Biogeographic Studies Research Articles

What Darwin could not see: island formation and historical sea levels shape genetic divergence and island biogeography in a coastal marine species

Oceanic islands play a central role in the study of evolution and island biogeography. The Galapagos Islands are one of the most studied oceanic archipelagos but research has almost exclusively focused on terrestrial organisms compared to marine species. Here we used the Galapagos bullhead shark (Heterodontus quoyi) and single nucleotide polymorphisms (SNPs) to examine evolutionary processes and their consequences for genetic divergence and island biogeography in a shallow-water marine species without larval dispersal. The sequential separation of individual islands from a central island cluster gradually established different ocean depths between islands that pose barriers to dispersal in H. quoyi. Isolation by resistance analysis suggested that ocean bathymetry and historical sea level fluctuations modified genetic connectivity. These processes resulted in at least three genetic clusters that exhibit low genetic diversity and effective population sizes that scale with island size and the level of geographic isolation. Our results exemplify that island formation and climatic cycles shape genetic divergence and biogeography of coastal marine organisms with limited dispersal comparable to terrestrial taxa. Because similar scenarios exist in oceanic islands around the globe our research provides a new perspective on marine evolution and biogeography with implications for the conservation of island biodiversity.

Rove beetle collection (Coleoptera: Staphylinidae: Aleocharinae) in the State Museum of Natural History (Lviv, Ukraine).

The collection of rove beetles of the subfamily Aleocharinae, stored in the State Museum of Natural History of the National Academy of Sciences of Ukraine (Lviv), has been catalogued. The catalog contains information about 2313 specimens of the collection, which belong to 278 species in 91 genera and 17 tribes. The overwhelming majority of the representatives of the subfamily Aleocharinae represented in the collection were collected on the territory of Ukraine, as well as in the modern territories of Europe, Africa, and Asia. The obtained data will later on provide an opportunity to expand the understanding of the distribution of species-specifically for faunal research, as well as for biogeographic study.

Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis.

Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards.

Journal of Biogeography Innovation Awards, 2023

Journal of Biogeography Innovation Awards, 2023

Sixty years of Halffter’s Mexican Transition Zone: a systematic review using bibliometric tools

The Mexican Transition Zone (MTZ) has become a key concept that has promoted the consolidation of an integrative field of research. We reviewed the scientific publications on the MTZ with bibliometric tools to detect trends through time and analyze the conceptual structure and historiographic citation. We also performed a content analysis considering the conceptualization of the MTZ, the application of Halffter’s patterns of distribution, and the different disciplines where the term has been used. The number of publications per year has not been constant, but since 2012 there has been a general increase, becoming the MTZ frequently cited in papers and in some cases constituting a research topic. We identified divergences in the conceptualization of the MTZ and discussed the implications for biogeographic studies. Halffter’s conceptualization of the Mexican Transition Zone has inspired other authors to produce research focused on this area and to set biogeographic hypotheses but also to redefine the concept and make it applicable through its incorporation in the biogeographical regionalization of the Americas.

CIGAF—a database and interactive platform for insect-associated trichomycete fungi

Trichomycete fungi are gut symbionts of arthropods living in aquatic habitats. The lack of a central platform with accessible collection records and associated ecological metadata has limited ecological investigations of trichomycetes. We present CIGAF (short for Collections of Insect Gut-Associated Fungi), a trichomycetes-focused digital database with interactive visualization functions enabled by the R Shiny web application. CIGAF curated 3120 collection records of trichomycetes across the globe, spanning from 1929 to 2022. CIGAF allows the exploration of nearly 100 years of field collection data through the web interface, including primary published data such as insect host information, collection site coordinates, descriptions and date of collection. When possible, specimen records are supplemented with climatic measures at collection sites. As a central platform of field collection records, multiple interactive tools allow users to analyze and plot data at various levels. CIGAF provides a comprehensive resource hub to the research community for further studies in mycology, entomology, symbiosis and biogeography.

