status are more diverse and extensive, are genetically discrete; call modification rarely leads to crossbill misclassification and overwhelmingly results in call divergence and enhanced discrimination; and are nearly completely reproductively isolated with little evidence of introgression from sympatric red crossbills. The differences in our conclusions result in part from H&P mischaracterizing and misconstruing the ecology of Cassia crossbills, geographic context of their divergence, and evidence for reproductive isolation. H&P seemingly require that crossbills must adhere to the typical model of bird speciation–protracted divergence in allopatry, followed by a gradual increase in sympatry if reproductive isolation and ecological divergence allow–and require evidence such as initial long periods of allopatry, FST values > 0.2, divergent mtDNA and intrinsic postzygotic isolation. Although such evidence commonly distinguishes bird species, an increasing number of studies show that such criteria are not necessary to indicate sympatric, evolutionarily independent lineages. [ABSTRACT FROM AUTHOR]

In this issue of Molecular Ecology, Poelstra et al. () use genomic data to show that cichlid species in the adaptive radiation in Lake Ejagham, Cameroon, experienced gene flow with a riverine relative, primarily prior to their diversification. Intriguingly, this introgression brought with it olfactory alleles that the authors suggest may play a sensory role in speciation. As a classic example of sympatric speciation due to the highly restricted geography of this small (0.49 km2) crater lake (Schliewen et al.,), this result sheds new light on the history of this fascinating radiation. As genomic data for cichlid radiations accumulate, finding evidence of introgression increasingly appears to be the rule rather than the exception (Kautt et al., ; Meier et al., ,). However, two points are pressing as evidence for introgression mounts: (a) It is crucial to understand the assumptions of analytical approaches used and (b) it is important to think clearly about the divergent contexts in which evidence for introgression has been invoked as an important feature of adaptive radiation. [ABSTRACT FROM AUTHOR]

Abstract: Theoretical models of sexual selection suggest that male courtship signals can evolve through the build‐up of genetic correlations between the male signal and female preference. When preference is mediated via increased sensitivity of the signal characteristics, correlations between male signal and perception/sensitivity are expected. When signal expression is limited to males, we would expect to find signal‐sensitivity correlations in males. Here, we document such a correlation within a breeding population of threespine stickleback mediated by differences in opsin expression. Males with redder nuptial coloration express more long‐wavelength‐sensitive (LWS) opsin, making them more sensitive to orange and red. This correlation is not an artifact of shared tuning to the optical microhabitat. Such correlations are an essential feature of many models of sexual selection, and our results highlight the potential importance of opsin expression variation as a substrate for signal‐preference evolution. Finally, these results suggest a potential sensory mechanism that could drive negative frequency‐dependent selection via male–male competition and thus maintain variation in male nuptial color. [ABSTRACT FROM AUTHOR]

Signal evolution is thought to depend on both a signal's detectability or conspicuousness (signal design) as well as any extractable information it may convey to a potential receiver (signal content). While theoretical and empirical work in sexual selection has largely focused on signal content, there has been a steady accrual of evidence that signal design is also important for trait evolution. Despite this, relatively little attention has been paid to spatial variation in the conspicuousness of a given signal, especially over small spatial scales (relative to an organism's dispersal distance). Here, we show that visual signals of male threespine stickleback vary in conspicuousness, depending on a male's nest depth within a given lake. Deeper nesting males were typically more chromatically conspicuous than shallow nesting males. This trend is partly because all male stickleback are more conspicuous in deep optical environments. However, deep males are even more conspicuous than environmentally driven null expectations, while shallow males tend to be disproportionally cryptic. Experimental manipulation of male nesting depth induced plastic changes in nuptial color that replicated the natural gradients in conspicuousness. We discuss a number of potential mechanisms that could produce depth gradients in conspicuousness in male stickleback, including concomitant depth gradients in diet, predation pressure, male/female density, female preference, and opportunity for sexual selection. [ABSTRACT FROM AUTHOR]

