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Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate divergences, as well as elucidate macroevolutionary dynamics. However, the effect fossils have on phylogenetic reconstruction from morphology remains controversial. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here, we use simulations to evaluate the performance of inference methods across different levels of fossil sampling and missing data. Our results show that fossil taxa improve phylogenetic analysis of morphological datasets, even when highly fragmentary. Irrespective of inference method, fossils improve the accuracy of phylogenies and increase the number of resolved nodes. They also induce the collapse of ancient and highly uncertain relationships that tend to be incorrectly resolved when sampling only extant taxa. Furthermore, tip-dated analyses under the fossilized birth–death process outperform undated methods of inference, demonstrating that the stratigraphic ages of fossils contain vital phylogenetic information. Fossils help to extract true phylogenetic signals from morphology, an effect that is mediated by both their distinctive morphology and their temporal information, and their incorporation in total-evidence phylogenetics is necessary to faithfully reconstruct evolutionary history.

The phylum of annelids is one of the most disparate animal phyla and encompasses ambush predators, suspension feeders and terrestrial earthworms 1 . The early evolution of annelids remains obscure or controversial 2 , 3 , partly owing to discordance between molecular phylogenies and fossils 2 , 4 . Annelid fossils from the Cambrian period have morphologies that indicate epibenthic lifestyles, whereas phylogenomics recovers sessile, infaunal and tubicolous taxa as an early diverging grade 5 . Magelonidae and Oweniidae (Palaeoannelida 1 ) are the sister group of all other annelids but contrast with Cambrian taxa in both lifestyle and gross morphology 2 , 6 . Here we describe a new fossil polychaete (bristle worm) from the early Cambrian Canglangpu formation 7 that we name Dannychaeta tucolus , which is preserved within delicate, dwelling tubes that were originally organic. The head has a well-defined spade-shaped prostomium with elongated ventrolateral palps. The body has a wide, stout thorax and elongated abdomen with biramous parapodia with parapodial lamellae. This character combination is shared with extant Magelonidae, and phylogenetic analyses recover Dannychaeta within Palaeoannelida. To our knowledge, Dannychaeta is the oldest polychaete that unambiguously belongs to crown annelids, providing a constraint on the tempo of annelid evolution and revealing unrecognized ecological and morphological diversity in ancient annelids. Dannychaeta tucolus , a bristle worm from the early Cambrian period, belongs to crown annelids, and has characters that provide evidence of ecological and morphological diversity in ancient annelids, thus reconciling the fossil record with molecular phylogenetic analyses.

Fossils are the only remaining evidence of the majority of species that have ever existed, providing a direct window into events in evolutionary history that shaped the diversification of life on Earth. Phylogenies underpin our ability to make sense of evolution but are routinely inferred using only data available from living organisms. Although extinct taxa have been shown to add crucial information for inferring macroevolutionary patterns and processes (such as ancestral states, paleobiogeography and diversification dynamics), the role fossils play in reconstructing phylogeny is controversial. Since the early years of phylogenetic systematics, different studies have dismissed the impact of fossils due to their incompleteness, championed their ability to overturn phylogenetic hypotheses or concluded that their behavior is indistinguishable from that of extant taxa. Based on taxon addition experiments on empirical data matrices, we show that the inclusion of paleontological data has a remarkable effect in phylogenetic inference. Incorporating fossils often (yet not always) induces stronger topological changes than increasing sampling of extant taxa. Fossils also produce unique topological rearrangements, allowing the exploration of regions of treespace that are never visited by analyses of only extant taxa. Previous studies have proposed a suite of explanations for the topological behavior of fossils, such as their retention of unique morphologies or their ability to break long branches. We develop predictive models that demonstrate that the possession of distinctive character state combinations is the primary predictor of the degree of induced topological change, and that the relative impact of taxa (fossil and extant) can be predicted to some extent before any phylogenetic analysis. Our results bolster the consensus of recent empirical studies by showing the unique role of paleontological data in phylogenetic inference, and provide the first quantitative assessment of its determinants, with broad consequences for the design of taxon sampling in both morphological and total-evidence analyses.

