Phylogenetic fields through time: temporal dynamics of geographical co-occurrence and phylogenetic structure within species ranges

Abstract

Species co-occur with different sets of other species across their geographical distribution, which can be either closely or distantly related. Such co-occurrence patterns and their phylogenetic structure within individual species ranges represent what we call the species phylogenetic fields (PFs). These PFs allow investigation of the role of historical processes—speciation, extinction and dispersal—in shaping species co-occurrence patterns, in both extinct and extant species. Here, we investigate PFs of large mammalian species during the last 3 Myr, and how these correlate with trends in diversification rates. Using the fossil record, we evaluate species' distributional and co-occurrence patterns along with their phylogenetic structure. We apply a novel Bayesian framework on fossil occurrences to estimate diversification rates through time. Our findings highlight the effect of evolutionary processes and past climatic changes on species' distributions and co-occurrences. From the Late Pliocene to the Recent, mammal species seem to have responded in an individualistic manner to climate changes and diversification dynamics, co-occurring with different sets of species from different lineages across their geographical ranges. These findings stress the difficulty of forecasting potential effects of future climate changes on biodiversity.

Cenozoic evolution of beta diversity and a Pleistocene emergence for modern mammal faunas in China

“…Incomplete taxonomic coverage might affect estimates of beta diversity, particularly when completeness varies in space and time (Darroch & Wagner, ). Older stratigraphic units tend to be preserved in fewer outcrops and over a smaller area than younger units (Villalobos et al, ), and this is also the case in our database (Figure ; Supporting Information Appendix S2, Table S2.1). Furthermore, the lack of useful fossil collections on the Tibetan Plateau (before the Miocene) and in Northeast China (before the Pleistocene) makes further interpretation of their palaeontological contexts challenging (Figure ; Supporting Information Appendix S2, Figure S2.8).…”

“…In particular, palaeontological data (e.g., fossil records) are prone to bias, because they are usually subjected to differences in preservation rates among taxa and by time averaging and are unevenly distributed in space and time (Figure ; Behrensmeyer, Kidwell, & Gastaldo, ). First, older stratigraphic units, on average, preserve fewer fossil assemblages (Figure a; Villalobos, Carotenuto, Raia, & Diniz‐Filho, ). Regarding the 856 faunas in our database, sampling varied from 55 faunas recorded in the Palaeocene to 239 faunas in the Pleistocene (Figure a; Supporting Information Appendix S2, Table S2.1).…”

Testing Darwin’s naturalization conundrum based on taxonomic, phylogenetic, and functional dimensions of vascular plants

“…The term focal species has been used previously, e.g., defined as a targeted species for conservation and management purposes (Lambeck 1997) and is conceptually similar to the α niche concept (Pickett and Bazzaz 1978), which can be interpreted as differences in functional traits between a given species and those of co‐occurring species (Pickett and Bazzaz 1978, Ackerly and Cornwell 2007). The focal‐species approach as extended here: (1) allows evaluation of phylogenetic and functional distances between the focal species and co‐occurring species, thus permitting the assessment of the potential community‐level consequences of focal‐species interactions as well as the influence of community‐wide interactions on the focal species; (2) is advantageous for incorporating different dimensions of biodiversity (i.e., taxonomic, functional, phylogenetic); (3) can be adapted to different spatial and temporal scales; and (4) facilitates consideration of environmental factors in driving species co‐occurrence (Villalobos et al 2013, 2016, Barnagaud et al 2014, Herrera‐Alsina and Villegas‐Patraca 2014, Miller et al 2017 b ).…”

“…Similarly, phylogenetic/functional fields can be used as metrics of species‐level coexistence. All three of these approaches, diversity, phylogenetic, and functional fields, are usually applied at macroecological scales (Arita et al 2008, Villalobos and Arita 2010, Villalobos et al 2013, 2016, 2017) with some local‐scale exceptions (e.g., Herrera‐Alsina and Villegas‐Patraca 2014, Miller et al 2017 b , Kusumoto et al 2019). Given that the observational units in our study are species within local communities, we downscale the concept of fields applied at large geographical scales to local communities in which phylogenetic/functional structure is measured on the set of species that co‐occur with a focal species in a particular community (Fig.…”

The challenges to inferring the regulators of biodiversity in deep time

“…Exploring the interactions of species and their geographical ranges over ecological and evolutionary timescales has been hard. In this volume, Villalobos et al [96] explore how species co-occur with other species and find that in the long term, species respond individualistically to major climatic shifts, while more stable climates allowed less phylogenetically variable, yet richer palaeocommunities to settle. The authors calculate phylogenetic fields, the co-occurrence patterns extinction diversification speciation biotic environment abiotic environment Figure 2.…”