LEPIDOPTERA TORTRICIDAE FROM THE SILA MASSIF AND SURROUNDING TERRITORY (SOUTHERN ITALY) WITH DESCRIPTION OF ACLERIS SILANA SP. N.

In the paper 89 species of Lepidoptera Tortricidae collected in the Sila Massif and surrounding territory (Calabria, southern Italy) are listed. Acleris silana sp. n. Trematerra is described and 17 species were added to the Calabrian fauna. Notes related to tortricid fauna of the region with biogeographic study and chorological analysis are also reported. Key Words: Lepidoptera Tortricidae, fauna, Calabria, new data, Sila Massif, southern Italy

Geological events and climate change drive diversification and speciation of mute cicadas in eastern continental Asia

The poor mobility of nymphs living underground, usually for many years, and the weak flying ability of adults make cicadas unique for evolutionary biology and bio-geographical study. Cicadas of the genus Karenia are unusual in Cicadidae in lacking the timbals that produce sound. Population differentiation, genetic structure, dispersal and evolutionary history of the eastern Asian mute cicada Karenia caelatata were investigated based on morphological, acoustic and molecular data. The results reveal a high level of genetic differentiation in this species. Six independent clades with nearly unique sets of haplotypes corresponding to geographically isolated populations are recognized. Genetic and geographic distances are significantly correlated among lineages. The phenotypic differentiation is generally consistent with the high levels of genetic divergence across populations. Results of ecological niche modeling suggest that the potential distribution range of this mountain-habitat specialist during the Last Glacial Maximum was broader than its current range, indicating this species had benefited from the climate change during the early Pleistocene in southern China. Geological events such as orogeny in Southwest China and Pleistocene climate oscillations have driven the differentiation and divergence of this species, and basins, plains and rivers function as natural “barriers” to block the gene flow. Besides significant genetic divergence being found among clades, the populations occurring in the Wuyi Mountains and the Hengduan Mountains are significantly different in the calling song structure from other populations. This may have resulted from significant population differentiation and subsequent adaptation of related populations. We conclude that ecological differences in habitats, coupled with geographical isolation, have driven population divergence and allopatric speciation. This study provides a plausible example of incipient speciation in Cicadidae and improves understanding of population differentiation, acoustic signal diversification and phylogeographic relationships of this unusual cicada species. It informs future studies on population differentiation, speciation and phylogeography of other mountain-habitat insects in the East Asian continent.

Fine‐scale variation in soil and topography influences herbaceous vegetation and the distribution of large mammalian herbivores

AbstractCurrent understanding of the distribution of vegetation and large mammalian herbivores (LMH) is based on a combination of biogeographic studies and highly controlled field experiments, but a more complete understanding of these patterns requires study of their natural co‐occurrence patterns at intermediate spatial scales. The study was conducted in the 120‐ha Mpala Forest Global Earth Observatory (ForestGEO) plot, Kenya. We examined differences in herbaceous plant communities and habitat use by LMH among three topographic habitats with distinct soil types, namely steep slopes, valley and plateau. Each pair of habitats differed in plant and animal composition. The steep slopes and plateau respectively had ≥1‐fold higher percentage herbaceous cover than the valley, whereas the steep slopes and valley had >1.5‐fold greater grass species richness and diversity than the plateau. The activity of LMH was ≥1.7‐fold higher in the valley than the steep slopes and plateau, reflecting a positive relationship between LMH activity index and richness and diversity of grass species. Results indicate that fine‐scale variation in topography and soil are associated with both the distribution of herbaceous vegetation and LMH, suggesting a need to account for local habitat characteristics when examining the distributions of plants, animals, and plant‐herbivore interactions in natural systems.

Biogeographical and Biodiversity Patterns of Marine Planktonic Bacteria Spanning from the South China Sea across the Gulf of Bengal to the Northern Arabian Sea.