A common pattern found in phylogeny-based empirical studies of diversification is a decrease in the rate of lineage accumulation toward the present. This early-burst pattern of cladogenesis is often interpreted as a signal of adaptive radiation or density-dependent processes of diversification. However, incomplete taxonomic sampling is also known to artifactually produce patterns of rapid initial diversification. The Monte Carlo constant rates (MCCR) test, based upon Pybus and Harvey's gamma (γ)-statistic, is commonly used to accommodate incomplete sampling, but this test assumes that missing taxa have been randomly pruned from the phylogeny. Here we use simulations to show that preferentially sampling disparate lineages within a clade can produce severely inflated type-I error rates of the MCCR test, especially when taxon sampling drops below 75%. We first propose two corrections for the standard MCCR test, the proportionally deeper splits that assumes missing taxa are more likely to be recently diverged, and the deepest splits only MCCR that assumes that all missing taxa are the youngest lineages in the clade, and assess their statistical properties. We then extend these two tests into a generalized form that allows the degree of nonrandom sampling (NRS)to be controlled by a scaling parameter, α. This generalized test is then applied to two recent studies. This new test allows systematists to account for nonrandom taxonomic sampling when assessing temporal patterns of lineage diversification in empirical trees. Given the dramatic affect NRS can have on the behavior of the MCCR test, we argue that evaluating the sensitivity of this test to NRS should become the norm when investigating patterns of cladogenesis in incompletely sampled phylogenies. [ABSTRACT FROM PUBLISHER]

Sexual selection is most often thought of as acting on organismal traits, such as size or color. However, individuals' habitat use may also affect mating success. Here, we show that, in threespine stickleback, nest depth can be a target of sexual selection. In postglacial lakes in British Columbia, male threespine stickleback nest in a narrow range of depths. Prior studies revealed heritable variation in males' preferred nest microhabitat. We surveyed four natural populations, finding that male stickleback with shallower nests were more successful at breeding. Indeed, nest depth was a much stronger predictor of male mating success than more commonly studied targets of sexual selection in stickleback (size, condition, shape, color, infection status). This selection on nest depth means that variance in fitness changed predictably across microhabitats, altering the opportunity for sexual selection to act on other traits. Accordingly, we show that sexual selection on other male traits is strongest where variance in nesting success is highest (at intermediate nest depths in some lakes). We conclude that males' choice of nesting microhabitat is an especially important target of sexual selection, resulting in fine-scale spatial variation in sexual selection on other traits. [ABSTRACT FROM AUTHOR]

A major challenge in evolutionary biology lies in explaining patterns of high species numbers found in biodiversity hot spots. Tropical coral reefs underlie most marine hot spots and reef-associated fish faunas represent some of the most diverse assemblages of vertebrates on the planet. Although the standing diversity of modern reef fish clades is usually attributed to their ecological association with corals, untangling temporal patterns of codiversification has traditionally proved difficult. In addition, owing to uncertainty in higher-level relationships among acanthomorph fish, there have been few opportunities to test the assumption that reef-association itself leads to higher rates of diversification compared to other habitats. Here we use relaxed-clock methods in conjunction with statistical measures of species accumulation and phylogenetic comparative methods to clarify the temporal pattern of diversification in reef and nonreef-associated lineages of tetraodontiforms, a morphologically diverse order of teleost fish. We incorporate 11 fossil calibrations distributed across the tetraodontiform tree to infer divergence times and compare results from models of autocorrelated and uncorrelated evolutionary rates. All major tetraodontiform reef crown groups have significantly higher rates of diversification than the order as a whole. None of the nonreef-associated families show this pattern with the exception of the aracanid boxfish. Independent contrasts analysis also reveals a significantly positive relationship between diversification rate and proportion of reef-associated species within each family when aracanids are excluded. Reef association appears to have increased diversification rate within tetraodontiforms. We suggest that both intrinsic factors of reef habitat and extrinsic factors relating to the provincialization and regionalization of the marine biota during the Miocene (about 23-5 MY) played a role in shaping these patterns of diversity. [ABSTRACT FROM AUTHOR]