Monitoring the distribution and abundance of hunted wildlife is critical to achieving sustainable resource use, yet adequate data are sparse for most tropical regions. Conventional methods for monitoring hunted forest-vertebrate species require intensive in situ survey effort, which severely constrains spatial and temporal replication. Integrating local ecological knowledge (LEK) into monitoring and management is appealing because it can be cost-effective, enhance community participation, and provide novel insights into sustainable resource use. We develop a technique to monitor population depletion of hunted forest wildlife in the Brazilian Amazon, based on the local ecological knowledge of rural hunters. We performed rapid interview surveys to estimate the landscape-scale depletion of ten large-bodied vertebrate species around 161 Amazonian riverine settlements. We assessed the explanatory and predictive power of settlement and landscape characteristics and were able to develop robust estimates of local faunal depletion. By identifying species-specific drivers of depletion and using secondary data on human population density, land form, and physical accessibility, we then estimated landscape- and regional-scale depletion. White-lipped peccary (Tayassu pecari), for example, were estimated to be absent from 17% of their putative range in Brazil’s largest state (Amazonas), despite 98% of the original forest cover remaining intact. We found evidence that bushmeat consumption in small urban centers has far-reaching impacts on some forest species, including severe depletion well over 100 km from urban centers. We conclude that LEK-based approaches require further field validation, but have significant potential for community-based participatory monitoring as well as cost-effective, large-scale monitoring of threatened forest species.

Machaeridians are Palaeozoic animals that are dorsally armoured with serialized, imbricating shell plates that cover or enclose the body. Prior to the discovery of an articulated plumulitid machaeridian from the Early Ordovician of Morocco that preserved unambiguous annelid characters (segmental parapodia with chaetae), machaeridians were a palaeontological mystery, having been previously linked to echinoderms, barnacles, tommotiids (putative stem-group brachiopods) or molluscs. Although the annelid affinities of machaeridians are now firmly established, their position within the phylum and relevance for understanding the early evolution of Annelida is less secure, with competing hypotheses placing Machaeridia in the stem or deeply nested within the crown group of annelids. We describe a scleritome of Plumulites bengtsoni from the Fezouata Formation of Morocco that preserves an anterior jaw apparatus consisting of at least two discrete elements that exhibit growth lines. Although jaws have multiple independent origins within the annelid crown group, comparable jaws are present only within Phyllodocida, the clade that contains modern aphroditiforms (scaleworms and relatives). Phylogenetic analysis places a monophyletic Machaeridia within the crown group of Phyllodocida in total-group Aphroditiformia, consistent with a common origin of machaeridian shell plates and scaleworm elytrae. The inclusion of machaeridians in Aphroditiformia truncates the ghost lineage of Phyllodocida by almost a hundred million years.

As a result of their plastic body plan, the relationships of the annelid worms and even the taxonomic makeup of the phylum have long been contentious. Morphological cladistic analyses have typically recovered a monophyletic Polychaeta, with the simple-bodied forms assigned to an early-diverging clade or grade. This is in stark contrast to molecular trees, in which polychaetes are paraphyletic and include clitellates, echiurans and sipunculans. Cambrian stem group annelid body fossils are complex-bodied polychaetes that possess well-developed parapodia and paired head appendages (palps), suggesting that the root of annelids is misplaced in morphological trees. We present a reinvestigation of the morphology of key fossil taxa and include them in a comprehensive phylogenetic analysis of annelids. Analyses using probabilistic methods and both equal- and implied-weights parsimony recover paraphyletic polychaetes and support the conclusion that echiurans and clitellates are derived polychaetes. Morphological trees including fossils depict two main clades of crown-group annelids that are similar, but not identical, to Errantia and Sedentaria, the fundamental groupings in transcriptomic analyses. Removing fossils yields trees that are often less resolved and/or root the tree in greater conflict with molecular topologies. While there are many topological similarities between the analyses herein and recent phylogenomic hypotheses, differences include the exclusion of Sipuncula from Annelida and the taxa forming the deepest crown-group divergences.

Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured but recent studies have shown that these approaches are less accurate than the Bayesian implementation of the Mk model. Here we expand on these findings in several ways: we assess the impact of tree shape and maximum-likelihood estimation using the Mk model, as well as analysing data composed of both binary and multistate characters. We find that all methods struggle to correctly resolve deep clades within asymmetric trees, and when analysing small character matrices. The Bayesian Mk model is the most accurate method for estimating topology, but with lower resolution than other methods. Equal weights parsimony is more accurate than implied weights parsimony, and maximum-likelihood estimation using the Mk model is the least accurate method. We conclude that the Bayesian implementation of the Mk model should be the default method for phylogenetic estimation from phenotype datasets, and we explore the implications of our simulations in reanalysing several empirical morphological character matrices. A consequence of our finding is that high levels of resolution or the ability to classify species or groups with much confidence should not be expected when using small datasets. It is now necessary to depart from the traditional parsimony paradigms of constructing character matrices, towards datasets constructed explicitly for Bayesian methods.

Tropical rainforest regions are urbanizing rapidly, yet the role of emerging metropolises in driving wildlife overharvesting in forests and inland waters is unknown. We present evidence of a large defaunation shadow around a rainforest metropolis. Using interviews with 392 rural fishers, we show that fishing has severely depleted a large-bodied keystone fish species, tambaqui (Colossoma macropomum), with an impact extending over 1,000 km from the rainforest city of Manaus (population 2.1 million). There was strong evidence of defaunation within this area, including a 50% reduction in body size and catch rate (catch per unit effort). Our findings link these declines to city-based boats that provide rural fishers with reliable access to fish buyers and ice and likely impact rural fisher livelihoods and flooded forest biodiversity. This empirical evidence that urban markets can defaunate deep into rainforest wilderness has implications for other urbanizing socioecological systems.

We examine ways in which the role of wild animals in the Amazonian food system may be socially differentiated and species-specific. We combine a hybrid framework of food choice preferences and theorizing on access to natural resources with fieldwork in Brazilian Amazon, where social and environmental challenges coalesce around the role of wildlife in feeding a growing urban population. Based on 798 household surveys across four towns, we found that consumption of, and taste preferences for, selected species of mammals, fishes, birds, and reptiles are related to variation in means of access (e.g., level of social trust - the basis of reciprocity and informal urban safety nets), and having rural cultural origins (marginal to migrants’ other socioeconomic differences). The likelihood of eating particular species was associated with taste preferences and household experiences of food insecurity. Hunting and fishing households consumed many wild species; it is unclear if they depend heavily on any in particular. Vulnerable species, including manatee, tortoise, and river turtle, were eaten mainly by relatively privileged households, and less so by other households (e.g., rural-urban migrants). Rural origins increased by 90% the likelihood of a strong wild meat preference, compared to other households. Evidently, wildlife consumption is a rural tradition that influences migrants’ dietary practices in towns, through the interplay of preferences, means of access, and context. Finally, severe and moderate food insecurity was associated with eating howler monkey and catfishes (barred and redtail) and not eating manatee and turtle. Hence, urban consumption of some, but not all, wild species is associated with household disadvantage and food insecurity. Amazonian town-dwellers consume many wild species, drawing on diverse means of access, which are species-specific and reflect social inequalities. Species-specific governance of wildlife consumption may help balance the risks of overharvesting against the well-being of Amazonia’s vulnerable town-dwellers.

Whilst the fossil record of polychaete worms extends to the early Cambrian, much data on this group derive from microfossils known as scolecodonts. These are sclerotized jaw elements, which generally range from 0.1–2 mm in size, and which, in contrast to the soft-body anatomy, have good preservation potential and a continuous fossil record. Here we describe a new eunicidan polychaete, Websteroprion armstrongi gen. et sp. nov., based primarily on monospecific bedding plane assemblages from the Lower-Middle Devonian Kwataboahegan Formation of Ontario, Canada. The specimens are preserved mainly as three-dimensional moulds in the calcareous host rock, with only parts of the original sclerotized jaw walls occasionally present. This new taxon has a unique morphology and is characterized by an unexpected combination of features seen in several different Palaeozoic polychaete families. Websteroprion armstrongi was a raptorial feeder and possessed the largest jaws recorded in polychaetes from the fossil record, with maxillae reaching over one centimetre in length. Total body length of the species is estimated to have reached over one metre, which is comparable to that of extant ‘giant eunicid’ species colloquially referred to as ‘Bobbit worms’. This demonstrates that polychaete gigantism was already a phenomenon in the Palaeozoic, some 400 million years ago.