Understanding the biogeographical and biodiversity patterns of bacterial communities is essential in unraveling their responses to future environmental changes. However, the relationships between marine planktonic bacterial biodiversity and seawater chlorophyll a are largely understudied. Here, we used high-throughput sequencing to study the biodiversity patterns of marine planktonic bacteria across a broad chlorophyll a gradient spanning from the South China Sea across the Gulf of Bengal to the northern Arabian Sea. We found that the biogeographical patterns of marine planktonic bacteria complied with the scenario of homogeneous selection, with chlorophyll a concentration being the key environmental selecting variable of bacteria taxa. The relative abundance of Prochlorococcus, the SAR11 clade, the SAR116 clade, and the SAR86 clade significantly decreased in habitats with high chlorophyll a concentrations (>0.5 μg/L). Free-living bacteria (FLB) and particle-associated bacteria (PAB) displayed contrasting alpha diversity and chlorophyll a relationships with a positive linear correlation for FLB but a negative correlation for PAB. We further found that PAB had a narrower niche breadth of chlorophyll a than did FLB, with far fewer bacterial taxa being favored at higher chlorophyll a concentrations. Higher chlorophyll a concentrations were linked to the enhanced stochastic drift and reduced beta diversity of PAB but to the weakened homogeneous selection, enhanced dispersal limitation, and increased beta diversity of FLB. Taken together, our findings might broaden our knowledge about the biogeography of marine planktonic bacteria and advance the understanding of bacterial roles in predicting ecosystem functioning under future environmental changes that are derived from eutrophication. IMPORTANCE One of the long-standing interests of biogeography is to explore diversity patterns and uncover their underlying mechanisms. Despite intensive studies on the responses of eukaryotic communities to chlorophyll a concentrations, we know little about how changes in seawater chlorophyll a concentrations affect free-living bacteria (FLB) and particle-associated bacteria (PAB) diversity patterns in natural systems. Our biogeography study demonstrated that marine FLB and PAB displayed contrasting diversity and chlorophyll a relationships and exhibited completely different assembly mechanisms. Our findings broaden our knowledge about the biogeographical and biodiversity patterns of marine planktonic bacteria in nature systems and suggest that PAB and FLB should be considered independently in predicting marine ecosystem functioning under future frequent eutrophication.

Biodiversity of epiphytic marine macroalgae in Mexico: composition and current status

Abstract Marine epiphyte studies in Mexico, including macroalgae, are lacking in the published literature. Floristic studies have been mainly focused on identifying the algae growing on rocky substrata, and epiphytic algae have been recorded, but only occasionally. The aim of this work is to establish the current state of knowledge of the epiphytic macroalgae and their hosts on the Mexican coasts. A systematic revision of the literature published from 1950 to 2021 is also reported, the literature information is included, and the composition, species richness, current state of knowledge of the epiphytic marine macroalgae, and their relationship with the various marine Mexican ecoregions are reported. Sixty-one publications since 1950 included at least one record of epiphytic macroalgae. In this study, 615 species of epiphytic macroalgae and 224 species of hosts for Mexico are reported. This checklist will provide a baseline for future taxonomic and biogeographic studies of the epiphytic marine algae in the country.

ArcticBirdSounds: An open-access, multiyear, and detailed annotated dataset of bird songs and calls.

Tracking biodiversity shifts is central to understanding past, present, and future global changes. Recent advances in bioacoustics and the low cost of high-quality automatic recorders are revolutionizing studies in biogeography and community and behavioral ecology with a robust assessment of phenology, species occurrence, and individual activity. This large volume of acoustic recordings has recently generated a plethora of datasets that can now be handled automatically, mostly via big data methods such as deep learning. These approaches need high-quality annotations to classify and detect recorded sounds efficiently. However, very few strongly annotated datasets-that is, with detailed information on start and end time of each vocalization-are openly accessible to the public. Moreover, these datasets mostly cover temperate species and are usually limited to a single year of recordings. Here, we present ArcticBirdSounds, the first open-access, multisite, and multiyear strongly annotated dataset of arctic bird vocalizations. ArcticBirdSounds offers 20 h of annotated recordings over 2 years (2018, 2019), taken from 15 distinct plots within six locations across the Arctic, from Alaska to Greenland. Recordings cover the arctic vertebrates' breeding period and are evenly spaced during the day; they capture most species breeding there with 12,933 temporal annotations in 49 classes of sounds. While these data can be used for many pressing ecological questions, it is also a unique resource for methodological development to help meet the challenges of fast ecosystem transformations such as those happening in the Arctic. All data, including audio files, annotation files, and companion spreadsheets, are available in an Open Science Framework repository published under a CC BY 4.0 License.