Bacterial endosymbionts are widespread across several insect orders and are involved in interactions ranging from obligate mutualism to reproductive parasitism. Candidatus Blochmannia gen. nov. ( Blochmannia ) is an obligate bacterial associate of Camponotus and related ant genera (Hymenoptera: Formicidae). The occurrence of Blochmannia in all Camponotus species sampled from field populations and its maternal transmission to host offspring suggest that this bacterium is engaged in a long-term, stable association with its ant hosts. However, evidence for cospeciation in this system is equivocal because previous phylogenetic studies were based on limited gene sampling, lacked statistical analysis of congruence, and have even suggested host switching. We compared phylogenies of host genes (the nuclear EF-1αF2 and mitochondrial COI/II ) and Blochmannia genes (16S ribosomal DNA [rDNA], groEL, gidA , and rpsB ), totaling more than 7 kilobases for each of 16 Camponotus species. Each data set was analyzed using maximum likelihood and Bayesian phylogenetic reconstruction methods. We found minimal conflict among host and symbiont phylogenies, and the few areas of discordance occurred at deep nodes that were poorly supported by individual data sets. Concatenated protein-coding genes produced a very well-resolved tree that, based on the Shimodaira-Hasegawa test, did not conflict with any host or symbiont data set. Correlated rates of synonymous substitution ( d S ) along corresponding branches of host and symbiont phylogenies further supported the hypothesis of cospeciation. These findings indicate that Blochmannia-Camponotus symbiosis has been evolutionarily stable throughout tens of millions of years. Based on inferred divergence times among the ant hosts, we estimated rates of sequence evolution of Blochmannia to be ∼0.0024 substitutions per site per million years (s/s/MY) for the 16S rDNA gene and ∼0.1094 s/s/MY at synonymous positions of the genes sampled. These rates are several-fold higher than those for related bacteria Buchnera aphidicola and Escherichia coli . Phylogenetic congruence among Blochmannia genes indicates genome stability that typifies primary endosymbionts of insects. [ABSTRACT FROM AUTHOR]

Multiple biological processes can generate sexual selection on male visual signals such as color. For example, females may prefer colorful males because those males are more readily detected (perceptual bias), or because male color conveys information about male quality and associated direct or indirect benefits to females. For example, male threespine stickleback often exhibit red throat coloration, which females prefer both because red is more visible in certain environments, and red color is correlated with male immune function and parasite load. However, not all light environments favor red nuptial coloration: more tannin-stained water tends to favor the evolution of a melanic male phenotype. Do such population differences in stickleback male color, driven by divergent light environments, lead to changes in the relationship between color and immunity? Here, we show that, within stickleback populations, multiple components of male color (brightness and hue of four body parts) are correlated with multiple immune variables (ROS production, phagocytosis rates, and lymphocyte:leukocyte ratios). Some of these color-immune associations persist across stickleback populations with very different male color patterns, whereas other color-immune associations are population-specific. Overall, lakes with red males exhibit stronger color-immune covariance while melanic male populations exhibit weak if any color-immune associations. Our finding that color-immunity relationships are labile implies that any evolution of male color traits (e.g., due to female perceptual bias in a given light environment), can alter the utility of color as an indicator of male quality. [ABSTRACT FROM AUTHOR]

Abstract: Homalopsid snakes are widely distributed throughout Southeast Asia and form the ecologically dominant component of the herpetofauna over much of their range. Although they are considered well differentiated from other colubrid lineages, several aspects of their radiation including within-family relationships, temporal patterns of species diversification, and biogeographic history remain under studied. We analyzed sequence data from four genes (three mitochondrial and one nuclear) for 22 species of the Homalopsidae to generate the most comprehensive phylogeny of the family to date. We also estimated divergence times within the family using a model of independent but log-normally distributed rates of evolution in conjunction with two external fossil calibrations. Using this chronogram, we inferred historical patterns of species diversification within the family. Finally, we used previously published sequence data for 172 snake species to test for the monophyly of the Homalopsidae. Phylogenetic analysis reveals strong support for homalopsid monophyly with an estimate age of the crown group of ∼22MYA. The family comprises three major clades which all originated 18–20MY. Lineage through time plots reveal that homalopsids experienced a significantly higher rate of effective cladogenesis in their early history, consistent with a hypothesis of adaptive radiation. We discuss several Miocene and Pliocene paleogeographic factors that might underlie observed patterns of temporal diversification and biogeography. [Copyright &y& Elsevier]