Records and palaeoenvironmental conditions of Early Miocene scleractinian corals from the Fırat formation (Diyarbakır, Turkey)

Miocene scleractinian corals were documented for the first time in the Fırat Formation of Sarıca village, Eğil district of Diyarbakır, SE Turkey. The fauna consists of four hermatypic species belonging to three families: Diploastrea taurinensis (d’Achiardi, 1868), Tarbellastraea reussiana (Milne-Edwards and Haime, 1850), Echinopora gemmacea (Lamarck, 1816) and Montastraea pelouaensis (Chevalier, 1954). The morphospecies described here are typical of the early Miocene (Aquitanian-Burdigalian) and show that the Fırat Formation coral community was composed of shallow and subtropical reefs of Mediterranean Tethys palaeobiogeographical affinity. The examined species are reef components found in tropical and subtropical oceans, as are the majority of zooxanthellae. The species were upper photic zone related, had massive colonial growth morphology, and lived in a shallow tropical-subtropical marine palaeoenvironment at a depth of up to 50m. They grew on hard ground, clean water, and normal salinity and required a minimum seawater temperature of 18̊C; however, they were most abundant at water temperatures ranging from 22 to 26̊C in high-moderate water energy. Consequently, this fossil assemblage will not only improve our knowledge of scleractinian coral diversity and morphological variation in SE Turkey but will also provide an important background for future studies of coral taxonomy, diversity and biogeography of the region.

Macrophyte islands as an experimental model: new perspectives and a step-by-step protocol to access assumptions of Island Biogeography theory and habitat fragmentation

To evaluate whether artificially built macrophyte islands could be used as a short-term and cost-effective experimental model for the study of island biogeography and habitat fragmentation, 20 islands of two different sizes were built and fishes were sampled. Habitat complexity and source-island distance were standardized. A macrophyte bank 200 times larger than the islands was used as a source of individuals. The results show that, in four days, several fish species colonized both small and large islands. After four days, larger islands bore significantly more species than smaller ones. We raise the caveats and new perspectives for studies using this methodology, which can be largely applicable due to its cost-effectiveness in terms of materials, short time required, and flexibility.

Paleoparasitological study of avian trace fossils from the Tremembé Formation (Oligocene of the Taubaté Basin), São Paulo, Brazil

Coprolites are promising tools for the understanding of paleoecological and paleoenvironmental aspects. Through its chemical composition and analysis of micro- and macrostructures, it is possible to obtain information about the diet of ancient animals and insights into the climate and vegetation of paleoenvironments. Paleoparasitological analysis of these trace fossils help to understand the parasite-host relationship and how parasitic infections were processed in the past. The present study aims to identify helminths in coprolites of the Tremembé Formation (Oligocene of the Taubaté Basin, São Paulo). Furthermore, we included the descriptive association of the paleoparasitological data with the paleoenvironmental information present in the literature for this geological formation. Eggs were identified through linear morphometry and morphology. The paleoparasitological analysis revealed the presence of Nematode eggs of Ascaridina, Spirurina, and Trichocephalida, with a prevalence of 5% for each group. The complex life cycle of some nematodes would be made possible by the wide faunal diversity of birds, fish, and arthropods that inhabited the Tremembé paleolake. The low prevalence of helminths in the samples may be related to taphonomic processes. This study represents the first paleoparasitological analysis of avian coprolites from the Tremembé Formation. In addition, the finding of these helminth records creates new perspectives for the studies of this geological unit through the epidemiological point of view associated with the local paleofauna and also provides new subsidies for the further development of evolutionary and biogeographic helminth studies.

A review of the Late Ordovician (Katian) Richmondian Invasion of eastern Laurentia

Biotic Immigration Events in which a group of organisms that originated in one geographic region invade and become established in a new geographic region are common during Earth history. Many such events have been documented from the fossil record and have significantly impacted diversification patterns and processes during the history of life. One of the best studied of these events is the Richmondian Invasion, which constituted several waves of biotic invasion from multiple source regions into the Cincinnati Basin of eastern Laurentia during the Katian Stage. The major features of this invasion were first appreciated during the early 1900s and have received significant study since that time. General patterns of the Richmondian Invasion, including the influx of >60 taxa that span ecological roles and taxonomic groups, differential survival of generalist taxa relative to specialist taxa, and significant restructuring of paleocommunities have been well documented and establish this invasion as a “coordinated invasion” within the Invasion Hierarchy of Stigall et al. (2019). Substantial research to further delineate and clarify the details of the Richmondian Invasion has progressed on multiple fronts over the past two decades. These novel analyses into sedimentology, stratigraphy, and geochemistry coupled with detailed paleoecology, evolutionary, and biogeographic studies provide a framework for increased synthesis and understanding of invasion dynamics during this interval. In this contribution, the current state of knowledge of the Richmondian Invasion is reviewed and some of the key implications for understanding both Ordovician diversification and other intervals of Earth history are examined.

Systematic and biogeographical aspects of the first Antarctic discovery of Orthoplana bregazzii Karling, 1973 (Proseriata, Otoplanidae)

ABSTRACT Three essential questions remain unresolved about the present Antarctic biota: its antiquity, origin, and ubiquity. Some benthic animals are capable of active self-dispersal following shallow corridors between islands. Identifying and characterizing the biota in such corridors is fundamental for biogeographic studies and the delimitation of priority sites to conserve biodiversity. The Scotia Arc provides an example of such passages, being a system of islands and underwater ridges connecting the Magellan Region to the Antarctic Peninsula and South Shetland Islands (Maritime Antarctic). Specimens of the free-living flatworm Orthoplana bregazzii Karling 1973 (Proseriata, Otoplanidae) were obtained in King George Island (South Shetland Islands). This is the first report of the family Otoplanidae from Antarctica, and the first rediscovery of the species 50 years after its original description. The present article provides a complete description of the Antarctic material of O. bregazzii, complements its original description, and provides an identification key to the species of Orthoplana. We analyze the distribution of the genus and species and argue that the range expansion reported here could be the result of a recent, successful colonization event. This work, therefore, gives insights into the systematics and biogeography of one of the lesser-known groups in the Antarctic fauna.

Nutrient availability of roughages in isocaloric and isonitrogenous diets alters the bacterial networks in the whole gastrointestinal tract of Hu sheep

BackgroundThe nutrient availability of roughages could affect the dietary utilization efficiency of ruminants even in isocaloric and isonitrogenous diets. Here, we analyzed the bacterial composition and their metabolic pathways in the gastrointestinal tracts (GITs) of Hu sheep fed with wheat straw (WS) instead of alfalfa (AL) in isocaloric and isonitrogenous diets, trying to explore the reasons from the perspective of GITs bacterial network structure changes.ResultsWe employed 16S rRNA gene sequencing in combination with the Kruskal–Wallis test, Spearman correlation analysis, and other statistical methods to describe the microbiota composition in the GITs of Hu sheep. The results showed after the roughage was replaced from AL to WS, the most positive response occurred in the rumen microbiota, resulting in a more obvious microbiological and functional redundancy phenomenon. Whereas extended biogeographic studies of the GITs bacterial community found opposite results for the hindgut microbiota and metabolism networks compared to the forestomach. The abundance of fiber-degrading bacteria such as Prevotella, Oscillospiraceae NK4A214 group, and Treponema was significantly increased in GITs, but low-efficiency crude fiber degradation inhibited energy use efficiency, the pentose phosphate pathway, gluconeogenesis, and volatile acid synthesis. In addition, dietary shifting from AL to WS decreased the abundance of beneficial bacteria such as the Lachnospiraceae NK3A20 group and Alistipes, thereby enhancing the underlying inflammatory response.ConclusionsThese findings suggest that feeding untreated WS affected the structure and function of the bacterial network in the GITs due to limited total digestible nutrients, and in particular increases the complexity of the rumen bacterial network, and limit the abundance of bacteria involved in the crude fiber degradation in the hindgut.

Temporal dynamics of geothermal microbial communities in Aotearoa-New Zealand.

Microbial biogeography studies, in particular for geothermal-associated habitats, have focused on spatial patterns and/or individual sites, which have limited ability to describe the dynamics of ecosystem behaviour. Here, we report the first comprehensive temporal study of bacterial and archaeal communities from an extensive range of geothermal features in Aotearoa-New Zealand. One hundred and fifteen water column samples from 31 geothermal ecosystems were taken over a 34-month period to ascertain microbial community stability (control sites), community response to both natural and anthropogenic disturbances in the local environment (disturbed sites) and temporal variation in spring diversity across different pH values (pH 3, 5, 7, 9) all at a similar temperature of 60-70°C (pH sites). Identical methodologies were employed to measure microbial diversity via 16S rRNA gene amplicon sequencing, along with 44 physicochemical parameters from each feature, to ensure confidence in comparing samples across timeframes. Our results indicated temperature and associated groundwater physicochemistry were the most likely parameters to vary stochastically in these geothermal features, with community abundances rather than composition more readily affected by a changing environment. However, variation in pH (pH ±1) had a more significant effect on community structure than temperature (±20°C), with alpha diversity failing to adequately measure temporal microbial disparity in geothermal features outside of circumneutral conditions. While a substantial physicochemical disturbance was required to shift community structures at the phylum level, geothermal ecosystems were resilient at this broad taxonomic rank and returned to a pre-disturbed state if environmental conditions re-established. These findings highlight the diverse controls between different microbial communities within the same habitat-type, expanding our understanding of temporal dynamics in extreme ecosystems.

ARCHAEOPHYTES IN THE FLORA OF EUROPEAN RUSSIA

The division of alien species into groups according to the time of invasion is widely used in biogeographic and floristic studies, but such information is not available for many regions of Russia. Based on the analysis of regional floras of European Russia (ER), 184 species of archaeophytes (i.e., alien species intentionally or unintentionally introduced by humans in the early historical period, until the end of the 16th century) were identified for ER regions. The substantiation of the prescription of their invasion was carried out by a number of criteria (type of habitat, presence of fossils and historical evidence, geographic distribution, frequency of known naturalizations, identification of possible means of introduction, human use). Some species are archaeophytes only for a part of the ER regions; in neighboring areas, they can be either species of natural flora or alien neophytes according to their status. Eighty one species of the archaeophytes are confirmed by archaeobotanical data belonged to some of the early historical periods, mostly to the Middle Ages, but from a limited number of regions. Taking into account the peculiarities of natural conditions, as well as the history of the development of anthropogenic cultures, the territory of the ER is divided into six regions: Karelian-Kola, East-Baltic, Dvina-Upper-Volga, Volga-Don and South-Eastern. For each of the big regions, the more or less unified set of archaeophytes has been proposed. For the entire group of archaeophytes in ER as a whole, it should be noted 1) the great similarity of the composition of archaeophytes with other European regions, 2) the low diversity compared to European countries, given the large area of ER, 3) the heterogeneity of the status of species in different regions and differences between different parts ER by species composition, 4) a large proportion of segetal weed species as a result of high contamination of crops with weed species at the beginning of the development of agricultural culture, 5) a significant percentage of species of Asian origin as evidence of the influence of eastern vectors on the formation of flora, including the eastern centers of agricultural culture. For a significant part of the species from the list of archaeophytes, species factsheets are presented according to the criteria mentioned above.